Efficient Blind Spectral Unmixing of Fluorescently Labeled Samples Using Multi-Layer Non-Negative Matrix Factorization

The ample variety of labeling dyes and staining methods available in fluorescence microscopy has enabled biologists to advance in the understanding of living organisms at cellular and molecular level. When two or more fluorescent dyes are used in the same preparation, or one dye is used in the presence of autofluorescence, the separation of the fluorescent emissions can become problematic. Various approaches have been recently proposed to solve this problem. Among them, blind non-negative matrix factorization is gaining interest since it requires little assumptions about the spectra and concentration of the fluorochromes. In this paper, we propose a novel algorithm for blind spectral separation that addresses some of the shortcomings of existing solutions: namely, their dependency on the initialization and their slow convergence. We apply this new algorithm to two relevant problems in fluorescence microscopy: autofluorescence elimination and spectral unmixing of multi-labeled samples. Our results show that our new algorithm performs well when compared with the state-of-the-art approaches for a much faster implementation.     

Identification of circRNA and mRNA expression profiles and functional networks of vascular tissue in lipopolysaccharide‐induced sepsis

Sepsis is the most common cause of death in intensive care units. This study investigated the circular RNA (circRNA) and mRNA expression profiles and functional networks of the aortic tissue in sepsis. We established a lipopolysaccharide (LPS)‐induced rat sepsis model. High‐throughput sequencing was performed on the aorta tissue to identify differentially expressed (DE) circRNAs and mRNAs, which were validated by real‐time quantitative polymerase chain reaction (RT‐qPCR). Bioinformatic analysis was carried out and coding and non‐coding co‐expression (CNC) and competing endogenous RNA (ceRNA) regulatory networks were constructed to investigate the mechanisms. In total, 373 up‐regulated and 428 down‐regulated circRNAs and 2063 up‐regulated and 2903 down‐regulated mRNAs were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of mRNAs showed that the down‐regulated genes were mainly enriched in the process of energy generation. CNC and ceRNA regulatory networks were constructed with seven DE circRNAs. The results of functional enrichment analysis of CNC target genes revealed the important role of circRNAs in inflammatory response. The ceRNA network also highlighted the significant enrichment in calcium signalling pathway. Significant alterations in circRNAs and mRNAs were observed in the aortic tissue of septic rats. In addition, CNC and ceRNA networks were established.     

A Paper-Fiber-Supported 3D SERS Substrate

Plasmonics - Surface-enhanced Raman scattering (SERS) spectroscopy is an effective approach for trace-level detection of molecular substance. Plasmonic metallic nanostructures with high...     

Osthole stimulates bone formation,drives vascularization and retards adipogenesis to alleviate alcohol‐induced osteonecrosis of the femoral head

Characteristic pathological changes in osteonecrosis of the femoral head (ONFH) include reduced osteogenic differentiation of bone mesenchymal stem cells (BMSCs), impaired osseous circulation and increased intramedullary adipocytes deposition. Osthole is a bioactive derivative from coumarin with a wide range of pharmacotherapeutic effects. The aim of this study was to unveil the potential protective role of osthole in alcohol‐induced ONFH. In vitro, ethanol (50 mmol/L) remarkably decreased the proliferation and osteogenic differentiation of BMSCs and impaired the proliferation and tube formation capacity of human umbilical vein endothelial cell (HUVECs), whereas it substantially promoted the adipogenic differentiation of BMSCs. However, osthole could reverse the effects of ethanol on osteogenesis via modulating Wnt/β‐catenin pathway, stimulate vasculogenesis and counteract adipogenesis. In vivo, the protective role of osthole was confirmed in the well‐constructed rat model of ethanol‐induced ONFH, demonstrated by a cascade of radiographical and pathological investigations including micro‐CT scanning, haematoxylin‐eosin staining, TdT‐mediated dUTP nick end labelling, immunohistochemical staining and fluorochrome labelling. Taken together, for the first time, osthole was demonstrated to rescue the ethanol‐induced ONFH via promoting bone formation, driving vascularization and retarding adipogenesis.     

Interface Engineering of Hierarchical Branched Mo‐Doped Ni3S2/NixPy Hollow Heterostructure Nanorods for Efficient Overall Water Splitting

Rational design and construction of bifunctional electrocatalysts with excellent activity and durability is imperative for water splitting. Herein, a novel top‐down strategy to realize a hierarchical branched Mo‐doped sulfide/phosphide heterostructure (Mo‐Ni₃S₂/Ni_xP_y hollow nanorods), by partially phosphating Mo‐Ni₃S₂/NF flower clusters, is proposed. Benefitting from the optimized electronic structure configuration, hierarchical branched hollow nanorod structure, and abundant heterogeneous interfaces, the as‐obtained multisite Mo‐Ni₃S₂/Ni_xP_y/NF electrode has remarkable stability and bifunctional electrocatalytic activity in the hydrogen evolution reaction (HER)/oxygen evolution reaction (OER) in 1 m KOH solutions. It possesses an extremely low overpotential of 238 mV at the current density of 50 mA cm^?2 for OER. Importantly, when assembled as anode and cathode simultaneously, it merely requires an ultralow cell voltage of 1.46 V to achieve the current density of 10 mA cm^?2, with excellent durability for over 72 h, outperforming most of the reported Ni‐based bifunctional materials. Density functional theory results further confirm that the doped heterostructure can synergistically optimize Gibbs free energies of H and O‐containing intermediates (OH*, O*, and OOH*) during HER and OER processes, thus accelerating the catalytic kinetics of electrochemical water splitting. This work demonstrates the importance of the rational combination of metal doping and interface engineering for advanced catalytic materials.     

Half‐Heusler Thermoelectric Module with High Conversion Efficiency and High Power Density

Half‐Heusler (HH) compounds have shown great potential in waste heat recovery. Among them, p‐type NbFeSb and n‐type ZrNiSn based alloys have exhibited the best thermoelectric (TE) performance. However, TE devices based on NbFeSb‐based HH compounds are rarely studied. In this work, bulk volumes of p‐type (Nb_0.8Ta_0.2)_0.8Ti_0.2FeSb and n‐type Hf_0.5Zr_0.5NiSn_0.98Sb_0.02 compounds are successfully prepared with good phase purity, compositional homogeneity, and matchable TE performance. The peak zTs are higher than 1.0 at 973 K for Hf_0.5Zr_0.5NiSn_0.98Sb_0.02 and at 1200 K for (Nb_0.8Ta_0.2)_0.8Ti_0.2FeSb. Based on an optimal design by a full‐parameters 3D finite element model, a single stage TE module with 8 n‐p HH couples is assembled. A high conversion efficiency of 8.3% and high power density of 2.11 W cm^?2 are obtained when hot and cold side temperatures are 997 and 342 K, respectively. Compared to the previous TE module assembled by the same materials, the conversion efficiency is enhanced by 33%, while the power density is almost the same. Given the excellent mechanical robustness and thermal stability, matchable thermal expansion coefficient and TE properties of NbFeSb and ZrNiSn based HH alloys, this work demonstrates their great promise for power generation with both high conversion efficiency and high power density.     

Enhanced regional terrestrial carbon uptake over Korea revealed by atmospheric CO2 measurements from 1999 to 2017

Understanding changes in terrestrial carbon balance is important to improve our knowledge of the regional carbon cycle and climate change. However, evaluating regional changes in the terrestrial carbon balance is challenging due to the lack of surface flux measurements. This study reveals that the terrestrial carbon uptake over the Republic of Korea has been enhanced from 1999 to 2017 by analyzing long‐term atmospheric CO₂ concentration measurements at the Anmyeondo Station (36.53°N, 126.32°E) located in the western coast. The influence of terrestrial carbon flux on atmospheric CO₂ concentrations (ΔCO₂) is estimated from the difference of CO₂ concentrations that were influenced by the land sector (through easterly winds) and the Yellow Sea sector (through westerly winds). We find a significant trend in ΔCO₂ of ?4.75 ppm per decade (p < .05) during the vegetation growing season (May through October), suggesting that the regional terrestrial carbon uptake has increased relative to the surrounding ocean areas. Combined analysis with satellite measured normalized difference vegetation index and gross primary production shows that the enhanced carbon uptake is associated with significant nationwide increases in vegetation and its production. Process‐based terrestrial model and inverse model simulations estimate that regional terrestrial carbon uptake increases by up to 18.9 and 8.0 Tg C for the study period, accounting for 13.4% and 5.7% of the average annual domestic carbon emissions, respectively. Atmospheric chemical transport model simulations indicate that the enhanced terrestrial carbon sink is the primary reason for the observed ΔCO₂ trend rather than anthropogenic emissions and atmospheric circulation changes. Our results highlight the fact that atmospheric CO₂ measurements could open up the possibility of detecting regional changes in the terrestrial carbon cycle even where anthropogenic emissions are not negligible.     

GPI7-mediated glycosylphosphatidylinositol anchoring regulates appressorial penetration and immune evasion during infection of Magnaporthe oryzae

Glycosylphosphatidylinositol (GPI) anchoring plays key roles in many biological processes by targeting proteins to the cell wall; however, its roles are largely unknown in plant pathogenic fungi. Here, we reveal the roles of the GPI anchoring in Magnaporthe oryzae during plant infection. The GPI-anchored proteins were found to highly accumulate in appressoria and invasive hyphae. Disruption of GPI7, a GPI anchor-pathway gene, led to a significant reduction in virulence. The Δgpi7 mutant showed significant defects in penetration and invasive growth. This mutant also displayed defects of the cell wall architecture, suggesting GPI7 is required for cell wall biogenesis. Removal of GPI-anchored proteins in the wild-type strain by hydrofluoric acid (HF) pyridine treatment exposed both the chitin and β-1,3-glucans to the host immune system. Exposure of the chitin and β-1,3-glucans was also observed in the Δgpi7 mutant, indicating GPI-anchored proteins are required for immune evasion. The GPI anchoring can regulate subcellular localization of the Gel proteins in the cell wall for appressorial penetration and abundance of which for invasive growth. Our results indicate the GPI anchoring facilitates the penetration of M. oryzae into host cells by affecting the cell wall integrity and the evasion of host immune recognition.     

The essential effector SCRE1 in Ustilaginoidea virens suppresses rice immunity via a small peptide region

The biotrophic fungal pathogen Ustilaginoidea virens causes rice false smut, a newly emerging plant disease that has become epidemic worldwide in recent years. The U. virens genome encodes many putative effector proteins that, based on the study of other pathosystems, could play an essential role in fungal virulence. However, few studies have been reported on virulence functions of individual U. virens effectors. Here, we report our identification and characterization of the secreted cysteine-rich protein SCRE1, which is an essential virulence effector in U. virens. When SCRE1 was heterologously expressed in Magnaporthe oryzae, the protein was secreted and translocated into plant cells during infection. SCRE1 suppresses the immunity-associated hypersensitive response in the nonhost plant Nicotiana benthamiana. Induced expression of SCRE1 in rice also inhibits pattern-triggered immunity and enhances disease susceptibility to rice bacterial and fungal pathogens. The immunosuppressive activity is localized to a small peptide region that contains an important ‘cysteine-proline-alanine-arginine-serine’ motif. Furthermore, the scre1 knockout mutant generated using the CRISPR/Cas9 system is attenuated in U. virens virulence to rice, which is greatly complemented by the full-length SCRE1 gene. Collectively, this study indicates that the effector SCRE1 is able to inhibit host immunity and is required for full virulence of U. virens.