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Up to now, three-dimensional temperature responses in mid-latitude shallow shelf seas to large-scale climate variabilities are still poorly understood. Combining observations and high-resolution numerical simulations, this study investigated the three-dimensional structure of interannual-to-decadal variations in water temperature in the Yellow Sea and underlying mechanisms during 1998‒2021. Both sea surface temperature (SST) and bottom layer temperature (BLT) in the majority of the Yellow Sea experienced decadal trends, which were negative during 1998‒2010 but were more significantly positive during 2011‒2021. Magnitudes of decadal SST trends had seasonal variations, being much larger in winter than in summer, but those of decadal BLT trends had no significant seasonal variations. Temperatures below the thermocline experienced more significant decadal trends than SST in spring‒summer seasons. This caused increasing trends during 1998‒2010 but decreasing trends during 2011‒2021 in summer stratification. Changes in decadal temperature trends were linked to activities of the Siberia High and Western Pacific pattern in winter. During 1998‒2010, strengthening Siberia High and weakening Western Pacific pattern enhanced surface heat loss and thus induced cooling trend throughout the water column in the Yellow Sea in winter. However, increasing surface heat gain in subsequent spring‒summer reduced the surface layer cooling trend and resulted in upper layer experiencing weaker cooling trend than lower layer. Seasonally reversing surface heat flux trends generated increasing summer stratification. During 2011‒2021, opposite but more intense situations occurred, with weakening Siberia High and strengthening Western Pacific pattern causing warming temperature and decreasing summer stratification in the Yellow Sea. [ABSTRACT FROM AUTHOR]

Abstract Cell therapy has emerged as a viable approach for treating damaged organs or tissues, particularly with advancements in stem cell research and regenerative medicine. The innovative technique of cell sheet engineering offers the potential to create a cell-dense lamellar structure that preserves the extracellular matrix (ECM) secreted by cells, along with the cell-matrix and intercellular junctions formed during in vitro cultivation. In recent years, significant progress has been made in developing cell sheet engineering technology. A variety of novel materials and methods were utilized for enzyme-free cell detachment during the cell sheet formation process. The complexity of cell sheet structures increased to meet advanced usage demands. This review aims to provide an overview of the preparation methods and types of cell sheets, thereby enhancing the understanding of this rapidly evolving technology and offering a fresh perspective on the development and future application of cell sheet engineering. Graphical Abstract

Zinc transporters (ZnTs) act as H+/Zn2+ antiporters, crucial for zinc homeostasis. Brain‐specific ZnT3 expressed in synaptic vesicles transports Zn2+ from the cytosol into vesicles and is essential for neurotransmission, with ZnT3 dysfunction associated with neurological disorders. Ubiquitously expressed ZnT4 localized to lysosomes facilitates the Zn2+ efflux from the cytosol to lysosomes, mitigating the cell injury risk. Despite their importance, the structures and Zn2+ transport mechanisms remain unclear. We characterized the three‐dimensional structures of human ZnT3 (inward‐facing) and ZnT4 (outward‐facing) using cryo‐electron microscopy. By combining these structures, we assessed the conformational changes that could occur within the transmembrane domain during Zn2+ transport. Our results provide a structural basis for a more comprehensive understanding of the H+/Zn2+ exchange mechanisms exhibited by ZnTs. [ABSTRACT FROM AUTHOR]

There is a long history of using VHF radar systems to detect ionospheric irregularities based on the theory of coherent scattering. According to previous work, there is a high occurrence of field-aligned irregularities (FAIs) in the ionospheric E-region over Kunming, China. In this paper, the VHF coherent scattering radar at Kunming is used to study the FAIs in the ionospheric E-region. Different arrangement of VHF radar antenna arrays, interferometry, and FAI echo parameter inversion methods are designed and tested. The measurement results show that the temporal and spatial characteristics of the irregularities can be obtained using these methods, as well as more refined spatial three-dimensional structure information. It is indicated that the new arrangement of the VHF radar antenna array is feasible to operate interferometry detection of E-region FAIs with the Kunming VHF radar. [ABSTRACT FROM AUTHOR]

The growth of bacteria and fungi may cause disease inf human or spoilage of food. New antimicrobial substances need to be discovered. Lactoferricin (LFcin) is a group of antimicrobial peptides derived from the N-terminal region of the milk protein lactoferrin (LF). LFcin has antimicrobial ability against a variety of microorganisms, which is significantly better than that of its parent version. Here, we review the sequences, structures, and antimicrobial activities of this family and elucidated the motifs of structural and functional significance, as well as its application in food. Using sequence and structural similarity searches, we identified 43 new LFcins from the mammalian LFs deposited in the protein databases, which are grouped into six families according to their origins (Primates, Rodentia, Artiodactyla, Perissodactyla, Pholidota, and Carnivora). This work expands the LFcin family and will facilitate further characterization of novel peptides with antimicrobial potential. Considering the antimicrobial effect of LFcin on foodborne pathogens, we describe the application of these peptides from the prospective of food preservation. [ABSTRACT FROM AUTHOR]

Hydroxides of nickel-cobalt have been widely employed as supercapacitor electrode materials. However, the shortcomings such as a low specific surface and an unstable structure made it difficult to display an excellent electrochemical performance. To address the said problems, carbon fibers were grown in situ on foam nickel by CVD method to prepare a three-dimensional foam nickel/carbon fiber composite collector, and then nickel-cobalt hydroxides were obtained on the composite current collector by a hydrothermal method with the aim of a superior supercapacitor electrode material (CF/Ni–Co). Effects of anions of metal salts (such as acetate, nitrate, sulfate and chloride) on the morphology, structure and electrochemical performance of the obtained electrodes were investigated. The results suggested that the sample CF/Ni–Co(SO4) synthesized with nickel sulfate and cobalt sulfate possessed large specific surface area. It also displayed outstanding capacitive performance with a superb specific capacitance of 3675.6 F/g at 1 A/g, a high capacitance retention rate of 70.6% as the current density increased to 15 A/g, and a good cycling stability of 66.4% after 2000 cycles of charge-discharge at 15 A/g, demonstrating CF/Ni–Co(SO4) with the three-dimensional nickel foam/carbon fiber composite as current collector had great potential for high-performance supercapacitor electrode materials. [ABSTRACT FROM AUTHOR]

Copyright of Rare Metals is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Cell therapy has emerged as a viable approach for treating damaged organs or tissues, particularly with advancements in stem cell research and regenerative medicine. The innovative technique of cell sheet engineering offers the potential to create a cell-dense lamellar structure that preserves the extracellular matrix (ECM) secreted by cells, along with the cell-matrix and intercellular junctions formed during in vitro cultivation. In recent years, significant progress has been made in developing cell sheet engineering technology. A variety of novel materials and methods were utilized for enzyme-free cell detachment during the cell sheet formation process. The complexity of cell sheet structures increased to meet advanced usage demands. This review aims to provide an overview of the preparation methods and types of cell sheets, thereby enhancing the understanding of this rapidly evolving technology and offering a fresh perspective on the development and future application of cell sheet engineering. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Harbin Institute of Technology. Social Sciences Edition / Haerbin Gongye Daxue Xuebao. Shehui Kexue Ban is the property of Harbin Institute of Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The superfamily of acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the structural catalytic core (SCC), which is conserved within each family of acid proteases, but varies between families, and thus can serve as a structural marker of four individual protease families. The SCC is a dimer of several structural blocks, such as the DD-link, D-loop, and G-loop, around two catalytic aspartates in each protease subunit or an individual chain. A dimer made of two (D-loop + DD-link) structural elements makes a DD-zone, and the D-loop + G-loop combination makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation, and protein engineering. [ABSTRACT FROM AUTHOR]

The wicking effect constitutes a pivotal determinant in facilitating the ingress and transference of liquid water within yarns and fabrics. Its significance looms prominently in the context of subsequent product processing, particularly concerning the immersion and interface bonding of textile matrix composites. The twist exerts profound influence over the fiber disposition and density within yarns, as well as the yarn and the wicking pathways for liquid water. We use a mathematical model grounded in the three-dimensional helical capillary permeation mechanism, inherently linked to the twist factor. This model operates under the assumption that the yarn's fibers exhibit uniform diameters and arrangements. Leveraging the macroscopic force equilibrium method, a function of liquid capillary rise with wicking time was deduced. and the dynamic progression of liquid water ascent within the yarn was simulated using the COMSOL platform. Subsequently, a series of wicking experiments were executed on polyester filament yarns, each characterized by varying twist levels. The results revealed that the experimental data coincided well with the theoretical prediction, thus affirming the model's accuracy. [ABSTRACT FROM AUTHOR]

Abstract Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already exist that can visualize molecules, and customize these visualizations, in many ways. However, software packages that can output projected 3D models onto a 2D canvas directly as SVG, while being programmatically accessible from Python, are lacking. Here, we introduce CineMol, which can draw vectorized approximations of three-dimensional small molecule models in seconds, without triangulation or ray tracing, resulting in files of around 50–300 kilobytes per molecule model for compounds with up to 45 heavy atoms. The SVGs outputted by CineMol can be readily modified in popular vector graphics editing software applications. CineMol is written in Python and can be incorporated into any existing Python cheminformatics workflow, as it only depends on native Python libraries. CineMol also provides programmatic access to all its internal states, allowing for per-atom and per-bond-based customization. CineMol’s capacity to programmatically create molecular visualizations suitable for post-production offers researchers and scientists a powerful tool for enhancing the clarity and visual impact of their scientific presentations and publications in cheminformatics, metabolomics, and related scientific disciplines. Scientific contribution We introduce CineMol, a Python-based tool that provides a valuable solution for cheminformatics researchers by enabling the direct generation of high-quality approximations of two-dimensional SVG visualizations from three-dimensional small molecule models, all within a programmable Python framework. CineMol offers a unique combination of speed, efficiency, and accessibility, making it an indispensable tool for researchers in cheminformatics, especially when working with SVG visualizations.

In order to understand the active mesoscale processes in the Kuroshio extension (KE) region, and reveal the three-dimensional structure of mesoscale eddies in this region, as well as the contributions of mesoscale eddies to water mass redistribution and ocean-atmosphere interactions, based on shipboard observations and satellite remote sensing data, this study investigates the three-dimensional structural characteristics of a typical eddy dipole composed of cyclonic eddy (CE) and an anticyclonic eddy (AE) distributed on the north and south sides of the KE axis, respectively, during June-July 2022. Results show that the CE has a southward cross-frontal motion dominated by shear forcing, while the AE remains relatively stable. The "cold tongue" structure of the CE gradually diminishes due to sea surface warming and heat diffusion from the KE axis, with the AE exhibiting a "reverse eddy sea surface temperature anomaly" structure due to the entrainment of cold water carried by the CE. The vertical multi-cores of internal temperature and salinity anomalies in the eddy dipole are related to the vertical redistribution of water masses with different characteristics. The AE's internal flow field is strongly baroclinic, with around 50% of it having a Richardson number less than the critical value of 0.25, indicating a tendency for turbulent mixing. The upper layer of the CE is barotropic, hindering substantial diapycnal mixing. This study helps to enhance understanding of the eddy dipole characteristics and internal structure of eddies in the KE region, providing information for further research on eddy dynamics. [ABSTRACT FROM AUTHOR]

Periodic eddies are a type of eddy that occur almost annually in fixed timeframes with similar patterns and trajectories. Nearly every year from April to June, under the combined effect of the barotropic instability of the mean flow and wind work, a cyclonic eddy (the Taiwan Cyclonic Eddy, TCE) forms in the southwest of Taiwan, then propagates westward, and finally dissipates near the Dongsha Islands. TCE exerts a significant impact on the Kuroshio intrusion into the South China Sea (SCS) and water exchange. Based on multi‐year in situ and satellite observations, this study reveals the thermohaline structure and evolutionary process of the TCE. The evolutions of the three‐dimensional structures of temperature, salinity, and geostrophic velocity of the TCE are analyzed based on reconstructed data. The TCE shows important interannual variations associated with El Niño–Southern Oscillation (ENSO), and the relationship between ENSO and the TCE is modulated by the Pacific Decadal Oscillation (PDO). In the negative phase of the PDO, the intensity of the TCE is significantly correlated with the Niño‐3.4 index. In contrast, in the positive phase, the ENSO–TCE relationship becomes weak and non‐significant. Further investigations indicate that these differences are related to the establishment of the low‐latitude Pacific–East Asian Teleconnection, influencing local wind stress curl in the region. This offers a new perspective on understanding the interannual variation of periodic mesoscale eddies in the SCS. Plain Language Summary: The Taiwan Cyclonic Eddy (TCE) represents a significant periodic mesoscale eddy in the South China Sea (SCS), demonstrating annual occurrences and profound impacts on regional oceanography and climatological dynamics. This study expands on multi‐year in situ and satellite observations to elaborate the three‐dimensional thermohaline structure and dynamic behavior of the TCE, emphasizing its seasonal consistency and interannual variability influenced by major climatic oscillations such as El Niño–Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO). The TCE's formation is primarily driven by the instability of the background current and significant wind forcing. Its interannual variation shows a non‐stationary relationship with ENSO, which is significantly modulated by the PDO. The study enhances our understanding of the interannual dynamics of the TCE by highlighting how shifts in large‐scale climatic conditions can directly alter the local structural and dynamic characteristics of the eddy. Understanding the TCE's formation and variation is vital as it affects water exchange in the SCS, and thus influences local marine ecosystems in the region. By studying this phenomenon, scientists can better predict the impacts of such eddies on marine and climatic environments. Key Points: The Taiwan Cyclonic Eddy (TCE) forms annually from April to June southwest of Taiwan due to current instability and wind forcingMulti‐year observations show the TCE has significant vertical extensions and temperature/salinity anomalies, impacting local conditionsThe TCE's evolution is tied to El Niño–Southern Oscillation and influenced by Pacific Decadal Oscillation phases, being stronger in negative phases due to enhanced teleconnections and wind adjustments [ABSTRACT FROM AUTHOR]

Mesoscale eddies are known to enhance diapycnal mixing in the ocean, yet direct observation of this effect remains a significant challenge, especially in the robust Antarctic Circumpolar Current (ACC). To quantify the diapycnal mixing induced by mesoscale eddies in the standing meander of the ACC, satellite altimeter and Argo profile data were combined to composite eddies, where the 1.6 m dynamic height contour was used for the first time instead of the climatological Northern Sub-Antarctic Front (SAFN) to define the northern boundary of the ACC to eliminate the influence of frontal shift. The 3D structures of the composite anticyclonic/cyclonic eddy (CAE/CCE) were obtained. Both the CAE and CCE were similar in shape to Taylor columns, from sea surface to the neutral surface of 28.085 kgm − 3 (1689 ± 66 dbar) for the CAE, and from sea surface to 28.01 kgm − 3 (1491 ± 202 dbar) for the CCE. On the same neutral surface, the diffusivity (κ) inside the CCE was one to two orders of magnitude higher than that inside the CAE. Vertically, the maximum influence depth of the CCE on κ reached 1200 dbar, while for the CAE, it reached 800 dbar, where κ exceeded O (10 − 4)   m 2 s − 1 , and κ gradually decreased from these depths downwards. [ABSTRACT FROM AUTHOR]

The growth and development of embryophytes is deeply influenced by environmental stimuli, such as light, temperature, and soil nutrients. Understanding the mechanisms underlying the growth response of plants to environmental stimuli is crucial for agriculture. In this study, we examined the morphology of a flowering plant, Arabidopsis thaliana, using microfocus X‐ray computed tomography (µCT), which enables non‐destructive analysis of the external and internal structures of plants. Three‐dimensional (3D) images of the plant, which were reconstructed from X‐ray scanned data, clearly showed the shapes of its leaves, stems, and buds from any angle. At a higher magnification, the µCT also revealed the small hair‐like structures called trichomes on the Arabidopsis leaf epidermis. However, motion artifacts found in the 3D‐reconstructed images indicated that plant's growth rate was faster than scanning speed. Thus, scan parameters must be accordingly optimized. Additionally, CT‐based 3D printing can be used to design micro devices that can be further used to monitor plant growth. These results suggest that µCT is a useful technique for analyzing morphology of growing plants. [ABSTRACT FROM AUTHOR]

Copyright of Chemical Engineering (China) / Huaxue Gongcheng is the property of Hualu Engineering Science & Technology Co Ltd. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

BACKGROUND: Biomimetic design of bioactive materials to restore, maintain or improve the function of tissue based on the understanding of anatomy on the function and structure of biological tissue is a research hotspot in the field of regenerative medicine at present. OBJECTIVE: To discuss the effect of mechanical properties, three-dimensional spatial structure, and biochemical activity of biomedical scaffolds on cell behavior and review the application of biomedical scaffolds in the field of tissue engineering. METHODS: The articles published in CNKI, Wanfang, Web of Science, and PubMed databases from January 2003 to April 2023 were searched by computer. The Chinese search terms were “extracellular matrix, tissue engineering, scaffolds, biomaterials, biomimetic structures, mechanical properties, three-dimensional structures, tendon-bone interface, osteochondral, neural conduits, artificial blood vessels”. English search terms were “extracellular matrix, tissue engineering, scaffolds, biomimetic structures, biomaterials, tendon bone interfaces, osteochondral, neural conduits, artificial blood vessels”. RESULTS AND CONCLUSION: Cells are in a complex and dynamic three-dimensional environment, so the extracellular matrix is the ultimate target of biomaterial simulation. The bionic structure of biomedical scaffolders needs to be similar to the real microenvironment, so that cells can stick to the wall, grow and migrate normally, and maintain their diverse physiological functions. Biomimetic design of extracellular matrix in terms of mechanical properties, threedimensional spatial structure, and biochemical properties of biomedical scaffolds can play a decisive role in tissue repair, thus affecting the final result of tissue repair. Biomimetic biomedical scaffolds have been widely used in tendon-bone interface, bone cartilage interface, nerve, vascular regeneration, and other fields, providing a promising new idea in clinical practice. [ABSTRACT FROM AUTHOR]

Effective visualization of small molecules is paramount in conveying concepts and results in cheminformatics. Scalable vector graphics (SVG) are preferred for creating such visualizations, as SVGs can be easily altered in post-production and exported to other formats. A wide spectrum of software applications already exist that can visualize molecules, and customize these visualizations, in many ways. However, software packages that can output projected 3D models onto a 2D canvas directly as SVG, while being programmatically accessible from Python, are lacking. Here, we introduce CineMol, which can draw vectorized approximations of three-dimensional small molecule models in seconds, without triangulation or ray tracing, resulting in files of around 50–300 kilobytes per molecule model for compounds with up to 45 heavy atoms. The SVGs outputted by CineMol can be readily modified in popular vector graphics editing software applications. CineMol is written in Python and can be incorporated into any existing Python cheminformatics workflow, as it only depends on native Python libraries. CineMol also provides programmatic access to all its internal states, allowing for per-atom and per-bond-based customization. CineMol’s capacity to programmatically create molecular visualizations suitable for post-production offers researchers and scientists a powerful tool for enhancing the clarity and visual impact of their scientific presentations and publications in cheminformatics, metabolomics, and related scientific disciplines. Scientific contribution We introduce CineMol, a Python-based tool that provides a valuable solution for cheminformatics researchers by enabling the direct generation of high-quality approximations of two-dimensional SVG visualizations from three-dimensional small molecule models, all within a programmable Python framework. CineMol offers a unique combination of speed, efficiency, and accessibility, making it an indispensable tool for researchers in cheminformatics, especially when working with SVG visualizations. [ABSTRACT FROM AUTHOR]

To maximize the active sites and accelerate the electron transfer are of significant importance for developing efficient MoS 2 -based catalysts towards hydrogen evolution reaction (HER). Herein, we report a facile one-step construction of three-dimensional assembly in which Co doped MoS 2 nanoflowers are attached on partially sulfided nickel foam (Co–MoS 2 /Ni 3 S 2 /Ni). The three-dimensional structure enables maximum exposure of the active sites. Besides, interfacial interaction between MoS 2 and Ni 3 S 2 accelerates the electron transfer kinetics and increases the electrochemically active surface area. Additionally, electronic synergy effect of Co to MoS 2 promotes the formation of 1T-MoS 2 phase. Consequently, the optimized Co–MoS 2 /Ni 3 S 2 /Ni catalyst shows a superior HER performance with low overpotentials of 43 mV and 201 mV to achieve the current densities of 10 mA/cm2 and 100 mA/cm2, as well as an excellent stability of 11 h. Besides, Co–MoS 2 /Ni 3 S 2 /Ni has a small Tafel slope of 53 mV dec−1 which indicates a combined Volmer-Heyrovsky mechanism during the HER process. This work provides a novel insight for designing excellent MoS 2 -based HER catalysts through electronic modulation and interfacial engineering. [Display omitted] • One-step construction of three-dimensional Co–MoS 2 /Ni 3 S 2 /Ni assembly was realized. • Interfacial effect and electronic modulation are conducive to improving the HER activity of MoS 2. • Low overpotential of 43 mV to reach current density at 10 mA cm−2 was achieved. • The Co–MoS 2 /Ni 3 S 2 /Ni shows excellent stability in alkaline media. [ABSTRACT FROM AUTHOR]

Motivation: In recent years, there have been significant advances in various chromatin conformation capture techniques, and annotating the topological structure from Hi-C contact maps has become crucial for studying the threedimensional structure of chromosomes. However, the structure and function of chromatin loops are highly dynamic and diverse, influenced by multiple factors. Therefore, obtaining the three-dimensional structure of the genome remains a challenging task. Among many chromatin loop prediction methods, it is difficult to fully extract features from the contact map and make accurate predictions at low sequencing depths. Results: In this study, we put forward a deep learning framework based on the diffusion model called CD-Loop for predicting accurate chromatin loops. First, by pre-training the input data, we obtain prior probabilities for predicting the classification of the Hi-C contact map. Then, by combining the denoising process based on the diffusion model and the prior probability obtained by pre-training, candidate loops were predicted from the input Hi-C contact map. Finally, CD-Loop uses a density-based clustering algorithm to cluster the candidate chromatin loops and predict the final chromatin loops. We compared CD-Loop with the currently popular methods, such as Peakachu, Chromosight, and Mustache, and found that in different cell types, species, and sequencing depths, CD-Loop outperforms other methods in loop annotation. We conclude that CD-Loop can accurately predict chromatin loops and reveal cell-type specificity. [ABSTRACT FROM AUTHOR]

This study presents a 3D regional modeling of seismic geology and shear wave velocity (Vs) in Metro Vancouver for seismic microzonation and hazard prediction. Leveraging an extensive geodatabase compiled from invasive and non-invasive in situ data, including lithological logs and seismic field data, we delineated four major geological units: Holocene post-glacial and Pleistocene inter/glacial sediments, and Tertiary sedimentary and Pre-Tertiary Coast Mountain plutonic rocks. Seismic geology model integrates the four primary geological formations, leveraging significant impedance-based surfaces derived from meticulously analyzed borehole stratigraphic logs and Vs depth profiles sourced from 2333 georecords, enhancing its depth and accuracy. Through a meticulous comparison with established interpreted geological cross-sections, we have reaffirmed the robustness and reliability of our seismic geology modeling approach. A numerical 3D “geotechnical layer” Vs model with 11 isovelocity surfaces was developed using 688 Vs depth profiles. Comparison with microtremor amplification spectra confirms our 3D models' reliable use in predicting site amplification. We find that the combination of local geology (thicknesses) and Vs information outperforms prediction in fundamental peak frequency compared to using only local geology combined with regional Vs information. Our study contributes to advancing understanding of seismic hazards in Metro Vancouver, highlighting the importance of incorporating localized seismic site conditions for precise regional seismic hazard assessments.

ABSTRACTDue to the strong penetrability, long-wavelength synthetic aperture radar (SAR) can provide an opportunity to reconstruct the three-dimensional structure of the penetrable media. SAR tomography (TomoSAR) technology can resynthesize aperture perpendicular to the slant-range direction and then obtain the tomographic profile consisting of power distribution of different heights, providing a powerful technical tool for reconstructing the three-dimensional structure of the penetrable ground objects. As an emerging technology, it is different from the traditional interferometric SAR (InSAR) technology and has advantages in reconstructing the three-dimensional structure of the illuminated media. Over the past two decades, many TomoSAR methods have been proposed to improve the vertical resolution, aiming to distinguish the locations of different scatters in the unit pixel. In order to cope with the forest mission of European Space Agency (ESA) that is designed to provide P-band SAR measurements to determine the amount of biomass and carbon stored in forests, it is necessary to systematically evaluate the performance of forest height and underlying topography inversion using TomoSAR technology. In this paper, we adopt three typical algorithms, namely, Capon, Multiple Signal Classification (MUSIC), and Compressed Sensing (CS), to evaluate the performance in forest height and underlying topography inversion. The P-band airborne full-polarization (FP) SAR data of Lopè National Park in the AfriSAR campaign implemented by ESA in 2016 is adopted to verify the experiment. Furthermore, we explore the effects of different baseline designs and filter methods on the reconstruction of the tomographic profile. The results show that a better tomographic profile can be obtained by using Hamming window filter and Capon algorithm in uniform baseline distribution and a certain number of acquisitions. Compared with LiDAR results, the root-mean-square error (RMSE) of forest height and underlying topography obtained by Capon algorithm is 2.17 m and 1.58 m, which performs the best among the three algorithms.

Gibberellins (GAs; tetracyclic di-terpenoid carboxylic acids) are endogenous plant growth regulators responsible for stimulating plant growth and development from seed germination to plant maturity. In potato (Solanum tuberosum L.), GA levels are known to be crucial in the complex process of tuberization. Gibberellin 2-oxidases (GA2oxs) inactivate bioactive GAs during stolon swelling and early stages of tuberization as evident from the predominant expression of a member of this gene family namely GA2ox1. We isolated and characterized a 1105-bp cDNA clone encoding a 340-aa GA2ox1 form, designated St-GA2ox1, using total RNA from growing tuber of a potato (Solanum tuberosum L.) cultivar, Kufri Chipsona-1 (KC-1) based on RT-PCR approach. A total of 26 GA2ox sequences were also retrieved from potato genome database and analysed. Multiple sequence alignment revealed sequence relatedness between the GA2oxs. Crucial protein motifs were identified. Phylogenetic analysis revealed the evolutionary relationships between the GA2oxs. Three-dimensional structure of St-GA2ox1 was predicted by using AlphaFold tool, validated by the predicted local-distance difference test and Ramachandran Plot. Structural analysis and molecular docking were carried out to identify domains, binding sites and affinity for the ligand. The STRING database and hydropathy analysis revealed the presence of a putative interaction site for other enzymes. Expression Atlas database and semi-quantitative RT-PCR revealed the expression patterns of various GA2ox forms in different potato organs. This comprehensive report would be useful in providing new insights into possible underlying mechanisms involved in tuber development, and could facilitate the targeted alteration of genes responsible to combat the stress and enhance tuber production. [ABSTRACT FROM AUTHOR]

Due to the strong penetrability, long-wavelength synthetic aperture radar (SAR) can provide an opportunity to reconstruct the three-dimensional structure of the penetrable media. SAR tomography (TomoSAR) technology can resynthesize aperture perpendicular to the slant-range direction and then obtain the tomographic profile consisting of power distribution of different heights, providing a powerful technical tool for reconstructing the three-dimensional structure of the penetrable ground objects. As an emerging technology, it is different from the traditional interferometric SAR (InSAR) technology and has advantages in reconstructing the three-dimensional structure of the illuminated media. Over the past two decades, many TomoSAR methods have been proposed to improve the vertical resolution, aiming to distinguish the locations of different scatters in the unit pixel. In order to cope with the forest mission of European Space Agency (ESA) that is designed to provide P-band SAR measurements to determine the amount of biomass and carbon stored in forests, it is necessary to systematically evaluate the performance of forest height and underlying topography inversion using TomoSAR technology. In this paper, we adopt three typical algorithms, namely, Capon, Multiple Signal Classification (MUSIC), and Compressed Sensing (CS), to evaluate the performance in forest height and underlying topography inversion. The P-band airborne full-polarization (FP) SAR data of Lopè National Park in the AfriSAR campaign implemented by ESA in 2016 is adopted to verify the experiment. Furthermore, we explore the effects of different baseline designs and filter methods on the reconstruction of the tomographic profile. The results show that a better tomographic profile can be obtained by using Hamming window filter and Capon algorithm in uniform baseline distribution and a certain number of acquisitions. Compared with LiDAR results, the root-mean-square error (RMSE) of forest height and underlying topography obtained by Capon algorithm is 2.17 m and 1.58 m, which performs the best among the three algorithms. [ABSTRACT FROM AUTHOR]

Zinc-ion hybrid capacitors (ZICs) can achieve high energy and power density, ultralong cycle life, and a wide operating voltage window, and they are widely used in wearable devices, portable electronics devices, and other energy storage fields. The design of advanced ZICs with high specific capacity and energy density remains a challenge. In this work, a novel kind of V, N dual-doped Ti3C2 film with a three-dimensional (3D) porous structure (3D V-, N-Ti3C2) based on Zn-ion pre-intercalation can be fabricated via a simple synthetic process. The stable 3D structure and heteroatom doping provide abundant ion transport channels and numerous surface active sites. The prepared 3D V-, N-Ti3C2 film can deliver unexpectedly high specific capacitance of 855 F g−1 (309 mAh g−1) and demonstrates 95.26% capacitance retention after 5000 charge/discharge cycles. In addition, the energy storage mechanism of 3D V-, N-Ti3C2 electrodes is the chemical adsorption of H+/Zn2+, which is confirmed by ex situ XRD and ex situ XPS. ZIC full cells with a competitive energy density (103 Wh kg−1) consist of a 3D V-, N-Ti3C2 cathode and a zinc foil anode. The impressive results provide a feasible strategy for developing high-performance MXene-based energy storage devices in various energy-related fields. [ABSTRACT FROM AUTHOR]

Using numerical and experimental methods, the mechanism of control of the transmission of a spin-wave signal in a three-dimensional magnon splitter, formed by an orthogonal junction of magnetic strips of yttrium iron garnet, has been investigated. It is shown that by variation the size of the air gap between the spin-waveguide sections, it is possible to control the selection of the signal propagating in the output sections of the structure. From an applied point of view, the results obtained can be used to create an interconnection element in multilevel magnon information processing devices for the formation of multilayer magnon network topologies and miniaturization of computing devices based on the principles of magnonics. [ABSTRACT FROM AUTHOR]

To rationally evaluate the seismic damage of RC structures comprehensively and multi-dimensionally, a damage index calculation method is proposed. This is a macroscopic global seismic damage model that considers torsional damage, damage in two perpendicular horizontal directions, as well as the overall damage, based on the modal characteristics of the three-dimensional structure and the multi-mode damage model. Formulas are derived, and the steps for damage evaluation are summarized. To better illustrate the results of the proposed method, an example of an asymmetric 6-story frame-shear wall structure is built using the OpenSees program. Thirteen ground motions are selected for incremental dynamic analysis. The structure's damage indexes are evaluated according to the proposed method and compared with the corresponding structural responses, He et al.'s index, and the Final Softening index. The results demonstrate that the proposed method can fully reflect the macroscopic damage state of the structure from different perspectives. Additionally, the results show that, despite the ground motion only acting in the y-direction, the structure exhibits responses and damage in both the x-direction and the torsional direction. The overall damage to the structure is primarily controlled by the torsional damage, attributed to the asymmetric arrangement of shear walls. The torsional effect is the key factor leading to the failure of asymmetric structures during earthquakes. Therefore, ensuring the torsional strength of the structure is crucial during the structural design process. [ABSTRACT FROM AUTHOR]

AbstractThe cultured meat technology has developed rapidly in recent years, but there are still many technical challenges that hinder the large-scale production and commercialization of cultured meat. Firstly, it is necessary to lay the foundation for cultured meat production by obtaining seed cells and maintaining stable cell functions. Next, technologies such as bioreactors are used to expand the scale of cell culture, and three-dimensional culture technologies such as scaffold culture or 3D printing are used to construct the three-dimensional structure of cultured meat. At the same time, it can reduce production costs by developing serum-free medium suitable for cultured meat. Finally, the edible quality of cultured meat is improved by evaluating food safety and sensory flavor, and combining ethical and consumer acceptability issues. Therefore, this review fully demonstrates the current development status and existing technical challenges of the cultured meat production technology with regard to the key points described above, in order to provide research ideas for the industrial production of cultured meat. [ABSTRACT FROM AUTHOR]

Comparative sequence analysis permits unraveling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly evolving sites, coevolving groups of residues, sites undergoing positive selection, or changes in evolutionary rates. Understanding the functional causes of these evolutionary patterns requires combining the results of these analyses and mapping them onto molecular structures, a complex task involving distinct coordinate referential systems. To ease this task, we introduce the site/group extended data format, a simple text format to store (groups of) site annotations. We developed a toolset, the SgedTools, which permits site/group extended data file manipulation, creating them from various software outputs and translating coordinates between individual sequences, alignments, and three-dimensional structures. The package also includes a Monte-Carlo procedure to generate random site samples, possibly conditioning on site-specific features. This eases the statistical testing of evolutionary hypotheses, accounting for the structural properties of the encoded molecules. [ABSTRACT FROM AUTHOR]

Murine norovirus (MNV) undergoes extremely large conformational changes in response to the environment. The T = 3 icosahedral capsid is composed of 180 copies of ~58-kDa VP1 comprised of N-terminus (N), shell (S), and C-terminal protruding (P) domains. At neutral pH, the P domains are loosely tethered to the shell and float ~15 Å above the surface. At low pH or in the presence of bile salts, the P domain drops onto the shell and this movement is accompanied by conformational changes within the P domain that enhance receptor interactions while blocking antibody binding. While previous crystallographic studies identified metal binding sites in the isolated P domain, the ~2.7-Å cryo-electron microscopy structures of MNV in the presence of Mg2+ or Ca2+ presented here show that metal ions can recapitulate the contraction observed at low pH or in the presence of bile. Further, we show that these conformational changes are reversed by dialysis against EDTA. As observed in the P domain crystal structures, metal ions bind to and contract the G’H’ loop. This movement is correlated with the lifting of the C’D’ loop and rotation of the P domain dimers about each other, exposing the bile salt binding pocket. Isothermal titration calorimetry experiments presented here demonstrate that the activation signals (bile salts, low pH, and metal ions) act in a synergistic manner that, individually, all result in the same activated structure. We present a model whereby these reversible conformational changes represent a uniquely dynamic and tissue-specific structural adaptation to the in vivo environment. IMPORTANCE The highly mobile protruding domains on the calicivirus capsids are recognized by cell receptor(s) and antibodies. At neutral pH, they float ~15 Å above the shell but at low pH or in the presence of bile salts, they contract onto the surface. Concomitantly, changes within the P domain block antibody binding while enhancing receptor binding. While we previously demonstrated that metals also block antibody binding, it was unknown whether they might also cause similar conformational changes in the virion. Here, we present the near atomic cryo-electron microscopy structures of infectious murine norovirus (MNV) in the presence of calcium or magnesium ions. The metal ions reversibly induce the same P domain contraction as low pH and bile salts and act in a synergistic manner with the other stimuli. We propose that, unlike most other viruses, MNV facilely changes conformations as a unique means to escape immune surveillance as it moves through various tissues. [ABSTRACT FROM AUTHOR]

Accurately modeling time-dependent coseismic crustal deformation as observed on high-rate Global Navigation Satellite System (HR-GNSS) lends insight into earthquake source processes and improves local earthquake and tsunami early warning algorithms. Currently, time-dependent crustal deformation modeling relies most frequently on simplified 1D radially symmetric Earth models. However, for shallow subduction zone earthquakes, even low-frequency shaking is likely affected by the many strongly heterogeneous structures such as the subducting slab, mantle wedge, and the overlying crustal structure. We demonstrate that including 3D structure improves the estimation of key features of coseismic HR-GNSS time series, such as the peak ground displacement (PGD), the time to PGD (tPGD), static displacements (SD), and waveform cross-correlation values. We computed synthetic 1D and 3D, 0.25 Hz and 0.5 Hz waveforms at HR-GNSS stations for four M7.3+ earthquakes in Japan using MudPy and SW4, respectively. From these synthetics, we computed intensity-measure residuals between the synthetic and observed GNSS waveforms. Comparing 1D and 3D residuals, we observed that the 3D simulations show better fits to the PGD and SD in the observed waveforms than the 1D simulations for both 0.25 Hz and 0.5 Hz simulations. We find that the reduction in PGD residuals in the 3D simulations is a combined effect of both shallow and deep 3D structures; hence incorporating only the upper 30 km of 3D structure will still improve the fit to the observed PGD values. Our results demonstrate that 3D simulations significantly improve models of GNSS waveform characteristics and will not only help understand the underlying processes, but also improve local tsunami warning.

Giant sequoias (Sequoiadendron giganteum) are some of the UK’s largest trees, despite only being introduced in the mid-nineteenth century. There are an estimated half a million giant sequoias and closely related coastal redwoods (Sequoia sempervirens) in the UK. Given the recent interest in planting more trees, partly due to their carbon sequestration potential and also their undoubted public appeal, an understanding of their growth capability is important. However, little is known about their growth and carbon uptake under UK conditions. Here, we focus on S. giganteum and use three-dimensional terrestrial laser scanning to perform detailed structural measurements of 97 individuals at three sites covering a range of different conditions, to estimate aboveground biomass (AGB) and annual biomass accumulation rates. We show that UK-grown S. giganteum can sequester carbon at a rate of 85 kg yr−1, varying with climate, management and age. We develop new UK-specific allometric models for S. giganteum that fit the observed AGB with r 2 > 0.93 and bias < 2% and can be used to estimate S. giganteum biomass more generally. This study provides the first estimate of the growth and carbon sequestration of UK open-grown S. giganteum and provides a baseline for estimating their longer-term carbon sequestration capacity.

Semiconductor catalytic materials have excellent photocatalytic degradation performance for organic pollutants, and photocatalytic degradation is considered to be the most promising technology for environmental pollution treatment. Bismuth-based bimetallic oxide CuBi 2 O 4 is widely recognized as one of the most valuable and promising semiconductor photocatalytic materials because of its narrow bandwidth, strong visible light absorption and excellent chemical stability. To further improve the photocatalytic activity of CuBi 2 O 4 , the Zn-doped CuBi 2 O 4 /montmorillonite composites were prepared by employing a synergistic control strategy of doping and oxygen vacancies (OVs), which efficiently regulated the electronic structure and the number of active sites to achieve a rapid separation of photogenerated charges. The doping of zn2+ significantly increased the quantity of oxygen vacancies in the prepared materials. The BET revealed that the incorporation of montmorillonite (MMT) greatly increased the specific surface area of CuBi 2 O 4. The experimental findings indicated that 5 % Zn–CuBi 2 O 4 /MMT0.6 possessed abundant oxygen vacancies and longer fluorescence lifetime, resulting in better photocatalytic performance. The removal rate of butyl xanthate was 99.31 % in 40 min, and the removal rate of tetracycline hydrochloride (TC) was 93.17 % in 180 min. The 5 % Zn–CuBi 2 O 4 /MMT0.6 could effectively inhibit e−/h+ complexation and provide richer catalytic active sites by doping to construct a flower-like oxygen-rich vacancy defect structure, which significantly improves its catalytic performance. The results of the cycling experiments showed that the stability and reproducibility of the 5 % Zn–CuBi 2 O 4 /MMT0.6 composites were excellent, the present study provides an innovative idea for the development of efficient and stable visible light photocatalytic applications. [ABSTRACT FROM AUTHOR]

Developing electrode materials with high voltage and high specific capacity has always been an important strategy for increasing the energy density of lithium-ion capacitors (LICs). However, organic-based electrolytes with lithium salts limit their potential for application in LICs to voltages below 3.8 V in terms of polarization reactions. In this work, we introduce Li[N(C2F5SO2)2] (lithium Bis (pentafluoroethanesulfonyl)imide or LiBETI), an electrolyte with high conductivity and superior electrochemical and mechanical stability, to construct a three-electrode LIC system. After graphite anode pre-lithiation, the anode potential was stabilized in the three-electrode LIC system, and a stable solid electrolyte interface (SEI) film formed on the anode surface as expected. Meanwhile, the LIC device using LiBETI as the electrolyte, and a self-synthesized graphene/single-walled carbon nanotube (SWCNT) composite as the cathode, showed a high voltage window, allowing the LIC to achieve an operating voltage of 4.5 V. As a result, the LIC device has a high energy density of up to 182 Wh kg−1 and a 2678 W kg−1 power density at 4.5 V. At a current density of 2 A g−1, the capacity retention rate is 72.7% after 10,000 cycles. [ABSTRACT FROM AUTHOR]

Introduction: Cancer stem cells have been described in lung adenocarcinoma‐associated malignant pleural effusion. They show clinically important features, including the ability to initiate new tumours and resistance to treatments. However, their correlation with the three‐dimensional tumour structures in the effusion is not well understood. Methods: Cell blocks produced from lung adenocarcinoma patients' pleural effusion were examined for cancer stem cell‐related markers Nanog and CD133 using immunocytochemistry. The three‐dimensional cancer cell structures and CD133 expression patterns were visualized with tissue‐clearing technology. The expression patterns were correlated with tumour cell structures, genetic variants and clinical outcomes. Results: Thirty‐nine patients were analysed. Moderate‐to‐strong Nanog expression was detected in 27 cases (69%), while CD133 was expressed by more than 1% of cancer cells in 11 cases (28%). Nanog expression was more homogenous within individual specimens, while CD133 expression was detected in single tumour cells or cells within small clusters instead of larger structures in 8 of the 11 positive cases (73%). Although no statistically significant correlation between the markers and tumour genetic variants or patient survival was observed, we recorded seven cases with follow‐up specimens after cancer treatment, and four (57%) showed a change in stem cell‐related marker expression corresponding to treatment response. Conclusions: Lung adenocarcinoma cells in the pleural effusion show variable expression of cancer stem cell‐related markers, some showing a correlation with the size of cell clusters. Their expression level is potentially correlated with cancer treatment effects. [ABSTRACT FROM AUTHOR]

The organic–inorganic hybrid compound, (o-BrAH)[H2Co(CN)6]0.5·(18-crown-6)0.5·H2O, was synthesized and characterized by variable-temperature X-ray diffraction, single-crystal diffraction, infrared spectroscopy, elemental analysis, thermogravimetric analysis, differential scanning calorimetry, and dielectric measurements. Single-crystal X-ray diffraction revealed a three-dimensional cage-like structure formed through the hydrogen bonds of cobalt hexacyanide, supermolecular cations, and water molecules. Temperature variation triggered an abrupt change in the cage structure and simultaneously caused dynamic oscillation of the supramolecules within the framework of [Co(CN)6]3−, inducing a phase transition accompanied by a step-like change in the dielectric physical properties. [ABSTRACT FROM AUTHOR]

The results of quasi-synchronous satellite and experimental field observations of two submesoscale eddy dipoles in the coastal zone of the southeastern Baltic Sea near the coast of Kaliningrad Region are presented. The parameters of eddy dipole dynamics, namely, the duration of the process in the sea water and its propagation velocity and direction, as well as atmospheric conditions favorable for the occurrence of eddy dipoles, are determined from consecutive satellite images of high resolution. The characteristics of the three-dimensional structure of eddy dipoles are determined using the data of an acoustic current profiler and a hydrological probe obtained concurrently with satellite survey. The depth of vortical motion penetration into the water column is discussed and it is shown that such processes are not purely surface phenomena but have their influence down to a depth of 20 m and more. Direct measurements of current velocities and directions within particular parts of an eddy dipole demonstrate significantly greater dynamics of waters inside such formations compared to their displacement velocity. The differences in the anticyclonic and cyclonic parts of the dipoles are evaluated. Hydrological observations show the influence of the active cyclonic part of a dipole on surrounding waters manifested in both capture (rise) of deeper water and accumulation of surfactants within it. [ABSTRACT FROM AUTHOR]

The SfL-1 isoform from the marine red algae Solieria filiformis was produced in recombinant form (rSfL-1) and showed hemagglutinating activity and inhibition similar to native SfL. The analysis of circular dichroism revealed the predominance of β-strands structures with spectra of βI-proteins for both lectins, which had Melting Temperature (Tm) between 41 °C and 53 °C. The three-dimensional structure of the rSfL-1 was determined by X-ray crystallography, revealing that it is composed of two β-barrel domains formed by five antiparallel β chains linked by a short peptide between the β-barrels. SfL and rSfL-1 were able to agglutinate strains of Escherichia coli and Staphylococcus aureus and did not show antibacterial activity. However, SfL induced a reduction in E. coli biomass at concentrations from 250 to 125 μg mL−1, whereas rSfL-1 induced reduction in all concentrations tested. Additionally, rSfL-1 at concentrations from 250 to 62.5 μg mL−1, showed a statistically significant reduction in the number of colony-forming units, which was not noticed for SfL. Wound healing assay showed that the treatments with SfL and rSfL-1 act in reducing the inflammatory response and in the activation and proliferation of fibroblasts by a larger and fast deposition of collagen. [Display omitted] • Lectin from S. filiformis was produced in wild (SfL) and recombinant (rSfL-1) form. • SfL is a member of the Oscillatoria agardhii Agglutinin Homolog Family. • Three-dimensional structure was determined and it is composed of two β-barrel domains. • SfL and rSfL-1 were able to inhibit the formation of biofilms of the E. coli strain. • The lectins presented pro-healing effects using a swiss albino mice model. [ABSTRACT FROM AUTHOR]

Bunyavirus is widely distributed, highly contagious, and has a high fatality rate. It is a negative- strand RNA virus that has a major impact on public health around the world. The development of vaccines and the search for drugs are the key to prevent bunyavirus infection. The nucleoprotein (NP) of viruses is necessary for the synthesis of viral RNA, which combines with viral RNA to form the nucleocapsid, participates in viral assembly and RNA transcription, and plays an important role in viral proliferation. In addition, NP also has B cell and T cell epitopes, which can induce cellular and humoral immunity, so NP is an ideal target for vaccine design and drug development. Given its abundance and specificity, NP is also commonly used in the detection of viral diseases. More and more bunyavirus NP structures and structures of NP-RNA complexes have been resolved. Researchers have discovered two important antiviral targets through these structures, the terminal arm and the RNA binding cleft. This paper reviews the function and three-dimensional structure of the bunyavirus NP and the research progress of NP as an antiviral target, in order to provide a theoretical basis for the prevention and treatment of the bunyavirus disease. [ABSTRACT FROM AUTHOR]

Abstract The forward calculation of magnetotelluric (MT) responses is generally assumed to be sufficiently accurate compared with typical observational errors in practical modeling and inversion studies. Although the uncertainty of the forward calculation may be examined by comparison with analytical or other numerical solutions for some simple models, such an examination does not guarantee that the uncertainty is similar for more realistic complex structures. In this study, I propose a simple method to evaluate the uncertainty of MT forward modeling for practical three-dimensional (3D) conductivity structure models in a Cartesian coordinate system. The method is based on the idea that the horizontal coordinate system can be selected arbitrarily for a general 3D structure. The synthesized MT responses are ideally identical irrespective of the selection but are different because of the difference in discretization angles, boundary values, and numerical errors. By synthesizing MT responses to the model in several different coordinate systems, the mean, standard deviation, and coefficient of variation can be calculated. These statistics provide quantitative information on how stably the forward calculations synthesize MT responses under the given conditions of the structure model, observation array, periods, numerical algorithm for the forward modeling, and mesh design. The proposed method was applied to two practical situations of seafloor MT arrays in the northwestern Pacific and southern Atlantic and a land MT array in Hokkaido, Japan. The results show that the uncertainty is comparable to real observation errors and is significantly dependent on the MT impedance element, period, site, structure model, and horizontal coordinate system. The uncertainty of the forward calculation should be considered for each element, period, and site to quantitatively evaluate how well a given model explains the data. I propose a new root-mean-square in which the residuals are normalized by both the standard errors of the MT responses observed and synthesized. This would help avoid overfitting data in the inversion analysis by ignoring the uncertainty of the forward calculation. This method is also useful for testing the appropriate selection of the coordinate system and mesh design. Graphical Abstract

The superfamily of acid proteases has two catalytic aspartates for proteolysis of their peptide substrates. Here, we show a minimal structural scaffold, the structural catalytic core (SCC), which is conserved within each family of acid proteases, but varies between families, and thus can serve as a structural marker of four individual protease families. The SCC is a dimer of several structural blocks, such as the DD-link, D-loop, and G-loop, around two catalytic aspartates in each protease subunit or an individual chain. A dimer made of two (D-loop + DD-link) structural elements makes a DD-zone, and the D-loop + G-loop combination makes a psi-loop. These structural markers are useful for protein comparison, structure identification, protein family separation, and protein engineering.

Mesoscale eddies are known to enhance diapycnal mixing in the ocean, yet direct observation of this effect remains a significant challenge, especially in the robust Antarctic Circumpolar Current (ACC). To quantify the diapycnal mixing induced by mesoscale eddies in the standing meander of the ACC, satellite altimeter and Argo profile data were combined to composite eddies, where the 1.6 m dynamic height contour was used for the first time instead of the climatological Northern Sub-Antarctic Front (SAFN) to define the northern boundary of the ACC to eliminate the influence of frontal shift. The 3D structures of the composite anticyclonic/cyclonic eddy (CAE/CCE) were obtained. Both the CAE and CCE were similar in shape to Taylor columns, from sea surface to the neutral surface of 28.085 kgm−3 (1689 ± 66 dbar) for the CAE, and from sea surface to 28.01 kgm−3 (1491 ± 202 dbar) for the CCE. On the same neutral surface, the diffusivity (κ) inside the CCE was one to two orders of magnitude higher than that inside the CAE. Vertically, the maximum influence depth of the CCE on κ reached 1200 dbar, while for the CAE, it reached 800 dbar, where κ exceeded O(10−4) m2s−1, and κ gradually decreased from these depths downwards.

As small ectotherms, insects need to cope with the challenges of winter cold by regulating the water content through water transport. Aquaporins (AQPs) are key players to enhance the cold resistance by mediating essential homeostatic processes in many animals but remain poorly characterized in insects. Agriphila aeneociliella is a newly discovered winter wheat pest in China, and its early-stage larvae have strong tolerance to low temperature stress. Six AQP genes were identified, which belong to five AQP subfamilies (RPIP, Eglp, AQP12L, PRIP, DRIP). All of them contained six hydrophobic transmembrane helices (TMHs) and two relatively conservative Asparagine-Proline-Alanine motifs. The three-dimensional homology modeling showed that the six TMHs folded into an hourglass-like shape, and the imperceptible replace of four ar/R residues in contraction region had critical effects on changing the pore size of channels. Moreover, the transcript levels of AaAQP 1, 3, and 6 increased significantly with the treatment time below 0 °C. Combined with the results of pore radius variation, it is suggested that AaAQP1 and AaAQP3 may be considered to be the key anti-hypothermia proteins in A. aeneociliella by regulating rapid cell dehydration and allowing the influx of extracellular cold resistance molecules, thus avoiding death in winter.

In the process of reconstructing the three-dimensional structure of the virus by using the icosahedral symmetry of the virus, the existence of the symmetry-mismatch problem hindered the analysis of the real structure of the virus and the acquisition of the high-resolution structure. In order to eliminate the influence of symmetric mismatch on the three-dimensional structure of the virus, a symmetry-mismatch three-dimensional reconstruction algorithm by using the special subgroup search of the icosahedral point group was proposed. By taking the Grass Corp Reovirus (GCRV) as the experimental material, the three-dimensional structure of GCRV was obtained by using the three-dimension reconstruction technique of cryo-electron microscopy. Then, the orientation information was obtained through the local three-dimensional reconstruction and symmetry-mismatch searching, by adding the search of GCRV-specific vertex. The results showed that: the algorithm improved the e任iciency of symmetry-mismatch orientation searching, and accurately reduced the orientation information of Grass Corp Reovirus (GCRV) by determining the icosahedral-specific apical position of the polymerase complex inside the virus. The results confirmed that the virus-deleted RdRp was in the pseudo-D3 symmetrical equatorial group, and it. provided a new method for resolving the whole-virus symmetry-mismatch structure of double-stranded RNA virus and exploring the molecular mechanism of endogenous transcription of double-stranded RNA virus. [ABSTRACT FROM AUTHOR]