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Objective: To explore the molecular etiology of Waardenburg syndrome type II (WS2) in a family from Yunnan province, China. Methods: A total of 406 genes related to hereditary hearing loss were sequenced using next‐generation sequencing. DNA samples were isolated from the peripheral blood DNA of probands. Those pathogenic mutations detected by next‐generation sequencing in probands and their parents were validated by Sanger sequencing. The conservatism of variation sites in genes was also analyzed. The protein expression was detected by flow cytometry. Results: A heterozygous mutation c.178delG (p.D60fs*49) in the SOX10 gene was identified in the proband, which is a frameshift mutation and may cause protein loss of function and considered to be a pathogenic mutation. This was determined to be a de novo mutation because her family were demonstrated to be wild‐type and symptom free. SOX10, FGFR3, SOX2, and PAX3 protein levels were reduced as determined by flow cytometry. Conclusion: A novel frameshift mutation in SOX10 gene was identified in this study, which may be the cause of WS2 in proband. In addition, FGFR3, SOX2, and PAX3 might also participate in promoting the progression of WS2. [ABSTRACT FROM AUTHOR]

As an important therapeutic target in breast cancer, HER2 expression assessed by immunohistochemistry plays a critical role in breast cancer treatment. Recent advances in HER2 antibody–drug conjugate therapy have enabled patients with HER2-low expression breast cancer to benefit from the drugs. However, it is not known whether the HER2-low expression in breast cancer FFPE blocks would be lost as storage time increased. In this study, we aimed to assess the loss of HER2 antigenicity in stored FFPE blocks of breast cancer and the rescue effect of modifying the protocol of antigen staining. We selected archived HER2-low breast cancer FFPE blocks with stored time ranging from 1 year to over 15 years and re-detected the expression of HER2. Our study showed that HER2 antigenicity loss increased with storage time and could cause false negativity in HER2-low detection. Moreover, we showed that by either increasing the antigen retrieval time or applying the tyramide signal amplification (TSA) kit, the HER2 signal can be rescued and detected in about half of the cases with HER2-low loss without causing false positivity. [ABSTRACT FROM AUTHOR]

Background: Single-cell RNA sequencing (scRNA-seq) enables the high-throughput profiling of gene expression at the single-cell level. However, overwhelming dropouts within data may obscure meaningful biological signals. Various imputation methods have recently been developed to address this problem. Therefore, it is important to perform a systematic evaluation of different imputation algorithms. Results: In this study, we evaluated 11 of the most recent imputation methods on 12 real biological datasets from immunological studies and 4 simulated datasets. The performance of these methods was compared, based on numerical recovery, cell clustering and marker gene analysis. Most of the methods brought some benefits on numerical recovery. To some extent, the performance of imputation methods varied among protocols. In the cell clustering analysis, no method performed consistently well across all datasets. Some methods performed poorly on real datasets but excellent on simulated datasets. Surprisingly and importantly, some methods had a negative effect on cell clustering. In marker gene analysis, some methods identified potentially novel cell subsets. However, not all of the marker genes were successfully imputed in gene expression, suggesting that imputation challenges remain. Conclusions: In summary, different imputation methods showed different effects on different datasets, suggesting that imputation may have dataset specificity. Our study reveals the benefits and limitations of various imputation methods and provides a data-driven guidance for scRNA-seq data analysis. [ABSTRACT FROM AUTHOR]

Motivation Emerging single-cell RNA sequencing (scRNA-seq) technology empowers biological research at cellular level. One of the most crucial scRNA-seq data analyses is clustering single cells into subpopulations. However, the high variability, high sparsity and high dimensionality of scRNA-seq data pose lots of challenges for clustering analysis. Although many single-cell clustering methods have been recently developed, few of them fully exploit latent relationship among cells, thus leading to suboptimal clustering results. Results Here, we propose a novel unsupervised clustering method, scGAC (single-cell Graph Attentional Clustering), for scRNA-seq data. scGAC firstly constructs a cell graph and refines it by network denoising. Then, it learns clustering-friendly representation of cells through a graph attentional autoencoder, which propagates information across cells with different weights and captures latent relationship among cells. Finally, scGAC adopts a self-optimizing method to obtain the cell clusters. Experiments on 16 real scRNA-seq datasets show that scGAC achieves excellent performance and outperforms existing state-of-art single-cell clustering methods. Availability and implementation Python implementation of scGAC is available at Github (https://github.com/Joye9285/scGAC) and Figshare (https://figshare.com/articles/software/scGAC/19091348). Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Abstract Insulin-responsive glucose transporter type 4 (GLUT4) translocation plays a major role in controlling glucose uptake in adipose tissue and muscle, maintaining homeostasis and preventing hyperglycemia. Screening for chemicals enhancing GLUT4 translocation is an approach for identifying hits of drug development for type 2 diabetes. Here we developed a novel functional dual-color probe, pHluorin-GLUT4-mOrange2, and constructed 3T3-L1 adipocytes based screening system to simply and efficiently screen new compounds stimulating GLUT4 translocation. Based on this system, we successfully identified a few hits facilitating GLUT4 translocation. In conclusion, we developed an easy-to-apply dual color GLUT4 probe to monitor GLUT4 translocation in insulin-responsive cells, which could be alternatively employed to high-throughput screen compounds regulating GLUT4 translocation and glucose uptake, even to dissect GLTU4 approaching, docking and fusion with the plasma membrane (PM), and to reveal relevant molecular mechanisms involved in these steps as expected. Highlights • We develop an easy-to-apply dual color GLUT4 probe to monitor GLUT4 translocation. • PHluorin-GLUT4-mOrange2 is a useful tool for the study of signaling pathway involved in GLUT4 translocation. • PHluorin-GLUT4-mOrange2 can be applied to high throughput screening of GLUT4 transport activators easily and handily. [ABSTRACT FROM AUTHOR]

Encrypted traffic classification (ETC) plays an important role in network management. In most research, the statistical features, transformed traffic images, or text are used for classification. However, the statistical features' design is time-consuming and labor-intensive, and the transformed traffic data lack spatial or semantic features. Considering that the headers of traffic packets have a uniform structure and are independent of each other, traffic data are most similar to tabular data. Thus we propose a data processing approach to convert packet headers into traffic tables in which each field is viewed as a column (feature). In addition, traffic data are hard to label in real traffic environments, and each field contributes differently to the classification. Therefore, a self-supervised learning algorithm, SubTab, is used as the baseline network to reduce the reliance on labeled data and assign different weights to different fields. To the best of our knowledge, this is the first time that the ETC problem is solved from the tabular domain. Experimental results on two real-world datasets, ISCX VPN-nonVPN and the self-collected dataset SHU-ET, demonstrate that our method surpasses state-of-the-art methods based on traffic images or text and proves that traffic tables are more suitable for ETC problems. In addition, our method achieves a great performance with only 10% of labeled data and reduces the reliance on labeling data. [ABSTRACT FROM AUTHOR]

This paper deals with the H ∞ state estimation problem for static neural networks subject to time-varying delays. First, an augmented Lyapunov-Krasovskii functional (LKF) is constructed for the use of the second-order Bessel–Legendre integral inequality. Second, by introducing some novel techniques to absorb the time-varying delay, the bounded real lemma (BRL) is expressed as matrix inequalities linearly dependent on the time-varying delay rather than in its quadratic form. By employing the linear convex approach, a less conservative BRL condition is derived for the estimation error system. Based on this condition, the state estimators can be calculated by solving a set of linear matrix inequalities. Finally, an example is used to illustrate the effectiveness of the proposed method. [ABSTRACT FROM AUTHOR]

This paper reports the results of a review of research articles on the teaching of Chinese as a second or foreign language published in four leading mainland Chinese journals during the years 2005–2015. The review found that Chinese language researchers are exploring a wide array of issues including language policy and planning, language learning and use, language pedagogy, teacher development and language testing. These studies document the efforts that Chinese language researchers and teachers have made to meet the explosively growing demand for Chinese language learning in the world. Furthermore, it was noted that the leading Chinese journals have become more receptive to empirical studies although a large number of non-empirical articles are still being published. Overall, research in these journals is still beset with different challenges, and there is a need for more rigorous scholarship on the part of researchers. For this reason, the review concludes with suggestions for Chinese journals so that they can promote high-quality research to support the global development of Chinese language education. [ABSTRACT FROM PUBLISHER]

Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interaction patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number of proteins need to work together to perform a job. Proteins densely interact with each other, forming large molecular machines or cellular building blocks. Identification of such densely interconnected clusters or protein complexes from PPI networks enables us to obtain a better understanding of the hierarchy and organization of biological processes and cellular components. However, most existing graph clustering algorithms on PPI networks often cannot effectively detect densely connected subgraphs and overlapped subgraphs. In this article, we formulate the problem of complex detection as diversified dense subgraph mining and introduce a novel approximation algorithm to efficiently enumerate putative protein complexes from biological networks. The key insight of our algorithm is that instead of enumerating all dense subgraphs, we only need to find a small diverse subset of subgraphs that cover as many proteins as possible. The problem is modeled as finding a diverse set of maximal dense subgraphs where we develop highly effective pruning techniques to guarantee efficiency. To scale up to large networks, we devise a divide-and-conquer approach to speed up the algorithm in a distributed manner. By comparing with existing clustering and dense subgraph-based algorithms on several yeast and human PPI networks, we demonstrate that our method can detect more putative protein complexes and achieves better prediction accuracy. [ABSTRACT FROM AUTHOR]

This inquiry explored 68 pre-service perceptions and aspirations of Teaching Chinese as an International Language (TCIL) teachers by analysing the metaphors they used to describe themselves as teachers. The inquiry revealed that the participants used a variety of metaphors to project the images of themselves as pre-service TCIL teachers. The results also confirm that the participants’ use of metaphors, as powerful tools to understand the complexity of teaching, reflects the mediation of cultural, historical and sociopolitical conditions. These findings help teacher educators to support TCIL teachers’ professional development by engaging them in critical dialogues about the metaphors they use to perceive themselves as TCIL teachers. They also help teacher educators to adopt tailor-made pedagogical content to address their development needs. [ABSTRACT FROM PUBLISHER]

The duck hepatitis A virus (DHAV), a member of the family Picornaviridae, is the major cause of outbreaks with high mortality rates in young ducklings. It has three distinctive serotypes and among them, serotypes 1 (DHAV-1) and 3 (DHAV-3) were recognized in China. To investigate evolutionary and antigenic properties of the major capsid protein VP1 of these two serotypes, a primary target of neutralizing antibodies, we determined the VP1 coding sequences of 19 DHAV-1 (spanning 2000-2012) and 11 DHAV-3 isolates (spanning 2008-2014) associated with disease outbreaks. By bioinformatics analysis of VP1 sequences of these isolates and other DHAV strains reported previously, we demonstrated that DHAV-1 viruses evolved into two genetic lineages, while DHAV-3 viruses exhibited three distinct lineages. The rate of nucleotide substitution for DHAV-1 VP1 genes was estimated to be 5.57 x 10-4 per site per year, which was about one-third times slower than that for DHAV-3 VP1 genes. The population dynamics analysis showed an upward trend for infection of DHAV-1 viruses over time with little change observed for DHAV-3 viruses. Antigenic study of representative DHAV-1 and DHAV-3 strains covering all observed major lineages revealed no detectable changes in viral neutralization properties within the serotype, despite the lack of cross-neutralization between serotypes 1 and 3 strains. Structural analysis identified VP1 mutations in DHAV-1 and DHAV-3 viruses that underpin the observed antigenic phenotypes. Results of our experiments described here shall give novel insights into evolution and antigenicity of duck picornaviruses. [ABSTRACT FROM AUTHOR]

In this work, a dummy molecularly imprinted polymers (MIPs) were developed as the selective sorbents for preparation of the high purity gingerols from ginger for the first time. The dummy template molecule with similar structural skeleton to gingerols, N-vanillylnonanamide, has been designed and synthesized. The performance of the MIPs and non-imprinted polymers (NIPs) were evaluated including selective recognition capacity, adsorption isotherm, and adsorption kinetics. Optimization of various parameters affecting dummy molecular imprinted solid phase extraction (MISPE), such as the type and flow rate of the loading solvent, the composition and volume of the eluting solvent, and the composition and volume of the washing solvent were investigated. Gingerols with the percent recovery of 80 and the percent purity of 99.1 were obtained from the extracts of ginger by MISPE. Besides, gingerols obtained by MISPE had more powerful activity of eliminating free radical compared with extracts before extraction with the MISPE column. Application of MIPs with a high affinity toward three gingerols provides a novel method for obtaining a group of compounds which have likely active groups from natural products. [ABSTRACT FROM AUTHOR]

In this work, dummy molecularly imprinted polymers with high selectivity and affinity to capsaicin and dihydrocapsaicin are designed using N-vanillylnonanamide as a dummy template. The performance of dummy molecularly imprinted polymers and nonimprinted polymers was evaluated using adsorption isotherms, adsorption kinetics, and selective recognition capacity. Dummy molecularly imprinted polymers were found to exhibit good site accessibility, taking just 20 min to achieve adsorption equilibrium; they were also highly selective toward capsaicin and dihydrocapsaicin. We successfully used dummy molecularly imprinted polymers as a specific sorbent for selectively enriching capsaicin and dihydrocapsaicin from chili pepper samples. In a scaled-up experiment, the selective recovery of capsaicinoids was calculated to be 77.8% using solid-phase extraction. To the best of our knowledge, this is the first example of the use of N-vanillylnonanamide as a dummy template in molecularly imprinted polymers to simultaneously enrich capsaicin and dihydrocapsaicin. [ABSTRACT FROM AUTHOR]

Dummy molecularly imprinted polymers (DMIPs) for simultaneously selective removal and enrichment of ginkgolic acids (GAs) during the processing of Ginkgo biloba leaves have been prepared. Two dummy template molecule with similar structural skeleton to GAs, 6-methoxysalicylic acid (MOSA, DT-1) and 6-hexadecyloxysalicylic acid (HOSA, DT-2), have been designed and synthesized. The performance of the DMIPs and NIPs were evaluated including selective recognition capacity, adsorption isotherm, and adsorption kinetics. The selective recognition capacity of the three GAs with four analogues on the sorbents illustrated that the DMIPs sorbents have high specificity for GAs. An efficient method based on DMIP-HOSA coupled with solid-phase extraction (SPE) was developed for simultaneously selective removal and enrichment of ginkgolic acids (GAs) during the processing of Ginkgo biloba leaves. The method showed excellent recoveries (82.5–88.7%) and precision (RSD 0.5–2.6%, n = 5) for licorice extracts, Gastrodia elata extracts and pepper extracts spiked at three concentration levels each (50, 100, 200 μg mL −1 ). The results indicated that GAs and standardized Ginkgo biloba leaves extracts could be obtained simultaneously through the DMIP-SPE. [ABSTRACT FROM AUTHOR]

Okihiro syndrome is an autosomal dominant condition characterized by Duane anomaly and radial ray defects. The present study aimed to analyze the clinical manifestations of a patient with Okihiro syndrome and perform genetic testing on the proband and his family to determine the biological pathogenesis. Clinical data were collected from the proband and his family and genomic DNA was extracted from peripheral blood. Whole exome sequencing was performed by high-throughput sequencing and mutation sites of the proband and his parents were validated by Sanger sequencing. The proband was diagnosed with Okihiro syndrome, which is characterized by bone abnormality in the arms and hands (radial ray malformation, absence of thumbs) and sensorineural hearing loss. A pathogenic heterozygous c.3060delG variant was identified in exon 4 of spalt-like transcription factor 4 (SALL4) gene in the proband. This is a frameshift mutation that changes increases the length of SALL4 protein from 1,053 to 1,076 amino acids. The variant was classed as a de novo mutation because the parents of the proband showed no variation at this site. This variant is not included in the ClinVar database and, to the best of our knowledge, has not previously been reported. The de novo heterozygous c.3060delG variant was the molecular pathological cause of Okihiro syndrome in the present study and expanded the database of known SALL4 variants. [ABSTRACT FROM AUTHOR]

Plasminogen activator inhibitor-1 (PAl- 1) is implicated in thrombogenesis, inflammation, and extracellular matrix remodeling. Previous studies indicated that oxidized low-density lipoprotein (LDL) stimulated the generation of PAI-1 in vascular endothelial cells (EC). The present study demonstrated that LDL oxidized by copper, iron, or 3-morpholinosydnonimine increased the expression of NADPH oxidase (NOX) 2, PAl-i, and heat shock factor-1 (HSF1) in human umbilical vein EC or coronary artery EC compared with LDL or vehicle. Diphenyleneiodonium, a NOX inhibitor, prevented the increases of the expression of HSF1 and PAL-1 in EC induced by oxidized LDLs. Small-interference RNA (siRNA) for p22[supphox], an essential subunit of NOX, prevented oxidized LDL-induced expression of NOX2, HSF1, and PAI-1 in EC. HSF1 siRNA inhibited oxidized LDL-induced expression of PAl-1 and HSF1, but not NOX2, in EC. The binding of HSF1 to PAl-1 promoter and the activity of PAI- 1 promoter in EC were enhanced by oxidized LDL. Butylated hydroxytulene, a potent anti- oxidant, inhibited oxidized LDL-induced release of hydrogen peroxide (H[sub2]O[sub2]) and the expression of NOX2, HSF1, and PAI-l in EC. Treatment with H202 increased the abundance of NOX2, HSF1, and PAI-1 in EC. The results of the present study indicate that oxidized LDL-induced expression of NOX may lead to the elevated release of reactive oxygen species, the activation of HSF1, and the enhancement of the transcription of PAI-1 gene in cultured vascular EC. [ABSTRACT FROM AUTHOR]

Milk coagulation is an important step in the production of fermented dairy products such as yogurt and cheese. Jujube is gaining popularity and acceptance as a food ingredient. In China, jujube yogurt is popular among consumers. However, there is limited information on the effect of jujube on acid- and rennet-induced coagulation properties of milk. The objective of this study was to evaluate the effects of jujube pulp at different concentrations on acid- and rennet-induced coagulation kinetics of milk and the microstructure of acid- and rennet-induced gels. During acid-induced coagulation, with increasing jujube pulp concentration, the initial pH value decreased; however, the final pH value increased. The initial elasticity index (EI) value increased, and the time point at which the mean square displacement curves lost the linear trend advanced. The sample with 10% jujube pulp had the densest structure and highest EI value. During rennet-induced coagulation, with increasing jujube pulp concentration, the production rate and amount of caseinomacropeptide decreased, and the final EI value increased. Protein aggregates in rennet-induced gels became rough, and the sample with 20% jujube pulp had the highest EI value. This study provides a new perspective and understanding of the application of jujube in fermented dairy products. [ABSTRACT FROM AUTHOR]

Sesame (Sesamum indicum) is a well-recognized food allergen, and sesame-related allergies have been increasingly reported worldwide. Patients with sesame allergy are specifically allergic to different sesame proteins (Ses i 1–7). Because of the increasing burden associated with allergies to sesame, there is an urgent need to develop sensitive and quantitative analytical methods capable of detecting sesame allergen contaminants. Targeted proteomic approach employing liquid chromatography/tandem mass spectrometry (LC-MS/MS) has emerged as a promising technique that offers increased specificity and reproducibility compared to antibody and DNA-based technologies. In this study, we developed a qualitative and absolute quantification method based on the LC-MS/MS-multiple reaction monitoring (MRM) system utilizing stable isotope-labeled internal standard (SIIS) peptides. We optimized extraction and trypsin digestion conditions and selected signature and absolute quantification (AQUA) peptides for seven sesame allergen proteins respectively. This quantitative method produced a linear relationship (R2 > 0.99) in a wide concentration range (0.4–2000 fmol/μL), and the overall coefficient of variation was <5% in multiple tests. Limits of detection (LOD) and Limits of quantification (LOQ) for the seven sesame allergens AQUA peptides were determined to range from 0.1 to 140.0 fmol/μL and 0.4–400 fmol/μL respectively. The results showed that the accuracy of 20, 50, 100 ppm incurred protein Ses i 2 were 90%, 92%, 94% in non-processed material and 92%, 95%,102% in processed material respectively. Overall, this method allowed for rapid and simultaneous absolute quantification of seven sesame allergens. The newly developed LC-MS/MS assay will likely increase the safety of sesame processed foods and add diagnostic value to the sesame allergy testing. • Targeted proteomic approach employing LC-MS/MS were used in this method. • Signature and AQUA peptides for seven sesame allergens were selected respectively. • The qualitative and quantitative method utilized LC-MS/MS-MRM and SIIS peptides. • We optimized extraction, trypsin digestion and LC-MS/MS-MRM analysis conditions. • Absolutely quantify seven sesame allergens rapidly and simultaneously in products. [ABSTRACT FROM AUTHOR]

Our previous studies have shown that the introduction of structurally diverse benzyl side chains at the C5-NH2 position of oseltamivir to occupy 150-cavity contributes to the binding affinity with neuraminidase and anti-influenza activity. To obtain broad-spectrum neuraminidase inhibitors, we designed and synthesised a series of novel oseltamivir derivatives bearing different N-heterocycles substituents that have been proved to induce opening of the 150-loop of group-2 neuraminidases. Among them, compound 6k bearing 4-((r)-2-methylpyrrolidin-1-yl) benzyl group exhibited antiviral activities similar to or weaker than those of oseltamivir carboxylate against H1N1, H3N2, H5N1, H5N6 and H5N1-H274Y mutant neuraminidases. More encouragingly, 6k displayed nearly 3-fold activity enhancement against H3N2 virus over oseltamivir carboxylate and 2-fold activity enhancement over zanamivir. Molecular docking studies provided insights into the explanation of its broad-spectrum potency against wild-type neuraminidases. Overall, as a promising lead compound, 6k deserves further optimisation by fully considering the ligand induced flexibility of the 150-loop. [ABSTRACT FROM AUTHOR]

We investigate the differential diagnostic value of tremor analysis of EMG on Parkinson’s disease (PD), essential tremor (ET), and enhanced physiological tremor (EPT). Clinical data from 25 patients with PD, 20 patients with ET, and 20 patients with EPT were collected. The tremor frequency and muscle contraction pattern of the resting, posture, and 500 g and 1000 g overload were recorded. The frequency of PD tremor was 4–6 Hz, and the frequency of ET was also in this range; the frequency of EPT is 6–12 hz having some overlap with PD. The muscle contraction patterns of the ET and EPT group were mainly synchronous contraction, and the muscle contraction mode of the PD group was mainly alternating contraction. Having tremor latency from rest to postural position and having changes in tremor amplitude after mental concentration in PD might distinguish ET. Tremor analysis of EMG was able to distinguish PD from ET and EPT by varying the tremor frequency and muscle contraction pattern. It can also differentiate between PD and ET by the latency and concentration effect and ET and EPT by weight load effect. [ABSTRACT FROM AUTHOR]

To address drug resistance to influenza virus neuraminidase inhibitors (NAIs), a series of novel boron-containing N-substituted oseltamivir derivatives were designed and synthesized to target the 150-cavity of neuraminidase (NA). In NA inhibitory assays, it was found that most of the new compounds exhibited moderate inhibitory potency against the wild-type NAs. Among them, compound 2c bearing 4-(3-boronic acid benzyloxy)benzyl group displayed weaker or slightly improved activities against group-1 NAs (H1N1, H5N1, H5N8 and H5N1-H274Y) compared to that of oseltamivir carboxylate (OSC). Encouragingly, 2c showed 4.6 times greater activity than OSC toward H5N1-H274Y NA. Moreover, 2c exerted equivalent or more potent antiviral activities than OSC against H1N1, H5N1 and H5N8. Additionally, 2c demonstrated low cytotoxicity in vitro and no acute toxicity at the dose of 1000 mg/kg in mice. Molecular docking of 2c was employed to provide a possible explanation for the improved anti-H274Y NA activity, which may be due to the formation of key additional hydrogen bonds with surrounding amino acid residues, such as Arg152, Gln136 and Val149. Taken together, 2c appeared to be a promising lead compound for further optimization. [ABSTRACT FROM AUTHOR]

Highlights: [•] Synthesis of MIPs with novel functional monomer as a selective sorbent for extraction of gastrodin. [•] An environment-friendly material with water used in the loading and eluting process of molecularly imprinted solid phase extraction. [•] Application of the optimized protocol for the extraction of gastrodin from the aqueous extract of Gastrodia elata roots. [Copyright &y& Elsevier]

Abstract: The genomic sequence of a strain of duck enteritis virus (DEV) was determined and analyzed in this study. The size of its genome is 158,091 bp in length and the genome is predicted to encode 78 putative proteins and resembles the members of the Alphaherpesvirinae in genomic organization and gene composition. The genome of the virus is composed of a unique long (UL) region, a unique short (US) region, a unique short internal repeat (IRS) region and a unique short terminal repeat (TRS) region. Its genomic arrangement pattern (UL-IRS-US-TRS) corresponds to D-type herpesvirus and is consistent with the members of Varicellovirus and Iltovirus genera. Sequence analysis reveals that the genome of the virus contains 67 genes having homologs in most members of the Alphaherpesvirinae. Out of these genes, one gene has a homolog in cercopithecine herpesvirus 8 which is a virus of Betaherpesvirinae, and 5 genes have homologs in avian herpesviruses. Furthermore, the genome possesses three unique genes without homologs in any other herpesviruses. Like most members of the Alphaherpesvirinae, the genes in the UL region of its genome are well conserved, whereas the gene arrangement of IRS-US is similar to that of Marek''s disease virus and equine herpesviruses 1. Therefore, our data based on the genomic analysis suggest that DEV represents an osculant taxonomic entity within the Alphaherpesvirinae. [Copyright &y& Elsevier]

To study the pathogenicity of new duck reovirus (NDRV) to chickens, eighty 3-day-old SPF chickens were equally divided into two groups. The experimental group was inoculated with a NDRV challenge strain of 100 μL (10–5.00 ELD50/0.1 mL) by the subcutaneous (s.c.) route, and the control group was inoculated with 100 μL of sterile phosphate-buffered saline (PBS) by the same route. In the experimental group, chickens exhibited introflexion of claws, performing of splits, stunting syndrome, weight loss and death. Gross lesions such as enlargement and yellowish-white focal necroses were observed in the liver and spleen. Microscopic changes were typical including varying degrees of hepatocyte steatosis and necrosis, splenic lymphocyte necrosis, interstitial pneumonia. Viral loads were detected in lung, liver, heart, spleen, duodenum, burse and kidney. The liver and spleen viral loads remained a much higher level and maintained for a longer time, suggesting that these tissues might be the target organs. In summary, NDRV can cause systemic infections and death in chickens, which indicated that chickens may be infected by NDRV in poultry production. [ABSTRACT FROM AUTHOR]

Reticuloendotheliosis virus (REV) is an important representative avian retrovirus. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of REV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect changes in protein levels in chicken embryo fibroblast cells (CEFs) that were infected with REV or mock infected. In total, 605 cellular proteins were differentially expressed, among which 196, 345, and 286 were differentially expressed in REV-infected CEFs at 1, 3, and 5 days postinfection, respectively. Gene Ontology analysis indicated that the biological processes of the differentially expressed proteins were primarily related to cellular processes, metabolic processes, biological regulation, response to stimulus, and immune system processes and that the molecular functions in which the differentially expressed proteins were mainly involved were binding, catalytic activity, and enzyme regulator activity. Pathway analysis showed that a total of 143, 167, and 179 pathways, including protein digestion and absorption, focal adhesion, ECM-receptor interaction, cytokine-cytokine receptor interaction, Toll-like receptors, and JAK-STAT signaling, were enriched in REV-infected CEFs at 1, 3, and 5 days postinfection, respectively. In conclusion, this study is the first to analyze the protein profile of REV-infected CEFs using an iTRAQ approach. The results of this study provide valuable information for better understanding the host response to REV infection. [ABSTRACT FROM AUTHOR]

Encouraged by our earlier discovery of neuraminidase inhibitors targeting 150-cavity or 430-cavity, herein, to yield more potent inhibitors, we designed, synthesized, and biologically evaluated a series of novel oseltamivir derivatives via modification of C-1 and C5–NH 2 of oseltamivir by exploiting 150-cavity and/or 430-cavity. Among the synthesized compounds, compound 15e , the most potent N1-selective inhibitor targeting 150-cavity, showed 1.5 and 1.8 times greater activity than oseltamivir carboxylate (OSC) against N1 (H5N1) and N1 (H5N1–H274Y). In cellular assays, 15e also exhibited greater potency than OSC against H5N1 with EC 50 of 0.66 μM. In addition, 15e demonstrated low cytotoxicity in vitro and low acute toxicity in mice. Molecular docking studies provided insights into the high potency of 15e against N1 and N1–H274Y mutant NA. Overall, we envisioned that the significant breakthrough in the discovery of potent group-1-specific neuraminidase inhibitors may lead to further investigation of more potent anti-influenza agents. Image 1 • By exploiting 150-cavity and/or 430-cavity of influenza virus neuraminidase, novel oseltamivir derivatives were reported. • Compound 15e showed similar or greater activity than OSC in both NA inhibitory activity and cellular assay. • Compound 15e demonstrated low cytotoxicity in vitro and low acute toxicity in mice. [ABSTRACT FROM AUTHOR]

Outbreaks of duck Tembusu virus (DTMUV) have caused substantial economic losses in the major duck-producing regions of China since 2010. To improve our understanding of the host cellular responses to virus infection and the pathogenesis of DTMUV infection, we applied isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with multidimensional liquid chromatography-tandem mass spectrometry to detect the protein changes in duck embryo fibroblast cells (DEFs) infected and mock-infected with DTMUV. In total, 434 cellular proteins were differentially expressed, among which 116, 76, and 339 proteins were differentially expressed in the DTMUV-infected DEFs at 12, 24, and 42 hours postinfection, respectively. The Gene Ontology analysis indicated that the biological processes of the differentially expressed proteins were primarily related to cellular processes, metabolic processes, biological regulation, response to stimulus, and cellular organismal processes and that the molecular functions in which the differentially expressed proteins were mainly involved were binding and catalytic activity. Some selected proteins that were found to be differentially expressed in DTMUV-infected DEFs were further confirmed by real-time PCR. The results of this study provide valuable insight into DTMUV-host interactions. This could lead to a better understanding of DTMUV infection mechanisms. [ABSTRACT FROM AUTHOR]

To yield potent neuraminidase inhibitors with improved drug resistance and favorable drug-like properties, two series of novel oseltamivir derivatives targeting the 150-cavity of neuraminidase were designed, synthesized, and biologically evaluated. Among the synthesized compounds, the most potent compound 43b bearing 3-floro-4-cyclopentenylphenzyl moiety exhibited weaker or slightly improved inhibitory activity against wild-type neuraminidases (NAs) of H1N1, H5N1, and H5N8 compared to oseltamivir carboxylate (OSC). Encouragingly, 43b displayed 62.70- and 5.03-fold more potent activity than OSC against mutant NAs of H5N1–H274Y and H1N1–H274Y, respectively. In cellular antiviral assays, 43b exerted equivalent or more potent activities against H1N1, H5N1, and H5N8 compared to OSC with no significant cytotoxicity up to 200 μM. Notably, 43b displayed potent antiviral efficacy in the embryonated egg model, in which achieved a protective effect against H5N1 and H5N8 similar to OSC. Molecular docking studies were implemented to reveal the binding mode of 43b in the binding pocket. Moreover, 43b possessed improved physicochemical properties and ADMET properties compared to OSC by in silico prediction. Taken together, 43b appeared to be a promising lead compound for further investigation. [Display omitted] • 43b exhibited similar inhibitory activity against NAs of H1N1, H5N1 and H5N8 compared to OSC. • 43b displayed more potent activity than OSC against H5N1–H274Y and H1N1–H274Y NAs. • 43b exerted equivalent or more potent activities against H1N1, H5N1 and H5N8 compared to OSC. • 43b displayed potent antiviral efficacy in the embryonated egg model against H5N1 and H5N8. [ABSTRACT FROM AUTHOR]

Specific molecularly imprinted polymers for dencichine were developed for the first time in this study by the bulk polymerization using phenylpyruvic acid and dl -tyrosine as multi-templates. The photographs confirmed that molecularly imprinted polymers prepared using N , N ′-methylene diacrylamide as cross-linker and glycol dimethyl ether as porogen displayed excellent hydrophilicity. Selectivity, adsorption isotherm and adsorption kinetics were investigated. The sample loading-washing-eluting solvent was optimized to evaluate the property of molecularly imprinted solid phase extract. Compared with LC/WCX-SPE, water-compatible molecularly imprinted solid phase extraction displayed more excellent specific adsorption performance. The extracted dencichine from Panax notoginseng with the purity of 98.5% and the average recovery of 85.6% ( n = 3) was obtained. [ABSTRACT FROM AUTHOR]

Downregulation of claudin 1, a critical tight junction protein, has been correlated with increased invasiveness in breast cancer. However, recent studies suggest that claudin 1 contributes to the progression of some molecular subtypes of breast cancer. In this study, claudin 1 promotes migration in luminal-like MCF7 human breast cancer cells and increases their sensitivity to tamoxifen, etoposide, and cisplatin. We also observed an inverse relationship between upregulation of claudin 1 and TGFβ. Collectively, our results suggest that claudin 1 has the potential to be used as a predictive marker for treatment efficacy for specific breast cancer patient subgroups. [ABSTRACT FROM PUBLISHER]

Todiscover group-1-specific neuraminidase (NA) inhibitors thatare especially involved in combating the H5N1 virus, two series ofoseltamivir derivatives were designed and synthesized by targetingthe 150-cavity. Among these, compound 20lwas the mostpotent N1-selective inhibitor, with IC50values of 0.0019,0.0038, and 0.0067 μM against NAs from three H5N1 viruses. Thesevalues are better than those of oseltamivir carboxylate. Compound 32was another potent N1-selective inhibitor that exhibiteda 12-fold increase in activity against the H274Y mutant relative tooseltamivir carboxylate. Molecular docking studies revealed that the150-cavity was an auxiliary binding site that may contribute to thehigh selectivity of these compounds. The present work is a significantbreakthrough in the discovery of potent group-1-specific neuraminidaseinhibitors, which may be further investigated for the treatment ofinfection by the H5N1 virus. [ABSTRACT FROM AUTHOR]

• An infectious DNA clone of duck Tembusu virus was constructed using the infectious-subgenomic-amplicons (ISA) method. • For the first time, duck embryo fibroblast cells were used for duck Tembusu virus reconstitution by ISA method. • The promoter pCMV worked well in duck embryo fibroblast cells for duck Tembusu virus reconstitution. • The ISA method is a valuable reverse genetic tool for the further study of duck Tembusu virus. Outbreaks of duck Tembusu virus (DTMUV) have caused serious economic losses in China since 2010. In this study, an infectious clone of the DTMUV BZ-2010strain, isolated from layer cherry duck in China, was constructed using the bacterium-free infectious subgenomic-amplicons method. The subgenomic-amplicons of the human cytomegalovirus promoter (pCMV) at the 5′ terminus of the first DNA fragment, the entire genome of DTMUV, and the hepatitis delta ribozyme followed by the simian virus 40 polyadenylation signal (HDR/SV40pA) at the 3′ terminus of the last DNA fragment were synthesized and amplified by PCR in three DNA fragments. The pCMV and HDR/SV40pA were used to drive the viral RNA transcription and generate a full-length RNA transcript of the virus, and were found to be effective in reassembling DTMUV in duck embryo fibroblast cells. The RNA transcripts from the infection clone were infectious in duck embryo fibroblast cells, generating the reconstituted DTMUV. This study provided a valuable reverse genetic tool for the further study DTMUV pathogenesis. [ABSTRACT FROM AUTHOR]

Since the first reported cases of ducks infected with a previously unknown flavivirus in eastern China in April 2010, the virus, provisionally designated Duck Tembusu Virus (DTMUV), has spread widely in domestic ducks in China and caused significant economic losses to poultry industry. In this study, we examined in detail structural, antigenic, and evolutionary properties of envelope (E) proteins of six DTMUV isolates spanning 2010–2012, each being isolated from individual farms with different geographical locations where disease outbreaks were documented. Structural analysis showed that E proteins of DTMUV and its closely related flavivirus (Japanese Encephalitis Virus) shared a conserved array of predicted functional domains and motifs. Among the six DTMUV strains, mutations were observed only at thirteen amino acid positions across three separate domains of the E protein. Interestingly, these genetic polymorphisms resulted in no detectable change in viral neutralization properties as demonstrated in a serum neutralization assay. Furthermore, phylogenetic analysis of the nucleotide sequences of the E proteins showed that viruses evolved into two distinct genotypes, termed as DTMUV.I and DTMUV.II, with II emerging as the dominant genotype. New findings described here shall give insights into the antigenicity and evolution of this new pathogen and provide guidance for further functional studies of the E protein for which no effective vaccine has yet been developed. [ABSTRACT FROM AUTHOR]

Background: Defects in tight junctions, gate-keepers of the integrity of the epidermal barrier function, are known to contribute to cancer development. As such, enhancing our understanding of how the expression of proteins involved in these junctions is regulated in cancer, remains a priority. Although the expression of one of these proteins, claudin 1, is down regulated in most invasive human breast cancers (HBC), we have recently shown that high levels of claudin 1, characterized tumors belonging to the very aggressive basal-like breast cancer (BLBC) subtype. In these tumors, the claudin 1 protein, usually localized in the cell membrane, is often mislocalized to the cytoplasm.Methods: To examine the clinical relevance of this observation, we have generated and analyzed an invasive HBC tissue microarray consisting of 151 breast tumor samples; 79 of which presented a basal-like phenotype (i.e. ER-ve, PR-ve HER2-ve, CK5/6 or EGFR+ve). We also interrogated the outcome of claudin 1 knockdown in a human BLBC cell line, BT-20.Results: Immunohistochemical analysis of this patient cohort revealed a significant association between high claudin 1 expression and BLBCs in women 55 years of age and older. Interestingly, no significant association was found between claudin 1 and nodal involvement, tumor grade or tumor size. Regression analysis however, showed a significant positive association between claudin 1 and claudin 4, even though claudin 4 did not significantly correlate with patient age. Claudin 1 knockdown in BT-20 cells resulted in decreased cell migration. It also significantly altered the expression of several genes involved in epithelial-mesenchymal-transition (EMT); in particular, SERPINE 1 (PAI1) and SSP1 (osteopontin), known to inhibit EMT and cancer cell migration. Conversely, genes known to maintain EMT through their interaction, SNAIL2, TCF4 and FOXC2 were significantly down regulated.Conclusions: The association of high claudin 1 protein levels observed in tumors derived from older women with BLBC, suggests that claudin 1 has the potential to serve as a marker which can identify a specific subgroup of patients within the BLBC subtype and thus, further contribute to the characterization of these ill-defined breast cancers. More importantly, our studies strongly suggest that claudin 1 directly participates in promoting breast cancer progression, possibly through the alteration of expression of EMT genes. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, we study the asymptotics of the finite-time ruin probability for a generalized renewal risk model with independent strong subexponential claim sizes and widely lower orthant dependent inter-occurrence times. This widely lower orthant dependence structure can include some common negative dependent random variables (r.v.s) such as negatively lower orthant dependent r.v.s, some positive dependent r.v.s and some other dependent r.v.s. For this generalized renewal risk model, we show that the asymptotics of the finite-time ruin probability hold uniformly for all times in the sense that the magnitude of the initial reserve of some insurance portfolio does not influence the length of the operating time. Further, the uniform asymptotics of the random-time ruin probability in the above model have been obtained. [Copyright &y& Elsevier]

Abstract: The formation of Aβ and its subsequent deposition in senile plaques are considered to be initial events that lead to a cascade of pathological changes in AD. Mediators of Aβ-induced oxidative stress are known to cause oxidative damage to macromolecules. However, the molecular mechanisms by which Aβ-induced oxidative stress leads to neuronal cell death are not fully understood. Here we show that Aβ-induced oxidative stress activates the pro-death gene BNIP3. Aβ treatment results in mitochondrial dysfunction, accumulation of reactive oxygen species, and subsequent expression of BNIP3 in rat primary cortical neurons. Pretreatment with antioxidants abolished Aβ-induced BNIP3 expression and attenuated cell death, demonstrating the role of oxidative stress in BNIP3 induction. Aβ-induced BNIP3 expression may be mediated by hypoxia-inducible factor-1 (HIF-1) because Aβ-treatment induced accumulation and nuclear translocation of HIF-1 and knock-down of HIF-1 by RNAi inhibited BNIP3 expression. Finally, knockdown of BNIP3 reduced Aβ-induced neuronal death. Together, these results suggest a potential pathological role of BNIP3 in the etiology of AD. [Copyright &y& Elsevier]

Encouraged by our earlier discovery of N1-selective inhibitors, the 150-cavity of influenza virus neuraminidases (NAs) could be further exploited to yield more potent oseltamivir derivatives. Herein, we report the design, synthesis and biological evaluation of a series of novel oseltamivir derivatives via the structural modifications at C 5 –NH 2 of oseltamivir targeting 150-cavity. Among them, compound 5c bearing 4-(3-methoxybenzyloxy)benzyl group exhibited the most potent activity, which was lower or modestly improved activities than oseltamivir carboxylate (OSC) against N1 (H1N1), N1 (H5N1) and N1 (H5N1–H274Y). Specifically, there was 30-fold loss of activity against the wild-type strain H1N1. However, 5c displayed 4.85-fold more potent activity than OSC against H5N1–H274Y NA. Also, 5c demonstrated low cytotoxicity in vitro and no acute toxicity in mice. Molecular docking studies provided insights into the high potency of 5c against N1 and N1–H274Y mutant NAs. Besides, the in silico prediction of physicochemical properties and CYP enzymatic inhibitory ability of representative compounds were conducted to evaluate their drug-like properties. Image 1 • Novel oseltamivir derivatives via modifying C 5 –NH 2 of oseltamivir were reported. • 5c showed lower or modestly improved activities than OSC against NAs. • 5c showed antiviral activities similar to those of OSC against H1N1 and H5N1. • 5c demonstrated low cytotoxicity in vitro and no acute toxicity in mice. [ABSTRACT FROM AUTHOR]

From our research group, it was noticed that oseltamivir derivatives targeting 150-cavity of neuraminidase enzyme (NA) could significantly increase antiviral activity. Thus, we further enriched the C5–NH 2 position of oseltamivir structure to obtain more potent oseltamivir derivatives. In this article a series of oseltamivir derivatives were synthesized by modifying C5–NH 2 position of oseltamivir. All the compounds were evaluated for in vitro antiviral activity against H5N1 and H5N8. Encouragingly, compounds 9a and 11e were exhibited prominent activity, which is similar to oseltamivir carboxylate (OSC) and in NAs inhibitory assay, 11e showed remarkable potency against N1 (H5N1), N2 (H5N2), N6 (H5N6) and N8 (H5N8). In addition, 11e demonstrated low cytotoxicity and no obvious toxicity at the dose of 1500 mg/kg in mice. Molecular docking studies of 9a and 11e provided a plausible rationale for the high potency against group-1 NAs. This work provided new insights to design further neuraminidase inhibitors, which can help to investigate new potent inhibitors for group-1 and group-2 shortly. Image 1 • By exploiting 150-cavity of influenza virus neuraminidase, novel oseltamivir derivatives were reported. • Compounds 9a and 11e showed similar or greater activity than OSC in both NA inhibitory activity and cellular assay. • Compound 11e demonstrated low cytotoxicity in vitro and low acute toxicity in mice. [ABSTRACT FROM AUTHOR]

To standardize the rice-specific quantification methods, the criteria of six genes of rice (gos9, PLD, SPS, RBE4, ppi-PPF and oriazain) were compared and evaluated by ddPCR. The results revealed that SPS, RBE4 and ppi-PPF were single copy genes per haploid genome and species specificity and stable among different rice cultivars, by employing Lectin gene of soybean as internal reference gene. The established ddPCR systems were precise and reliable with an absolute LOQ of 10–20 copies/reaction. Furthermore, the robustness of these three assays was verified by performing an intra-laboratory repeatability validation and the results showed that the three endogenous genes of rice could be quantitated repeatedly and precisely above the LOQ. These ddPCR methods can reliably quantified the GM content even if the content was low to 0.1%, which were much more reliable than the results from real-time PCR using the same primers and probes. Image 1 • SPS, RBE4 and ppi-PPF were single copy genes and stable among different rice cultivars. • The established ddPCR methods were precise with a LOQ of 10–20 copies/reaction. • An intra-laboratory validation was performed to verify the robustness of the developed methods. • GM rice content of 0.1% (w/w) could be quantified with the developed methods. [ABSTRACT FROM AUTHOR]

Edible bird's nest (EBN) has been traditionally regarded as a kind of medicinal and healthy food in Asia. However, economically motivated adulteration (EMA) has been an issue in the EBN supply chain. To develop an accurate high-throughput approach for detecting EBN and its adulterants (exemplified by porcine skin, swim bladder, white fungus, and egg white), shotgun proteomics was applied for discovery of specific peptides that were subsequently converted into scheduled multiple reaction monitoring (MRM) transitions. Totally, 28 specific peptides were verified as unique to EBN and its adulterants by tandem mass spectrometry. Subsequently, 9 quantitative MRM-transitions of peptides from adulterants and 2 internal standard references from EBN were screened for the quantitative analysis of the adulterants, which allowed detection of adulterants in EBN matrix in the range of 1–80%. These results suggested that integration of shotgun proteomics and scheduled MRM had potential for the authentication of EBN and its adulterants. Unlabelled Image • A Proteomics method was reported for authentication of edible bird's nest. • 28 specific peptides were discovered as unique to edible bird's nest or its 4 common adulterants by shotgun proteomics. • 11 quantitative MRM-transitions of peptides were screened for quantitation of adulterants by scheduled MRM. • Characteristics of quantitative MRM-transitions were described. • An optimal workflow of discovering specific peptide markers of protein-containing food was proposed. [ABSTRACT FROM AUTHOR]

Adenanthin, a natural ent-kaurane diterpenoid extracted from the herb Isodon adenantha, has been reported to increase intracellular reactive oxygen species in leukemic and hepatocellular carcinoma cells. However, the function and mechanism of the compound in adipogenesis and the development of obesity is still unknown. In this study, we demonstrated that adenanthin inhibited adipogenesis of 3T3-L1 and mouse embryonic fibroblasts, and the underlying mechanism included two processes: a delayed mitotic clonal expansion via G0/G1 cell cycle arrest by inhibiting the RB-E2F1 signaling pathway and a reduced C/EBPβ signaling by inhibiting the expression and activity of C/EBPβ during mitotic clonal expansion. Furthermore, adenanthin significantly reduced the growing body weight and adipose tissue mass during high-fat diet-inducing obesity of mice, indicating the beneficial effects of adenanthin as a potential agent for prevention of obesity. [ABSTRACT FROM AUTHOR]