OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

The Cornella Health Interview Survey Follow-Up (CHIS.FU) Study: design, methods, and response rate

Background: The aim of this report is to describe the main characteristics of the design, including response rates, of the Cornella Health Interview Survey Follow-up Study. Methods: The original cohort consisted of 2,500 subjects (1,263 women and 1,237 men) interviewed as part of the 1994 Cornella Health Interview Study. A record linkage to update the address and vital status of the cohort members was carried out using, first a deterministic method, and secondly a probabilistic one, based on each subject's first name and surnames. Subsequently, we attempted to locate the cohort members to conduct the phone follow-up interviews. A pilot study was carried out to test the overall feasibility and to modify some procedures before the field work began. Results: After record linkage, 2,468 (98.7%) subjects were successfully traced. Of these, 91 (3.6%) were deceased, 259 (10.3%) had moved to other towns, and 50 (2.0%) had neither renewed their last municipal census documents nor declared having moved. After using different strategies to track and to retain cohort members, we traced 92% of the CHIS participants. From them, 1,605 subjects answered the follow-up questionnaire. Conclusion: The computerized record linkage maximized the success of the follow-up that was carried out 7 years after the baseline interview. The pilot study was useful to increase the efficiency in tracing and interviewing the respondents.

Cardiac injuries in blunt chest trauma

Blunt chest traumas are a clinical challenge, both for diagnosis and treatment. The use ofCardiovascular Magnetic Resonance can play a major role in this setting. We present two cases: a12-year-old boy and 45-year-old man. Late gadolinium enhancement imaging enabled visualizationof myocardial damage resulting from the trauma.

The role of computational fluid dynamics in the management of unruptured intracranial aneurysms: a clinicians' view

Objective: The importance of hemodynamics in the etiopathogenesis of intracranial aneurysms (IAs) is widely accepted.Computational fluid dynamics (CFD) is being used increasingly for hemodynamic predictions. However, alogn with thecontinuing development and validation of these tools, it is imperative to collect the opinion of the clinicians. Methods: A workshopon CFD was conducted during the European Society of Minimally Invasive Neurological Therapy (ESMINT) Teaching Course,Lisbon, Portugal. 36 delegates, mostly clinicians, performed supervised CFD analysis for an IA, using the @neuFuse softwaredeveloped within the European project @neurIST. Feedback on the workshop was collected and analyzed. The performancewas assessed on a scale of 1 to 4 and, compared with experts’ performance. Results: Current dilemmas in the management ofunruptured IAs remained the most important motivating factor to attend the workshop and majority of participants showedinterest in participating in a multicentric trial. The participants achieved an average score of 2.52 (range 0–4) which was 63% (range 0–100%) of an expert user. Conclusions: Although participants showed a manifest interest in CFD, there was a clear lack ofawareness concerning the role of hemodynamics in the etiopathogenesis of IAs and the use of CFD in this context. More effortstherefore are required to enhance understanding of the clinicians in the subject.

A WiMAX-based implementation of network MIMO for indoor wireless systems

It is well known that multiple-input multiple-output (MIMO) techniques can bring numerous benefits, such as higher spectral efficiency, to point-to-point wireless links. More recently, there has been interest in extending MIMO concepts tomultiuser wireless systems. Our focus in this paper is on network MIMO, a family of techniques whereby each end user in a wireless access network is served through several access points within its range of influence. By tightly coordinating the transmission and reception of signals at multiple access points, network MIMO can transcend the limits on spectral efficiency imposed by cochannel interference. Taking prior information-theoretic analyses of networkMIMO to the next level, we quantify the spectral efficiency gains obtainable under realistic propagation and operational conditions in a typical indoor deployment. Our study relies on detailed simulations and, for specificity, is conducted largely within the physical-layer framework of the IEEE 802.16e Mobile WiMAX system. Furthermore,to facilitate the coordination between access points, we assume that a high-capacity local area network, such as Gigabit Ethernet,connects all the access points. Our results confirm that network MIMO stands to provide a multiple-fold increase in spectralefficiency under these conditions.

3GPP LTE and LTE-Advanced

Editorial introductòria del número de la revista, en la qual s'exposa el tema del nou estàndard de mòbil, anomenatLong-TermEvolution (LTE),també referenciat com Evolved UMTS Terrestrial Radio Access(E-UTRA), que s'està definint com el substitut del sistema UMTSde tercera generació. LTE-Advanced, al seu torn, es refereix a la versió més avançada de LTE.

A two-stage approach for tonic identification in indian art music

In this paper we propose a new approach for tonic identification in Indian art music and present a proposal for acomplete iterative system for the same. Our method splits the task of tonic pitch identification into two stages. In the first stage, which is applicable to both vocal and instrumental music, we perform a multi-pitch analysis of the audio signal to identify the tonic pitch-class. Multi-pitch analysisallows us to take advantage of the drone sound, which constantlyreinforces the tonic. In the second stage we estimate the octave in which the tonic of the singer lies and is thusneeded only for the vocal performances. We analyse the predominant melody sung by the lead performer in order to establish the tonic octave. Both stages are individually evaluated on a sizable music collection and are shown toobtain a good accuracy. We also discuss the types of errors made by the method.Further, we present a proposal for a system that aims to incrementally utilize all the available data, both audio and metadata in order to identify the tonic pitch. It produces a tonic estimate and a confidence value, and is iterative in nature. At each iteration, more data is fed into the systemuntil the confidence value for the identified tonic is above a defined threshold. Rather than obtain high overall accuracy for our complete database, ultimately our goal is to develop a system which obtains very high accuracy on a subset of the database with maximum confidence.

Applause identification and its relevance to archival of Carnatic music

A Carnatic music concert is made up of a sequence of pieces, where each piece corresponds to a particular genre and ra¯aga (melody). Unlike a western music concert, the artist may be applauded intra-performance inter-performance. Most Carnatic music that is archived today correspond to a single audio recordings of entire concerts.The purpose of this paper is to segment single audio recordings into a sequence of pieces using thecharacteristic features of applause and music. Spectral flux, spectral entropy change quite significantly from music to applause and vice-versa. The characteristics of these features for a subset of concerts was studied. A threshold based approach was used to segment the pieces into music fragments and applauses. Preliminary resultson recordings 19 concerts from matched microphones show that the EER is about 17% for a resolution of 0.25 seconds. Further, a parameter called CUSUM is estimatedfor the applause regions. The CUSUM values determine the strength of the applause. The CUSUM is used to characterise the highlights of a concert.

A method for extracting semantic information from on-line art music discussion forums

In this paper a method for extracting semantic informationfrom online music discussion forums is proposed. The semantic relations are inferred from the co-occurrence of musical concepts in forum posts, using network analysis. The method starts by defining a dictionary of common music terms in an art music tradition. Then, it creates a complex network representation of the online forum by matchingsuch dictionary against the forum posts. Once the complex network is built we can study different network measures, including node relevance, node co-occurrence andterm relations via semantically connecting words. Moreover, we can detect communities of concepts inside the forum posts. The rationale is that some music terms are more related to each other than to other terms. All in all, this methodology allows us to obtain meaningful and relevantinformation from forum discussions.

Analysis of the folksonomy of freesound

User generated content shared in online communities is often described using collaborative tagging systems where users assign labels to content resources. As a result, a folksonomy emerges that relates a number of tags with the resources they label and the users that have used them. In this paper we analyze the folksonomy of Freesound, an online audio clip sharing site which contains more than two million users and 150,000 user-contributed sound samplescovering a wide variety of sounds. By following methodologies taken from similar studies, we compute some metrics that characterize the folksonomy both at the globallevel and at the tag level. In this manner, we are able to betterunderstand the behavior of the folksonomy as a whole, and also obtain some indicators that can be used as metadata for describing tags themselves. We expect that such a methodology for characterizing folksonomies can be useful to support processes such as tag recommendation or automatic annotation of online resources.

A Musically aware system for browsing and interacting with audio music collections

In the context of the CompMusic project we are developing methods to automatically describe/annotate audio music recordings pertaining to various music cultures. As away to demonstrate the usefulness of the methods we are also developing a system to browse and interact with specific audio collections. The system is an online web application that interfaces with all the data gathered (audio, scores plus contextual information) and all the descriptions that are automatically generated with the developed methods. In this paper we present the basic architecture of the proposed system, the types of data sources that it includes,and we mention some of the culture specific issues that we are working on for its development. The system is in a preliminary stage but it shows the potential that MIR technologies can have in browsing and interacting with musiccollections of various cultures.

Opportunities for a cultural specific approach in the computational description of music

The current research in Music Information Retrieval (MIR) is showing the potential that the Information Technologies can have in music related applications. Amajor research challenge in that direction is how to automaticallydescribe/annotate audio recordings and how to use the resulting descriptions to discover and appreciate music in new ways. But music is a complex phenomenonand the description of an audio recording has to deal with this complexity. For example, each musicculture has specificities and emphasizes different musicaland communication aspects, thus the musical recordings of each culture should be described differently. At the same time these cultural specificities give us the opportunity to pay attention to musical concepts andfacets that, despite being present in most world musics, are not easily noticed by listeners. In this paper we present some of the work done in the CompMusic project, including ideas and specific examples on how to take advantage of the cultural specificities of differentmusical repertoires. We will use examples from the art music traditions of India, Turkey and China.

PANACEA (Platform for Automatic, Normalised Annotation and Cost-Effective Acquisition of Language Resources for Human Language Technologies)

The objective of PANACEA is to build a factory of LRs that automates the stages involved in the acquisition, production, updating and maintenance of LRs required by MT systems and by other applications based on language technologies, and simplifies eventual issues regarding intellectual property rights. This automation will cut down the cost, time and human effort significantly. These reductions of costs and time are the only way to guarantee the continuous supply of LRs that MT and other language technologies will be demanding in the multilingual Europe.

Using qualia information to identify lexical semantic classes in an unsupervised clustering task

Acquiring lexical information is a complex problem, typically approached by relying on a number of contexts to contribute information for classification. One of the first issues to address in this domain is the determination of such contexts. The work presented here proposes the use of automatically obtained FORMAL role descriptors as features used to draw nouns from the same lexical semantic class together in an unsupervised clustering task. We have dealt with three lexical semantic classes (HUMAN, LOCATION and EVENT) in English. The results obtained show that it is possible to discriminate between elements from different lexical semantic classes using only FORMAL role information, hence validating our initial hypothesis. Also, iterating our method accurately accounts for fine-grained distinctions within lexical classes, namely distinctions involving ambiguous expressions. Moreover, a filtering and bootstrapping strategy employed in extracting FORMAL role descriptors proved to minimize effects of sparse data and noise in our task.

Automatic Extraction of Polar Adjectives for the Creation of Polarity Lexicons

Automatic creation of polarity lexicons is a crucial issue to be solved in order to reduce time andefforts in the first steps of Sentiment Analysis. In this paper we present a methodology based onlinguistic cues that allows us to automatically discover, extract and label subjective adjectivesthat should be collected in a domain-based polarity lexicon. For this purpose, we designed abootstrapping algorithm that, from a small set of seed polar adjectives, is capable to iterativelyidentify, extract and annotate positive and negative adjectives. Additionally, the methodautomatically creates lists of highly subjective elements that change their prior polarity evenwithin the same domain. The algorithm proposed reached a precision of 97.5% for positiveadjectives and 71.4% for negative ones in the semantic orientation identification task.