bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of water film evaporation on the shale gas transmission in inorganic nanopores under viscosity
Authors: Wang Haoyi , Peng Weihong , Hu Liangyu , Zhang Wei 
Published: April 2024

Shale gas reservoirs generally have ultra-low water saturation, and the water in reservoirs is closely bound to the walls of inorganic nanopores, forming a water film structure on the hydrophilic surface. When shale gas enters the inorganic nanopores, the water films in the inorganic pores will be removed by evaporation instead of being driven away by the gas, which increases the difficulty of predicting production during shale gas extraction. Based on molecular dynamics simulations, a water film evaporation model is proposed, considering the evaporation of water films during shale gas transport and the influence of water film evaporation on the shale gas transport mechanism. The Green–Kubo method is employed to calculate the viscosity of the water film. The evaporation flux of the water film under the influence of viscosity is discussed in the evaporation model. The transport mechanisms of shale gas in nanopores and the effect of water film evaporation on shale gas transport mechanisms are analyzed in detail. The result indicates that the water films in the inorganic nanopores are constrained on the hydrophilic surface, and the viscosity normal to the surface of the water film of 4 Å is 0.005 26 Pa⋅S, which is 6.12 times the reference value of viscosity at 298 K. In the process of water film evaporation, the evaporation flux of the water film is influenced by viscosity. In the study of the shale gas transport mechanism, water films in inorganic nanopores can hinder the surface diffusion of the methane molecules adsorbed on boundary and significantly reduce the mass flux of shale gas.
A dual-ring network design for the fast orbit feedback system of the storage ring
Authors: Liang Yu , Zhu Wenchao , Xie Chunjie , Wei Zhengyu , Luo Qing , Sun Baogen , Zhou Zeran 
Published: April 2024

Building reliable fast orbit feedback (FOFB) systems to offer high stability of the beam orbit becomes more challenging for the diffraction-limited storage ring due to the smaller beam size. The beam position measurement and control (BPMC) processor has been developed to streamline the FOFB system architecture by integrating BPM (Beam Position Monitor) electronics and an orbit feedback controller. This paper designs a hierarchical dual-ring network topology based on BPMC processors using parameters derived from the storage ring of the Hefei Advanced Light Facility. To reduce latency and prevent data transmission collisions, we propose a multi-forwarding communication scheme and a communication controller design in a field-programmable gate array. Experimental results verify that this topology operates reliably with the multi-forwarding scheme, providing an approximate communication latency as low as 17.336 μs to support the 30 kHz orbit feedback update rate.
Dissociative photoionization of phenyl triflate, a photoacid generator for photolithography, at 92 eV
Authors: Laffert V. , Sajjadian F. S. , Richter R. , van Setten M. J. , Holzmeier F. 
Published: April 2024

The dissociative photoionization of phenyl triflate (C6H5OSO2CF3), a neutral photoacid generator used in photolithography, was investigated in a gas phase experiment employing extreme ultraviolet (EUV) synchrotron radiation at 92 eV and photoelectron–photoion coincidence detection. The interaction of EUV photons with the molecule leads almost exclusively to dissociation, which is dominated by a sequential fragmentation mechanism, in which SO2, CF3, CO, and C2H2 are lost. For lithographic purposes, the lack of the observation of a fragment that could serve as a precursor for the formation of triflic acid means that the effective photoacid generator concentration in a photoresist is reduced, impacting its patterning performance in EUV lithography. A better understanding of the dissociative photoionization of photoresist components and proxies thereof can provide a crucial handle that guides the design of photoresists for the upcoming technology nodes with ever decreasing feature sizes for more powerful computer chips.
Rotating effects on the thermophysical properties of a two-dimensional GaAs quantum ring
Authors: Ghanbari Ahmad 
Published: April 2024

Abstract
In this work, we have investigated the rotating effect on the thermodynamic properties of a 2D quantum ring. Accordingly, we have considered the radial potential of a 2D quantum ring and solved the Schrödinger equation in the presence of the Aharonov–Bohm effect and a uniform magnetic field for the considered potential. According to the solution of the equation, we calculated the eigenvalues and eigenfunctions of the considered system. Using the calculated energy spectrum, we obtained the partition function and thermodynamic properties of the system, such as the mean energy, specific heat, entropy and free energy. Our results show that the rotating effect has a significant influence on the thermophysical properties of a 2D quantum ring. We also study other effects of the rotating term: (1) the effect of different values of rotating parameters, and (2) the effect of negative rotation on the thermodynamic properties of the system. Our results are discussed in detail.
Capture Efficiency Analysis in the Circular Restricted Three-body Problem
Authors: Miao Yu-Xuan , Hou Xi-Yun 
Published: April 2024

Abstract
Temporary capture efficiency is studied in the framework of the circular restricted three-body problem in two steps. First, a non-uniform distribution of test particles around the secondary’s orbit is obtained by fully accounting the secondary’s gravitational influence. Second, the capture efficiency is computed based on the non-uniform distribution. Several factors influencing the result are discussed. By studying the capture efficiency in the circular restricted three-body problem of different mass ratios, a power-law relation between the capture efficiency (p) and the mass ratio (μ) is established, which is given by p ≈ 0.27 × μ
0.53, within the range of 3.0035 ×10−6 ≤ μ ≤ 3.0034 × 10−5. Taking the Sun–Earth system as an example, the influence from the orbit eccentricity of the secondary on the non-uniform distribution and the capture efficiency is studied. Our studies find that the secondary’s orbit eccentricity has a negative influence on the capture efficiency.
The penetration depth of atomic radicals in tubes with catalytic surface properties
Authors: PAUL Domen , MOZETIČ Miran , ZAPLOTNIK Rok , VESEL Alenka , PRIMC Gregor , ÐONLAGIČ Denis 
Published: April 2024

Abstract
Catalysis of molecular radicals is often performed in interesting experimental configurations. One possible configuration is tubular geometry. The radicals are introduced into the tubes on one side, and stable molecules are exhausted on the other side. The penetration depth of radicals depends on numerous parameters, so it is not always feasible to calculate it. This article presents systematic measurements of the penetration depth of oxygen atoms along tubes made from nickel, cobalt, and copper. The source of O atoms was a surfatron-type microwave plasma. The initial density of O atoms depended on the gas flow and was 0.7×1021 m−3, 2.4×1021 m−3, and 4.2×1021 m−3 at the flow rates of 50, 300, and 600 sccm, and pressures of 10, 35, and 60 Pa, respectively. The gas temperature remained at room temperature throughout the experiments. The dissociation fraction decreased exponentially along the length of the tubes in all cases. The penetration depths for well-oxidized nickel were 1.2, 1.7, and 2.4 cm, respectively. For cobalt, they were slightly lower at 1.0, 1.3, and 1.6 cm, respectively, while for copper, they were 1.1, 1.3, and 1.7 cm, respectively. The results were explained by gas dynamics and heterogeneous surface association. These data are useful in any attempt to estimate the loss of molecular fragments along tubes, which serve as catalysts for the association of various radicals to stable molecules.
IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data
Authors: Gerault Marc-Antoine , Granjeaud Samuel , Camoin Luc , Nordlund Pär , Dai Lingyun 
Published: April 2024

Abstract
IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States—Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS.CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
SpatialcoGCN: deconvolution and spatial information–aware simulation of spatial transcriptomics data via deep graph co-embedding
Authors: Yin Wang , Wan You , Zhou Yuan 
Published: April 2024

Abstract
Spatial transcriptomics (ST) data have emerged as a pivotal approach to comprehending the function and interplay of cells within intricate tissues. Nonetheless, analyses of ST data are restricted by the low spatial resolution and limited number of ribonucleic acid transcripts that can be detected with several popular ST techniques. In this study, we propose that both of the above issues can be significantly improved by introducing a deep graph co-embedding framework. First, we establish a self-supervised, co-graph convolution network–based deep learning model termed SpatialcoGCN, which leverages single-cell data to deconvolve the cell mixtures in spatial data. Evaluations of SpatialcoGCN on a series of simulated ST data and real ST datasets from human ductal carcinoma in situ, developing human heart and mouse brain suggest that SpatialcoGCN could outperform other state-of-the-art cell type deconvolution methods in estimating per-spot cell composition. Moreover, with competitive accuracy, SpatialcoGCN could also recover the spatial distribution of transcripts that are not detected by raw ST data. With a similar co-embedding framework, we further established a spatial information–aware ST data simulation method, SpatialcoGCN-Sim. SpatialcoGCN-Sim could generate simulated ST data with high similarity to real datasets. Together, our approaches provide efficient tools for studying the spatial organization of heterogeneous cells within complex tissues.
Graphormer supervised de novo protein design method and function validation
Authors: Mu Junxi , Li Zhengxin , Zhang Bo , Zhang Qi , Iqbal Jamshed , Wadood Abdul , Wei Ting , Feng Yan , Chen Hai-Feng 
Published: April 2024

Abstract
Protein design is central to nearly all protein engineering problems, as it can enable the creation of proteins with new biological functions, such as improving the catalytic efficiency of enzymes. One key facet of protein design, fixed-backbone protein sequence design, seeks to design new sequences that will conform to a prescribed protein backbone structure. Nonetheless, existing sequence design methods present limitations, such as low sequence diversity and shortcomings in experimental validation of the designed functional proteins. These inadequacies obstruct the goal of functional protein design. To improve these limitations, we initially developed the Graphormer-based Protein Design (GPD) model. This model utilizes the Transformer on a graph-based representation of three-dimensional protein structures and incorporates Gaussian noise and a sequence random masks to node features, thereby enhancing sequence recovery and diversity. The performance of the GPD model was significantly better than that of the state-of-the-art ProteinMPNN model on multiple independent tests, especially for sequence diversity. We employed GPD to design CalB hydrolase and generated nine artificially designed CalB proteins. The results show a 1.7-fold increase in catalytic activity compared to that of the wild-type CalB and strong substrate selectivity on p-nitrophenyl acetate with different carbon chain lengths (C2–C16). Thus, the GPD method could be used for the de novo design of industrial enzymes and protein drugs. The code was released at https://github.com/decodermu/GPD.
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles
Authors: Wei Junkang , Xiao Jin , Chen Siyuan , Zong Licheng , Gao Xin , Li Yu 
Published: April 2024

Abstract
The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures poses a significant challenge for computational biology in leveraging structural information and accurate representation of protein surface properties. Recently, AlphaFold2 released the comprehensive proteomes of various species, and protein surface property representation plays a crucial role in protein-molecule interaction predictions, including those involving proteins, nucleic acids and compounds. Here, we proposed the first extensive database, namely ProNet DB, that integrates multiple protein surface representations and RNA-binding landscape for 326 175 protein structures. This collection encompasses the 16 model organism proteomes from the AlphaFold Protein Structure Database and experimentally validated structures from the Protein Data Bank. For each protein, ProNet DB provides access to the original protein structures along with the detailed surface property representations encompassing hydrophobicity, charge distribution and hydrogen bonding potential as well as interactive features such as the interacting face and RNA-binding sites and preferences. To facilitate an intuitive interpretation of these properties and the RNA-binding landscape, ProNet DB incorporates visualization tools like Mol* and an Online 3D Viewer, allowing for the direct observation and analysis of these representations on protein surfaces. The availability of pre-computed features enables instantaneous access for users, significantly advancing computational biology research in areas such as molecular mechanism elucidation, geometry-based drug discovery and the development of novel therapeutic approaches.
Database URL: https://proj.cse.cuhk.edu.hk/aihlab/pronet/.
Effects of different dietary lipid levels on physiological metabolism and odor quality of hepatopancreas in adult female Chinese mitten crab (Eriocheir sinensis)
Authors: Wu Jingjing , Zhang Long , Jiang Xiaodong , Wu Xugan , Wang Xichang 
Published: April 2024

Abstract

Objectives
This study aimed to investigate the impact of different dietary lipid levels on the physiological metabolism and odor quality of adult female Eriocheir sinensis during the fattening phase.

Materials and Methods
Five dietary schemes, each containing different total lipid levels (4%, 7%, 10%, 13%, and 16%), were administered over a 60-d fattening period for adult female crab (approximately 50 g, n=60). Chromatography and spectroscopy techniques were used for the detection of aroma and key aroma precursors.

Results
Dietary lipids had no significant effect on growth performance and hepatopancreas index (P&lt;0.05). The carotenoid content showed an increasing and then decreasing trend, with a significant increase to 1312.51 mg/kg (P&lt;0.05) at 7% lipid content of the diet. In contrast, a diet with a 13% lipid level led to a significant increase in total unsaturated fatty acids (115.3 mg/g, P&lt;0.05), which maximized the contents of major fatty acids (oleic, linoleic, and linolenic, among others), and presented a fluctuating trend. A diet with higher lipid levels (16%) inhibited fatty acid accumulation. Moreover, a 13% dietary lipid level enhanced characteristic aroma compounds (for example, nonanal, octanal, hexanal, 3-methylbutanal, and 2-heptanone) in E. sinensis cooked hepatopancreas. Through an orthogonal partial least squares discriminant analysis model, it becomes evident that lipids and carotenoids together promote aroma formation in hepatopancreas.

Conclusions
Based on the current findings, the optimal dietary lipid level for enhancing the odor quality of hepatopancreas in adult female E. sinensis during the fattening phase was 13%. This study provides more precise options for the high-quality cultivation of E. sinensis.
Quantitative genetic analysis of attractiveness of yeast products to Drosophila
Authors: Yan Weiru , Li Yishen , Louis Edward J , Kyriacou Charalambos P , Hu Yue , Cordell Rebecca L , Xie Xiaodong 
Published: April 2024

Abstract
An attractive perfume is a complex mixture of compounds, some of which may be unpleasant on their own. This is also true for the volatile combinations from yeast fermentation products in vineyards and orchards when assessed by Drosophila. Here, we used crosses between a yeast strain with an attractive fermentation profile and another strain with a repulsive one and tested fly responses using a T-maze. QTL analysis reveals allelic variation in four yeast genes, namely PTC6, SAT4, YFL040W, and ARI1, that modulated expression levels of volatile compounds [assessed by gas chromatography–mass spectrometry (GC–MS)] and in different combinations, generated various levels of attractiveness. The parent strain that is more attractive to Drosophila has repulsive alleles at two of the loci, while the least attractive parent has attractive alleles. Behavioral assays using artificial mixtures mimicking the composition of odors from fermentation validated the results of GC–MS and QTL mapping, thereby directly connecting genetic variation in yeast to attractiveness in flies. This study can be used as a basis for dissecting the combination of olfactory receptors that mediate the attractiveness/repulsion of flies to yeast volatiles and may also serve as a model for testing the attractiveness of pest species such as Drosophila suzukii to their host fruit.
Inhibition of DAPK3 Suppresses Radiation-Induced Cellular Senescence by Activation of a PGC1α-Dependent Metabolism Pathway in Brain Endothelial Cells
Authors: Park Ji-Eun , Park Jeong Woo , Sim Myong-Kyu , Kim So Ra , Kim Kwang Seok 
Published: April 2024

Abstract
In the brain, environmental changes, such as neuroinflammation, can induce senescence, characterized by the decreased proliferation of neurons and dendrites and synaptic and vascular damage, resulting in cognitive decline. Senescence promotes neuroinflammatory disorders by senescence-associated secretory phenotypes and reactive oxygen species. In human brain microvascular endothelial cells (HBMVECs), we demonstrate that chronological aging and irradiation increase death-associated protein kinase 3 (DAPK3) expression. To confirm the role of DAPK3 in HBMVEC senescence, we disrupted DAPK3 activity using small interfering RNA (siRNA) or a dominant-negative mutant (DAPK3-P216S), which reduced cellular senescence phenotypes, as assessed by changes in tube formation, senescence-associated beta-galactosidase activity, and cell proliferation. In endothelial cells, DAPK3 promotes cellular senescence by regulating the phosphorylation and inactivation of peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α) via the protein kinase B pathway, resulting in the decreased expression of mitochondrial metabolism-associated genes, such as ATP5G1, BDNF, and COX5A. Our studies show that DAPK3 is involved in cellular senescence and PGC1α regulation, suggesting that DAPK3 regulation may be important for treating aging-related brain diseases or the response to radiation therapy.
Base editing correction of OCRL in Lowe syndrome: ABE-mediated functional rescue in patient-derived fibroblasts
Authors: Chen Siyu , Lo Chien-Hui , Liu Zhiquan , Wang Qing , Ning Ke , Li Tingting , Sun Yang 
Published: April 2024

Abstract
Lowe syndrome, a rare X-linked multisystem disorder presenting with major abnormalities in the eyes, kidneys, and central nervous system, is caused by mutations in OCRL gene (NG_008638.1). Encoding an inositol polyphosphate 5-phosphatase, OCRL catalyzes the hydrolysis of PI(4,5)P2 into PI4P. There are no effective targeted treatments for Lowe syndrome. Here, we demonstrate a novel gene therapy for Lowe syndrome in patient fibroblasts using an adenine base editor (ABE) that can efficiently correct pathogenic point mutations. We show that ABE8e-NG-based correction of a disease-causing mutation in a Lowe patient-derived fibroblast line containing R844X mutation in OCRL gene, restores OCRL expression at mRNA and protein levels. It also restores cellular abnormalities that are hallmarks of OCRL dysfunction, including defects in ciliogenesis, microtubule anchoring, α-actinin distribution, and F-actin network. The study indicates that ABE-mediated gene therapy is a feasible treatment for Lowe syndrome, laying the foundation for therapeutic application of ABE in the currently incurable disease.
Naringin Alleviates Intestinal Fibrosis by Inhibiting ER Stress–Induced PAR2 Activation
Authors: Liu Jinguo , Xu Lei , Wang Li , Wang Qianqian , Yu Liangliang , Zhang Shuo 
Published: April 2024

Abstract
Fibrosis characterized by intestinal strictures is a common complication of Crohn’s disease (CD), without specific antifibrotic drugs, which usually relies on surgical intervention. The transcription factor XBP1, a key component of endoplasmic reticulum (ER) stress, is required for degranulation of mast cells and linked to PAR2 activation and fibrosis. Many studies have confirmed that naringin (NAR) can inhibit ER stress and reduce organ fibrosis. We hypothesized that ER stress activated the PAR2-induced epithelial-mesenchymal transition process by stimulating mast cell degranulation to release tryptase and led to intestinal fibrosis in CD patients; NAR might play an antifibrotic role by inhibiting ER stress–induced PAR2 activation. We report that the expression levels of XBP1, mast cell tryptase, and PAR2 are upregulated in fibrotic strictures of CD patients. Molecular docking simulates the interaction of NAR and spliced XBP1. ER stress stimulates degranulation of mast cells to secrete tryptase, activates PAR2-induced epithelial-mesenchymal transition process, and promotes intestinal fibrosis in vitro and vivo experiments, which is inhibited by NAR. Moreover, F2rl1 (the coding gene of PAR2) deletion in intestinal epithelial cells decreases the antifibrotic effect of NAR. Hence, the ER stress–mast cell tryptase–PAR2 axis can promote intestinal fibrosis, and NAR administration can alleviate intestinal fibrosis by inhibiting ER stress–induced PAR2 activation.