Quark-gluon vertex in general kinematics

The original publication can be found at www.springerlink.com Submitted to Cornell University’s online archive www.arXiv.org in 2007 by Jon-Ivar Skullerud. Post-print sourced from www.arxiv.org.We compute the quark–gluon vertex in quenched lattice QCD in the Landau gauge, using an off-shell mean-field O(a)-improved fermion action. The Dirac-vector part of the vertex is computed for arbitrary kinematics. We find a substantial infrared enhancement of the interaction strength regardless of the kinematics.Ayse Kizilersu, Derek B. Leinweber, Jon-Ivar Skullerud and Anthony G. William

BarkBase: Epigenomic annotation of canine genomes

Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans

Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

Background: Dissecting the role copy number variants (CNVs) play in disease pathogenesis is directly reliant on accurate methods for quantification. The Shar-Pei dog breed is predisposed to a complex autoinflammatory disease with numerous clinical manifestations. One such sign, recurrent fever, was previously shown to be significantly associated with a novel, but unstable CNV (CNV_16.1). Droplet digital PCR (ddPCR) offers a new mechanism for CNV detection via absolute quantification with the promise of added precision and reliability. The aim of this study was to evaluate ddPCR in relation to quantitative PCR (qPCR) and to assess the suitability of the favoured method as a genetic test for Shar-Pei Autoinflammatory Disease (SPAID). Results: One hundred and ninety-six individuals were assayed using both PCR methods at two CNV positions (CNV_14.3 and CNV_16.1). The digital method revealed a striking result. The CNVs did not follow a continuum of alleles as previously reported, rather the alleles were stable and pedigree analysis showed they adhered to Mendelian segregation. Subsequent analysis of ddPCR case/control data confirmed that both CNVs remained significantly associated with the subphenotype of fever, but also to the encompassing SPAID complex (p < 0.001). In addition, harbouring CNV_16.1 allele five (CNV_16.1 vertical bar 5) resulted in a four-fold increase in the odds for SPAID (p < 0.001). The inclusion of a genetic marker for CNV_16.1 in a genome-wide association test revealed that this variant explained 9.7 % of genetic variance and 25.8 % of the additive genetic heritability of this autoinflammatory disease. Conclusions: This data shows the utility of the ddPCR method to resolve cryptic copy number inheritance patterns and so open avenues of genetic testing. In its current form, the ddPCR test presented here could be used in canine breeding to reduce the number of homozygote CNV_16.1 broken vertical bar 5 individuals and thereby to reduce the prevalence of disease in this breed

Additional file 1: Table S1. of Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

Summary information for each individual included in the current study. (XLSX 69 kb

Additional file 2: Table S2. of Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

Phenotypic overlap observed within the genetic test cohort. Table S3. Primers and Probes used in analysis. Figure S1. Illustrative plots for two individuals showing the results obtained for each assay and methodology. Figure S2. Five pedigrees illustrating the segregation of copy number variant (CNV) alleles. Figure S3. The relationship of increased HAS2 and HAS2as gene expression with increased CNV_16.1 copy number holds with droplet digital PCR (ddPCR) CNV measures. (DOCX 1628 kb

Community Educators and the Struggle for Recognition Theorising meaning, educator and institution in Ireland’s community education field using a generative grounded theory approach.

This thesis explores community education in Ireland in a threefold enquiry examining; (a) the core meaning which community education holds for practitioners in the field, (b) how the role of community educators shares a connectedness with liberatory struggle for social justice, and (c) what space community education and its educators occupy within its institutional provider, the Vocational Education Committees (VECs). Community education in Ireland is a vibrant field of practice operating on the fringes of mainstream education. Its origins can be traced to the early instructors of the Vocational Education Committees in the early part of the last century. Women’s community education has shaped the practice in Ireland since the 1970s. The year 2000 marked a significant step forward in terms of recognition for community education with the publication of the White Paper on Adult Education. In this thesis the author draws on his experience working in the community education sector to engage with other community educators to reflect on the generative themes of meaning, educator role and institution in this field of practice. The first aspect of the research explores the meaning of community education from the practitioner perspective, and finds a clear preference for an empowerment meaning. However, the findings suggest there is no clear settlement on the meaning of empowerment, and concludes there is a need to articulate an understanding of empowerment in the context of a critical analysis of power. The second aspect of the research concerns the role of the community educator and the connectedness of this role to a broader liberatory struggle for social justice. Using Honneth’s concept of a struggle for recognition, the findings point to a critical role which is poorly recognized within the education field in Ireland. A key purpose of the research is to rediscover the roots of this role in Gramsci’s organic intellectuals and Freire’s radicals and reclaim the critical role of the community educator within the Irish education site. The third aspect of this research examines the space which community education occupies within its institutional provider, the Vocational Education Committees in Ireland. The research presents an assessment of the institutional culture of the VECs. The findings recall the VEC’s radical origins, and its later immersion within the mainstream educational apparatus. Findings point to the tensions between a dominant school ethos and subordinate community education ethos in the VEC and proposes a critical coalition for the future. The findings suggest that community education facilitators have a role to play in occupying a critical space within the VECs. The unique contribution of this research is that it presents a theorized community education from the perspective of its workers, the community educators. The research methodology combines Charmaz’s constructivist grounded theory with Freirean liberatory pedagogy. The result is a unique contribution to a generative grounded theorization of community education in Ireland today

Top 10 differentially expressed genes by the risk haplotype at each locus.

<p>Top 10 differentially expressed genes by the risk haplotype at each locus.</p

Differentially expressed genes by the risk alleles at 29 Mb and 33 Mb play important role in T-cell immunity.

<p>A. The risk allele at the 29 Mb at homozygous state has a clear cis-regulation effect on the expression levels of <i>TRPC6</i>, <i>KIAA1377</i>, and <i>ANGPTL5</i>, three of the most proximal genes. <i>BIRC3</i>, which is also proximal to the 29 Mb risk locus, had a significant p-value, however the FDR value was slightly above the threshold of 0.05. The risk allele at 29 Mb was also associated with a regulatory effect on genes near the 33 Mb locus and a change in the expression of <i>PIK3R6</i> significantly. B. A large network of molecules that play a major role in activation of T-lymphocyte and other immune cells (IPA category: cell-to-cell signaling and interaction, hematological system development and function). This network includes 15 molecules of which expressions are significantly altered in individuals carrying at least one copy of the shared risk allele at the 33 Mb locus. The outcomes of such expression changes are significantly linked to decrease in T-cell activation.</p

List of significantly associated haplotypes.

<p>List of significantly associated haplotypes.</p

Two neighboring loci on chromosome 5 are independently associated with disease risk.

<p>A. The top SNP of the first peak (29 Mb) is in high LD with nearby variants and shows no evidence of linkage to the top SNPs in the second peak (33 Mb). B. The 29 Mb peak is comprised of two haplotype blocks, and C. the risk haplotypes for the 29 Mb peak are rather common in the population. Similarly, D. the second peak also shows no linkage with the first peak in the combined analysis, whereas E. analysis of only B-cell lymphoma shows SNPs in strong LD within the second peak and in moderate LD with SNPs in the first peak. The top SNPs in the combined analysis and B-cell-lymphoma-only analysis are independent, and F. make up separate haplotypes at the second locus. G. Both risk haplotypes at the second locus are rare. Color-coding of SNPs in A, D, E, reflects their r² value relative the top SNP of that region, ranging from grey (not in LD) to red (strong LD).</p