Computers in biology and medicine最新文献

{"title":"Quantifying the frequency modulation in electrograms during simulated atrial fibrillation in 2D domains.","authors":"Juan P Ugarte, Alejandro Gómez-Echavarría, Catalina Tobón","doi":"10.1016/j.compbiomed.2024.109228","DOIUrl":"https://doi.org/10.1016/j.compbiomed.2024.109228","url":null,"abstract":"<p><p>Atrial fibrillation (AF) affects millions of people in the world, causing increased morbidity and mortality. Treatment involves antiarrhythmic drugs and catheter ablation, showing high success for paroxysmal AF but challenges for persistent AF. Experimental evidence suggests reentrant waves and rotors contribute to AF substrates. Ablation procedures rely on electroanatomical maps and electrogram (EGM) signals; however, current methods used in clinical practice lack consideration for time-frequency varying EGM components. The fractional Fourier transform (FrFT) can be adopted to capture time-varying frequency components, thereby enhancing the comprehension of arrhythmogenic substrates during AF for improved ablation strategies. To this end, a FrFT-based algorithm is developed to characterize non-stationary components in EGM signals from simulated AF episodes. The proposed algorithm comprises a pre-processing step to enhance the coarser features of the EGM waveform, a windowing process for dynamic assessment of the EGM, and a FrFT order optimization stage that seeks compact signal representations in fractional Fourier domains. The resulting order is related to the rate of frequency change in the signal, making it a useful indicator for frequency-modulated components. The FrFT-based algorithm is implemented on EGM signals from AF simulations in 2D domains representing a region of the atrial tissue. Consequently, the computed optimum FrFT orders are used to build maps that are spatially correlated to the underlying propagation dynamics of the simulated AF episode. The results evince that the extreme values in the optimum orders map pinpoint the localization of fibrillatory mechanisms, generating EGM activation waveforms with varying frequency content over time.</p>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multimodal brain tumor segmentation and classification from MRI scans based on optimized DeepLabV3+ and interpreted networks information fusion empowered with explainable AI.","authors":"Muhammad Sami Ullah, Muhammad Attique Khan, Hussain Mubarak Albarakati, Robertas Damaševičius, Shrooq Alsenan","doi":"10.1016/j.compbiomed.2024.109183","DOIUrl":"https://doi.org/10.1016/j.compbiomed.2024.109183","url":null,"abstract":"<p><p>Explainable artificial intelligence (XAI) aims to offer machine learning (ML) methods that enable people to comprehend, properly trust, and create more explainable models. In medical imaging, XAI has been adopted to interpret deep learning black box models to demonstrate the trustworthiness of machine decisions and predictions. In this work, we proposed a deep learning and explainable AI-based framework for segmenting and classifying brain tumors. The proposed framework consists of two parts. The first part, encoder-decoder-based DeepLabv3+ architecture, is implemented with Bayesian Optimization (BO) based hyperparameter initialization. The different scales are performed, and features are extracted through the Atrous Spatial Pyramid Pooling (ASPP) technique. The extracted features are passed to the output layer for tumor segmentation. In the second part of the proposed framework, two customized models have been proposed named Inverted Residual Bottleneck 96 layers (IRB-96) and Inverted Residual Bottleneck Self-Attention (IRB-Self). Both models are trained on the selected brain tumor datasets and extracted features from the global average pooling and self-attention layers. Features are fused using a serial approach, and classification is performed. The BO-based hyperparameters optimization of the neural network classifiers is performed and the classification results have been optimized. An XAI method named LIME is implemented to check the interpretability of the proposed models. The experimental process of the proposed framework was performed on the Figshare dataset, and an average segmentation accuracy of 92.68 % and classification accuracy of 95.42 % were obtained, respectively. Compared with state-of-the-art techniques, the proposed framework shows improved accuracy.</p>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Frontoparietal atrophy trajectories in cognitively unimpaired elderly individuals using longitudinal Bayesian clustering.","authors":"G Lorenzon, K Poulakis, R Mohanty, M Kivipelto, M Eriksdotter, D Ferreira, E Westman","doi":"10.1016/j.compbiomed.2024.109190","DOIUrl":"https://doi.org/10.1016/j.compbiomed.2024.109190","url":null,"abstract":"<p><strong>Introduction: </strong>Frontal and/or parietal atrophy has been reported during aging. To disentangle the heterogeneity previously observed, this study aimed to uncover different clusters of grey matter profiles and trajectories within cognitively unimpaired individuals.</p><p><strong>Methods: </strong>Structural magnetic resonance imaging (MRI) data of 307 Aβ-negative cognitively unimpaired individuals were modelled between ages 60-85 from three cohorts worldwide. We applied unsupervised clustering using a novel longitudinal Bayesian approach and characterized the clusters' cerebrovascular and cognitive profiles.</p><p><strong>Results: </strong>Four clusters were identified with different grey matter profiles and atrophy trajectories. Differences were mainly observed in frontal and parietal brain regions. These distinct frontoparietal grey matter profiles and longitudinal trajectories were differently associated with cerebrovascular burden and cognitive decline.</p><p><strong>Discussion: </strong>Our findings suggest a conciliation of the frontal and parietal theories of aging, uncovering coexisting frontoparietal GM patterns. This could have important future implications for better stratification and identification of at-risk individuals.</p>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Histopathology-driven prostate cancer identification: A VBIR approach with CLAHE and GLCM insights.","authors":"Pramod K B Rangaiah, B P Pradeep Kumar, Robin Augustine","doi":"10.1016/j.compbiomed.2024.109213","DOIUrl":"https://doi.org/10.1016/j.compbiomed.2024.109213","url":null,"abstract":"<p><p>Efficient extraction and analysis of histopathological images are crucial for accurate medical diagnoses, particularly for prostate cancer. This research enhances histopathological image reclamation by integrating Visual-Based Image Reclamation (VBIR) techniques with contrast-limited adaptive Histogram Equalization (CLAHE) and the Gray-Level Co-occurrence Matrix (GLCM) algorithm. The proposed method leverages CLAHE to improve image contrast and visibility, crucial for regions with varying illumination, and employs a non-linear Support Vector Machine (SVM) to incorporate GLCM features. Our approach achieved a notable success rate of 89.6%, demonstrating significant improvement in image analysis. The average execution time for matched tissues was 41.23 s (standard deviation 36.87 s), and for unmatched tissues, 21.22 s (standard deviation 29.18 s). These results underscore the method's efficiency and reliability in processing histopathological images. The findings from this study highlight the potential of our method to enhance image reclamation processes, paving the way for further research and advancements in medical image analysis. The superior performance of our approach signifies its capability to significantly improve histopathological image analysis, contributing to more accurate and efficient diagnostic practices.</p>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-invasive regional parameter identification of degenerated human meniscus.","authors":"Jonas Schwer, Fabio Galbusera, Anita Ignatius, Lutz Dürselen, Andreas Martin Seitz","doi":"10.1016/j.compbiomed.2024.109230","DOIUrl":"https://doi.org/10.1016/j.compbiomed.2024.109230","url":null,"abstract":"<p><p>Accurate identification of local changes in the biomechanical properties of the normal and degenerative meniscus is critical to better understand knee joint osteoarthritis onset and progression. Ex-vivo material characterization is typically performed on specimens obtained from different locations, compromising the tissue's structural integrity and thus altering its mechanical behavior. Therefore, the aim of this in-silico study was to establish a non-invasive method to determine the region-specific material properties of the degenerated human meniscus. In a previous experimental magnetic resonance imaging (MRI) study, the spatial displacement of the meniscus and its root attachments in mildly degenerated (n = 12) and severely degenerated (n = 12) cadaveric knee joints was determined under controlled subject-specific axial joint loading. To simulate the experimental response of the lateral and medial menisci, individual finite element models were created utilizing a transverse isotropic hyper-poroelastic constitutive material formulation. The superficial displacements were applied to the individual models to calculate the femoral reaction force in an inverse finite element analysis. During particle swarm optimization, the four most sensitive material parameters were varied to minimize the error between the femoral reaction force and the force applied in the MRI loading experiment. Individual global and regional parameter sets were identified. In addition to in-depth model verification, prediction errors were determined to quantify the reliability of the identified parameter sets. Both compressibility of the solid meniscus matrix (+141 %, p ≤ 0.04) and hydraulic permeability (+53 %, p ≤ 0.04) were significantly increased in the menisci of severely degenerated knees compared to mildly degenerated knees, irrespective of the meniscus region. By contrast, tensile and shear properties were unaffected by progressive knee joint degeneration. Overall, the optimization procedure resulted in reliable and robust parameter sets, as evidenced by mean prediction errors of <1 %. In conclusion, the proposed approach demonstrated high potential for application in clinical practice, where it might provide a non-invasive diagnostic tool for the early detection of osteoarthritic changes within the knee joint.</p>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhancing ensemble classifiers utilizing gaze tracking data for autism spectrum disorder diagnosis","authors":"","doi":"10.1016/j.compbiomed.2024.109184","DOIUrl":"10.1016/j.compbiomed.2024.109184","url":null,"abstract":"<div><h3>Problem:</h3><div>Diagnosing Autism Spectrum Disorder (ASD) remains a significant challenge, especially in regions where access to specialists is limited. Computer-based approaches offer a promising solution to make diagnosis more accessible. Eye tracking has emerged as a valuable technique in aiding the diagnosis of ASD. Typically, individuals’ gaze patterns are monitored while they view videos designed according to established paradigms. In a previous study, we developed a method to classify individuals as having ASD or Typical Development (TD) by processing eye-tracking data using Random Forest ensembles, with a focus on a paradigm known as joint attention.</div></div><div><h3>Aim:</h3><div>This article aims to enhance our previous work by evaluating alternative algorithms and ensemble strategies, with a particular emphasis on the role of anticipation features in diagnosis.</div></div><div><h3>Methods:</h3><div>Utilizing stimuli based on joint attention and the concept of “floating regions of interest” from our earlier research, we identified features that indicate gaze anticipation or delay. We then tested seven class balancing strategies, applied seven dimensionality reduction algorithms, and combined them with five different classifier induction algorithms. Finally, we employed the stacking technique to construct an ensemble model.</div></div><div><h3>Results:</h3><div>Our findings showed a significant improvement, achieving an F1-score of 95.5%, compared to the 82% F1-score from our previous work, through the use of a heterogeneous stacking meta-classifier composed of diverse induction algorithms.</div></div><div><h3>Conclusion:</h3><div>While there remains an opportunity to explore new algorithms and features, the approach proposed in this article has the potential to be applied in clinical practice, contributing to increased accessibility to ASD diagnosis.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142359431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patient-based multilevel transcriptome exploration highlights relevant chemokines and chemokine receptor axes in glioblastoma.","authors":"Giulia D'Uonnolo, Damla Isci, Bakhtiyor Nosirov, Amandine Kuppens, May Wantz, Petr V Nazarov, Anna Golebiewska, Bernard Rogister, Andy Chevigné, Virginie Neirinckx, Martyna Szpakowska","doi":"10.1016/j.compbiomed.2024.109197","DOIUrl":"https://doi.org/10.1016/j.compbiomed.2024.109197","url":null,"abstract":"<p><p>Chemokines and their receptors form a complex interaction network, crucial for precise leukocyte positioning and trafficking. In cancer, they promote malignant cell proliferation and survival but are also critical for immune cell infiltration in the tumor microenvironment. Glioblastoma (GBM) is the most common and lethal brain tumor, characterized by an immunosuppressive TME, with restricted immune cell infiltration. A better understanding of chemokine-receptor interactions is therefore essential for improving tumor immunogenicity. In this study, we assessed the expression of all human chemokines in adult-type diffuse gliomas, with particular focus on GBM, based on patient-derived samples. Publicly available bulk RNA sequencing datasets allowed us to identify the chemokines most abundantly expressed in GBM, with regard to disease severity and across different tumor subregions. To gain insight into the chemokines-receptor network at the single cell resolution, we explored GBmap, a curated resource integrating multiple scRNAseq datasets from different published studies. Our study constitutes the first patient-based handbook highlighting the relevant chemokine-receptor crosstalks, which are of significant interest in the perspective of a therapeutic modulation of the TME in GBM.</p>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142364649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visual interpretation of deep learning model in ECG classification: A comprehensive evaluation of feature attribution methods","authors":"","doi":"10.1016/j.compbiomed.2024.109088","DOIUrl":"10.1016/j.compbiomed.2024.109088","url":null,"abstract":"<div><div>Feature attribution methods can visually highlight specific input regions containing influential aspects affecting a deep learning model's prediction. Recently, the use of feature attribution methods in electrocardiogram (ECG) classification has been sharply increasing, as they assist clinicians in understanding the model's decision-making process and assessing the model's reliability. However, a careful study to identify suitable methods for ECG datasets has been lacking, leading researchers to select methods without a thorough understanding of their appropriateness. In this work, we conduct a large-scale assessment by considering eleven popular feature attribution methods across five large ECG datasets using a model based on the ResNet-18 architecture. Our experiments include both automatic evaluations and human evaluations. Annotated datasets were utilized for automatic evaluations and three cardiac experts were involved for human evaluations. We found that Guided Grad-CAM, particularly when its absolute values are utilized, achieves the best performance. When Guided Grad-CAM was utilized as the feature attribution method, cardiac experts confirmed that it can identify diagnostically relevant electrophysiological characteristics, although its effectiveness varied across the 17 different diagnoses that we have investigated.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142359430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification, isoform classification, ligand binding, and database construction of the protein-tyrosine sulfotransferase family in metazoans","authors":"","doi":"10.1016/j.compbiomed.2024.109208","DOIUrl":"10.1016/j.compbiomed.2024.109208","url":null,"abstract":"<div><div>Protein tyrosine sulfonation (PTS) influences various crucial physiological and pathological processes in animals. Protein-tyrosine sulfotransferase (TPST) serves as a pivotal enzyme in this process. Research on TPST is still in its early stages, and current identification methods have not yet effectively differentiated TPST from other type II sulfotransferases. Furthermore, this study has revealed that TPST in animals is highly conserved and exhibits significant differences when compared to other sulfotransferases and TPSTs in non-animal species. However, precise and efficient methods for identifying TPST, conducting subfamily classification, performing functional and sequence analyses, and accessing corresponding databases and analytical platforms for the entire TPST family of metazoan species are lacking. These findings provide a foundation for more in-depth research on TPST in animals and are crucial for advancing the understanding of PTS and its broader impacts.</div><div>In this study, a Hidden Markov Model (TPST-HMM) was formulated based on the conserved motifs binding to the substrate PAPS and the ligand tyrosine in metazoan TPSTs. TPST-HMM successfully identified more than 91.8 % of metazoan TPSTs in UniProt (e-value &lt; 1e-5). When the threshold was adjusted to 1e-20, the identification rate of TPST was 83.9 % in metazoans and approximately 0 % in other species (fungi, bacteria, etc.). Subsequently, 5638 TPSTs were identified from 1311 metazoan genomes, and these TPSTs were classified into three subfamilies. The classification of the TPST1 and TPST2 subtypes, which were initially annotated in mammals, was extended across vertebrates. Additionally, a novel subtype, TPST3, belonging to a distinct subfamily, was discovered in invertebrates. We proposed a molecular docking prediction method for TPST and tyrosine ligands based on the observation that TPST-tyrosine binding recognition and binding in metazoans were primarily driven by electrostatic interactions.</div><div>Finally, a database website for animal TPST sequences was established (<span><span>http://sz.bjfskj.com/</span><svg><path></path></svg></span>). The website included an online tool for identifying TPST protein sequences, enabling annotation and visualization of functional motifs and active amino acids. Its design aimed to assist users in studying TPST in animals.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 circRNA regulation with ADARB2 enrichment in inhibitory neurons","authors":"","doi":"10.1016/j.compbiomed.2024.109212","DOIUrl":"10.1016/j.compbiomed.2024.109212","url":null,"abstract":"<div><div>This study investigates the regulation of circular RNAs (circRNAs) with Adenosine Deaminase RNA Specific B2 (ADARB2) enrichment specifically in inhibitory neurons. Using an integrated analysis combining high-throughput sequencing and bioinformatics approaches, we identified a group of circRNAs that are potentially enhanced by ADARB2. Our findings highlight the pivotal role of ADARB2 in circRNA synthesis within inhibitory neurons, likely through its specific binding to precursor RNAs, which facilitates circRNA biogenesis.</div></div>","PeriodicalId":10578,"journal":{"name":"Computers in biology and medicine","volume":null,"pages":null},"PeriodicalIF":7.0,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142343050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}