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Computational Optical Sensing and Imaging, COSI 2020 - Part of Imaging and Applied Optics Congress 2020

作者： Yanny, Kyrollos Antipa, Nick Liberti, William Dehaeck, Sam Monakhova, Kristina Liu, Fanglin Linda Shen, Konlin Ng, Ren Waller, Laura UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States Department of Electrical Engineering and Computer Sciences University of California Berkeley United States Brussels1050 Belgium

We demonstrate a single-shot miniature 3D computational microscope with an optimized phase encoder. Our method uses sparsity-based reconstruction to achieve a 2.76µm lateral and 15µm axial resolution across ... 详细信息

ISBN: (纸本)9781557528209

关键词： Fluorescence microscopy

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In Silico Assessment of Arrhythmic Risk in Infarcted Ventricles Engrafted with Engineered Heart Tissues

In Silico Assessment of Arrhythmic Risk in Infarcted Ventric...

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Computers in Cardiology (CinC)

作者： Ricardo M Rosales Konstantinos A Mountris Manuel Doblare Manuel M Mazo Esther Pueyo Aragon Institute of Engineering Research University of Zaragoza IIS Aragon Zaragoza Spain CIBER in Bioengineering Biomaterials & Nanomedicine (CIBER-BBN) Spain Department of Mechanical Engineering University College London London United Kingdom Regenerative Medicine Program CIMA Universidad de Navarra Pamplona Spain Hematology and Cell Therapy Clinica Universidad de Navarra Pamplona Spain

Engineered heart tissues (EHTs) from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent novel alternatives to repair damaged cardiac tissue after myocardial infarction (MI). However, their associated slow conduction and prolonged action potential duration (APD) can favor proarrhythmicity. We coupled biventricular (BiV) and EHT in silico elec-trophysiological models. The BiV model, defined from magnetic resonance imaging, included an MI region. The EHT model was deformed to follow the epicardial surface. Different values of EHT electrical conductivity (EHTc) and degree of myocardial attachment (EHTa) were tested. Results showed that even a minimum degree of EHTa inhibited EHT automaticity. Activation time and APD were driven by myocardial tissue when engrafted. Importantly, higher EHTc and EHTa led to lower repolarization gradients (RTGs), considered as a surrogate of arrhythmic risk. Maximum RTG decreased by 52.3 ms/mm when EHTa var-iedfrom 25 % to 100 % under low EHTc and decreased by 98.8 ms/mm when EHTc raised to 90 % of the myocardium conductivity under low EHTa. Proarrhythmicity in cardiac tissue engineering highly depends on EHT conductivity and degree of engraftment on the myocardium.

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DACIT: Device for Axon - Cancer Cell Interaction Testing in 2D & 3D

SSRN

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SSRN 2025年

作者： Velazquez-Quesada, Ines Alizadeh, Vahid Allison, Kara Belova, Elizaveta Kallogjerovic, Svetllana Hesketh, Natasha Zhang, Xiaotian Thomas, Gareth Tuzel, Erkan Gligorijevic, Bojana Temple University Hospital United States Bioengineering Department Temple University PhiladelphiaPA19122 United States Lewis Katz School of Medicine Temple University PhiladelphiaPA19140 United States Cancer Signaling and Microenvironment Program Fox Chase Cancer Center PhiladelphiaPA19111 United States Fels Cancer Institute for Personalized Medicine Lewis Katz School of Medicine Temple University PhiladelphiaPA19140 United States

There is increasing interest in studying the role of peripheral innervation in tumor growth and metastasis. However, in vitro studies of interactions between cancer cells and axonal projections are technically challenging. To address this, we have developed a microfluidic Device for Axon-Cancer cell Interaction Testing in 2D and 3D (DACIT). We show that DACIT successfully separates neuronal soma from the axons and cancer cells into two compartments, which can be exposed to similar, or different growth conditions, depending on the experimental needs. We compare neoaxonogenesis using either the PC-12 cell line or primary embryonic or adult sensory neurons, demonstrating superior neurite growth in primary cells. Additionally, we show that DACIT can accommodate assessing growth and 3D invasion of tumor spheroids, due to its unique height profile. Hence, DACIT can be used to analyze cancer cell interactions with axons in most typical cell biology assays such as proliferation, invasion, and calcium activity which we demonstrate on examples of imaging transients in GCaMP6-labeled neurons, invadopodia assay, and 3D cancer spheroid invasion. © 2025, The Authors. All rights reserved.

关键词： Cancer cells

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eVision: Forecasting the spread of Tuberculosis in India with Deep Learning

eVision: Forecasting the spread of Tuberculosis in India wit...

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International Conference on Computational Science and Computational Intelligence (CSCI)

作者： Juan Zuluaga Michael Castillo Divya Syal Andres Calle Navid Shaghaghi Department of Bioengineering (BIOE) Computer Science & Engineering (CSEN) Ethical Pragmatic & Intelligent Computing (EPIC) Laboratory in collaboration with the Healthcare Innovation & Design (HID) Program Information Systems & Analytics (ISA) and Mathematics & Computer Science (MCS) Santa Clara University Santa Clara California USA

Humanity has battled tuberculosis for all of recorded history. Some studies estimate that Mycobacterium tuberculosis may have been around as long as 3 million years but it was only in 1834 when Johann Schonlein officially presented the characteristics of it. Even though the TB epidemic has touched all corners of the world, Africa and Asia are the regions that currently suffer the worst consequences. The purpose of this study is to construct a model within the eVision forecasting environment, capable of forecasting the trend of Tuberculosis cases in India, as India is the country that accounts for the largest percentage of TB cases and deaths worldwide. And being able to make predictions for India may also lead to successful results for other regions in Asia and Africa. In order to do so, this study presents different test cases that show the effectiveness of the model, varying the number of steps for each one of the data sets created. It's important to note, that these data sets are combinations of data gathered from the states with the most TB cases in India in the last years, as well as the total data for India, and supplemental data from Google Trends, as a way to facilitate the machine learning model. Even though the final results were respectable compared to past research done on India and other countries, the model nevertheless has a limitation on the number of weeks ahead which the predictions are still considered to be good; with 7 weeks being the optimal result.

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A DISEASE-SPECIFIC FOUNDATION MODEL USING OVER 100K FUNDUS IMAGES: RELEASE AND VALIDATION FOR ABNORMALITY AND MULTI-DISEASE CLASSIFICATION ON DOWNSTREAM TASKS

arXiv

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arXiv 2024年

作者： Jang, Boa Ahn, Youngbin Choe, Eun Kyung Yoon, Chang Ki Choi, Hyuk Jin Kim, Young-Gon Interdisciplinary Program in Bioengineering College of Engineering Seoul National University Korea Republic of Department of Transdisciplinary Medicine Seoul National University Hospital Korea Republic of Interdisciplinary Program of Medical Informatics Seoul National University College of Medicine Korea Republic of Department of Surgery Seoul National University Hospital Healthcare System Gangnam Center Korea Republic of Department of Ophthalmology Seoul National University College of Medicine Korea Republic of Department of Ophthalmology Seoul National University Hospital Healthcare System Gangnam Center Korea Republic of Department of Medicine Seoul National University College of Medicine Korea Republic of

Artificial intelligence applied to retinal images offers significant potential for recognizing signs and symptoms of retinal conditions and expediting the diagnosis of eye diseases and systemic disorders. However, developing generalized artificial intelligence models for medical data often requires a large number of labeled images representing various disease signs, and most models are typically task-specific, focusing on major retinal diseases. In this study, we developed a Fundus-Specific Pretrained Model (Image+Fundus), a supervised artificial intelligence model trained to detect abnormalities in fundus images. A total of 57,803 images were used to develop this pretrained model, which achieved superior performance across various downstream tasks, indicating that our proposed model outperforms other general methods. Our Image+Fundus model offers a generalized approach to improve model performance while reducing the number of labeled datasets required. Additionally, it provides more disease-specific insights into fundus images, with visualizations generated by our model. These disease-specific foundation models are invaluable in enhancing the performance and efficiency of deep learning models in the field of fundus imaging. Copyright © 2024, The Authors. All rights reserved.

关键词： Ophthalmology

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Effects of Polyvinyl Chloride and Low-Density Polyethylene Microplastics on Oxidative Stress and Mitochondria Function of Earthworm (Eisenia Foetida)

SSRN

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SSRN 2024年

作者： Lee, Songhee Choi, Jisun Jho, Eun Hea Shin, Sooim Interdisciplinary Program of Bioenergy and Biomaterials Graduate School Chonnam National University 77 Yongbong-ro Buk-gu Gwangju61186 Korea Republic of Department of Biotechnology and Bioengineering Chonnam National University Gwangju61186 Korea Republic of Korea Water Resources Corporation Daejeon34045 Korea Republic of Department of Agricultural and Biological Chemistry Chonnam National University 77 Yongbong-ro Buk-gu Gwangju61186 Korea Republic of

Plastics are widely used worldwide due to their convenience. However, microplastics (MPs) accumulation poses a serious threat to ecosystem health. Therefore, understanding the effects of MPs on living organisms within their native ecosystem is crucial. Previous studies have primarily focused on the impacts of MPs in aquatic environments, whereas the effects of MPs on terrestrial ecosystems have remained largely understudied. Therefore, our study assessed the impacts of MPs on soil ecosystems by characterizing their toxic effects on earthworms (Eisenia foetida). Here, we exposed earthworms to two representative plastics within soil environments: polyvinyl chloride (PVC) and low-density polyethylene (LDPE). Given the known link between MPs and oxidative stress, we next quantified oxidative stress markers and mitochondrial function to assess the effects of MPs on the redox and energy metabolism of earthworms. Mitochondria are crucial metabolic organelles that generate reactive oxygen species via uncontrolled ATP production. Our findings demonstrated that MPs exert different effects depending on their type. Neither the PVC-exposed groups nor the LDPE-exposed groups exhibited changes in oxidative stress (ROS/RNS), as worked by the strong action of glutathione (GSH). While treatment of the two types of MP did not significantly affect the amount of ROS/RNS generated, PVC exhibited a more pronounced effect on antioxidant system compared to LDP. However, mitochondrial function was markedly decreased in the group exposed to high LDPE concentrations, suggesting that the examined LDPE concentrations were too low to activate compensatory mechanisms to protect energy production. Collectively, our findings demonstrated that exposure of MPs not only influences the antioxidant defense mechanisms of earthworms but also alters their mitochondrial function depending on their types. © 2024, The Authors. All rights reserved.

关键词： Microplastic

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Acromion and Scapular Spine Fractures in Reverse Total Shoulder Arthroplasty An XFEM Study

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Journal of shoulder and elbow surgery 2025年

作者： Shuchun Sun Jian Chen Farhad Ahmadi Jichao Zhao Josef K Eichinger Brandon L Rogalski Hai Yao Richard J Friedman Clemson-MUSC Joint Bioengineering Program Clemson University Clemson SC USA. Department of Orthopedics and Physical Medicine Medical University of South CarolinaCharlestonSCUSA. Clemson-MUSC Joint Bioengineering Program Clemson University Clemson SC USA Department of Orthopedics and Physical Medicine Medical University of South CarolinaCharlestonSCUSA. Electronic address: friedman@musc.edu.

BACKGROUND:Reverse total shoulder arthroplasty (rTSA) is widely used to restore shoulder function and alleviate pain. In approximately 1-4% of patients, acromion and scapular spine fractures (ASF) occur and present a clinical challenge for orthopedic surgeons. While impact trauma, impingement, and excessive muscle forces are proposed causes, the relationship between these loading conditions and ASF types remains unclear, hindering targeted prevention strategies. The objective of this study is to identify the biomechanical relationship between loading conditions and ASF types, with the goal of informing targeted preventive strategies to reduce fracture incidence. METHODS:An extended finite element model (XFEM) was developed using computed tomography (CT)-derived shoulder geometry from virtual surgeries to simulate ASF. Bone material properties were based on CT Hounsfield units (HU). Loading scenarios, including impact trauma, impingement, and excessive deltoid force, were informed by existing literature. Simulations were performed in Abaqus, with mesh independence testing ensuring result accuracy. Fracture locations were analyzed according to the modified Levy ASF classification. RESULTS:For impact traumas, the analysis identified that fractures occurred primarily at the initial contact point of the acromion, predominantly in the lateral region. Specifically, forward and sideway impact traumas typically resulted in modified Levy Type I ASF, while backward impact traumas could produce modified Levy Type IIA ASF. Lateral impingement typically led to lateral fractures, specifically modified Levy Type I ASF. The effects of deltoid force varied with the type of shoulder activity; excessive movements during shoulder abduction and forward flexion could cause modified Levy Type IIA ASF. In contrast, hyperextension of the shoulder could shift the fracture location to the medial region, leading to modified Levy Type III ASF. CONCLUSION:Impact trauma, impingement, and excessive

关键词： Acromion and Spine Fractures Biomechanics Extended Finite Element Analysis Reverse Total Shoulder Arthroplasty

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Guiding Brain-to-Vocalization Decoder Design Using Structured Generalization Error 46

Guiding Brain-to-Vocalization Decoder Design Using Structure...

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46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024

作者： Huang, Jingya Tostado-Marcos, Pablo Narasimha, Sowmya Manojna Patel, Aashish N. Arneodo, Ezequiel. M. Gentner, Timothy Q. Mishne, Gal Gilja, Vikash University of California San Diego Department of Electrical and Computer Engineering La Jolla CA92092 United States University of California San Diego Department of Bioengineering La Jolla CA92092 United States University of California San Diego Institute for Neural Computation La Jolla CA92092 United States University of California San Diego Neuroscience Graduate Program La Jolla CA92092 United States University of California San Diego Department of Physics La Jolla CA92092 United States University of California San Diego Department of Psychology La Jolla CA92092 United States University of California San Diego Halicioǧlu Data Science Institute La Jolla CA92092 United States

ISBN: (纸本)9798350371499

State-of-the-art intracortical neuroprostheses currently enable communication at 60+ words per minute for anarthric individuals by training on over 10K sentences to account for phoneme variability in different word contexts. There is limited understanding about whether this performance can be maintained in decoding naturalistic speech with 40K+ word vocabularies across elicited, spontaneous, and conversational speech contexts. We introduce a vocal-unit-level generalization test to explicitly evaluate neural decoder performance with an expanded and more diverse behavioral repertoire. Tested on neural decoders modeling zebra finch vocalization, an analog to human vocal production, we compare three decoders with different input types: spike trains, neural factors, and firing rates. The factors and rates are latent neural features inferred using trained Latent Factor Analysis via Dynamical Systems (LFADS) models that capture the population neural dynamics during vocal production. While the conventional random holdout generalization error measure is similar for all three decoders, factor- and rate-based decoders outperform spike-based decoders when testing vocal-unit-holdout generalization error. These results suggest the later models better adapt to flexible vocalization inference when trained with partial observation of data variation, motivating further exploration of decoders incorporating latent neural and vocalization dynamics. © 2024 IEEE.

关键词： Errors

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Dynamic Time-Over-Threshold Readout for Improved Energy Linearity in PET Detectors that Achieve 100 ps CTR

Dynamic Time-Over-Threshold Readout for Improved Energy Line...

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2021 IEEE Nuclear Science Symposium and Medical Imaging Conference, NSS/MIC 2021

作者： Pourashraf, Shirin Gonzalez-Montoro, Andrea Cates, Joshua W. Zhao, Zhixiang Won, Jun Yeon Sung Lee, Jae Levin, Craig S. Stanford University Department of Radiology StanfordCA94305 United States Berkeley National Laboratory Applied Nuclear Physics Program at Lawrence BerkeleyCA94720 United States Shanghai Jiao Tong University School of Biomedical Engineering Shanghai China Seoul National University Department of Nuclear Medicine and Biomedical Sciences Seoul110-744 Korea Republic of Stanford University Molecular Imaging Program Departments of Radiology Bioengineering Physics and Electrical Engineering StanfordCA94305 United States

ISBN: (纸本)9781665421133

We have embedded a dynamic time-over-threshold (DynTOT) block in our scalable TOF-PET detector readout electronics to linearize the multiplexed energy spectra while keeping 100 ps FWHM Coincidence Time Resolution (CTR) performance. This DynTOT block is constructed by off-the-shelve components and consumes only 20 mW power per detector 'layer' in our design. Using 3×3×10 mm3 "LGSO"crystals coupled to arrays of 3×3 mm² SiPMs, energy resolution of 13.8±0.1%, 13.9±0.3%, and 17.1±0.6% were experimentally achieved for conventional pulse height, DynTOT, and conventional TOT methods, respectively. Including the DynTOT method, coincidence data were experimentally acquired using a low jitter FPGA-based TDC, and 103.6 ± 1.1 ps FWHM CTR was achieved, demonstrating the robustness of our novel and scalable timing electronic chain. © 2021 IEEE.

关键词： Medical imaging

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De Novo Design of a Highly Stable Ovoid TIM Barrel:Unlocking Pocket Shape towards Functional Design

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BioDesign Research 2022年第1期2022卷 68-80页

作者： Alexander E.Chu Daniel Fernandez Jingjia Liu Raphael R.Eguchi Po-Ssu Huang Biophysics Program Stanford UniversityStanfordCAUSA Department of Bioengineering Stanford UniversityStanfordCAUSA Program in Chemistry EngineeringAnd Medicine for Human Health(ChEM-H)Stanford UniversityStanfordCAUSA Stanford ChEM-H Macromolecular Structure Knowledge CenterStanford UniversityStanfordCAUSA Department of Biochemistry Stanford UniversityStanfordCAUSA Bio-X Institute Stanford UniversityStanfordCAUSA

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrelfold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel proteinhas been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the foldremains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold)symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbonesampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequencedesign protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences arehighly stable and fold to the designed barrel curvature as determined by a 2.1Å resolution crystal structure. The designs showrobustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in thehydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diversehydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major steptowards the de novo design of functional TIM barrels.

关键词： structure curvature backbone

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