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Hierarchical and periodic nanostructures of dielectrics or metals are highly demanded for wide applications in optical, electrical, biological, and quantum devices. In this work, programmable plasmonic–photonic hierarchical nanostructures are fabricated using a facile and effective method with high controllability and stable reproducibility. The fabrication involves colloidal self-assembly, metal film deposition, and pulsed laser-induced dewetting in sequence for controllably pairing metal nanostructures on dielectric nanospheres in either large area or a local precision. Au nanostructures including Au nanocrown (AuNC), large Au nanosphere (AuNS), and multiple small Au nanoparticles (AuNPs) have been paired one-on-one on assembled SiO2 nanosphere (SiO2NS) arrays, with size and shape controlled by correlating the laser fluence and irradiation time, and the Au film thickness. The fabricated hierarchical nanostructures demonstrate synergistic effect of the photonic effects from the monolayer SiO2NS arrays and the surface plasma resonance effect from the Au nanostructures. The dewetting induced metal film reshaping has been modeled theoretically corresponding to observed experimental results. We can directly “write” the plasmonic Au nanostructures on the photonic crystal array using a focused laser beam to form encode patterns, showing angle-dependent structural colors for anti-counterfeiting information storage and display in rigid/flexible and opaque/transparent devices. It provides a promising path to actively construct on-demand pixelated plasmonic–photonic arrays for optical multiplexing technology in sensing, information encryption, and display.

Bursting is a crucial form of firing in neurons, laden with substantial information. Studying it can aid in understanding the neural coding to identify human behavioral characteristics conducted by these neurons. However, the high-dimensionality of many neuron models imposes a difficult challenge in studying the generative mechanisms of bursting. On account of the high complexity and nonlinearity characteristic of these models, it becomes nearly impossible to theoretically study and analyze them. Thus, this paper proposed to address these issues by focusing on the midbrain dopamine neurons, serving as the central neuron model for the investigation of the bursting mechanisms and bifurcation behaviors exhibited by the neuron. In this study, we considered the dimensionality reduction of a high-dimensional neuronal model and analyzed the dynamical properties of the reduced system. To begin, for the original thirteen-dimensional model, using the correlation between variables, we reduced its dimensionality and obtained a simplified three-dimensional system. Then, we discussed the changing characteristics of the number of spikes within a burst by simultaneously varying two parameters. Finally, we studied the co-dimension-2 bifurcation in the reduced system and presented the bifurcation behavior near the Bogdanov-Takens bifurcation. [ABSTRACT FROM AUTHOR]

Interactions between proteins and glycans are critical to various biological processes. With databases of carbohydrate-interacting proteins and increasing amounts of structural data, the three-sided right-handed β-helix (RHBH) has emerged as a significant structural fold for glycan interactions. In this review, we provide an overview of the sequence, mechanistic, and structural features that enable the RHBH to interact with glycans. The RHBH is a prevalent fold that exists in eukaryotes, prokaryotes, and viruses associated with adhesin and carbohydrate-active enzyme (CAZyme) functions. An evolutionary trajectory analysis on structurally characterized RHBH-containing proteins shows that they likely evolved from carbohydrate-binding proteins with their carbohydrate-degrading activities evolving later. By examining three polysaccharide lyase and three glycoside hydrolase structures, we provide a detailed view of the modes of glycan binding in RHBH proteins. The 3-dimensional shape of the RHBH creates an electrostatically and spatially favorable glycan binding surface that allows for extensive hydrogen bonding interactions, leading to favorable and stable glycan binding. The RHBH is observed to be an adaptable domain capable of being modified with loop insertions and charge inversions to accommodate heterogeneous and flexible glycans and diverse reaction mechanisms. Understanding this prevalent protein fold can advance our knowledge of glycan binding in biological systems and help guide the efficient design and utilization of RHBH-containing proteins in glycobiology research. [ABSTRACT FROM AUTHOR]

Introduction: The objective of this study was to examine the utility of protein kinase N1 (PKN1) as a biomarker of cardiac surgery-associated AKI (CSA-AKI). Methods: A prospective cohort study of 110 adults undergoing on-pump cardiac surgery was conducted. The associations between post-operative PKN1 and CSA-AKI, AKI severity, need for renal replacement therapy (RRT), duration of AKI, length of ICU stay, and post-operative hospital stay were evaluated. Results: Patients were categorized into three groups according to PKN1 tertiles. The incidence of CSA-AKI in the third tertile was 3.4-fold higher than that in the first. PKN1 was an independent risk factor for CSA-AKI. The discrimination of PKN1 to CSA-AKI assessed by ROC curve indicated that the AUC was 0.70, and the best cutoff was 5.025 ng/mL. This group (>5.025 ng/mL) was more likely to develop CSA-AKI (p < 0.001). The combined AUC of EuroSCORE, aortic cross-clamp time, and PKN1 was 0.82 (p < 0.001). A higher level of PKN1 was related to increased need for RRT, longer duration of AKI, and length of ICU and post-operative hospital stays. Conclusions: PKN1 could be a potential biomarker for the prediction of CSA-AKI. The combination of PKN1, EuroSCORE, and aortic cross-clamp time was likely to predict the occurrence of CSA-AKI. [ABSTRACT FROM AUTHOR]

Intrinsic bursting neurons represent a common neuronal type that displays bursting patterns upon depolarization stimulation. These neurons can be described by a system of seven-dimensional equations, which pose a challenge for dynamical analysis. To overcome this limitation, we employed the projection reduction method to reduce the dimensionality of the model. Our approach demonstrated that the reduced model retained the inherent bursting characteristics of the original model. Following reduction, we investigated the bi-parameter bifurcation of the equilibrium point in the reduced model. Specifically, we analyzed the Bogdanov-Takens bifurcation that arises in the reduced system. Notably, the topological structure of the neuronal model near the bifurcation point can be effectively revealed with our proposed method. By leveraging the proposed projection reduction method, we could explore the bursting mechanism in the reduced Pospischil model with greater precision. Our approach offers an effective foundation for generating theories and hypotheses that can be tested experimentally. Furthermore, it enables links to be drawn between neuronal morphology and function, thereby facilitating a deeper understanding of the complex dynamical behaviors that underlie intrinsic bursting neurons. [ABSTRACT FROM AUTHOR]

Soil ecosystem provides a guarantee for the ecological environment. Soil salinization is a typical land degradation problem. In order to explore the applicability of GF-5, Sentinel-1, and Sentinel-2 remote sensing data in soil salinity research, this study selected Golmud of Qaidam Basin in China as the study area, using particle swarm optimization-artificial neural network (PSO-ANN), partial least squares regression (PLSR), and whale optimization algorithm-extreme learning machine (WOA-ELM) to predict soil salinity. The research results indicated that the correlation between Sentinel-2 and electric conductivity (EC) was higher than GF-5 and Sentinel-1. The simulation accuracy of models based on Sentinel-2 was slightly higher than that based on GF-5 and Sentinel-1. The three models' mean values of root mean square error (RMSE), R2, and mean absolute error (MAE) of Sentinel-2 were slightly better than those of GF-5 and Sentinel-1, and the fitting accuracy of GF-5 was similar to that of Sentinel-1 on the whole. The result proved that Sentinel-1, GF-5, and Sentinel-2 were suitable for salinity monitoring because the strong penetrability and sensitivity of Sentinel-1, the high spectral resolution of GF-5, and the high spatial resolution of Sentinel-2. The performance of PSO-ANN was the best, and that of PLSR was the worst. The salinity mapping result of Sentinel-2 coupled with PSO-ANN proved that machine learning methods and spaceborne data could be used to study large-scale soil salinization. [ABSTRACT FROM AUTHOR]

Reported data of measured slip lengths in nanostructures span several orders of magnitude, from a few nanometers to tens of micrometers. Small roughness on surfaces caused by structural defects or thermal fluctuations dramatically reduces slippage. Tiny bubbles entrapped on rough surfaces can also affect slippage. We used an asymptotic solution and a high density-ratio pseudopotential lattice Boltzmann model to systematically study the drag resistance of a rough surface with attached bubbles. As bubbles nucleate and grow, drag resistance is slightly reduced until the tri-phase contact line reaches the edges of roughness, where bubbles with small angles substantially reduce drag resistance. As bubbles grow to become a continuous gas layer on the surface, the drag resistance greatly decreases. However, the interface deformation from flat to curved shape greatly hinders liquid flow, and the vortex structures cause a wave-like fluctuation in the effective slip length. This finding sheds light on the controversies of reported large variations in the slip length of super-hydrophobic surfaces in nanostructures, e.g., carbon nanotubes. [ABSTRACT FROM AUTHOR]

Motivation The discovery of the genetic features that underly a phenotype is a fundamental task in microbial genomics. With the growing number of microbial genomes that are paired with phenotypic data, new challenges, and opportunities are arising for genotype-phenotype inference. Phylogenetic approaches are frequently used to adjust for the population structure of microbes but scaling them to trees with thousands of leaves representing heterogeneous populations is highly challenging. This greatly hinders the identification of prevalent genetic features that contribute to phenotypes that are observed in a wide diversity of species. Results In this study, Evolink was developed as an approach to rapidly identify genotypes associated with phenotypes in large-scale multispecies microbial datasets. Compared with other similar tools, Evolink was consistently among the top-performing methods in terms of precision and sensitivity when applied to simulated and real-world flagella datasets. In addition, Evolink significantly outperformed all other approaches in terms of computation time. Application of Evolink on flagella and gram-staining datasets revealed findings that are consistent with known markers and supported by the literature. In conclusion, Evolink can rapidly detect phenotype-associated genotypes across multiple species, demonstrating its potential to be broadly utilized to identify gene families associated with traits of interest. Availability and implementation The source code, docker container, and web server for Evolink are freely available at https://github.com/nlm-irp-jianglab/Evolink. [ABSTRACT FROM AUTHOR]

Materials with large optical nonlinearity are highly desired for various applications such as all-optical signal processing and storage. Recently, indium tin oxide (ITO) has been found to possess strong optical nonlinearity in the spectral region where its permittivity vanishes. Here, we demonstrate that ITO/Ag/ITO trilayer coatings, deposited by magnetron sputtering with high-temperature heat treatment, can significantly enhance the nonlinear response in their effective epsilon-near-zero (ENZ) regions. The obtained results show that the carrier concentrations of our trilayer samples can reach 7.25 × 1021 cm−3, and the ENZ region can shift to the spectrum close to the visible range. In the ENZ spectral region, the ITO/Ag/ITO samples exhibit enhanced nonlinear refractive indices as large as 2.397 × 10−15 m2 W−1, over 27 times larger than that of an individual ITO layer. Such a nonlinear optical response is well described using a two-temperature model. Our findings provide a new paradigm for developing nonlinear optical devices for applications requiring low power. [ABSTRACT FROM AUTHOR]

The CRISPR-Cas system is an adaptive immune system for many bacteria and archaea to defend against foreign nucleic acid invasion, and this system is conserved in the genome of M. tuberculosis (Mtb). Although the CRISPR-Cas system-mediated immune defense mechanism has been revealed in Mtb, the regulation of cas gene expression is poorly understood. In this study, we identified a transcription factor, CasR (CRISPR-associated protein repressor, encoded by Rv1776c), and it could bind to the upstream DNA sequence of the CRISPR-Cas gene cluster and regulate the expression of cas genes. EMSA and ChIP assays confirmed that CasR could interact with the upstream sequence of the csm6 promoter, both in vivo and in vitro. Furthermore, DNA footprinting assay revealed that CasR recognized a 20 bp palindromic sequence motif and negatively regulated the expression of csm6. In conclusion, our research elucidates the regulatory effect of CasR on the expression of CRISPR-associated genes in mycobacteria, thus providing insight into gene expression regulation of the CRISPR-Cas system. [ABSTRACT FROM AUTHOR]