NasalSeg: A Dataset for Automatic Segmentation of Nasal Cavity and Paranasal Sinuses from 3D CT Images.

Modern facial surgical planning and therapeutic strategies rely heavily on the precise segmentation of the nasal cavity and paranasal sinuses from computed tomography (CT) images for quantitative analysis. Nevertheless, manual segmentation is labor-intensive and prone to inconsistencies, highlighting the need for automatic segmentation methods. A significant challenge in this field is the lack of publicly available clinical datasets for research.

A general temperature-guided language model to design proteins of enhanced stability and activity.

Designing protein mutants with both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants with improved stability and activity without any prior experimental mutagenesis data for the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive ability compared to current state-of-the-art models on the public mutagenesis dataset across 283 protein assays.

Simple, Efficient, and Scalable Structure-Aware Adapter Boosts Protein Language Models.

Fine-tuning pretrained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in natural language processing, employing parameter-efficient fine-tuning techniques could potentially enhance the performance of PLMs. However, the direct transfer to life science tasks is nontrivial due to the different training strategies and data forms.

PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications.

Protein language models (PLMs) play a dominant role in protein representation learning. Most existing PLMs regard proteins as sequences of 20 natural amino acids. The problem with this representation method is that it simply divides the protein sequence into sequences of individual amino acids, ignoring the fact that certain residues often occur together.

Enhancing efficiency of protein language models with minimal wet-lab data through few-shot learning.

Accurately modeling the protein fitness landscapes holds great importance for protein engineering. Pre-trained protein language models have achieved state-of-the-art performance in predicting protein fitness without wet-lab experimental data, but their accuracy and interpretability remain limited. On the other hand, traditional supervised deep learning models require abundant labeled training examples for performance improvements, posing a practical barrier.

Icariin attenuates the calcification of vascular smooth muscle cells through ERα - p38MAPK pathway.

Objective: To investigate the relationship between icariin and the osteoblastic differentiation of vascular smooth muscle cells (VSMCs) and the signal pathway involved.

Methods: We applied a universally accepted calcification model of VSMCs induced by β glycerophosphate. Then the VSMCs calcification was observed by treatment with icariin and/or inhibitors of estrogen receptors (ERs) and p38-mitogen-activated protein kinase (MAPK) signaling.

Effects of irradiation behavior on physicochemical properties of glassy radioactive contaminated soil containing various contents of actinides nuclear waste.

The evaluation of radiation resistance of the treated radioactive contaminated soil is crucial. The irradiation behavior of simulated radioactive soil waste irradiated with 1.5 MeV Xe ions at fluences of 1 × 10-1 × 10 ions/cm was studied.

Cinepazide maleate promotes recovery from spinal cord injury by inhibiting inflammation and prolonging neuronal survival.

This study aimed to investigate the therapeutic effects of cinepazide maleate (CM) on spinal cord injury (SCI) in rats, thereby providing an experimental basis for the use of CM as a preventative and therapeutic strategy for SCI. Terminal deoxynucleotidyl transferase dUTP nick end labeling staining and western blot analysis were used to assess neural cell apoptosis. enzyme-linked immunosorbent assay was used to analyze the expression of interleukin (IL)-1β, IL-6, and tumor necrosis factor-α (TNF-α) in spinal cord tissues and cerebrospinal fluid.

The evolution of anionic nanoclusters at the electrode interface in water-in-salt electrolytes.

Water-in-salt electrolytes (WiSEs) have attracted extensive attention as promising alternatives to organic electrolytes. The limited electrochemical stability windows (ESWs) of aqueous electrolytes are significantly widened by WiSEs. However, the actual ESWs are lower than predicted as the interphase with WiSEs is not as stable as the solid electrolyte interphase (SEI) in conventional lithium-ion batteries.

Discontinuous low temperature stress and plant growth regulators during the germination period promote roots growth in alfalfa (Medicago sativa L.).

In high-cold regions, alfalfa is susceptible to cold damage during the seed germination. The effects of discontinuous low temperature stress and plant growth regulators (PGRs) on alfalfa were studied in response to the high day/night temperature differentials in the area. The experiments included seed germination, seedling cold tolerance and plant recovery.

SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism.

Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria.

Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes.

A random batch Ewald method for charged particles in the isothermal-isobaric ensemble.

We develop an accurate, highly efficient, and scalable random batch Ewald (RBE) method to conduct molecular dynamics simulations in the isothermal-isobaric ensemble (the NPT ensemble) for charged particles in a periodic box. After discretizing the Langevin equations of motion derived using suitable Lagrangians, the RBE method builds the mini-batch strategy into the Fourier space in the Ewald summation for the pressure and forces such that the computational cost is reduced to O(N) per time step. We implement the method in the Large-scale Atomic/Molecular Massively Parallel Simulator package and report accurate simulation results for both dynamical quantities and statistics for equilibrium for typical systems including all-atom bulk water and a semi-isotropic membrane system.

Dynamics of soil properties and bacterial community structure by mulched fertigation system in semi-arid area of Northeast China.

The agricultural irrigation and fertigation systems have a non-negligible impact on the soil microenvironment in arid and semi-arid areas. Therefore, studying the processes and changes of soil microenvironment under different plastic mulch drip irrigation systems can reveal the "soil-microbe" mechanism and provide a theoretical support for the optimal irrigation and nutrition management of maize in the semi-arid area of Northeast China. Three treatments were used for this study in the semi-arid area of northeast China, namely; mulched fertigation system (MF), drip irrigation system (DI), and farmers' practices system (FP).

Investigating Morphology and Breakage Evolution Characteristics of Railroad Ballasts over Distinct Supports Subjected to Impact Loading.

The ballast bed constantly degrades under the repeated applications of impact loading exerted by passing trains in terms of the particle size, shape, breakage, fouling, etc., thus significantly jeopardizing the in-service performance and operational safety of ballasted tracks. In this study, the morphology and breakage evolution characteristics of railroad ballasts of single- and multiple-size ranges were investigated from laboratory impact-load tests.

Effects of rehabilitation management on lifestyle and quality of life of patients with coronary heart disease after percutaneous coronary intervention based on behavior change theory.

Background: The aim of this study was to assess the effects of rehabilitation management on the lifestyle and quality of life of patients with coronary heart disease (CHD) after percutaneous coronary intervention (PCI) based on the behavior change theory.

Methods: A total of 222 CHD patients admitted from January 2019 to April 2021 were randomly divided into research and control groups (N.=111).

Dynamic assessment of coronary artery during different cardiac cycle in patients with coronary artery disease using coronary CT angiography.

Introduction: To evaluate the effect of the cardiac cycle for the coronary artery opening and coronary stenosis at the plaque to determine the phase of measuring maximum diameters required for coronary artery disease (CAD).

Methods: This retrospective study assessed data for 208 consecutive patients who underwent coronary computed tomography angiography (CTA). The cross-sectional area and diameters of the opening of the left main coronary artery (LM), left anterior descending branch (LAD), left circumflex branch (LCX) and right coronary artery (RCA), the stenosis rate of involved vessels were measured in 10 cardiac cycles.

Universal dynamical onset in water at distinct material interfaces.

Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials.

Dual-layer spectral detector CT for contrast agent concentration, dose and injection rate reduction: Utility in imaging of the superior mesenteric artery.

Purpose: To investigate the feasibility of contrast agent and injection rate reduction for dual-layer spectral detector computed tomography (SDCT) imaging of the superior mesenteric artery (SMA) using virtual monochromatic image (VMI).

Methods: A total of 102 patients who underwent abdominal arterial phase-enhanced SDCT examination due to suspected abdominal diseases were prospectively selected and divided into control group, low concentration/dose groups (groups 370-0.7, 300-1.

Superscalability of the random batch Ewald method.

Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular dynamics simulations, which are major tools for problems at the nano-/micro-scale. Various algorithms are developed to calculate the pairwise Coulomb interactions to a linear scale, but poor scalability limits the size of simulated systems.

Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells.

Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated protein powder, a concentrated protein solution, and in living () cells. Anomalous sub-diffusion of water is observed in all samples, which is alleviated upon increasing the water content.

Decoupling between the translation and rotation of water in the proximity of a protein molecule.

The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation.

Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System.

DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties.