Delve into Multiple Sclerosis (MS) lesion exploration: A modified attention U-Net for MS lesion segmentation in Brain MRI.

Multiple Sclerosis (MS) is a Central Nervous System (CNS) disease that Magnetic Resonance Imaging (MRI) system can detect and segment its lesions. Artificial Neural Networks (ANNs) recently reached a noticeable performance in finding MS lesions from MRI. U-Net and Attention U-Net are two of the most successful ANNs in the field of MS lesion segmentation. In this work, we proposed a framework to segment MS lesions in Fluid-Attenuated Inversion Recovery (FLAIR) and T2 MRI images by modified U-Net and modified Attention U-Net. For this purpose, we developed some extra preprocessing on MRI scans, made modifications in the loss function of U-Net and Attention U-Net, and proposed using the union of FLAIR and T2 predictions to reach a better performance. Results show that the union of FLAIR and T2 predicted masks by the modified Attention U-Net reaches the performance of 82.30% in terms of Dice Similarity Coefficient (DSC) in the test dataset, which is a considerable improvement compared to the previous works.

The association between cardiac injury and outcomes in hospitalized patients with COVID-19.

In this study, we aimed to assess the association between development of cardiac injury and short-term mortality as well as poor in-hospital outcomes in hospitalized patients with COVID-19. In this prospective, single-center study, we enrolled hospitalized patients with laboratory-confirmed COVID-19 and highly suspicious patients with compatible chest computed tomography features. Cardiac injury was defined as a rise of serum high sensitivity cardiac Troponin-I level above 99th percentile (men: > 26 ng/mL, women: > 11 ng/mL). A total of 386 hospitalized patients with COVID-19 were included. Cardiac injury was present among 115 (29.8%) of the study population. The development of cardiac injury was significantly associated with a higher in-hospital mortality rate compared to those with normal troponin levels (40.9% vs 11.1%, p value < 0.001). It was shown that patients with cardiac injury had a significantly lower survival rate after a median follow-up of 18 days from symptom onset (p log-rank < 0.001). It was further demonstrated in the multivariable analysis that cardiac injury could possibly increase the risk of short-term mortality in hospitalized patients with COVID-19 (HR = 1.811, p-value = 0.023). Additionally, preexisting cardiovascular disease, malignancy, blood oxygen saturation < 90%, leukocytosis, and lymphopenia at presentation were independently associated with a greater risk of developing cardiac injury. Development of cardiac injury in hospitalized patients with COVID-19 was significantly associated with higher rates of in-hospital mortality and poor in-hospital outcomes. Additionally, it was shown that development of cardiac injury was associated with a lower short-term survival rate compared to patients without myocardial damage and could independently increase the risk of short-term mortality by nearly two-fold.

ECG fiducial point extraction using switching Kalman filter.

In this paper, we propose a novel method for extracting fiducial points (FPs) of the beats in electrocardiogram (ECG) signals using switching Kalman filter (SKF). In this method, according to McSharry's model, ECG waveforms (P-wave, QRS complex and T-wave) are modeled with Gaussian functions and ECG baselines are modeled with first order auto regressive models. In the proposed method, a discrete state variable called "switch" is considered that affects only the observation equations. We denote a mode as a specific observation equation and switch changes between 7 modes and corresponds to different segments of an ECG beat. At each time instant, the probability of each mode is calculated and compared among two consecutive modes and a path is estimated, which shows the relation of each part of the ECG signal to the mode with the maximum probability. ECG FPs are found from the estimated path. For performance evaluation, the Physionet QT database is used and the proposed method is compared with methods based on wavelet transform, partially collapsed Gibbs sampler (PCGS) and extended Kalman filter. For our proposed method, the mean error and the root mean square error across all FPs are 2 ms (i.e. less than one sample) and 14 ms, respectively. These errors are significantly smaller than those obtained using other methods. The proposed method achieves lesser RMSE and smaller variability with respect to others.

ECG segmentation and fiducial point extraction using multi hidden Markov model.

In this paper, we propose a novel method for extracting fiducial points (FPs) of electrocardiogram (ECG) signals. We propose the use of multi hidden Markov model (MultiHMM) as opposed to the traditional use of Classic HMM. In the MultiHMM method, each segment of an ECG beat is represented by a separate ergodic continuous density HMM. Each HMM has different state number and is trained separately. In the test step, the log-likelihood of two consecutive HMMs is compared and a path is estimated, which shows the correspondence of each part of the ECG signal to the HMM with the maximum log-likelihood. Fiducial points are estimated from the obtained path. For performance evaluation, the Physionet QT database and a Swine ECG database are used and the proposed method is compared with the Classic HMM and a method based on partially collapsed Gibbs sampler (PCGS). In our evaluation using the QT database, we also compare the results with low-pass differentiation, hybrid feature extraction algorithm, a method based on the wavelet transform and three HMM-based approaches. For the Swine database, the root mean square error (RMSE) values, across all FPs for MultiHMM, Classic HMM and PCGS methods are 13, 21 and 40ms, respectively and the MultiHMM exhibits smaller error variability than other methods. For the QT database, RMSE values for MultiHMM, Classic HMM, Wavelet and PCGS methods are 10, 17, 26 and 38ms, respectively. Our results demonstrate that our proposed MultiHMM approach outperforms other benchmark methods that exist in the literature; therefore can be used in practical ECG fiducial point extraction.

ECG denoising and fiducial point extraction using an extended Kalman filtering framework with linear and nonlinear phase observations.

In this paper we propose an efficient method for denoising and extracting fiducial point (FP) of ECG signals. The method is based on a nonlinear dynamic model which uses Gaussian functions to model ECG waveforms. For estimating the model parameters, we use an extended Kalman filter (EKF). In this framework called EKF25, all the parameters of Gaussian functions as well as the ECG waveforms (P-wave, QRS complex and T-wave) in the ECG dynamical model, are considered as state variables. In this paper, the dynamic time warping method is used to estimate the nonlinear ECG phase observation. We compare this new approach with linear phase observation models. Using linear and nonlinear EKF25 for ECG denoising and nonlinear EKF25 for fiducial point extraction and ECG interval analysis are the main contributions of this paper. Performance comparison with other EKF-based techniques shows that the proposed method results in higher output SNR with an average SNR improvement of 12 dB for an input SNR of -8 dB. To evaluate the FP extraction performance, we compare the proposed method with a method based on partially collapsed Gibbs sampler and an established EKF-based method. The mean absolute error and the root mean square error of all FPs, across all databases are 14 ms and 22 ms, respectively, for our proposed method, with an advantage when using a nonlinear phase observation. These errors are significantly smaller than errors obtained with other methods. For ECG interval analysis, with an absolute mean error and a root mean square error of about 22 ms and 29 ms, the proposed method achieves better accuracy and smaller variability with respect to other methods.

ECG denoising using angular velocity as a state and an observation in an Extended Kalman Filter framework.

In this paper an efficient filtering procedure based on Extended Kalman Filter (EKF) has been proposed. The method is based on a modified nonlinear dynamic model, previously introduced for the generation of synthetic ECG signals. The proposed method considers the angular velocity of ECG signal, as one of the states of an EKF. We have considered two cases for observation equations, in one case we have assumed a corresponding observation to angular velocity state and in the other case, we have not assumed any observations for it. Quantitative evaluation of the proposed algorithm on the MIT-BIH Normal Sinus Rhythm Database (NSRDB) shows that an average SNR improvement of 8 dB is achieved for an input signal of -4 dB.