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<!DOCTYPE html>
<html>
<head>
<title>John Squire</title>
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John Squire
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<div class="w3-content w3-padding" style="max-width:1000px">
<h1 style="padding-top: 70px">Research</h1>
<hr>
<p>I have been actively involved in a range of undergraduate and graduate research projects, with a growing focus on the intersection of machine learning and medicine. Throughout medical school, I developed an interest in the field of radiology, leading me to pursue research that explores how machine learning can support radiologists in diagnosing pathology more accurately and efficiently.</p>
<p>Currently, my primary research centers on applying machine learning techniques to magnetic resonance elastography (MRE), with the goal of identifying and masking brain structures in an image. MRE holds promise for earlier detection of degenerative neurological diseases, but its widespread use is limited by the time-intensive image processing required. My work aims to develop AI tools that streamline this processing, potentially accelerating research and clinical workflows.</p>
<h2 style="padding-top: 30px">Poster Presentations</h2>
<hr>
<p>Here is a collection of past poster presentations I have presented at various conferences. If you're interested in one, click on it to see the full poster!</p>
<div id="carouselExampleIndicators" class="carousel slide" data-ride="carousel" style="max-height:500px; background-color:rgba(0,0,0,0.8 )">
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<a href="./archive/presentations/mreureka-poster/mreureka-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/mreureka-poster/mreureka-poster.png" alt="MREureka!: Efficiently and Effectively Segmenting Brain Elastographs with nnU-Net">
</a>
</div>
<div class="carousel-item">
<a href="./archive/presentations/arthritis-to-meningitis-poster/arthritis-to-meningitis-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/arthritis-to-meningitis-poster/arthritis-to-meningitis-poster.png" alt="Arthritis to Meningitis: A Rare Case of Rheumatoid Meningitis">
</a>
</div>
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<a href="./archive/presentations/cozad-2025-poster/cozad-2025-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/cozad-2025-poster/cozad-2025-poster.png" alt="The Intra-Fallopian Device">
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<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/sorad-poster/sorad-poster.png" alt="Between a Liver and a Hard Place: A Case of Chilaiditi Syndrome">
</a>
</div>
<div class="carousel-item">
<a href="./archive/presentations/embc-poster/embc-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/embc-poster/embc-poster.png" alt="ANTs, BET, or…neither? An exploration of brain masking and machine learning tools applied to magnetic resonance elastography">
</a>
</div>
<div class="carousel-item">
<a href="./archive/presentations/cozad-2024-poster/cozad-2024-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/cozad-2024-poster/cozad-2024-poster.png" alt="Tumestent">
</a>
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<a href="./archive/presentations/discovery-learning-poster/discovery-learning-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/discovery-learning-poster/discovery-learning-poster.png" alt="Becoming a Military Clinician">
</a>
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<a href="./archive/presentations/green-fellowship-poster/green-fellowship-poster.pdf" target="_blank">
<img class="d-block mx-auto" style="max-height:500px; max-width: 100%; opacity: 0.5" src="./archive/presentations/green-fellowship-poster/green-fellowship-poster.png" alt="Efficacy of Nanoformulation-Enhanced Photodynamic Therapy Excited by Radiation in Head and Neck Cancer Cells">
</a>
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<a href="./archive/presentations/clark-poster/clark-poster.pdf" target="_blank">
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</a>
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<h2 style="padding-top: 30px">Publications</h2>
<hr>
<a href="https://ieeexplore.ieee.org/abstract/document/10781675" target="_blank">
<h4><b>ANTs, BET, or…neither? An exploration of brain masking and machine learning tools applied to magnetic resonance elastography</b></h4>
</a>
<p>IEEE | Dec 17, 2024</p>
<p>Magnetic resonance elastography is a quantitative MRI modality that can aid in diagnosis of disease by detecting altered tissue mechanical properties. While brain masking tools exist for common MRI sequences, such as T1-weighted and T2-weighted imaging, there is no reliable masking tool for MRE. In this research, our innovation involves applying machine learning methods to a problem where no existing tools exist within the MRE research space. The demonstrated machine learning model shows potential for improvement in masking out distorted regions in brain elastography when compared to current non-machine learning masking methods not meant for MRE. This tool will enable automated and reproducible MRE results for neuroimaging applications.</p>
<hr>
<a href="https://www.sciencedirect.com/science/article/pii/S1930043324009919" target="_blank">
<h4><b>Dural arteriovenous fistula mimicking a stroke: A misdiagnosis of two months</b></h4>
</a>
<p>Radiology Case Reports | Sep 19, 2024</p>
<p>We present a case of a 70-year-old male who presented with left-sided weakness and dysarthria. Cranial imaging was suggestive of a cerebellar infarct and the patient was treated with aspirin and clopidogrel. Two months later a fall prompted further cranial imaging, which was concerning for an intracranial mass with vasogenic edema. Computed tomography angiogram (CTA) was negative for vascular lesion. Ultimately, a DSA revealed a Borden III dAVF between the right occipital artery and the posterior cerebellar vein that was treated with endovascular embolization.</p>
<hr>
<a href="https://www.mdpi.com/2072-6694/14/8/2004" target="_blank">
<h4><b>Deep-Tissue Activation of Photonanomedicines: An Update and Clinical Perspectives</b></h4>
</a>
<p>MDPI | Apr 15, 2022</p>
<p>Photodynamic therapy (PDT) is a light-activated treatment modality, which is being clinically used and further developed for a number of premalignancies, solid tumors, and disseminated cancers. Nanomedicines that facilitate PDT (photonanomedicines, PNMs) have transformed its safety, efficacy, and capacity for multifunctionality. This review focuses on the state of the art in deep-tissue activation technologies for PNMs and explores how their preclinical use can evolve towards clinical translation by harnessing current clinically available instrumentation.</p>
<h2 style="padding-top: 30px">Research Experience</h2>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://mrfilbioen.web.illinois.edu/" target="_blank"><img class="container" src="images/mrfil-logo.png" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://mrfilbioen.web.illinois.edu/" target="_blank">Magnetic Resonance Functional Imaging Laboratory</a></h2>
<p><i>Graduate Researcher | December 2022 – present</i></p>
<br>
<ul>
<li style="font-size: 14pt">Developed machine learning methods to extract information about the brain in magnetic resonance elastography data</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://mfp.hk.illinois.edu/" target="_blank"><img class="container" src="images/mfp-logo.jpg" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://mfp.hk.illinois.edu/" target="_blank">Mobility and Fall Prevention Research Laboratory</a></h2>
<p><i>Graduate Researcher | December 2022 – December 2024</i></p>
<br>
<ul>
<li style="font-size: 14pt">Characterized cognitive and motor function in gait with the goal of developing objective and standardized diagnostic measures of motor impairment and treatment</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://labs.utdallas.edu/obaid-mion/" target="_blank"><img class="container" src="images/mion-logo.png" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://labs.utdallas.edu/obaid-mion/" target="_blank">Obaid Lab for Molecular Imaging and Optical Nanotherapeutics</a></h2>
<p><i>Undergraduate Researcher | August 2021 – June 2022</i></p>
<ul>
<li style="font-size: 14pt">Continuation of research at UT Southwestern</li>
<li style="font-size: 14pt">Characterized various nanoscale drugs for head and neck cancers under light-activated, x-ray activated, and γ-ray activated conditions</li>
<li style="font-size: 14pt">Co-authored review artice: <i>Deep tissue activation of photonanomedicines: an update and clinical perspectives (accepted)</i></li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://afciviliancareers.com/" target="_blank"><img class="container" src="images/afcs-logo.jpg" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://afciviliancareers.com/" target="_blank">Air Force Civilian Service</a></h2>
<p><i>Premier College Intern | May 2021 – August 2021</i></p>
<ul>
<li style="font-size: 14pt">Premier College Intern as a part of the <a href="https://afciviliancareers.com/student-roa/" target="_blank">Premier College Intern Program</a></li>
<li style="font-size: 14pt">Worked in the 711th Human Performance Wing in the Bioanalytics Section at Wright-Patterson Air Force Base in the Air Force Research Laboratory</li>
<li style="font-size: 14pt">Research project involves developing an application for toxicological analysis integrated with machine learning applications</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://www.utsouthwestern.edu/education/graduate-school/" target="_blank"><img class="container" src="https://s3-us-west-2.amazonaws.com/utsw-patientcare-web-production/static/img/UTSouthwestern-Medical-Center.svg" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://www.utsouthwestern.edu/education/graduate-school/" target="_blank">UT Southwestern Graduate School of Biomedical Sciences</a></h2>
<p><i>Green Fellow | January 2021 – May 2021</i></p>
<ul>
<li style="font-size: 14pt">A research partnership between UT Dallas and UT Southwestern under the <a href="https://www.utsouthwestern.edu/education/graduate-school/research-opportunities/green-fellows.html" target="_blank">2021 Green Fellowship</a></li>
<li style="font-size: 14pt">Worked in the <a href="https://labs.utsouthwestern.edu/saha-lab" target="_blank">Saha Lab</a> in the Radiation Oncology/Molecular Radiation Biology Department at UT Southwestern</li>
<li style="font-size: 14pt">Acquired imaging data in 3D tumor models for head and neck cancer as well as imaged and modeled time-dependent distribution of x-ray responsive nanoparticles in response to varying doses of radiation therapy</li>
<li style="font-size: 14pt">Investigated the use of light-activatable nanotechnology as a facilitator for radiation therapy in radiation-resistant tumors of the head and neck</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://be.utdallas.edu/" target="_blank"><img class="container" src="images/utd-logo.jpg" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://be.utdallas.edu/" target="_blank">The Systems for Augmenting Human Mechanics Lab at UTD</a></h2>
<p><i>Undergraduate Researcher | January 2020 – Dec 2020</i></p>
<ul>
<li style="font-size: 14pt">Utilized neural network architecture to build a neural network to identify diseases related to the hip joint</li>
<li style="font-size: 14pt">Mainly used MATLAB</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://be.utdallas.edu/" target="_blank"><img class="container" src="images/utd-logo.jpg" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://be.utdallas.edu/" target="_blank">The Speech Disorders and Technology Lab at UTD</a></h2>
<p><i>Undergraduate Researcher | June 2018 – June 2019</i></p>
<ul>
<li style="font-size: 14pt"><a href="https://honors.utdallas.edu/research/clark-program/" target="_blank">Clark Summer Research Program</a> participant</li>
<li style="font-size: 14pt">Developed speech analysis programs</li>
<li style="font-size: 14pt">Mainly used MATLAB for data extraction and analysis</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://new.trinity.edu/" target="_blank"><img class="container" src="images/trinity-university-logo.jpg" /></a>
</div>
<div class="col-md-8">
<h2><a href="https://new.trinity.edu/" target="_blank">Trinity University Bioinformatics Department</a></h2>
<p><i>High School Researcher | January 2018 – April 2018</i></p>
<ul>
<li style="font-size: 14pt">Developed programs to analyze hybrid incompatiblities between strains of <em>Arabidopsis Thaliana</em></li>
<li style="font-size: 14pt">Mainly used Python for data extraction and analysis</li>
</ul>
</div>
</div>
<h3 style="padding-top: 30px">Other Employment Experience</h3>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://msegroup.com/" target="_blank"><img class="container" src="images/mse-logo.png" /></a>
</div>
<div class="col-md-8">
<br>
<h2><a href="https://msegroup.com/" target="_blank">MSE Group, LLC</a></h2>
<br>
<ul>
<li style="font-size: 14pt">Staff I IT Intern</li>
<li style="font-size: 14pt">Participated in general IT management</li>
<li style="font-size: 14pt">Submitted a TCEQ Air Quality Permit</li>
<li style="font-size: 14pt">Designed promotional material and editing the project outline for the electric vehicle plan for Electric Vehicles San Antonio</li>
<li style="font-size: 14pt">Digitized company reference material</li>
<li style="font-size: 14pt">EPA TRI Reporting</li>
<li style="font-size: 14pt">Electronic Stormwater Pollution Prevention Plan (eSWPPP) Development</li>
</ul>
</div>
</div>
<hr>
<div class="w3-container w3-padding-32 row">
<div class="col-md-4">
<a href="https://texasdls.com/" target="_blank"><img class="container" src="https://texasdls.com/wp-content/uploads/2018/05/TD-Logo-NEW-FOOTER.png" /></a>
</div>
<div class="col-md-8">
<br>
<h2><a href="https://texasdls.com/" target="_blank">Texas Dermatology and Laser Specialists</a></h2>
<br>
<ul>
<li style="font-size: 14pt">Company Intern (2016)</li>
<li style="font-size: 14pt">Updated personnel files, input patient data into database, took basic patient data, edited firm website</li>
<li style="font-size: 14pt">Mainly used HTML/CSS as well as customer interaction</li>
</ul>
</div>
</div>
</div>
</body>
</html>