Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization.

Introduction: The evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profound comprehension of potential variations is crucial to effectively mitigate the impact of viral evolution. Yet, this task still faces considerable challenges.

DGCPPISP: a PPI site prediction model based on dynamic graph convolutional network and two-stage transfer learning.

Background: Proteins play a pivotal role in the diverse array of biological processes, making the precise prediction of protein-protein interaction (PPI) sites critical to numerous disciplines including biology, medicine and pharmacy. While deep learning methods have progressively been implemented for the prediction of PPI sites within proteins, the task of enhancing their predictive performance remains an arduous challenge.

Results: In this paper, we propose a novel PPI site prediction model (DGCPPISP) based on a dynamic graph convolutional neural network and a two-stage transfer learning strategy.

DSnet: a new dual-branch network for hippocampus subfield segmentation.

The hippocampus is a critical component of the brain and is associated with many neurological disorders. It can be further subdivided into several subfields, and accurate segmentation of these subfields is of great significance for diagnosis and research. However, the structures of hippocampal subfields are irregular and have complex boundaries, and their voxel values are close to surrounding brain tissues, making the segmentation task highly challenging.

A machine learning based method for constructing group profiles of university students.

This study facilitates university student profiling by constructing a prediction model to forecast the classification of future students participating in a survey, thereby enhancing the utility and effectiveness of the questionnaire approach. In the context of the ongoing digital transformation of campuses, higher education institutions are increasingly prioritizing student educational development. This shift aligns with the maturation of big data technology, prompting scholars to focus on profiling university student education.

Deep fusion of multi-modal features for brain tumor image segmentation.

Accurate segmentation of pathological regions in brain magnetic resonance images (MRI) is essential for the diagnosis and treatment of brain tumors. Multi-modality MRIs, which offer diverse feature information, are commonly utilized in brain tumor image segmentation. Deep neural networks have become prevalent in this field; however, many approaches simply concatenate different modalities and input them directly into the neural network for segmentation, disregarding the unique characteristics and complementarity of each modality.

Deep convolutional neural network for hippocampus segmentation with boundary region refinement.

Accurately segmenting the hippocampus from magnetic resonance (MR) brain images is a crucial step in studying brain disorders. However, this task is challenging due to the low signal contrast of hippocampal images, the irregular shape, and small structural size of the hippocampi. In recent years, several deep convolutional networks have been proposed for hippocampus segmentation, which have achieved state-of-the-art performance.

Patch tensor decomposition and non-local means filter-based hybrid ASL image denoising.

Background: Arterial spin labeling magnetic resonance imaging (ASL MRI) is a noninvasive technique to measure cerebral blood flow (CBF). It is widely used in the study of neurodegenerative diseases. Image denoising is an important step in ASL image processing because the signal-to-noise ratio (SNR) of an ASL CBF perfusion image is very small.

Functional parcellation of the hippocampus by semi-supervised clustering of resting state fMRI data.

Many unsupervised methods are widely used for parcellating the brain. However, unsupervised methods aren't able to integrate prior information, obtained from such as exiting functional neuroanatomy studies, to parcellate the brain, whereas the prior information guided semi-supervised method can generate more reliable brain parcellation. In this study, we propose a novel semi-supervised clustering method for parcellating the brain into spatially and functionally consistent parcels based on resting state functional magnetic resonance imaging (fMRI) data.

Multi-Scale Context-Guided Deep Network for Automated Lesion Segmentation With Endoscopy Images of Gastrointestinal Tract.

Accurate lesion segmentation based on endoscopy images is a fundamental task for the automated diagnosis of gastrointestinal tract (GI Tract) diseases. Previous studies usually use hand-crafted features for representing endoscopy images, while feature definition and lesion segmentation are treated as two standalone tasks. Due to the possible heterogeneity between features and segmentation models, these methods often result in sub-optimal performance.

FCN Based Label Correction for Multi-Atlas Guided Organ Segmentation.

Segmentation of medical images using multiple atlases has recently gained immense attention due to their augmented robustness against variabilities across different subjects. These atlas-based methods typically comprise of three steps: atlas selection, image registration, and finally label fusion. Image registration is one of the core steps in this process, accuracy of which directly affects the final labeling performance.

Multi-atlas label fusion with random local binary pattern features: Application to hippocampus segmentation.

Automatic and reliable segmentation of the hippocampus from magnetic resonance (MR) brain images is extremely important in a variety of neuroimage studies. To improve the hippocampus segmentation performance, a local binary pattern based feature extraction method is developed for machine learning based multi-atlas hippocampus segmentation. Under the framework of multi-atlas image segmentation (MAIS), a set of selected atlases are registered to images to be segmented using a non-linear image registration algorithm.

Dilated Dense U-Net for Infant Hippocampus Subfield Segmentation.

Accurate and automatic segmentation of infant hippocampal subfields from magnetic resonance (MR) images is an important step for studying memory related infant neurological diseases. However, existing hippocampal subfield segmentation methods were generally designed based on adult subjects, and would compromise performance when applied to infant subjects due to insufficient tissue contrast and fast changing structural patterns of early hippocampal development. In this paper, we propose a new fully convolutional network (FCN) for infant hippocampal subfield segmentation by embedding the dilated dense network in the U-net, namely DUnet.

Arterial spin labeling perfusion MRI signal denoising using robust principal component analysis.

Background: Arterial spin labeling (ASL) perfusion MRI provides a non-invasive way to quantify regional cerebral blood flow (CBF) and has been increasingly used to characterize brain state changes due to disease or functional alterations. Its use in dynamic brain activity study, however, is still hampered by the relatively low signal-to-noise-ratio (SNR) of ASL data.

New Method: The aim of this study was to validate a new temporal denoising strategy for ASL MRI.

Patch-based local learning method for cerebral blood flow quantification with arterial spin-labeling MRI.

Arterial spin-labeling (ASL) perfusion MRI is a non-invasive method for quantifying cerebral blood flow (CBF). Standard ASL CBF calibration mainly relies on pair-wise subtraction of the spin-labeled images and controls images at each voxel separately, ignoring the abundant spatial correlations in ASL data. To address this issue, we previously proposed a multivariate support vector machine (SVM) learning-based algorithm for ASL CBF quantification (SVMASLQ).

Metric Learning for Multi-atlas based Segmentation of Hippocampus.

Automatic and reliable segmentation of hippocampus from MR brain images is of great importance in studies of neurological diseases, such as epilepsy and Alzheimer's disease. In this paper, we proposed a novel metric learning method to fuse segmentation labels in multi-atlas based image segmentation. Different from current label fusion methods that typically adopt a predefined distance metric model to compute a similarity measure between image patches of atlas images and the image to be segmented, we learn a distance metric model from the atlases to keep image patches of the same structure close to each other while those of different structures are separated.

Investigation on the mechanisms for biotransformation of saponins to diosgenin.

In order to improve the efficiency of biotransformation of saponins in Dioscorea zingiberensis to diosgenin, a new enzymatic model was developed to investigate the mechanism of the metabolic systems. Four main saponin hydrolases (E1, E2, E3 and E4) were purified from Trichoderma reesei. Using progracillin as substrate, the enzymatic hydrolysis experiments with E1, E2, E3 and E4 were carried out respectively.