Cestyll yn y Cymylau

Morgan, Mihangel, Cestyll yn y Cymylau (Talybont: Y Lolfa, 2007)

Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals

Kingston-Smith, A. H., Merry, R. J., Leemans, D. K., Thomas, Howard, Theodorou, M. K. (2005). Evidence in support of a role for plant-mediated proteolysis in the rumens of grazing animals. British Journal of Nutrition, 93(1), 73-79. Sponsorship: DEFRA / BBSRC RAE2008

Construction of a Festuca pratensis BAC library for map-based cloning in IFestulolium substitution lines

Iain S. Donnison, Donal M. O Sullivan, Ann Thomas, Peter Canter, Beverley Moore, Ian Armstead, Howard Thomas, Keith J. Edwards and Ian P. King (2005). Construction of a Festuca pratensis BAC library for map-based cloning in Festulolium substitution lines. Theoretical and Applied Genetics, 110 (5) pp.846-851 Sponsorship: BBSRC;BBSRC RAE2008

Effects of a stay-green mutation on plant nitrogen relations in Lolium perenne during N starvation and after defoliation

Macduff, J. H., Humphreys, M. O., Thomas, Howard (2002). Effects of a stay-green mutation on plant nitrogen relations in Lolium perenne during N starvation and after defoliation. Annals of Botany, 89 (1), 11-21. Sponsorship: BBSRC RAE2008

Modification of nitrogen remobilisation, grain fill and leaf senescence in maize (Zea mays L.) by transposon insertional mutagenensis in a protease gene

Donnison, I. S., Gay, A. P., Thomas, Howard, Edwards, K. J., Edwards, D., James, C. L., Thomas, A. M., Ougham, H. J. (2007). Modification of nitrogen remobilization, grain fill and leaf senescence in maize (Zea mays) by transposon insertional mutagenensis in a protease gene. New Phytologist, 173 (3), 481-494. Sponsorship: BBSRC RAE2008

Analysis of the chlorophyll catabolism pathway in leaves of an introgression senescence mutant of Lolium temulentum

Maria Roca, Caron James, Adriana Pruzinsk?, Stefan H?rtensteiner, Howard Thomas and Helen Ougham. Analysis of the chlorophyll catabolism pathway in leaves of an introgression senescence mutant of Lolium temulentum. Phytochemistry, 65 (9), 1231-1238. Sponsorship: BBSRC RAE2008

In the Far East : letters from Geraldine Guinness in China / edited by her sister.

http://www.archive.org/details/infareastletters00tayliala

Narratives of Holiness Identity: The "Sanctified Person" in the Church of the Nazarene

This dissertation is an exercise in practical theology, which investigates and responds to the problem of changing holiness identity in the Church of the Nazarene. The first part of the study is an empirical investigation into the social context of contemporary Nazarene holiness identity and practices among Nazarenes in three congregations located in the Northeast United States. Previous research relied too heavily on secularization and sect-church theory to understand the dynamics of religious identity change among Nazarenes. The theological result was a pessimistic appraisal of the future possibilities of holiness identity and practice in the Church of the Nazarene. This study employs an alternative theory—Nancy T. Ammerman's theory of narrative religious identity—to understand the dynamics of lived religious life within these congregations and to identify the various holiness narratives at play. Ammerman's theory facilitates an empirical description of the multiple holiness identities emerging out of the social contexts of these Nazarene congregations and offers a way to account for identity change. At the heart of this research is the theoretical notion that a particular religious identity, in the case of the Church of the Nazarene, the "sanctified person," emerges out of a particular ecclesial context characterized by religious narratives and practices that shape this identity. Chapter one reviews the problem of holiness identity in the Church of the Nazarene and offers an analysis of recent sociological attempts to understand the changing identity among Nazarenes. Chapter two draws on sociological research to describe and depict the range of views of holiness held by some contemporary Nazarenes. Chapter three identifies the varieties of holiness identity within the three Nazarene congregations that are part of the study. Chapter four investigates the social sources that shape the various holiness identities discovered in these congregations. Chapter five is a description of the many ways religious narratives are enacted and engaged within these congregations. The second part of the study is a theological critique of contemporary Nazarene holiness identity. Chapter six draws on the theory of narrative identity proposed by Nancy Ammerman and outlines a theoretical model which describes the social conditions necessary to shape holiness identity, "the sanctified person," within the context of the local congregation. Finally, chapter seven draws on the theological resources of Mennonite scholar and historian John Howard Yoder to propose a way of construing and facilitating holiness identity formation that takes the ecclesiality of hoilness more seriously, emphasizes a clearer relationship between Jesus and the "Christlikeness" that is central to holiness, and highlights the importance of religious practices in the formation of a holiness identity.

The impact of learning context on the acquisition of sociopragmatic variation patterns in non-native speaker teachers of English

The study is a cross-linguistic, cross-sectional investigation of the impact of learning contexts on the acquisition of sociopragmatic variation patterns and the subsequent enactment of compound identities. The informants are 20 non-native speaker teachers of English from a range of 10 European countries. They are all primarily mono-contextual foreign language learners/users of English: however, they differ with respect to the length of time accumulated in a target language environment. This allows for three groups to be established – those who have accumulated 60 days or less; those with between 90 days and one year and the final group, all of whom have accumulated in excess of one year. In order to foster the dismantling of the monolith of learning context, both learning contexts under consideration – i.e. the foreign language context and submersion context are broken down into micro-contexts which I refer to as loci of learning. For the purpose of this study, two loci are considered: the institutional and the conversational locus. In order to make a correlation between the impact of learning contexts and loci of learning on the acquisition of sociopragmatic variation patterns, a two-fold study is conducted. The first stage is the completion of a highly detailed language contact profile (LCP) questionnaire. This provides extensive biographical information regarding language learning history and is a powerful tool in illuminating the intensity of contact with the L2 that learners experience in both contexts as well as shedding light on the loci of learning to which learners are exposed in both contexts. Following the completion of the LCP, the informants take part in two role plays which require the enactment of differential identities when engaged in a speech event of asking for advice. The enactment of identities then undergoes a strategic and linguistic analysis in order to investigate if and how differences in the enactment of compound identities are indexed in language. Results indicate that learning context has a considerable impact not only on how identity is indexed in language, but also on the nature of identities enacted. Informants with very low levels of crosscontextuality index identity through strategic means – i.e. levels of directness and conventionality; however greater degrees of cross-contextuality give rise to the indexing of differential identities linguistically by means of speaker/hearer orientation and (non-) solidary moves. When it comes to the nature of identity enacted, it seems that more time spent in intense contact with native speakers in a range of loci of learning allows learners to enact their core identity; whereas low levels of contact with over-exposure to the institutional locus of learning fosters the enactment of generic identities.

Study abroad and complexity, accuracy and fluency (CAF) development: a longitudinal investigation of French and Chinese Learners of L2 English

This longitudinal study tracked third-level French (n=10) and Chinese (n=7) learners of English as a second language (L2) during an eight-month study abroad (SA) period at an Irish university. The investigation sought to determine whether there was a significant relationship between length of stay (LoS) abroad and gains in the learners' oral complexity, accuracy and fluency (CAF), what the relationship was between these three language constructs and whether the two learner groups would experience similar paths to development. Additionally, the study also investigated whether specific reported out-of-class contact with the L2 was implicated in oral CAF gains. Oral data were collected at three equidistant time points; at the beginning of SA (T1), midway through the SA sojourn (T2) and at the end (T3), allowing for a comparison of CAF gains arising during one semester abroad to those arising during a subsequent semester. Data were collected using Sociolinguistic Interviews (Labov, 1984) and adapted versions of the Language Contact Profile (Freed et al., 2004). Overall, the results point to LoS abroad as a highly influential variable in gains to be expected in oral CAF during SA. While one semester in the TL country was not enough to foster statistically significant improvement in any of the CAF measures employed, significant improvement was found during the second semester of SA. Significant differences were also revealed between the two learner groups. Finally, significant correlations, some positive, some negative, were found between gains in CAF and specific usage of the L2. All in all, the disaggregation of the group data clearly illustrates, in line with other recent enquiries (e.g. Wright and Cong, 2014) that each individual learner's path to CAF development was unique and highly individualised, thus providing strong evidence for the recent claim that SLA is "an individualized nonlinear endeavor" (Polat and Kim, 2014: 186).

Postoperative statin use and risk of biochemical recurrence following radical prostatectomy: results from the Shared Equal Access Regional Cancer Hospital (SEARCH) database.

OBJECTIVE: To investigate the effect of statin use after radical prostatectomy (RP) on biochemical recurrence (BCR) in patients with prostate cancer who never received statins before RP. PATIENTS AND METHODS: We conducted a retrospective analysis of 1146 RP patients within the Shared Equal Access Regional Cancer Hospital (SEARCH) database. Multivariable Cox proportional hazards analyses were used to examine differences in risk of BCR between post-RP statin users vs nonusers. To account for varying start dates and duration of statin use during follow-up, post-RP statin use was treated as a time-dependent variable. In a secondary analysis, models were stratified by race to examine the association of post-RP statin use with BCR among black and non-black men. RESULTS: After adjusting for clinical and pathological characteristics, post-RP statin use was significantly associated with 36% reduced risk of BCR (hazard ratio [HR] 0.64, 95% confidence interval [CI] 0.47-0.87; P = 0.004). Post-RP statin use remained associated with reduced risk of BCR after adjusting for preoperative serum cholesterol levels. In secondary analysis, after stratification by race, this protective association was significant in non-black (HR 0.49, 95% CI 0.32-0.75; P = 0.001) but not black men (HR 0.82, 95% CI 0.53-1.28; P = 0.384). CONCLUSION: In this retrospective cohort of men undergoing RP, post-RP statin use was significantly associated with reduced risk of BCR. Whether the association between post-RP statin use and BCR differs by race requires further study. Given these findings, coupled with other studies suggesting that statins may reduce risk of advanced prostate cancer, randomised controlled trials are warranted to formally test the hypothesis that statins slow prostate cancer progression.

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species.

Cells are fundamental units of life, but little is known about evolution of cell states. Induced pluripotent stem cells (iPSCs) are once differentiated cells that have been re-programmed to an embryonic stem cell-like state, providing a powerful platform for biology and medicine. However, they have been limited to a few mammalian species. Here we found that a set of four mammalian transcription factor genes used to generate iPSCs in mouse and humans can induce a partially reprogrammed pluripotent stem cell (PRPSCs) state in vertebrate and invertebrate model organisms, in mammals, birds, fish, and fly, which span 550 million years from a common ancestor. These findings are one of the first to show cross-lineage stem cell-like induction, and to generate pluripotent-like cells for several of these species with in vivo chimeras. We suggest that the stem-cell state may be highly conserved across a wide phylogenetic range. DOI:http://dx.doi.org/10.7554/eLife.00036.001.

Characterization of B cells in muscle-specific kinase antibody myasthenia gravis.

OBJECTIVE: To characterize B-cell subsets in patients with muscle-specific tyrosine kinase (MuSK) myasthenia gravis (MG). METHODS: In accordance with Human Immunology Project Consortium guidelines, we performed polychromatic flow cytometry and ELISA assays in peripheral blood samples from 18 patients with MuSK MG and 9 healthy controls. To complement a B-cell phenotype assay that evaluated maturational subsets, we measured B10 cell percentages, plasma B cell-activating factor (BAFF) levels, and MuSK antibody titers. Immunologic variables were compared with healthy controls and clinical outcome measures. RESULTS: As expected, patients treated with rituximab had high percentages of transitional B cells and plasmablasts and thus were excluded from subsequent analysis. The remaining patients with MuSK MG and controls had similar percentages of total B cells and naïve, memory, isotype-switched, plasmablast, and transitional B-cell subsets. However, patients with MuSK MG had higher BAFF levels and lower percentages of B10 cells. In addition, we observed an increase in MuSK antibody levels with more severe disease. CONCLUSIONS: We found prominent B-cell pathology in the distinct form of MG with MuSK autoantibodies. Increased BAFF levels have been described in other autoimmune diseases, including acetylcholine receptor antibody-positive MG. This finding suggests a role for BAFF in the survival of B cells in MuSK MG, which has important therapeutic implications. B10 cells, a recently described rare regulatory B-cell subset that potently blocks Th1 and Th17 responses, were reduced, which suggests a potential mechanism for the breakdown in immune tolerance in patients with MuSK MG.