Lactylation prediction models based on protein sequence and structural feature fusion.

Lysine lactylation (Kla) is a newly discovered posttranslational modification that is involved in important life activities, such as glycolysis-related cell function, macrophage polarization and nervous system regulation, and has received widespread attention due to the Warburg effect in tumor cells. In this work, we first design a natural language processing method to automatically extract the 3D structural features of Kla sites, avoiding potential biases caused by manually designed structural features. Then, we establish two Kla prediction frameworks, Attention-based feature fusion Kla model (ABFF-Kla) and EBFF-Kla, to integrate the sequence features and the structure features based on the attention layer and embedding layer, respectively. The results indicate that ABFF-Kla and Embedding-based feature fusion Kla model (EBFF-Kla), which fuse features from protein sequences and spatial structures, have better predictive performance than that of models that use only sequence features. Our work provides an approach for the automatic extraction of protein structural features, as well as a flexible framework for Kla prediction. The source code and the training data of the ABFF-Kla and the EBFF-Kla are publicly deposited at: https://github.com/ispotato/Lactylation_model.

Multi-Feature Automatic Extraction for Detecting Obstructive Sleep Apnea Based on Single-Lead Electrocardiography Signals.

Obstructive sleep apnea (OSA), a prevalent sleep disorder, is intimately associated with various other diseases, particularly cardiovascular conditions. The conventional diagnostic method, nocturnal polysomnography (PSG), despite its widespread use, faces challenges due to its high cost and prolonged duration. Recent developments in electrocardiogram-based diagnostic techniques have opened new avenues for addressing these challenges, although they often require a deep understanding of feature engineering. In this study, we introduce an innovative method for OSA classification that combines a composite deep convolutional neural network model with a multimodal strategy for automatic feature extraction. This approach involves transforming the original dataset into scalogram images that reflect heart rate variability attributes and Gramian angular field matrix images that reveal temporal characteristics, aiming to enhance the diversity and richness of data features. The model comprises automatic feature extraction and feature enhancement components and has been trained and validated on the PhysioNet Apnea-ECG database. The experimental results demonstrate the model's exceptional performance in diagnosing OSA, achieving an accuracy of 96.37%, a sensitivity of 94.67%, a specificity of 97.44%, and an AUC of 0.96. These outcomes underscore the potential of our proposed model as an efficient, accurate, and convenient tool for OSA diagnosis.

IoT Traffic Analyzer Tool with Automated and Holistic Feature Extraction Capability.

The Internet of Things (IoT) is an emerging technology that attracted considerable attention in the last decade to become one of the most researched topics in computer science studies. This research aims to develop a benchmark framework for a public multi-task IoT traffic analyzer tool that holistically extracts network traffic features from an IoT device in a smart home environment that researchers in various IoT industries can implement to collect information about IoT network behavior. A custom testbed with four IoT devices is created to collect real-time network traffic data based on seventeen comprehensive scenarios of these devices' possible interactions. The output data is fed into the IoT traffic analyzer tool for both flow and packet levels analysis to extract all possible features. Such features are ultimately classified into five categories: IoT device type, IoT device behavior, Human interaction type, IoT behavior within the network, and Abnormal behavior. The tool is then evaluated by 20 users considering three variables: usefulness, accuracy of information being extracted, performance and usability. Users in three groups were highly satisfied with the interface and ease of use of the tool, with scores ranging from 90.5% to 93.8% and with an average score between 4.52 and 4.69 with a low standard deviation range, indicating that most of the data revolve around the mean.

Morphological Autoencoders for Beat-by-Beat Atrial Fibrillation Detection Using Single-Lead ECG.

Engineered feature extraction can compromise the ability of Atrial Fibrillation (AFib) detection algorithms to deliver near real-time results. Autoencoders (AEs) can be used as an automatic feature extraction tool, tailoring the resulting features to a specific classification task. By coupling an encoder to a classifier, it is possible to reduce the dimension of the Electrocardiogram (ECG) heartbeat waveforms and classify them. In this work we show that morphological features extracted using a Sparse AE are sufficient to distinguish AFib from Normal Sinus Rhythm (NSR) beats. In addition to the morphological features, rhythm information was included in the model using a proposed short-term feature called Local Change of Successive Differences (LCSD). Using single-lead ECG recordings from two referenced public databases, and with features from the AE, the model was able to achieve an F1-score of 88.8%. These results show that morphological features appear to be a distinct and sufficient factor for detecting AFib in ECG recordings, especially when designed for patient-specific applications. This is an advantage over state-of-the-art algorithms that need longer acquisition times to extract engineered rhythm features, which also requires careful preprocessing steps. To the best of our knowledge, this is the first work that presents a near real-time morphological approach for AFib detection under naturalistic ECG acquisition with a mobile device.

Intelligent Detection of a Planetary Gearbox Composite Fault Based on Adaptive Separation and Deep Learning.

Due to the existence of multiple rotating parts in the planetary gearbox-such as the sun gear, planet gears, planet carriers, and its unique planetary motion, etc.-the vibration signals generated under multiple fault conditions are time-varying and nonstable, thus making fault diagnosis difficult. In order to solve the problem of planetary gearbox composite fault diagnosis, an improved particle swarm optimization variational mode decomposition (IPVMD) and improved convolutional neural network (I-CNN) are proposed. The method takes as input the spectrum of the original vibration signal that contains rich information. First, the automatic feature extraction of signal spectrum is performed by I-CNN, while a classifier is used to diagnose the fault modes. Second, the composite fault signal is decomposed into multiple single fault signals by adaptive variational mode, and the signal is decomposed as a model input to diagnose the single fault component. Finally, a complete intelligent diagnosis of planetary gearboxes is conducted. Through experimental verification, the composite fault diagnosis method combining IPVMD and I-CNN will diagnose the composite fault and effectively diagnose the sub-fault included in the composite fault.

ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology.

Artificial intelligence (AI) has extensive applications in a wide range of disciplines including healthcare and clinical practice. Advances in high-resolution whole-slide brightfield microscopy allow for the digitization of histologically stained tissue sections, producing gigapixel-scale whole-slide images (WSI). The significant improvement in computing and revolution of deep neural network (DNN)-based AI technologies over the last decade allow us to integrate massively parallelized computational power, cutting-edge AI algorithms, and big data storage, management, and processing. Applied to WSIs, AI has created opportunities for improved disease diagnostics and prognostics with the ultimate goal of enhancing precision medicine and resulting patient care. The National Institutes of Health (NIH) has recognized the importance of developing standardized principles for data management and discovery for the advancement of science and proposed the Findable, Accessible, Interoperable, Reusable, (FAIR) Data Principles1 with the goal of building a modernized biomedical data resource ecosystem to establish collaborative research communities. In line with this mission and to democratize AI-based image analysis in digital pathology, we propose ComPRePS: an end-to-end automated Computational Renal Pathology Suite which combines massive scalability, on-demand cloud computing, and an easy-to-use web-based user interface for data upload, storage, management, slide-level visualization, and domain expert interaction. Moreover, our platform is equipped with both in-house and collaborator developed sophisticated AI algorithms in the back-end server for image analysis to identify clinically relevant micro-anatomic functional tissue units (FTU) and to extract image features.

ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology.

Artificial intelligence (AI) has extensive applications in a wide range of disciplines including healthcare and clinical practice. Advances in high-resolution whole-slide brightfield microscopy allow for the digitization of histologically stained tissue sections, producing gigapixel-scale whole-slide images (WSI). The significant improvement in computing and revolution of deep neural network (DNN)-based AI technologies over the last decade allow us to integrate massively parallelized computational power, cutting-edge AI algorithms, and big data storage, management, and processing. Applied to WSIs, AI has created opportunities for improved disease diagnostics and prognostics with the ultimate goal of enhancing precision medicine and resulting patient care. The National Institutes of Health (NIH) has recognized the importance of developing standardized principles for data management and discovery for the advancement of science and proposed the Findable, Accessible, Interoperable, Reusable, (FAIR) Data Principles1 with the goal of building a modernized biomedical data resource ecosystem to establish collaborative research communities. In line with this mission and to democratize AI-based image analysis in digital pathology, we propose ComPRePS: an end-to-end automated Computational Renal Pathology Suite which combines massive scalability, on-demand cloud computing, and an easy-to-use web-based user interface for data upload, storage, management, slide-level visualization, and domain expert interaction. Moreover, our platform is equipped with both in-house and collaborator developed sophisticated AI algorithms in the back-end server for image analysis to identify clinically relevant micro-anatomic functional tissue units (FTU) and to extract image features.

On Extracting Digitized Spiral Dynamics' Representations: A Study on Transfer Learning for Early Alzheimer's Detection.

This work proposes a decision-aid tool for detecting Alzheimer's disease (AD) at an early stage, based on the Archimedes spiral, executed on a Wacom digitizer. Our work assesses the potential of the task as a dynamic gesture and defines the most pertinent methodology for exploiting transfer learning to compensate for sparse data. We embed directly in spiral trajectory images, kinematic time functions. With transfer learning, we perform automatic feature extraction on such images. Experiments on 30 AD patients and 45 healthy controls (HC) show that the extracted features allow a significant improvement in sensitivity and accuracy, compared to raw images. We study at which level of the deep network features have the highest discriminant capabilities. Results show that intermediate-level features are the best for our specific task. Decision fusion of experts trained on such descriptors outperforms low-level fusion of hybrid images. When fusing decisions of classifiers trained on the best features, from pressure, altitude, and velocity images, we obtain 84% of sensitivity and 81.5% of accuracy, achieving an absolute improvement of 22% in sensitivity and 7% in accuracy. We demonstrate the potential of the spiral task for AD detection and give a complete methodology based on off-the-shelf features.

Multi-labeled neural network model for automatically processing cardiomyocyte mechanical beating signals in drug assessment.

High-throughput cardiotoxicity assessment is important for large-scale preclinical screening in novel drug development. To improve the efficiency of drug development and avoid drug-induced cardiotoxicity, there is a huge demand to explore the automatic and intelligent drug assessment platforms for preclinical cardiotoxicity investigations. In this work, we proposed an automatic and intelligent strategy that combined automatic feature extraction and multi-labeled neural network (MLNN) to process cardiomyocytes mechanical beating signals detected by an interdigital electrode biosensor for the assessment of drug-induced cardiotoxicity. Taking advantages of artificial neural network, our work not only classified different drugs inducing different cardiotoxicities but also predicted drug concentrations representing severity of cardiotoxicity. This has not been achieved by conventional strategies like principal component analysis and visualized heatmap. MLNN analysis showed high accuracy (up to 96%) and large AUC (more than 98%) for classification of different drug-induced cardiotoxicities. There was a high correlation (over 0.90) between concentrations reported by MLNN and experimentally treated concentrations of various drugs, demonstrating great capacity of our intelligent strategy to predict the severity of drug-induced cardiotoxicity. This new intelligent bio-signal processing algorithm is a promising method for identification and classification of drug-induced cardiotoxicity in cardiological and pharmaceutical applications.

Original Research: Label-free detection for radiation-induced apoptosis in glioblastoma cells.

Current flow cytometry (FCM) requires fluorescent dyes labeling cells which make the procedure costly and time consuming. This manuscript reports a feasibility study of detecting the cell apoptosis with a label-free method in glioblastoma cells. A human glioma cell line M059K was exposed to 8 Gy dose of radiation, which enables the cells to undergo radiation-induced apoptosis. The rates of apoptosis were studied at different time points post-irradiation with two different methods: FCM in combination with Annexin V-FITC/PI staining and a newly developed technique named polarization diffraction imaging flow cytometry. Totally 1000 diffraction images were acquired for each sample and the gray level co-occurrence matrix (GLCM) algorithm was used in morphological characterization of the apoptotic cells. Among the feature parameters extracted from each image pair, we found that the two GLCM parameters of angular second moment (ASM) and sum entropy (SumEnt) exhibit high sensitivities and consistencies as the apoptotic rates (Pa) measured with FCM method. In addition, no significant difference exists between Pa and ASM_S, Pa and SumEnt_S, respectively (P > 0.05). These results demonstrated that the new label-free method can detect cell apoptosis effectively. Cells can be directly used in the subsequent biochemical experiments as the structure and function of cells and biomolecules are well-preserved with this new method.