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•PS could improve the immunosuppressive effects caused by CTX on silkworm.•PS exhibited antioxidant activity by increasing the SOD, CAT, GSH-Px and decreasing ROS level.•PS could ...regulate the immunity of silkworm by reprogramming of lipid and amino acid metabolisms.
The present study investigated the immune regulatory mechanisms of Poria cocos polysaccharides (PS) in a cyclophosphamide (CTX)-induced immunosuppression silkworm model. We found that PS increased the superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) activities, as well as reactive oxygen species (ROS) levels in the fat body or haemocytes of CTX-treated silkworms. PS also strongly stimulated the immunity of silkworms by increasing haemocyte counts and PO activity and upregulating the mRNA expression of immune-related genes. We further investigated the metabolic profile of the fat body after PS treatment using liquid chromatography–massspectrometry/mass spectrometry (LC–MS/MS) and identified 236 differentially expressed metabolites. Among them, nine metabolites related to amino acid metabolism were present at high levels in the PS-treated group, whereas the contents of metabolites involved in sphingolipid metabolism and alpha-linolenic acid metabolism were significantly decreased after PS treatment. The amino acid metabolism pathways and lipid metabolism pathways were found to be significantly altered in the PS-treated group, which indicates that PS may regulate the immune system of silkworms by reprogramming lipid and amino acid metabolism. This study provides new insight into the immune regulatory effect of PS in animals.
Entity linking is a task to extract query mentions in documents, and then link them to their corresponding entities in a knowledge base. It can improve the performances of knowledge network ...construction, knowledge fusion, information retrieval, natural language processing, and knowledge base population. In this paper, we introduce the difficulties and applications of entity linking and focus on the main methods to address this issue. At last, we list the knowledge bases, data sets, and the evaluation criterion and some challenges of entity linking.
Poria cocos
polysaccharides (PS) have been used as Chinese traditional medicine with various pharmacological effects, including antiviral, anti-oxidative, and immunomodulatory activities. Herein
...Bombyx mori
silkworm was used as a model animal to evaluate the immunomodulatory effects of PS
via
detecting the changes of innate immune parameters and explore the underlying molecular mechanism of the immunoregulatory effect of PS using Illumina HiSeq Xten platform. The results presented here demonstrated that a hemocoel injection of PS significantly enhanced the cellular immunity of silkworm, including hemocyte phagocytosis, microaggregation, and spreading ability. A total of 335 differentially expressed genes (DEGs) were screened, including 214 upregulated genes and 121 downregulated genes by differential expression analysis. Gene annotation and enrichment analyses showed that many DEGs related to immune signal recognition, detoxification, proPO activation, carbohydrate metabolism, and lipid metabolism were significantly upregulated in the treatment group. The Kyoto Encyclopedia of Genes and Genomes-based Gene Set Enrichment Analysis also revealed that the more highly expressed gene sets in the PS treatment silkworm were mainly related to immune signal transduction pathways and energy metabolism. In addition, the activity of four enzymes related to immunity and energy metabolism—including phenoloxidase, glucose-6-phosphate dehydrogenase, hexokinase, and fatty acid synthetase—were all significantly increased in the larvae injected with PS. We performed qRT-PCR to examine the expression profile of immune and metabolic-related genes, which further verified the reliability of our transcriptome data and suggested that PS can regulate the immunity of silkworm by enhancing the cellular immunity and modulating the expression levels of genes related to immune responses and physiological metabolism. These findings will lay a scientific foundation for the use of PS as an immunomodulator in disease prevention in human beings or animals.
Aeromonas hydrophila is a conditional pathogen impacting public hygiene and safety. Hemolysin is a virulence factor of Aeromonas hydrophila that causes erythrocyte hemolysis, yet its transcriptional ...response to Cyprinus rubrofuscus remains unknown. Our investigation confirmed the hemolysis of hemolysin from A. hydrophila. Serum enzyme activity was evaluated weekly after C. rubrofuscus were immunized with hemolysin Ahh1. The results showed that the hemolysin enhances the serum superoxide dismutase (SOD), lysozyme (LZM), and catalase (CAT) activity, which reached a maximum on day 14. To elucidate the molecular interaction between hemolysin from A. hydrophila and the host, we performed transcriptome sequencing on the spleen of C. rubrofuscus 14 days post hemolysin infection. The total number of clean reads was 41.37 Gb, resulting in 79,832 unigenes with an N50 length of 1863 bp. There were 1982 significantly differentially expressed genes (DEGs), including 1083 upregulated genes and 899 downregulated genes. Transcript levels of the genes, such as LA6BL, CD2, and NLRC5, were significantly downregulated, while those of IL11, IL1R2, and IL8 were dramatically upregulated. The DEGs were mainly enriched in the immune disease, viral protein interaction with cytokine and cytokine receptor, and toll-like receptor pathways, suggesting that hemolysin stimulation can activate the transcriptional responses. RT-qPCR experiments results of seven genes, IL-8, STAT2, CTSK, PRF1, CXCL9, TLR5, and SACS, showed that their expression was highly concordant with RNA-seq data. We clarified for the first time the key genes and signaling pathways response to hemolysin from A. hydrophila, which offers strategies for treating and preventing diseases.
•Hemolysin from A. hydrophila enhances serum SOD, LZM, and CAT activities of Cyprinus rubrofuscus.•Transcriptome sequencing showed 1982 significantly DEGs post hemolysin mediated responses.•Hemolysin regulates the expression of immune-related genes, and DEGs are enriched in the immune disease pathway.
Knowledge Engineering with Big Data Wu, Xindong; Chen, Huanhuan; Wu, Gongqing ...
IEEE intelligent systems,
2015-Sept.-Oct., 2015-9-00, 20150901, Letnik:
30, Številka:
5
Journal Article
Recenzirano
In the era of big data, knowledge engineering faces fundamental challenges induced by fragmented knowledge from heterogeneous, autonomous sources with complex and evolving relationships. The ...knowledge representation, acquisition, and inference techniques developed in the 1970s and 1980s, driven by research and development of expert systems, must be updated to cope with both fragmented knowledge from multiple sources in the big data revolution and in-depth knowledge from domain experts. This article presents BigKE, a knowledge engineering framework that handles fragmented knowledge modeling and online learning from multiple information sources, nonlinear fusion on fragmented knowledge, and automated demand-driven knowledge navigation.
Although invertebrates are incapable of adaptive immunity, immunal reactions which are functionally similar to the adaptive immunity of vertebrates have been described in many studies of ...invertebrates including insects. The phenomenon was termed immune priming. In order to understand the molecular mechanism of immune priming, we employed Illumina/Solexa platform to investigate the transcriptional changes of the hemocytes and fat body of Helicoverpa armigera larvae immune-primed with the pathogenic bacteria Photorhabdus luminescens TT01. A total of 43.6 and 65.1 million clean reads with 4.4 and 6.5 gigabase sequence data were obtained from the TT01 (the immune-primed) and PBS (non-primed) cDNA libraries and assembled into 35,707 all-unigenes (non-redundant transcripts), which has a length varied from 201 to 16,947 bp and a N50 length of 1,997 bp. For 35,707 all-unigenes, 20,438 were functionally annotated and 2,494 were differentially expressed after immune priming. The differentially expressed genes (DEGs) are mainly related to immunity, detoxification, development and metabolism of the host insect. Analysis on the annotated immune related DEGs supported a hypothesis that we proposed previously: the immune priming phenomenon observed in H. armigera larvae was achieved by regulation of key innate immune elements. The transcriptome profiling data sets (especially the sequences of 1,022 unannotated DEGs) and the clues (such as those on immune-related signal and regulatory pathways) obtained from this study will facilitate immune-related novel gene discovery and provide valuable information for further exploring the molecular mechanism of immune priming of invertebrates. All these will increase our understanding of invertebrate immunity which may provide new approaches to control insect pests or prevent epidemic of infectious diseases in economic invertebrates in the future.
The present study explored the ability of a novel spent chrysanthemum adsorbent prepared from acid acetaldehyde for the removal of Cu2+ from an aqueous solution. The effect of various parameters, ...including solution pH, adsorbent dosage, contact time and temperature on adsorption of Cu2+ were studied by batch experiments. According to the experimental results, the optimal pH range and optimum dosage were found to be 3.0–5.0 and 6.0g/L, respectively. The adsorption amount at equilibrium decreased with the increase of temperature. Freudlich model provided better correlation for the adsorption of Cu2+ by modified spent Chrysanthemum (MSC) (R=0.99)and spent Chrysanthemum (SC)(R=0.98). Adsorption capacity of MSC was 692mg/g at 293K, but it was 400mg/g at 293K for SC. The adsorption process on Cu2+ proceeded rapidly and almost reached adsorption equilibrium within 20min. The kinetics data of MSC were analyzed using the pseudo-first-order equations and pseudo-second-order equations. The pseudo-second-order equation fitted the experimental data very well (R=0.99). The adsorption amount at equilibrium decreased with the increase of temperature. The thermodynamic parameters showed that the biosorption was exothermic and spontaneous. Experimental results showed that MSC could be used as an effective biosorbent for Cu2+ removal from aqueous solutions.
The improvement of file access performance is a great challenge in real-time cloud services. In this paper, we analyze preconditions of dealing with this problem considering the aspects of ...requirements, hardware, software, and network environments in the cloud. Then we describe the design and implementation of a novel distributed layered cache system built on the top of the Hadoop Distributed File System which is named HDFS-based Distributed Cache System (HDCache). The cache system consists of a client library and multiple cache services. The cache services are designed with three access layers an in-memory cache, a snapshot of the local disk, and the actual disk view as provided by HDFS. The files loading from HDFS are cached in the shared memory which can be directly accessed by a client library. Multiple applications integrated with a client library can access a cache service simultaneously. Cache services are organized in the P2P style using a distributed hash table. Every file cached has three replicas in different cache service nodes in order to improve robustness and alleviates the workload. Experimental results show that the novel cache system can store files with a wide range in their sizes and has the access performance in a millisecond level in highly concurrent environments.
•Two transcriptomes were generated from the hemocytes of the PBS- and Bt-injected B. mori larvae.•We identified 217 DEGs between the PBS and Bt-injected groups, of which 133 genes were upregulated ...and 84 genes were downregulated.•The qRT-PCR results showed significant identical expression tendency as the deep sequencing data.•A large number of immune-related genes of the hemocyte in silkworm were found after exposure to Bt by RNA-seq.
In this study, we describe RNA-seq expression profiling of larval Bombyx mori response to hemocoel injection of Bacillus thuringiensis (Bt). Two transcriptomes were generated from the hemocytes of the PBS- and Bt-injected B. mori larvae. More than 49 million 100-bp paired-end reads, encompassing over 7.3 Gb of sequence data, were generated for each library. After filtering the raw reads and removing the rRNA mapped reads, more than 89% of the reads in each library could be mapped to the silkworm genome reference sequence. Comparison of gene expression levels revealed that a total of 133 unigenes were upregulated while 84 unigenes were downregulated in PBS vs Bt. To further investigate the biological functions of different expression genes (DEGs), gene ontology (GO) and functional enrichment analysis were performed to map all the DEGs to terms in the GO, euKaryotic Ortholog Groups of proteins (KOG) and Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. Among these DEGs, many genes involved in immunity against Bt challenge were identified. These included genes participated in pattern recognition, antimicrobial peptides, insecticide resistance or detoxification, immune melanization, cytoskeleton reorganization and many other immune effectors. To confirm the gene expression patterns identified by the RNA-seq data, the transcript levels of 10 immune related DEGs were examined by quantitative real-time PCR (qRT-PCR). The results showed that the DEGs obtained from the deep sequencing data were accurate and gene expression profiles from RNA-Seq data were reliable. Our studies provide insights into the to immune response of B. mori underling the stress of Bt, which is valuable to understand how Bt affects the innate immune system of silkworm and provide new approaches to control insect pests by using Bt as a biological insecticide.
The multivariate time series (MTS) classification is an important classification problem in which data has the temporal attribute. Because relationships between many variables of the MTS are complex ...and time-varying, existing methods perform not well in MTS classification with many attribute variables. Thus, in this paper, we propose a novel model-based classification method, called Kullback-Leibler Divergence-based Gaussian Model Classification (KLD-GMC), which converts the original MTS data into two important parameters of the multivariate Gaussian model: the mean vector and the inverse covariance matrix. The inverse covariance is the most important parameter, which can obtain the information between the variables. So that the more variables, the more information could be obtained by the inverse covariance, KLD-GMC can deal with the relationship between variables well in the MTS. Then the sparse inverse covariance of each subsequence is solved by Graphical Lasso. Furthermore, the Kullback-Leibler divergence is used as the similarity measurement to implement the classification of unlabeled subsequences, because it can effectively measure the similarity between different distributions. Experimental results on classical MTS datasets demonstrate that our method can improve the performance of multivariate time series classification and outperform the state-of-the-art methods.
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