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Medical Imaging 2020: Digital Pathology

作者： Dammak, Salma Cecchini, Matthew Baranova, Katherina Palma, David Kwan, Keith Ward, Aaron D. School of Biomedical Engineering Biomedical Engineering Graduate Program Western University LondonON Canada Department of Medical Biophysics Western University LondonON Canada Department of Oncology Western University LondonON Canada Schulich School of Medicine and Dentistry Western University LondonON Canada Department of Pathology and Laboratory Medicine Western University LondonON Canada

ISBN: (纸本)9781510634077

Immunotherapy is a novel anti-cancer treatment that shows significant improvements in outcomes for lung cancer patients. However, this treatment has the potential for substantial side effects in a minority of patients, and many lung cancer patients do not benefit from it. programmed-death ligand-1 expression in tumour cells is currently the main biomarker used to identify those who might benefit but it is not very accurate. Tumour mutational burden (TMB) is a promising alternative, with lung cancers having more than 10 mutations/megabase being more likely to respond to immunotherapy. However, the cost and time it takes to obtain TMB makes it difficult to implement in the clinic. In this study, we used the deep learning technique of transfer learning with Alexnet to obtain a model that can estimate whether a cancer is highly mutated or not based on digitized hematoxylin and eosin histology slides that are routinely obtained from surgical resection of squamous cell carcinoma. The system was developed using images from 20 patients obtained through The Cancer Genome Atlas, five of which were reserved for validation. On this validation set, the system had an area under the receiver operator characteristic curve of 0.80, error rate of 24%, false negative rate of 26%, and false positive rate of 22%. This motivates additional work in this direction to build a system that can be used in the future to inform physicians as to which patients with squamous lung carcinoma would benefit from immunotherapy. © 2020 SPIE. All rights reserved.

关键词： Cancer Lung cancer Genetics Medicine Lung Computer aided diagnosis and therapy Convolutional neural networks Decision support systems Medical imaging Pathology

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Review of Image-Guided Percutaneous Coronary Interventions

Review of Image-Guided Percutaneous Coronary Interventions

引用

2019 Advances in Science and engineering Technology International Conferences, ASET 2019

作者： Alatoom, Aseel Farhat, Jumana Dhou, Salam Biomedical Engineering Graduate Program American University of Sharjah Sharjah United Arab Emirates Department of Computer Science and Engineering Biomedical Engineering Graduate Program Biosciences and Bioengineering Research Institute American University of Sharjah Sharjah United Arab Emirates

ISBN: (纸本)9781538682715

Image-guided surgery (IGS) involves using surgical instruments tracking system to guide the surgeon during invasive surgical procedures. The use of preoperative or intraoperative images is very essential in providing navigation for different medical applications. In this paper, a literature review of different imaging modalities that aid in the diagnosis and treatment of coronary artery disease (CAD) is proposed. The imaging modalities discussed include x-ray fluoroscopy, coronary computed tomography angiography (CCTA), fractional flow reserve (FFR), cardiac single-photon emission computed tomography (SPECT), cardiovascular magnetic resonance imaging (CMRI) and ultrasound. Additionally, pseudoaneurysms, which can result from percutaneous coronary interventions (PCI) procedure, are reviewed as well as the treatment procedure. Finally, a comparison between the different imaging modalities is carried out, based on the number of papers that have been published, in addition to the sensitivity and specificity for each modality according to PubMed and Web of Science databases. © 2019 IEEE.

关键词： Ultrasonics

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Hierarchical Assembly and Dynamic Reinforced Woven Biotextiles for Anisotropic and Viscoelastic Tendon Tissue Regeneration

SSRN

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SSRN 2025年

作者： Wang, Tzu-Wei Chen, Hao-Xuan Chen, Shih-Heng Chen, Shih-Hsien Liu, Yu-Chung Wu, Chen-Te Kuan, Chen-Hsiang Huang, Wei-Yuan Department of Materials Science and Engineering National Tsing Hua University Hsinchu Taiwan Department of Plastic and Reconstructive Surgery Chang-Gung Memorial Hospital Chang-Gung University Medical College Taoyuan Taiwan Department of Biomedical Engineering University of Michigan Ann ArborMI United States Department of Medical Imaging and Intervention Chang Gung Memorial Hospital Taoyuan Taiwan Taipei Taiwan Graduate Institute of Clinical Medicine College of Medicine National Taiwan University Taipei Taiwan Research Center for Developmental Biology and Regenerative Medicine National Taiwan University Taipei Taiwan Precision Medicine Program National Tsing Hua University Hsinchu Taiwan Institute of Oral Biology National Yang Ming Chiao Tung University Taiwan Department of Biomedical Engineering Linkou Chang Gung Memorial Hospital Taiwan

Currently used tendon grafts, including autologous and allogeneic options, are hindered by limitations such as availability, donor site morbidity, and the risk of immune rejection. While offering potential alternatives, artificial tendons still have drawbacks, including creep, stress relaxation, fatigue, and poor tissue integration. To overcome these challenges with unmet clinical needs, this study develops a biomimetic tendon graft using interfacial polyelectrolyte complexation spinning techniques combined with customized twisting and weaving reinforcements. Hierarchical tendon biomimicry addresses anatomical and physiological features crucial for tendon repair and regeneration. The dynamic strengthening culture and growth factor incorporation with spatial-controlled delicacy further enhance the integration and functionality of the substitute with tendon-related protein secretion, both of which are valuable characteristics in native tissues. As demonstrated in fatigue tests, the durability and viscoelasticity of the braided scaffolds under loading-unloading cycles highlight their suitability for daily activities. This bottom-up assembly approach replicates the physiological, biological, and mechanical properties of native tendon tissue. For future perspective, this study represents a significant advancement in tendon tissue engineering, offering bioinspired woven biotextiles that hold great promise for tendon replacement. © 2025, The Authors. All rights reserved.

关键词： Tissue regeneration

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ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing

arXiv

引用

arXiv 2023年

作者： Kuczynski, Michael T. Neeteson, Nathan J. Stok, Kathryn S. Burghardt, Andrew J. Espinosa Hernandez, Michelle A. Vicory, Jared Tse, Justin J. Durongbhan, Pholpat Bonaretti, Serena Wong, Andy Kin On Boyd, Steven K. Manske, Sarah L. McCaig Institute for Bone and Joint Health University of Calgary Calgary Canada Biomedical Engineering Graduate Program University of Calgary Calgary Canada Department of Biomedical Engineering The University of Melbourne Parkville Australia Department of Radiology and Biomedical Imaging University of California San Francisco United States Rehabilitation Sciences Institute The University of Toronto Toronto Canada Joint Department of Medical Imaging University Health Network Toronto Canada Kitware Inc. CarrboroNC United States Department of Radiology Cumming School of Medicine University of Calgary Calgary Canada Swiss Center for Musculoskeletal Imaging Balgrist Campus Zurich Switzerland Department of Epidemiology Dalla Lana School of Public Health University of Toronto Toronto Canada

High resolution peripheral quantitative computed tomography (HR-pQCT) is animaging technique capable of imaging trabecular bone in-vivo. HR-pQCT has awide range of applications, primarily focused on bone to improve ourunderstanding of musculoskeletal diseases, assess epidemiological associations,and evaluate the effects of pharmaceutical interventions. Processing HR-pQCTimages has largely been supported using the scanner manufacturer scriptinglanguage (Image Processing Language, IPL, Scanco Medical). However, byexpanding image processing workflows outside of the scanner manufacturersoftware environment, users have the flexibility to apply more advancedmathematical techniques and leverage modern software packages to improve imageprocessing. The ORMIR_XCT Python package was developed to reimplement someexisting IPL workflows and provide an open and reproducible package allowingfor the development of advanced HR-pQCT data processing workflows. © 2023, CC BY-SA.

关键词： High level languages

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ShapeY: Measuring shape recognition capacity using nearest neighbor matching

arXiv

引用

arXiv 2021年

作者： Nam, Jong Woo Rios, Amanda S. Mel, Bartlett W. Neuroscience Graduate Program University of Southern California Los AngelesCA90007 United States Biomedical Engineering Department University of Southern California Los AngelesCA90007 United States

Object recognition in humans depends primarily on shape cues. We have developed a new approach to measuring the shape recognition performance of a vision system based on nearest neighbor view matching within the system's embedding space. Our performance benchmark, ShapeY, allows for precise control of task difficulty, by enforcing that view matching span a specified degree of 3D viewpoint change and/or appearance change. As a first test case we measured the performance of ResNet50 pre-trained on ImageNet. Matching error rates were high. For example, a 27° change in object pitch led ResNet50 to match the incorrect object 45% of the time. Appearance changes were also highly disruptive. Examination of false matches indicates that ResNet50's embedding space is severely "tangled". These findings suggest ShapeY can be a useful tool for charting the progress of artificial vision systems towards human-level shape recognition capabilities. © 2021, CC BY.

关键词： Embeddings

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Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy

引用

Nanoscale 2021年第15期13卷 7285-7293页

作者： Casasanta, Michael A. Jonaid, G.M. Kaylor, Liam Luqiu, William Y. Solares, Maria J. Schroen, Mariah L. Dearnaley, William J. Wilson, Jarad Dukes, Madeline J. Kelly, Deborah F. Department of Biomedical Engineering Pennsylvania State University University Park 16802 PA United States Materials Research Institute Pennsylvania State University University Park 16802 PA United States Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park 16802 PA United States Molecular Cellular and Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park 16802 PA United States Department of Electrical and Computer Engineering Duke University Durham 27708 NC United States RayBiotech Life Peachtree Corners 30092 GA United States Applications Science Protochips Inc Morrisville 27560 NC United States

Interest in cryo-Electron Microscopy (EM) imaging has skyrocketed in recent years due to its pristine views of macromolecules and materials. As advances in instrumentation and computing algorithms spurred this progress, there is renewed focus to address specimen-related challenges. Here we contribute a microchip-based toolkit to perform complementary structural and biochemical analysis on low-molecular weight proteins. As a model system, we used the SARS-CoV-2 nucleocapsid (N) protein (48 kDa) due to its stability and important role in therapeutic development. Cryo-EM structures of the N protein monomer revealed a flexible N-terminal "top hat"motif and a helical-rich C-terminal domain. To complement our structural findings, we engineered microchip-based immunoprecipitation assays that led to the discovery of the first antibody binding site on the N protein. The data also facilitated molecular modeling of a variety of pandemic and common cold-related coronavirus proteins. Such insights may guide future pandemic-preparedness protocols through immuno-engineering strategies to mitigate viral outbreaks. This journal is © The Royal Society of Chemistry.

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Microwell-Patterned Microfluidic Device for Rapid Identification of High-Affinity Anti-Tumor T Cells

Microwell-Patterned Microfluidic Device for Rapid Identifica...

引用

IEEE International Conference on Micro Electro Mechanical Systems

作者： Kavya L. Singampalli Desh Deepak Dixit Peixin Jiang Alexandre Reuben Peter B. Lillehoj Department of Bioengineering Rice University Houston TX USA Medical Scientist Training Program Baylor College of Medicine Houston TX USA Department of Mechanical Engineering Rice University Houston TX USA Department of Thoracic/ Head and Neck Medical Oncology The University of Texas MD Anderson Cancer Center Houston TX USA The University of Texas MD Anderson Cancer Center UT Health Houston Graduate School of Biomedical Sciences Houston TX USA

This paper presents a microfluidic device for the rapid identification of high-affinity anti-tumor T cells. This device consists of a polymethyl methacrylate (PMMA) microchannel containing a dense array of circular microwells fabricated using a unique CO 2 laser etching process. Using this device, OT-I T cells and LLC-OVA tumor cells were incubated within microwells to identify high-affinity T cells in <1 hour, which is significantly faster than existing T cell screening methods (requiring weeks/months) while being simpler to operate without requiring sophisticated instrumentation. Furthermore, this method is compatible with adherent and nonadherent tumor cells, making it a versatile platform for T cell-tumor cell interaction studies and T cell screening.

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Thermography for the detection of Secondary Raynaud's Phenomenon by means of the Distal-Dorsal Distance

Thermography for the detection of Secondary Raynaud's Phenom...

引用

Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： J.R. Viana D. Campos L. Ulbricht G.Y. Sato W.L. Ripka Universidade Tecnológica Federal do Paraná with the Graduate Program in Biomedical Engineering Curitiba Brazil Federal University of Paraná with the Graduate Program in Physical Education

ISBN: (数字)9781728119908

ISBN: (纸本)9781728119915

Raynaud's phenomenon (RP) is a disease characterized by a transient ischemic process, in an exaggerated vascular response to cold or emotional stress. Thermography is a resource applied to support diagnosis of changes in the circulatory system. The aim of the study was to use the DistalDorsal Thermography Difference (DDD) in thermographic images to assess thermal behavior in individuals with secondary RP. The research was carried out in the period between 2018 and 2019. The sample means of the Distal-consisted of 44 individuals in a control group (Control) and 44 individuals in a pathological group (RP2). The participants, after acclimatization, were submitted to the cold stress protocol. The protocol consisted of immersing hands in a container of water at a temperature of 15°C for 60 seconds. The acquisition of thermographic images was performed at the pre-test moment and at the 1st, 3rd, 5th, 7th, 10th and 15th minute. At each time, the DDD values (of all fingers - minimum, maximum and sum) between the groups were analyzed. For statistical analysis, the independent t test and Cohen's d test were used. Regarding the results, there was a difference in relation to the rate of temperature recovery between the groups. The first group showed a rate of reheating just after the first minute subsequent to the cold stress test, while the RP2 group was unable to recover the temperature over 15 minutes. DDD, regardless of the selected criterion, proved to be a valid index for verifying the temperature gradient in the study with individuals identified with secondary RP.

关键词： Thumb Temperature measurement Diseases Stress Protocols Temperature sensors

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Optogenetic Neural Probes: Fiberless, High-Density, Artifact-Free Neuromodulation : (Invited)

Optogenetic Neural Probes: Fiberless, High-Density, Artifact...

引用

International Electron Devices Meeting (IEDM)

作者： Eunah Ko Kanghwan Kim Mihály Vöröslakos Sungjin Oh György Buzsáki Kensall D. Wise Euisk Yoon Department of Electrical Engineering and Computer Science University of Michigan Ann Arbor MI USA Center for BioMicrosystems Brain Science Institute Korea Institute of Science and Technology Seoul Korea Neuroscience Institute Langone Medical Center New York University New York NY USA Department of Biomedical Engineering University of Michigan Ann Arbor MI USA Center for Nanomedicine Institute for Basic Science (IBS) and Graduate Program of Nano Biomedical Engineering (Nano BME) Advanced Science Institute Yonsei University Seoul Korea

ISBN: (纸本)9781665489607

Evolution of “Michigan Probes” has enabled unraveling the connectivity of neurons at cellular resolution and their dynamic interaction within and across brain areas that underlie behavioral and cognitive functions. Recently, micro-LEDs were monolithically integrated for optogenetic neuromodulation at scale without requiring external optical fiber connection. The ‘hectoSTAR’ micro-LED optoelectrode features 256 recording electrodes and 128 stimulation micro-LEDs in four silicon micro-needle shanks, covering a large volume with 1.3-mm × 0.9-mm cross-sectional area located as deep as 6 mm inside the brain. Technical challenges to overcome in scaling of optogenetic probes will be discussed, followed by future direction.

关键词： Optical fibers Electrodes Brain Optogenetics Silicon Recording Optical fiber devices

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Towards Robust Natural-Looking Mammography Lesion Synthesis on Ipsilateral Dual-Views Breast Cancer Analysis

arXiv

引用

arXiv 2023年

作者： Nguyen, Thanh-Huy Kha, Quang Hien Truong, Thai Ngoc Toan Lam, Ba Thinh Ngo, Ba Hung Dinh, Quang Vinh Le, Nguyen Quoc Khanh Department of Biomedical Engineering National Cheng Kung University Taiwan International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taiwan Viet Nam Ho Chi Minh City International University Viet Nam Graduate School of Data Science Chonnam National University Korea Republic of Vietnamese-German University Viet Nam Research Center for Artificial Intelligence in Medicine Taipei Medical University Taiwan Professional Master Program in Artificial Intelligence in Medicine Taiwan

In recent years, many mammographic image analysis methods have been introduced for improving cancer classification tasks. Two major issues of mammogram classification tasks are leveraging multi-view mammographic information and class-imbalance handling. In the first problem, many multi-view methods have been released for concatenating features of two or more views for the training and inference stage. Having said that, most multi-view existing methods are not explainable in the meaning of feature fusion, and treat many views equally for diagnosing. Our work aims to propose a simple but novel method for enhancing examined view (main view) by leveraging low-level feature information from the auxiliary view (ipsilateral view) before learning the high-level feature that contains the cancerous features. For the second issue, we also propose a simple but novel malignant mammogram synthesis framework for upsampling minor class samples. Our easy-to-implement and no-training framework has eliminated the current limitation of the CutMix algorithm which are unreliable synthesized images with random pasted patches, hard-contour problems, and domain shift problems. Our results on VinDr-Mammo and CMMD datasets show the effectiveness of our two new frameworks for both multi-view training and synthesizing mammographic images, outperforming the previous conventional methods in our experimental settings. © 2023, CC BY-NC-SA.

关键词： Mammography

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