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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

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]

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]

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]

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.

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]

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]

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.

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]

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]

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]

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]

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

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.

All adeno-associated virus (AAV) vectors currently used in clinical trials or approved gene therapy biologics are based on human or non-human primate AAVs. A major challenge for AAV gene therapy is the high prevalence of circulating neutralizing antibodies (NAbs) in the general population targeting the virus capsids leading to vector inactivation and a loss of treatment efficacy. A strategy to escape detection by NAbs is the utilization of AAVs that do not disseminate in the primate population and exhibit low or no antigenicity. One such example is avian AAV (AAAV), which was first identified in preparations of the Olson strain of quail bronchitis, an avian adenovirus. AAAV shows very low sequence identities (~54–58%) to the AAV serotypes including to the sequences of the structurally diverse AAV4 and AAV5. In this study, the structure of empty and genome-filled AAAV capsids was determined by cryo-electron microscopy (cryo-EM) at 2.5 and 3.1 Å resolution. Furthermore, AAAV was found to utilize galactose for cell attachment, similar to AAV9 and AAVrh.10. Characterization of AAAV’s antigenic properties revealed that 30% of human sera from healthy individuals were capable of neutralizing transduction. This high rate of antigenicity is caused by conserved epitopes around the fivefold channel of the capsid allowing cross-reactivity of NAbs. This was further confirmed by mapping a cross-reactive human anti-AAV9 monoclonal antibody using cryo-EM. This structure-function characterization will be beneficial to further expand the current repertoire of AAV vectors in human gene therapy applications. IMPORTANCE AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity. [ABSTRACT FROM AUTHOR]

In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins. [ABSTRACT FROM AUTHOR]

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Abstract Cell therapy is an accessible method for curing damaged organs or tissues. Yet, this approach is limited by the delivery efficiency of cell suspension injection. Over recent years, biological scaffolds have emerged as carriers of delivering therapeutic cells to the target sites. Although they can be regarded as revolutionary research output and promote the development of tissue engineering, the defect of biological scaffolds in repairing cell-dense tissues is apparent. Cell sheet engineering (CSE) is a novel technique that supports enzyme-free cell detachment in the shape of a sheet-like structure. Compared with the traditional method of enzymatic digestion, products harvested by this technique retain extracellular matrix (ECM) secreted by cells as well as cell-matrix and intercellular junctions established during in vitro culture. Herein, we discussed the current status and recent progress of CSE in basic research and clinical application by reviewing relevant articles that have been published, hoping to provide a reference for the development of CSE in the field of stem cells and regenerative medicine.

Beta-lactams are the main antibiotics for the treatment of invasive meningococcal disease. However, reduced susceptibility to penicillin G is increasingly reported in Neisseria meningitidis and reduced susceptibility to third-generation cephalosporines (3GC) and the rare acquisition of ROB-1 beta-lactamase were also described. Modifications of penicillin-binding protein 2 (PBP2) encoded by the penA gene are the main described mechanism for the reduced susceptibility to penicillin and to other beta-lactams. penA modifications were analyzed using the sequences of all penA genes from cultured isolates between 2017–2021 in France (n = 1255). Data showed an increasing trend of reduced susceptibility to penicillin from 36% in 2017 to 58% in 2021. Reduced susceptibility to 3GC remained limited at 2.4%. We identified 74 different penA alleles and penA1 was the most frequent wild-type allele and represented 29% of all alleles while penA9 was the most frequently altered allele and represented 17% of all alleles. Reduced susceptibility to 3GC was associated with the penA327 allele. The amino acid sequences of wild-type and altered PBP2 were modeled. The critical amino acid substitutions were shown to change access to the active S310 residue and hence hinder the binding of beta-lactams to the active site of PBP2. [ABSTRACT FROM AUTHOR]

A proper canopy light distribution in fruit trees can improve photosynthetic efficiency, which is important for improving fruit yield and quality. Traditional methods of measuring light intensity in the canopy of fruit trees are time consuming, labor intensive and error prone. Therefore, a method for predicting canopy light distribution in cherry trees was proposed based on a three-dimensional (3D) cherry tree canopy point cloud model fused by multiple sources. First, to quickly and accurately reconstruct the 3D cherry tree point cloud model, we propose a global cherry tree alignment method based on a binocular depth camera vision system. For the point cloud data acquired by the two cameras, a RANSAC-based orb calibration method is used to externally calibrate the cameras, and the point cloud is coarsely aligned using the pose transformation matrix between the cameras. For the point cloud data collected at different stations, a coarse point cloud alignment method based on intrinsic shape signature (ISS) key points is proposed. In addition, an improved iterative closest point (ICP) algorithm based on bidirectional KD-tree is proposed to precisely align the coarse-aligned cherry tree point cloud data to achieve point cloud data fusion and obtain a complete 3D cherry tree point cloud model. Finally, to reveal the pattern between the fruit tree canopy structure and the light distribution, a GBRT-based model for predicting the cherry tree canopy light distribution is proposed based on the established 3D cherry tree point cloud model, which takes the relative projected area features, relative surface area and relative volume characteristics of the minimum bounding box of the point cloud model as inputs and the relative light intensity as output. The experiment results show that the GBRT-based model for predicting the cherry tree canopy illumination distribution has good feasibility. The coefficient of determination between the predicted value and the actual value is 0.932, and the MAPE is 0.116, and the model can provide technical support for scientific and reasonable cherry tree pruning. [ABSTRACT FROM AUTHOR]

The conventional wisdom is that liquids are completely disordered and lack nontrivial structure beyond nearest-neighbor distances. Recent observations have upended this view and demonstrated that the microstructure in liquids is surprisingly rich and plays a critical role in numerous physical, biological, and industrial processes. However, approaches to uncover this structure are either system-specific or yield results that are not physically intuitive. Here, through single-particle resolved three-dimensional confocal microscope imaging and the use of a recently introduced four-point correlation function, we show that bidisperse colloidal liquids have a highly nontrivial structure comprising alternating layers with icosahedral and dodecahedral order, which extends well beyond nearest-neighbor distances and grows with supercooling. By quantifying the dynamics ofthe system on the particle level, we establish that it is this intermediate- range order, and not the short-range order, which has a one-to-one correlation with dynamical heterogeneities, a property directly related to the relaxation dynamics of glassy liquids. Our experimental findings provide a direct and much sought-after link between the structure and dynamics of liquids and pave the way for probing the consequences of this intermediate-range order in other liquid state processes. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The Drake Passage is known for its abundant mesoscale eddies, but little is known about their three-dimensional characteristics, which hinders our understanding of their impact on eddy-induced transport and deep-sea circulation. A 10-year study was conducted using GLORYS12 Mercator Ocean reanalysis data from 2009 to 2018. The study analyzed the statistical characteristics of eddies in the Drake Passage, spanning from the surface down to a depth of 2000 m in three dimensions. The findings indicate that the mean radius of the eddies is 35.5 km, with a mean lifespan of 12.3 weeks and mean vorticity of 2.2 × 10−5 s−1. The eddies are most active and energetic near the three main fronts and propagate north-eastward at an average distance of 97.8 km. The eddy parameters vary with water depth, with more anticyclones detected from the surface to 400 m, displaying a larger radius and longer propagation distance. Cyclones have longer lifespans and greater vorticity. However, beyond 400 m, there is not much difference between anticyclones and cyclones. Approximately 23.3% of the eddies reach a depth of 2000 m, with larger eddies tending to penetrate deeper. The eddies come in three different shapes, bowl-shaped (52.7%), lens-shaped (27.1%) and cone-shaped (20.2%). They exhibit annual and monthly distribution patterns. Due to its high latitude location, the Drake Passage has strong rotation and weak stratification, resulting in the generation of small and deep-reaching eddies. These eddies contribute to the formation of Antarctic intermediate water and lead to modulation of turbulent dissipation. [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.

Autoimmune diseases, which affect approximately 5% of human population, are a range of diseases in which the immune response to self-antigens results in damage or dysfunction of tissues. Recent genome wide association studies (GWAS) have successfully identified novel autoimmune disease-associated loci, with many of them shared by multiple disease-associated pathways but much of the genetics and pathophysiological mechanisms remain still obscure. Considering that most of the potential causal variants are still unknown, many studies showed that the missense variant rs35667974 at interferon-induced with helicase C domain 1 (IFIH1) gene is protective for type 1 diabetes (T1D), psoriasis (PS) and psoriatic arthritis (PsA). Recently, this variant was found to be also associated with ankylosing spondylitis (AS), Crohn’s disease (CD) and ulcerative colitis (UC). The IFIH1 gene encodes a cytoplasmic RNA helicase otherwise known as melanoma differentiation-associated 5 (MDA5) that recognizes viral RNA and is involved in innate immunity through recognition of viral RNA. In the present study we sought to investigate the association of the rare rs35667974 variant of IFIH1 gene, which resides in exon 14 and changes a conserved isoleucine at position #923 to valine, in the development of various autoimmune diseases and give a reason for the selectivity affecting different autoimmune diseases. Evolutionary studies and three-dimensional (3 D) homology modelling were employed on the MDA5 protein product, through its association with dsRNA, recognition factor controlling cytokine and chemokine signalling, to investigate the protective role of the MDA5 variant for certain autoimmune diseases.

ABSTRACT The SARS-CoV-2 nucleocapsid (N) protein is highly immunogenic, and anti-N antibodies are commonly used as markers for prior infection. While several studies have examined or predicted the antigenic regions of N, these have lacked consensus and structural context. Using COVID-19 patient sera to probe an overlapping peptide array, we identified six public and four private epitope regions across N, some of which are unique to this study. We further report the first deposited X-ray structure of the stable dimerization domain at 2.05 Å as similar to all other reported structures. Structural mapping revealed that most epitopes are derived from surface-exposed loops on the stable domains or from the unstructured linker regions. An antibody response to an epitope in the stable RNA binding domain was found more frequently in sera from patients requiring intensive care. Since emerging amino acid variations in N map to immunogenic peptides, N protein variation could impact detection of seroconversion for variants of concern. IMPORTANCE As SARS-CoV-2 continues to evolve, a structural and genetic understanding of key viral epitopes will be essential to the development of next-generation diagnostics and vaccines. This study uses structural biology and epitope mapping to define the antigenic regions of the viral nucleocapsid protein in sera from a cohort of COVID-19 patients with diverse clinical outcomes. These results are interpreted in the context of prior structural and epitope mapping studies as well as in the context of emergent viral variants. This report serves as a resource for synthesizing the current state of the field toward improving strategies for future diagnostic and therapeutic design.

Cell therapy is an accessible method for curing damaged organs or tissues. Yet, this approach is limited by the delivery efficiency of cell suspension injection. Over recent years, biological scaffolds have emerged as carriers of delivering therapeutic cells to the target sites. Although they can be regarded as revolutionary research output and promote the development of tissue engineering, the defect of biological scaffolds in repairing cell-dense tissues is apparent. Cell sheet engineering (CSE) is a novel technique that supports enzyme-free cell detachment in the shape of a sheet-like structure. Compared with the traditional method of enzymatic digestion, products harvested by this technique retain extracellular matrix (ECM) secreted by cells as well as cell-matrix and intercellular junctions established during in vitro culture. Herein, we discussed the current status and recent progress of CSE in basic research and clinical application by reviewing relevant articles that have been published, hoping to provide a reference for the development of CSE in the field of stem cells and regenerative medicine. [ABSTRACT FROM AUTHOR]

The structure of the maize kernels plays a critical role in determining maize yield and quality, and high-throughput, non-destructive microscope phenotypic characteristics acquisition and analysis are of great importance. In this study, Micro-CT technology was used to obtain images of maize kernels. An automatic CT image analysis pipeline was then developed to extract 20 traits related to the three-dimensional structure of kernel, embryo, endosperm, and cavity. The determination coefficients for five volume-related traits (embryo, endosperm, silty endosperm, embryo cavity, and endosperm cavity) were 0.95, 0.95, 0.77, 0.73, and 0.94, respectively. Further, we analyzed the phenotypic variations among a group of 303 inbred lines and conducted genome-wide association studies (GWAS). A total of 26 significant SNP loci were associated with these traits that are closely related to kernel volume, and 62 candidate genes were identified. Functional analysis revealed that most candidate genes corresponding to cavity traits encoded stress resistance proteins, while those corresponding to embryo and endosperm traits encoded proteins involved in regulating plant growth and development. These results will improve the understanding of the phenotypic traits of maize kernels and will provide new theoretical support for in-depth analysis of the genetic mechanism of kernel structure traits. [ABSTRACT FROM AUTHOR]

The effectiveness of electrochemical systems in various applications (e.g., energy storage and conversion, wastewater treatment, ammonia synthesis) is, in essence, dependent on the electrode materials employed in such systems. The emphasis of research on electrochemical systems is given to developing electrode materials that would offer cost-effectiveness, stability, and reliable results that can be practical for commercial scaling. However, the operation of these systems also relies on other various components that include electrode fabrication, electrolytes, system architecture, the durability of the systems, and supporting components (i.e., substrate/current collector). On the choice of the current collector, nickel foam (NF) has enjoyed widespread attention as a favourable substrate in various electrochemical systems. This growing trend is attributed to its unique interlinked three-dimensional structure that offers advantages such as light weight, high porosity, great mechanical strength, chemical stability, and promising electrical and thermal conductivity. These traits are favourable for maximized contact areas between the current collector, the active materials, and charged species, resulting in the reduction of charge transport pathways, which is a vital step for improving the electrochemical performance. This review aims at highlighting the use of NF as a substrate of choice in developing effective electrodes for various electrochemical systems and can serve as a navigational tool for the literature involving the use of NF as the current collector. It also shows, to a certain extent, the impact of NF on electrochemical performance as compared with other current collectors. [ABSTRACT FROM AUTHOR]

Elevenins are peptides found in a range of organisms, including arthropods, annelids, nematodes, and molluscs. They consist of 17 to 19 amino acid residues with a single conserved disulfide bond. The subject of this study, elevenin-Vc1, was first identified in the venom of the cone snail Conus victoriae (Gen. Comp. Endocrinol. 2017, 244, 11–18). Although numerous elevenin sequences have been reported, their physiological function is unclear, and no structural information is available. Upon intracranial injection in mice, elevenin-Vc1 induced hyperactivity at doses of 5 or 10 nmol. The structure of elevenin-Vc1, determined using nuclear magnetic resonance spectroscopy, consists of a short helix and a bend region stabilised by the single disulfide bond. The elevenin-Vc1 structural fold is similar to that of α-conotoxins such as α-RgIA and α-ImI, which are also found in the venoms of cone snails and are antagonists at specific subtypes of nicotinic acetylcholine receptors (nAChRs). In an attempt to mimic the functional motif, Asp-Pro-Arg, of α-RgIA and α-ImI, we synthesised an analogue, designated elevenin-Vc1-DPR. However, neither elevenin-Vc1 nor the analogue was active at six different human nAChR subtypes (α1β1εδ, α3β2, α3β4, α4β2, α7, and α9α10) at 1 µM concentrations. [ABSTRACT FROM AUTHOR]

Polyamines (PAs) are positively charged amines that are present in all organisms. In addition to their functions specific to growth and development, they are involved in responding to various biotic and abiotic stress tolerance functions. The appropriate concentration of PA in the cell is maintained by a delicate balance between the catabolism and anabolism of PAs, which is primarily driven by two enzymes, namely diamine oxidase and polyamine oxidase (PAO). PAOs have been found to be localized in multiple subcellular locations, including peroxisomes. This paper presents a holistic account of peroxisomal PAOs. PAOs are flavin adenine dinucleotide-dependent enzymes with varying degrees of substrate specificity. They are expressed differentially upon various abiotic stress conditions, namely heat, cold, salinity, and dehydration. It has also been observed that in a particular species, the various PAO isoforms are expressed differentially with a spatial and temporal distinction. PAOs are targeted to peroxisome via a peroxisomal targeting signal (PTS) type 1. We conducted an extensive bioinformatics analysis of PTS1s present in various peroxisomal PAOs and present a consensus peroxisome targeting signal present in PAOs. Furthermore, we also propose an evolutionary perspective of peroxisomal PAOs. PAOs localized in plant peroxisomes are of potential importance in abiotic stress tolerance since peroxisomes are one of the nodal centers of reactive oxygen species (ROS) homeostasis and an increase in ROS is a major indicator of the plant being in stress conditions; hence, in the future, PAO enzymes could be used as a key candidate for generating abiotic stress tolerant crops. [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.

Intercropping creates a heterogeneous canopy and triggers plastic responses in plant growth and structural development. In order to quantify the effect of planting pattern, strip width and row position on the structural development and light capture of maize and soybean in simultaneous intercropping, both experimental and modelling approaches were used. Field experiments were conducted in 2017－2018 with two sole crops (maize and soybean) and two intercrops: Two rows of maize alternating with two rows of soybeans (2:2 MS) and three rows of maize alternating with six rows of soybean (3:6 MS). The morphological traits of maize and soybean e.g., leaf length and width, internode length and diameter, leaf and petiole declination angle in different rows and different planting patterns, and photosynthetically active radiation (PAR) above and below the canopy of 2:2 MS were measured throughout the growing season. A functional-structural plant model of maize-soybean intercropping was developed in the GroIMP platform. The model was parameterized based on the morphological data set of 2017, and was validated with the leaf area index (LAI), plant height and PAR data set of 2018. The model simulated the morphological development of individual organs based on growing degree days (thermal time) and calculated the light capture at leaf level. The model well reproduced the observed dynamics of leaf area index and plant height (RMSE: 0.24－0.70 m2/m2 for LAI and 0.06－0.17 m for plant height), and the fraction of light capture in the 2:2 MS intercropping (RMSE: 0.06－0.10). Maize internode diameter in intercrops increased, but the internode length did not change. Soybean internodes in intercrops became longer and thinner compared to sole soybean probably caused by the shading imposed by maize, and the 2:2 MS had longer internodes than the 3:6 MS, indicating the effects of strip width. Simulated light capture of maize in 2:2 MS intercropping was 35.6% higher than sole maize. For maize in 3:6 MS intercropping, the light capture of the border rows and inner row were 27.8% and 20.3% higher than sole maize, respectively. Compared to sole soybean, the simulated light capture of soybean in border rows was 36.0% lower in 2:2 MS intercropping, and was 28.8% lower in 3:6 MS intercropping. For 3:6 MS intercropping, light capture of soybean in inner rows I and inner rows II were 4.1% and 1.8% lower than sole soybean, respectively. In the future, the model could be further developed and used to explore and optimize the planting patterns of maize soybean intercropping under different environmental conditions using light capture as an indicator.

Molecular dynamic (MD) simulation provides an insight into the behavior of a protein under applied processing at the molecular level. The behavior of glutelin type-B 5-like protein, a type of glutelin protein from proso millet was studied, in solution under different temperatures (300, 350, and 400 K) and pressure (1 bar, 3 kbar, and 6 kbar) levels using a molecular dynamics simulation approach. The combined treatment effect (400 K, 6 kbar) increased the compaction of the protein compared to the level at (300 K, 1 bar) as shown by the decreased radius of gyration values from 3.26 to 2.92 nm, decreased solvent accessibility surface area from 327.47 to 311.06 nm2 and decreased volume from 108.35 to 105.04 nm3. The root means square deviation increased with increasing temperature but decreased with increasing pressure while the root means square fluctuations increased significantly with increased in temperature and pressure. A snapshot of the three-dimensional structure of the protein revealed compression of its occluded cavities at higher pressure levels but no obvious disruption to the secondary structure elements of the protein was observed, except for the loss of a few amino acid residues that comprise the secondary structure element. [ABSTRACT FROM AUTHOR]

A series of three-dimensional porous composite α-MnO2/reduced graphene oxides (α-MnO2/RGO) were prepared by nano-assembly in a hydrothermal environment at pH 9.0–13.0 using graphene oxide as the precursor, KMnO4 and MnCl2 as the manganese sources and F− as the control agent of the α-MnO2 crystal form. The α-MnO2/RGO composites prepared at different hydrothermal pH levels presented porous network structures but there were significant differences in these structures. The special pore structure promoted the migration of ions in the electrolyte in the electrode material, and the larger specific surface area promoted the contact between the electrode material and the electrolyte ions. The introduction of graphene solved the problem of poor conductivity of MnO2, facilitated the rapid transfer of electrons, and significantly improved the electrochemical performance of materials. When the pH was 12.0, the specific surface area of the 3D porous composite material αMGs-12.0 was 264 m2·g−1, and it displayed the best super-capacitive performance; in Na2SO4 solution with 1.0 mol·L−1 electrolyte, the specific capacitance was 504 F·g−1 when the current density was 0.5 A·g−1 and the specific capacitance retention rate after 5000 cycles was 88.27%, showing that the composite had excellent electrochemical performance. [ABSTRACT FROM AUTHOR]

Objective: To predict the tertiary structure of human interferon alpha/beta receptor 2 protein. Study Design: Structure prediction by using bio informatics tools. Place and Duration of Study: Department of Biochemistry, Swat Medical College (STMC), Saidu Shareef, Swat, Pakistan, from Aug 2019 to Dec 2019. Methodology: All protein sequences of human interferon alpha/beta receptor 2 (isoforma, b and c) (IFNAR-2) were retrieved through the BLAST search (The Basic Local Alignment Search Tool) from available databases ‘NCBI’ (National Centre for Biotechnology Information) and ‘Uni Prot KB’ (The Universal Protein Resource). Sequence alignment was conducted by using Clustal Omega, to get the consensus sequence for IFNAR-2 protein. Consensus protein sequence of human IFNAR-2 was used for the prediction of the three-dimensional structure by employing Swiss-Model Server. Moreover, subcellular localization analysis was also performed by using CELLO2GO program. Results: Structural model of human IFNAR-2 protein was predicted and evaluated by Ramachandran dimension. Cellular localization of tertiary topological domains of the predicted models were revealed probability of localization of IFNAR-2 protein (isoform a, b & c) is highest in the plasma membrane due to the presence of the transmembrane alpha helical regions. Conclusion: This study predicted the tertiary structural dimensions of human IFNAR-2 protein, including the specific topological domains that contribute towards the subcellular compartmentalization and functional characteristics.

As primitive metazoa, sea anemones are rich in various bioactive peptide neurotoxins. These peptides have been applied to neuroscience research tools or directly developed as marine drugs. To date, more than 1100 species of sea anemones have been reported, but only 5% of the species have been used to isolate and identify sea anemone peptide neurotoxins. There is an urgent need for more systematic discovery and study of peptide neurotoxins in sea anemones. In this review, we have gathered the currently available methods from crude venom purification and gene cloning to venom multiomics, employing these techniques for discovering novel sea anemone peptide neurotoxins. In addition, the three-dimensional structures and targets of sea anemone peptide neurotoxins are summarized. Therefore, the purpose of this review is to provide a reference for the discovery, development, and utilization of sea anemone peptide neurotoxins.