Pompeu Fabra University

About: Pompeu Fabra University is a education organization based out in Barcelona, Spain. It is known for research contribution in the topics: Population & Context (language use). The organization has 8093 authors who have published 23570 publications receiving 858431 citations. The organization is also known as: Universitat Pompeu Fabra & UPF.

Nextflow enables reproducible computational workflows

Abstract: 1. Weinstein, J.N. et al. Nat. Genet. 45, 1113–1120 (2013). 2. Zhang, J. et al. Database. http://dx.doi.org/10.1093/ database/bar026 (2011) 3. Siva, N. Lancet 385, 103–104 (2015). 4. McKenna, A. et al. Genome Res. 20, 1297–1303 (2010). 5. UNC Bioinformatics. TCGA mRNA-seq pipeline for UNC data. https://webshare.bioinf.unc.edu/public/ mRNAseq_TCGA/UNC_mRNAseq_summary.pdf (2013). 6. Albrecht, M., Michael, A., Patrick, D., Peter, B. & Douglas, T. in Proceedings of the 1st ACM SIGMOD Workshop on Scalable Workflow Execution Engines and Technologies (SWEET ’12) 1. ACM (Association of Computing Machinery. http://dx.doi. org/10.1145/2443416.2443417 (2012). 7. Bernhardsson, E. & Frieder, E. Luigi. Github https:// github.com/spotify/luigi (2016). 8. Goecks, J., Nekrutenko, A. & Taylor, J. Genome Biol. 11, R86 (2010). 9. UCSC. Xena http://xena.ucsc.edu (2016). comprehensive analyses. Further, it means that results can be reproduced using the original computation’s set of tools and parameters. If we had run the original TCGA best-practices RNA-seq pipeline with one sample per node, it would have cost ~$800,000. Through the use of efficient algorithms (STAR and Kallisto) and Toil, we were able to reduce the final cost to $26,071 (Supplementary Note 9). We have demonstrated the utility of Toil by creating one of the single largest, consistently analyzed, public human RNA-seq expression repositories, which we hope the community will find useful.

A mutation in the LDL receptor-related protein 5 gene results in the autosomal dominant high-bone-mass trait.

Abstract: Osteoporosis is a complex disease that affects >10 million people in the United States and results in 1.5 million fractures annually. In addition, the high prevalence of osteopenia (low bone mass) in the general population places a large number of people at risk for developing the disease. In an effort to identify genetic factors influencing bone density, we characterized a family that includes individuals who possess exceptionally dense bones but are otherwise phenotypically normal. This high–bone-mass trait (HBM) was originally localized by linkage analysis to chromosome 11q12-13. We refined the interval by extending the pedigree and genotyping additional markers. A systematic search for mutations that segregated with the HBM phenotype uncovered an amino acid change, in a predicted β-propeller module of the low-density lipoprotein receptor–related protein 5 (LRP5), that results in the HBM phenotype. During analysis of >1,000 individuals, this mutation was observed only in affected individuals from the HBM kindred. By use of in situ hybridization to rat tibia, expression of LRP5 was detected in areas of bone involved in remodeling. Our findings suggest that the HBM mutation confers a unique osteogenic activity in bone remodeling, and this understanding may facilitate the development of novel therapies for the treatment of osteoporosis.

Capital in the 21st Century

Abstract: On 19 December 2014, the Centre for Economic Policy Research and the Bank of England hosted a discussion forum based around Thomas Piketty’s book, Capital in the twenty-first century, with a number of economists from academia, public sector bodies and private sector institutions. Four speakers presented research on various issues relating to inequality, including: access to education; wealth and taxation policy; and the role of governance and institutions. This article presents each speaker’s key arguments, and includes a summary of the open-floor debate that followed.

Ensuring Positiveness of the Scaled Difference Chi-square Test Statistic.

Abstract: A scaled difference test statistic \(\tilde{T}{}_{d}\) that can be computed from standard software of structural equation models (SEM) by hand calculations was proposed in Satorra and Bentler (Psychometrika 66:507–514, 2001). The statistic \(\tilde{T}_{d}\) is asymptotically equivalent to the scaled difference test statistic \(\bar{T}_{d}\) introduced in Satorra (Innovations in Multivariate Statistical Analysis: A Festschrift for Heinz Neudecker, pp. 233–247, 2000), which requires more involved computations beyond standard output of SEM software. The test statistic \(\tilde{T}_{d}\) has been widely used in practice, but in some applications it is negative due to negativity of its associated scaling correction. Using the implicit function theorem, this note develops an improved scaling correction leading to a new scaled difference statistic \(\bar{T}_{d}\) that avoids negative chi-square values.

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.