Markov basis and Groebner basis of Segre-Veronese configuration for testing independence in group-wise selections

We consider testing independence in group-wise selections with some restrictions on combinations of choices. We present models for frequency data of selections for which it is easy to perform conditional tests by Markov chain Monte Carlo (MCMC) methods. When the restrictions on the combinations can be described in terms of a Segre-Veronese configuration, an explicit form of a Gr\"obner basis consisting of moves of degree two is readily available for performing a Markov chain. We illustrate our setting with the National Center Test for university entrance examinations in Japan. We also apply our method to testing independence hypotheses involving genotypes at more than one locus or haplotypes of alleles on the same chromosome.Comment: 25 pages, 5 figure

Characterization of the binding of botulinum type B 16S toxin to human intestinal epithelial cells

Botulinum neurotoxin produced by Clostridium botulinum type B is a complex of 12S and 16S toxins. 12S toxin consists of a neurotoxin and a nontoxic non-HA (NTNH). The 16S toxin consists of a neurotoxin, an NTNH, and a hemagglutinin (HA). Food-borne botulism is caused by these complex toxins, which are ingested orally and absorbed from the digestive tract across the epithelial barrier lining the gut. Here we show that the type B 16S toxin, but not the 12S toxin or the neurotoxin, binds to the T84 human intestinal epithelial cell line. We also demonstrate that the HA moiety in the 16S toxin mediates the toxin binding to the cells. The carbohydrates containing a galactose moiety inhibited the binding of the 16S toxin to the T84 cells, and neuraminidase treatment of the cells increased the 16S toxin binding. The binding of the 16S toxin to the neuraminidase-treated cells was also inhibited by carbohydrates containing a galactose moiety. These results suggest that the type B 16S toxin binds to human intestinal epithelial cells via the galactose moiety in the carbohydrate chain on the cell surface

Geodemographics profiling of influenza A and B virus infections in community neighborhoods in Japan

<p>Abstract</p> <p>Background</p> <p>The spread of influenza viruses in a community are influenced by several factors, but no reports have focused on the relationship between the incidence of influenza and characteristics of small neighborhoods in a community. We aimed to clarify the relationship between the incidence of influenza and neighborhood characteristics using GIS and identified the type of small areas where influenza occurs frequently or infrequently.</p> <p>Methods</p> <p>Of the 19,077 registered influenza cases, we analyzed 11,437 influenza A and 5,193 influenza B cases that were diagnosed by the rapid antigen test in 66-86 medical facilities in Isahaya City, Japan, from 2004 to 2008. We used the commercial geodemographics dataset, Mosaic Japan to categorize and classify each neighborhood. Furthermore, we calculated the index value of influenza in crude and age adjusted rates to evaluate the incidence of influenza by Mosaic segmentation. Additional age structure analysis was performed to geodemographics segmentation to explore the relationship between influenza and family structure.</p> <p>Results</p> <p>The observed number of influenza A and B patients in the neighborhoods where young couples with small children lived was approximately 10-40% higher than the expected number (p < 0.01) during all seasons. On the contrary, the number of patients in the neighborhoods of the aging society in a rural area was 20-50% lower than the expected number (p < 0.01) during all seasons. This tendency was consistent after age adjustment except in the case of influenza B, which lost significance in higher incidence areas, but the overall results indicated high transmission of influenza in areas where young families with children lived.</p> <p>Conclusions</p> <p>Our analysis indicated that the incidence of influenza A and B in neighborhood groups is related to the family structure, especially the presence of children in households. Simple statistical analysis of geodemographics data is an effective method to understand the differences in the incidence of influenza among neighborhood groups, and it provides a valuable basis for community strategies to control influenza.</p

Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements

<p>Abstract</p> <p>Background</p> <p><it>Clostridium botulinum </it>strains can be divided into four physiological groups that are sufficiently diverged to be considered as separate species. Here we present the first complete genome of a <it>C. botulinum </it>strain from physiological group III, causing animal botulism. We also compare the sequence to three new draft genomes from the same physiological group.</p> <p>Results</p> <p>The 2.77 Mb chromosome was highly conserved between the isolates and also closely related to that of <it>C. novyi</it>. However, the sequence was very different from the human <it>C. botulinum </it>group genomes. Replication-directed translocations were rare and conservation of synteny was high. The largest difference between <it>C. botulinum </it>group III isolates occurred within their surprisingly large plasmidomes and in the pattern of mobile elements insertions. Five plasmids, constituting 13.5% of the total genetic material, were present in the completed genome. Interestingly, the set of plasmids differed compared to other isolates. The largest plasmid, the botulinum-neurotoxin carrying prophage, was conserved at a level similar to that of the chromosome while the medium-sized plasmids seemed to be undergoing faster genetic drift. These plasmids also contained more mobile elements than other replicons. Several toxins and resistance genes were identified, many of which were located on the plasmids.</p> <p>Conclusions</p> <p>The completion of the genome of <it>C. botulinum </it>group III has revealed it to be a genome with dual identity. It belongs to the pathogenic species <it>C. botulinum</it>, but as a genotypic species it should also include <it>C. novyi </it>and <it>C. haemolyticum</it>. The genotypic species share a conserved chromosomal core that can be transformed into various pathogenic variants by modulation of the highly plastic plasmidome.</p

M2 Macrophages Activate WNT Signaling Pathway in Epithelial Cells: Relevance in Ulcerative Colitis

Macrophages, which exhibit great plasticity, are important components of the inflamed tissue and constitute an essential element of regenerative responses. Epithelial Wnt signalling is involved in mechanisms of proliferation and differentiation and expression of Wnt ligands by macrophages has been reported. We aim to determine whether the macrophage phenotype determines the expression of Wnt ligands, the influence of the macrophage phenotype in epithelial activation of Wnt signalling and the relevance of this pathway in ulcerative colitis. Human monocyte-derived macrophages and U937-derived macrophages were polarized towards M1 or M2 phenotypes and the expression of Wnt1 and Wnt3a was analyzed by qPCR. The effects of macrophages and the role of Wnt1 were analyzed on the expression of β-catenin, Tcf-4, c-Myc and markers of cell differentiation in a co-culture system with Caco-2 cells. Immunohistochemical staining of CD68, CD206, CD86, Wnt1, β-catenin and c-Myc were evaluated in the damaged and non-damaged mucosa of patients with UC. We also determined the mRNA expression of Lgr5 and c-Myc by qPCR and protein levels of β-catenin by western blot. Results show that M2, and no M1, activated the Wnt signaling pathway in co-culture epithelial cells through Wnt1 which impaired enterocyte differentiation. A significant increase in the number of CD206+ macrophages was observed in the damaged mucosa of chronic vs newly diagnosed patients. CD206 immunostaining co-localized with Wnt1 in the mucosa and these cells were associated with activation of canonical Wnt signalling pathway in epithelial cells and diminution of alkaline phosphatase activity. Our results show that M2 macrophages, and not M1, activate Wnt signalling pathways and decrease enterocyte differentiation in co-cultured epithelial cells. In the mucosa of UC patients, M2 macrophages increase with chronicity and are associated with activation of epithelial Wnt signalling and diminution in enterocyte differentiation

"Predictability of body mass index for diabetes: Affected by the presence of metabolic syndrome?"

<p>Abstract</p> <p>Background</p> <p>Metabolic syndrome (MetS) and body mass index (BMI, kg.m^-2) are established independent risk factors in the development of diabetes; we prospectively examined their relative contributions and joint relationship with incident diabetes in a Middle Eastern cohort.</p> <p>Method</p> <p>participants of the ongoing Tehran lipid and glucose study are followed on a triennial basis. Among non-diabetic participants aged≥ 20 years at baseline (8,121) those with at least one follow-up examination (5,250) were included for the current study. Multivariate logistic regression models were used to estimate sex-specific adjusted odd ratios (ORs) and 95% confidence intervals (CIs) of baseline BMI-MetS categories (normal weight without MetS as reference group) for incident diabetes among 2186 men and 3064 women, aged ≥ 20 years, free of diabetes at baseline.</p> <p>Result</p> <p>During follow up (median 6.5 years); there were 369 incident diabetes (147 in men). In women without MetS, the multivariate adjusted ORs (95% CIs) for overweight (BMI 25-30 kg/m2) and obese (BMI≥30) participants were 2.3 (1.2-4.3) and 2.2 (1.0-4.7), respectively. The corresponding ORs for men without MetS were 1.6 (0.9-2.9) and 3.6 (1.5-8.4) respectively. As compared to the normal-weight/without MetS, normal-weight women and men with MetS, had a multivariate-adjusted ORs for incident diabetes of 8.8 (3.7-21.2) and 3.1 (1.3-7.0), respectively. The corresponding ORs for overweight and obese women with MetS reached to 7.7 (4.0-14.9) and 12.6 (6.9-23.2) and for men reached to 3.4(2.0-5.8) and 5.7(3.9-9.9), respectively.</p> <p>Conclusion</p> <p>This study highlights the importance of screening for MetS in normal weight individuals. Obesity increases diabetes risk in the absence of MetS, underscores the need for more stringent criteria to define healthy metabolic state among obese individuals. Weight reduction measures, thus, should be encouraged in conjunction with achieving metabolic targets not addressed by current definition of MetS, both in every day encounter and public health setting.</p

Race, colonial history and national identity: Resident Evil 5 as a Japanese game

Resident Evil 5 is a zombie game made by Capcom featuring a White American protagonist and set in Africa. This paper argues that approaching this as a Japanese game reveals aspects of a Japanese racial and colonial social imaginary that are missed if this context of production is ignored. In terms of race, the game presents hybrid racial subjectivities that can be related to Japanese perspectives of Blackness and Whiteness where these terms are two poles of difference and identity through which an essentialised Japanese identity is constructed in what Iwabuchi calls “strategic hybridism” (Iwabuchi, 2002). In terms of colonialism, the game echoes structures of Japanese colonialism through which Japanese colonialism is obliquely memorialised and a “normal” Japanese global subjectivity can be performed

Role of lysophosphatidic acid receptor LPA2 in the development of allergic airway inflammation in a murine model of asthma

<p>Abstract</p> <p>Background</p> <p>Lysophosphatidic acid (LPA) plays a critical role in airway inflammation through G protein-coupled LPA receptors (LPA_1-3). We have demonstrated that LPA induced cytokine and lipid mediator release in human bronchial epithelial cells. Here we provide evidence for the role of LPA and LPA receptors in Th2-dominant airway inflammation.</p> <p>Methods</p> <p/> <p>Wild type, LPA₁heterozygous knockout mice (LPA₁^+/-), and LPA₂heterozygous knockout mice (LPA₂^+/-) were sensitized with inactivated <it>Schistosoma mansoni </it>eggs and local antigenic challenge with <it>Schistosoma mansoni </it>soluble egg Ag (SEA) in the lungs. Bronchoalveolar larvage (BAL) fluids and lung tissues were collected for analysis of inflammatory responses. Further, tracheal epithelial cells were isolated and challenged with LPA.</p> <p>Results</p> <p>BAL fluids from <it>Schistosoma mansoni </it>egg-sensitized and challenged wild type mice (4 days of challenge) showed increase of LPA level (~2.8 fold), compared to control mice. LPA₂^+/-mice, but not LPA₁^+/-mice, exposed to <it>Schistosoma mansoni </it>egg revealed significantly reduced cell numbers and eosinophils in BAL fluids, compared to challenged wild type mice. Both LPA₂^+/-and LPA₁^+/-mice showed decreases in bronchial goblet cells. LPA₂^+/-mice, but not LPA₁^+/-mice showed the decreases in prostaglandin E2 (PGE2) and LPA levels in BAL fluids after SEA challenge. The PGE2 production by LPA was reduced in isolated tracheal epithelial cells from LPA₂^+/-mice. These results suggest that LPA and LPA receptors are involved in <it>Schistosoma mansoni </it>egg-mediated inflammation and further studies are proposed to understand the role of LPA and LPA receptors in the inflammatory process.</p