Probabilistic Radiomics: Ambiguous Diagnosis with Controllable Shape Analysis

Radiomics analysis has achieved great success in recent years. However, conventional Radiomics analysis suffers from insufficiently expressive hand-crafted features. Recently, emerging deep learning techniques, e.g., convolutional neural networks (CNNs), dominate recent research in Computer-Aided Diagnosis (CADx). Unfortunately, as black-box predictors, we argue that CNNs are "diagnosing" voxels (or pixels), rather than lesions; in other words, visual saliency from a trained CNN is not necessarily concentrated on the lesions. On the other hand, classification in clinical applications suffers from inherent ambiguities: radiologists may produce diverse diagnosis on challenging cases. To this end, we propose a controllable and explainable {\em Probabilistic Radiomics} framework, by combining the Radiomics analysis and probabilistic deep learning. In our framework, 3D CNN feature is extracted upon lesion region only, then encoded into lesion representation, by a controllable Non-local Shape Analysis Module (NSAM) based on self-attention. Inspired from variational auto-encoders (VAEs), an Ambiguity PriorNet is used to approximate the ambiguity distribution over human experts. The final diagnosis is obtained by combining the ambiguity prior sample and lesion representation, and the whole network named $DenseSharp^{+}$ is end-to-end trainable. We apply the proposed method on lung nodule diagnosis on LIDC-IDRI database to validate its effectiveness.Comment: MICCAI 2019 (early accept), with supplementary material

Modified Discrete Grey Wolf Optimizer Algorithm for Multilevel Image Thresholding

The computation of image segmentation has become more complicated with the increasing number of thresholds, and the option and application of the thresholds in image thresholding fields have become an NP problem at the same time. The paper puts forward the modified discrete grey wolf optimizer algorithm (MDGWO), which improves on the optimal solution updating mechanism of the search agent by the weights. Taking Kapur’s entropy as the optimized function and based on the discreteness of threshold in image segmentation, the paper firstly discretizes the grey wolf optimizer (GWO) and then proposes a new attack strategy by using the weight coefficient to replace the search formula for optimal solution used in the original algorithm. The experimental results show that MDGWO can search out the optimal thresholds efficiently and precisely, which are very close to the result examined by exhaustive searches. In comparison with the electromagnetism optimization (EMO), the differential evolution (DE), the Artifical Bee Colony (ABC), and the classical GWO, it is concluded that MDGWO has advantages over the latter four in terms of image segmentation quality and objective function values and their stability

Heat shock factor 1-mediated transcription activation of Omi/HtrA2 induces myocardial mitochondrial apoptosis in the aging heart.

BACKGROUND: Increased cardiac apoptosis is a hallmark of the elderly, which in turn increases the risk for developing cardiac disease. The overexpression of Omi/HtrA2 mRNA and protein contributes to apoptosis in the aged heart. Heat shock factor 1 (HSF1) is a transcription factor that binds to the promoter of Omi/HtrA2 in the aging myocardium. However, whether HSF1 participates in cardiomyocyte apoptosis via transcriptional regulation of Omi/HtrA2 remains unclear. The present study was designed to investigate whether HSF1 plays a role in Omi/HtrA2 transcriptional regulation and myocardial apoptosis. METHODS AND RESULTS: Assessment of the hearts of mice of different ages was performed, which indicated a decrease in cardiac function reserve and an increase in mitochondrial apoptosis. Omi/HtrA2 overexpression in the elderly was negatively correlated with left ventricular function after exercise overload and positively correlated with myocardial Caspase-9 apoptosis. Chromatin immunoprecipitation (ChIP) of aging hearts and plasmid transfection/RNA interference of H9C2 cells revealed that enhancement of HSF1 expression promotes Omi/HtrA2 expression by inducing the promoter activity of Omi/HtrA2 while also increasing mitochondrial apoptosis by upregulating Omi/HtrA2 expression. CONCLUSIONS: HSF1 acts as a transcriptional factor that induces Omi/HtrA2 expression and Caspase-9 apoptosis in aged cardiomyocytes, while also decreasing cardiac function reserve

A Quick Artificial Bee Colony Algorithm for Image Thresholding

The computational complexity grows exponentially for multi-level thresholding (MT) with the increase of the number of thresholds. Taking Kapur’s entropy as the optimized objective function, the paper puts forward the modified quick artificial bee colony algorithm (MQABC), which employs a new distance strategy for neighborhood searches. The experimental results show that MQABC can search out the optimal thresholds efficiently, precisely, and speedily, and the thresholds are very close to the results examined by exhaustive searches. In comparison to the EMO (Electro-Magnetism optimization), which is based on Kapur’s entropy, the classical ABC algorithm, and MDGWO (modified discrete grey wolf optimizer) respectively, the experimental results demonstrate that MQABC has exciting advantages over the latter three in terms of the running time in image thesholding, while maintaining the efficient segmentation quality

SYNONYMOUS CONDON USAGE BIAS AND OVEREXPRESSION OF A SYNTHETIC xynB GENE FROM Aspergillus niger NL-1 IN Pichia pastoris

To further improve the expression level of recombinant xylanase in Pichia pastoris, the xynB gene, encoding the mature peptide from Aspergillus niger NL-1, was designed and synthesized based on the synonymous condon bias of P. pastoris and optimized G+C content. 155 nucleotides were changed, and the GC content decreased from 57.7% to 43.6%. The synthetic xynB was inserted into the pPICZaA and then integrated into P. pastoris GS115. The activity of the recombinant xylanase reached 1414.7 U/mL, induced with 0.8% methanol after 14-day cultivation at a temperature of 28oC in shake flasks, which was 267% higher than that of the native gene. Furthermore, the maximum xylanase activity of 20424.2 U/mL was obtained by high-density fermentation in a 5-L fermenter, which was the highest xylanase expression in P. pastoris yet reported. The recombinant xylanase had its optimal activity at a pH of 5.0 and temperature of 50oC. The recombinant xylanase was stable over a pH range of 4.5 to 8.0. Thus, this report provides an industrial means to produce the recombinant xylanase in P. pastoris

Integrated decision-making model for groundwater potential evaluation in mining areas using the cusp catastrophe model and principal component analysis

10.1016/j.ejrh.2021.100891Journal of Hydrology: Regional Studies3710089

An Improved Frequency-Adaptive Virtual Variable Sampling-Based Repetitive Control for an Active Power Filter

To eliminate the harmonics caused by nonlinear loads, repetitive controllers are widely applied as current controllers for active power filters (APF). In practice, a variation in grid frequency leads to the appearance of a fractional-order delay filter. As a result, the resonant frequency of the repetitive controller will deviate from the fundamental frequency and the controller cannot compensate for harmonics accurately. To solve this problem, an improved frequency-adaptive repetitive controller based on virtual variable sampling (IMFA-VVS-RC) for APF is proposed in this paper. To enhance the system stability margin, the proposed RC introduces an infinite impulse response (IIR) low-pass filter. The proposed RC has a high stability margin at high frequencies due to the low gain of the IIR low-pass filter in the region above the cutoff frequency. In this way, the influence of model uncertainty and parameter uncertainty on system stability are reduced at high frequencies. At the same time, compared with the conventional repetitive controller (CRC), the proposed RC for APF has a better harmonic suppression ability when the frequency varies. Experiments have verified the effectiveness of the scheme adopted for APF