bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure, physicochemical properties, and biological activities of protein hydrolysates from Zanthoxylum seed
Authors: Dong Si‐Yu , Li Ying‐Qiu , Sun Xin , Sun Gui‐Jin , Wang Chen‐Ying , Liang Yan , Hua Dong‐Liang , Chen Lei , Mo Hai‐Zhen 
Published: December 2023

AbstractBACKGROUNDZanthoxylum seed, as a low‐cost and easily accessible plant protein resource, has good potential in the food industry. But protein and its hydrolysates from Zanthoxylum seed are underutilized due to the dearth of studies on them. This study aimed to investigate the structure and physicochemical and biological activities of Zanthoxylum seed protein (ZSP) hydrolysates prepared using Protamex®, Alcalase®, Neutrase®, trypsin, or pepsin.RESULTSHydrolysis using each of the five enzymes diminished average particle size and molecular weight of ZSP but increased random coil content. ZSP hydrolysate prepared using pepsin had the highest degree of hydrolysis (24.07%) and the smallest molecular weight (<13 kDa) and average particle size (129.80 nm) with the highest solubility (98.9%). In contrast, ZSP hydrolysate prepared using Alcalase had the highest surface hydrophobicity and foaming capacity (88.89%), as well as the lowest foam stability (45.00%). Moreover, ZSP hydrolysate prepared using Alcalase exhibited the best hydroxyl‐radical scavenging (half maximal inhibitory concentration (IC50) 1.94 mg mL−1) and ferrous‐ion chelating (IC50 0.61 mg mL−1) activities. Additionally, ZSP hydrolysate prepared using pepsin displayed the highest angiotensin‐converting enzyme inhibition activity (IC50 0.54 mg mL−1).CONCLUSIONThese data showed that enzyme hydrolysis improved the physicochemical properties of ZSP, and enzymatic hydrolysates of ZSP exhibited significant biological activity. These results provided validation for application of ZSP enzymatic hydrolysates as antioxidants and antihypertensive agents in the food or medicinal industries. © 2023 Society of Chemical Industry.
Characteristics of microplastics in dryland soils after long‐term film mulching and the effect of cropping type in western Liaoning Province, China
Authors: Luo Qing , Zhang Xinyu , Wang Congcong , Yang Ning , Sun Zhanxiang , Feng Liangshan 
Published: December 2023

AbstractMicroplastic (MP) pollution poses a significant environmental challenge on a global scale. In the semi‐arid region of western Liaoning, China, agricultural films have been widely utilized to enhance crop production over an extended period. However, there is a scarcity of research on the presence of MPs in the soil of farmlands in this area. Consequently, a total of 25 dryland soil samples from western Liaoning that had been mulched for more than 10 years and had been used to grow a variety of crops were gathered for the current study. The abundance, particle size, shape, and potential sources of MPs were examined, and the impact of different crop varieties on MPs characteristics was investigated. MPs abundance ranged from 6960 ± 1939 to 34,710 ± 9974 n kg−1, with the average and median of 14,305 ± 7015 and 12,270 ± 1621 n kg−1. MPs with sizes of less than 0.05, 0.05–0.1, and 0.1–0.4 mm were found in 42.7%, 33.8%, and 18.8% of cases, respectively. The most common shapes were fragments, microbeads, and films, with percentages of 47.1%, 22.3%, and 17.9%, respectively. A total of three polymers were found: polyethylene, polypropylene, and polystyrene in a proportion of 44.8%, 43.7%, and 11.5%, respectively. Based on the shape of the MPs, principal component analysis and cluster analysis revealed that the primary sources for MPs may be agricultural mulch, irrigation water, and the weathering of hard plastics like agricultural packaging. Compared to other crop types, soils growing sweet potato and peanut had significantly higher MP abundances. Moreover, soils growing sweet potato had significantly higher percentages of MPs with 0.05–0.1 mm particle size. Regardless of the crop type grown, fragments are the most common shape, while the proportion of other shapes varies depending on the crop type. The aforementioned findings suggest that MP pollution in farmland soil in western Liaoning is more severe and that the kind of crop cultivation affects the characteristics of MPs in the soil.
Novel insights into HBV‐hepatocellular carcinoma at single‐cell sequencing
Authors: Yin Dandan , Zhou Tao , Xia Xuyang , Han Chang , Liu Zhaoqian , Li Qiu , Shu Yang , Xu Heng 
Published: December 2023

AbstractA significant proportion of hepatocellular carcinoma (HCC) is pathologically associated with hepatitis B virus (HBV) infection, followed by unsatisfied clinical outcomes. The increasing unmet need for HBV‐associated hepatocellular carcinoma (HBV‐HCC) treatment drives to deeper understand the role of the intricate immune microenvironment, tumor cell plasticity and dynamics of tumor evolution in HBV‐associated hepatic carcinogenesis. Thus, a comprehensive understanding of cross‐talk between HBV, host cells, and tumor microenvironment is of fundamental importance for identifying immune imbalance and heterogeneity in HBV‐HCC. Over the past 5 years, the application of single‐cell RNA sequencing (scRNA‐seq) in the understanding of heterogeneity and dynamics of immune cells, clonal evolution, and cancer stem cell (CSC) subsets of tumor cells has established a landscape for HBV‐HCC tumor ecosystem. Novel insights into anatomizing immune escape mechanisms and tumor drug resistance have remarkably facilitated the revolution of HBV‐HCC clinical treatment. Here, we provided a summary of HCC at single‐cell resolution and details on the basic workflow, limitations, and improvements of scRNA‐seq. The review highlights novel insights derived from scRNA‐seq on advances in the immune microenvironment and tumor heterogeneity of HBV‐HCC.
Mechanical response of concrete pipe rehabilitated by liner under external load: Analytical solution
Authors: Zhai Kejie , Fang Hongyuan , Wang Niannian , Li Bin , Dong Jiaxiu , Xue Binghan 
Published: December 2023

AbstractUsing pipe lines to rehabilitate concrete drainage pipes is a popular trenchless technique. In this paper, the concrete pipe and liner are equivalent to a symmetrical structural mechanics problem, and the mechanical solution of the composite structure is obtained using the force method. Subsequently, the analytical solutions are compared with the test and finite element results. The distribution law of axial force, bending moment, and shear force of the composite structure are obtained, and the circumferential strain law of the inner and outer surfaces of the host pipe is analyzed. Lastly, the influence of pipe diameter and liner thickness on the bearing capacity of the host pipe is examined. The results indicate that the axial and shear force distribution of the composite structure remains the same for different pipe diameters, as the distribution diagrams of shear and axial force along the circumferential direction coincide. While the elastic modulus and thickness of the liner have no effect on the internal force distribution of the composite structure, they do directly affect the stress state of the host pipe. Additionally, the bottom support causes abrupt changes in the bending moments and strains of the host pipe.
Museum experience and its impact on visitor reactions
Authors: Addis Michela , Copat Valentina , Martorana Cecilia 
Published: December 2023

AbstractDesigning engaging visitor experiences has become a paramount concern for museums; however, a comprehensive understanding of the impact of museum experiences on visitors' reactions remains incomplete. Our paper aims to assist museums in implementing more effective strategies. By examining three distinct characteristics of museum experiences—subjectivity, multidimensionality, and co‐creation—we formulate four hypotheses to assess the influence of visitor journeys on their reactions. We concentrate on the journey at the Capitoline Museums, employing qualitative and quantitative methods (in‐depth interviews, subjective personal introspection, non‐participant observation, and questionnaires) involving 110 participants. Our findings indicate that (a) Visitor attitudinal and behavioral reactions exhibit consistency for the overall experience but not when analyzed for specific areas; (b) Visitor satisfaction is correlated with the number of companions but not with the number of visited areas in the museum experience; (c) Visitor's apparent dominance over visitor satisfaction is not linked to visitor satisfaction. We develop a managerial decision‐making framework that empowers museums to create captivating experiences for their visitors.
Control‐oriented models of the shallow water equations using energy‐conserving discretization schemes
Authors: Mayer Luca , Wurm Jens , Woittennek Frank 
Published: December 2023

AbstractIn this study, we introduce higher‐order approximation schemes for a 1D shallow‐water model with a moving boundary and arbitrary cross‐section. The model equations are formulated using Lagrange coordinates to handle the time‐varying spatial domain. By discretizing the action functional on a material‐fixed grid and applying an appropriate quadrature scheme, we derive a finite‐dimensional model. This model, taking mass conservation into account as an auxiliary condition, results in a system of semi‐explicit differential‐algebraic equations (DAE). Unlike previous work, we employ higher‐order quadrature formulae to enhance numerical accuracy, albeit at the cost of more complex nonlinear DAE. In order to compare the performance of the resulting models obtained from using different quadrature schemes, a comprehensive simulation study is conducted.
Soybean oil‐based nanocomposites for dye adsorption: AESO‐chitosan‐graphene oxide synergy in water treatment
Authors: Dare Masoud Tavakoli , Bazmi Maryam , Khosravi Amirhosein , Monem Mohammad , Jafari Aliakbar , Khonakdar Hossein Ali 
Published: December 2023

AbstractThis study presents the synthesis and characterization of a bio‐adsorbent (A‐C2‐G3) based on the acrylated epoxidized soybean oil (AESO) for the efficient removal of methylene blue (MB) dye from aqueous solutions. The adsorbent was synthesized by incorporating chitosan and nano graphene oxide into the AESO matrix, followed by crosslinking through the UV curing process. The effects of various parameters, including pH, contact time, initial dye concentration, adsorbent dosage, and ionic strength, on the adsorption performance were systematically investigated. The experimental data were best fitted by the Langmuir isotherm model, suggesting a monolayer adsorption process, with a maximum adsorption capacity of 263.87 mg g−1. The adsorption kinetics followed the pseudo‐second‐order model, indicating the significance of electron exchange between the adsorbate and adsorbent during the process. Three primary interaction mechanisms at the interface between MB and A‐C2‐G3 and the A‐C2‐G3 bio‐adsorbent were identified: electrostatic interactions, hydrogen bond formation, and π–π stacking. The reusability of the synthesized adsorbent was evaluated through a series of adsorption–desorption cycles, maintaining high adsorption capacities for up to three cycles. These findings highlight the potential of the AESO‐based bio‐adsorbent for effective MB dye removal from wastewater.
Assessing computational tools for predicting protein stability changes upon missense mutations using a new dataset
Authors: Zheng Feifan , Liu Yang , Yang Yan , Wen Yuhao , Li Minghui 
Published: December 2023

AbstractInsight into how mutations affect protein stability is crucial for protein engineering, understanding genetic diseases, and exploring protein evolution. Numerous computational methods have been developed to predict the impact of amino acid substitutions on protein stability. Nevertheless, comparing these methods poses challenges due to variations in their training data. Moreover, it is observed that they tend to perform better at predicting destabilizing mutations than stabilizing ones. Here, we meticulously compiled a new dataset from three recently published databases: ThermoMutDB, FireProtDB, and ProThermDB. This dataset, which does not overlap with the well‐established S2648 dataset, consists of 4038 single‐point mutations, including over 1000 stabilizing mutations. We assessed these mutations using 27 computational methods, including the latest ones utilizing mega‐scale stability datasets and transfer learning. We excluded entries with overlap or similarity to training datasets to ensure fairness. Pearson correlation coefficients for the tested tools ranged from 0.20 to 0.53 on unseen data, and none of the methods could accurately predict stabilizing mutations, even those performing well in anti‐symmetric property analysis. While most methods present consistent trends for predicting destabilizing mutations across various properties such as solvent exposure and secondary conformation, stabilizing mutations do not exhibit a clear pattern. Our study also suggests that solely addressing training dataset bias may not significantly enhance accuracy of predicting stabilizing mutations. These findings emphasize the importance of developing precise predictive methods for stabilizing mutations.
Predicting the functional state of protein kinases using interpretable graph neural networks from sequence and structural data
Authors: Ravichandran Ashwin , Araque Juan C. , Lawson John W. 
Published: December 2023

AbstractProtein kinases are central to cellular activities and are actively pursued as drug targets for several conditions including cancer and autoimmune diseases. Despite the availability of a large structural database for kinases, methodologies to elucidate the structure–function relationship of these proteins (without manual intervention) are lacking. Such techniques are essential in structural biology and to accelerate drug discovery efforts. Here, we implement an interpretable graph neural network (GNN) framework for classifying the functionally active and inactive states of a large set of protein kinases by only using their tertiary structure and amino acid sequence. We show that the GNN models can classify kinase structures with high accuracy (>97%). We implement the Gradient‐weighted Class Activation Mapping for graphs (Graph Grad‐CAM) to automatically identify structurally important residues and residue‐residue contacts of the kinases without any a priori input. We show that the motifs identified through the Graph Grad‐CAM methodology are functionally critical, consistent with the existing kinase literature. Notably, the highly conserved DFG and HRD motifs of the well‐known hydrophobic spine are identified by the interpretable framework in addition to some of the lesser known motifs. Further, using Grad‐CAM maps as the vector embedding of the protein structures, we identify the subtle differences in the crystal structures among different sub‐classes of kinases in the Protein Data Bank (PDB). Frameworks such as the one implemented here, for high‐throughput identification of protein structure–function relationships are essential in designing targeted small molecules therapies as well as in engineering new proteins for novel applications.
Metameric influences on conformational selectivity for zwitterionic pyridinium cyclopentadienide and its aza analogues. Quantum mechanical studies on linear and nonlinear optoelectronic properties
Authors: Sitha Sanyasi 
Published: December 2023

AbstractThis contribution reports the structure–property correlations for few already synthesized bi‐aryl types of zwitterionic molecules. Quantum mechanical methodologies like, HF, MP2, B3LYP, CAM‐B3LYP, LC‐ωPBE, M06‐2X, and ωB97xD were used to investigate the optoelectronic properties of some interesting metameric pairs, where the molecules were bonded either through Reichardt's or Brooker's modes. Different bonding modes and inter‐ring attractive forces are assigned to investigate three distinct cases (i) metameric enforcements & preferential resonance stabilizations, (ii) inter‐ring hydrogen bonded stabilizations through hetero‐atoms in the ring, and (iii) an amalgamation of these two forces. Computations indicate unusual structural preferences (planar vs. twisted) by the metameric pairs, and thus direct reflections of these behaviors on some of the important tensorial properties like, dipole moments, polarizabilities, hyperpolarizabilities, and so forth were observed. The metameric manipulation on structure–property correlations shown by these molecules can be utilized as useful strategies for efficient chromophore design, not only in the field of nonlinear optics, but also in other areas of research connecting to advanced functional materials for technological applications.
A fast, accurate and uncalibrated robotic puncture method
Authors: Li ShangHong , Wang Qiwan , Yan Biao , Yang Rongqian , Zhan Yinwei 
Published: December 2023

AbstractBackgroundRobotic puncture system (RPS) consists of an optical tracking system (OTS) and a robotic arm gripping the puncture needle. Typically, the RPS requires hand‐eye calibration before the surgery in order to obtain the relative position between the OTS and the robotic arm. However, if there is any displacement or angular deviation in either the robotic arm or the OTS, the calibration results become invalid, necessitating recalibration.MethodsWe propose an uncalibrated robotic puncture method that does not rely on the hand‐eye relationship of the RPS. By constructing angle and position graph jacobian matrices respectively, and employing Square Root Cubature Kalman Filter for online estimation. This enables obtaining control variables for the robot to perform puncture operations.ResultsIn simulation experiments, our method achieves an average error of 1.3495 mm and an average time consumption of 39.331 s.ConclusionsExperimental results indicate that our method possesses high accuracy, low time consumption, and strong robustness.
The changing epidemiology of preterm labour and delivery: A systematic literature review
Authors: Li Tina , Rochon Hannah , Szabo Shelagh M. , Kourmaeva Emilia , Manuel Megan , Patel Vanessa Perez 
Published: December 2023

AbstractObjectiveTo identify and synthesize epidemiologic data for preterm labour (PTL) and preterm birth (PTB).MethodsA systematic search, with protocol registered in PROSPERO, was implemented in MEDLINE and EMBASE and supplemented by web‐based and grey literature searches. Observational, population‐based studies in the United States, Canada, United Kingdom, France, Germany, Spain, and Italy, published in English between 2012 and 2022 were considered for inclusion. Estimates by country were reported and stratified by gestational age, birth plurality, and race/ethnicity, data permitting.ResultsTen publications and nine grey literature reports were included. Epidemiologic estimates of PTL were reported for the United Kingdom and France: PTL was diagnosed in 2.2% of pregnancies and preceded 50% of PTBs. PTB rates were reported for the United States, Canada, United Kingdom, France, and Spain. Among live births in these countries, annual PTB incidence ranged from 5.9% (Spain, 2020) to 10.2% (United States, 2019). Most countries reported the PTB incidence by gestational age; reports by birth plurality or race/ethnicity were scarce. PTB rates for Germany or Italy were not identified.ConclusionsWhile PTBs were well‐reported overall and by gestational age, how rates varied by plurality, race/ethnicity and etiology is unclear. Epidemiologic estimates for PTL, a leading cause of PTB, were rarely reported in the literature. Population‐based research is needed to understand the burden of PTL and for decision making regarding the management of this condition.
Revealing cation and metal gradients in and underneath passive films of the stainless steel 1.4652 in acidic and alkaline electrolytes with angular resolved dual energy X‐ray photo‐electron spectroscopy
Authors: Olsson Claes‐Olof A. , Hauert Roland , Neus Igual‐Muñoz Anna , Mischler Stefano , Schmutz Patrik 
Published: December 2023

AbstractPassive films on the superaustenitic stainless steel 1.4652 were studied using angular resolved hard X‐ray photo‐electron spectroscopy (HAXPES), which provides an increased information depth compared to conventional X‐ray photo‐electron spectroscopy (XPS). Elemental depth profiles in the oxide as well as gradients in the underlying metal were established using a dedicated algorithm. The utility was exemplified for three different conditions of film formation: (i) as polished and as polarized to the high passive end in (ii) 1 M H2SO4 and (iii) 1 M NaOH. The use of a superaustenitic material ascertained that metal signals from the main contributors to film formation: Fe, Cr, Ni, and Mo remained above the detection limit throughout the data set. With the dual‐source technique (XPS, HAXPES), it was possible to investigate metal gradients underneath the passive film. For polarizations in an acidic environment, a metallic nickel enrichment of the order of 5 Å was found. For a corresponding polarization in an alkaline environment, the metal region closest to the oxide/metal interface was enriched in iron, followed by concentration gradients down to about 50 Å into the metal.
Interface‐Guided Computational Protein Design Reveals Bebtelovimab‐Resistance Mutations in SARS‐CoV‐2 RBD: Correlation with Global Viral Genomes and Bebtelovimab‐Escape Mutations
Authors: Maurya Shweata , Kumar Shivank , Padhi Aditya K. 
Published: December 2023

AbstractThe emergence of novel mutations in the SARS‐CoV‐2 spike protein challenges monoclonal antibody (mAb) effectiveness. Comprehending resistance mutations and pinpointing vulnerable spike protein residues is vital for enhanced antibody design. To address this issue, we employed an interface‐guided computational protein design (CPD) approach to decode bebtelovimab‐resistance mutations and uncover susceptible residues within the receptor‐binding domain (RBD). Utilizing structural‐modeling and high‐throughput techniques, we mapped the bebtelovimab‐RBD interface, identifying critical resistance mutations through analysis of binding energetics and residue interactions. Our design protocol integrated stability predictions, side‐chain conformational sampling, and binding affinity calculations to prioritize substitutions that restore antibody recognition and neutralization. Previously unexplored susceptible RBD residues were also discovered, offering new therapeutic avenues. Comparative analysis with COVID‐19 patient data validated the predicted resistance mutations (69 %–100 % correlation, based on different MinProp cut‐offs). Precision and recall values, calculated by comparing our predictions with experimentally reported bebtelovimab‐escape mutants, demonstrated the performance and accuracy of our predictions. Investigation of intermolecular interactions highlighted the importance of van der Waals forces, hydrogen bond energy, and electrostatic contributions in bebtelovimab‐RBD binding affinity. This computational design empowers the decoding of resistance mutations and the development of next‐generation antibodies against viral variants, strengthening our response to SARS‐CoV‐2 and related coronaviruses.