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.

Many Languages, One Parser

Abstract: We train one multilingual model for dependency parsing and use it to parse sentences in several languages. The parsing model uses (i) multilingual word clusters and embeddings; (ii) token-level language information; and (iii) language-specific features (fine-grained POS tags). This input representation enables the parser not only to parse effectively in multiple languages, but also to generalize across languages based on linguistic universals and typological similarities, making it more effective to learn from limited annotations. Our parser's performance compares favorably to strong baselines in a range of data scenarios, including when the target language has a large treebank, a small treebank, or no treebank for training.

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Abstract: Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction (∼80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.

Outcome of protracted hypoparathyroidism after total thyroidectomy

Abstract: Background: Although the variables that influence the development of post-thyroidectomy hypocalcaemia are now better understood, the risk factors and long-term outcome of persistent hypoparathyroidism (HPP) are poorly defined. A retrospective review of a prospective protocol for the management of post-thyroidectomy hypocalcaemia was performed. Methods: Patients with a serum calcium level below 8 mg/dl (2 mmol/l) 24 h after total thyroidectomy were prescribed oral calcium with or without calcitriol and followed for at least 1 year. Protracted HPP was defined as an intact parathyroid hormone (iPTH) level below 13 pg/ml and need for calcium medication at 1 month after thyroidectomy. Results: Of 442 patients (343 with goitre, 99 with carcinoma) undergoing total thyroidectomy, 222 (50·2 per cent) developed postoperative hypocalcaemia. Eleven patients were lost to follow-up. Parathyroid function recovered in 131 patients within 1 month and 80 developed protracted HPP, which was associated with lymphadenectomy, fewer than three glands left in situ and incidental parathyroidectomy. Parathyroid function recovered within 1 year in 78 per cent of patients with protracted HPP. Factors associated with late recovery of parathyroid function were higher serum calcium and low but detectable iPTH levels 1 month after surgery. These factors were associated with higher calcitriol and calcium dosages at hospital discharge. Parathyroid autotransplantation did not protect against permanent HPP. Conclusion: Higher serum calcium levels at 1 month after total thyroidectomy are associated with recovery of parathyroid function. It is hypothesized that intensive medical treatment of hypocalcaemia—‘parathyroid splinting’—may improve the outcome of patients with protracted HPP. Copyright © 2010 British Journal of Surgery Society Ltd. Published by John Wiley & Sons, Ltd.