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.

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Abstract: While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Interpreter, a versatile platform that automates the interpretation of newly sequenced cancer genomes, annotating the potential of alterations detected in tumors to act as drivers and their possible effect on treatment response. The results are organized in different levels of evidence according to current knowledge, which we envision can support a broad range of oncology use cases. The resource is publicly available at http://www.cancergenomeinterpreter.org .

Facial point detection using boosted regression and graph models

Abstract: Finding fiducial facial points in any frame of a video showing rich naturalistic facial behaviour is an unsolved problem. Yet this is a crucial step for geometric-feature-based facial expression analysis, and methods that use appearance-based features extracted at fiducial facial point locations. In this paper we present a method based on a combination of Support Vector Regression and Markov Random Fields to drastically reduce the time needed to search for a point's location and increase the accuracy and robustness of the algorithm. Using Markov Random Fields allows us to constrain the search space by exploiting the constellations that facial points can form. The regressors on the other hand learn a mapping between the appearance of the area surrounding a point and the positions of these points, which makes detection of the points very fast and can make the algorithm robust to variations of appearance due to facial expression and moderate changes in head pose. The proposed point detection algorithm was tested on 1855 images, the results of which showed we outperform current state of the art point detectors.

Discourse, context and cognition

Abstract: In this article the relevance of a sociocognitive approach to discourse is shown by presenting a new theory of context, defined as subjective participants’ constructs of communicative situations, a...

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Abstract: Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidron cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidron Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.