RNA 3D structure prediction is a long-standing challenge. Inspired by the recent breakthrough in protein structure prediction, we developed trRosettaRNA, an automated deep learning-based approach to RNA 3D structure prediction. The trRosettaRNA pipeline comprises two major steps: 1D and 2D geometries prediction by a transformer network; and 3D structure folding by energy minimization. Benchmark tests suggest that trRosettaRNA outperforms traditional automated methods. In the blind tests of the 15 ^th Critical Assessment of Structure Prediction (CASP15) and the RNA-Puzzles experiments, the automated trRosettaRNA predictions for the natural RNAs are competitive with the top human predictions. trRosettaRNA also outperforms other deep learning-based methods in CASP15 when measured by the Z-score of the Root-Mean-Square Deviation. Nevertheless, it remains challenging to predict accurate structures for synthetic RNAs with an automated approach. We hope this work could be a good start toward solving the hard problem of RNA structure prediction with deep learning.

The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous methods and produces the best results in a large-scale protein dynamics dataset; this model can accurately infer the dynamic information of a protein in only a few seconds. By learning effectively from experimental protein structure data and cryo-electron microscopy (cryo-EM) data integration, our approach is able to accurately identify the interactive bidirectional constraints and supervision between cryo-EM maps and PDB models in maximizing the dynamic prediction efficacy. Rigorous 5-fold cross-validation on the dataset demonstrates that RMSF-net achieves test correlation coefficients of 0.746 ± 0.127 at the voxel level and 0.765 ± 0.109 at the residue level, showcasing its ability to deliver dynamic predictions closely approximating molecular dynamics simulations. Additionally, it offers real-time dynamic inference with minimal storage overhead on the order of megabytes. RMSF-net is a freely accessible tool and is anticipated to play an essential role in the study of protein dynamics.

Electron tomography (ET) plays an important role in revealing biological structures, ranging from macromolecular to subcellular scale. Due to limited tilt angles, ET reconstruction always suffers from the 'missing wedge' artifacts, thus severely weakens the further biological interpretation. In this work, we developed an algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-sensing and the assumption of sparsity of biological specimens. ICON can significantly restore the missing information in comparison with other reconstruction algorithms. More importantly, we used the leave-one-out method to verify the validity of restored information for both simulated and experimental data. The significant improvement in sub-tomogram averaging by ICON indicates its great potential in the future application of high-resolution structural determination of macromolecules in situ.

The size and number of cloud data centers (CDCs) have grown rapidly with the increasing popularity of cloud computing and high-performance computing. This has the unintended consequences of creating new challenges due to inefficient use of resources and high energy consumption. Hence, this necessitates the need to maximize resource utilization and ensure energy efficiency in CDCs. One viable approach to achieve energy efficiency and resource utilization in CDC is task scheduling. While several task scheduling approaches have been proposed in the literature, there appears to be a lack of classification-based merging concept for real-time tasks in these existing approaches. Thus, an energy-efficient dynamic scheduling scheme (EDS) of real-time tasks for virtualized CDC is presented in this paper. In the scheduling scheme, the heterogeneous tasks and virtual machines are first classified based on a historical scheduling record. Then, similar type of tasks are merged and scheduled to maximally utilize an operational state of the host. In addition, energy efficiencies and optimal operating frequencies of heterogeneous physical hosts are employed to attain energy preservation while creating and deleting the virtual machines. Experimental results show that, in comparison with existing techniques, EDS significantly improves overall scheduling performance, achieves a higher CDC resource utilization, increases task guarantee ratio, minimizes the mean response time, and reduces energy consumption.

Survival analysis is a significant study in cancer prognosis, and the multi-modal data, including histopathological images, genomic data, and clinical information, provides unprecedented opportunities for its development. However, because of the high dimensionality and the heterogeneity of histopathological images and genomic data, acquiring effective predictive characters from these multi-modal data has always been a challenge for survival analysis. In this study, we propose a transformer-based survival analysis model (TransSurv) for colorectal cancer that can effectively integrate intra-modality and inter-modality features of histopathological images, genomic data, and clinical information. Specifically, to integrate the intra-modality relationship of image patches, we develop a multi-scale histopathological features fusion transformer (MS-Trans). Furthermore, we provide a cross-modal fusion transformer based on cross attention for multi-scale pathological representation and multi-omics representation, which includes RNA-seq expression and copy number alteration (CNA). At the output layer of the TransSurv, we adopt the Cox layer to integrate multi-modal fusion representation with clinical information for end-to-end survival analysis. The experimental results on the Cancer Genome Atlas (TCGA) colorectal cancer cohort demonstrate that the proposed TransSurv outperforms the existing methods and improves the prognosis prediction of colorectal cancer.