PLoS One. 2024 Nov 21;19(11):e0313261. doi: 10.1371/journal.pone.0313261. eCollection 2024.

ABSTRACT

Motor imagery (MI) classification has been commonly employed in making brain-computer interfaces (BCI) to manage the outside tools as a substitute neural muscular path. Effectual MI classification in BCI improves communication and mobility for people with a breakdown or motor damage, delivering a bridge between the brain's intentions and exterior actions. Employing electroencephalography (EEG) or aggressive neural recordings, machine learning (ML) methods are used to interpret patterns of brain action linked with motor image tasks. These models frequently depend upon models like support vector machine (SVM) or deep learning (DL) to distinguish among dissimilar MI classes, such as visualizing left or right limb actions. This procedure allows individuals, particularly those with motor disabilities, to utilize their opinions to command exterior devices like robotic limbs or computer borders. This article presents a Boosted Harris Hawks Shuffled Shepherd Optimization Augmented Deep Learning (BHHSHO-DL) technique based on Motor Imagery Classification for BCI. The BHHSHO-DL technique mainly exploits the hyperparameter-tuned DL approach for MI identification for BCI. Initially, the BHHSHO-DL technique performs data preprocessing utilizing the wavelet packet decomposition (WPD) model. Besides, the enhanced densely connected networks (DenseNet) model extracts the preprocessed data's complex and hierarchical feature patterns. Meanwhile, the BHHSHO technique-based hyperparameter tuning process is accomplished to elect optimal parameter values of the enhanced DenseNet model. Finally, the classification procedure is implemented by utilizing the convolutional autoencoder (CAE) model. The simulation value of the BHHSHO-DL methodology is performed on a benchmark dataset. The performance validation of the BHHSHO-DL methodology portrayed a superior accuracy value of 98.15% and 92.23% over other techniques under BCIC-III and BCIC-IV datasets.

PMID:39570847 | DOI:10.1371/journal.pone.0313261

J Chem Inf Model. 2024 Nov 21. doi: 10.1021/acs.jcim.4c01554. Online ahead of print.

ABSTRACT

Identifying drug-target interactions (DTIs) is essential for drug discovery and development. Existing deep learning approaches to DTI prediction often employ powerful feature encoders to represent drugs and targets holistically, which usually cause significant redundancy and noise by neglecting the restricted binding regions. Furthermore, many previous DTI networks ignore or simplify the complex intermolecular interaction process involving diverse binding types, which significantly limits both predictive ability and interpretability. We propose ReduMixDTI, an end-to-end model that addresses feature redundancy and explicitly captures complex local interactions for DTI prediction. In this study, drug and target features are encoded by using graph neural networks and convolutional neural networks, respectively. These features are refined from channel and spatial perspectives to enhance the representations. The proposed attention mechanism explicitly models pairwise interactions between drug and target substructures, improving the model's understanding of binding processes. In extensive comparisons with seven state-of-the-art methods, ReduMixDTI demonstrates superior performance across three benchmark data sets and external test sets reflecting real-world scenarios. Additionally, we perform comprehensive ablation studies and visualize protein attention weights to enhance the interpretability. The results confirm that ReduMixDTI serves as a robust and interpretable model for reducing feature redundancy, contributing to advances in DTI prediction.

PMID:39570771 | DOI:10.1021/acs.jcim.4c01554

Bioinformatics. 2024 Nov 21:btae675. doi: 10.1093/bioinformatics/btae675. Online ahead of print.

ABSTRACT

MOTIVATION: Post-translational modification (PTM) crosstalk events play critical roles in biological processes. Several machine learning methods have been developed to identify PTM crosstalk within proteins, but the accuracy is still far from satisfactory. Recent breakthroughs in deep learning and protein structure prediction could provide a potential solution to this issue.

RESULTS: We proposed DeepPCT, a deep learning algorithm to identify PTM crosstalk using AlphaFold2-based structures. In this algorithm, one deep learning classifier was constructed for sequence-based prediction by combining the residue and residue pair embeddings with cross-attention techniques, while the other classifier was established for structure-based prediction by integrating the structural embedding and a graph neural network. Meanwhile, a machine learning classifier was developed using novel structural descriptors and a random forest model to complement the structural deep learning classifier. By integrating the three classifiers, DeepPCT outperformed existing algorithms in different evaluation scenarios and showed better generalizability on new data owing to its less distance dependency.

AVAILABILITY: Datasets, codes, and models of DeepPCT are freely accessible at https://github.com/hzau-liulab/DeepPCT/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:39570595 | DOI:10.1093/bioinformatics/btae675

Traffic Inj Prev. 2024 Nov 21:1-8. doi: 10.1080/15389588.2024.2402936. Online ahead of print.

ABSTRACT

OBJECTIVE: The objective of this study is to conduct precise risk prediction of traffic accidents using vehicle trajectory data.

METHODS: For urban road and highway scenarios, a scheme was developed to gather vehicle kinematic data and driving operation records from an in-vehicle device. The raw trajectory samples of over 3000 vehicles were processed through cleaning, filtering, interpolation, and normalization for preprocessing. Three deep learning frameworks based on RNN, CNN, and LSTM were compared. An end-to-end LSTM accident risk prediction model was constructed, and the model was trained using the cross-entropy loss function with Adam optimizer.

RESULTS: The LSTM model is capable of directly extracting accident-related hazardous state features from low-quality raw trajectory data, thereby enabling the prediction of accident probability with fine-grained time resolution. In tests conducted under complex traffic scenarios, the model successfully identifies high-risk driving behaviors in high-speed road sections and intersections with a prediction accuracy of 0.89, demonstrating strong generalization performance.

CONCLUSIONS: The LSTM accident risk prediction model, based on vehicle trajectory, developed in this study, is capable of intelligently extracting dangerous driving features. It can accurately warn about the risk of traffic accidents and provides a novel approach to enhancing road safety.

PMID:39570198 | DOI:10.1080/15389588.2024.2402936

SICOT J. 2024;10:49. doi: 10.1051/sicotj/2024044. Epub 2024 Nov 21.

ABSTRACT

The integration of artificial intelligence (AI) into orthopaedic care has gained considerable interest in recent years, evidenced by the growing body of literature boasting wide-ranging applications across the perioperative setting. This includes automated diagnostic imaging, clinical decision-making tools, optimisation of implant design, robotic surgery, and remote patient monitoring. Collectively, these advances propose to enhance patient care and improve system efficiency. Musculoskeletal pathologies represent the most significant contributor to global disability, with roughly 1.71 billion people afflicted, leading to an increasing volume of patients awaiting planned orthopaedic surgeries. This has exerted a considerable strain on healthcare systems globally, compounded by both the COVID-19 pandemic and the effects of an ageing population. Subsequently, patients face prolonged waiting times for surgery, with further deterioration and potentially poorer outcomes as a result. Furthermore, incorporating AI technologies into clinical practice could provide a means of addressing current and future service demands. This review aims to present a clear overview of AI applications across preoperative, intraoperative, and postoperative stages to elucidate its potential to transform planned orthopaedic care.

PMID:39570038 | DOI:10.1051/sicotj/2024044

Phys Med Biol. 2024 Nov 20. doi: 10.1088/1361-6560/ad953e. Online ahead of print.

ABSTRACT

The latest developments combining deep learning technology and medical image data have attracted wide attention and provide efficient noninvasive methods for the early diagnosis of breast cancer. The success of this task often depends on a large amount of data annotated by medical experts, which is time-consuming and may not always be feasible in the biomedical field. The lack of interpretability has greatly hindered the application of deep learning in the medical field. Currently, deep stable learning, including causal inference, make deep learning models more predictive and interpretable. In this study, to distinguish malignant tumors in Breast Imaging-Reporting and Data System (BI-RADS) category 3-4A breast lesions, we propose BD-StableNet, a deep stable learning model for the automatic detection of lesion areas. In this retrospective study, we collected 3103 breast ultrasound images (1418 benign and 1685 malignant lesions) from 493 patients (361 benign and 132 malignant lesion patients) for model training and testing. Compared with other mainstream deep learning models, BD-StableNet has better prediction performance (accuracy = 0.952, area under the curve (AUC) = 0.982, precision = 0.970, recall = 0.941, F1-score = 0.955 and specificity = 0.965). The lesion area prediction and class activation map (CAM) results both verify that our proposed model is highly interpretable. The results indicate that BD-StableNet significantly enhances diagnostic accuracy and interpretability, offering a promising noninvasive approach for the diagnosis of BI-RADS category 3-4A breast lesions. Clinically, the use of BD-StableNet could reduce unnecessary biopsies, improve diagnostic efficiency, and ultimately enhance patient outcomes by providing more precise and reliable assessments of breast lesions.

PMID:39569908 | DOI:10.1088/1361-6560/ad953e

J Neural Eng. 2024 Nov 19. doi: 10.1088/1741-2552/ad94a4. Online ahead of print.

ABSTRACT

OBJECTIVE: Visual prostheses are effective tools for restoring vision, yet real-world complexities pose ongoing challenges. The progress in AI has led to the emergence of the concept of intelligent visual prosthetics with auditory support, leveraging deep learning to create practical artificial vision perception beyond merely restoring natural sight for the blind.

APPROACH: This study introduces an object-based attention mechanism that simulates human gaze points when observing the external world to descriptions of physical regions. By transforming this mechanism into a ranking problem of salient entity regions, we introduce prior visual attention cues to build a new salient object ranking dataset, and propose a salient object ranking (SaOR) network aimed at providing depth perception for prosthetic vision. Furthermore, we propose a SaOR-guided image description method to align with human observation patterns, toward providing additional visual information by auditory feedback. Finally, the integration of the two aforementioned algorithms constitutes an audiovisual cognitive optimization strategy for prosthetic vision.

MAIN RESULTS: Through conducting psychophysical experiments based on scene description tasks under simulated prosthetic vision, we verify that the SaOR method improves the subjects' performance in terms of object identification and understanding the correlation among objects. Additionally, the cognitive optimization strategy incorporating image description further enhances their prosthetic visual cognition.

SIGNIFICANCE: This offers valuable technical insights for designing next-generation intelligent visual prostheses and establishes a theoretical groundwork for developing their visual information processing strategies. Code will be made publicly available.

PMID:39569905 | DOI:10.1088/1741-2552/ad94a4

Phys Med Biol. 2024 Nov 19. doi: 10.1088/1361-6560/ad94c7. Online ahead of print.

ABSTRACT

Magnetic resonance imaging (MRI) provides detailed structural information of the internal body organs and soft tissue regions of a patient in clinical diagnosis for disease detection, localization, and progress monitoring. MRI scanner hardware manufacturers incorporate various post-acquisition image-processing techniques into the scanner's computer software tools for different post-processing tasks. These tools provide a final image of adequate quality and essential features for accurate clinical reporting and predictive interpretation for better treatment planning. Different post-acquisition image-processing tasks for MRI quality enhancement include noise removal, motion artifact reduction, magnetic bias field correction, and eddy electric current effect removal. Recently, deep learning (DL) methods have shown great success in many research fields, including image and video applications. DL-based data-driven feature-learning approaches have great potential for MR image denoising and image-quality-degrading artifact correction. Recent studies have demonstrated significant improvements in image-analysis tasks using DL-based convolutional neural network (CNN) techniques. The promising capabilities and performance of DL techniques in various problem-solving domains have motivated researchers to adapt DL methods to medical image analysis and quality enhancement tasks. This paper presents a comprehensive review of DL-based state-of-the-art MRI quality enhancement and artifact removal methods for regenerating high-quality images while preserving essential anatomical and physiological feature maps without destroying important image information. Existing research gaps and future directions have also been provided by highlighting potential research areas for future developments, along with their importance and advantages in medical imaging.

PMID:39569887 | DOI:10.1088/1361-6560/ad94c7

Biomed Phys Eng Express. 2024 Nov 19. doi: 10.1088/2057-1976/ad947b. Online ahead of print.

ABSTRACT


This paper introduces a deep learning method for myocardial strain analysis while also evaluating the efficacy of the method across a public and a private dataset for cardiac pathology discrimination.
Methods:
We measure the global and regional myocardial strain in cSAX CMR images by first identifying a ROI centered in the LV, obtaining the cardiac structures (LV, RV and Myo) and estimating the motion of the myocardii. Finally we compute the strain for the heart coordinate system and report the global and regional strain.
Results:
We validated our method in two public datasets (ACDC, 80 subjects and CMAC, 16 subjects) and a private dataset (SSC, 75 subjects), containing healthy and pathological cases (acute myocardial infarct, DCM and HCM). We measured the mean Dice coefficient and Haussdorff distance for segmentation accuracy, the absolute end point error for motion accuracy, and we conducted a study of the discrimination power of the strain and strain rate between populations of healthy and pathological subjects. The results demonstrated that our method effectively quantifies myocardial strain and strain rate, showing distinct patterns across different cardiac conditions achieving notable statistical significance. Results also show that the method's accuracy is on par with iterative non-parametric registration methods and is also capable of estimating regional strain values.
Conclusion:
Our method proves to be a powerful tool for cardiac strain analysis, achieving results comparable to other state of the art methods, and computational efficiency over traditional methods.&#xD.

PMID:39569845 | DOI:10.1088/2057-1976/ad947b

Med Phys. 2024 Nov 21. doi: 10.1002/mp.17512. Online ahead of print.

ABSTRACT

BACKGROUND: PET/CT and planning CT are commonly used medical images in radiotherapy for esophageal and nasopharyngeal cancer. However, repeated scans will expose patients to additional radiation doses and also introduce registration errors. This multimodal treatment approach is expected to be further improved.

PURPOSE: A new Transformer model is proposed to obtain pseudo-PET/CT fusion images for esophageal and nasopharyngeal cancer radiotherapy.

METHODS: The data of 129 cases of esophageal cancer and 141 cases of nasopharyngeal cancer were retrospectively selected for training, validation, and testing. PET and CT images are used as input. Based on the Transformer model with a "focus-disperse" attention mechanism and multi-consistency loss constraints, the feature information in two images is effectively captured. This ultimately results in the synthesis of pseudo-PET/CT fusion images with enhanced tumor region imaging. During the testing phase, the accuracy of pseudo-PET/CT fusion images was verified in anatomy and dosimetry, and two prospective cases were selected for further dose verification.

RESULTS: In terms of anatomical verification, the PET/CT fusion image obtained using the wavelet fusion algorithm was used as the ground truth image after correction by clinicians. The evaluation metrics, including peak signal-to-noise ratio, structural similarity index, mean absolute error, and normalized root mean square error, between the pseudo-fused images obtained based on the proposed model and ground truth, are represented by means (standard deviation). They are 37.82 (1.57), 95.23 (2.60), 29.70 (2.49), and 9.48 (0.32), respectively. These numerical values outperform those of the state-of-the-art deep learning comparative models. In terms of dosimetry validation, based on a 3%/2 mm gamma analysis, the average passing rates of global and tumor regions between the pseudo-fused images (with a PET/CT weight ratio of 2:8) and the planning CT images are 97.2% and 95.5%, respectively. These numerical outcomes are superior to those of pseudo-PET/CT fusion images with other weight ratios.

CONCLUSIONS: This pseudo-PET/CT fusion images obtained based on the proposed model hold promise as a new modality in the radiotherapy for esophageal and nasopharyngeal cancer.

PMID:39569842 | DOI:10.1002/mp.17512

Med Phys. 2024 Nov 21. doi: 10.1002/mp.17521. Online ahead of print.

ABSTRACT

BACKGROUND: Mammographic imaging is essential for breast cancer detection and diagnosis. In addition to masses, calcifications are of concern and the early detection of breast cancer also heavily relies on the correct interpretation of suspicious microcalcification clusters. Even with advances in imaging and the introduction of novel techniques such as digital breast tomosynthesis and contrast-enhanced mammography, a correct interpretation can still be challenging given the subtle nature and large variety of calcifications.

PURPOSE: Computer simulated lesion models can serve to develop, optimize, or improve imaging techniques. In addition to their use in comparative (virtual clinical trial) detection experiments, these models have potential application in training deep learning models and in the understanding and interpretation of breast lesions. Existing simulation methods, however, often lack the capacity to model the diversity occurring in breast lesions or to generate models relevant for a specific case. This study focuses on clusters of microcalcifications and introduces an automated, flexible toolbox designed to generate microcalcification cluster models customized to specific tasks.

METHODS: The toolbox allows users to control a large number of simulation parameters related to model characteristics such as lesion size, calcification shape, or number of microcalcifications per cluster. This leads to the capability of creating models that range from regular to complex clusters. Based on the input parameters, which are either tuned manually or pre-set for a specific clinical type, different sets of models can be simulated depending on the use case. Two lesion generation methods are described. The first method generates three-dimensional microcalcification clusters models based on geometrical shapes and transformations. The second method creates two-dimensional (2D) microcalcification cluster models for a specific 2D mammographic image. This novel method employs radiomics analysis to account for local textures, ensuring the simulated microcalcification cluster is appropriately integrated within the existing breast tissue. The toolbox is implemented in the Python language and can be conveniently run through a Jupyter Notebook interface, openly accessible at https://gitlab.kuleuven.be/medphysqa/deploy/breast-calcifications. Validation studies performed by radiologists assessed the level of malignancy and realism of clusters tuned with specific parameters and inserted in mammographic images.

RESULTS: The flexibility of the toolbox with multiple simulation methods is illustrated, as well as the compatibility with different simulation frameworks and image types. The automation allows for the straightforward and fast generation of diverse microcalcification cluster models. The generated models are most likely applicable for various tasks as they can be configured in a variety of ways and inserted in different types of mammographic images of multiple acquisition systems. Validation studies confirmed the capacity to simulate realistic clusters and capture clinical properties when tuned with appropriate parameter settings.

CONCLUSION: This simulation toolbox offers a flexible means of simulating microcalcification cluster models with potential use in both technical and clinical research in mammography imaging. The 3D generation methods allow for specifying many characteristics regarding the calcification shape and cluster architecture, and the 2D generation method presents a novel manner to create microcalcification clusters tailored to existing breast textures.

PMID:39569820 | DOI:10.1002/mp.17521

Anal Methods. 2024 Nov 21. doi: 10.1039/d4ay01755b. Online ahead of print.

ABSTRACT

Light sources exhibit significant absorption and scattering effects during the transmission through biological tissues, posing challenges in identifying heterogeneities in multi-spectral images. This paper introduces a fusion of techniques encompassing the spatial pyramid matching model (SPM), modulation and demodulation (M_D), and frame accumulation (FA). These techniques not only elevate image quality but also augment the precision of heterogeneous classification in multi-spectral transmission images (MTI) within deep learning network models (DLNM). Initially, experiments are designed to capture MTI of phantoms. Subsequently, the images are preprocessed separately through a combination of different techniques such as SPM, M_D and FA. Ultimately, multi-spectral fusion pseudo-color images derived from U-Net semantic segmentation are fed into VGG16/19 and ResNet50/101 networks for heterogeneous classification. Among them, different combinations of SPM, M_D and FA significantly enhance the quality of images, facilitating the extraction of heterogeneous feature information from multi-spectral images. In comparison to the classification accuracy achieved in the original image VGG and ResNet network models, all images after preprocessing effectively improved the classification accuracy of heterogeneities. Following scatter correction, images processed with 3.5 Hz modulation-demodulation combined with frame accumulation (M_D-FA) attain the highest classification accuracy for heterogeneities in the VGG19 and ResNet101 models, achieving accuracies of 95.47% and 98.47%, respectively. In conclusion, this paper utilizes different combinations of SPM, M_D and FA techniques to not only enhance the quality of images but also further improve the accuracy of DLNM in heterogeneous classification, which will promote the clinical application of MTI technique in breast tumor screening.

PMID:39569814 | DOI:10.1039/d4ay01755b

Trends Hear. 2024 Jan-Dec;28:23312165241298606. doi: 10.1177/23312165241298606.

ABSTRACT

Cochlear implant (CI) users, even with substantial speech comprehension, generally have poor sensitivity to pitch information (or fundamental frequency, F0). This insensitivity is often attributed to limited spectral and temporal resolution in the CI signals. However, the pitch sensitivity markedly varies among individuals, and some users exhibit fairly good sensitivity. This indicates that the CI signal contains sufficient information about F0, and users' sensitivity is predominantly limited by other physiological conditions such as neuroplasticity or neural health. We estimated the upper limit of F0 information that a CI signal can convey by decoding F0 from simulated CI signals (multi-channel pulsatile signals) with a deep neural network model (referred to as the CI model). We varied the number of electrode channels and the pulse rate, which should respectively affect spectral and temporal resolutions of stimulus representations. The F0-estimation performance generally improved with increasing number of channels and pulse rate. For the sounds presented under quiet conditions, the model performance was at best comparable to that of a control waveform model, which received raw-waveform inputs. Under conditions in which background noise was imposed, the performance of the CI model generally degraded by a greater degree than that of the waveform model. The pulse rate had a particularly large effect on predicted performance. These observations indicate that the CI signal contains some information for predicting F0, which is particularly sufficient for targets under quiet conditions. The temporal resolution (represented as pulse rate) plays a critical role in pitch representation under noisy conditions.

PMID:39569552 | DOI:10.1177/23312165241298606

J Am Med Inform Assoc. 2024 Nov 21:ocae271. doi: 10.1093/jamia/ocae271. Online ahead of print.

ABSTRACT

OBJECTIVE: Machine learning applications for longitudinal electronic health records often forecast the risk of events at fixed time points, whereas survival analysis achieves dynamic risk prediction by estimating time-to-event distributions. Here, we propose a novel conditional variational autoencoder-based method, DySurv, which uses a combination of static and longitudinal measurements from electronic health records to estimate the individual risk of death dynamically.

MATERIALS AND METHODS: DySurv directly estimates the cumulative risk incidence function without making any parametric assumptions on the underlying stochastic process of the time-to-event. We evaluate DySurv on 6 time-to-event benchmark datasets in healthcare, as well as 2 real-world intensive care unit (ICU) electronic health records (EHR) datasets extracted from the eICU Collaborative Research (eICU) and the Medical Information Mart for Intensive Care database (MIMIC-IV).

RESULTS: DySurv outperforms other existing statistical and deep learning approaches to time-to-event analysis across concordance and other metrics. It achieves time-dependent concordance of over 60% in the eICU case. It is also over 12% more accurate and 22% more sensitive than in-use ICU scores like Acute Physiology and Chronic Health Evaluation (APACHE) and Sequential Organ Failure Assessment (SOFA) scores. The predictive capacity of DySurv is consistent and the survival estimates remain disentangled across different datasets.

DISCUSSION: Our interdisciplinary framework successfully incorporates deep learning, survival analysis, and intensive care to create a novel method for time-to-event prediction from longitudinal health records. We test our method on several held-out test sets from a variety of healthcare datasets and compare it to existing in-use clinical risk scoring benchmarks.

CONCLUSION: While our method leverages non-parametric extensions to deep learning-guided estimations of the survival distribution, further deep learning paradigms could be explored.

PMID:39569428 | DOI:10.1093/jamia/ocae271

J Hepatocell Carcinoma. 2024 Nov 16;11:2223-2239. doi: 10.2147/JHC.S493478. eCollection 2024.

ABSTRACT

PURPOSE: To construct a 2.5-dimensional (2.5D) CT radiomics-based deep learning (DL) model to predict early postoperative recurrence of hepatocellular carcinoma (HCC).

PATIENTS AND METHODS: We retrospectively analyzed the data of patients who underwent HCC resection at 2 centers. The 232 patients from center 1 were randomly divided into the training (162 patients) and internal validation cohorts (70 patients); 91 patients from center 2 formed the external validation cohort. We developed a 2.5D DL model based on a central 2D image with the maximum tumor cross-section and adjacent slices. Multiple views (transverse, sagittal, and coronal) and phases (arterial, plain, and portal) were incorporated. Multi-instance learning techniques were applied to the extracted data; the resulting comprehensive feature set was modeled using Logistic Regression, RandomForest, ExtraTrees, XGBoost, and LightGBM, with 5-fold cross validation and hyperparameter optimization with Grid-search. Receiver operating characteristic curves, calibration curves, DeLong test, and decision curve analysis were used to evaluate model performance.

RESULTS: The 2.5D DL model performed well in the training (AUC: 0.920), internal validation (AUC: 0.825), and external validation cohorts (AUC: 0.795). The 3D DL model performed well in the training cohort and poorly in the internal and external validation cohorts (AUCs: 0.751, 0.666, and 0.567, respectively), indicating overfitting. The combined model (2.5D DL+clinical) performed well in all cohorts (AUCs: 0.921, 0.835, 0.804). The Hosmer-Lemeshow test, DeLong test, and decision curve analysis confirmed the superiority of the combined model over the other signatures.

CONCLUSION: The combined model integrating 2.5D DL and clinical features accurately predicts early postoperative HCC recurrence.

PMID:39569409 | PMC:PMC11577935 | DOI:10.2147/JHC.S493478

iScience. 2024 Oct 21;27(11):111209. doi: 10.1016/j.isci.2024.111209. eCollection 2024 Nov 15.

ABSTRACT

Noninvasive magnetic resonance imaging (MRI) of the relayed nuclear Overhauser effect (rNOE) constitutes a promising approach for gaining biological insights into various pathologies, including brain cancer, kidney injury, ischemic stroke, and liver disease. However, rNOE imaging is time-consuming and prone to biases stemming from the water T1 and the semisolid magnetization transfer (MT) contrasts. Here, we developed a rapid rNOE quantification approach, combining magnetic resonance fingerprinting (MRF) acquisition with deep-learning-based reconstruction. The method was systematically validated using tissue-mimicking phantoms, wild-type mice (n = 7), and healthy human volunteers (n = 5). In vitro rNOE parameter maps generated by MRF were highly correlated with ground truth (r > 0.98, p < 0.001). Simultaneous mapping of the rNOE and the semisolid MT exchange parameters in mice and humans were in agreement with previously reported literature values. Whole-brain 3D parameter mapping in humans took less than 5 min (282 s for acquisition and less than 2 s for reconstruction). With its demonstrated ability to rapidly extract quantitative molecular maps, deep rNOE-MRF can potentially serve as a valuable tool for the characterization and detection of molecular abnormalities in vivo.

PMID:39569380 | PMC:PMC11576397 | DOI:10.1016/j.isci.2024.111209

Patterns (N Y). 2024 Sep 30;5(10):101063. doi: 10.1016/j.patter.2024.101063. eCollection 2024 Oct 11.

ABSTRACT

Organoids and 3D imaging techniques are crucial for studying human tissue structure and function, but traditional 3D reconstruction methods are expensive and time consuming, relying on complete z stack confocal microscopy data. This paper introduces VONet, a deep learning-based system for 3D organoid rendering that uses a fully convolutional neural network to reconstruct entire 3D structures from a minimal number of z stack images. VONet was trained on a library of over 39,000 virtual organoids (VOs) with diverse structural features and achieved an average intersection over union of 0.82 in performance validation. Remarkably, VONet can predict the structure of deeper focal plane regions, unseen by conventional confocal microscopy. This innovative approach and VO dataset offer significant advancements in 3D bioimaging technologies.

PMID:39569212 | PMC:PMC11573902 | DOI:10.1016/j.patter.2024.101063

RSC Adv. 2024 Nov 20;14(50):37035-37044. doi: 10.1039/d4ra05422a. eCollection 2024 Nov 19.

ABSTRACT

Semi-empirical quantum chemistry methods estimate the binding free energies of protein-ligand complexes. We present an integrated approach combining the GFN2-xTB method with de novo design for the generation and evaluation of potential inhibitors of acetylcholinesterase (AChE). We employed chemical language model-based molecule generation to explore the synthetically accessible chemical space around the natural product Huperzine A, a potent AChE inhibitor. Four distinct molecular libraries were created using structure- and ligand-based molecular de novo design with SMILES and SELFIES representations, respectively. These libraries were computationally evaluated for synthesizability, novelty, and predicted biological activity. The candidate molecules were subjected to molecular docking to identify hypothetical binding poses, which were further refined using Gibbs free energy calculations. The structurally novel top-ranked molecule was chemically synthesized and biologically tested, demonstrating moderate micromolar activity against AChE. Our findings highlight the potential and certain limitations of integrating deep learning-based molecular generation with semi-empirical quantum chemistry-based activity prediction for structure-based drug design.

PMID:39569121 | PMC:PMC11577348 | DOI:10.1039/d4ra05422a

Front Neurorobot. 2024 Nov 6;18:1484751. doi: 10.3389/fnbot.2024.1484751. eCollection 2024.

ABSTRACT

INTRODUCTION: Slip detection is crucial for achieving stable grasping and subsequent operational tasks. A grasp action is a continuous process that requires information from multiple sources. The success of a specific grasping maneuver is contingent upon the confluence of two factors: the spatial accuracy of the contact and the stability of the continuous process.

METHODS: In this paper, for the task of perceiving grasping results using visual-haptic information, we propose a new method for slip detection, which synergizes visual and haptic information from spatial-temporal dual dimensions. Specifically, the method takes as input a sequence of visual images from a first-person perspective and a sequence of haptic images from a gripper. Then, it extracts time-dependent features of the whole process and spatial features matching the importance of different parts with different attention mechanisms. Inspired by neurological studies, during the information fusion process, we adjusted temporal and spatial information from vision and haptic through a combination of two-step fusion and gate units.

RESULTS AND DISCUSSION: To validate the effectiveness of method, we compared it with traditional CNN net and models with attention. It is anticipated that our method achieves a classification accuracy of 93.59%, which is higher than that of previous works. Attention visualization is further presented to support the validity.

PMID:39569062 | PMC:PMC11576469 | DOI:10.3389/fnbot.2024.1484751

Front Surg. 2024 Nov 6;11:1458569. doi: 10.3389/fsurg.2024.1458569. eCollection 2024.

ABSTRACT

OBJECTIVE: To develop and validate an artificial intelligence diagnostic model for identifying calcified lumbar disc herniation based on lateral lumbar magnetic resonance imaging(MRI).

METHODS: During the period from January 2019 to March 2024, patients meeting the inclusion criteria were collected. All patients had undergone both lumbar spine MRI and computed tomography(CT) examinations, with regions of interest (ROI) clearly marked on the lumbar sagittal MRI images. The participants were then divided into separate sets for training, testing, and external validation. Ultimately, we developed a deep learning model using the ResNet-34 algorithm model and evaluated its diagnostic efficacy.

RESULTS: A total of 1,224 eligible patients were included in this study, consisting of 610 males and 614 females, with an average age of 53.34 ± 10.61 years. Notably, the test datasets displayed an impressive classification accuracy rate of 91.67%, whereas the external validation datasets achieved a classification accuracy rate of 88.76%. Among the test datasets, the ResNet34 model outperformed other models, yielding the highest area under the curve (AUC) of 0.96 (95% CI: 0.93, 0.99). Additionally, the ResNet34 model also exhibited superior performance in the external validation datasets, exhibiting an AUC of 0.88 (95% CI: 0.80, 0.93).

CONCLUSION: In this study, we established a deep learning model with excellent performance in identifying calcified intervertebral discs, thereby offering a valuable and efficient diagnostic tool for clinical surgeons.

PMID:39569028 | PMC:PMC11576459 | DOI:10.3389/fsurg.2024.1458569