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Understanding ADC variation by fat content effect using a dual-function MRI phantom

European Radiology Experimental 2024年第1期8卷 1-11页

作者： Liu, Yi-Jui Tsai, Tung-Sheng Li, Ya-Hui Peng, Jo-Hua Chang, Hing-Chiu Peng, Hsu-Hsia Lee, Ying-Chieh Lee, Tung-Yang Liou, Chang-Hsien Lin, Tz-Feng Chew, Fatt-Yang Chou, Ruey-Hwang Juan, Chun-Jung Department of Automatic Control Engineering Feng Chia University Taichung Taiwan Ph.D. Program in Electrical and Communication Engineering Feng Chia University Taichung Taiwan Department of Medical Imaging China Medical University Hsinchu Hospital 199 Sec. 1 Xinglong Rd. Hsinchu County Zhubei City 302 Taiwan Department of Biomedical Engineering and Environmental Sciences National Tsing Hua University Hsinchu Taiwan Department of Biomedical Engineering Chinese University of Hong Kong Hong Kong Master’s Program of Biomedical Informatics and Biomedical Engineering Feng Chia University Taichung Taiwan Cheng Ching Hospital Taichung Taiwan Institute of Nuclear Engineering and Science National Tsing Hua University Hsinchu Taiwan Department of Fiber and Composite Materials Feng Chia University Taichung Taiwan Department of Medical Imaging China Medical University Hospital Taichung Taiwan Department of Radiology School of Medicine China Medical University Taichung Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung 406 Taiwan Center for Molecular Medicine China Medical University Hospital Taichung Taiwan Department of Medical Laboratory and Biotechnology Asia University Taichung Taiwan

Background: A dual-function phantom designed to quantify the apparent diffusion coefficient (ADC) in different fat contents (FCs) and glass bead densities (GBDs) to simulate the human tissues has not been documented yet. We propose a dual-function phantom to quantify the FC and to measure the ADC at different FCs and different GBDs. Methods: A fat-containing diffusion phantom comprised by 30 glass-bead-containing fat-water emulsions consisting of six different FCs (0, 10, 20, 30, 40, and 50%) multiplied by five different GBDs (0, 0.1, 0.25, 0.5, and 1.0 g/50 mL). The FC and ADC were measured by the “iterative decomposition of water and fat with echo asymmetry and least squares estimation-IQ,” IDEAL-IQ, and single-shot echo-planar diffusion-weighted imaging, SS-EP-DWI, sequences, respectively. Linear regression analysis was used to evaluate the relationship among the fat fraction (FF) measured by IDEAL-IQ, GBD, and ADC. Results: The ADC was significantly, negatively, and linearly associated with the FF (the linear slope ranged from -0.005 to -0.017, R² = 0.925 to 0.986, all p < 0.001). The slope of the linear relationship between the ADC and the FF, however, varied among different GBDs (the higher the GBD, the lower the slope). ADCs among emulsions across different GBDs and FFs were overlapped. Emulsions with low GBDs plus high FFs shared a same lower ADC range with those with median or high GBDs plus median or lower FFs. Conclusions: A novel dual-function phantom simulating the human tissues allowed to quantify the influence of FC and GBD on ADC. Relevance statement: The study developed an innovative dual-function MRI phantom to explore the impact of FC on ADC variation that can affect clinical results. The results revealed the superimposed effect on FF and GBD density on ADC measurements. Key points: • A dual-function phantom made of glass bead density (GBD) and fat fraction (FF) emulsion has been developed. • Apparent diffusion coefficient (ADC) values

关键词： Adipose tissue Diffusion magnetic resonance imaging Phantoms (imaging) Quality assurance (healthcare) Quality control

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The Effect of Epidemiological Cohort Creation on the Machine Learning Prediction of Homelessness and Police Interaction Outcomes Using Administrative Health Care Data

arXiv

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arXiv 2023年

作者： Shahidi, Faezehsadat MacDonald, M. Ethan Seitz, Dallas Messier, Geoffrey Electrical and Software Engineering Schulich School of Engineering University of Calgary CalgaryAB Canada Biomedical Engineering Schulich School of Engineering University of Calgary CalgaryAB Canada Hotchkiss Brain Institute University of Calgary CalgaryAB Canada Department of Psychiatry Cumming School of Medicine University of Calgary CalgaryAB Canada

Background: Mental illness can lead to adverse outcomes such as homelessness and police interaction and understanding of the events leading up to these adverse outcomes is important. Predictive models may help identify individuals at risk of such adverse outcomes. Using a fixed observation window cohort with logistic regression (LR) or machine learning (ML) models can result in lower performance when compared with adaptive and parcellated windows. Method: An administrative healthcare dataset was used, comprising of 240,219 individuals in Calgary, Alberta, Canada who were diagnosed with addiction or mental health (AMH) between April 1, 2013, and March 31, 2018. The cohort was followed for 2 years to identify factors associated with homelessness and police interactions. To understand the benefit of flexible windows to predictive models, an alternative cohort was created. Then LR and ML models, including random forests (RF), and extreme gradient boosting (XGBoost) were compared in the two cohorts. Results: Among 237,602 individuals, 0.8% (1,800) experienced first homelessness, while 0.32% (759) reported initial police interaction among 237,141 individuals. Male sex (AORs: H=1.51, P=2.52), substance disorder (AORs: H=3.70, P=2.83), psychiatrist visits (AORs: H=1.44, P=1.49), and drug abuse (AORs: H=2.67, P=1.83) were associated with initial homelessness (H) and police interaction (P). XGBoost showed superior performance using the flexible method (sensitivity =91%, AUC =90% for initial homelessness, and sensitivity =90%, AUC=89% for initial police interaction) Conclusion: This study identified key features associated with initial homelessness and police interaction and demonstrated that flexible windows can improve predictive modeling. © 2023, CC BY-NC-ND.

关键词： Law enforcement

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Mesenchymal stromal cell-derived small extracellular vesicles modulate macrophage polarization and enhance angio-osteogenesis to promote bone healing

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Genes & Diseases 2022年第4期9卷 841-844页

作者： Shang Jiunn Chuah Chee Weng Yong Kristeen Ye Wen Teo Jacob Ren Jie Chew Yi Ann Cheow Shipin Zhang Raymond Chung Wen Wong Asher Ah Tong Lim Sai Kiang Lim Wei Seong Toh Faculty of Dentistry National University of Singapore119085Singapore Institute of Molecular and Cell Biology Agency for ScienceTechnology and Research138648Singapore Department of Orthopaedic Surgery Yong Loo Lin School of MedicineNational University of Singapore119288Singapore Department of Biomedical Engineering Faculty of EngineeringNational University of Singapore117583Singapore Tissue Engineering Program Life Sciences InstituteNational University of Singapore117456Singapore Integrative Sciences and Engineering Program NUS Graduate SchoolNational University of Singapore119077Singapore

Mesenchymal stem/stromal cells(MSCs)have demonstrated therapeutic efficacy for bone regeneration in animal and clinical *** MSCs were initially thought to differentiate to various cell types to replace the injured/diseased tissue,it is now accepted that these cells secrete factors to promote tissue repair.1 Among these factors,small extracellular vesicles(sEVs)of size 50–200 nm,which include the exosomes,have been identified as the principal agent mediating the wide-ranging therapeutic efficacy of MSCs.2 Several studies have also reported the therapeutic effects of MSC-sEVs to enhance bone repair in animal models,as recently reviewed.3 However,the cellular processes and mechanisms mediated by MSC-sEVs in bone regeneration remain to be fully elucidated.

关键词： healing clinical macrophage

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Reflectance outperforms force and position in model-free needle puncture detection

Reflectance outperforms force and position in model-free nee...

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

作者： Rachael L’Orsa Anupam Bisht Linhui Yu Kartikeya Murari David T. Westwick Garnette R. Sutherland Katherine J. Kuchenbecker Engineering’s Department of Electrical and Software Engineering Schulich School University of Calgary Calgary Canada Project NeuroArm Cumming School of Medicine University of Calgary Calgary Canada Haptic Intelligence Department Max Planck Institute for Intelligent Systems Stuttgart Germany Hotchkiss Brain Institute Cumming School of Medicine University of Calgary Calgary Canada Department of Biomedical Engineering Schulich School of Engineering’s University of Calgary Calgary Canada

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

The surgical procedure of needle thoracostomy temporarily corrects accidental over-pressurization of the space between the chest wall and the lungs. However, failure rates of up to 94.1% have been reported, likely because this procedure is done blind: operators estimate by feel when the needle has reached its target. We believe instrumented needles could help operators discern entry into the target space, but limited success has been achieved using force and/or position to try to discriminate needle puncture events during simulated surgical procedures. We thus augmented our needle insertion system with a novel in-bore double-fiber optical setup. Tissue reflectance measurements as well as 3D force, torque, position, and orientation were recorded while two experimenters repeatedly inserted a bevel-tipped percutaneous needle into ex vivo porcine ribs. We applied model-free puncture detection to various filtered time derivatives of each sensor data stream offline. In the held-out test set of insertions, puncture-detection precision improved substantially using reflectance measurements compared to needle insertion force alone (3.3-fold increase) or position alone (11.6-fold increase).

关键词： Reflectivity Force measurement Torque Three-dimensional displays Force Surgery Position measurement Aerospace electronics Needles Torque measurement

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Title: Challenges in single cells sequencing Microbial community and biofilm: A case of Oleidesulfovibrio alaskensis G20 NGS protocol

Title: Challenges in single cells sequencing Microbial commu...

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2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022

作者： Singh, Ram Nageena Gnimpieba, Etienne Z. Sani, Rajesh Kumar Chemical and Biological Engineering South Dakota School of Mines and Technology Rapid City United States University of South Dakota Gear Center Biomedical Engineering Program Sioux Falls United States

ISBN: (纸本)9781665468190

Biofilm, is a special-complex organization of bacterial cells with multiple layers, formed in certain environmental conditions. In the complex biofilm different bacterial (single) cells perform different functions and contribute to overall biofilm activity, where single bacterial cells are in different physiological states of growth, stress and signaling. Sulphate reducing bacteria (SRB) contributes to huge economic loss ({}4B) causing microbial induced corrosion. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and biocorrosion. Single Cell Genomics (single cell transcriptomics) is a technique which investigates the gene expression at the level of a single biological cell and could not be attainable in bulk analysis (RNASeq) could decipher the uniqueness of each cell in complex group. We are developing a NGS (oxford Nanopore)-workflow for single cell transcriptomics of biofilms using Oleidesulfovibrio alaskensis (earlier Desulfovibrio alaskensis) strain G20 (OA-G20) as a model. We encountered several challenges to design and develop the workflow such 1) absence of ploy(A) tail in mRNAs, 2) amount of total RNA, 3) half-lives of mRNAs, 4) perforation of cell membrane, 5) low copy number of mRNAs, 6) single cell suspension and cell sorting, 7) quantification of bacterial cells, 8) fixation of cells, 9) designing of probes, 10) hybridization of probes and 11) amplification of mRNAs. Here, we are presenting how we resolved some of these challenges to design and develop a single cell genomics (transcriptomics) workflow for SRB biofilms. © 2022 IEEE.

关键词： Genome

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A comprehensive overview of diffuse correlation spectroscopy: theoretical framework, recent advances in hardware, analysis, and applications

arXiv

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arXiv 2024年

作者： Wang, Quan Pan, Mingliang Kreiss, Lucas Samaei, Saeed Carp, Stefan A. Johansson, Johannes D. Zhang, Yuanzhe Wu, Melissa Horstmeyer, Roarke Diop, Mamadou Li, David Day-Uei University of Strathclyde Department of Biomedical Engineering Faculty of Engineering Glasgow United Kingdom Duke University Department of Biomedical Engineering DurhamNC United States Western University Department of Medical and Biophysics Schulich School of Medical & Dentistry LondonON Canada Harvard Medical School Massachusetts General Hospital Optics at Athinoula A. Martinos Center for Biomedical Imaging CharlestownMA United States Linköping University Department of Biomedical Engineering Linköping Sweden Imaging Program Lawson Health Research Institute LondonON Canada

Diffuse correlation spectroscopy (DCS) is a powerful tool for assessing microvascular hemodynamic in deep tissues. Recent advances in sensors, lasers, and deep learning have further boosted the development of new DCS methods. However, newcomers might feel overwhelmed, not only by the already complex DCS theoretical framework but also by the broad range of component options and system architectures. To facilitate new entry into this exciting field, we present a comprehensive review of DCS hardware architectures (continuous-wave, frequency-domain, and time-domain) and summarize corresponding theoretical models. Further, we discuss new applications of highly integrated silicon single-photon avalanche diode (SPAD) sensors in DCS, compare SPADs with existing sensors, and review other components (lasers, fibers, and correlators), as well as new data analysis tools, including deep learning. Potential applications in medical diagnosis are discussed, and an outlook for the future directions is provided, to offer effective guidance to embark on DCS research. Copyright © 2024, The Authors. All rights reserved.

关键词： Correlators

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Detection of physiological changes in rheumatoid arthritis using time-domain near-infrared imaging: an in silico phantom study 15

Detection of physiological changes in rheumatoid arthritis u...

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Optical Tomography and Spectroscopy of Tissue XV 2023

作者： Ioussoufovitch, Seva Diop, Mamadou School of Biomedical Engineering Collaborative Training Program in Musculoskeletal Health Research Bone & Joint Institute Western University London Canada Dept. of Medical Biophysics Western University London Canada Imaging Program Lawson Health Research Institute London Canada

ISBN: (纸本)9781510658578

Early treatment improves rheumatoid arthritis (RA) prognosis;however, 30% of patients still fail their first treatment and current methods can take as long as 3–6 months to detect treatment failure. Time-domain near-infrared diffuse optical imaging (TD-DOI) has the potential to track gradual changes in RA disease activity and could be a more sensitive technique for RA treatment monitoring. Nevertheless, there has been very little investigation into the relationships between TD-DOI and the specific physiological changes that occur in RA. To this end, this work’s objective was to investigate the effects of RA-associated physiological changes on TD-DOI images in silico. Virtual finger phantoms—derived from an MRI segmentation of a healthy human finger—were used to simulate changes in 5 physiological parameters that are typically affected in RA. Four levels of disease activity were considered for each parameter and each parameter was altered individually;parameter alterations were then translated into changes in phantom geometry and optical properties. MCXLAB was used to simulate the propagation of time-domain light (800 nm) through phantoms’ proximal interphalangeal joints and Poisson noise was added to the TD-DOI data to simulate experimental conditions. Spatiotemporal Fourier decomposition was applied to the TD-DOI data to extract image components, which were grouped into datasets based on the physiological parameter that was altered. Component sensitivity to each physiological parameter was assessed using the ratio between a component’s range and standard deviation within each dataset (range-to-error ratio;RER). Mean RER was highest for changes in synovial membrane and fluid volume, suggesting that this parameter may be a primary source of contrast for monitoring RA treatment response with TD-DOI. © 2023 SPIE.

关键词： Phantoms

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Denoising Simulated Low-Field MRI (70mT) using Denoising Autoencoders (DAE) and Cycle-Consistent Generative Adversarial Networks (Cycle-GAN)

arXiv

引用

arXiv 2023年

作者： Vega, Fernando Addeh, Abdoljalil MacDonald, M. Ethan Department of Biomedical Engineering Schulich School of Engineering University of Calgary CalgaryAB Canada Department of Electrical & Software Engineering Schulich School of Engineering University of Calgary CalgaryAB Canada Hotchkiss Brain Institute Cumming School of Medicine University of Calgary CalgaryAB Canada Department of Radiology Cumming School of Medicine University of Calgary CalgaryAB Canada

In this work, a denoising Cycle-GAN (Cycle Consistent Generative Adversarial Network) is implemented to yield high-field, high resolution, high signal-to-noise ratio (SNR) Magnetic Resonance Imaging (MRI) images from simulated low-field, low resolution, low SNR MRI images. Resampling and additive Rician noise were used to simulate low-field MRI. Images were utilized to train a Denoising Autoencoder (DAE) and a Cycle-GAN, with paired and unpaired cases. Both networks were evaluated using SSIM and PSNR image quality metrics. This work demonstrates the use of a generative deep learning model that can outperform classical DAEs to improve low-field MRI images and does not require image pairs. Copyright © 2023, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Amyloid-Beta Axial Plane PET Synthesis from Structural MRI: An Image Translation Approach for Screening Alzheimer’s Disease

arXiv

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arXiv 2023年

In this work, an image translation model is implemented to produce synthetic amyloid-beta PET images from structural MRI that are quantitatively accurate. Image pairs of amyloid-beta PET and structural MRI were used to train the model. We found that the synthetic PET images could be produced with a high degree of similarity to truth in terms of shape, contrast and overall high SSIM and PSNR. This work demonstrates that performing structural to quantitative image translation is feasible to enable the access of amyloid-beta information from only MRI. Copyright © 2023, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Optical tissue clearing enables rapid,precise and comprehensive assessment of three-dimensional morphology in experimental nerve regeneration research

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Neural Regeneration Research 2022年第6期17卷 1348-1356页

作者： Simeon C.Daeschler Jennifer Zhang Tessa Gordon Gregory H.Borschel SickKids Research Institute Neuroscience and Mental Health ProgramTorontoONCanada Institute of Biomaterials and Biomedical Engineering University of TorontoTorontoONCanada Division of Plastic and Reconstructive Surgery the Hospital for Sick ChildrenTorontoONCanada Indiana University School of Medicine IndianapolisINUSA

Morphological analyses are key outcome assessments for nerve regeneration studies but are historically limited to tissue *** optical tissue clearing techniques enabling three-dimensional imaging of entire organs at a subcellular resolution have revolutionized morphological studies of the *** extend their applicability to experimental nerve repair studies we adapted these techniques to nerves and their motor and sensory targets in *** solvent-based protocols rendered harvested peripheral nerves and their target organs transparent within 24 hours while preserving tissue architecture and *** optical clearing was compatible with conventional laboratory techniques,including retrograde labeling studies,and computational image segmentation,providing fast and precise cell ***,optically cleared organs enabled three-dimensional morphometry at an unprecedented scale including dermatome-wide innervation studies,tracing of intramuscular nerve branches or mapping of neurovascular *** their wide-ranging applicability,rapid processing times,and low costs,tissue clearing techniques are likely to be a key technology for next-generation nerve repair *** procedures were approved by the Hospital for Sick Children’s Laboratory Animal Services Committee(49871/9)on November 9,2019.

关键词： histology image segmentation morphometry nerve regeneration outcome assessment peripheral nerve three-dimensional imaging tissue clearing

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