All-organic polymeric materials with high refractive index and excellent transparency.

High refractive index polymers (HRIPs) have drawn attention for their optoelectronic applications and HRIPs with excellent transparency and facile preparation are highly demanded. Herein, sulfur-containing all organic HRIPs with refractive indices up to 1.8433 at 589 nm and excellent optical transparency even in one hundred micrometre scale in the visual and RI region as well as high weight-average molecular weights (up to 44500) are prepared by our developed organobase catalyzed polymerization of bromoalkynes and dithiophenols in yields up to 92%. Notably, the fabricated optical transmission waveguides using the resultant HRIP with the highest refractive index display a reduced propagation loss compared with that generated by the commercial material of SU-8. In addition, the tetraphenylethylene containing polymer not only exhibits a reduced propagation loss, but also is used to examine the uniformity and continuity of optical waveguides with naked eyes because of its aggregation-induced emission feature.

Thermosensitive Microgels Containing AIEgens: Enhanced Luminescence and Distinctive Photochromism for Dynamic Anticounterfeiting.

The proposal of the aggregation-induced emission (AIE) effect shines a light on the practical application of luminescent materials. The AIE-active luminescence microgels (TPEC MGs) with photo-induced color-changing behavior were developed by integrating positively charged AIE luminogens (AIEgens) into the anionic network of microgels, where AIEgens of TPEC were obtained from the quaternization reaction between tetra-(4-pyridylphenyl)ethylene (TPE-4Py) and 7-(6-bromohexyloxy)-coumarin. The aqueous suspensions of TPEC MGs exhibit a significant AIE effect following the enhancement of quantum yield. In addition, further increase in fluorescence intensity and blueshift occur at elevated temperatures due to the collapse of microgels. The distinctive photochromic behavior of TPEC MGs was observed, which presents as the transition from orange-yellow to blue-green color under UV irradiation, which is different from TPEC in good organic solvents. The phenomenon of color changing can be ascribed to the competition between photodimerization of the coumarin part and photocyclization of TPE-4Py in TPEC. The photochromic TPEC MG aqueous suspensions can be conducted as aqueous microgel inks for information display, encryption, and dynamic anticounterfeiting.

Sulfur Conversion to Multifunctional Poly(O-thiocarbamate)s through Multicomponent Polymerizations of Sulfur, Diols, and Diisocyanides.

Sulfur, which is generated from the waste byproducts in the oil and gas refinery industry, is an abundant, cheap, stable, and readily available source in the world. However, the utilization of excessive amounts of sulfur is mostly limited, and developing novel methods for sulfur conversion is still a global concern. Here, we report a facile one-step conversion from elemental sulfur to functional poly(O-thiocarbamate)s through a multicomponent polymerization of sulfur, diols, and diisocyanides, which possesses a series of advantages such as mild condition (55 °C), short reaction time (1 h), 100% atom economy, and transition-metal free in the catalyst system. Seven poly(O-thiocarbamate)s are constructed with high yields (up to 95%), large molecular weight (up to 53100 of Mw), good solubility in organic solvents, and completely new polymer structures. The poly(O-thiocarbamate)s possess a high refractive index above 1.7 from 600 to 1700 nm by adjusting the sulfur content. By incorporating tetraphenylethene (TPE) moieties into the polymer structure, the poly(O-thiocarbamate)s can also be designed as fluorescent sensors to detect harmful metal cation of Hg2+ in a turn-on mode with high sensitivity (LOD = 32 nM) and excellent selectivity (over interference cations of Pb2+, Au3+, Ag+). Different from the previous reports, the exact coordination structure is first identified by single-crystal X-ray diffraction, which is revealed in a tetracoordination fashion (two sulfur and two chloride) using a model coordination compound.

Comprehensive analysis of differentially expressed profiles of non­coding RNAs in peripheral blood and ceRNA regulatory networks in non­syndromic orofacial clefts.

Non­syndromic orofacial clefts (NSOC), which include cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO), are common congenital birth defects in humans. Accumulating evidence indicates that long non­coding RNAs (lncRNAs) and microRNAs (miRNAs or miRs) play important roles in NSOC; however, the potential regulatory associations between them remain largely unknown. In this study, we performed next­generation RNA sequencing (RNA­seq) to identify transcriptome profiles, including mRNAs, lncRNAs and miRNAs, in patients with CL/P and CPO. A total of 36 lncRNAs, 1,341 mRNAs and 60 miRNAs were found to be differentially expressed in the CL/P group compared to the control group, and 57 lncRNAs, 1,255 mRNAs and 162 miRNAs were found to be differentially expressed in the CPO group compared to the control group. Subsequently, reverse transcription­quantitative polymerase chain reaction (RT­qPCR) was performed to validate the expression of selected lncRNAs, miRNAs and mRNAs. In addition, bioinformatics methods were employed to explore the potential functions of ncRNAs and to construct lncRNA­miRNA­mRNA regulatory networks. To the best of our knowledge, this is the first study to comprehensively analyze regulated non­coding RNAs (ncRNAs) in CL/P and CPO, providing a novel perspective on the etiology of NSOC and laying the foundation for future research into the potential regulatory mechanisms of ncRNAs and mRNAs in NSOC.

Emission enhancement and high sensitivity of a π-conjugated dye towards pressure: the synergistic effect of supramolecular interactions and H-aggregation.

Piezoresponsive fluorescent (PRF) materials are highly promising for applications in deformation, flaw detection and haptic sensing. However, traditional PRF materials generally suffer from low sensitivity and fluorescence quenching processes. This study involved the preparation of H-aggregated dyes with weak supramolecular interactions, which showed enhanced emission under a low pressure.

Excitation Wavelength Dependent Fluorescence of an ESIPT Triazole Derivative for Amine Sensing and Anti-Counterfeiting Applications.

Excitation wavelength dependent (Ex-De) emission materials have potential applications in anti-counterfeiting labels and bioimaging. Nevertheless, few purely organic chromophores are used in these areas. In this study, multiple excited states were incorporated into a molecule that was excited state intramolecular proton transfer (ESIPT) active, with the goal of manipulating the relaxation pathways of the excited states. The triazole derivative exhibits Ex-De photoluminescence (PL), and the maximum PL wavelength is located at 526 nm and 593 nm under a series of excitation wavelengths. Spectral identification indicates that the excimer and ESIPT processes are responsible for the green (526 nm) and orange (593 nm) fluorescence, respectively. Importantly, the quick response code and test strip prepared with this triazole derivative can be used for anti-counterfeiting and food spoilage detection applications, respectively. This research opens the door for developing novel Ex-De materials for anti-counterfeiting purposes.

Red-emissive azabenzanthrone derivatives for photodynamic therapy irradiated with ultralow light power density and two-photon imaging.

Photodynamic therapy has proved to be an effective strategy for cancer therapy, and advanced photosensitizers for image-guided photodynamic therapy require biocompatibility, intense absorption, high ROS generation efficiency, phototoxicity, low irradiation power density and efficient emission. In this work, four red emissive azabenzanthrone derivatives have been designed and synthesized, which generally exhibit efficient aggregated state emission. Through structural optimization, 3-diphenylamino-11-azabenzanthrone was found to show satisfactory photo-induced ROS generation and high emission efficiency in the aggregated state. Under the irradiation of a white LED lamp with an ultralow power density of 1.67 mW cm-2, this compound demonstrates significant photo-induced cytotoxicity toward HeLa cells. Moreover, deep tissue penetration can be realized by two-photon imaging of mouse brain vessels with these azabenzanthrone derivatives at vertical depths of up to 280 µm, attributed to the large emission wavelength and efficient emission.

Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data.

BACKGROUND: Copy number variations (CNVs) are the main genetic structural variations in cancer genome. Detecting CNVs in genetic exome region is efficient and cost-effective in identifying cancer associated genes. Many tools had been developed accordingly and yet these tools lack of reliability because of high false negative rate, which is intrinsically caused by genome exonic bias. RESULTS: To provide an alternative option, here, we report Anaconda, a comprehensive pipeline that allows flexible integration of multiple CNV-calling methods and systematic annotation of CNVs in analyzing WES data. Just by one command, Anaconda can generate CNV detection result by up to four CNV detecting tools. Associated with comprehensive annotation analysis of genes involved in shared CNV regions, Anaconda is able to deliver a more reliable and useful report in assistance with CNV-associate cancer researches. CONCLUSION: Anaconda package and manual can be freely accessed at http://mcg.ustc.edu.cn/bsc/ANACONDA/ .

CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data.

SUMMARY: Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of supported species from 10 to 48; (ii) improved strategies applied to detect ncRNAs; (iii) more ncRNAs can be detected and profiled, such as lncRNA and circRNA; (iv) identification of differentially expressed ncRNAs among multiple samples; (v) enhanced visualization interface containing graphs and charts in detailed analysis results. The new version of CPSS is an efficient bioinformatics tool for users in non-coding RNA research. AVAILABILITY AND IMPLEMENTATION: CPSS 2.0 is implemented in PHP + Perl + R and can be freely accessed at http://114.214.166.79/cpss2.0/. CONTACT: zyuanwei@ustc.edu.cn or qshi@ustc.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bright and photostable fluorescent probe with aggregation-induced emission characteristics for specific lysosome imaging and tracking.

We develop a new lysosome-targeting AIE fluorescent probe tetraphenylethene-morpholine (TPE-MPL), by incorporating a typical lysosome-targeting moiety of morpholine into a stable tetraphenylethene skeleton. Due to both the AIE and antenna effects, TPE-MPL possesses superior photostability, appreciable tolerance to microenvironment change and high lysosome targeting ability. Our findings confirm that TPE-MPL is a well-suited imaging agent for targeting lysosome and tracking dynamic movement of lysosome. Moreover, due to its synthetic accessibility, TPE-MPL could be further modified as a dual-functional probe for lysosome, thereby gain further insight into the role of lysosome in biomedical applications.

DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.

Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing data is still in great demand. Here, we present an online tool, DeAnnIso (Detection and Annotation of IsomiRs from sRNA sequencing data). DeAnnIso can detect all the isomiRs in an uploaded sample, and can extract the differentially expressing isomiRs from paired or multiple samples. Once the isomiRs detection is accomplished, detailed annotation information, including isomiRs expression, isomiRs classification, SNPs in miRNAs and tissue specific isomiR expression are provided to users. Furthermore, DeAnnIso provides a comprehensive module of target analysis and enrichment analysis for the selected isomiRs. Taken together, DeAnnIso is convenient for users to screen for isomiRs of their interest and useful for further functional studies. The server is implemented in PHP + Perl + R and available to all users for free at: http://mcg.ustc.edu.cn/bsc/deanniso/ and http://mcg2.ustc.edu.cn/bsc/deanniso/.

IsomiR Bank: a research resource for tracking IsomiRs.

UNLABELLED: : Next-Generation Sequencing (NGS) technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent differences from their corresponding mature reference sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). These isomiRs mainly originate via the imprecise and alternative cleavage during the pre-miRNA processing and post-transcriptional modifications that influence miRNA stability, their sub-cellular localization and target selection. Although several tools for the identification of isomiR have been reported, no bioinformatics resource dedicated to gather isomiRs from public NGS data and to provide functional analysis of these isomiRs is available to date. Thus, a free online database, IsomiR Bank has been created to integrate isomiRs detected by our previously published algorithm CPSS. In total, 2727 samples (Small RNA NGS data downloaded from ArrayExpress) from eight species (Arabidopsis thaliana, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Oryza sativa, Solanum lycopersicum and Zea mays) are analyzed. At present, 308 919 isomiRs from 4706 mature miRNAs are collected into IsomiR Bank. In addition, IsomiR Bank provides target prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. AVAILABILITY AND IMPLEMENTATION: IsomiR Bank is implemented in PHP/PERL + MySQL + R format and can be freely accessed at http://mcg.ustc.edu.cn/bsc/isomir/ CONTACTS: : aoli@ustc.edu.cn or qshi@ustc.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

NIR light controlled release of caged hydrogen sulfide based on upconversion nanoparticles.

A NIR light induced H2S release platform based on UCNPs was constructed. Under NIR light excitation, UCNPs can emit UV light which triggers H2S release in a spatial and temporal pattern. The platform was also employed to real-time monitor the delivery process in vivo, which may provide a new way for the use of H2S-based therapeutics for a variety of diseases.