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Gene Regulatory Network Inference From Perturbed Time-Series Expression Data Via Ordered Dynamical Expansion Of Non-Steady State Actors, Mahdi Zamanighomi, Mostafa Zamanian, Michael J. Kimber, Zhengdao Wang 2018 Stanford University

Gene Regulatory Network Inference From Perturbed Time-Series Expression Data Via Ordered Dynamical Expansion Of Non-Steady State Actors, Mahdi Zamanighomi, Mostafa Zamanian, Michael J. Kimber, Zhengdao Wang

Zhengdao Wang

The reconstruction of gene regulatory networks from gene expression data has been the subject of intense research activity. A variety of models and methods have been developed to address different aspects of this important problem. However, these techniques are narrowly focused on particular biological and experimental platforms, and require experimental data that are typically unavailable and difficult to ascertain. The more recent availability of higher-throughput sequencing platforms, combined with more precise modes of genetic perturbation, presents an opportunity to formulate more robust and comprehensive approaches to gene network inference. Here, we propose a step-wise framework for identifying gene-gene regulatory interactions ...


Transcranial Magnetic Stimulation-Coil Design With Improved Focality, Priyam Rastogi, E. G. Lee, Ravi L. Hadimani, David C. Jiles 2018 Iowa State University

Transcranial Magnetic Stimulation-Coil Design With Improved Focality, Priyam Rastogi, E. G. Lee, Ravi L. Hadimani, David C. Jiles

Ravi L Hadimani

Transcranial Magnetic Stimulation (TMS) is a technique for neuromodulation that can be used as a non-invasive therapy for various neurological disorders. In TMS, a time varying magnetic field generated from an electromagnetic coilplaced on the scalp is used to induce an electric field inside the brain. TMS coilgeometry plays an important role in determining the focality and depth of penetration of the induced electric field responsible for stimulation. Clinicians and basic scientists are interested in stimulating a localized area of the brain,while minimizing the stimulation of surrounding neural networks. In this paper, a novel coil has been proposed, namely ...


Optimal Decomposition Strategy For Tree Edit Distance, Shaofeng Jiang 2017 The University of Western Ontario

Optimal Decomposition Strategy For Tree Edit Distance, Shaofeng Jiang

Electronic Thesis and Dissertation Repository

An ordered labeled tree is a tree where the left-to-right order among siblings is significant. Given two ordered labeled trees, the edit distance between them is the minimum cost edit operations that convert one tree to the other.

In this thesis, we present an algorithm for the tree edit distance problem by using the optimal tree decomposition strategy. By combining the vertical compression of trees with optimal decomposition we can significantly reduce the running time of the algorithm. We compare our method with other methods both theoretically and experimentally. The test results show that our strategies on compressed trees are ...


Portable 6 Lead 4 Electrode Ekg, Cody Magnuson, Wes Archbold 2017 California Polytechnic State University, San Luis Obispo

Portable 6 Lead 4 Electrode Ekg, Cody Magnuson, Wes Archbold

Electrical Engineering

This project focused on designing a small, portable, 6 lead 4 electrode electrocardiogram (EKG) machine with enough accuracy and resolution to successfully diagnose clinical issues. The electrical design used to measure signals originating from the heart can be broken up into three stages. The first stage is the human device interface. Next, is the analog block that filters out common mode noise and conditions the signal for digital encoding using instrumentation amplifiers, a right leg circuit, high pass, low pass, and an amplifier. This circuit filters all frequencies above and below the frequency band of meaningful data (1-160Hz), rejects signals ...


Design And Evaluation Of Neurosurgical Training Simulator, Trinette L. Wright 2017 Western University

Design And Evaluation Of Neurosurgical Training Simulator, Trinette L. Wright

Electronic Thesis and Dissertation Repository

Surgical simulators are becoming more important in surgical training. Consumer smartphone technology has improved to allow deployment of VR applications and are now being targeted for medical training simulators. A surgical simulator has been designed using a smartphone, Google cardboard 3D glasses, and the Leap Motion (LM) hand controller. Two expert and 16 novice users were tasked with completing the same pointing tasks using both the LM and the medical simulator NeuroTouch. The novice users had an accuracy of 0.2717 bits (SD 0.3899) and the experts had an accuracy of 0.0925 bits (SD 0.1210) while using ...


Force Sensing Surgical Grasper With Folding Capacitive Sensor, Dave BP Tripp 2017 The University of Western Ontario

Force Sensing Surgical Grasper With Folding Capacitive Sensor, Dave Bp Tripp

Electronic Thesis and Dissertation Repository

Minimally-invasive surgery (MIS) has brought many benefits to the operating room, however, MIS procedures result in an absence of force feedback, and surgeons cannot as accurately feel the tissue they are working on, or the forces that they are applying. One of the barriers to introducing MIS instruments with force feedback systems is the high cost of manufacturing and assembly. Instruments must also be sterilized before every use, a process that can destroy embedded sensing systems. An instrument that can be disposed of after a single use and produced in bulk at a low cost is desirable. Printed circuit micro-electro-mechanical ...


Pulmonary Image Segmentation And Registration Algorithms: Towards Regional Evaluation Of Obstructive Lung Disease, Fumin Guo 2017 The University of Western Ontario

Pulmonary Image Segmentation And Registration Algorithms: Towards Regional Evaluation Of Obstructive Lung Disease, Fumin Guo

Electronic Thesis and Dissertation Repository

Pulmonary imaging, including pulmonary magnetic resonance imaging (MRI) and computed tomography (CT), provides a way to sensitively and regionally measure spatially heterogeneous lung structural-functional abnormalities. These unique imaging biomarkers offer the potential for better understanding pulmonary disease mechanisms, monitoring disease progression and response to therapy, and developing novel treatments for improved patient care. To generate these regional lung structure-function measurements and enable broad clinical applications of quantitative pulmonary MRI and CT biomarkers, as a first step, accurate, reproducible and rapid lung segmentation and registration methods are required. In this regard, we first developed a 1H MRI lung segmentation algorithm that ...


Gui For Mri-Compatible Neural Stimulator And Recorder, Soo Han Soon, Nishant Babaria, Ranajay Mandal, Zhongming Liu 2017 Purdue University

Gui For Mri-Compatible Neural Stimulator And Recorder, Soo Han Soon, Nishant Babaria, Ranajay Mandal, Zhongming Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) are useful tools to analyze brain activities given active stimulation. However, the electromagnetic noise from the MRI distorts the brain signal recording and damages the subject with excessive heat generated on the electrodes attached to the skin. MRI-compatible recording and stimulation systems previously developed at LIBI lab were capable of removing the electromagnetic noise during the imaging process. Previously, the hardware systems had required the integrative software that could control both circuits simultaneously and enable users to easily change recording and stimulation parameters. Graphical user interface (GUI) programmed with computer language informed ...


Optimization Of Prosthetic Hands: Utilizing Modularity To Improve Grip Force, Grasp, And Versatility, Jordan William Harris 2017 University of Nevada, Las Vegas

Optimization Of Prosthetic Hands: Utilizing Modularity To Improve Grip Force, Grasp, And Versatility, Jordan William Harris

UNLV Theses, Dissertations, Professional Papers, and Capstones

It has been demonstrated that although many varieties of upper limb prosthetics exist, commercially available prosthetics are outdated and unsatisfactory. Ineffectiveness and limitations have led to some prosthesis wearers having to own multiple devices, whereas others have given up on them entirely. Even though ample research has been conducted to design and test new hand designs, the industry appears to rest in an overall stagnated state.

It was proposed here, that one problem with prosthetic research is an excess of variables involved in testing, and therefore the improper application of the scientific method. It seems that each time a research ...


Design And Implementation Of A Low‐Power Wireless Respiration Monitoring Sensor, Ifana Mahbub 2017 Univeristy of Tennessee, Knoxville

Design And Implementation Of A Low‐Power Wireless Respiration Monitoring Sensor, Ifana Mahbub

Doctoral Dissertations

Wireless devices for monitoring of respiration activities can play a major role in advancing modern home-based health care applications. Existing methods for respiration monitoring require special algorithms and high precision filters to eliminate noise and other motion artifacts. These necessitate additional power consuming circuitry for further signal conditioning. This dissertation is particularly focused on a novel approach of respiration monitoring based on a PVDF-based pyroelectric transducer. Low-power, low-noise, and fully integrated charge amplifiers are designed to serve as the front-end amplifier of the sensor to efficiently convert the charge generated by the transducer into a proportional voltage signal. To transmit ...


Wax Bee Gone: A Safe, Effective Solution To Ear Wax Removal, Robert G. Shenon, Shanvir S. Dhinsa 2017 California Polytechnic State University, San Luis Obispo

Wax Bee Gone: A Safe, Effective Solution To Ear Wax Removal, Robert G. Shenon, Shanvir S. Dhinsa

Electrical Engineering

This project sought to combine conventional methods such as scraping and water pressure to removal ear wax, but with electronic automation to removal the potential for human error as much as possible. Through the use of a 9V battery, and Arduino microcontroller, DC motors, and other circuitry, this project has developed a prototype for a device that can properly remove ear wax without any discomfort or risk to the user. Much of this project involved learning how to properly manipulate and provide the necessary power requirements DC motors from an Arduino and a 9V battery. Additionally, creating a 3D printed ...


Poly Drop, Zachary T. Scott, Lilly J. Paul 2017 California Polytechnic State University, San Luis Obispo

Poly Drop, Zachary T. Scott, Lilly J. Paul

Computer Engineering

Poly Drop is a software interface to control an Open Drop digital micro-fluidics system. We obtained a hardware system from Gaudi labs. Our task was to create a Graphical User Interface that made the control of the device easier and more automated for better testing. We created software that had 3 parts: a control GUI, arduino code to control the hardware, and Image Analysis that gives the user information such as location and color of liquid drops as they move across the electrode grid of the Open Drop system. The GUI was developed using Java Swing. The communication between the ...


Pulse Oximetry, Yitzhak Mendelson 2017 Worcester Polytechnic Institute

Pulse Oximetry, Yitzhak Mendelson

UMass Center for Clinical and Translational Science Research Retreat

As part of the mini-symposium entitled "Bench to Bedside: Engineering Technology Translation," Dr. Mendelson describes pulse oximetry technology and how that technology idea successfully developed into a real world medical product.


Pet/Mr Imaging Of Hypoxic Atherosclerotic Plaque Using 64cu-Atsm, Xingyu Nie 2017 Washington University in St. Louis

Pet/Mr Imaging Of Hypoxic Atherosclerotic Plaque Using 64cu-Atsm, Xingyu Nie

Engineering and Applied Science Theses & Dissertations

ABSTRACT OF THE DISSERTATION

PET/MR Imaging of Hypoxic Atherosclerotic Plaque Using 64Cu-ATSM

by

Xingyu Nie

Doctor of Philosophy in Biomedical Engineering

Washington University in St. Louis, 2017

Professor Pamela K. Woodard, Chair

Professor Suzanne Lapi, Co-Chair

It is important to accurately identify the factors involved in the progression of atherosclerosis because advanced atherosclerotic lesions are prone to rupture, leading to disability or death. Hypoxic areas have been known to be present in human atherosclerotic lesions, and lesion progression is associated with the formation of lipid-loaded macrophages and increased local inflammation which are potential major factors in the formation of ...


The Electrophysiology Of Resting State Fmri Networks, Carl David Hacker 2017 Washington University in St. Louis

The Electrophysiology Of Resting State Fmri Networks, Carl David Hacker

Engineering and Applied Science Theses & Dissertations

Traditional research in neuroscience has studied the topography of specific brain functions largely by presenting stimuli or imposing tasks and measuring evoked brain activity. This paradigm has dominated neuroscience for 50 years. Recently, investigations of brain activity in the resting state, most frequently using functional magnetic resonance imaging (fMRI), have revealed spontaneous correlations within widely distributed brain regions known as resting state networks (RSNs). Variability in RSNs across individuals has found to systematically relate to numerous diseases as well as differences in cognitive performance within specific domains. However, the relationship between spontaneous fMRI activity and the underlying neurophysiology is not ...


An Exact Analysis For Four-Order Acousto-Optic Bragg Diffraction Which Incorporates Both Incident Light Angle And Sound Frequency Dependencies, Adeyinka Sunday Ademola 2017 University of Texas at Tyler

An Exact Analysis For Four-Order Acousto-Optic Bragg Diffraction Which Incorporates Both Incident Light Angle And Sound Frequency Dependencies, Adeyinka Sunday Ademola

Electrical Engineering Theses

This thesis extends the prior work which produced an exact solution to the four-order acousto-optic (AO) Bragg cell with assumed fixed center frequency and with exact Bragg angle incident light. The extension predicts the model that incorporates the dependencies of both the input angle of light and the sound frequency. Specifically, a generalized 4th order linear differential equation (DE), is developed from a simultaneous analysis of four coupled AO system of DEs. Through standard methods, the characteristic roots, which requires solving a quartic equation, is produced. Subsequently, a derived system of homogeneous solutions, which absorbs the roots obtained using ...


Development Of A Low Cost Biosensing Platform For Highly Sensitive And Specific On-Site Detection Of Pathogens And Infections, Cheng Cheng 2017 University of Tennessee, Knoxville

Development Of A Low Cost Biosensing Platform For Highly Sensitive And Specific On-Site Detection Of Pathogens And Infections, Cheng Cheng

Doctoral Dissertations

A highly sensitive, specific, real time, and field-deployable surveillance tool is critical to the control of pathogens and infections, as well as ecological impact of chemicals exposure. This work investigates the development of a low cost biosensing platform that can be used for viral disease diagnosis and chemical detection. The sensing mechanism is known as AC electrokinetics (ACEK) capacitive sensing. By applying an inhomogeneous AC electric field on sensor electrodes, positive dielectrophoresis is induced to accelerate the travel of analytes. The same applied AC signal also directly measures the capture of target by the probe on sensor surface. The realized ...


Development Of An Oxygen Saturation Monitoring System By Embedded Electronics, Manikandan Venkatesan Gomathy 2017 University of Arkansas, Fayetteville

Development Of An Oxygen Saturation Monitoring System By Embedded Electronics, Manikandan Venkatesan Gomathy

Theses and Dissertations

Measuring Oxygenation of blood (SaO2) plays a vital role in patient’s health monitoring. This is often measured by pulse oximeter, which is standard measure during anesthesia, asthma, operative and post-operative recoveries. Despite all, monitoring Oxygen level is necessary for infants with respiratory problems, old people, and pregnant women and in other critical situations.

This paper discusses the process of calculating the level of oxygen in blood and heart-rate detection using a non-invasive photo plethysmography also called as pulsoximeter using the MSP430FG437 microcontroller (MCU). The probe uses infrared lights to measure and should be in physical contact with any peripheral ...


Basic Science To Clinical Research: Segmentation Of Ultrasound And Modelling In Clinical Informatics, Ali K. Hamou 2017 The University of Western Ontario

Basic Science To Clinical Research: Segmentation Of Ultrasound And Modelling In Clinical Informatics, Ali K. Hamou

Electronic Thesis and Dissertation Repository

The world of basic science is a world of minutia; it boils down to improving even a fraction of a percent over the baseline standard. It is a domain of peer reviewed fractions of seconds and the world of squeezing every last ounce of efficiency from a processor, a storage medium, or an algorithm. The field of health data is based on extracting knowledge from segments of data that may improve some clinical process or practice guideline to improve the time and quality of care. Clinical informatics and knowledge translation provide this information in order to reveal insights to the ...


Advanced Signal Processing Methods For Plane-Wave Color Doppler Ultrasound Imaging, Omar Mansour 2017 The University of Western Ontario

Advanced Signal Processing Methods For Plane-Wave Color Doppler Ultrasound Imaging, Omar Mansour

Electronic Thesis and Dissertation Repository

Conventional medical ultrasound imaging uses focused beams to scan the imaging scene line-by-line, but recently however, plane-wave imaging, in which plane-waves are used to illuminate the entire imaging scene, has been gaining popularity due its ability to achieve high frame rates, thus allowing the capture of fast dynamic events and producing continuous Doppler data. In most implementations, multiple low-resolution images from different plane wave tilt angles are coherently averaged (compounded) to form a single high-resolution image, albeit with the undesirable side effect of reducing the frame rate, and attenuating signals with high Doppler shifts.

This thesis introduces a spread-spectrum color ...


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