International Journal for Numerical Methods in Biomedical Engineering最新文献

{"title":"Quantifying the efficacy of voltage protocols in characterising ion channel kinetics: A novel information-theoretic approach","authors":"Matthew W. Jennings,&nbsp;Perumal Nithiarasu,&nbsp;Sanjay Pant","doi":"10.1002/cnm.3815","DOIUrl":"10.1002/cnm.3815","url":null,"abstract":"<p>Voltage-clamp experiments are commonly utilised to characterise cellular ion channel kinetics. In these experiments, cells are stimulated using a known time-varying voltage, referred to as the voltage protocol, and the resulting cellular response, typically in the form of current, is measured. Parameters of models that describe ion channel kinetics are then estimated by solving an inverse problem which aims to minimise the discrepancy between the predicted response of the model and the actual measured cell response. In this paper, a novel framework to evaluate the information content of voltage-clamp protocols in relation to ion channel model parameters is presented. Additional quantitative information metrics that allow for comparisons among various voltage protocols are proposed. These metrics offer a foundation for future optimal design frameworks to devise novel, information-rich protocols. The efficacy of the proposed framework is evidenced through the analysis of seven voltage protocols from the literature. By comparing known numerical results for inverse problems using these protocols with the information-theoretic metrics, the proposed approach is validated. The essential steps of the framework are: (i) generate random samples of the parameters from chosen prior distributions; (ii) run the model to generate model output (current) for all samples; (iii) construct reduced-dimensional representations of the time-varying current output using proper orthogonal decomposition (POD); (iv) estimate information-theoretic metrics such as mutual information, entropy equivalent variance, and conditional mutual information using non-parametric methods; (v) interpret the metrics; for example, a higher mutual information between a parameter and the current output suggests the protocol yields greater information about that parameter, resulting in improved identifiability; and (vi) integrate the information-theoretic metrics into a single quantitative criterion, encapsulating the protocol's efficacy in estimating model parameters.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cnm.3815","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A probabilistic neural twin for treatment planning in peripheral pulmonary artery stenosis","authors":"John D. Lee,&nbsp;Jakob Richter,&nbsp;Martin R. Pfaller,&nbsp;Jason M. Szafron,&nbsp;Karthik Menon,&nbsp;Andrea Zanoni,&nbsp;Michael R. Ma,&nbsp;Jeffrey A. Feinstein,&nbsp;Jacqueline Kreutzer,&nbsp;Alison L. Marsden,&nbsp;Daniele E. Schiavazzi","doi":"10.1002/cnm.3820","DOIUrl":"10.1002/cnm.3820","url":null,"abstract":"<p>The substantial computational cost of high-fidelity models in numerical hemodynamics has, so far, relegated their use mainly to <i>offline</i> treatment planning. New breakthroughs in data-driven architectures and optimization techniques for fast surrogate modeling provide an exciting opportunity to overcome these limitations, enabling the use of such technology for time-critical decisions. We discuss an application to the repair of multiple stenosis in peripheral pulmonary artery disease through either transcatheter pulmonary artery rehabilitation or surgery, where it is of interest to achieve desired pressures and flows at specific locations in the pulmonary artery tree, while minimizing the risk for the patient. Since different degrees of success can be achieved in practice during treatment, we formulate the problem in probability, and solve it through a sample-based approach. We propose a new offline–online pipeline for probabilistic real-time treatment planning which combines <i>offline</i> assimilation of boundary conditions, model reduction, and training dataset generation with <i>online</i> estimation of marginal probabilities, possibly conditioned on the degree of augmentation observed in already repaired lesions. Moreover, we propose a new approach for the parametrization of arbitrarily shaped vascular repairs through iterative corrections of a zero-dimensional approximant. We demonstrate this pipeline for a diseased model of the pulmonary artery tree available through the Vascular Model Repository.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Numerical study of doxorubicin transdermal delivery for breast cancer treatment using microneedles","authors":"Houda Barhoumi,&nbsp;Marie Carole Kouassi,&nbsp;Achraf Kallel","doi":"10.1002/cnm.3812","DOIUrl":"10.1002/cnm.3812","url":null,"abstract":"<p>The lack of in vivo studies on the delivery of doxorubicin within human skin, especially the absence of data on the doxorubicin diffusion coefficient, has made understanding its transdermal delivery kinetics challenging. In this study, as a first step, governing equations and finite element methods were employed to reproduce Franz diffusion cell experiment in human cadaver skin. The application of this experiment representative model with a fitting method resulted in approximate values for the diffusivity of doxorubicin across various skin layers. The estimated values were used later to conduct a comprehensive examination of doxorubicin administration for breast tumor treatments. In a 2D axisymmetric model using Fick's Law and then a microneedles array 3D model, crucial parameters effects on delivery efficiency were examined, such as the microneedle tip diameter, tip-to-tip distance, and tumor depth. As highlighted by the findings of this study, these parameters have an impact on the effectiveness of doxorubicin delivery for treating breast tumors. The focus of this research is on the potential of numerical methods in biomedical engineering, which addresses the urgent need for data on doxorubicin diffusion in human skin and offers valuable insights into optimizing drug delivery strategies for enhanced therapeutic outcomes.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140307690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alzheimer's disease progression detection based on optical fluence rate measurements using alternative laser wavelengths","authors":"Shimaa Mahdy,&nbsp;Hala S. Abuelmakarem","doi":"10.1002/cnm.3816","DOIUrl":"10.1002/cnm.3816","url":null,"abstract":"<p>Alzheimer's disease (AD) levels have increased globally, which is considered the sixth reason for deaths. So, a requirement exists for economic and quantitative methods to follow up the gradual progression of AD. The current study presents a simulation for a non-irradiated, safe, wearable, and noninvasive mobile approach for detecting the progression of Alzheimer's brain atrophy using the optical diffusion technique and for investigating the difference between the normal and the diseased brain. The virtual study was accomplished using COMSOL Multiphysics. The simulated head is implemented as the following: scalp, skull, cerebrospinal fluid, gray matter, and white matter. The optical properties of the heterogeneous tissue are observed using the fluence rate after irradiating the head with different wavelengths (630, 700, 810, 915, and 1000 nm) of lasers. Two assessment techniques were applied to evaluate the brain atrophy measurements; the first technique was an array of photodetectors, which were lined at the head posterior, while a matrix of photodetectors was applied over the head surface in the second technique. The results show that the surface photodetectors approach differentiates the normal from AD brains without measuring the brain atrophy percentages by applying 630 nm. The array of photodetectors distinguishes normal from AD brains without detecting the brain atrophy percentages when the wavelengths 630, 700, and 810 nm were applied. The line detector at 1000 nm evaluates the brain atrophy percentages with AD. The future explores applying those techniques in vivo and analyzing the information by the spectrometer for extensively safer early detection of neural disorders.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An in silico analysis of neuromodulation for pain relief: Determining the role of classical electrodynamics","authors":"Philip Cornish,&nbsp;Nabil Humphrey,&nbsp;Anne Cornish,&nbsp;R. Branden Emmerson","doi":"10.1002/cnm.3813","DOIUrl":"10.1002/cnm.3813","url":null,"abstract":"<p>There has been ongoing debate about the efficacy and mechanism of action of neuromodulation devices in pain relief applications. It has recently been suggested that both issues may be resolved if electromagnetic theory is incorporated into the understanding and application of this technology, and we therefore undertook an in silico analysis to further explore this idea. We created a CAD replication of a standard neuromodulation electrode array with a generic linear 3/6 mm 8-contact lead, developed a parameterized algorithmic model for the pulse delivered by the device and assigned material properties to biologic media to accurately reflect their electromagnetic properties. We then created a physical simulation of the device's output both in air and in the biophysical environment. The simulations confirmed the presence of an electromagnetic field (EM field). Variations in programming of the device affected the strength of the EM field by orders of magnitude. The biologic media all absorbed the EM field, an effect which was particularly pronounced in cerebrospinal fluid and muscle. We discuss the implications of all these findings in relation to the literature. We suggest that knowledge of electromagnetic theory and its application within the biophysical space is required for the optimal use of neuromodulation devices in pain relief applications.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cnm.3813","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Left atrial appendage occlusion: On the need of a numerical model to simulate the implant procedure","authors":"Francesca Danielli,&nbsp;Francesca Berti,&nbsp;Benigno Marco Fanni,&nbsp;Emanuele Gasparotti,&nbsp;Simona Celi,&nbsp;Giancarlo Pennati,&nbsp;Lorenza Petrini","doi":"10.1002/cnm.3814","DOIUrl":"10.1002/cnm.3814","url":null,"abstract":"<p>Left atrial appendage occlusion (LAAO) is a percutaneous procedure to prevent thromboembolism in patients affected by atrial fibrillation. Despite its demonstrated efficacy, the LAA morphological complexity hinders the procedure, resulting in postprocedural drawbacks (device-related thrombus and peri-device leakage). Local anatomical features may cause difficulties in the device's positioning and affect the effectiveness of the device's implant. The current work proposes a detailed FE model of the LAAO useful to investigate implant scenarios and derive clinical indications. A high-fidelity model of the Watchman FLX device and simplified parametric conduits mimicking the zone of the LAA where the device is deployed were developed. Device-conduit interactions were evaluated by looking at clinical indicators such as device-wall gap, possible cause of leakage, and device protrusion. As expected, the positioning of the crimped device before the deployment was found to significantly affect the implant outcomes: clinician's choices can be improved if FE models are used to optimize the pre-operative planning. Remarkably, also the wall mechanical stiffness plays an important role. However, this parameter value is unknown for a specific LAA, a crucial point that must be correctly defined for developing an accurate FE model. Finally, numerical simulations outlined how the device's configuration on which the clinician relies to assess the implant success (i.e., the deployed configuration with the device still attached to the catheter) may differ from the actual final device's configuration, relevant for achieving a safe intervention.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DGAMDA: Predicting miRNA-disease association based on dynamic graph attention network","authors":"ChangXin Jia,&nbsp;FuYu Wang,&nbsp;Baoxiang Xing,&nbsp;ShaoNa Li,&nbsp;Yang Zhao,&nbsp;Yu Li,&nbsp;Qing Wang","doi":"10.1002/cnm.3809","DOIUrl":"10.1002/cnm.3809","url":null,"abstract":"<p>MiRNA (microRNA)-disease association prediction has essential applications for early disease screening. The process of traditional biological experimental validation is both time-consuming and expensive. However, as artificial intelligence technology continues to advance, computational methods have become efficient tools for predicting miRNA-disease associations. These methods often rely on the combination of multiple sources of association data and require improved feature mining. This study proposes a dynamic graph attention-based association prediction model, DGAMDA, which combines feature mapping and dynamic graph attention mechanisms through feature mining on a single miRNA-disease association network. DGAMDA effectively solves the problems of feature heterogeneity and inadequate feature mining by previous static graph attention mechanisms and achieves high-precision feature mining and association scoring prediction. We conducted a five-fold cross-validation experiment and obtained the mean values of Accuracy, Precision, Recall, and F1-score, which were .8986, .8869, .9115, and .8984, respectively. Our proposed model outperforms other advanced models in terms of experimental results, demonstrating its effectiveness in feature mining and association prediction based on a single association network. In addition, our model can also be used to predict miRNAs associated with unknown diseases.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140112139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The biomechanical effects of bimaxillary osteotomies to the patients with mandibular retraction under incisal clenching","authors":"Haotian Luo,&nbsp;Haidong Teng,&nbsp;Desmond Y. R. Chong,&nbsp;Zhan Liu","doi":"10.1002/cnm.3810","DOIUrl":"10.1002/cnm.3810","url":null,"abstract":"<p>The purpose of this study is to investigate the biomechanical effect of bimaxillary osteotomies on patients with mandibular retraction. Mandibular retraction, as a typical maxillofacial deformity, and has great adverse effects on TMJ. Bimaxillary osteotomies are widely used to correct symptoms of mandibular retraction. It is necessary to understand the effect of surgery on temporomandibular disc (TMJ). Five patients with mandibular retraction and 10 asymptomatic subjects were involved in this study. Finite element models of preoperative, postoperative and control group were constructed based on the CT data. Nine sets of concentrated forces were used to simulate the muscle effect and contact method was used to simulate the interaction within the TMJs and dentitions. The results showed that bimaxillary osteotomies could effectively improve the maxillofacial morphology and alleviate the overload in TMJ. The facial asymmetry and right chewing side preference could cause imbalanced stress distributions in the TMJs and interfere the surgical treatment.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140112140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Numerical modelling of the interaction between dialysis catheter, vascular vessel and blood considering elastic structural deformation","authors":"Zihan Chen,&nbsp;Qijun Zheng,&nbsp;Zhenbo Tong,&nbsp;Xianchen Huang,&nbsp;Aibing Yu","doi":"10.1002/cnm.3811","DOIUrl":"10.1002/cnm.3811","url":null,"abstract":"<p>The dialysis catheter indwelling in human bodies has a high risk of inducing thrombus and stenosis. Biomechanical research showed that such physiological complications are triggered by the wall shear stress of the vascular vessel. This study aimed to assess the impact of CVC implantation on central venous haemodynamics and the potential alterations in the haemodynamic environment related to thrombus development. The SVC structure was built from the images from computed tomography. The blood flow was calculated using the Carreau model, and the fluid domain was determined by CFD. The vascular wall and the CVC were computed using FEA. The elastic interaction between the vessel wall and the flow field was considered using FSI simulation. With consideration of the effect of coupling, it was shown that the catheter vibrated in the vascular systems due to the periodic variation of blood pressure, with an amplitude of up to 10% of the vessel width. Spiral flow was observed along the catheter after CVC indwelling, and recirculation flow appeared near the catheter tip. High OSI and WSS regions occurred at the catheter tip and the vascular junction. The arterial lumen tip had a larger effect on the WSS and OSI values on the vascular wall. Considering FSI simulation, the movement of the catheter inside the blood flow was simulated in the deformable vessel. After CVC indwelling, spiral flow and recirculation flow were observed near the regions with high WSS and OSI values.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 5","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140102795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A real-time patient-specific treatment strategy for enhanced external counterpulsation","authors":"Bao Li,&nbsp;Youjun Liu,&nbsp;Guangfei Li,&nbsp;Zhe Zhang,&nbsp;Yue Feng,&nbsp;Boyan Mao","doi":"10.1002/cnm.3808","DOIUrl":"10.1002/cnm.3808","url":null,"abstract":"<p>Diastolic/systolic blood pressure ratio (D/S) ≥ 1.2 is the gold standard of enhanced external counterpulsation (EECP) treatment, but it does not show a clear clinical correspondence with the configuration of the EECP mode. As such, a single target results in different treatment effects in different individuals. The local haemodynamic effect (wall shear stress, WSS) of EECP on vascular endothelial cells is conducive to promote the growth of collateral circulation vessels and restore the blood supply distal to the stenosis lesion. Considering the haemodynamic effects of WSS on human arteries, this study developed a real-time patient-specific treatment strategy of EECP for patients with cardio-cerebrovascular diseases. Based on patient-specific haemodynamic data from 113 individuals, an optimization algorithm was developed to achieve the individualization of a 0D lumped-parameter model of the human circulatory system, thereby simulating the patient-specific global haemodynamic effects. 0D/3D coupled cardio-cerebrovascular models of two subjects were established to simulate the local WSS. We then established statistical models to evaluate clinically unmeasurable WSS based on measurable global haemodynamic indicators. With the aim of attaining appropriate area- and time-averaged WSS (ATAWSS, 4–7 Pa), as evaluated by global haemodynamic indicators, a closed-loop feedback tuning method was developed to provide patient-specific EECP treatment strategies. Results showed that for clinical data collected from 113 individuals, the individualized 0D model can accurately simulate patient-specific global haemodynamic effects (average error &lt;5%). Based on two subjects, the statistical models can be used to evaluate local ATAWSS (error &lt;6%) for coronary arteries and for cerebral arteries. An EECP mode planned by the patient-specific treatment strategy can promote an appropriate ATAWSS within a 16 s calculation time. The real-time patient-specific treatment strategy of EECP is expected to improve the long-term outcome for each patient and have potential clinical significance.</p>","PeriodicalId":50349,"journal":{"name":"International Journal for Numerical Methods in Biomedical Engineering","volume":"40 4","pages":""},"PeriodicalIF":2.1,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139974273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}