Itaconate and citrate releasing polymer attenuates foreign body response in biofabricated cardiac patches.

Application of cardiac patches to the heart surface can be undertaken to provide support and facilitate regeneration of the damaged cardiac tissue following ischemic injury. Biomaterial composition is an important consideration in the design of cardiac patch materials as it governs host response to ultimately prevent the undesirable fibrotic response. Here, we investigate a novel patch material, poly (itaconate-co-citrate-co-octanediol) (PICO), in the context of cardiac implantation. Citric acid (CA) and itaconic acid (ITA), the molecular components of PICO, provided a level of protection for cardiac cells during ischemic reperfusion injury in vitro. Biofabricated PICO patches were shown to degrade in accelerated and hydrolytic conditions, with CA and ITA being released upon degradation. Furthermore, the host response to PICO patches after implantation on rat epicardium in vivo was explored and compared to two biocompatible cardiac patch materials, poly (octamethylene (anhydride) citrate) (POMaC) and poly (ethylene glycol) diacrylate (PEGDA). PICO patches resulted in less macrophage infiltration and lower foreign body giant cell reaction compared to the other materials, with corresponding reduction in smooth muscle actin-positive vessel infiltration into the implant region. Overall, this work demonstrates that PICO patches release CA and ITA upon degradation, both of which demonstrate cardioprotective effects on cardiac cells after ischemic injury, and that PICO patches generate a reduced inflammatory response upon implantation to the heart compared to other materials, signifying promise for use in cardiac patch applications.

Advances in cardiac tissue engineering and heart-on-a-chip.

Recent advances in both cardiac tissue engineering and hearts-on-a-chip are grounded in new biomaterial development as well as the employment of innovative fabrication techniques that enable precise control of the mechanical, electrical, and structural properties of the cardiac tissues being modelled. The elongated structure of cardiomyocytes requires tuning of substrate properties and application of biophysical stimuli to drive its mature phenotype. Landmark advances have already been achieved with induced pluripotent stem cell-derived cardiac patches that advanced to human testing. Heart-on-a-chip platforms are now commonly used by a number of pharmaceutical and biotechnology companies. Here, we provide an overview of cardiac physiology in order to better define the requirements for functional tissue recapitulation. We then discuss the biomaterials most commonly used in both cardiac tissue engineering and heart-on-a-chip, followed by the discussion of recent representative studies in both fields. We outline significant challenges common to both fields, specifically: scalable tissue fabrication and platform standardization, improving cellular fidelity through effective tissue vascularization, achieving adult tissue maturation, and ultimately developing cryopreservation protocols so that the tissues are available off the shelf.

Hyper-Dense_Lung_Seg: Multimodal-Fusion-Based Modified U-Net for Lung Tumour Segmentation Using Multimodality of CT-PET Scans.

The majority of cancer-related deaths globally are due to lung cancer, which also has the second-highest mortality rate. The segmentation of lung tumours, treatment evaluation, and tumour stage classification have become significantly more accessible with the advent of PET/CT scans. With the advent of PET/CT scans, it is possible to obtain both functioning and anatomic data during a single examination. However, integrating images from different modalities can indeed be time-consuming for medical professionals and remains a challenging task. This challenge arises from several factors, including differences in image acquisition techniques, image resolutions, and the inherent variations in the spectral and temporal data captured by different imaging modalities. Artificial Intelligence (AI) methodologies have shown potential in the automation of image integration and segmentation. To address these challenges, multimodal fusion approach-based U-Net architecture (early fusion, late fusion, dense fusion, hyper-dense fusion, and hyper-dense VGG16 U-Net) are proposed for lung tumour segmentation. Dice scores of 73% show that hyper-dense VGG16 U-Net is superior to the other four proposed models. The proposed method can potentially aid medical professionals in detecting lung cancer at an early stage.

3-D Quantum-Inspired Self-Supervised Tensor Network for Volumetric Segmentation of Medical Images.

This article introduces a novel shallow 3-D self-supervised tensor neural network in quantum formalism for volumetric segmentation of medical images with merits of obviating training and supervision. The proposed network is referred to as the 3-D quantum-inspired self-supervised tensor neural network (3-D-QNet). The underlying architecture of 3-D-QNet is composed of a trinity of volumetric layers, viz., input, intermediate, and output layers interconnected using an S -connected third-order neighborhood-based topology for voxelwise processing of 3-D medical image data, suitable for semantic segmentation. Each of the volumetric layers contains quantum neurons designated by qubits or quantum bits. The incorporation of tensor decomposition in quantum formalism leads to faster convergence of network operations to preclude the inherent slow convergence problems faced by the classical supervised and self-supervised networks. The segmented volumes are obtained once the network converges. The suggested 3-D-QNet is tailored and tested on the BRATS 2019 Brain MR image dataset and the Liver Tumor Segmentation Challenge (LiTS17) dataset extensively in our experiments. The 3-D-QNet has achieved promising dice similarity (DS) as compared with the time-intensive supervised convolutional neural network (CNN)-based models, such as 3-D-UNet, voxelwise residual network (VoxResNet), Dense-Res-Inception Net (DRINet), and 3-D-ESPNet, thereby showing a potential advantage of our self-supervised shallow network on facilitating semantic segmentation.

Robust Brain Age Estimation Based on sMRI via Nonlinear Age-Adaptive Ensemble Learning.

Precise prediction on brain age is urgently needed by many biomedical areas including mental rehabilitation prognosis as well as various medicine or treatment trials. People began to realize that contrasting physical (real) age and predicted brain age can help to highlight brain issues and evaluate if patients' brains are healthy or not. Such age prediction is often challenging for single model-based prediction, while the conditions of brains vary drastically over age. In this work, we present an age-adaptive ensemble model that is based on the combination of four different machine learning algorithms, including a support vector machine (SVR), a convolutional neural network (CNN) model, and the popular GoogLeNet and ResNet deep networks. The ensemble model proposed here is nonlinearly adaptive, where age is taken as a key factor in the nonlinear combination of various single-algorithm-based independent models. In our age-adaptive ensemble method, the weights of each model are learned automatically as nonlinear functions over age instead of fixed values, while brain age estimation is based on such an age-adaptive integration of various single models. The quality of the model is quantified by the mean absolute errors (MAE) and spearman correlation between the predicted age and the actual age, with the least MAE and the highest Spearman correlation representing the highest accuracy in age prediction. By testing on the Predictive Analysis Challenge 2019 (PAC 2019) dataset, our novel ensemble model has achieved a MAE down to 3.19, which is a significantly increased accuracy in this brain age competition. If deployed in the real world, our novel ensemble model having an improved accuracy could potentially help doctors to identify the risk of brain diseases more accurately and quickly, thus helping pharmaceutical companies develop drugs or treatments precisely, and potential offer a new powerful tool for researchers in the field of brain science.

Efficient Quantum Image Classification Using Single Qubit Encoding.

The domain of image classification has been seen to be dominated by high-performing deep-learning (DL) architectures. However, the success of this field, as seen over the past decade, has resulted in the complexity of modern methodologies scaling exponentially, commonly requiring millions of parameters. Quantum computing (QC) is an active area of research aimed toward greatly reducing problems of complexity faced in classical computing. With growing interest toward quantum machine learning (QML) for applications of image classification, many proposed algorithms require usage of numerous qubits. In the noisy intermediate-scale quantum (NISQ) era, these circuits may not always be feasible to execute effectively; therefore, we should aim to use each qubit as effectively and efficiently as possible, before adding additional qubits. This article proposes a new single-qubit-based deep quantum neural network for image classification that mimics traditional convolutional neural network (CNN) techniques, resulting in a reduced number of parameters compared with previous works. Our aim is to prove the concept of the initial proposal by demonstrating classification performance of the single-qubit-based architecture, as well as to provide a tested foundation for further development. To demonstrate this, our experiments were conducted using various datasets including MNIST, Fashion-MNIST, and ORL face datasets. To further our proposal in the context of the NISQ era, our experiments were intentionally conducted in noisy simulation environments. Initial test results appear promising, with classification accuracies of 94.6%, 89.5%, and 82.5% achieved on the subsets of MNIST, FMNIST, and ORL face datasets, respectively. In addition, proposals for further investigation and development were considered, where it is hoped that these initial results can be improved.

Towards robust diagnosis of COVID-19 using vision self-attention transformer.

The outbreak of COVID-19, since its appearance, has affected about 200 countries and endangered millions of lives. COVID-19 is extremely contagious disease, and it can quickly incapacitate the healthcare systems if infected cases are not handled timely. Several Conventional Neural Networks (CNN) based techniques have been developed to diagnose the COVID-19. These techniques require a large, labelled dataset to train the algorithm fully, but there are not too many labelled datasets. To mitigate this problem and facilitate the diagnosis of COVID-19, we developed a self-attention transformer-based approach having self-attention mechanism using CT slices. The architecture of transformer can exploit the ample unlabelled datasets using pre-training. The paper aims to compare the performances of self-attention transformer-based approach with CNN and Ensemble classifiers for diagnosis of COVID-19 using binary Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and multi-class Hybrid-learning for UnbiaSed predicTion of COVID-19 (HUST-19) CT scan dataset. To perform this comparison, we have tested Deep learning-based classifiers and ensemble classifiers with proposed approach using CT scan images. Proposed approach is more effective in detection of COVID-19 with an accuracy of 99.7% on multi-class HUST-19, whereas 98% on binary class SARS-CoV-2 dataset. Cross corpus evaluation achieves accuracy of 93% by training the model with Hust19 dataset and testing using Brazilian COVID dataset.

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods.

Identifying the reactions that govern a dynamical biological system is a crucial but challenging task in systems biology. In this work, we present a data-driven method to infer the underlying biochemical reaction system governing a set of observed species concentrations over time. We formulate the problem as a regression over a large, but limited, mass-action constrained reaction space and utilize sparse Bayesian inference via the regularized horseshoe prior to produce robust, interpretable biochemical reaction networks, along with uncertainty estimates of parameters. The resulting systems of chemical reactions and posteriors inform the biologist of potentially several reaction systems that can be further investigated. We demonstrate the method on two examples of recovering the dynamics of an unknown reaction system, to illustrate the benefits of improved accuracy and information obtained.

Private Facial Prediagnosis as an Edge Service for Parkinson's DBS Treatment Valuation.

Facial phenotyping for medical prediagnosis has recently been successfully exploited as a novel way for the preclinical assessment of a range of rare genetic diseases, where facial biometrics is revealed to have rich links to underlying genetic or medical causes. In this paper, we aim to extend this facial prediagnosis technology for a more general disease, Parkinson's Diseases (PD), and proposed an Artificial-Intelligence-of-Things (AIoT) edge-oriented privacy-preserving facial prediagnosis framework to analyze the treatment of Deep Brain Stimulation (DBS) on PD patients. In the proposed framework, a novel edge-based privacy-preserving framework is proposed to implement private deep facial diagnosis as a service over an AIoT-oriented information theoretically secure multi-party communication scheme, while data privacy has been a primary concern toward a wider exploitation of Electronic Health and Medical Records (EHR/EMR) over cloud-based medical services. In our experiments with a collected facial dataset from PD patients, for the first time, we proved that facial patterns could be used to evaluate the facial difference of PD patients undergoing DBS treatment. We further implemented a privacy-preserving information theoretical secure deep facial prediagnosis framework that can achieve the same accuracy as the non-encrypted one, showing the potential of our facial prediagnosis as a trustworthy edge service for grading the severity of PD in patients.

Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators.

BACKGROUND: Approximate Bayesian Computation (ABC) has become a key tool for calibrating the parameters of discrete stochastic biochemical models. For higher dimensional models and data, its performance is strongly dependent on having a representative set of summary statistics. While regression-based methods have been demonstrated to allow for the automatic construction of effective summary statistics, their reliance on first simulating a large training set creates a significant overhead when applying these methods to discrete stochastic models for which simulation is relatively expensive. In this τ work, we present a method to reduce this computational burden by leveraging approximate simulators of these systems, such as ordinary differential equations and τ-Leaping approximations. RESULTS: We have developed an algorithm to accelerate the construction of regression-based summary statistics for Approximate Bayesian Computation by selectively using the faster approximate algorithms for simulations. By posing the problem as one of ratio estimation, we use state-of-the-art methods in machine learning to show that, in many cases, our algorithm can significantly reduce the number of simulations from the full resolution model at a minimal cost to accuracy and little additional tuning from the user. We demonstrate the usefulness and robustness of our method with four different experiments. CONCLUSIONS: We provide a novel algorithm for accelerating the construction of summary statistics for stochastic biochemical systems. Compared to the standard practice of exclusively training from exact simulator samples, our method is able to dramatically reduce the number of required calls to the stochastic simulator at a minimal loss in accuracy. This can immediately be implemented to increase the overall speed of the ABC workflow for estimating parameters in complex systems.

Associations of longitudinal D-Dimer and Factor II on early trauma survival risk.

BACKGROUND: Trauma-induced coagulopathy (TIC) is a disorder that occurs in one-third of severely injured trauma patients, manifesting as increased bleeding and a 4X risk of mortality. Understanding the mechanisms driving TIC, clinical risk factors are essential to mitigating this coagulopathic bleeding and is therefore essential for saving lives. In this retrospective, single hospital study of 891 trauma patients, we investigate and quantify how two prominently described phenotypes of TIC, consumptive coagulopathy and hyperfibrinolysis, affect survival odds in the first 25 h, when deaths from TIC are most prevalent. METHODS: We employ a joint survival model to estimate the longitudinal trajectories of the protein Factor II (% activity) and the log of the protein fragment D-Dimer ([Formula: see text]g/ml), representative biomarkers of consumptive coagulopathy and hyperfibrinolysis respectively, and tie them together with patient outcomes. Joint models have recently gained popularity in medical studies due to the necessity to simultaneously track continuously measured biomarkers as a disease evolves, as well as to associate them with patient outcomes. In this work, we estimate and analyze our joint model using Bayesian methods to obtain uncertainties and distributions over associations and trajectories. RESULTS: We find that a unit increase in log D-Dimer increases the risk of mortality by 2.22 [1.57, 3.28] fold while a unit increase in Factor II only marginally decreases the risk of mortality by 0.94 [0.91,0.96] fold. This suggests that, while managing consumptive coagulopathy and hyperfibrinolysis both seem to affect survival odds, the effect of hyperfibrinolysis is much greater and more sensitive. Furthermore, we find that the longitudinal trajectories, controlling for many fixed covariates, trend differently for different patients. Thus, a more personalized approach is necessary when considering treatment and risk prediction under these phenotypes. CONCLUSION: This study reinforces the finding that hyperfibrinolysis is linked with poor patient outcomes regardless of factor consumption levels. Furthermore, it quantifies the degree to which measured D-Dimer levels correlate with increased risk. The single hospital, retrospective nature can be understood to specify the results to this particular hospital's patients and protocol in treating trauma patients. Expanding to a multi-hospital setting would result in better estimates about the underlying nature of consumptive coagulopathy and hyperfibrinolysis with survival, regardless of protocol. Individual trajectories obtained with these estimates can be used to provide personalized dynamic risk prediction when making decisions regarding management of blood factors.

Epidemiological modeling in StochSS Live!

SUMMARY: We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. AVAILABILITY AND IMPLEMENTATION: StochSS Live! is freely available at https://live.stochss.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Role for 2D image generated 3D face models in the rehabilitation of facial palsy.

The outcome for patients diagnosed with facial palsy has been shown to be linked to rehabilitation. Dense 3D morphable models have been shown within the computer vision to create accurate representations of human faces even from single 2D images. This has the potential to provide feedback to both the patient and medical expert dealing with the rehabilitation plan. It is proposed that a framework for the creation and measuring of patient facial movement consisting of a hybrid 2D facial landmark fitting technique which shows better accuracy in testing than current methods and 3D model fitting.

Live-cell tracking using SIFT features in DIC microscopic videos.

In this paper, a novel motion-tracking scheme using scale-invariant features is proposed for automatic cell motility analysis in gray-scale microscopic videos, particularly for the live-cell tracking in low-contrast differential interference contrast (DIC) microscopy. In the proposed approach, scale-invariant feature transform (SIFT) points around live cells in the microscopic image are detected, and a structure locality preservation (SLP) scheme using Laplacian Eigenmap is proposed to track the SIFT feature points along successive frames of low-contrast DIC videos. Experiments on low-contrast DIC microscopic videos of various live-cell lines shows that in comparison with principal component analysis (PCA) based SIFT tracking, the proposed Laplacian-SIFT can significantly reduce the error rate of SIFT feature tracking. With this enhancement, further experimental results demonstrate that the proposed scheme is a robust and accurate approach to tackling the challenge of live-cell tracking in DIC microscopy.