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Bioimaging and Biomedical Optics Commons

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6d Single-Fluorogen Orientation-Localization Microscopy For Elucidating The Architecture Of Beta-Sheet Assemblies And Biomolecular Condensates, Tingting Wu, Weiyan Zhou, Jai S. Rudra, Rohit V. Pappu, Matthew D. Lew 2024 Washington University in St. Louis

6d Single-Fluorogen Orientation-Localization Microscopy For Elucidating The Architecture Of Beta-Sheet Assemblies And Biomolecular Condensates, Tingting Wu, Weiyan Zhou, Jai S. Rudra, Rohit V. Pappu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We develop six-dimensional single-molecule orientation-localization microscopy (SMOLM) to measure the 3D positions and 3D orientations simultaneously of single fluorophores. We show how careful optimization of phase and polarization modulation components can encode phase, polarization, and angular spectrum information from each fluorescence photon into a microscope’s dipole-spread function. We used the transient binding and blinking of Nile red (NR) to characterize the helical structure of fibrils formed by designed amphipathic peptides, KFE8L and KFE8D, and the pathological amyloid-beta peptide Aβ42. We also deployed merocyanine 540 to uncover the interfacial architectures of biomolecular condensates.


Development Of An In Vitro 3-Dimensional Co-Culture Human Colorectal Cancer Model In Microfluidic Devices, Abby Jens 2024 California Polytechnic State University, San Luis Obispo

Development Of An In Vitro 3-Dimensional Co-Culture Human Colorectal Cancer Model In Microfluidic Devices, Abby Jens

Master's Theses

Colorectal cancer is the second most common cause of cancer-related deaths in the United States, with the relative 5-year survival rate for distant stage cancer being only 14%. The most common treatment for colorectal cancer is with chemotherapeutic drugs; however, the discovery of these drugs is costly, time-consuming, and often requires the use of animal models that do not yield results that translate to clinical trials. Due to these shortcomings, researchers seek to develop physiologically relevant in vitro tumor models that more accurately mimic the tumor microenvironment for cheaper and faster high-throughput drug screening. The aim of this research was …


Comparison Of Scanning Electron Microscopy And Confocal Laser Microscopy For Tissue Surface Roughness Characterization, Tarnvir Dhaliwal 2024 California Polytechnic State University, San Luis Obispo

Comparison Of Scanning Electron Microscopy And Confocal Laser Microscopy For Tissue Surface Roughness Characterization, Tarnvir Dhaliwal

Master's Theses

It was found that the measurements captured by confocal microscopy and scanning electron microscopy had a statistically significant difference for bovine tissue. There was not a statistically significant for porcine and poultry tissue.

The intent of the study is to perform a comparative study to examine efficacy of two distinct technologies for a singular purpose: tissue surface roughness characterization. The two technologies compared are a confocal reflectance microscope and a scanning electron microscope. The comparison was made by comparing two surface roughness parameters [Ra and Rq] within ImageJ.

The study examined three different animal species [porcine, bovine, and poultry] to …


Plasma Protein Signatures Of Adult Asthma, Gordon J. Smilnak, Yura Lee, Abhijnan Chattopadhyay, Annah B. Wyss, Julie D. White, Sinjini Sikdar, Jianping Jin, Andrew J. Grant, Alison A. Motsinger-Reif, Jian-Liang Li, Mikyeong Lee, Bing Yu, Stephanie J. London 2024 National Institutes of Health

Plasma Protein Signatures Of Adult Asthma, Gordon J. Smilnak, Yura Lee, Abhijnan Chattopadhyay, Annah B. Wyss, Julie D. White, Sinjini Sikdar, Jianping Jin, Andrew J. Grant, Alison A. Motsinger-Reif, Jian-Liang Li, Mikyeong Lee, Bing Yu, Stephanie J. London

Mathematics & Statistics Faculty Publications

Background: Adult asthma is complex and incompletely understood. Plasma proteomics is an evolving technique that can both generate biomarkers and provide insights into disease mechanisms. We aimed to identify plasma proteomic signatures of adult asthma.

Methods: Protein abundance in plasma was measured in individuals from the Agricultural Lung Health Study (ALHS) (761 asthma, 1095 non-case) and the Atherosclerosis Risk in Communities study (470 asthma, 10,669 non-case) using the SOMAScan 5K array. Associations with asthma were estimated using covariate adjusted logistic regression and meta-analyzed using inverse-variance weighting. Additionally, in ALHS, we examined phenotypes based on both asthma and seroatopy (asthma with …


Deep Learning And Generative Ai Approaches For Automated Diagnosis And Personalized Treatment: Bridging Machine Learning, Medicine, And Biomechanics In Predicting Tissue Mechanics And Biomaterial Properties., Yasin Shokrollahi 2023 Florida Institute of Technology

Deep Learning And Generative Ai Approaches For Automated Diagnosis And Personalized Treatment: Bridging Machine Learning, Medicine, And Biomechanics In Predicting Tissue Mechanics And Biomaterial Properties., Yasin Shokrollahi

Theses and Dissertations

Machine learning, particularly deep neural networks, has demonstrated significant potential in predicting high-dimensional tasks across various domains. This work encompasses a detailed review of Generative AI in healthcare and three studies integrating machine learning with finite element analysis for predicting biomechanical behaviors and properties. Initially, we provide a comprehensive overview of Generative AI applications in healthcare, focusing on Transformers and Denoising Diffusion models and suggesting potential research avenues to address existing challenges.

Subsequently, we addressed soccer-related ocular injuries by combining finite element analysis and machine learning to predict retinal mechanics following a soccer ball hit rapidly. The prediction errors are …


Characterizing Intervertebral Disc Strain Under Dynamic Loading Conditions Using Ultrasound Texture Analysis, Radhika Kulkarni 2023 Purdue University

Characterizing Intervertebral Disc Strain Under Dynamic Loading Conditions Using Ultrasound Texture Analysis, Radhika Kulkarni

Discovery Undergraduate Interdisciplinary Research Internship

Herniated discs in the spine are a significant patient burden, with potential links to lower back and leg discomfort and a considerable impact on daily life. These discs, located between spinal vertebrae, are comprised of the annulus fibrosus (AF) and the nucleus pulposus (NP). Herniations happen when the NP protrudes through a full-thickness annular tear, possibly compressing spinal nerves. The mechanical factors underlying herniated discs are poorly understood, necessitating research into these mechanisms and accessible diagnostic techniques. Our study employs high-resolution ultrasound and texture correlation to quantify strain patterns in intervertebral discs during dynamic loading.

A motion segment from the …


Reactive Chemistries For Protein Labeling, Degradation, And Stimuli Responsive Delivery, Myrat Kurbanov 2023 University of Massachusetts Amherst

Reactive Chemistries For Protein Labeling, Degradation, And Stimuli Responsive Delivery, Myrat Kurbanov

Doctoral Dissertations

Reactive chemistries for protein chemical modification play an instrumental role in chemical biology, proteomics, and therapeutics. Depending on the application, the selectivity of these modifications can range from precise modification of an amino acid sequence by genetic manipulation of protein expression machinery to a stochastic modification of lysine residues on the protein surface. Ligand-Directed (LD) chemistry is one of the few methods for targeted modification of endogenous proteins without genetic engineering. However, current LD strategies are limited by stringent amino acid selectivity. To bridge this gap, this thesis focuses on the development of highly reactive LD Triggerable Michael Acceptors (LD-TMAcs) …


Free-Hand Photoacoustic Imaging Of Breast Cancer Tissue, Elina Rascevska 2023 Western University

Free-Hand Photoacoustic Imaging Of Breast Cancer Tissue, Elina Rascevska

Electronic Thesis and Dissertation Repository

Approximately 19% of breast cancer patients undergoing breast conserving surgery (BCS) must return for a re-excision surgery due to positive margin reported by pathology. This problem is mainly associated with lack of intraoperative cancer margin assessment tools. Our previous work demonstrated that lipid-weighted photoacoustic imaging (PAI) can be used intraoperatively to successfully differentiate between cancerous and healthy tissue with high sensitivity. However, the technology was cumbersome and significantly prolonged the procedure time. The goal of this work was to develop a compact hand-held probe, working on lipid-weighted PAI principles, that can provide feedback during BSC without significantly altering the surgical …


Characterization Of Mammographic Dense Tissue Sub-Types Using Classification Algorithms On Metric Space Technique Output Functions, Madison Raza 2023 University of Maine

Characterization Of Mammographic Dense Tissue Sub-Types Using Classification Algorithms On Metric Space Technique Output Functions, Madison Raza

Electronic Theses and Dissertations

In recent years breast cancer has become the leading cause of global cancer incidence. One of the most common forms of screening is through the use of digital x-ray screening mammography. Risk assessment models which help predict a patient’s risk of developing breast cancer rely mainly on patient history and qualitative breast density assessment from screening. The 2D wavelet transform maxima modulus (2D WTMM) method uses a sliding window approach to quantify the spatial organization of underlying mammographic tissue according to Hurst- exponent ranges (H) as fatty (H ≤ 0.45), healthy dense (H ≥ 0.55) and …


Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke 2023 Duquesne University

Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke

Electronic Theses and Dissertations

The number of daily bacterial infections is climbing and the CDC explains that this is due to the antibiotic-resistant threat in the United States. Finding a faster way of bacterial identification is necessary as it currently takes 1-4 days for a medical lab to culture and identify bacteria. Photoacoustic flow cytometry (PAFC) can be used as an alternative method resulting in swift identification within an hour (Edgar, 2019). Pseudomonas aeruginosa, cell line PA01, will be coated in up to a few hundred red dyed phages making it detectible by the photoacoustic flow cytometry system. Bacteriophages (phages) are viruses that …


Scanning Electron Microscopy Analysis Of Murine Renal, Aortic, And Cardiac Tissue, Sarah E. Grev, Luke E. Schepers, Jennifer Anderson, Craig J. Goergen 2023 Purdue University

Scanning Electron Microscopy Analysis Of Murine Renal, Aortic, And Cardiac Tissue, Sarah E. Grev, Luke E. Schepers, Jennifer Anderson, Craig J. Goergen

Discovery Undergraduate Interdisciplinary Research Internship

Scanning electron microscopy (SEM) is a tool that provides detailed insight into objects invisible to the human eye. As the name suggests, an electron beam is used to create an image down to the nanometer scale. The beam focuses on the surface of a sample using lenses in the electron column. In this project, we use SEM to study three types of murine tissue. First, we examine the glomerulus, found in the kidney, that is primarily responsible for filtering blood. Following a left renal vein (LRV) stenosis, SEM is used to observe changes to the glomeruli. Differences in the left …


Novel Magnetic Resonance Imaging-Compatible Mechatronic Needle Guidance System For Prostate Focal Laser Ablation Therapy, Eric R. Knull 2023 Western University

Novel Magnetic Resonance Imaging-Compatible Mechatronic Needle Guidance System For Prostate Focal Laser Ablation Therapy, Eric R. Knull

Electronic Thesis and Dissertation Repository

Advances in prostate cancer (PCa) screening techniques have led to diagnosis of many cases of low-grade and highly localized disease. Conventional whole-gland therapies often result in overtreatment in such cases and debate still surrounds the optimal method of oncologic control. MRI-guided prostate focal laser ablation (FLA) is a minimally invasive treatment option, which has demonstrated potential to destroy localized lesions while sparing healthy prostatic tissue, thereby reducing treatment-related side effects. Many challenges still exist in the development of FLA, including patient selection; tumour localization, visualization, and characterization; needle guidance; and evaluation of treatment efficacy. The objective of this thesis work …


Cad System For Early Diagnosis Of Diabetic Retinopathy Based On 3d Extracted Imaging Markers., Ahmed Sleman 2023 University of Louisville

Cad System For Early Diagnosis Of Diabetic Retinopathy Based On 3d Extracted Imaging Markers., Ahmed Sleman

Electronic Theses and Dissertations

This dissertation makes significant contributions to the field of ophthalmology, addressing the segmentation of retinal layers and the diagnosis of diabetic retinopathy (DR). The first contribution is a novel 3D segmentation approach that leverages the patientspecific anatomy of retinal layers. This approach demonstrates superior accuracy in segmenting all retinal layers from a 3D retinal image compared to current state-of-the-art methods. It also offers enhanced speed, enabling potential clinical applications. The proposed segmentation approach holds great potential for supporting surgical planning and guidance in retinal procedures such as retinal detachment repair or macular hole closure. Surgeons can benefit from the accurate …


Design Of Asic Based Electrical Impedance Tomography Microendoscopic System For Prostate Cancer Surgical Marginal Assessment, Mohsen Shahghasemi 2023 Dartmouth College

Design Of Asic Based Electrical Impedance Tomography Microendoscopic System For Prostate Cancer Surgical Marginal Assessment, Mohsen Shahghasemi

Dartmouth College Ph.D Dissertations

Prostate cancer is the second most common cancer in the United States. It is typically treated by surgically excising the cancerous section of the prostate. Because there is not always a visible distinction between the healthy and cancerous sections, surgery often leaves some cancerous tissue behind. This is referred to as a positive surgical margin and it requires adjuvant treatment with adverse side effects. Electrical impedance tomography (EIT) is a low-cost low-form-factor method that can be used to assess surgical marginal intraoperatively to ensure that no cancerous tissue is left behind. EIT-based surgical margin assessment works on the principle that …


List Of 121 Papers Citing One Or More Skin Lesion Image Datasets, Neda Alipour 2023 Technological University Dublin

List Of 121 Papers Citing One Or More Skin Lesion Image Datasets, Neda Alipour

Other resources

No abstract provided.


Mechanisms Of Theta Burst Transcranial Ultrasound Induced Plasticity In The Human Motor Cortex, Yazan Shamli Oghli, Talyta Grippe, Tarun Arora, Tasnuva Hoque, Ghazaleh Darmani, Robert Chen 2023 Thomas Jefferson University

Mechanisms Of Theta Burst Transcranial Ultrasound Induced Plasticity In The Human Motor Cortex, Yazan Shamli Oghli, Talyta Grippe, Tarun Arora, Tasnuva Hoque, Ghazaleh Darmani, Robert Chen

Department of Medicine Faculty Papers

BACKGROUND: Transcranial ultrasound stimulation (TUS) is a novel non-invasive brain stimulation technique with high depth penetrance and spatial resolution. Theta-burst TUS (tbTUS) is a plasticity-inducing protocol which increases motor cortical excitability for up to 30 min following 80s of sonication. While this protocol may have therapeutic potential for the treatment of psychiatric and neurological disorders, the mechanisms of action of TUS remain unclear.

OBJECTIVE: We conducted the first pharmacological study to examine the mechanisms of TUS in human primary motor cortex. By administering brain-active drugs with known mechanisms of action, we aimed to elucidate the mechanisms of tbTUS.

METHODS: Fourteen …


Intraoperative Quantification Of Bone Perfusion In Lower Extremity Injury Surgery, Xinyue Han 2023 Dartmouth College

Intraoperative Quantification Of Bone Perfusion In Lower Extremity Injury Surgery, Xinyue Han

Dartmouth College Ph.D Dissertations

Orthopaedic surgery is one of the most common surgical categories. In particular, lower extremity injuries sustained from trauma can be complex and life-threatening injuries that are addressed through orthopaedic trauma surgery. Timely evaluation and surgical debridement following lower extremity injury is essential, because devitalized bones and tissues will result in high surgical site infection rates. However, the current clinical judgment of what constitutes “devitalized tissue” is subjective and dependent on surgeon experience, so it is necessary to develop imaging techniques for guiding surgical debridement, in order to control infection rates and to improve patient outcome.

In this thesis work, computational …


Neural Correlates Of Post-Traumatic Brain Injury (Tbi) Attention Deficits In Children, Meng Cao 2023 New Jersey Institute of Technology

Neural Correlates Of Post-Traumatic Brain Injury (Tbi) Attention Deficits In Children, Meng Cao

Dissertations

Traumatic brain injury (TBI) in children is a major public health concern worldwide. Attention deficits are among the most common neurocognitive and behavioral consequences in children post-TBI which have significant negative impacts on their educational and social outcomes and compromise the quality of their lives. However, there is a paucity of evidence to guide the optimal treatment strategies of attention deficit related symptoms in children post-TBI due to the lack of understanding regarding its neurobiological substrate. Thus, it is critical to understand the neural mechanisms associated with TBI-induced attention deficits in children so that more refined and tailored strategies can …


Methodology For Formalin Fixed Paraffin Embedded Cardiac Tissue Analysis, Leah G. Gutzwiller, Colleen Crouch 2023 University of Tennessee Knoxville

Methodology For Formalin Fixed Paraffin Embedded Cardiac Tissue Analysis, Leah G. Gutzwiller, Colleen Crouch

Haslam Scholars Projects

No abstract provided.


Noninvasively Monitoring Of Cerebral Blood Flow In Piglet Models Of Graded Hemorrhage And Hypoxic Ischemic Brain Injury Using Diffuse Correlation Spectroscopy And Near-Infrared Spectroscopy, Randolph Sinahon, Danielle Shoshany, Shadi Malaeb, Mert Deniz Polat, Meltem Izzetoglu, Kurtulus Izzetoglu 2023 Drexel University

Noninvasively Monitoring Of Cerebral Blood Flow In Piglet Models Of Graded Hemorrhage And Hypoxic Ischemic Brain Injury Using Diffuse Correlation Spectroscopy And Near-Infrared Spectroscopy, Randolph Sinahon, Danielle Shoshany, Shadi Malaeb, Mert Deniz Polat, Meltem Izzetoglu, Kurtulus Izzetoglu

St. Chris Research Day

No abstract provided.


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