Managing polyglot systems metadata with hypergraphs

A single type of data store can hardly fulfill every end-user requirements in the NoSQL world. Therefore, polyglot systems use different types of NoSQL datastores in combination. However, the heterogeneity of the data storage models makes managing the metadata a complex task in such systems, with only a handful of research carried out to address this. In this paper, we propose a hypergraph-based approach for representing the catalog of metadata in a polyglot system. Taking an existing common programming interface to NoSQL systems, we extend and formalize it as hypergraphs for managing metadata. Then, we define design constraints and query transformation rules for three representative data store types. Furthermore, we propose a simple query rewriting algorithm using the catalog itself for these data store types and provide a prototype implementation. Finally, we show the feasibility of our approach on a use case of an existing polyglot system.Peer ReviewedPostprint (author's final draft

Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region

Molecular and serological characterization of a distinct potyvirus causing latent infection in calla lilies

A virus (isolate: Ca-M19) capable of inducing local lesions on Chenopodium quinoa Willd. was isolated from calla lilies (Zantedeschia spp.). Subculture of Ca-M19 was easily maintained in C. quinoa, but a back inoculation from single lesion of C. quinoa to calla lilies has so far not been successful. Typical potyvirus-like flexuous particles were consistently detected in Ca-M19 infected plants, and a 1.3-kb DNA fragment was amplifiedfrom these plants by reverse-transcription polymerase chain reaction (RT-PCR) using potyvirus degenerate primers. The PCR product was cloned and its sequence analyzed (AF469171). The amplicon was revealed to correspond to the 3’ terminal region of a potyviral genome. After comparing this sequence with known potyvirus sequences in the GenBank, we considered the virus a new species of Potyvirus based on the uniqueness in its coat protein gene (CP) and the 3’ non-coding region (NCR). Comparative studies showed that Soybean mosaic virus (SMV) and Watermelon mosaic virus 2 (WMV 2) were the two most similar potyviruses with Ca-M19, but they shared only 80% of nucleotide identities in CP and NCR with Ca-M19. Attempts to purify a sufficient quantity of Ca-M19 from C. quinoa for preparation of antibodies were unsuccessful. Alternatively, Ca-M19 CP was expressed by the vector pET28b and puri-fied from E. coli culture, and polyclonal antibodies were prepared in rabbits. The antibody was applied in ELISA, Western blotting, SDS-immunodiffusion and immuno-specific electron microscopy for the detection of Ca-M19 in calla lilies. It did not react with at least five calla lily infecting potyviruses, including Dasheen mosaic virus, Bean yellow mosaic virus, Konjak mosaic virus, Turnip mosaic virus, and Zantedeschia mild mosaic virus. Indirect ELISA and SDS-immunodiffusion tests showed that Ca-M19 was serologically related, but distinct from Bean common mosaic virus (BCMV), Black cowpea mosaic virus (BlCMV), Melon vein banding mosaic virus (MVbMV), Passionfruit mottle virus (PaMV), Passionfruit crinkle virus (PCV), Pas-sionfruit woodness virus (PWV), Soybean mosaic virus (SMV), Watermelon mosaic virus 2 (WMV 2), and Zucchini yellow mosaic virus (ZYMV). Besides serological techniques, a primer pair (M19u/M19d) and a DNA probe were designed which could also specifically detect and differentiate Ca-M19 from other viruses. By the use of specific antibodies in ELISA, Ca-M19 was frequently detected in calla lily plants collected from several major calla lily production townships in Taiwan. Among 86 field samples positively reacting to the antibody, 77 of them exhibited evident systemic mosaic symptoms, but these symptomatic plants were confirmed to be infected simultaneously by other viruses. Nine plants were found to be infected by Ca-M19 alone. These plants were confirmed to have remained symptomless throughout a 6-month observation period. Therefore, we propose naming this isolate Calla lily latent virus (CLLV) for its inability to develop any visible symptoms on calla lily

Macrophage expression of E3 ubiquitin ligase Grail protects mice from lipopolysaccharide-induced hyperinflammation and organ injury.

Multiple organ dysfunction caused by hyperinflammation remains the major cause of mortality during sepsis. Excessive M1-macrophage activation leads to systemic inflammatory responses. Gene related to anergy in lymphocytes (Grail) is regarded as an important regulator of T cells that functions by diminishing cytokine production. However, its role in regulating macrophage activation and organ injury during sepsis remains unclear. Our aim was to examine the effects of Grail on macrophage reactivity and organ injury in endotoxemic animals. Wild-type and Grail knockout mice were injected with vehicle or Escherichia coli lipopolysaccharide and observed for 24 h. Changes in blood pressure, heart rate, blood glucose, and biochemical variables were then examined. Moreover, levels of neutrophil infiltration, MMP-9, and caspase 3 were analyzed in the lungs of animals. The expression of pro-inflammatory cytokines in J774A, RAW264.7, and primary peritoneal macrophages stimulated with LPS were also assessed in the presence or absence of Grail. Results indicated that loss of Grail expression enhances the induction of pro-inflammatory cytokines in J774A, RAW264.7, and primary peritoneal macrophages treated with LPS. Furthermore, LPS-induced macrophage hyperactivation was alleviated by ectopic Grail overexpression. In vivo studies showed that Grail deficiency exacerbates organ damage in endotoxemic animals. Levels of neutrophil infiltration, MMP-9, and caspase 3 were significantly increased in the lungs of Grail-deficient endotoxemic mice. Thus, these results suggest that Grail contributes to the attenuation of hyperinflammation caused by activated macrophages and prevents organ damage in endotoxemic mice. We suggest that Grail signaling could be a therapeutic target for endotoxemia