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Bioimaging and Biomedical Optics Commons

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Water Exchange Rate Across The Blood-Brain Barrier Is Associated With Csf Amyloid-Β 42 In Healthy Older Adults, Brian T. Gold, Xingfeng Shao, Tiffany L. Sudduth, Gregory A. Jicha, Donna M. Wilcock, Elayna R. Seago, Danny J. J. Wang 2021 University of Kentucky

Water Exchange Rate Across The Blood-Brain Barrier Is Associated With Csf Amyloid-Β 42 In Healthy Older Adults, Brian T. Gold, Xingfeng Shao, Tiffany L. Sudduth, Gregory A. Jicha, Donna M. Wilcock, Elayna R. Seago, Danny J. J. Wang

Sanders-Brown Center on Aging Faculty Publications

INTRODUCTION: We tested if water exchange across the blood-brain barrier (BBB), estimated with a noninvasive magnetic resonance imaging (MRI) technique, is associated with cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) and neuropsychological function.

METHODS: Forty cognitively normal older adults (67–86 years old) were scanned with diffusion‐prepared, arterial spin labeling (DP‐ASL), which estimates water exchange rate across the BBB (kw). Participants also underwent CSF draw and neuropsychological testing. Multiple linear regression models were run with kw as a predictor of CSF concentrations and neuropsychological scores.

RESULTS: In multiple brain regions, BBB kw was positively associated ...


Biomedical Applications And Syntheses Of Selected Anthraquinone Dyes, Richard Sirard 2021 Liberty University

Biomedical Applications And Syntheses Of Selected Anthraquinone Dyes, Richard Sirard

Senior Honors Theses

Anthraquinones are aromatic organic compounds that have multiple applications in the biomedical field. Some anthraquinone-based compounds are used as fluorophores to contrast cell nuclei while others act as chemotherapeutic agents. However, there are not many fluorescent anthraquinone cell stains currently available. In this study, commercially available anthraquinone dyes, in addition to other dye families and compounds, were reviewed for their unique properties, advantages, and drawbacks. The development and characterization of three novel anthraquinone fluorophores revealed promising photophysical characteristics, like large Stokes shifts. One of the compounds, RBS3, was chosen for fixed and live cell staining and exhibited desirable biomedical properties ...


A Brief Bibliometric Survey Of Explainable Ai In Medical Field, Nilkanth Mukund Deshpande, Shilpa Shailesh Gite 2021 Department of Electronics and Telecommunication, Symbiosis Institute of Technology, Symbiosis International( Deemed University), Lavale, Pune-412115 and Dr. Vithalrao Vikhe Patil College of Engingeering, Ahmednagar

A Brief Bibliometric Survey Of Explainable Ai In Medical Field, Nilkanth Mukund Deshpande, Shilpa Shailesh Gite

Library Philosophy and Practice (e-journal)

Background: This study aims to analyze the work done in the field of explainability related to artificial intelligence, especially in the medical field from 2004 onwards using the bibliometric methods.

Methods: different articles based on the topic leukemia detection were retrieved using one of the most popular database- Scopus. The articles are considered from 2004 onwards. Scopus analyzer is used for different types of analysis including documents by year, source, county and so on. There are other different analysis tools such as VOSviewer Version 1.6.15. This is used for the analysis of different units such as co-authorship, co-occurrences ...


Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber 2021 University of Nebraska - Lincoln

Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber

Biological Systems Engineering--Dissertations, Theses, and Student Research

High resolution, long-term monitoring of key biological analytes would improve patient outcomes by providing earlier detection of disease states and improved efficacy of treatment. One class of biosensors that have gained much attention in recent years are optical biosensors. Optical probes are attractive biosensors due to their noninvasive nature of detection, as certain light can pass through tissue, water, and blood. Single walled carbon nanotubes (SWNT) are a specific type of optical biosensor that fluoresce in the near infrared range of the electromagnetic spectrum and offer unparalleled spatial and temporal resolution. SWNT have been applied as biosensors in vitro, ex ...


Nnemo (Neonatal Neuromonitor) - A Hybrid Optical System To Characterize Perfusion And Metabolism In The Newborn Brain, Ajay Rajaram 2021 The University of Western Ontario

Nnemo (Neonatal Neuromonitor) - A Hybrid Optical System To Characterize Perfusion And Metabolism In The Newborn Brain, Ajay Rajaram

Electronic Thesis and Dissertation Repository

Premature birth, defined as a gestational period less than 37 weeks, occurs in 8% of infants born in Canada. These births are associated with a higher risk of developing neurological complications. Infants born with very low birth weights (VLBW, < 1500 g) experience cognitive or behavioural deficits at a rate of 40-50%, while a further 5-10% develop major disorders such as cerebral palsy. The likelihood of injury increases with a shorter gestational period and/or a lower birthweight. Intraventricular hemorrhaging (IVH) occurs in 20-25% of VLBW infants, characterized by bleeding in the germinal matrix and surrounding white matter. This highly vascularized region is particularly susceptible to bleeds due to underdeveloped cerebrovascular structures. Severe IVH causes an inflammatory response and subsequent obstruction of cerebrospinal fluid (CSF) drainage, resulting in enlargement of the brain’s ventricles, referred to as post-hemorrhagic ventricular dilatation (PHVD). PHVD increases intracranial pressure and can result in compression/damage of brain tissue.

Diagnosis of IVH and PHVD is regularly performed using cranial ultrasound. Clinicians can visually assess and grade hemorrhaging/ventricle dilatation. Ultrasound, however, is limited in its ability to continuously monitor and only detects irreversible damage. NNeMo (Neonatal NeuroMonitor) is a hybrid optical device combining diffuse correlation (DCS) and near-infrared spectroscopy (NIRS) to simultaneous monitor cerebral blood flow (CBF) and metabolism at ...


Laparoscopic Image Recovery And Stereo Matching, Wenyao Xia 2021 The University of Western Ontario

Laparoscopic Image Recovery And Stereo Matching, Wenyao Xia

Electronic Thesis and Dissertation Repository

Laparoscopic imaging can play a significant role in the minimally invasive surgical procedure. However, laparoscopic images often suffer from insufficient and irregular light sources, specular highlight surfaces, and a lack of depth information. These problems can negatively influence the surgeons during surgery, and lead to erroneous visual tracking and potential surgical risks. Thus, developing effective image-processing algorithms for laparoscopic vision recovery and stereo matching is of significant importance. Most related algorithms are effective on nature images, but less effective on laparoscopic images.

The first purpose of this thesis is to restore low-light laparoscopic vision, where an effective image enhancement method ...


Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew 2021 Washington University in St. Louis

Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

The following sections are included:

  • Present State of Computational Modelling in Fluorescence Nanoscopy

  • Recent Contributions to Computational Modelling in Fluorescence Nanoscopy

  • Outlook on Computational Modelling in Fluorescence Nanoscopy

  • Acknowledgments

  • References


Fmri Feature Extraction Model For Adhd Classification Using Convolutional Neural Network, Senuri De Silva, Sanuwani Udara Dayarathna, Gangani Ariyarathne, Dulani Meedeniya, Sampath Jayarathna 2021 Old Dominion University

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 ...


Perceptually Improved Medical Image Translations Using Conditional Generative Adversarial Networks, Anurag Vaidya, Joshua Stough, Aalpen Patel, Benjamin Wheatley, Dan Cavanagh 2021 Bucknell University

Perceptually Improved Medical Image Translations Using Conditional Generative Adversarial Networks, Anurag Vaidya, Joshua Stough, Aalpen Patel, Benjamin Wheatley, Dan Cavanagh

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 ...


Understanding Radiation Resistance In Head And Neck Tumor Xenografts Using Diffuse Reflectance And Raman Spectroscopy, Sina Dadgar 2020 University of Arkansas, Fayetteville

Understanding Radiation Resistance In Head And Neck Tumor Xenografts Using Diffuse Reflectance And Raman Spectroscopy, Sina Dadgar

Theses and Dissertations

Each year, 800,000 new patients are diagnosed with head and neck squamous cell carcinoma (HNSCC), a majority of whom are treated with a combination of daily fractions of radiation and weekly chemotherapy sessions for up to seven weeks. Current methods to evaluate treatment response of individual patients are limited to anatomical measurements of tumor burden using CT scan or MRI 4-8 weeks after completion of treatment. However, earlier knowledge of radiation-response prior to or at early days after commencement of therapy can aid oncologist with escalating and de-escalating treatment plans for exceptionally non-responding and responding patients. Such a knowledge ...


3-D Fabry–Pérot Cavities Sculpted On Fiber Tips Using A Multiphoton Polymerization Process, Jonathan W. Smith, Jeremiah C. Williams, Joseph S. Suelzer, Nicholas G. Usechak, Hengky Chandrahalim 2020 Air Force Institute of Technology

3-D Fabry–Pérot Cavities Sculpted On Fiber Tips Using A Multiphoton Polymerization Process, Jonathan W. Smith, Jeremiah C. Williams, Joseph S. Suelzer, Nicholas G. Usechak, Hengky Chandrahalim

Faculty Publications

This paper presents 3-D Fabry–Pérot (FP) cavities fabricated directly onto cleaved ends of low-loss optical fibers by a two-photon polymerization (2PP) process. This fabrication technique is quick, simple, and inexpensive compared to planar microfabrication processes, which enables rapid prototyping and the ability to adapt to new requirements. These devices also utilize true 3-D design freedom, facilitating the realization of microscale optical elements with challenging geometries. Three different device types were fabricated and evaluated: an unreleased single-cavity device, a released dual-cavity device, and a released hemispherical mirror dual-cavity device. Each iteration improved the quality of the FP cavity's reflection ...


Deep Reinforcement Learning In Medical Object Detection And Segmentation, Dong Zhang 2020 The University of Western Ontario

Deep Reinforcement Learning In Medical Object Detection And Segmentation, Dong Zhang

Electronic Thesis and Dissertation Repository

Medical object detection and segmentation are crucial pre-processing steps in the clinical workflow for diagnosis and therapy planning. Although deep learning methods have achieved considerable performance in this field, they impose several shortcomings, such as computational limitations, sub-optimal parameter optimization, and weak generalization. Deep reinforcement learning as the newest artificial intelligence algorithm has great potential to address the limitation of traditional deep learning methods, as well as obtaining accurate detection and segmentation results. Deep reinforcement learning has a cognitive-like process to propose the area of desirable objects, thereby facilitating accurate object detection and segmentation. In this thesis, we deploy deep ...


Lipophilic Dye-Compatible Brain Clearing Technique Allowing Correlative Magnetic Resonance/High-Resolution Fluorescence Imaging In Rat Models Of Glioblastoma, Marco Peviani, Giorgia Spano, Antonella Pagani, Gianluca Brugnara, Cesare Covino, Rossella Galli, Alessandra Biffi, Letterio S. Politi 2020 Harvard Medical School

Lipophilic Dye-Compatible Brain Clearing Technique Allowing Correlative Magnetic Resonance/High-Resolution Fluorescence Imaging In Rat Models Of Glioblastoma, Marco Peviani, Giorgia Spano, Antonella Pagani, Gianluca Brugnara, Cesare Covino, Rossella Galli, Alessandra Biffi, Letterio S. Politi

Open Access Publications by UMMS Authors

In this work we optimized a novel approach for combining in vivo MRI and ex vivo high-resolution fluorescence microscopy that involves: (i) a method for slicing rat brain tissue into sections with the same thickness and spatial orientation as in in vivo MRI, to better correlate in vivo MRI analyses with ex-vivo imaging via scanning confocal microscope and (ii) an improved clearing protocol compatible with lipophilic dyes that highlight the neurovascular network, to obtain high tissue transparency while preserving tissue staining and morphology with no significant tissue shrinkage or expansion. We applied this methodology in two rat models of glioblastoma ...


A Polymer Gel Index-Matched To Water Enables Diverse Applications In Fluorescence Microscopy [Preprint], Xiaofei Han, Yijun Su, Hamilton White 2020 Tsinghua University

A Polymer Gel Index-Matched To Water Enables Diverse Applications In Fluorescence Microscopy [Preprint], Xiaofei Han, Yijun Su, Hamilton White

University of Massachusetts Medical School Faculty Publications

We demonstrate diffraction-limited and super-resolution imaging through thick layers (tens-hundreds of microns) of BIO-133, a biocompatible, UV-curable, commercially available polymer with a refractive index (RI) matched to water. We show that cells can be directly grown on BIO-133 substrates without the need for surface passivation and use this capability to perform extended time-lapse volumetric imaging of cellular dynamics 1) at isotropic resolution using dual-view light-sheet microscopy, and 2) at super-resolution using instant structured illumination microscopy. BIO-133 also enables immobilization of 1) Drosophila tissue, allowing us to track membrane puncta in pioneer neurons, and 2) Caenorhabditis elegans, which allows us to ...


The Clinical Utilities Of Multi-Pinhole Single Photon Emission Computed Tomography, Ilker Ozsahin, Ling Chen, Arda Konik, Michael A. King, Freek J. Beekman, Greta S. P. Mok 2020 University of Macau

The Clinical Utilities Of Multi-Pinhole Single Photon Emission Computed Tomography, Ilker Ozsahin, Ling Chen, Arda Konik, Michael A. King, Freek J. Beekman, Greta S. P. Mok

Open Access Publications by UMMS Authors

Single photon emission computed tomography (SPECT) is an important imaging modality for various applications in nuclear medicine. The use of multi-pinhole (MPH) collimators can provide superior resolution-sensitivity trade-off when imaging small field-of-view compared to conventional parallel-hole and fan-beam collimators. Besides the very successful application in small animal imaging, there has been a resurgence of the use of MPH collimators for clinical cardiac and brain studies, as well as other small field-of-view applications. This article reviews the basic principles of MPH collimators and introduces currently available and proposed clinical MPH SPECT systems.


Simulation Approaches To X-Ray C-Arm-Based Interventions, Daniel R. Allen 2020 The University of Western Ontario

Simulation Approaches To X-Ray C-Arm-Based Interventions, Daniel R. Allen

Electronic Thesis and Dissertation Repository

Mobile C-Arm systems have enabled interventional spine procedures, such as facet joint injections, to be performed minimally-invasively under X-ray or fluoroscopy guidance. The downside to these procedures is the radiation exposure the patient and medical staff are subject to, which can vary greatly depending on the procedure as well as the skill and experience of the team. Standard training methods for these procedures involve the use of a physical C-Arm with real X-rays training on either cadavers or via an apprenticeship-based program. Many guidance systems have been proposed in the literature which aim to reduce the amount of radiation exposure ...


A 3d Printed Axon-Mimetic Diffusion Mri Phantom, Tristan K. Kuehn 2020 The University of Western Ontario

A 3d Printed Axon-Mimetic Diffusion Mri Phantom, Tristan K. Kuehn

Electronic Thesis and Dissertation Repository

Diffusion MRI is used to non-invasively characterize the microstructure of the brain. However, the accuracy of the characterization is difficult to verify because no other non-invasive imaging modality provides the same information. This thesis presents a novel 3D printed axon-mimetic (3AM) diffusion MRI phantom, a synthetic object designed to mimic the brain's microstructure.

The phantoms were characterized using microscopy, synchrotron micro-computed tomography, and diffusion MRI, and found to have sufficiently axon-mimetic properties to be useful as diffusion MRI phantoms. A set of phantoms designed to have anatomically realistic and complex fibre structures was used to test the response of ...


Investigation Of Axial And Angular Sampling In Multi-Detector Pinhole-Spect Brain Imaging, Navid Zeraatkar, Kesava S. Kalluri, Benjamin Auer, Arda Konik, Timothy J. Fromme, Lars R. Furenlid, Phillip H. Kuo, Michael A. King 2020 University of Massachusetts Medical School

Investigation Of Axial And Angular Sampling In Multi-Detector Pinhole-Spect Brain Imaging, Navid Zeraatkar, Kesava S. Kalluri, Benjamin Auer, Arda Konik, Timothy J. Fromme, Lars R. Furenlid, Phillip H. Kuo, Michael A. King

Radiology Publications

We designed a dedicated multi-detector multi-pinhole brain SPECT scanner to generate images of higher quality compared to general-purpose systems. The system, AdaptiSPECT-C, is intended to adapt its sensitivity-resolution trade-off by varying its aperture configurations allowing both high-sensitivity dynamic and high-spatial-resolution static imaging. The current system design consists of 23 detector heads arranged in a truncated spherical geometry. In this work, we investigated the axial and angular sampling capability of the current stationary system design. Two data acquisition schemes using limited rotation of the gantry and two others using axial translation of the imaging bed were also evaluated concerning their impact ...


Model-Based Approach For Diffuse Glioma Classification, Grading, And Patient Survival Prediction, Zeina A. Shboul 2020 Old Dominion University

Model-Based Approach For Diffuse Glioma Classification, Grading, And Patient Survival Prediction, Zeina A. Shboul

Electrical & Computer Engineering Theses & Disssertations

The work in this dissertation proposes model-based approaches for molecular mutations classification of gliomas, grading based on radiomics features and genomics, and prediction of diffuse gliomas clinical outcome in overall patient survival. Diffuse gliomas are types of Central Nervous System (CNS) brain tumors that account for 25.5% of primary brain and CNS tumors and originate from the supportive glial cells. In the 2016 World Health Organization’s (WHO) criteria for CNS brain tumor, a major reclassification of the diffuse gliomas is presented based on gliomas molecular mutations and the growth behavior. Currently, the status of molecular mutations is determined ...


A Neurovascular High-Frequency Optical Coherence Tomography System Enables In Situ Cerebrovascular Volumetric Microscopy, Giovanni J. Ughi, Miklos G. Marosfoi, Robert M. King, Jildaz Caroff, Lindsy M. Peterson, Benjamin H. Duncan, Erin T. Langan, Amanda J. Collins, Anita M. Leporati, Serge Rousselle, Demetrius K. Lopes, Matthew J. Gounis, Ajit S. Puri 2020 University of Massachusetts Medical School

A Neurovascular High-Frequency Optical Coherence Tomography System Enables In Situ Cerebrovascular Volumetric Microscopy, Giovanni J. Ughi, Miklos G. Marosfoi, Robert M. King, Jildaz Caroff, Lindsy M. Peterson, Benjamin H. Duncan, Erin T. Langan, Amanda J. Collins, Anita M. Leporati, Serge Rousselle, Demetrius K. Lopes, Matthew J. Gounis, Ajit S. Puri

Radiology Publications

Intravascular imaging has emerged as a valuable tool for the treatment of coronary and peripheral artery disease; however, no solution is available for safe and reliable use in the tortuous vascular anatomy of the brain. Endovascular treatment of stroke is delivered under image guidance with insufficient resolution to adequately assess underlying arterial pathology and therapeutic devices. High-resolution imaging, enabling surgeons to visualize cerebral arteries' microstructure and micron-level features of neurovascular devices, would have a profound impact in the research, diagnosis, and treatment of cerebrovascular diseases. Here, we present a neurovascular high-frequency optical coherence tomography (HF-OCT) system, including an imaging console ...


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