On the geometry of C^3/D_27 and del Pezzo surfaces

We clarify some aspects of the geometry of a resolution of the orbifold X = C3/D_27, the noncompact complex manifold underlying the brane quiver standard model recently proposed by Verlinde and Wijnholt. We explicitly realize a map between X and the total space of the canonical bundle over a degree 1 quasi del Pezzo surface, thus defining a desingularization of X. Our analysis relys essentially on the relationship existing between the normalizer group of D_27 and the Hessian group and on the study of the behaviour of the Hesse pencil of plane cubic curves under the quotient.Comment: 23 pages, 5 figures, 2 tables. JHEP style. Added references. Corrected typos. Revised introduction, results unchanged

Transmutations and spectral parameter power series in eigenvalue problems

We give an overview of recent developments in Sturm-Liouville theory concerning operators of transmutation (transformation) and spectral parameter power series (SPPS). The possibility to write down the dispersion (characteristic) equations corresponding to a variety of spectral problems related to Sturm-Liouville equations in an analytic form is an attractive feature of the SPPS method. It is based on a computation of certain systems of recursive integrals. Considered as families of functions these systems are complete in the $L_{2}$-space and result to be the images of the nonnegative integer powers of the independent variable under the action of a corresponding transmutation operator. This recently revealed property of the Delsarte transmutations opens the way to apply the transmutation operator even when its integral kernel is unknown and gives the possibility to obtain further interesting properties concerning the Darboux transformed Schr\"{o}dinger operators. We introduce the systems of recursive integrals and the SPPS approach, explain some of its applications to spectral problems with numerical illustrations, give the definition and basic properties of transmutation operators, introduce a parametrized family of transmutation operators, study their mapping properties and construct the transmutation operators for Darboux transformed Schr\"{o}dinger operators.Comment: 30 pages, 4 figures. arXiv admin note: text overlap with arXiv:1111.444

Algorithm of OMA for large-scale orthology inference

Since the publication of our article (Roth, Gonnet, and Dessimoz: BMC Bioinformatics 2008 9: 518), we have noticed several errors, which we correct in the following

Understanding the links between hearing impairment and dementia : development and validation of the social and emotional impact of hearing impairment (SEI-HI) questionnaire

Background The links between hearing impairment (HI) and dementia have been well documented, but factors mediating this relationship remain unknown. Major consequences of HI are social and emotional dysfunction, and as the risk of dementia increases linearly with the severity of HI, it is plausible that socio-emotional difficulties may play a role in this association. Objective The aim of this study was to develop and validate a tool to analyse levels of hearing-related disability, to investigate ultimately whether subjective disability contributes to risk of cognitive impairment compared with hearing thresholds alone. Methods Development and validation of the questionnaire, the Social and Emotional Impact of Hearing Impairment (SEI-HI), was conducted in four phases: (1) content; (2) scoring and outcomes; (3) validation; (4) feasibility in a sample of people with cognitive impairment. Results Considerable evidence was found for the internal and external reliability of the tool with high construct validity, concurrent validity and test-retest values of the SEI-HI questionnaire. A feasibility check on 31 patients with mild cognitive impairment or dementia showed the SEI-HI questionnaire was easy to administer and well-received. Conclusion The SEI-HI questionnaire is a relevant instrument to assess hearing-related disability which can be used in people with cognitive decline to assess further impact on risk of developing dementia

Persistence of accuracy of genomic estimated breeding values over generations in layer chickens

<p>Abstract</p> <p>Background</p> <p>The predictive ability of genomic estimated breeding values (GEBV) originates both from associations between high-density markers and QTL (Quantitative Trait Loci) and from pedigree information. Thus, GEBV are expected to provide more persistent accuracy over successive generations than breeding values estimated using pedigree-based methods. The objective of this study was to evaluate the accuracy of GEBV in a closed population of layer chickens and to quantify their persistence over five successive generations using marker or pedigree information.</p> <p>Methods</p> <p>The training data consisted of 16 traits and 777 genotyped animals from two generations of a brown-egg layer breeding line, 295 of which had individual phenotype records, while others had phenotypes on 2,738 non-genotyped relatives, or similar data accumulated over up to five generations. Validation data included phenotyped and genotyped birds from five subsequent generations (on average 306 birds/generation). Birds were genotyped for 23,356 segregating SNP. Animal models using genomic or pedigree relationship matrices and Bayesian model averaging methods were used for training analyses. Accuracy was evaluated as the correlation between EBV and phenotype in validation divided by the square root of trait heritability.</p> <p>Results</p> <p>Pedigree relationships in outbred populations are reduced by 50% at each meiosis, therefore accuracy is expected to decrease by the square root of 0.5 every generation, as observed for pedigree-based EBV (Estimated Breeding Values). In contrast the GEBV accuracy was more persistent, although the drop in accuracy was substantial in the first generation. Traits that were considered to be influenced by fewer QTL and to have a higher heritability maintained a higher GEBV accuracy over generations. In conclusion, GEBV capture information beyond pedigree relationships, but retraining every generation is recommended for genomic selection in closed breeding populations.</p

Pilot evaluation of a walking school bus program in a low-income, urban community

<p>Abstract</p> <p>Background</p> <p>To evaluate the impact of a walking school bus (WSB) program on student transport in a low-income, urban neighborhood.</p> <p>Methods</p> <p>The design was a controlled, quasi-experimental trial with consecutive cross-sectional assessments. The setting was three urban, socioeconomically disadvantaged, public elementary schools (1 intervention vs. 2 controls) in Seattle, Washington, USA. Participants were ethnically diverse students in kindergarten-5^thgrade (aged 5–11 years). The intervention was a WSB program consisting of a part-time WSB coordinator and parent volunteers. Students' method of transportation to school was assessed by a classroom survey at baseline and one-year follow-up. The Pearson Chi-squared test compared students transported to school at the intervention versus control schools at each time point. Due to multiple testing, we calculated adjusted p-values using the Ryan-Holm stepdown Bonferroni procedure. McNemar's test was used to examine the change from baseline to 12-month follow-up for walking versus all other forms of school transport at the intervention or control schools.</p> <p>Results</p> <p>At baseline, the proportions of students (n = 653) walking to the intervention (20% +/- 2%) or control schools (15% +/- 2%) did not differ (<it>p </it>= 0.39). At 12-month follow up, higher proportions of students (n = 643, <it>p </it>= 0.001)) walked to the intervention (25% +/- 2%) versus the control schools (7% +/- 1%). No significant changes were noted in the proportion of students riding in a car or taking the school bus at baseline or 12-month follow up (all <it>p </it>> 0.05). Comparing baseline to 12-month follow up, the numbers of students who walked to the intervention school increased while the numbers of students who used the other forms of transport did not change (<it>p </it>< 0.0001). In contrast, the numbers of students who walked to the control schools decreased while the numbers of students who used the other forms of transport did not change (<it>p </it>< 0.0001).</p> <p>Conclusion</p> <p>A WSB program is a promising intervention among urban, low-income elementary school students that may promote favorable changes toward active transport to school.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov NCT00402701</p

BranchClust: a phylogenetic algorithm for selecting gene families

BACKGROUND: Automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. The first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. Phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is often unknown, and that from the analyses of single gene families the branching order between related organisms frequently is unresolved. RESULTS: Here we describe an algorithm for the automated selection of orthologous genes that recognizes orthologous genes from different species in a phylogenetic tree for any number of taxa. The algorithm is capable of distinguishing complete (containing all taxa) and incomplete (not containing all taxa) families and recognizes in- and outparalogs. The BranchClust algorithm is implemented in Perl with the use of the BioPerl module for parsing trees and is freely available at . CONCLUSION: BranchClust outperforms the Reciprocal Best Blast hit method in selecting more sets of putatively orthologous genes. In the test cases examined, the correctness of the selected families and of the identified in- and outparalogs was confirmed by inspection of the pertinent phylogenetic trees