Ammonium Arylspiroborate Compounds: Synthesis, Crystal Structure, Fluorescence Properties, and Antibacterial Activity

A series of R-substituted ammonium arylspiroborate compounds (R = CH₃, H, F, Cl, Br) have been synthesized via a facile one-pot method. The structures of these new kinds of boron compounds were characterized by IR, NMR spectra, elemental analysis and X-ray diffraction techniques, and their possible formation mechanism was proposed. Surprisingly, the as-synthesized boron compounds showed multifunctional character with not only excellent fluorescence properties (high quantum yields and large Stokes shift) in both the liquid and solid state but also high antibacterial activity against both Gram-negative (E. coli) and Gram-positive (S. aureus) bacteria. The chlorine-substituted boron compound even possessed antibacterial activity comparable with that of commercial antibiotics. More importantly, the fluorescence properties and antibacterial activity of these boron compounds could be easily mediated by the variation of the substituents, which was proved to regulate the conjugated system, modify the hydrophobic character, and adjust the electric charge on the surface of boron compounds. In addition, the influence of different factors including solvent (i.e., polarity, concentration), temperature, and pH on the fluorescence properties of boron compounds was discussed in detail. This work provides a new strategy for the design of multifunctional organoboron compounds and the mediation of their properties

Emergy ecological model for sponge cities: A case study of China

Sponge cities have been recognized as the major measures to deal with urban drainage and waterlogging and restore urban water ecology in China. However, the existing evaluation indices could not calculate ecological benefits of the whole sponge city system. The objective of this study is to develop an emergy ecological model for evaluating the ecological benefits and sustainability of the urban stormwater system with a sponge city case in Xiamen, China. To achieve this objective, this study adopts the emergy analysis method and proposed the emergy flow diagrams of grey and green water networks. The results confirmed that the green water network was more sustainable. Additionally, this study selected the Wastewater Reuse Rate and Rainwater Utilization Rate as the variables to optimize the green water network. The analysis results showed that the optimized green water network received significantly better Emergy Index of Sustainable Development (0.82), by setting Volume Capture Ratio of annual rainfall, Wastewater Reuse Rate and Rainwater Utilization Rate at 75%, 40% and 50%, respectively. The case study verified that the proposed emergy model can be used as a generic model to quantitatively evaluate the ecological benefits of sponge cities, and the construction of sponge cities could promote water circulation and improve the sustainability of the system

Generating risk response measures for subway construction by fusion of knowledge and deep learning

This study aims to propose a method to generate response measures for subway construction risks. The HowNet semantic theoretical system was selected and incorporated the knowledge of subway construction risk management to develop the semantic knowledge base. Then, a risk response generation algorithm was designed based on Knowledge-enabled Bidirectional Encoder Representation from Transformers (K-BERT) to fuse knowledge and deep learning (DL). Meanwhile, the BERT in the original K-BERT model was replaced by the Masked Language Model (MLM) as correction BERT (MacBERT) pre-training model suitable for Chinese natural language processing (NLP) tasks. The data-driven and knowledge-driven approaches were combined for better performance of DL. The pre-training model based on MacBERT was selected to undertake the comparative experiment of fusing knowledge and DL. The results showed that the proposed algorithm with the K-BERT fusion of knowledge and DL had better performance than the MacBERT-based model without the knowledge base

DNAzyme Based Nanomachine for <i>in Situ</i> Detection of MicroRNA in Living Cells

The capability of <i>in situ</i> detection of microRNA in living cells with signal amplification strategy is of fundamental importance, and it will open up a new opportunity in development of diagnosis and prognosis of many diseases. Herein we report a swing DNA nanomachine for intracellular microRNA detection. The surfaces of Au nanoparticles (NPs) are modified by two hairpin DNA. We observe that one DNA (MB2) will open its hairpin structure upon partial hybridization with target miR-21 after entering into cells, and the other part of its hairpin structure could further react with the other hairpin DNA (MB1) to form a Zn²⁺-specific DNAzyme. This results in the disruption of MB1 through shearing action and the release of fluorescein Cy5. To provide an intelligent DNA nanomachine, MB2 is available again with the shearing action to bind with MB1, which provides effective signal amplification. This target-responsive, DNA nanomachine-based method showed a detection limit of 0.1 nM <i>in vitro</i>, and this approach could be an important step toward intracellular amplified detection and imaging of various analytes in living cells

High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains

<div><p>Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >10⁵ binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3–3.9; median: 2.1; standard deviation: 1.1) supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site.</p></div

Classification of Time Series Gene Expression in Clinical Studies via Integration of Biological Network

<div><p>The increasing availability of time series expression datasets, although promising, raises a number of new computational challenges. Accordingly, the development of suitable classification methods to make reliable and sound predictions is becoming a pressing issue. We propose, here, a new method to classify time series gene expression via integration of biological networks. We evaluated our approach on 2 different datasets and showed that the use of a hidden Markov model/Gaussian mixture models hybrid explores the time-dependence of the expression data, thereby leading to better prediction results. We demonstrated that the biclustering procedure identifies function-related genes as a whole, giving rise to high accordance in prognosis prediction across independent time series datasets. In addition, we showed that integration of biological networks into our method significantly improves prediction performance. Moreover, we compared our approach with several state-of–the-art algorithms and found that our method outperformed previous approaches with regard to various criteria. Finally, our approach achieved better prediction results on early-stage data, implying the potential of our method for practical prediction.</p> </div

Flexible Gold Electrode Array for Multiplexed Immunoelectrochemical Measurement of Three Protein Biomarkers for Prostate Cancer

In this work, we report a simple and novel electrochemical multiplexed immunosensor on a flexible polydimethylsiloxane (PDMS) slice deposited with 8 × 8 nano-Au film electrodes for simultaneous detection of prostate specific antigen (PSA), prostate specific membrane antigen (PSMA), and interleukin-6 (IL-6). Primary antibodies linked with magnetic beads (Ab₁-MBs) were modified on the nano-Au film electrodes via magnetic force. In the presence of corresponding antigen, horse radish peroxidase–secondary antibody-conjugated gold nanorods (HRP-Ab₂-gold NRs) were brought into the surface of electrodes, generating obvious electrochemical signals of H₂O₂ reduction reactions. Based on this, the designed immunosensor provide good performance in sensitivity and specificity during the detection of above three biomarkers for prostate cancer. The electrochemical multiplexed immunosensor was verified for selective and accurate detection of complex samples in human serum. Data suggested that the reported multiplexed immunosensing strategy holds great promise for applications in clinical assay and diseases diagnosis

Membrane Insertion and Phospholipids Extraction by Graphyne Nanosheets

The presence of both sp¹- and sp²-hybridized carbon atoms in graphyne (GY), a nanomaterial resembling the 2D graphene, has led researchers to speculate possible outstanding properties of this material. Recent studies have also been successful in synthesizing derivatives of GY, such as graphdiyne (GY-2), which holds promises in various applications, notably biomedicine. In anticipation of successful synthesis and wide applications of GY as a novel 2D nanomaterial in the near future, we utilized <i>in silico</i> molecular modeling to examine and predict the material’s potential impacts while placed in a biological system, in particular its interactions with cell membranes. Intriguingly, we found that while in the vicinity, GY can be spontaneously inserted into POPC membrane and extract large amounts of phospholipids from it. When compared with graphene, GY shows a relatively weaker capability of lipid extraction though, which is also confirmed by free energy perturbation (FEP) calculations where the POPC lipid molecule shows a larger reduction in free energy when being extracted from the membrane to the graphene surface than to the graphyne surface. This difference in lipid-extraction capability was mainly due to the significantly different carbon density in nanosheets

Classification accuracies of PPI-SVM-KNN with the change of parameter C.

<p>The bars and error ticks represent mean values and standard deviations respectively. (A) shows the result for Baranzini dataset. (B) shows the result for Goertsches dataset.</p

Amino acid diversity encoded in first generation library.

<p>Each row was constructed as a separate sublibrary. CDR’ refers to a degenerate codon with the following nucleotide frequencies: 20% A, 15% C, 25% G, and 40% T at site 1, 50% A, 25% C, 15% G, and 10% T at site 2, and 0% A, 45% C, 10% G, and 45% T at site 3. Loop length diversity was afforded at mid-loop positions by inserting CDR’ diversity sites between sites P25-V29 and G79-S85 of the BC and FG loop, respectively, as denoted by subscripts within table. Length diversity at the DE loop occurred between S53-S55, consisting of diversity matching that of K54 as shown below. Note that throughout the manuscript, a series of unseparated capital amino acid abbreviations refer to equally possible amino acids; for example, SYNT indicates 25% each of serine, tyrosine, asparagine, and threonine at that site.</p