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, Huilin Zhou, Fuhui Zhou, Yongpeng Wu, Senior Member, IEEE, Victor C. ... Zhou, H. Zhou and F. ...arXiv:1809.01518v1 fatcat:n3pnalxwzrel3mravbau27vbk4
Each genome has a stable distribution of the combined frequency for each k-mer and its reverse complement measured in sequence fragments as short as 1000 bps across the whole genome, for 1<k<6. The collection of these k-mer frequency distributions is unique to each genome and termed the genome's barcode. Results: We found that for each genome, the majority of its short sequence fragments have highly similar barcodes while sequence fragments with different barcodes typically correspond to genesdoi:10.1186/1471-2105-9-546 pmid:19091119 pmcid:PMC2621371 fatcat:vxmm6nri3re3tptb2apw6gt6aq
more »... hat are horizontally transferred or highly expressed. This observation has led to new and more effective ways for addressing two challenging problems: metagenome binning problem and identification of horizontally transferred genes. Our barcode-based metagenome binning algorithm substantially improves the state of the art in terms of both binning accuracies and the scope of applicability. Other attractive properties of genomes barcodes include (a) the barcodes have different and identifiable characteristics for different classes of genomes like prokaryotes, eukaryotes, mitochondria and plastids, and (b) barcodes similarities are generally proportional to the genomes' phylogenetic closeness. Conclusion: These and other properties of genomes barcodes make them a new and effective tool for studying numerous genome and metagenome analysis problems.
Protein & Cell
Programmed necrosis, also known as necroptosis, has recently drawn great attention. As an important cellular regulation mechanism, knowledge of its signaling components is expanding. Necroptosisis demonstrated to be regulated by the RIP1 and RIP3 kinases, and its pathophysiological importance has been confirmed in a number of disease models. Here we review the new members of this necroptosis pathway, MLKL, PGAM5, Drp1 and DAI, and discuss some of their possible applications according to recent findings.doi:10.1007/s13238-012-2083-9 pmid:23073834 pmcid:PMC4875459 fatcat:cih7hz4f7nbfdb4nawakgnapiu
Dielectric failure as well as optical switching failure in electrofluidic display (EFD) are still a bottleneck for sufficient device lifetime. In this study, a dielectric redundancy-designed multilayer insulator of ParyleneC/AF1600X was applied in an EFD device. The reliability performance was systematically studied by tracking the applied voltage-dependent leakage current and capacitance changes (I-V and C-V curves) with thermal ageing time. The multilayer insulator shows a more stabledoi:10.1098/rsos.181121 pmid:30564404 pmcid:PMC6281906 fatcat:q2gsbevbkrgc7bsiatfevfllri
more »... nce in leakage current compared to a single-layer insulator. The failure modes during operation underlying the single-layer and the multilayer dielectric appear to be different as exemplified by microscopic images. The single-layer AFX shows significant detachment. In addition, by quantitatively analysing the C-V curves with ageing time, we find that for the single AFX device, the dominant failure mode is 'no-opening' of the pixels. For the multilayer device, the dominant failure mode is 'no-closing' of the pixels. This study provides tools for distinguishing the basic failure modes of an EFD device and demonstrates a quantitative method for evaluating the reliability performance of the device under thermal ageing.
2.763 (2) 168 O1ÐH1AÁ Á ÁN9 O1ÐH1BÁ Á ÁO1 ii O1ÐH1CÁ Á ÁO1 iii 0.86 (2) 0.86 (3) 0.85 (3) 2.05 (3) 1.92 (3) 2.01 (4) 2.901 (3) 2.726 (4) 2.744 (4) 171 (3) 156 (6) 143 (5) Symmetry codes: o370 Sun, Zhou ...doi:10.1107/s1600536802002921 fatcat:uh2e4uwvlbailaycxagbcyhoqy
Graph Convolution Network (GCN) has been widely applied in recommender systems for its representation learning capability on user and item embeddings. However, GCN is vulnerable to noisy and incomplete graphs, which are common in real world, due to its recursive message propagation mechanism. In the literature, some work propose to remove the feature transformation during message propagation, but making it unable to effectively capture the graph structural features. Moreover, they model usersarXiv:2111.10536v1 fatcat:k3rekddj5japxgaa774k5trjam
more »... d items in the Euclidean space, which has been demonstrated to have high distortion when modeling complex graphs, further degrading the capability to capture the graph structural features and leading to sub-optimal performance. To this end, in this paper, we propose a simple yet effective Quaternion-based Graph Convolution Network (QGCN) recommendation model. In the proposed model, we utilize the hyper-complex Quaternion space to learn user and item representations and feature transformation to improve both performance and robustness. Specifically, we first embed all users and items into the Quaternion space. Then, we introduce the quaternion embedding propagation layers with quaternion feature transformation to perform message propagation. Finally, we combine the embeddings generated at each layer with the mean pooling strategy to obtain the final embeddings for recommendation. Extensive experiments on three public benchmark datasets demonstrate that our proposed QGCN model outperforms baseline methods by a large margin.
The overexpression and hypersecretion of mucus is a hallmark of chronic pulmonary inflammatory disease. Mucin5AC (MUC5AC) is a major component of airway gel-forming mucin. Members of the Unc13 (Munc13) protein family act as important activators of granule exocytosis from various types of mammalian cells. The present study aimed to determine the role of Munc13 family proteins in MUC5AC secretion via an in vitro study with BEAS-2B and Calu-3 cell lines. Reverse transcription-quantitativedoi:10.3892/mmr.2018.9015 pmid:29767240 fatcat:alof4tfdozhkhhd74ygpnbvkju
more »... e chain reaction and western blotting indicated that stimulation of the cells with 100 nM human neutrophil elastase (hNE) for 1 h did not affect the expression of either unc13 homolog B (Munc13-2) or unc13 homolog D (Munc13-4), but immunofluorescence analysis demonstrated that hNE treatment was associated with the recruitment of Munc13-4 to the plasma membrane. Co-immunoprecipitation analysis indicated increased binding between Munc13-4 and syntaxin2 followingh NE stimulation; however, Munc13-2 formed a stable interaction with syntaxin2 with or without hNE stimulation. Subsequently, Munc13-2 and Munc13-4 expression levels were downregulated in BEAS-2B and Calu-3 cells using small interfering RNA (siRNA). ELISAs and immunofluorescence analysis were performed to assess MUC5AC secretion and intracellular retention, respectively. Munc13-2 siRNA transfection did not alter the expression levels of intracellular or secreted MUC5AC following hNE stimulation in either cell line; however, it increased the baseline intracellular levels of MUC5AC and decreased the amount of secreted MUC5AC. Conversely, Munc13-4 siRNA transfection increased the intracellular levels of MUC5AC and decreased the amount of secreted MUC5AC following hNE stimulation, but did not affect their baseline quantities. The results of the present study indicate that Munc13-2 may be an essential regulator of basal MUC5AC exocytosis, while Munc13-4 appears to be a Munc13 protein subtype that may to be sensitive to hNE stimulation during airway MUC5AC hypersecretion.
Cellulases are important glycosyl hydrolases (GHs) that hydrolyze cellulose polymers into smaller oligosaccharides by breaking the cellulose β (1→4) bonds, and they are widely used to produce cellulosic ethanol from the plant biomass. N-linked and O-linked glycosylations were proposed to impact the catalytic ef f iciency, cellulose binding af f inity and the stability of cellulases based on observations of individual cellulases. As far as we know, there has not been any systematic analysis ofdoi:10.1016/s1672-0229(08)60049-2 pmid:20172492 pmcid:PMC5054413 fatcat:n7375ydo7zd6tfnsoioxfpmkze
more »... e distributions of N-linked and O-linked glycosylated residues in cellulases, mainly due to the limited annotations of the relevant functional domains and the glycosylated residues. We have computationally annotated the functional domains and glycosylated residues in cellulases, and conducted a systematic analysis of the distributions of the N-linked and O-linked glycosylated residues in these enzymes. Many N-linked glycosylated residues were known to be in the GH domains of cellulases, but they are there probably just by chance, since the GH domain usually occupies more than half of the sequence length of a cellulase. Our analysis indicates that the O-linked glycosylated residues are signif icantly enriched in the linker regions between the carbohydrate binding module (CBM) domains and GH domains of cellulases. Possible mechanisms are discussed.
This is an Open Access article licensed under the terms of the Creative Commons Attribution-NonCommercial 3.0 Unported license (CC BY-NC) (www.karger.com/OA-license), applicable to the online version of the article only. Distribution permitted for non-commercial purposes only. Abstract Aims: Secretoneurin(SN), a neuropeptide, has been considered a reliable marker of allergenic stimulation. However, the relationship between SN and the secretion of airway mucin remains unclear. In this study, wedoi:10.1159/000358625 pmid:24556756 fatcat:rvzeaextwrczvdkx3zg4atbfqm
more »... imed to examine the in vitro relationship between SN and airway mucin over synthesis, as well as the signaling pathways involved. Methods and Results: Exogenous SN was added to two human airway epithelial cell lines (16HBE and NCI-H292). Measured by real-time quantitative polymerase chain reaction (qPCR) and enzyme-linked immuno sorbent assay (ELISA) respectively, the intracellular mucin(MUC)5AC mRNA and MUC5AC protein of culture supernates exhibited a time-and dose-dependent increase after stimulation of SN. Based on the evidence of an increased phosphorylation of ERK1/2 induced by exogenous SN, we performed the radioactive binding assay. We failed to find direct binding of SN to either epidermal growth factor receptor (EGFR) or Neuropilin-1(NRP1), the co-receptor of EGFR. But we detected an enhanced binding of EGF to NRP1 in the two airway epithelial cell lines induced by exogenous SN. Either EGF neutralizing antibody or MEK specific inhibitor (PD-98059) could attenuate the over synthesis of MUC5AC induced by exogenous SN, indicating an endogenous EGF dependent mechanism in MUC5AC over synthesis induced by SN. Conclusions: We conclude that SN induces MUC5AC hypersecretion in a dose-and time-dependent manner; moreover, the MUC5AC over synthesis induced by SN is strongly associated with the enhanced binding of EGF to NRP1 and the activation of EGFR and ERK1/2 subsequently. could be blocked by EGF-Ab (1:500 dilution) indicating that SN-induced MUC5AC oversynthesis depended on endogenous EGF (Fig. 4a) . To analyze the secreted MUC5AC protein levels, supernatants were collected from the 16HBE cells and were subjected to ELISA analysis. Both 16HBE and NCI-H292 cell lines were treated similarly as mentioned above. EGF-Ab (1:500 dilution) or PD-98059 significantly attenuated the hypersecretion of MUC5AC induced by SN (Fig. 4b) .
Cognitive radio (CR) and non-orthogonal multiple access (NOMA) are two promising technologies in the next generation wireless communication systems. The security of a NOMA CR network (CRN) is important but lacks of study. In this paper, a multiple-input single-output NOMA CRN relying on simultaneous wireless information and power transfer is studied. In order to improve the security of both the primary and secondary network, an artificial noise-aided cooperative jamming scheme is proposed.arXiv:1802.03908v1 fatcat:2alopdm7z5ecnl3ickk6k3zyh4
more »... rent from the most existing works, a power minimization problem is formulated under a practical non-linear energy harvesting model. A suboptimal scheme is proposed to solve this problem based on semidefinite relaxation and successive convex approximation. Simulation results show that the proposed cooperative jamming scheme is efficient to achieve secure communication and NOMA outperforms the conventional orthogonal multiple access in terms of the power consumption.
Densely-connected networks are prominent among natural systems, exhibiting structural characteristics often optimized for biological function. To reveal such features in highly-connected networks, we introduce a new network characterization determined by a decomposition of networkconnectivity into low-rank and sparse components. Based on these components, we discover a new class of networks we define as amalgamated networks, which exhibit large functional groups and dense connectivity.doi:10.1038/srep10611 pmid:26035066 pmcid:PMC4451842 fatcat:nvizo4xhybadjetiqqvnxuhop4
more »... recent experimental findings on cerebral cortex, food-web, and gene regulatory networks, we establish the unique importance of amalgamated networks in fostering biologically advantageous properties, including rapid communication among nodes, structural stability under attacks, and separation of network activity into distinct functional modules. We further observe that our network characterization is scalable with network size and connectivity, thereby identifying robust features significant to diverse physical systems, which are typically undetectable by conventional characterizations of connectivity. We expect that studying the amalgamation properties of biological networks may offer new insights into understanding their structure-function relationships.
Zhou). ...doi:10.1172/jci74368 pmid:25365073 pmcid:PMC4347226 fatcat:qos236tvfzhgzg6z4uzcfgxnau
To purchase reprints of this article, contact: Reprints@BioTechniques.com Victor 000112435 Figure 1 . 0001124351 Vassar, Crystal Hagen, Jeffrey Ludwig, Richard Thomas, and Jiming Zhou Avanir Pharmaceuticals ...doi:10.2144/000112435 pmid:17489229 fatcat:lot4y2ku6vh7hcswjkfd4fj5aq
Increased intestinal permeability and translocation of gut bacteria trigger various polyaetiological diseases associated with chronic inflammation and underlie a variety of poorly treatable pathologies. Previous studies have established a primary role of the microbiota composition and intestinal permeability in such pathologies. Using a rat model, we examined the effects of exposure to a bacteriophage cocktail on intestinal permeability and relative abundance of taxonomic units in the gutdoi:10.1038/s41598-017-07278-6 pmid:28765534 pmcid:PMC5539208 fatcat:lie3auluqfgkbbz4qv3zxifjvm
more »... ial community. There was an increase in markers of impaired gut permeability, such as the lactulose/mannitol ratio, plasma endotoxin concentrations, and serum levels of inflammationrelated cytokines, following the bacteriophage challenge. We observed significant differences in the alpha diversity of faecal bacterial species and found that richness and diversity index values increased following the bacteriophage challenge. There was a reduction in the abundance of Blautia, Catenibacterium, Lactobacillus, and Faecalibacterium species and an increase in Butyrivibrio, Oscillospira and Ruminococcus after bacteriophage administration. These findings provide novel insights into the role of bacteriophages as potentially pathogenic for mammals and their possible implication in the development of diseases associated with increased intestinal permeability. Our knowledge of the intestinal microbiota has greatly expanded over the last decade, and growing evidence suggests that alterations of the intestinal microbiota are critical pathogenic factors that trigger various polyaetiological diseases associated with increased intestinal permeability and chronic inflammation 1-3 . Previous studies have established a clear correlation between chronic inflammation and a variety of pathologies, including neurodegenerative and cardiovascular diseases, cancer, inflammatory bowel disease (IBD), rheumatoid arthritis, diabetes, aging, among others 4-7 . The primary causes of chronic inflammation in the gut are activation of immunoreactive submucosa and endotoxemia, resulting from the impaired gut barrier function. Understanding the factors that modulate microbiota, leading to an increase in intestinal permeability, is essential to determine the direct and indirect causes of these diseases, which have emerged in Western countries as a major health issue during the past several decades, and to find new approaches to their treatment and prevention. The microbiota of the human intestinal tract is comprised of bacteria, fungi, and viruses, including bacteriophages. This highly diverse and complex ecosystem is characterised by dynamic stability of each of its components in the context of the host organism. The gut microbiota directly or indirectly modulates all components of the gut barrier function, such as the mucus integrity and transcellular and paracellular transport 8, 9 . The human gut contains approximately 10 15 bacteriophages, which >10 times of the number of bacterial cells and 100 times of the number of human cells 10 . Although recent studies have shown that the number of free lytic phages in the mammalian gastrointestinal tract is relatively low and prophages are dominant, phages are nevertheless considered important regulators of the microbiota stability 11 . Although it is established that regulators of microbiota can contribute to various pathological conditions in humans, and bacterial viruses are important regulators, there are very few studies of the role of bacteriophages in human health. Until recently, bacteriophages have been considered not to be harmful to humans since they selectively interact with bacteria and do not affect eukaryotic cells. Therefore, bacteriophages were used in a number of experimental and clinical therapeutic studies 12, 13 .
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