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Machine Learning-Based Prediction of Pulmonary Thromboembolism to Reduce Unnecessary Computed Tomography Scans in Gastrointestinal Cancer Patients: A Retrospective Multicenter Study

SSRN

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SSRN 2023年

作者： Kim, Joo Seong Kwon, Doyun Kim, Kyungdo Lee, Sang Hyub Lee, Seung-Bo Kim, Kwangsoo Kim, Dongmin Lee, Min Woo Park, Namyoung Choi, Jin Ho Jang, Eun Sun Cho, In Rae Paik, Woo Hyun Lee, Jun Kyu Ryu, Ji Kon Kim, Yong-Tae Department of Internal Medicine Liver Research Institute Seoul National University Hospital Seoul National University College of Medicine Seoul Korea Republic of Department of Internal Medicine Dongguk University College of Medicine Dongguk University Ilsan Hospital Goyang-si Korea Republic of Interdisciplinary Program of Medical Informatics Seoul National University College of Medicine Seoul Korea Republic of Department of Biomedical Engineering Pratt School of Engineering Duke University DurhamNC27708 United States Transdisciplinary Department of Medicine & Advanced Technology Seoul National University Hospital Seoul Korea Republic of Department of Medicine Seoul National University College of Medicine Seoul Korea Republic of Department of Medical Informatics Keimyung University School of Medicine Daegu Korea Republic of Biomedical Research Institute Seoul National University Hospital Seoul Korea Republic of Department of Medicine Kyung Hee University Gangdong Hospital Seoul Korea Republic of Department of Medicine Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea Republic of Department of Internal Medicine Seoul National University Bundang Hospital Seongnam-si Korea Republic of

Background: Pulmonary thromboembolism (PTE) is one of the most important complications in cancer patients. Gastrointestinal cancers entail an increased risk of PTE. However, there were few research on predicting pulmonary embolism using machine learning (ML) in cancer patients. The purpose of this study was to develop an ML based prediction model for PTE in gastrointestinal cancer ***: We conducted a retrospective, multicenter study in which ML model was developed and subsequently internally and externally validated. We reviewed gastrointestinal cancer patients who had undergone computed tomographic pulmonary angiography (CTPA) from 2010 to 2020. Demographic and predictor variables including the Wells score and D-dimer were investigated. The ML model was based on the random forest model. The area under receiver operating curve (AUROC) was used to evaluate the performance of ML ***: 446 patients in hospital A and 139 patients in hospital B were analyzed in this study. The training set comprised 356 patients in hospital A. The ML model was validated both internally (90 patients) and externally (139 patients). AUROC was 0.736 in hospital A and 0.669 in hospital B. The number of patients classified as requiring CTPA was significantly reduced according to the prediction with ML (hospital A;100.0% vs 91.1%, P Conclusion: Prediction model based on ML might have advantages in reducing the number of CTPA compared to the conventional diagnostic strategy for PTE in patients with gastrointestinal cancer. © 2023, The Authors. All rights reserved.

关键词： Hospitals

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2 x 3 Arrayed CMOS Capacitive Biosensors for Detection of microRNAs on a Microfluidic System

2 x 3 Arrayed CMOS Capacitive Biosensors for Detection of mi...

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IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS)

作者： Yu-Husan Kuo Chi-Chien Huang Yi-Sin Chen Po-Chiun Huang Gwo-Bin Lee Institute of Nano Engineering and Microsystems National Tsing Hua University Hsinchu Taiwan Interdisciplinary Program of Life Science National Tsing Hua University Hsinchu Taiwan National Tsing Hua University Hsinchu Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu Taiwan

ISBN: (数字)9781728172309

ISBN: (纸本)9781728172316

Breast cancer is one of the most important cancers among women worldwide. Since breast cancer is prone to metastasis and recurrence, mortality is relatively high if not diagnosed early. Therefore, it is important to develop a device that can quickly and accurately diagnose breast cancer. Recently, microRNAs such as microRNA-195 and microRNA-126 have been reported to act as biomarkers for breast cancer diagnosis. Therefore, this study reported an integrated microfluidic system capable of extracting microRNAs by microfluidic techniques, detecting and quantifying microRNAs by using complementary-metal-oxide-semiconductor (CMOS) capacitive biosensors for rapid and accurate diagnosis of breast cancer. Monolithic sensor with integrated-circuits reduces parasitic effects and submicron interdigitated microelectrodes as sensing interfaces significantly improves sensitivity. microRNA-195 detection for concentrations ranging from 1 fM to 10 pM could be successfully obtained, allowing detection in physiological conditions for cancer patients in the near future.

关键词： Cancer Breast cancer Microfluidics Biomarkers Capacitance Surface treatment Sensors

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Nanomaterials-based flexible and stretchable bioelectronics

Nanomaterials-based flexible and stretchable bioelectronics

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作者： Song, Jun-Kyul Do, Kyungsik Koo, Ja Hoon Son, Donghee Kim, Dae-Hyeong School of Chemical and Biological Engineering Seoul National University Korea Republic of Interdisciplinary Program for Bioengineering Seoul National University Korea Republic of Biomedical Research Institute Korea Institute of Science and Technology Korea Republic of Seoul National University Korea Republic of

Conventional silicon-based electronics have faced challenges in the realization of soft bioelectronics, such as wearable and implantable integrated devices, which necessitate electrically and mechanically interactive biotic-abiotic interfacing without disturbing the daily life of the user or posing biocompatibility issues. Recently, much effort has been directed at overcoming the mechanical limitations of conventional rigid electronics by replacement of bulky, thick, and rigid electronic materials with biocompatible, soft, and nanoscale electronic materials, which exhibit intrinsic mechanical deformability as well as superior electrical properties. Recent advances in the synthesis of unconventional nanomaterials, surface functionalization methods, and integrated device fabrication techniques have resulted in further improvements in the performance of nanomaterials-based soft bioelectronics. Numerous studies have focused on the biological, electrical, and mechanical analyses of heterogeneous nanomaterial-biosystem interfaces as well as the development of efficient integration processes of soft nanomaterials into devices. In this article, we summarize the latest advances and future prospects in nanomaterials synthesis, processing, and integration strategies for flexible and stretchable bioelectronics, and their application to wearable and implantable devices. © Materials Research Society 2019.

关键词： Flexible electronics

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Sequence and phylogenetic analysis of the complete mitochondrial genome for the grey stingfishMinous monodactylus(Scorpaeniformes:Synanceiidae)

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Mitochondrial DNA Part B 2019年第1期4卷 1377-1378页

作者： Hyun-Woo Kim Md. Jobaidul Alam Ah-Ran Kim Hyun Park Sapto Andriyono Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of Korea Korea Polar Research Institute Korea Ocean Research and Development Institute Incheon Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFisheries and Marine Faculty C Campus Jl. Mulyorejo Universitas Airlangga Surabaya Indonesia

The mitochondrial genome sequence ofMinous monodactylus(16,459 bp) was determined by the MiSeq platform for the first time in the genusMinous. It encoded the 37 genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs) and two conserved noncoding regions; control region (D-loop) and the origin of light strand (OL). Twenty-eight genes were encoded on the heavy (H) strand, while eight tRNAs andND6genes were on the light (L) strand. According to the phylogenetic analysis with other complete mitogenomes from order Scorpaeniformes,M. monodactyluswas clustered withSynanceia verrucosaas familySynanceiidaewith 81% sequence identity.

关键词： Next-generation sequencing Minous monodactylus mitochondrial genome stingfish

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Characterization of complete mitochondrial genome and gene organization of sharp-spined notothenia,Trematomus pennellii(Perciformes: Nototheniidae)

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Mitochondrial DNA Part B 2019年第1期4卷 648-649页

作者： Md. Jobaidul Alam Jeong-Hoon Kim Sapto Andriyono Ji-Hyun Lee Soo Rin Lee Hyun Park Hyun-Woo Kim Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of Korea Korea Polar Research Institute Korea Ocean Research and Development Institute Incheon Republic of Korea Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFisheries and Marine Faculty Universitas Airlangga Surabaya East Java Indonesia Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea

The complete mitochondrial genome ofTrematomus pennelliiwas determined by MiSeq platform. The mitogenome ofT. pennelliiwas 15,976 bp in length and encoded 37 genes (13 proteins, 22 tRNAs, 2 ribosomal RNAs) and a non-coding control region (D-Loop). Overall A + T contents (54.10%) in the mitogenome was higher than G + C contents (45.90%). Twenty-nine genes were located on H strand, whereas eight genes were identified on L strand. Among 13 protein-coding genes, unusual start codons were identified inCOX1(GTG),ND6(ATT),COX2(ATC), andATP6(ATC). The incomplete stop codon (T–) was identified in six genes includingCOXII,COXIII,NAD2,NAD3,NAD4, andCytb. The phylogenetic tree of complete genome indicated thatTrematomus pennelliiwas most closely related toTrematomus bernacchiiwith 91.65% DNA sequence identity.

关键词： Next generation sequencing Trematomus pennellii mitochondrial genome Antarctica Notothenioidei

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Melanoma Detection by AFM Indentation of Histological Specimens

Research Square

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Research Square 2021年

作者： Jeon, ByoungJun Jung, Hyo Gi Lee, Sang Won Lee, Gyudo Shim, Jung Hee Kim, Mi Ok Kim, Byung Jun Kim, Sang-Hyon Lee, Hyungbeen Lee, Sang Woo Yoon, Dae Sung Jo, Seong Jin Choi, Tae Hyun Lee, Wonseok Interdisciplinary Program for Bioengineering Seoul National University Seoul08826 Korea Republic of School of Biomedical Engineering Korea University Seoul02841 Korea Republic of Interdisciplinary Program in Precision Public Health Korea University Seoul02841 Korea Republic of Department of Biotechnology and Bioinformatics Korea University Sejong30019 Korea Republic of Department of Plastic and Reconstructive Surgery Research Services Seoul National University Bundang Hospital Seongnam13620 Korea Republic of Department of Plastic and Reconstructive Surgery Institute of Human Environment Interface Biology Seoul National University College of Medicine Seoul03087 Korea Republic of Department of Internal Medicine Keimyung University Dongsan Medical Center Daegu41931 Korea Republic of Department of Biomedical Engineering Yonsei University Wonju26493 Korea Republic of R&D Center of Curigin Ltd. Seoul04778 Korea Republic of Department of Dermatology Seoul National University College of Medicine Seoul03087 Korea Republic of Department of Electrical Engineering Korea National University of Transportation Chungju27469 Korea Republic of

Melanoma is visible unlike other types of cancer, but it is still challenging to diagnose correctly because of the difficulty in distinguishing between benign nevus and melanoma. We conducted a robust investigation of melanoma, identifying considerable differences in local elastic properties between nevus and melanoma tissues by using atomic force microscopy (AFM) indentation of histological specimens. Specifically, the histograms of the elasticity of melanoma displayed multimodal Gaussian distributions, exhibiting the heterogeneous mechanical properties, in contrast with the unimodal distributions of elasticity in the benign nevus. We identified this notable signature was consistent regardless of blotch incidence by sex, age, anatomical site (e.g., thigh, calf, arm, eyelid, and cheek), or cancer stage (I, IV, and V). In addition, we found that the non-linearity of the force-distance curves for melanoma is increased compared to benign nevus. We believe that AFM indentation of histological specimens may technically complement conventional histopathological analysis for earlier and more precise melanoma detection. © 2021, CC BY.

关键词： Elasticity

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The molecular characterization of complete mitochondrial genome of spotted snakehead fish,Channa punctata(Bloch 1793)

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Mitochondrial DNA Part B 2019年第1期4卷 547-548页

作者： Md. Jobaidul Alam Sapto Andriyono Sinar Pagi Sektiana Md. Mofizur Rahman Hyun-Woo Kim Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Fisheries Ministry of Fisheries and Livestock Dhaka Bangladesh Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaFisheries and Marine Faculty Universitas Airlangga Surabaya East Java Indonesia Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaAquaculture Technology Study Program Sekolah Tinggi Perikanan Jakarta Indonesia Department of Marine Biology Pukyong National University Busan Republic of KoreaDepartment of Fisheries and Marine Science Noakhali Science and Technology University Sonapur Noakhali Bangladesh Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Pukyong National University Busan Republic of KoreaDepartment of Marine Biology Pukyong National University Busan Republic of Korea

The complete mitochondrial genome of spotted snakehead fish,Channa punctata(Bloch 1793) was determined by MiSeq platform. The genome was 16,409 bp in length, in which canonical 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (D-Loop) were encoded. Relatively higher overall A + T contents (53.70%) was identified compared with G + C contents (46.30%). Among 13 protein-coding genes, only one unusual start condon (GTG) was identified in COX1, whereas six genes includingCOXII,COXIII,NAD2,NAD3,NAD4, andCytbwere ended with the incomplete stop codons (TA-/T–). Based on the currently identified mitogenomes of Channa fish species,C. punctatawas most closely related toChanna gachuawith 82% sequence identity.

关键词： Next generation sequencing Channa punctata mitochondrial genome phylogeny snakehead fish

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A sharp interface Lagrangian-Eulerian method for flexible-body fluid-structure interaction

arXiv

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arXiv 2022年

作者： Kolahdouz, Ebrahim M. Wells, David R. Rossi, Simone Aycock, Kenneth I. Craven, Brent A. Griffith, Boyce E. Center for Computational Biology Flatiron Institute Simons Foundation New YorkNY United States Department of Mathematics University of North Carolina Chapel HillNC United States Division of Applied Mechanics Office of Science and Engineering Laboratories Center for Devices and Radiological Health United States Food and Drug Administration Silver SpringMD United States Departments of Mathematics and Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina Chapel HillNC United States McAllister Heart Institute University of North Carolina Chapel HillNC United States

This paper introduces a sharp-interface approach to simulating fluid-structure interaction (FSI) involving flexible bodies described by general nonlinear material models and across a broad range of mass density ratios. This new flexible-body immersed Lagrangian-Eulerian (ILE) scheme extends our prior work on integrating partitioned and immersed approaches to rigid-body FSI. Our numerical approach incorporates the geometrical and domain solution flexibility of the immersed boundary (IB) method with an accuracy comparable to body-fitted approaches that sharply resolve flows and stresses up to the fluid-structure interface. Unlike many IB methods, our ILE formulation uses distinct momentum equations for the fluid and solid subregions with a Dirichlet-Neumann coupling strategy that connects fluid and solid subproblems through simple interface conditions. As in earlier work, we use approximate Lagrange multiplier forces to treat the kinematic interface conditions along the fluid-structure interface. This penalty approach simplifies the linear solvers needed by our formulation by introducing two representations of the fluid-structure interface, one that moves with the fluid and another that moves with the structure, that are connected by stiff springs. This approach also enables the use of multi-rate time stepping, which allows us to use different time step sizes for the fluid and structure subproblems. Our fluid solver relies on an immersed interface method (IIM) for discrete surfaces to impose stress jump conditions along complex interfaces while enabling the use of fast structured-grid solvers for the incompressible Navier-Stokes equations. The dynamics of the volumetric structural mesh are determined using a standard finite element approach to large-deformation nonlinear elasticity via a nearly incompressible solid mechanics formulation. This formulation also readily accommodates compressible structures with a constant total volume, and it can handle fully compressibl

关键词： Fluid structure interaction

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A Nodal Immersed Finite Element-Finite Difference Method

SSRN

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SSRN 2022年

作者： Wells, David Vadala-Roth, Ben Lee, Jae Ho Griffith, Boyce E. Department of Mathematics University of North Carolina Chapel HillNC United States U.S. Army Corps of Engineers Engineer Research and Development Center Coastal and Hydraulic Laboratory VicksburgMS United States Department of Mechanical Engineering Institute for Computational Medicine Johns Hopkins University BaltimoreMD United States Departments of Mathematics Applied Physical Sciences and Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina Chapel HillNC United States McAllister Heart Institute University of North Carolina Chapel HillNC United States

The immersed finite element-finite difference (IFED) method is a computational approach to modeling interactions between a fluid and an immersed structure. The IFED method uses a finite element (FE) method to approximate the stresses and forces on a structural mesh and a finite difference (FD) method to approximate the momentum of the entire fluid-structure system on a Cartesian grid. The fundamental approach used by this method follows the immersed boundary framework for modeling fluid-structure interaction (FSI), in which a force spreading operator prolongs structural forces to a Cartesian grid, and a velocity interpolation operator restricts a velocity field defined on that grid back onto the structural mesh. With an FE structural mechanics framework, force spreading first requires that the force itself be projected onto the finite element space. Similarly, velocity interpolation requires projecting velocity data onto the FE basis functions. Consequently, evaluating either coupling operator requires solving a matrix equation at every time step. Mass lumping, in which the projection matrices are replaced by diagonal approximations, has the potential to accelerate this method considerably. This paper provides both numerical and computational analyses of the effects of this replacement for evaluating the force projection and for the IFED coupling operators. Constructing the coupling operators also requires determining the locations on the structure mesh where the forces and velocities are sampled. Here we show that sampling the forces and velocities at the nodes of the structural mesh is equivalent to using lumped mass matrices in the IFED coupling operators. A key theoretical result of our analysis is that if both of these approaches are used together, the IFED method permits the use of lumped mass matrices derived from nodal quadrature rules for any standard interpolatory element. This is different from standard FE methods, which require specialized treatments to

关键词： Fluid structure interaction

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Clinical text generation through leveraging medical concept and relations

arXiv

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arXiv 2019年

作者： Lee, Wangjin Park, Hyeryun Yoon, Jooyoung Kim, Kyeongmo Choi, Jinwook Interdisciplinary Program in Bioengineering Graduate School Seoul National University Department of Biomedical Engineering College of Medicine Seoul National University

With a neural sequence generation model, this study aims to develop a method of writing the patient clinical texts given a brief medical history. As a proof-of-a-concept, we have demonstrated that it can be workable to use medical concept embedding in clinical text generation. Our model was based on the Sequence-to-Sequence architecture and trained with a large set of de-identified clinical text data. The quantitative result shows that our concept embedding method decreased the perplexity of the baseline architecture. Also, we discuss the analyzed results from a human evaluation performed by medical doctors. Copyright © 2019, The Authors. All rights reserved.

关键词： Embeddings

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