Detailed Structure Research Articles

BODIPY-Based NIR Trackers with Acidity-Driven Amphiphilicity for STED Super-Resolution Imaging of Lysosomal Membranes.

Although super-resolution imaging provides a great opportunity to disclose the structures of living cells at the nanoscale level, resolving the structural details of organelles is highly dependent on the targeting accuracy and photophysical properties of fluorescence trackers. Herein, we report a series of ultrabright and photostable trackers of lysosomal membranes for super-resolution imaging using stimulated emission depletion microscopy (STED). These trackers are composed of lipophilic NIR BODIPY derivatives and ionizable tertiary amines. This structural feature enables accurate targeting of the lysosomal membrane through the formation of transient amphiphilicity driven by the acidity in the lysosome. As a representative, Lyso-700 is applied for STED-based super-resolution imaging of the lysosomal membrane of living macrophages. By use of Lyso-700, the interaction details between lysosomes of macrophages and fungi are visualized. Overall, these trackers display great potential as advanced lysosome trackers and merit further evaluation for lysosome-related studies.

Shallow Convection Dataset Simulated by Three Different Large Eddy Models

Shallow convection plays an important role in transporting heat and moisture from the near-surface to higher altitudes, yet its parameterization in numerical models remains a great challenge, partly due to the lack of high-resolution observations. This study describes a large eddy simulation (LES) dataset for four shallow convection cases that differ primarily in inversion strength, which can be used as a surrogate for real data. To reduce the uncertainty in LES modeling, three different large eddy models were used, including SAM (System for Atmospheric Modeling), WRF (Weather Research and Forecasting model), and UCLA-LES.Results show that the different models generally exhibit similar behavior for each shallow convection case, despite some differences in the details of the convective structure. In addition to grid-averaged fields, conditionally sampled variables, such as in-cloud moisture and vertical velocity, are also provided, which are indispensable for calculation of the entrainment/detrainment rate. Considering the essentiality of the entraining/detraining process in the parameterization of cumulus convection, the dataset presented in this study is potentially useful for validation and improvement of the parameterization of shallow convection.

Structural Assignment of the Product Ion Generated from a Natural Ciguatoxin-3C Congener, 51-Hydroxyciguatoxin-3C, and Discovery of Distinguishable Signals in Congeners Bearing the 51-Hydroxy Group.

Ciguatoxins (CTXs) stand as the primary toxins causing ciguatera fish poisoning (CFP) and are essential compounds distinguished by their characteristic polycyclic ether structure. In a previous report, we identified the structures of product ions generated via homolytic fragmentation by assuming three charge sites in the mass spectrometry (MS)/MS spectrum of ciguatoxin-3C (CTX3C) using LC-MS. This study aims to elucidate the homolytic fragmentation of a ciguatoxin-3C congener. We assigned detailed structures of the product ions in the MS/MS spectrum of a naturally occurring ciguatoxin-3C congener, 51-hydroxyciguatoxin-3C (51-hydoxyCTX3C), employing liquid chromatography/quadrupole time-of-flight mass spectrometry with an atmospheric pressure chemical ionization (APCI) source. The introduction of a hydroxy substituent on C51 induced different fragmentation pathways, including a novel cleavage mechanism of the M ring involving the elimination of 51-OH and the formation of enol ether. Consequently, new cleavage patterns generated product ions at m/z 979 (C55H79O15), 439 (C24H39O7), 149 (C10H13O), 135 (C9H11O), and 115 (C6H11O2). Additionally, characteristic product ions were observed at m/z 509 (C28H45O8), 491 (C28H43O7), 481 (C26H41O8), 463 (C26H39O7), 439 (C24H39O7), 421 (C24H37O6), 171 (C9H15O3), 153 (C9H13O2), 141 (C8H13O2), and 123 (C8H11O).

A CRITICAL REVIEW ON FATIGUE ASSESSMENT APPROACH IN SHIP STRUCTURAL DETAILS

Review of the methods used in the fatigue analysis of structures has been widely used. The resulting fatigue is primarily the result of repeated loads acting on the structure both internally and externally. Internal loads are caused by the cargo loading and unloading process, while external loads are caused by sea waves. The interaction of the two loads affects the strength of the structure. In this paper, we will discuss materials, residual stresses and environmental factors that cause fatigue in structures. The focus of analysis in this critical review is on the structural details of the ship. In determining fatigue in detailed structures, it can occur in welded joints, section cuts and shape imperfections.

Influence of variation in grain boundary parameters on the evolution of atomic structure and properties of [111] tilt boundaries in aluminum

Grain boundaries (GBs) are fundamental planar defects in metallic materials, exerting a profound influence on material behaviour and properties. Understanding the influence of GB structure on material performance presents challenges due to the intricate atomic arrangements involved. To overcome inconsistencies observed in previous simulations, experimental validation is necessary. However, research on [111] tilt GBs in metals other than copper, such as aluminium, remains limited. This study aims to address these gaps by investigating the characterization of [111] tilt GBs in Al, employing advanced experimental techniques and validating the findings through simulations. By exploring a range of misorientation angles and plane inclinations, two distinct misorientation groups are identified, each exhibiting unique structural configurations. However, the structural differences resulting from plane inclination are more pronounced than those stemming from misorientation angle. Additionally, it is found that deviations from precise misorientation angles and different plane inclinations significantly influence the excess properties of GBs, such as GB energy and excess volume, etc. Furthermore, comparisons between Al and Cu structures enhance our understanding of GB behaviour in different metallic materials. This study lays the foundation for robust structure-property correlations in GBs and emphasizes the importance of considering intricate GB structural details to better understand and predict their properties accurately.

Fatigue analysis of concrete structures using AI with the introduction of fractal corrosion detection

The article is devoted to the study of fatigue of concrete structures using modern artificial intelligence technologies. The main attention is paid to the use of machine vision for the fractal analysis of reinforced concrete structures. The article presents models optimized for operation in machine vision conditions, which makes it possible to detect signs of corrosion and fatigue with high accuracy and speed. A feature of the presented method is the use of a unique method of infinite fractal discrimination, which allows you to analyze the concrete structure in detail at the micro level. This method reveals unique features and heterogeneities in the structure of the material, which contributes to a more accurate prediction of its behavior under various influences. The application of this approach can become revolutionary in the field of diagnostics and maintenance of infrastructure facilities.

Mitochondrial Cytochrome bc1 Complex as Validated Drug Target: A Structural Perspective.

Mitochondrial respiratory chain Complex III, also known as cytochrome bc1 complex or cyt bc1, is a validated target not only for antibiotics but also for pesticides and anti-parasitic drugs. Although significant progress has been made in understanding the mechanisms of cyt bc1 function and inhibition by using various natural and synthetic compounds, important issues remain in overcoming drug resistance in agriculture and in evading cytotoxicity in medicine. In this review, we look at these issues from a structural perspective. After a brief description of the essential and common structural features, we point out the differences among various cyt bc1 complexes of different organisms, whose structures have been determined to atomic resolution. We use a few examples of cyt bc1 structures determined via bound inhibitors to illustrate both conformational changes observed and implications to the Q-cycle mechanism of cyt bc1 function. These structures not only offer views of atomic interactions between cyt bc1 complexes and inhibitors, but they also provide explanations for drug resistance when structural details are coupled to sequence changes. Examples are provided for exploiting structural differences in evolutionarily conserved enzymes to develop antifungal drugs for selectivity enhancement, which offer a unique perspective on differential interactions that can be exploited to overcome cytotoxicity in treating human infections.

Finite Element Model for Local Instantaneous Impact Protection Analysis Based on Digital Arm

Background: This study investigates the damage in human tissue in regions subjected to stress when the human body experiences localized, instantaneous impact loads. Methods: Utilizing 727 images spanning from the shoulder to the fingertip of a digital human model based on Chinese demographics, the geometric details of tissue structures were derived via tissue segmentation, 3D modeling, and reverse engineering. A stress-induced damage model for the human forearm was created using the finite element simulation software, commercial software COMSOL Multiphysics 5.5 in the college edition. By applying an impact load of 6.4×106 N m2 to the load surface, a response time of 1×10−3 s was determined. Subsequently, the force transmission mechanism was examined when the human forearm was under stress. This approach represents the unique aspect of our patent study. Results: The modeling and analysis revealed that skin, fat, and muscle -being viscoelastic tissues -undergo deformation upon experiencing stress impacts. This deformation aids in dissipating energy. In transient states, the body does not sustain severe damage, and the impact-induced damage to these tissues is relatively minimal. However, if the force duration is prolonged or if the impact load is exceedingly high, exceeding the critical limit of adhesive tissue may result in penetration of the tissue at the stress point. Notably, tissues beyond the direct impact area remain largely unharmed. Conclusion: Damage due to localized, instantaneous impact loads is primarily concentrated on the immediate stress surface, while regions beyond this point incur minimal to no damage. Calculations indicate that, while such impacts can cause penetrating injuries, the resulting wounds are typically small. With prompt medical intervention, these injuries are not debilitating to the human body.

Collaborative Filter Pruning for Efficient Automatic Surface Defect Detection

Surface defect detection is a critical task in industrial production, and numerous methods have been proposed to achieve high detection accuracy. Although deep learning-based approaches have achieved state-of-the-art performances, their vast computational cost and high memory footprint prevent their deployment in resource-constrained environments. To address this problem, we propose a collaborative filter pruning method for the defect detection model, which significantly reduces the number of required calculations and parameters while maintaining high performance, even in cases with tasks suffering from the class imbalance problem. Our method aims to obtain lightweight pruned models by removing unimportant filters according to their importance evaluated by both structural similarity and detail richness of corresponding feature maps. Moreover, to improve the performance of pruned models, we propose a knowledge-fused fine-tuning approach that fuses the knowledge derived from two teacher networks to look after both representation learning and classifier learning, alleviating the class imbalance problem. Experimental results on four public datasets demonstrate that the proposed approach performs favorably relative to the state-of-the-art methods. In particular, the proposed method achieves 39× and 59× parameter compression for VGG-16 and ResNet-50, respectively, on the NEU-CLS dataset, with a very small detection accuracy loss (< 0.2%). The code is available at <uri xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/HXuan-Wang/CFP</uri> .

Spectroscopic Characterization of Mn1+ Low Oxidation State in Prussian Blue-Based Battery Anodes.

Stabilization of ions in exotic oxidation states is beneficial for the development of new materials for green energy technologies. Exotic Mn1+ was proposed to play a role in the function of sodium-based Prussian blue analogues (PBA) batteries, a highly sought-out technology for industrial energy storage. Here, we report the detailed electronic structure characterization of uncharged and charged sodium-based manganese hexacyanomanganate anodes via Mn K-edge X-ray absorption spectroscopy (XAS), Kβ nonresonant X-ray emission (XES), and resonant inelastic X-ray scattering (RIXS). The latter allowed us to obtain site-selective XANES information about two distinct Mn centers. The obtained spectroscopic data represent the first electronic structure characterization of low-spin Mn1+ using hard X-ray RIXS and XES and allowed us to confirm its role in anode reduction. Our experimental approach can be expanded to analysis of analogues with other 3d transition metals broadening the application of exotic ionic states in materials engineering.

Advances in machine learning optimization for classical and quantum photonics

The development and optimization of photonic devices and various other nanostructure electromagnetic devices present a computationally intensive task. Much optimization relies on finite-difference time-domain or finite element analysis simulations, which can become very computationally demanding for finely detailed structures and dramatically reduce the available optimization space. In recent years, various inverse design machine learning (ML) techniques have been successfully applied to realize previously unexplored optimization spaces for photonic and quantum photonic devices. In this review, recent results using conventional optimization methods, such as the adjoint method and particle swarm, are examined along with ML optimization using convolutional neural networks, Bayesian optimizations with deep learning, and reinforcement learning in the context of new applications to photonics and quantum photonics.

Detection of new pioneer transcription factors as cell-type-specific nucleosome binders.

Wrapping of DNA into nucleosomes restricts accessibility to DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, initiate local chromatin opening, and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding, and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2, and HeLa-S3 cell lines. Last, we systematically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.

Detection of new pioneer transcription factors as cell-type-specific nucleosome binders

Wrapping of DNA into nucleosomes restricts accessibility to DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, initiate local chromatin opening, and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding, and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2, and HeLa-S3 cell lines. Last, we systematically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.

Hydroponic Trough Systems for Maximising Cucumber Production

Abstract: Hydroponics is a promising solution to address the increasing demand for food caused by limited arable land and a growing global population. This article focuses on the use of hydroponics in cucumber cultivation, specifically highlighting the adaptability of hydroponic trough system. It explains the design elements of the trough system in detail, including configuration, growing medium, nutrient solution, and support structures. The article emphasises the advantages of hydroponic trough systems in cucumber cultivation, such as precise nutrient dispensation, space efficiency, water conservation, and potential for automation. It discusses strategies for optimal cucumber production within these systems, including temperature control, pollination techniques, pruning, and pH monitoring. The article also addresses the challenges of insect and pest attacks, introducing common pests and presenting integrated pest management strategies for effective control. It explores diseases that can affect cucumber crops in hydroponic systems, such as powdery mildew, downy mildew, Pythium root rot, and Fusarium wilt. It discusses strategies to prevent these diseases, including preventive measures, disease-resistant cucumber varieties, cultural practices, and bio methods. By considering all these aspects, a comprehensive approach to disease management can be established. Overall, adopting hydroponic trough systems in cucumber cultivation offers a sustainable and efficient solution to traditional farming challenges. By incorporating preventive measures, disease-resistant cultivars, and organic remedies, farmers can ensure a thriving cucumber harvest and contribute to a productive and sustainable agricultural future.

CG-CFPANet: a multi-task network for built-up area extraction from SDGSAT-1 and Sentinel-2 remote sensing images

ABSTRACT Accurate extraction of built-up areas is helpful to urban development and map updating. Nighttime light (NTL) data can capture the lighting signal of ground objects. However, most built-up area extraction is conducted on public limited coarse spatial resolution NTL images. The Sustainable Development Science Satellite-1 (SDGSAT-1) provides 10 m spatial resolution panchromatic NTL images, making it possible to map detailed urban lighting structures. In urban extraction, the boundaries of urban areas are easily confused with background objects due to the similar spectral and textual features. To address this problem, we proposed a multi-task deep learning model, CG-CFPANet, to extract illuminated built-up areas by synthesizing SDGSAT-1 NTL data and optical remote sensing images. In CG-CFPANet, a convolutional feature pyramid attention (CFPA) module for better contextual recognition and a concatenation group (CG) module to merge the two remote sensing images are developed. Our proposed CG-CFPANet achieved 1.3% higher precision in built-up area extraction than ten other recently proposed network structures: UNet, UNet++, PSPNet, DeeplabV3, FCN, ExtremeC3Net, SegNet, BiseNet, Res2-UNet, and CBRNet. It shows higher applicability for large-scale built-up area extraction.

Structural and Functional Analysis of Groundnut bud necrosis virus (GBNV) Using Computational and Biochemical Approaches.

Groundnut bud necrosis virus (GBNV) belonging to the genus Orthotospovirus is transmitted by its vector Thrips palmi. It is a tri-segmented RNA virus that consists of L, M, and S RNA segments. We analysed the secondary structure features of GBNV proteins through various software and predicted the transmembrane helix, glycosylation, and signal peptidase sites within the GBNV protein sequences (GN, GC, N, NSm, and NSs). In glycoprotein sequence, extended strands are predominant (52.87%) whereas the N protein sequence mostly contains alpha helices (47.46%). The random coils are present in movement protein (43.97%) and structural protein (39.41%). We generated the 3D structure of GN and N protein using SWISS MODEL software and quality is validated through PROCHECK and PDBsum software. We also expressed the GBNV proteins (GN, GC, N, NSm, and NSs) in bacterial expression system. The recombinant proteins were used to raise polyclonal antibodies in mice. Our study will be useful in understanding GBNV protein structures in further detail by analysing the important domains that interact with the thrips proteins. This will further aid us in understanding virus-vector relationship through the application of protein-protein interaction and other immunodiagnostic techniques.

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM.

Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions.

Structural Design of RCC Building Using Integrated BIM-Based Design Workflow and Analysis Result Comparison between ETABS and RSAP

Rapid computerization and stakeholder integration in the construction industry stressed the need for a new design methodology that was only possible through BIM. To address the inefficiency and limitations of conventional design flow that lead to design clashes, information loss, delays, and poor stakeholders’ coordination throughout the design phase, as well as the designer’s reluctance to use BIM-integrated software for design. This study aims to develop an integrated design flow using the Autodesk system followed by structural design through the developed flow. Further, the study also aims to identify and resolve design clashes between architectural and structural models and incorporate analysis results comparison of RSAP and ETABS. The results of the study revealed that BIM design flow provided better coordination between stakeholders, speedy clash detection, and resolved bi-directional interoperability issues using an extension (structural analysis toolkit). Furthermore, design through BIM provided better visualization i.e., both 2D and 3D, and final documentation in the shape of structural detailing of designed elements. Navisworks successfully identified coordinate and element clashes between architectural and structural models and provided a virtual 3D representation of the facility before the construction phase. The analysis results of RSAP and ETABS revealed that RSAP gives higher analysis results than ETABS due to the different analysis procedures of the two software packages thus yielding safer design.

Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23.

Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.

Huge mobility difference between the neutral and charged steps on 180° domain walls of PbTiO3 by first-principles calculations

The microscopic mechanism of ferroelectric switching is the motion of domain walls, which is actually accomplished by the movement of tiny steps on the domain walls. Using first-principles calculations, the detailed polarization structures and the motion barriers of neutral and charged steps on 180° domain walls of prototypical ferroelectrics PbTiO3 are elaborately revealed in this study. While the Bloch components get weakened near all neutral steps, they become weakened/strengthened near the head-to-head/tail-to-tail charged steps. The neutral step possesses a lower formation energy but a higher migration barrier, indicating that the charged step could move faster. Based on these results, the possible motion picture of steps on one 180° domain wall of tetragonal ferroelectrics is proposed, which provides a better understanding of the mechanism of domain wall motion and may shed light on the future development of domain wall–based functional devices.