Neural Related Work Summarization with a Joint Context-driven Attention Mechanism

Conventional solutions to automatic related work summarization rely heavily on human-engineered features. In this paper, we develop a neural data-driven summarizer by leveraging the seq2seq paradigm, in which a joint context-driven attention mechanism is proposed to measure the contextual relevance within full texts and a heterogeneous bibliography graph simultaneously. Our motivation is to maintain the topic coherency between a related work section and its target document, where both the textual and graphic contexts play a big role in characterizing the relationship among scientific publications accurately. Experimental results on a large dataset show that our approach achieves a considerable improvement over a typical seq2seq summarizer and five classical summarization baselines.Comment: 11 pages, 3 figures, in the Proceedings of EMNLP 201

Stroke and Liver Cirrhosis: A Brief Review of Current Evidence

Stroke and liver cirrhosis are common in our everyday clinical practice, both of which can lead to serious complications. Their association is unclear. In this chapter, we briefly summarized the epidemiology of liver cirrhosis in stroke, reviewed the current evidence regarding the association between liver cirrhosis and stroke, and discussed the potential mechanisms for explaining such an association, such as coagulopathy, hypoperfusion, cardiac diseases, diabetes, and dyslipidemia

CpG oligonucleotides suppress HepG2 cells-induced Jurkat cell apoptosis via the Fas-FasL-mediated pathway

<p>Abstract</p> <p>Objective</p> <p>To explore the potential role of CpG motif-containing oligonucleotides (CpG-ODN) in modulating the expression of FasL in HepG2 and Fas in Jurkat cells <it>in vitro</it>, and to examine the effect of CpG-ODN treatment on the HepG2 cells-mediated Jurkat cell apoptosis <it>in vitro</it>.</p> <p>Methods</p> <p>The expressions of FasL in HepG2 and Fas in Jurkat cells were examined by real time PCR and flow cytometry (FCM). HepG2 and Jurkat cells were co-cultured, and the frequency of apoptotic Jurkat cells and levels of activated caspase-3 were determined by FCM.</p> <p>Results</p> <p>Treatment with CpG-ODN down-regulated the expression of FasL in HepG2 cells in a dose- and time-dependent manner. In addition, treatment with CpG-ODN down-regulated the Fas mRNA transcription and protein expression in Jurkat cells. Treatment of HepG2 cells or Jurkat cells with FasL-neutralizing antibody NOK-2 remarkably inhibited the HepG2-medaited Jurkat cell apoptosis. Pre-treatment of HepG2 or Jurkat cells with CpG-ODN significantly reduced the frequency of HepG2-mediated apoptotic Jurkat cells and inhibited the activation of caspase-3 in Jurkat cells <it>in vitro</it>.</p> <p>Conclusions</p> <p>Our data indicated that treatment with CpG-ODN inhibited the HepG2 cells-mediated Jurkat cell apoptosis by modulating the Fas/FasL pathway. Apparently, CpG-ODN treatment may be a potential therapeutic reagent for HCC.</p

Personalized community detection in scholarly network

Most graph clustering methods partition a network into communities based solely on the topology and structure of the network. Due to this, the means via which communities are detected on a network are insensitive to the preferences of a user who is searching the network with a specific, personalized information need. Such partition algorithms may be of diminished value for scholars exploring networks of research if these scholars possess prior preferences on what information they consider relevant. To better address this type of information seeking behavior, we introduce a personalized community detection algorithm that provides higher-resolution partitioning of areas of the network that are more relevant to a provided seed query. This algorithm utilizes the divisive Girvan-Newman approach but incorporates a user's personal preferences as a prior. We show that this personalized algorithm can produce a more fine-tuned partition of a scholarly network when compared to existing prior-insensitive approaches

Regulatory divergence of homeologous Atlantic salmon elovl5 genes following the salmonid-specific whole genome duplication

Fatty acyl elongase 5 (elovl5) is a critical enzyme in the vertebrate biosynthetic pathway which produces the physiologically essential long chain polyunsaturated fatty acids (LC-PUFA), docosahexenoic acid (DHA) and eicosapentenoic acid (EPA) from 18 carbon fatty acids precursors. In contrast to most other vertebrates, Atlantic salmon possess two copies of elovl5 (elovl5a and elovl5b) as a result of a whole genome duplication (WGD) which occurred at the base of the salmonid lineage. WGDs have had a major influence on vertebrate evolution, providing extra genetic material, enabling neofunctionalization to accelerate adaptation and speciation. However, little is known about the mechanisms by which such duplicated homeologous genes diverge. Here we show that homeologous Atlantic salmon elovl5a and elovl5b genes have been asymmetrically colonised by transposon-like elements. Identical locations and identities of insertions are also present in the rainbow trout duplicate elovl5 genes, but not in the nearest extant representative preduplicated teleost, the northern pike. Both elovl5 salmon duplicates possessed conserved regulatory elements that promoted Srebp1- and Srebp2-dependent transcription, and differences in the magnitude of Srebp response between promoters could be attributed to a tandem duplication of SRE and NF-Y cofactor binding sites in elovl5b. Furthermore, an insertion in the promoter region of elovl5a confers responsiveness to Lxr/Rxr transcriptional activation. Our results indicate that most, but not all transposon mobilisation into elovl5 genes occurred after the split from the common ancestor of pike and salmon, but before more recent salmonid speciations, and that divergence of elovl5 regulatory regions have enabled neofuntionalization by promoting differential expression of these homeologous genes

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page

Molecular and Functional Characterization and Expression Analysis of a Delta6 Fatty Acyl Desaturase cDNA of European Sea Bass (Dicentrarchus labrax L.)

The extent to which fish species can produce highly unsaturated fatty acids (HUFA) from C18 fatty acids varies with their complement of fatty acyl desaturase (FAD) enzymes. Marine fish are unable to produce HUFA at a significant rate due to apparent deficiencies in one or more enzymatic steps in the desaturation/ elongation pathway. It is not known if this is due to a lack of the genes or to tight regulation of the enzymatic activity in some of the transformation steps. In the present study, we report molecular cloning, cDNA, protein and functional analysis of a Δ6 FAD of European sea bass (Dicentrarchus labrax L.), and describe its tissue expression and nutritional regulation. An FAD cDNA contig sequence from brain tissue of sea bass was obtained by gene walking, and full-length cDNA was obtained by amplification using 5′end forward and 3′ end reversed primers. The full length of the sea bass FAD cDNA was 2089 bp, which included a 5′-UTR (untranslated region) of 267 bp, a 3′-UTR of 484 bp and an open reading frame (ORF) of 1338 bp, which specified a protein of 445 amino acids. The mRNA size, estimated by northern blot analysis was 2.1 kb, consistent with the cDNA. Transient expression of Δ6-FAD-EGFP in HeLa cells showed the protein compartmentalized to the endoplasmic reticulum. Functional expression in yeast showed the sea bass cDNA encoded a unifunctional Δ6 FAD enzyme. The sea bass FAD was more active towards 18:3n-3 with 14.5% being converted to 18:4n-3 compared to 5.6% of 18:2n-6 converted to 18:3n-6. Expression of the Δ6 FAD gene in the sea bass tissues showed a rank order of heart, brain, ovary, kidney, adipose tissue and liver as determined by RT-qPCR. Nutritional regulation of gene expression was studied. Diets containing partial substitution of fish oil with rapeseed or linseed oils induced up-regulation of the Δ6 FAD gene; whereas, a diet containing olive oil did not influence the expression. Similarly, when fish oil was partially replaced by blends of vegetable oils, one increased expression and one did not

Effects of diets containing vegetable oil on expression of genes involved in highly unsaturated fatty acid biosynthesis in liver of Atlantic salmon (Salmo salar)

Fish are an important dietary source of the long-chain C20 and C22 highly unsaturated fatty acids (HUFA), arachidonate (20:4n-6), eicosapentaenoate (20:5n-3) and docosahexaenoate (22:6n-3), that are crucial to the health of higher vertebrates and that can be beneficial in human diets. Δ5 and Δ6 fatty acid desaturases, and fatty acid elongases are critical enzymes in the biosynthetic pathways of HUFA from shorter chain C18 polyunsaturated fatty acids (PUFA) such as linoleic (18:2n-6) and α-linolenic (18:3n-3) acids. Recently, full-length cDNAs for fatty acid desaturase and elongase enzymes have been cloned from Atlantic salmon. Functional characterisation of the desaturase revealed n-3 Δ5 desaturase activity, whereas the elongase had broad substrate specificity for PUFA with a range of chain lengths from C18 to C22. The study described here was primarily focused on the nutritional regulation of genes involved in the HUFA biosynthetic pathway in Atlantic salmon. A feeding trial was performed whereby salmon smolts in seawater pens were fed for 40 weeks on five different diets. The diets consisted of a control diet containing fish oil (FO) and four diets in which the FO was replaced in a graded manner by linseed oil (LO). Specifically, in terms of added oils, the five diets were 100% FO (FO), 100%LO (LO100) and FO/LO in ratios of 3:1 (LO25), 1:1 (LO50) and 1:3 (LO75). Fish were sampled at 20 and 40 weeks, and samples of liver were collected for lipid analyses and total RNA extraction. Hepatocytes were also prepared and the activity of the HUFA biosynthetic pathway determined. Expression of fatty acid desaturase and elongase genes was determined by quantitative real time PCR and the ratio of the copy number of the targeted gene against that of β-actin was calculated. The results showed that after 20 weeks of feeding, desaturase and elongase gene expression in liver was increased in a graded manner by increasing dietary LO. Expression of both genes was positively and negatively correlated with dietary 18:3n-3 and n-3 HUFA, respectively. By 40 weeks of feeding, expression of neither gene showed the same degree of correlation with dietary fatty acid composition. In contrast, activity of the HUFA biosynthetic pathway, which showed some association with diet at 20 weeks, was positively and significantly correlated with dietary LO after 40 weeks of feeding. Elongation activity reflected the overall activity of the HUFA biosynthetic pathway to a greater degree than Δ5 desaturation activity. The possible mechanisms underlying the observed results and the regulation of the HUFA biosynthetic pathway are discussed

Multiple genes for functional delta6 fatty acyl desaturases (Fad) in Atlantic salmon (Salmo salar L.): Gene and cDNA characterization, functional expression, tissue distribution and nutritional regulation

Fish are the primary source in the human food basket of the n-3 long-chain polyunsaturated fatty acids (LC-PUFA), eicosapentaenoate (EPA; 20:5n-3) and docosahexaenoate (DHA; 22:6n-3), that are crucial to the health of higher vertebrates. Atlantic salmon are able to synthesis EPA and DHA from 18:3n-3 through reactions catalyzed by fatty acyl desaturases (Fad) and elongases of very long fatty acids (Elovl). Previously, two cDNAs encoding functionally distinct Δ5 and Δ6 Fads were isolated, but screening of a genomic DNA library revealed the existence of more putative fad genes in the Atlantic salmon genome. In the present study, we show that there are at least four genes encoding putative Fad proteins in Atlantic salmon. Two genes, Δ6fad_a and Δ5fad, corresponded to the previously cloned Δ6 and Δ5 Fad cDNAs. Functional characterization by heterologous expression in yeast showed that the cDNAs for both the two further putative fad genes, Δ6fad_b and Δ6fad_c, had only Δ6 activity, converting 47 and 12 % of 18:3n-3 to 18:4n-3, and 25 and 7 % of 18:2n-6 to 18:3n-6, for ∆6Fad_b and Δ6Fad_c, respectively. Both ∆6fad_a and ∆6fad_b genes were highly expressed in intestine (pyloric caeca), liver and brain, with ∆6fad_b also highly expressed in gill, whereas ∆6fad_c transcript was found predominantly in brain, with lower expression levels in all other tissues. The expression levels of the ∆6fad_a gene in liver and the ∆6fad_b gene in intestine were significantly higher in fish fed diets containing vegetable oil compared to fish fed fish oil suggesting up-regulation in response to reduced dietary EPA and DHA. In contrast, no significant differences were found between transcript levels for ∆6fad_a in intestine, ∆6fad_b in liver, or ∆6fad_c in liver or intestine of fish fed vegetable oil compared to fish fed fish oil. The observed differences in tissue expression and nutritional regulation of the fad genes were discussed in relation to gene structures and fish physiology