PTransIPs: Identification of phosphorylation sites based on protein pretrained language model and Transformer

Phosphorylation is central to numerous fundamental cellular processes, influencing the onset and progression of a variety of diseases. The correct identification of these phosphorylation sites is of great importance to unravel the intricate molecular mechanisms within cells and during viral infections, potentially leading to the discovery of new therapeutic targets. In this study, we introduce PTransIPs, a novel deep learning model for the identification of phosphorylation sites. PTransIPs treat amino acids within protein sequences as words, extracting unique encodings based on their type and sequential position. The model also incorporates embeddings from large pretrained protein models as additional data inputs. PTransIPS is further trained on a combination model of convolutional neural network with residual connections and Transformer model equipped with multi-head attention mechanisms. At last, the model outputs classification results through a fully connected layer. The results of independent testing reveal that PTransIPs outperforms existing state-of-the-art(SOTA) methods, achieving AUROCs of 0.9232 and 0.9660 for identifying phosphorylated S/T and Y sites respectively. In addition, ablation studies prove that pretrained model embeddings contribute to the performance of PTransIPs. Furthermore, PTransIPs has interpretable amino acid preference, visible training process and shows generalizability on other bioactivity classification tasks. To facilitate usage, our code and data are publicly accessible at \url{https://github.com/StatXzy7/PTransIPs}

Short-range correlations and momentum distributions in mirror nuclei 3H and 3He

Motivated by recent high-energy electron and $\rm ^3H$ and $\rm ^3He$ nuclei scattering experiment in Jefferson Lab (Nature 609, 41 (2022)), the short-range correlations (SRCs) between nucleon pairs for 3-nucleon systems are microscopically studied using realistic $NN$ 2-body interaction and two-Gaussian type $NNN$ 3-body interaction. The wave functions of both $\rm ^3H$ and $\rm ^3He$ are obtained by solving 3-body Schr\"{o}dinger equations using Gaussian expansion method (GEM). The differences of one-nucleon and nucleon-nucleon momentum distributions between $\rm ^3H$ and $\rm ^3He$ are analyzed in detail. The results show that the percentages of $pn$-SRC pairs are significantly enhanced as compared with those of $nn(pp)$-SRC ones in $\rm ^3H$ and $\rm ^3He$ nuclei, which is consistent with the experimental findings.Comment: 6 pages, 5 figures, to appear in Phys. Rev.

Numerical Simulation of Hydraulic Fracturing in Enhanced Geothermal Systems Considering Thermal Stress Cracks

With the increasing attention to clean and economical energy resources, geothermal energy and enhanced geothermal systems (EGS) have gained much importance in recent years. For the efficient development of deep geothermal reservoirs, it is crucial to understand the mechanical behavior of reservoir rock and its interaction with injected fluid under high-temperature and high confining pressure environments for employing hydraulic stimulation technologies. In the present study, we develop a novel numerical scheme based on the distinct element method (DEM) to simulate the failure behavior of rock by considering the influence of thermal stress cracks and high confining pressure for EGS. The proposed methodology is validated by comparing uniaxial compression tests at various temperatures and biaxial compression tests at different confining pressures with laboratory experimental results. The numerical results indicate a good agreement in terms of failure models and stress-strain curves with those of laboratory experiments. We then apply the developed scheme to the hydraulic fracturing simulations under various temperatures, confining pressures, and injection fluid conditions. Based on our numerical results, the number of hydraulic cracks is proportional to the temperature. At a high-temperature and low confining pressure environment, a complex crack network with large crack width can be observed, whereas the generation of the micro-cracks is suppressed in high confining pressure conditions. In addition, high-viscosity injection fluid tends to induce more hydraulic cracks. Since the crack network in the geothermal reservoir is an essential factor for the efficient production of geothermal energy, the combination of the above factors should be considered in hydraulic fracturing treatment in EGS

Exploration of a New Model of "Highway + Tourism" Development from the Perspective of 5G——Taking the Yichang Road Tourism Economic Belt as an Example

The innovation of 5G technology is the characteristics of the progress and development of the times, now Yibin City Yichang Road construction has been basically perfect, along the way tourism in this network era and the epidemic epidemic intersection can be described as ready to go, in the typical mode of "highway + tourism", with the help of 5G advantages, Yichang Road tourism economic belt innovation into "5G + highway + tourist attractions + tourism services" integrated tourism comprehensive development model, adapt to the development of the times and the diversification characteristics of tourists, explore new directions of industry development, draw a new main line for high-quality tourism development. 5G is a mobile communication technology, but also a trend of future development, in the development of Yibin Yichang Road tourism, seize the new opportunities of 5G mobile communication development, rely on the "Internet of Things", "cloud computing" and "smart city" common development, combined with the current situation, with the help of "highway + tourism" typical model, strive to explore a new development model for Yichang Road tourism economy