SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse.

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.

Soil N2 O emissions from specialty crop systems: A global estimation and meta-analysis.

Nitrous oxide (N2 O) exacerbates the greenhouse effect and thus global warming. Agricultural management practices, especially the use of nitrogen (N) fertilizers and irrigation, increase soil N2 O emissions. As a vital sector of global agriculture, specialty crop systems usually require intensive input and management. However, soil N2 O emissions from global specialty crop systems have not been comprehensively evaluated. Here, we synthesized 1137 observations from 114 published studies, conducted a meta-analysis to evaluate the effects of agricultural management and environmental factors on soil N2 O emissions, and estimated global soil N2 O emissions from specialty crop systems. The estimated global N2 O emission from specialty crop soils was 1.5 Tg N2 O-N year-1 , ranging from 0.5 to 4.5 Tg N2 O-N year-1 . Globally, soil N2 O emissions exponentially increased with N fertilizer rates. The effect size of N fertilizer on soil N2 O emissions generally increased with mean annual temperature, mean annual precipitation, and soil organic carbon concentration but decreased with soil pH. Global climate change will further intensify the effect of N fertilizer on soil N2 O emissions. Drip irrigation, fertigation, and reduced tillage can be used as essential strategies to reduce soil N2 O emissions and increase crop yields. Deficit irrigation and non-legume cover crop can reduce soil N2 O emissions but may also lower crop yields. Biochar may have a relatively limited effect on reducing soil N2 O emissions but be effective in increasing crop yields. Our study points toward effective management strategies that have substantial potential for reducing N2 O emissions from global agricultural soils.

Gelatin sponge functionalized with gold/silver clusters for antibacterial application.

Pathogenic bacterial infection, especially in the wound, may threaten human health. Developing new antibacterial materials for wound healing is still urgent. Metal nanoclusters have been explored as a novel antibacterial agent. Herein, biomolecule gelatin was chosen as a substrate and functionalized with gold/silver clusters for bacterial killing. Through a simple amidation reaction, gold/silver clusters were successfully conjugated in a gelatin substrate to obtain a Au/Ag@gelatin sponge. The presence of gold/silver clusters modified the porous structure of the gelatin. Thus, the water absorption and water retention of the Au/Ag@gelatin sponge were enhanced. More importantly, the gold/silver clusters show aggregation-enhanced emission and strong reactive oxygen generation, that endow the Au/Ag@gelatin sponge with a good antibacterial property. The good physical performance and favorable bactericidal activity of the Au/Ag@gelatin sponge suggest its potential for application as a wound dressing.

Amorphous Nanocages of Cu-Ni-Fe Hydr(oxy)oxide Prepared by Photocorrosion For Highly Efficient Oxygen Evolution.

Electrochemical water splitting requires efficient, low-cost water oxidation catalysts to accelerate the sluggish kinetics of the water oxidation reaction. A rapid photocorrosion method is now used to synthesize the homogeneous amorphous nanocages of Cu-Ni-Fe hydr(oxy)oxide as a highly efficient electrocatalyst for the oxygen evolution reaction (OER). The as-fabricated product exhibits a low overpotential of 224 mV on a glassy carbon electrode at 10 mA cm-2 (even lower down to 181 mV when supported on Ni foam) with a Tafel slope of 44 mV dec-1 for OER in an alkaline solution. The obtained catalyst shows an extraordinarily large mass activity of 1464.5 A g-1 at overpotential of 300 mV, which is the highest mass activity for OER. This synthetic strategy may open a brand new pathway to prepare copper-based ternary amorphous nanocages for greatly enhanced oxygen evolution.

A Diarylethene-Based Photoswitch and its Photomodulation of the Fluorescence of Conjugated Polymers.

Photochromic diarylethene derivatives, which can reversibly switch the fluorescence of adjacent fluorophores between the ON and OFF states under light irradiation, have been widely used to construct photoswitchable materials. Herein, eight dithienylethene (DTE) groups are integrated onto one polyhedral oligomeric silsesquioxane (POSS) core, obtaining a novel super molecular photoswitch. After being doped into conjugated polymer nanoparticles, the POSS-DTE8 molecules show a higher contrast on/off photoswitching performance and a quicker responsive speed than free DTE molecules at same molar concentration of photochromic units. This enhanced photoswitching efficiency is attributed to the increased molecular interaction of the ring-open form and lowered energy of the ring-closed form of the DTE units on the POSS core, which is beneficial for the ring-closing reaction and subsequent energy transfer between photoswitch and fluorophores. In addition, POSS-DTE8 also exhibits good photomodulation behavior in the conjugated polymer film, giving it potential applications in optical devices.

Graphitic Carbon Nitride as a Distinct Solid Stabilizer for Emulsion Polymerization.

g-C3 N4 has been found to be highly functional in many fields, such as photocatalysis, electrocatalysis, and chemical analysis. Pickering emulsion polymerization is a fascinating strategy to fabricate a range of nanomaterials, in which the emulsion is stabilized by solid particles, rather than molecular surfactants. Herein, we demonstrate that g-C3 N4 can act as a remarkable stabilizer for Pickering emulsion polymerization. Contrary to normal Pickering systems, monodisperse polystyrene microspheres with tunable size, surface charge, and morphology were achieved using this approach. Importantly, the g-C3 N4 hybridized latex is highly processable and has exhibited multiple functions: manufacture of photonic crystals via self-organization, stabilizing Pickering emulsion owing to proper wettability, and acting as bioimaging agents with enriched fluorescent colors. Considering the easy synthesis and low cost of g-C3 N4 , our approach has a high potential for scale-up synthesis and practical translation.

Mild Synthesis of Copper Nanoparticles with Enhanced Oxidative Stability and Their Application in Antibacterial Films.

Copper nanoparticles possess unique physical and chemical properties; however, their application is often restricted, owing to their tendency to oxidize. In this work, we prepared copper nanoparticles with enhanced oxidative stability via a simple and low-cost method, where a modified starch was used as an environmentally friendly reducing agent and biocompatible polyethylenimine was used as a stabilizer. The prepared copper nanoparticles could be stored in air for at least 6 months without any oxidation in a dried state. Interestingly, our synthesis could even be performed at room temperature with a longer reaction time. We used various characterization methods to study the reaction mechanism. The prepared copper nanoparticles were further uniformly doped into an agar film, and this composite showed excellent bacterial killing efficiency, owing to the antibacterial properties of the copper nanoparticles. Our composite film shows potential for various clinical applications, such as wound dressing materials.

Synthesis of photothermal nanocomposites and their application to antibacterial assays.

In this work, we report a novel gold nanorod (AuNR)-based nanocomposite that shows strong binding to bacterium and high antibacterial efficiency. The AuNRs were used as a photothermal material to transform near-infrared radiation (NIR) into heat. We selected poly (acrylic acid) to modify the surface of the AuNRs based on a simple self-assembly method. After conjugation of the bacterium-binding molecule vancomycin, the nanocomposites were capable of efficiently gathering on the cell walls of bacteria. The nanocomposites exhibited a high bacterial inhibition capability owing to NIR-induced heat generation in situ. Therefore, the prepared photothermal nanocomposites show great potential for use in antibacterial assays.

Tunable fluorescence behaviors of a supramolecular system based on a fluorene derivative and cucurbit[8]uril and its application for ATP sensing.

In this work, we developed a supramolecular fluorescent system based on host-guest interactions between a fluorene derivative carrying two bispyridinium units (FPy) and cucurbit[8]uril (CB[8]). In aqueous solution, the system showed outstanding tunable emission properties. After being encapsulated into the rigid hydrophobic cavity of the CB[8] host, the fluorescence emission of fluorene had an obvious red-shift with enhanced quantum yield. Interestingly, the emission behavior of the FPy/CB[8] complex showed a two-step self-assembly process when the molar ratio of FPy to CB[8] changed from 1 : 1 to 1 : 2. Besides, the influence of several factors on the emission properties of the FPy/CB[8] complex was also investigated, like pH value, salt concentration, and temperature. Finally, the fluorescent FPy/CB[8] complexes displayed a good performance for detection of adenosine-5'-triphosphate (ATP), which can cause aggregation-induced quenching of the complexes via electrostatic attraction.

Phenyl-Modified Carbon Nitride Quantum Dots with Distinct Photoluminescence Behavior.

A novel type of quantum dot (Ph-CN) is manufactured from graphitic carbon nitride by "lining" the carbon nitride structure with phenyl groups through supramolecular preorganization. This approach requires no chemical etching or hydrothermal treatments like other competing nanoparticle syntheses and is easy and safe to use. The Ph-CN nanoparticles exhibit bright, tunable fluorescence, with a high quantum yield of 48.4 % in aqueous colloidal suspensions. Interestingly, the observed Stokes shift of approximately 200 nm is higher than the maximum values reported for carbon nitride based fluorophores. The high quantum yield and the large Stokes shift are related to the structural surface organization of the phenyl groups, which affects the π-electron delocalization in the conjugated carbon nitride networks and induces colloidal stability. The remarkable performance of the Ph-CN nanoparticles in imaging is demonstrated by a simple incubation study with HeLa cells.

Synthesis of Au@Pt bimetallic nanoparticles with concave Au nanocuboids as seeds and their enhanced electrocatalytic properties in the ethanol oxidation reaction.

Herein, a new type of uniform and well-structured Au@Pt bimetallic nanoparticles (BNPs) with highly active concave Au nanocuboids (NCs) as seeds was successfully synthesized by using the classic seed-mediated method. Electrochemical measurements were conducted to demonstrate their greatly enhanced catalytic performance in the ethanol oxidation reaction (EOR). It was found that the electrochemical performance for Au@Pt BNPs with the concave Au NCs as seeds, which were enclosed by {611} high-index facets, could be seven times higher than that of the Au@Pt bimetallic nanoparticles with regular spherical Au NPs as seeds. Furthermore, our findings show that the morphology and electrocatalytic activity of the Au@Pt BNPs can be tuned simply by changing the compositional ratios of the growth solution. The lower the amount of H2PtCl6 used in the growth solution, the thinner the Pt shell grew, and the more high-index facets of concave Au NCs seeds were exposed in Au@Pt BNPs, leading to higher electrochemical activity. These as-prepared concave Au@Pt BNPs will open up new strategies for improving catalytic efficiency and reducing the use of the expensive and scarce resource of platinum in the ethanol oxidation reaction, and are potentially applicable as electrochemical catalysts for direct ethanol fuel cells.

Two-dimensional structure Au nanosheets are super active for the catalytic reduction of 4-nitrophenol.

Two-dimensional structure Au nanosheets with a polygon morphology and controlled thicknesses of ∼15 nm, ∼35 nm, and ∼50 nm were successfully synthesized by a one-step solution reduction method. Scanning and transmission electron microscopy (SEM and TEM), selected area electron diffraction (SEAD) analyses, and X-ray diffraction (XRD) were used to thoroughly study the structure and the formation mechanism of the nanosheets. The catalytic activity of the Au nanosheets was investigated for the reduction of 4-nitrophenol (4-NP) by UV-visible absorption spectroscopy. Against all expectation, the Au nanosheets with such a big lateral (more than 1 µm) size exhibited superior catalytic activity on the selective reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) in the presence of NaBH4. On the other hand, the catalytic activity does closely depend on the thickness of the nanosheets; that is, it decreases with increasing thickness. The reaction can be completed in less than 1 min when catalyzed by Au nanosheets about 15 nm thick. The 100% conversion efficiency was further demonstrated after two catalytic cycles with the thinnest Au nanosheets.

Sensitive detection of acetylcholine based on a novel boronate intramolecular charge transfer fluorescence probe.

A highly sensitive and selective fluorescence method for the detection of acetylcholine (ACh) based on enzyme-generated hydrogen peroxide (H2O2) and a new boronate intramolecular charge transfer (ICT) fluorescence probe, 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-N-butyl-1,8-naphthalimide (BN), was developed. This strategy involves the reaction of ACh with acetylcholinesterase (AChE) to produce choline, which is further oxidized by choline oxidase (ChOx) to obtain betaine and H2O2. The enzyme-generated H2O2 reacts with BN and results in hydrolytic deprotection of BN to generate fluorescent product (4-hydroxyl-N-butyl-1,8-naphthalimide, ON). Two consecutive linear response ranges allow determining ACh in a wide concentration range with a low detection limit of 2.7 nM (signal/noise=3). Compared with other fluorescent probes based on the mechanism of nonspecific oxidation, this reported boronate probe has the advantage of no interference from other biologically relevant reactive oxygen species (ROS) on the detection of ACh. This study provides a new method for the detection of ACh with high selectivity and sensitivity.

One-step synthesis of diazaspiro[4.5]decane scaffolds with exocyclic double bonds.

Unactivated yne-en-ynes reacted with a range of substituted aryl halides in the presence of Pd(OAc)2-PPh3 to afford diazaspiro[4.5]decane with exocyclic double bonds. Three carbon-carbon bonds are formed in this domino reaction, which involves highly regioselective C-C coupling and spiro scaffold steps.

Point decoration of silicon nanowires: an approach toward single-molecule electrical detection.

Probing interactions of biological systems at the molecular level is of great importance to fundamental biology, diagnosis, and drug discovery. A rational bioassay design of lithographically integrating individual point scattering sites into electrical circuits is capable of realizing real-time, label-free biodetection of influenza H1N1 viruses with single-molecule sensitivity and high selectivity by using silicon nanowires as local reporters in combination with microfluidics. This nanocircuit-based architecture is complementary to more conventional optical techniques, but has the advantages of no bleaching problems and no fluorescent labeling. These advantages offer a promising platform for exploring dynamics of stochastic processes in biological systems and gaining information from genomics to proteomics to improve accurate molecular and even point-of-care clinical diagnosis.

Tunable Fluorescence, Morphology, and Antibacterial Behaviors of Conjugated Oligomers via Host-Guest Supramolecular Self-Assembly.

Host-guest supramolecular self-assembly has become one facile but efficient way to regulate the optical properties of conjugated oligomers and construct promising photofunctional materials. Herein, we design two linear conjugated oligomers terminated with two or four pyridinium moieties, which show different 1:1 'head-to-tail' binding patterns with cucurbit[8]uril (CB[8]) to form host-guest supramolecules. After being encapsulated in the hydrophobic cavity of the CB[8] host, the fluorescence emission of the conjugated oligomers undergoes significant changes, resulting in tunable fluorescence color with enhanced quantum yields. Triggered by the aggregation of supramolecules, the regular or rigid binding modes lead to the formation of cuboids and spheroids in nanoscale, respectively. Due to the macrocyclic-confinement effect, the light-driven reactive oxygen species (ROS) production of the host-guest complex is increased significantly, thereby improving the photodynamic antibacterial performance toward Staphylococcus aureus (S. aureus).

Photofunctional Gold Nanocluster Composites for Bioapplications.

Gold nanoclusters (AuNCs), with customized structures and diverse optical properties, are promising optical materials. Constructing composite systems by the assembly and incorporation of AuNCs can utilize their optical properties to achieve diagnostic and therapeutic applications in the biological field. Therefore, the exploration of the assembly behaviors of AuNCs and the enhancement of their performance has attracted widespread interest. In this review, we introduce multiple interactions and assembly modes that are prevalent in nanocomposites and microcomposites based on AuNCs. Then, the functions of AuNC composites for bioapplications are demonstrated in detail. These composite systems have inherited and enhanced the inherent optical performances of the AuNCs to meet diverse requirements for biological sensing and optical treatments. Finally, we discuss the prospects of AuNC composites and highlight the challenges and opportunities in biomedical applications.

Coupling vibration analysis of heat exchanger tube bundles under different stiffness conditions.

A two-dimensional tube bundles fluid-structure coupling model was developed using the CFD approach, with a rigid body motion equation and the Newmark integral method. The numerical simulations were performed to determine the vibration coupling properties between various tube bundles of stiffness. Take the corner square tube bundles with a pitch ratio of 1.28 as the research object. The influence of adjacent tubes with different stiffness on the vibration of the central target tube was analyzed. The research results show that the vibration characteristic of tube bundles is affected by the flow field dominant frequency and the inherent frequency of tube bundles. The vibration of adjacent tube bundles significantly impacts the amplitude and frequency of the central target tube. The equal stiffness and large stiffness tubes upstream or downstream inhibit the vibration displacement of the target tube to some extent. The low-stiffness tubes upstream or downstream significantly enhanced the amplitude of the target tube. The findings can be used to provide a basis for reasonable design and vibration suppression of shell-and-tube heat exchangers.

Structure-dependent electrocatalysis of Ni(OH)2 hourglass-like nanostructures towards L-histidine.

As the properties of nanomaterials are strongly dependent on their size, shape and nanostructures, probing the relations between macro-properties and nanostructures is challenging for nanoscientists. Herein, we deliberately chose three types of Ni(OH)(2) with hexagonal, truncated trigonal, and trigonal hourglass-like nanostructures, respectively, as the electrode modifier to demonstrate the correlation between the nanostructures and their electrocatalytic performance towards L-histidine. It was found that the hexagonal hourglass-like Ni(OH)(2) sample had the best electrocatalytic activity, which can be understood by a cooperative mechanism: on one hand, the hexagonal sample possesses the largest specific surface area and the tidiest nanostructure, resulting in the most orderly packing on the electrode surface; on the other hand, its internal structure with the most stacking faults would generate a lot of unstable protons, leading to an enhanced electronic conductivity. The findings are important because they provide a clue for materials design and engineering to meet a specific requirement for electrocatalysis of L-histidine, possibly even for other biomolecules. In addition, the hexagonal Ni(OH)(2)-based biosensor shows excellent sensitivity and selectivity in the determination of L-histidine and offers a promising feature for the analytical application in real biological samples.

Preparation of bimetallic nanoparticles using a facile green synthesis method and their application.

A straightforward, economically viable, and green approach for the synthesis of well-stabilized Au/Ag bimetallic nanoparticles is described; this method uses nontoxic and renewable degraded pueraria starch (DPS) as a matrix and mild reaction conditions. The DPS acted as both a reducing agent and a capping agent for the bimetallic nanoparticles. Au/Ag bimetallic nanoparticles were successfully grown within the DPS matrixes, and the bimetallic structures were characterized using various methods, including high-resolution transmission electron microscopy, energy-dispersive X-ray, and X-ray diffraction. Moreover, it was shown that these DPS-capped Au/Ag bimetallic nanoparticles could function as catalysts for the reduction of 4-nitrophenol in the presence of NaBH4 and were more effective than Au or Ag monometallic nanoparticles.