{"title":"EthoWatcher OS: improving the reproducibility and quality of categorical and morphologic/kinematic data from behavioral recordings in laboratory animals.","authors":"João Antônio Marcolan, José Marino-Neto","doi":"10.1007/s11517-024-03212-x","DOIUrl":"https://doi.org/10.1007/s11517-024-03212-x","url":null,"abstract":"<p><p>Behavioral recordings annotated by human observers (HOs) from video recordings are a fundamental component of preclinical animal behavioral models of neurobiological diseases. These models are often criticized for their vulnerability to reproducibility issues. Here, we present the EthoWatcher-Open Source (EW-OS), with tools and procedures for the use of blind-to-condition categorical transcriptions that are simultaneous with tracking, for the assessment of HOs intra- and interobserver reliability during training and data collection, for producing video clips of samples of behavioral categories that are useful for observer training. The use of these tools can inform and optimize the performance of observers, thus favoring the reproducibility of the data obtained. Categorical and machine vision-derived outputs are presented in an open data format for increased interoperability with other applications, where behavioral categories are associated frame-by-frame with tracking, morphological and kinematic attributes of an animal's image. The center of mass (X and Y pixel coordinates), the animal's area in square millimeters, the length and width in millimeters, and the angle in degrees were recorded. It also assesses the variation in each morphological descriptor to produce kinematic descriptors. While the initial measurements are in pixels, they are later converted to millimeters using the scale calibrated by the user via the graphical user interfaces. This process enables the creation of databases suitable for machine learning processing and behavioral pharmacology studies. EW-OS is constructed for continued collaborative development, available through an open-source platform, to support initiatives toward the adoption of good scientific practices in behavioral analysis, including tools for evaluating the quality of the data that can alleviate problems associated with low reproducibility in the behavioral sciences.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479179","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}
Lizhi Pan, Zhongyi Ding, Haifeng Zhao, Ruinan Mu, Jianmin Li
{"title":"Comparing on-line continuous movement decoding with joints unconstrained and constrained based on a generic musculoskeletal model.","authors":"Lizhi Pan, Zhongyi Ding, Haifeng Zhao, Ruinan Mu, Jianmin Li","doi":"10.1007/s11517-024-03207-8","DOIUrl":"https://doi.org/10.1007/s11517-024-03207-8","url":null,"abstract":"<p><p>Human-machine interface (HMI) has been extensively developed and applied in rehabilitation. However, the performance of amputees on continuous movement decoding was significantly decreased compared with that of able-bodied individuals. To explore the impact of the absence of joint movements on the performance of HMI in rehabilitation, a generic musculoskeletal model (MM) was employed in this study to evaluate and compare the performance of subjects completing a series of on-line tasks with the wrist and metacarpophalangeal (MCP) joints unconstrained and constrained. The performance of the generic MM has been demonstrated in previous studies. The electromyography (EMG) signals of four muscles were employed as inputs of the generic MM to realize the continuous movement decoding of wrist and MCP joints. Ten able-bodied subjects were recruited to perform the on-line tasks. The completion time, the number of overshoots, and the path efficiency of the tasks were taken as the indexes to quantify the subjects' performance. The muscle activation associated with the movement was analyzed. Across all tasks and subjects, the average values of the three indexes with the joints unconstrained were 7.7 s, 0.59, and 0.38, respectively, while those with the joints constrained were 17.86 s, 1.47, and 0.22, respectively. The results demonstrated that the subjects performed better with the wrist and MCP joints unconstrained than with those joints constrained in the on-line tasks, suggesting that the absence of joint movements can be a reason of the decreased performance of continuous movement decoding with HMIs. Meanwhile, it is revealed that the different performance on motion behaviors is caused by the absence of joint movements.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479175","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":"Cancer-on-chip: a breakthrough organ-on-a-chip technology in cancer cell modeling.","authors":"Babak Nejati, Reza Shahhosseini, Mobasher Hajiabbasi, Nastaran Safavi Ardabili, Kosar Bagtashi Baktash, Vahid Alivirdiloo, Sadegh Moradi, Mohammadreza Farhadi Rad, Fatemeh Rahimi, Marzieh Ramezani Farani, Farhood Ghazi, Ahmad Mobed, Iraj Alipourfard","doi":"10.1007/s11517-024-03199-5","DOIUrl":"https://doi.org/10.1007/s11517-024-03199-5","url":null,"abstract":"<p><p>Cancer remains one of the leading causes of death worldwide. The unclear molecular mechanisms and complex in vivo microenvironment of tumors make it difficult to clarify the nature of cancer and develop effective treatments. Therefore, the development of new methods to effectively treat cancer is urgently needed and of great importance. Organ-on-a-chip (OoC) systems could be the breakthrough technology sought by the pharmaceutical industry to address ever-increasing research and development costs. The past decade has seen significant advances in the spatial modeling of cancer therapeutics related to OoC technology, improving physiological exposition criteria. This article aims to summarize the latest achievements and research results of cancer cell treatment simulated in a 3D microenvironment using OoC technology. To this end, we will first discuss the OoC system in detail and then demonstrate the latest findings of the cancer cell treatment study by Ooc and how this technique can potentially optimize better modeling of the tumor. The prospects of OoC systems in the treatment of cancer cells and their advantages and limitations are also among the other points discussed in this study.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479174","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":"Digital transformation of mental health therapy by integrating digitalized cognitive behavioral therapy and eye movement desensitization and reprocessing.","authors":"Ju-Yu Wu, Ying-Ying Tsai, Yu-Jie Chen, Fan-Chi Hsiao, Ching-Han Hsu, Yen-Feng Lin, Lun-De Liao","doi":"10.1007/s11517-024-03209-6","DOIUrl":"https://doi.org/10.1007/s11517-024-03209-6","url":null,"abstract":"<p><p>Digital therapy has gained popularity in the mental health field because of its convenience and accessibility. One major benefit of digital therapy is its ability to address therapist shortages. Posttraumatic stress disorder (PTSD) is a debilitating mental health condition that can develop after an individual experiences or witnesses a traumatic event. Digital therapy is an important resource for individuals with PTSD who may not have access to traditional in-person therapy. Cognitive behavioral therapy (CBT) and eye movement desensitization and reprocessing (EMDR) are two evidence-based psychotherapies that have shown efficacy in treating PTSD. This paper examines the mechanisms and clinical symptoms of PTSD as well as the principles and applications of CBT and EMDR. Additionally, the potential of digital therapy, including internet-based CBT, video conferencing-based therapy, and exposure therapy using augmented and virtual reality, is explored. This paper also discusses the engineering techniques employed in digital psychotherapy, such as emotion detection models and text analysis, for assessing patients' emotional states. Furthermore, it addresses the challenges faced in digital therapy, including regulatory issues, hardware limitations, privacy and security concerns, and effectiveness considerations. Overall, this paper provides a comprehensive overview of the current state of digital psychotherapy for PTSD treatment and highlights the opportunities and challenges in this rapidly evolving field.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479178","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":"Ultra-short-term stress measurement using RGB camera-based remote photoplethysmography with reduced effects of Individual differences in heart rate.","authors":"Seungkeon Lee, Young Do Song, Eui Chul Lee","doi":"10.1007/s11517-024-03213-w","DOIUrl":"https://doi.org/10.1007/s11517-024-03213-w","url":null,"abstract":"<p><p>Stress is linked to health problems, increasing the need for immediate monitoring. Traditional methods like electrocardiograms or contact photoplethysmography require device attachment, causing discomfort, and ultra-short-term stress measurement research remains inadequate. This paper proposes a method for ultra-short-term stress monitoring using remote photoplethysmography (rPPG). Previous predictions of ultra-short-term stress have typically used pulse rate variability (PRV) features derived from time-segmented heart rate data. However, PRV varies at the same stress levels depending on heart rates, necessitating a new method to account for these differences. This study addressed this by segmenting rPPG data based on normal-to-normal intervals (NNIs), converted from peak-to-peak intervals, to predict ultra-short-term stress indices. We used NNI counts corresponding to average durations of 10, 20, and 30 s (13, 26, and 39 NNIs) to extract PRV features, predicting the Baevsky stress index through regressors. The Extra Trees Regressor achieved R<sup>2</sup> scores of 0.6699 for 13 NNIs, 0.8751 for 26 NNIs, and 0.9358 for 39 NNIs, surpassing the time-segmented approach, which yielded 0.4162, 0.6528, and 0.7943 for 10, 20, and 30-s intervals, respectively. These findings demonstrate that using NNI counts for ultra-short-term stress prediction improves accuracy by accounting for individual bio-signal variations.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401794","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":"Integrated analysis of gene expressions and targeted mirnas for explaining crosstalk between oral and esophageal squamous cell carcinomas through an interpretable machine learning approach.","authors":"Khushi Yadav, Yasha Hasija","doi":"10.1007/s11517-024-03210-z","DOIUrl":"https://doi.org/10.1007/s11517-024-03210-z","url":null,"abstract":"<p><p>This study explores the bidirectional relation of esophageal squamous cell carcinoma (ESCC) and oral squamous cell carcinoma (OSCC), examining shared risk factors and underlying molecular mechanisms. By employing random forest (RF) classifier, enhanced with interpretable machine learning (IML) through SHapley Additive exPlanations (SHAP), we analyzed gene expression from two GEO datasets (GSE30784 and GSE44021). The GSE30784 dataset comprises 167 OSCC samples and 45 control group, whereas the GSE44021 dataset encompasses 113 ESCC samples and 113 control group. Our analysis led to identification of 20 key genes, such as XBP1, VGLL1, and RAD1, which are significantly associated with development of ESCC and OSCC. Further investigations were conducted using tools like NetworkAnalyst 3.0, Single Cell Portal, and miRNET 2.0, which highlighted complex interactions between these genes and specific miRNA targets including hsa-mir-124-3p and hsa-mir-1-3p. Our model achieved high precision in identifying genes linked to crucial processes like programmed cell death and cancer pathways, suggesting new avenues for diagnosis and treatment. This study confirms the bidirectional relationship between OSCC and ESCC, laying groundwork for targeted therapeutic approaches. This study helps to identify shared biological pathways and genetic factors of these conditions for designing personalized medicine strategies and to improve disease management.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142394778","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}
Roberta Scuoppo, Salvatore Castelbuono, Stefano Cannata, Giovanni Gentile, Valentina Agnese, Diego Bellavia, Caterina Gandolfo, Salvatore Pasta
{"title":"Generation of a virtual cohort of TAVI patients for in silico trials: a statistical shape and machine learning analysis.","authors":"Roberta Scuoppo, Salvatore Castelbuono, Stefano Cannata, Giovanni Gentile, Valentina Agnese, Diego Bellavia, Caterina Gandolfo, Salvatore Pasta","doi":"10.1007/s11517-024-03215-8","DOIUrl":"https://doi.org/10.1007/s11517-024-03215-8","url":null,"abstract":"<p><strong>Purpose: </strong>In silico trials using computational modeling and simulations can complement clinical trials to improve the time-to-market of complex cardiovascular devices in humans. This study aims to investigate the significance of synthetic data in developing in silico trials for assessing the safety and efficacy of cardiovascular devices, focusing on bioprostheses designed for transcatheter aortic valve implantation (TAVI).</p><p><strong>Methods: </strong>A statistical shape model (SSM) was employed to extract uncorrelated shape features from TAVI patients, enabling the augmentation of the original patient population into a clinically validated synthetic cohort. Machine learning techniques were utilized not only for risk stratification and classification but also for predicting the physiological variability within the original patient population.</p><p><strong>Results: </strong>By randomly varying the statistical shape modes within a range of ± 2σ, a hundred virtual patients were generated, forming the synthetic cohort. Validation against the original patient population was conducted using morphological measurements. Support vector machine regression, based on selected shape modes (principal component scores), effectively predicted the peak pressure gradient across the stenosis (R-squared of 0.551 and RMSE of 11.67 mmHg). Multilayer perceptron neural network accurately predicted the optimal device size for implantation with high sensitivity and specificity (AUC = 0.98).</p><p><strong>Conclusion: </strong>The study highlights the potential of integrating computational predictions, advanced machine learning techniques, and synthetic data generation to improve predictive accuracy and assess TAVI-related outcomes through in silico trials.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401783","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}
Christoph Schmidt, Wasilios Hatziklitiu, Frederik Trinkmann, Giorgio Cattaneo, Johannes Port
{"title":"Investigation of inert gas washout methods in a new numerical model based on an electrical analogy.","authors":"Christoph Schmidt, Wasilios Hatziklitiu, Frederik Trinkmann, Giorgio Cattaneo, Johannes Port","doi":"10.1007/s11517-024-03200-1","DOIUrl":"https://doi.org/10.1007/s11517-024-03200-1","url":null,"abstract":"<p><p>Inert gas washout methods have been shown to detect pathological changes in the small airways that occur in the early stages of obstructive lung diseases such as asthma and COPD. Numerical lung models support the analysis of characteristic washout curves, but are limited in their ability to simulate the complexity of lung anatomy over an appropriate time period. Therefore, the interpretation of patient-specific washout data remains a challenge. A new numerical lung model is presented in which electrical components describe the anatomical and physiological characteristics of the lung as well as gas-specific properties. To verify that the model is able to reproduce characteristic washout curves, the phase 3 slopes (S<sub>3</sub>) of helium washouts are simulated using simple asymmetric lung anatomies consisting of two parallel connected lung units with volume ratios of <math> <mfrac><mrow><mn>1.25</mn></mrow> <mrow><mn>0.75</mn></mrow> </mfrac> </math> , <math> <mfrac><mrow><mn>1.50</mn></mrow> <mrow><mn>0.50</mn></mrow> </mfrac> </math> , and <math> <mfrac><mrow><mn>1.75</mn></mrow> <mrow><mn>0.25</mn></mrow> </mfrac> </math> and a total volume flow of 250 ml/s which are evaluated for asymmetries in both the convection- and diffusion-dominated zone of the lung. The results show that the model is able to reproduce the S<sub>3</sub> for helium and thus the processes underlying the washout methods, so that electrical components can be used to model these methods. This approach could form the basis of a hardware-based real-time simulator.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142382181","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 cascaded FAS-UNet+ framework with iterative optimization strategy for segmentation of organs at risk.","authors":"Hui Zhu, Shi Shu, Jianping Zhang","doi":"10.1007/s11517-024-03208-7","DOIUrl":"https://doi.org/10.1007/s11517-024-03208-7","url":null,"abstract":"<p><p>Segmentation of organs at risks (OARs) in the thorax plays a critical role in radiation therapy for lung and esophageal cancer. Although automatic segmentation of OARs has been extensively studied, it remains challenging due to the varying sizes and shapes of organs, as well as the low contrast between the target and background. This paper proposes a cascaded FAS-UNet+ framework, which integrates convolutional neural networks and nonlinear multi-grid theory to solve a modified Mumford-shah model for segmenting OARs. This framework is equipped with an enhanced iteration block, a coarse-to-fine multiscale architecture, an iterative optimization strategy, and a model ensemble technique. The enhanced iteration block aims to extract multiscale features, while the cascade module is used to refine coarse segmentation predictions. The iterative optimization strategy improves the network parameters to avoid unfavorable local minima. An efficient data augmentation method is also developed to train the network, which significantly improves its performance. During the prediction stage, a weighted ensemble technique combines predictions from multiple models to refine the final segmentation. The proposed cascaded FAS-UNet+ framework was evaluated on the SegTHOR dataset, and the results demonstrate significant improvements in Dice score and Hausdorff Distance (HD). The Dice scores were 95.22%, 95.68%, and HD values were 0.1024, and 0.1194 for the segmentations of the aorta and heart in the official unlabeled dataset, respectively. Our code and trained models are available at https://github.com/zhuhui100/C-FASUNet-plus .</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373364","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":"Comparative biomechanical analysis of a conventional/novel hip prosthetic socket.","authors":"Yu Qian, Yunzhang Cheng, Shiyao Chen, Mingwei Zhang, Yingyu Fang, Tianyi Zhang","doi":"10.1007/s11517-024-03206-9","DOIUrl":"https://doi.org/10.1007/s11517-024-03206-9","url":null,"abstract":"<p><p>The aim of this study was to investigate and compare the biomechanical properties of the conventional and novel hip prosthetic socket by using the finite element and gait analysis. According to the CT scan model of the subject's residual limb, the bones, soft tissues, and the socket model were reconstructed in three dimensions by using inverse modeling. The distribution of normal and shear stresses at the residual limb-socket interface under the standing condition was investigated using the finite element method and verified by designing a pressure acquisition module system. The gait experiment compared and analyzed the conventional and novel sockets. The results show that the simulation results are consistent with the experimental data. The novel socket exhibited superior stress performance and gait outcomes compared to the conventional design. Our findings provide a research basis for evaluating the comfort of the hip prosthetic socket, optimizing and designing the structure of the socket of the hip.</p>","PeriodicalId":49840,"journal":{"name":"Medical & Biological Engineering & Computing","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367226","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}