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Prediction tools for assessing functional impacts of gene mutations in Clear Cell Renal Cell Carcinoma: A comparative study

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Computers in Biology and Medicine 2025年第Pt A期192卷 110187-110187页

作者： Yang, Cheng-Hong Lin, Guan-Cheng Wu, Chih-Hsien Chen, Jin-Bor Chuang, Li-Yeh Department of Information Management Tainan University of Technology Tainan Taiwan Department of Electronic Engineering National Kaohsiung University of Science and Technology Kaohsiung Taiwan Drug Development and Value Creation Research Center Kaohsiung Taiwan Ph. D. Program in Biomedical Engineering Kaohsiung Medical University Kaohsiung Taiwan Division of Nephrology Department of Internal Medicine Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Taiwan Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering I-Shou University Kaohsiung Taiwan Taiwan

Renal cell carcinoma (RCC) is a well-known malignancy characterized by specific gene mutations that elevate its occurrence. It can be categorized into clear cell RCC (ccRCC), papillary RCC, and chromophobe RCC, which account for approximately 85 % of all primary RCC cases. The mutations typically involve single-nucleotide variants (SNVs) that lead to amino acid substitutions, which influence various biological functions, including gene expression. Therefore, predicting the functional consequences of RCC-related single-nucleotide polymorphisms (SNPs), including substitutions, insertions, deletions, and duplications, is crucial for the effective clinical management of RCC. In recent years, the accessibility and popularity of tools for predicting SNP functional variations have grown, especially in research concerning the potential risks associated with key gene mutations in cancer. Accordingly, this study focused on commonly mutated genes in ccRCC, namely VHL, BAP1, PBRM1, and SETD2. Public data from sources such as The Cancer Genome Atlas and the National Center for Biotechnology Information were used to identify 61 gene mutation positions. Nine nonsynonymous mutation prediction tools were used for analysis, namely SIFT, Polyphen-2, Mutation Assessor, Fathmm, MutPred, CHASM, Revel, Provean, and SNP&GO. The tools were evaluated by their statistical performance, prediction distribution, and receiver operating characteristic curves. The three tools with the highest accuracy for predicting the functional consequences of mutations in the four frequently mutated genes associated with ccRCC were SIFT (accuracy of 0.75), Provean (0.7), and Polyphen-2 (0.69). These findings offer valuable insights into predicting ccRCC-related gene mutation effects, but further research and validation are essential to support their clinical applications. © 2025

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PULSE TRANSMISSION AND IMPEDANCE CHARACTERISTICS OF A NONUNIFORM CIRCULATORY MODEL

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JOURNAL OF biomedical engineering 1992年第5期14卷 390-396页

作者： EINAV, S AHARONI, S MANOACH, M Biomedical Engineering Program Tel Aviv University Israel

In recent years, the technique of non-uniform transmission lines has been utilized in the synthesis of lines feeding antennae from transmitters, thereby maintaining matching over a wide band of frequencies and with varying load For this reason, an electrical model based on that technique stems from the resemblance between the two systems: in both the feeding medium is non-uniform, and it is necessary to maintain a good response over a wide range of frequencies. Our non-uniform transmission line model of the arterial system, introduced in an earlier publication, supplies comprehensive answers to many questions dealing with the research into this system. Whereas in our earlier model the ohmic resistance R was considered small and not considered in the calculations, it is included in the present study. We have calculated the variation of the input impedance with the frequency and distance from the source, the effect of occluded main branches, augmentation of the pressure wave, the relationship between body size and heart rate and the matching of impedances at large bifurcations. We found that our calculated results agree very well with the quantitative results measured by other investigators in the field.

关键词： NONUNIFORM CIRCULATORY MODEL ARTERIAL SYSTEM OHMIC RESISTANCE

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IS THERE AN OPTIMAL LASER TREATMENT FOR PORT WINE STAINS

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LASERS IN SURGERY AND MEDICINE 1986年第1期6卷 76-83页

作者： VANGEMERT, MJC WELCH, AJ AMIN, AP Biomedical Engineering Program The University of Texas at Austin Austin

Optimization of laser treatment of port wine stains (PWS) is discussed from the standpoint of heat production. Laser wavelength, irradiation time, heat conduction, and external epidermal cooling are the variables considered in conjunction with absorbing and scattering behavior of a PWS-model consisting of epidermis, dermis, and ectatic blood vessel. Ideal treatment is defined as minimal heating of the epidermis and upper dermis, but with irreversible damage to the capillary wall. The analysis shows that irradiation times of 1-10 ms in conjunction with external epidermal cooling may give optimal results. The wavelength of choice is 577 nm, followed by 540, 415, 560, and 500 nm (argon laser). The ruby and Nd-YAG lasers are predicted to damage the epidermis and dermis at all times when the capillary is coagulated. Concurrent cooling to prevent epidermal-dermal damage is also recommended here. The CO2 laser is predicted to be the worst laser and, according to our analysis, should not be used to treat PWS. Both upper dermal and capillary destruction can only result from heat conduction from the damaged epidermis and external cooling cannot be applied here.

关键词： port wine stain ideal laser treatment modeling Kr Ar dye ruby Nd-YAG CO2 lasers

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HIGH-FREQUENCY ELECTROCARDIOGRAM ANALYSIS OF THE ENTIRE QRS IN THE DIAGNOSIS AND ASSESSMENT OF CORONARY-ARTERY DISEASE

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PROGRESS IN CARDIOVASCULAR DISEASES 1993年第5期35卷 311-328页

作者： ABBOUD, S Biomedical Engineering Program Faculty of Engineering Tel Aviv University Israel

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NONINVASIVE TRANS-CUTANEOUS MONITORING OF ARTERIAL BLOOD-GASES

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IEEE TRANSACTIONS ON biomedical engineering 1984年第12期31卷 792-800页

作者： MENDELSON, Y PEURA, RA Biomedical Engineering Program Worcester Polytechnic Institute Worcester MA USA

Valuable clinical and physiological data concerning the function of the cardiopulmonary system can be obtained from continuous monitoring of hemoglobin oxygen saturation (SaO2), oxygen tension (PO2), and carbon dioxide tension (PCO2) in blood. While periodic blood sampling is still used clinically to determine arterial blood gases, it is becoming apparent that the recent introduction of continuous noninvasive monitoring of blood gases can offer many advantages. This paper discusses the historical development and significant accomplishments of various techniques available for transcutaneous blood gas monitoring. Four major areas are reviewed: electrochemistry, spectrophotometry, mass spectrometry, and gas chromatography. For each of these techniques, the theoretical basis, instrumentation, and clinical applications are discussed.

关键词： Monitoring Blood Gases Skin Epidermis Dermis Humans Instruments Carbon dioxide Sampling methods

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A MODEL FOR OPTICAL AND THERMAL-ANALYSIS OF LASER BALLOON ANGIOPLASTY

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IEEE TRANSACTIONS ON biomedical engineering 1989年第12期36卷 1233-1243页

作者： CHEONG, WF WELCH, AJ Biomedical Engineering Program University of Texas Austin Austin TX USA

Laser balloon angioplasty is modeled using an infinitely long, axisymmetric cylinder. The balloon surface is assumed to be uniformly irradiated by diffuse light at 1060 nm delivered from within the balloon core. The diffusion approximation to the radiative transport equation is solved for a single-layer homogeneous medium enclosing the transparent fluid-filled balloon. The computed light fluence rate (W-cm/sup -2/) just beneath the tissue surface is 4.7 times the primary irradiance, owing to scattering and secondary irradiance from the integrating cylinder effect of light backscattered into the inner core. The transient temperature response of the heated tissue is then calculated using an implicit finite-difference solution of the heat conduction equation for concentric layers of varying thermal properties. The extent of damage is analyzed using the Arrhenius rate process model. Changes in optical and thermal properties with temperature and thermal phase transitions have been omitted in all of the analyses.< >

关键词： Laser modes Angioplasty Optical scattering Equations Temperature Light scattering Finite difference methods Thermal conductivity

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DiffEGG: Diffusion-Driven Edge Generation as a Pixel-Annotation-Free Alternative for Instance Annotation

arXiv

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arXiv 2025年

作者： Jo, Sanghyun Lee, Ziseok Lee, Wooyeol Kim, Kyungsu OGQ Seoul Korea Republic of Department of Biomedical Sciences Seoul National University Seoul Korea Republic of Department of Computer Science and Engineering Seoul National University Seoul Korea Republic of School of Transdisciplinary Innovations Interdisciplinary Program in Artificial Intelligence Seoul National University Seoul Korea Republic of

Achieving precise panoptic segmentation heavily relies on pixel-wise instance annotations, but obtaining such datasets is costly. Unsupervised instance segmentation (UIS) eliminates annotation requirements but struggles with adjacent instance merging and single-instance fragmentation, largely due to the limitations of DINO-based backbones, which lack strong instance separation cues. Weakly-supervised panoptic segmentation (WPS) reduces annotation costs by using sparse labels (e.g., points, boxes), yet these annotations remain expensive and introduce human bias and boundary errors, limiting performance. To address these challenges, we propose DiffEGG (Diffusion-Driven EdGe Generation), a fully annotation-free method that extracts instance-aware features from pretrained diffusion models to generate precise instance edge maps. DiffEGG fundamentally differs from prior UIS and WPS approaches by leveraging pretrained diffusion models as a backbone. Unlike DINO-based UIS methods, diffusion models inherently capture fine-grained, instance-aware features, enabling more precise boundary delineation. DiffEGG further enhances edge connectivity through self-supervised fine-tuning, progressively improving instance separation. For WPS, DiffEGG completely eliminates annotation costs and human bias by operating without any form of manual supervision, addressing the key limitations of prior best methods. Additionally, we introduce RIP, a post-processing technique that fuses DiffEGG’s edge maps with segmentation masks in a task-agnostic manner. This broad applicability allows DiffEGG to be seamlessly integrated into various segmentation frameworks. When applied to UIS, DiffEGG and RIP achieve an average +4.4 AP improvement over prior best UIS methods. When combined with weakly-supervised semantic segmentation (WSS), DiffEGG enables WPS without instance annotations, outperforming prior best point-supervised WPS methods by +1.7 PQ. These results demonstrate that DiffEGG’s edge maps serv

关键词： Semantic Segmentation

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Monte Carlo model for determination of the role of heat generation in laser-irradiated tissue

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JOURNAL OF BIOMECHANICAL engineering-TRANSACTIONS OF THE ASME 1997年第4期119卷 489-495页

作者： Welch, AJ Gardner, CM Biomedical Engineering Program The University of Texas at Austin Austin TX 78712

A Monte Carlo model is described for modeling photo propagation in a scattering medium. The fraction of locally absorbed photons is proportional to the local rate of heat generation in laser-irradiated tissue and the associated distribution of light (fluence rate) is obtained by dividing the rate of heat generation by the local absorption coefficient. Examples of computed distributions of the rate of heat generation are presented for situations where light scattering in tissue is important. The method is applied to analyze treatment of Port Wine Stain and the selection of laser wavelengths for cyclophotocoagulation.

关键词： Light scattering Laser Ablation Cyclophotocoagulation Hypoderma Heat generation Port-Wine Stain

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STATISTICALLY TAILORED NEURAL-NETWORK APPROACH TO TOMOGRAPHIC IMAGE-RECONSTRUCTION

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MEDICAL PHYSICS 1995年第5期22卷 601-610页

作者： KERR, JP BARTLETT, EB Biomedical Engineering Program Iowa State University Ames Iowa 50011

In previous work it has been shown that a standard backpropagation neural network can be trained to reconstruct sections of single photon emission computed tomography (SPECT) images based on the planar image projections as inputs. In this study, it is demonstrated that an artificial neural network (ANN) trained on a series of simulated SPECT images or trained on a set of rudimentary geometric images can learn the planar data-to-tomographic image relationship for 64×64 tomograms. As a result, a properly trained ANN can produce accurate, novel image reconstructions but without the high computational cost inherent in some traditional reconstruction techniques. We also present a method of deriving activation functions for a backpropagation ANN that make it readily trainable for cardiac SPECT image reconstruction. The activation functions are derived from the estimated probability density functions (p.d.f.s) of the ANN training set data. The performance of the statistically tailored ANNs are compared with the performance of standard sigmoidal backpropagation ANNs, both in terms of their trainability and generalization ability. The results presented demonstrate that statistically tailored ANNs are significantly better than standard sigmoidal ANNs at reconstructing novel tomographic images based on a simulated SPECT image training set or a rudimentary geometric image training set. Neural network based image reconstruction has two potential advantages over conventional reconstruction methods. The first advantage is that ANNs can rapidly reconstruction tomograms. Secondly, the quality of the reconstructions produced are directly correlated to the quality of the images used to train the ANN.

关键词： ARTIFICIAL NEURAL NETWORK BACKPROPAGATION PROBABILITY DENSITY FUNCTION SINGLE PHOTON EMISSION COMPUTED TOMOGRAPHY (SPECT) STATISTICALLY TAILORED NEURAL NETWORK

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Cobalt-Chromium-Molybdenum Femoral Knee Implant Damage Correlates With Elevated Periprosthetic Metal Concentrations

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Journal of Arthroplasty 2025年

作者： Kurtz, Peter W. Aslani, Shabnam Kurtz, Michael A. Taylor, Lilliana M. Barnes, Emma R. MacDonald, Daniel W. Piuzzi, Nicolas S. Mihalko, William M. Kurtz, Steven M. Gilbert, Jeremy L. Department of Bioengineering Clemson University Clemson SC United States The Clemson University-Medical University of South Carolina Bioengineering Program Charleston South Carolina United States Department of Biomedical Engineering Drexel University Implant Research Core Philadelphia Pennsylvania United States Department of Orthopaedic Surgery Cleveland Clinic Adult Reconstruction Research (CCARR) Cleveland Clinic Cleveland Ohio United States Department of Biomedical Engineering Cleveland Clinic Cleveland Ohio United States Campbell Clinic Department of Orthopaedic Surgery and Biomedical Engineering University of Tennessee Health Science Center Memphis TN United States

Background: Total knee arthroplasty (TKA) device systems frequently include cast cobalt chrome alloy (CoCrMo) femoral components. However, compared to total hip arthroplasty (THA), gaps persist in our understanding of the correlations between femoral component damage, local metal release, and potential biological effects. Additionally, it remains unclear how TKA metal release affects clinical success or patient satisfaction. In this study, we investigated the associations between implant damage and metal release in the periprosthetic tissues following TKA. We asked: (1) does damage severity correlate with increased metal concentrations within the periprosthetic tissue? and (2) does the magnitude of metal released from CoCrMo femoral components merit clinical concern? Methods: There were 51 CoCrMo femoral components and synovial samples that were prospectively collected by an institutional review board–exempt retrieval program. Devices received damage scores ranging from minimal (1) to severe (4). Tissue metal concentrations for cobalt (Co), chromium (Cr), molybdenum (Mo), and titanium (Ti) were quantified using inductively coupled plasma mass spectroscopy. Results: Visual damage correlated with increases in Co, Cr, and Mo concentrations in the periprosthetic tissue (P = 0.0008, 0.029, and 0.007, respectively). Within the tissue adjacent to severely damaged implants, we measured median Co, Cr, and Mo concentrations of 7.81, 5.26, and 0.713 μg/mL, respectively. For minimally damaged implants, we report median Co, Cr, and Mo concentrations of 0.111, 1.80, and 0.179 μg/mL, respectively. In several of the 51 (14%) tissue samples, we measured Co and Cr concentrations > 10 μg/mL. Additionally, within periprosthetic tissues of devices with Ti tibial trays, Ti concentrations increased (P = 0.0052) arising, in part, from tibial-femoral component contact during arthroplasty. Conclusions: We (1) showed elevated periprosthetic tissue metal concentrations in TKA patients and (2)

关键词： cobalt-chromium-molybdenum femoral component metal concentration titanium total knee arthroplasty

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