A behavioral ecology of shermen: hidden stories from trajectory data in the Northern Humboldt Current System

This work proposes an original contribution to the understanding of shermen spatial behavior, based on the behavioral ecology and movement ecology paradigms. Through the analysis of Vessel Monitoring System (VMS) data, we characterized the spatial behavior of Peruvian anchovy shermen at di erent scales: (1) the behavioral modes within shing trips (i.e., searching, shing and cruising); (2) the behavioral patterns among shing trips; (3) the behavioral patterns by shing season conditioned by ecosystem scenarios; and (4) the computation of maps of anchovy presence proxy from the spatial patterns of behavioral mode positions. At the rst scale considered, we compared several Markovian (hidden Markov and semi-Markov models) and discriminative models (random forests, support vector machines and arti cial neural networks) for inferring the behavioral modes associated with VMS tracks. The models were trained under a supervised setting and validated using tracks for which behavioral modes were known (from on-board observers records). Hidden semi-Markov models performed better, and were retained for inferring the behavioral modes on the entire VMS dataset. At the second scale considered, each shing trip was characterized by several features, including the time spent within each behavioral mode. Using a clustering analysis, shing trip patterns were classi ed into groups associated to management zones, eet segments and skippers' personalities. At the third scale considered, we analyzed how ecological conditions shaped shermen behavior. By means of co-inertia analyses, we found signi cant associations between shermen, anchovy and environmental spatial dynamics, and shermen behavioral responses were characterized according to contrasted environmental scenarios. At the fourth scale considered, we investigated whether the spatial behavior of shermen re ected to some extent the spatial distribution of anchovy. Finally, this work provides a wider view of shermen behavior: shermen are not only economic agents, but they are also foragers, constrained by ecosystem variability. To conclude, we discuss how these ndings may be of importance for sheries management, collective behavior analyses and end-to-end models.

A Smartphone-Based Prototype System for Incident/Work Zone Management Driven by Crowd-Sourced Data, 2015

This project develops a smartphone-based prototype system that supplements the 511 system to improve its dynamic traffic routing service to state highway users under non-recurrent congestion. This system will save considerable time to provide crucial traffic information and en-route assistance to travelers for them to avoid being trapped in traffic congestion due to accidents, work zones, hazards, or special events. It also creates a feedback loop between travelers and responsible agencies that enable the state to effectively collect, fuse, and analyze crowd-sourced data for next-gen transportation planning and management. This project can result in substantial economic savings (e.g. less traffic congestion, reduced fuel wastage and emissions) and safety benefits for the freight industry and society due to better dissemination of real-time traffic information by highway users. Such benefits will increase significantly in future with the expected increase in freight traffic on the network. The proposed system also has the flexibility to be integrated with various transportation management modules to assist state agencies to improve transportation services and daily operations.

Urotensin-II System in Genetic Control of Blood Pressure and Renal Function.

Urotensin-II controls ion/water homeostasis in fish and vascular tone in rodents. We hypothesised that common genetic variants in urotensin-II pathway genes are associated with human blood pressure or renal function. We performed family-based analysis of association between blood pressure, glomerular filtration and genes of the urotensin-II pathway (urotensin-II, urotensin-II related peptide, urotensin-II receptor) saturated with 28 tagging single nucleotide polymorphisms in 2024 individuals from 520 families; followed by an independent replication in 420 families and 7545 unrelated subjects. The expression studies of the urotensin-II pathway were carried out in 97 human kidneys. Phylogenetic evolutionary analysis was conducted in 17 vertebrate species. One single nucleotide polymorphism (rs531485 in urotensin-II gene) was associated with adjusted estimated glomerular filtration rate in the discovery cohort (p = 0.0005). It showed no association with estimated glomerular filtration rate in the combined replication resource of 8724 subjects from 6 populations. Expression of urotensin-II and its receptor showed strong linear correlation (r = 0.86, p<0.0001). There was no difference in renal expression of urotensin-II system between hypertensive and normotensive subjects. Evolutionary analysis revealed accumulation of mutations in urotensin-II since the divergence of primates and weaker conservation of urotensin-II receptor in primates than in lower vertebrates. Our data suggest that urotensin-II system genes are unlikely to play a major role in genetic control of human blood pressure or renal function. The signatures of evolutionary forces acting on urotensin-II system indicate that it may have evolved towards loss of function since the divergence of primates.

Cross-species analysis of the replication complex of Old World arenaviruses reveals two nucleoprotein sites involved in L protein function.

Lassa virus (LASV) causing hemorrhagic Lassa fever in West Africa, Mopeia virus (MOPV) from East Africa, and lymphocytic choriomeningitis virus (LCMV) are the main representatives of the Old World arenaviruses. Little is known about how the components of the arenavirus replication machinery, i.e., the genome, nucleoprotein (NP), and L protein, interact. In addition, it is unknown whether these components can function across species boundaries. We established minireplicon systems for MOPV and LCMV in analogy to the existing LASV system and exchanged the components among the three systems. The functional and physical integrity of the resulting complexes was tested by reporter gene assay, Northern blotting, and coimmunoprecipitation studies. The minigenomes, NPs, and L proteins of LASV and MOPV could be exchanged without loss of function. LASV and MOPV L protein was also active in conjunction with LCMV NP, while the LCMV L protein required homologous NP for activity. Analysis of LASV/LCMV NP chimeras identified a single LCMV-specific NP residue (Ile-53) and the C terminus of NP (residues 340 to 558) as being essential for LCMV L protein function. The defect of LASV and MOPV NP in supporting transcriptional activity of LCMV L protein was not caused by a defect in physical NP-L protein interaction. In conclusion, components of the replication complex of Old World arenaviruses have the potential to functionally and physically interact across species boundaries. Residue 53 and the C-terminal domain of NP are important for function of L protein during genome replication and transcription.

Juvenile Justice System Planning Data Iowa’s Juvenile Justice Advisory Council Three Year Comprehensive Plan with Additional Juvenile Justice System Information, November 2015

This report provides key juvenile justice system planning data, most of which are taken from Iowa’s 2015 Juvenile Justice and Delinquency Prevention Act Three Year Plan. The data and related descriptions serve as an overview of decision making for major juvenile justice system processing points, and also assist state and local officials with policy and practice. Included in the report are school discipline data and data related to juvenile in the adult criminal justice system.

Juvenile Justice System Planning Data Iowa’s Juvenile Justice Advisory Council Three Year Comprehensive Plan with Additional Juvenile Justice System Information, November 2015

This report provides key juvenile justice system planning data, most of which are taken from Iowa’s 2015 Juvenile Justice and Delinquency Prevention Act Three Year Plan. The data and related descriptions serve as an overview of decision making for major juvenile justice system processing points, and also assist state and local officials with policy and practice. Included in the report are school discipline data and data related to juvenile in the adult criminal justice system.

An Italian to Catalan RBMT system reusing data from existing language pairs

This paper presents an Italian to CatalanRBMT system automatically built bycombining the linguistic data of theexisting pairs Spanish-Catalan andSpanish-Italian. A lightweight manualpostprocessing is carried out in order tofix inconsistencies in the automaticallyderived dictionaries and to add very frequentwords that are missing accordingto a corpus analysis. The system isevaluated on the KDE4 corpus and outperformsGoogle Translate by approximatelyten absolute points in terms ofboth TER and GTM.

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature and linked to an improved annotation system

Résumé: L'automatisation du séquençage et de l'annotation des génomes, ainsi que l'application à large échelle de méthodes de mesure de l'expression génique, génèrent une quantité phénoménale de données pour des organismes modèles tels que l'homme ou la souris. Dans ce déluge de données, il devient très difficile d'obtenir des informations spécifiques à un organisme ou à un gène, et une telle recherche aboutit fréquemment à des réponses fragmentées, voir incomplètes. La création d'une base de données capable de gérer et d'intégrer aussi bien les données génomiques que les données transcriptomiques peut grandement améliorer la vitesse de recherche ainsi que la qualité des résultats obtenus, en permettant une comparaison directe de mesures d'expression des gènes provenant d'expériences réalisées grâce à des techniques différentes. L'objectif principal de ce projet, appelé CleanEx, est de fournir un accès direct aux données d'expression publiques par le biais de noms de gènes officiels, et de représenter des données d'expression produites selon des protocoles différents de manière à faciliter une analyse générale et une comparaison entre plusieurs jeux de données. Une mise à jour cohérente et régulière de la nomenclature des gènes est assurée en associant chaque expérience d'expression de gène à un identificateur permanent de la séquence-cible, donnant une description physique de la population d'ARN visée par l'expérience. Ces identificateurs sont ensuite associés à intervalles réguliers aux catalogues, en constante évolution, des gènes d'organismes modèles. Cette procédure automatique de traçage se fonde en partie sur des ressources externes d'information génomique, telles que UniGene et RefSeq. La partie centrale de CleanEx consiste en un index de gènes établi de manière hebdomadaire et qui contient les liens à toutes les données publiques d'expression déjà incorporées au système. En outre, la base de données des séquences-cible fournit un lien sur le gène correspondant ainsi qu'un contrôle de qualité de ce lien pour différents types de ressources expérimentales, telles que des clones ou des sondes Affymetrix. Le système de recherche en ligne de CleanEx offre un accès aux entrées individuelles ainsi qu'à des outils d'analyse croisée de jeux de donnnées. Ces outils se sont avérés très efficaces dans le cadre de la comparaison de l'expression de gènes, ainsi que, dans une certaine mesure, dans la détection d'une variation de cette expression liée au phénomène d'épissage alternatif. Les fichiers et les outils de CleanEx sont accessibles en ligne (http://www.cleanex.isb-sib.ch/). Abstract: The automatic genome sequencing and annotation, as well as the large-scale gene expression measurements methods, generate a massive amount of data for model organisms. Searching for genespecific or organism-specific information througout all the different databases has become a very difficult task, and often results in fragmented and unrelated answers. The generation of a database which will federate and integrate genomic and transcriptomic data together will greatly improve the search speed as well as the quality of the results by allowing a direct comparison of expression results obtained by different techniques. The main goal of this project, called the CleanEx database, is thus to provide access to public gene expression data via unique gene names and to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and crossdataset comparisons. A consistent and uptodate gene nomenclature is achieved by associating each single gene expression experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of genes from model organisms, such as human and mouse. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing crossreferences to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resources, such as cDNA clones or Affymetrix probe sets. The Affymetrix mapping files are accessible as text files, for further use in external applications, and as individual entries, via the webbased interfaces . The CleanEx webbased query interfaces offer access to individual entries via text string searches or quantitative expression criteria, as well as crossdataset analysis tools, and crosschip gene comparison. These tools have proven to be very efficient in expression data comparison and even, to a certain extent, in detection of differentially expressed splice variants. The CleanEx flat files and tools are available online at: http://www.cleanex.isbsib. ch/.

Semantic data integration in a newspaper content management system

A newspaper content management system has to deal with a very heterogeneous information space as the experience in the Diari Segre newspaper has shown us. The greatest problem is to harmonise the different ways the involved users (journalist, archivists...) structure the newspaper information space, i.e. news, topics, headlines, etc. Our approach is based on ontology and differentiated universes of discourse (UoD). Users interact with the system and, from this interaction, integration rules are derived. These rules are based on Description Logic ontological relations for subsumption and equivalence. They relate the different UoD and produce a shared conceptualisation of the newspaper information domain.

Breast imaging reporting and data system (BI-RADS™): como tem sido utilizado?

O Breast Imaging Reporting and Data System (BI-RADS™), do American College of hRadiology, foi concebido para padronizar o laudo mamográfico e reduzir os fatores de confusão na descrição e interpretação das imagens, além de facilitar o monitoramento do resultado final. OBJETIVO: Identificar a maneira como vem sendo utilizado o BI-RADS™, gerando informações que possam auxiliar o Colégio Brasileiro de Radiologia a desenvolver estratégias para aperfeiçoar o seu uso. MATERIAIS E MÉTODOS: Os dados foram coletados na cidade de Goiânia, GO. Foram solicitados os exames de mamografia anteriores a todas as mulheres que se dirigiram ao serviço para realização de mamografia entre janeiro/2003 e junho/2003. Foram incluídos na análise exames anteriores, realizados entre 1/7/2001 e 30/6/2003. RESULTADOS: Foram coletados 104 laudos anteriores, emitidos por 40 radiologistas de 33 diferentes serviços. Dos 104 laudos, 77% (n = 80) utilizavam o BI-RADS™. Destes, apenas 15% (n = 12) eram concisos, nenhum utilizava a estrutura e organização recomendadas pelo sistema, 98,75% (n = 79) não respeitavam o léxico e 65% (n = 51) não faziam recomendação de conduta. CONCLUSÃO: O BI-RADS™, apesar de bastante utilizado, não foi reconhecido como sistema para padronização dos laudos. Foi usado quase exclusivamente como forma de classificação final dos exames.

Breast Imaging Reporting and Data System - BI-RADS®: valor preditivo positivo das categorias 3, 4 e 5. revisão sistemática da literatura

OBJETIVO: Avaliar artigos, na literatura, que verificam o valor preditivo positivo das categorias 3, 4 e 5 do Breast Imaging Reporting and Data System (BI-RADS®). MATERIAIS E MÉTODOS: Foi realizada pesquisa na base de dados Medline utilizando os termos "predictive value" e "BI-RADS". Foram incluídos 11 artigos nesta revisão. RESULTADOS: O valor preditivo positivo das categorias 3, 4 e 5 variou entre 0% e 8%, 4% e 62%, 54% e 100%, respectivamente. Três artigos avaliaram, concomitantemente, os critérios morfológicos das lesões que apresentaram maior valor preditivo positivo na mamografia, sendo nódulo espiculado o critério com maior valor preditivo positivo. CONCLUSÃO: Houve grande variabilidade do valor preditivo positivo das categorias 3, 4 e 5 do BI-RADS® em todos os estudos, porém foram identificadas diferenças metodológicas que limitaram a comparação desses estudos.

Valor preditivo positivo das categorias 3, 4 e 5 do Breast Imaging Reporting and Data System (BI-RADS®)

OBJETIVO: O objetivo deste trabalho foi avaliar o BI-RADS® como fator preditivo de suspeição de malignidade em lesões mamárias não palpáveis nas categorias 3, 4 e 5, correlacionando as mamografias com os resultados histopatológicos através do cálculo do valor preditivo positivo do exame mamográfico. MATERIAIS E MÉTODOS: Trezentas e setenta e uma pacientes encaminhadas a um serviço de referência em tratamento de câncer em Teresina, PI, para realização de exames histopatológicos em mama no período de julho de 2005 a março de 2008, por terem mamografia de categorias 3, 4 ou 5, tiveram seus exames revisados. Das 371 pacientes, 265 foram submetidas a biópsia por agulha grossa e 106, a marcação pré-cirúrgica. RESULTADOS: Em relação às mamografias, 11,32% foram classificadas como categoria 3, 76,28% como categoria 4 e 12,4% como categoria 5. Os resultados histológicos demonstraram 24% de exames positivos para malignidade. Os valores preditivos positivos das categorias 3, 4 e 5 foram, respectivamente, de 7,14%, 16,96% e 82,61%. Foram calculados os valores preditivos positivos, separadamente, para as biópsias percutâneas (7,14%, 15,76%, 76,47%) e para as marcações pré-cirúrgicas (7,14%, 20%, 100%). CONCLUSÃO: Achados malignos foram subestimados pelo laudo radiológico e houve superestimação de achados benignos, o que resultou na realização desnecessária de alguns procedimentos invasivos.

Positive predictive values of Breast Imaging Reporting and Data System (BI-RADS®) categories 3, 4 and 5 in breast lesions submitted to percutaneous biopsy

Objective To evaluate the BI-RADS as a predictive factor of suspicion for malignancy in breast lesions by correlating radiological with histological results and calculating the positive predictive value for categories 3, 4 and 5 in a breast cancer reference center in the city of São Paulo. Materials and Methods Retrospective, analytical and cross-sectional study including 725 patients with mammographic and/or sonographic findings classified as BI-RADS categories 3, 4 and 5 who were referred to the authors' institution to undergo percutaneous biopsy. The tests results were reviewed and the positive predictive value was calculated by means of a specific mathematical equation. Results Positive predictive values found for categories 3, 4 and 5 were respectively the following: 0.74%, 33.08% and 92.95%, for cases submitted to ultrasound-guided biopsy, and 0.00%, 14.90% and 100% for cases submitted to stereotactic biopsy. Conclusion The present study demonstrated high suspicion for malignancy in lesions classified as category 5 and low risk for category 3. As regards category 4, the need for systematic biopsies was observed.

Construction and validation of a scoring system for the selection of high-quality data in a Spanish population primary care database (SIDIAP)

Background Computerised databases of primary care clinical records are widely used for epidemiological research. In Catalonia, the InformationSystem for the Development of Research in Primary Care (SIDIAP) aims to promote the development of research based on high-quality validated data from primary care electronic medical records. Objective The purpose of this study is to create and validate a scoring system (Registry Quality Score, RQS) that will enable all primary care practices (PCPs) to be selected as providers of researchusable data based on the completeness of their registers. Methods Diseases that were likely to be representative of common diagnoses seen in primary care were selected for RQS calculations. The observed/ expected cases ratio was calculated for each disease. Once we had obtained an estimated value for this ratio for each of the selected conditions we added up the ratios calculated for each condition to obtain a final RQS. Rate comparisons between observed and published prevalences of diseases not included in the RQS calculations (atrial fibrillation, diabetes, obesity, schizophrenia, stroke, urinary incontinenceand Crohn’s disease) were used to set the RQS cutoff which will enable researchers to select PCPs with research-usable data. Results Apart from Crohn’s disease, all prevalences were the same as those published from the RQS fourth quintile (60th percentile) onwards. This RQS cut-off provided a total population of 1 936 443 (39.6% of the total SIDIAP population). Conclusions SIDIAP is highly representative of the population of Catalonia in terms of geographical, age and sex distributions. We report the usefulness of rate comparison as a valid method to establish research-usable data within primary care electronic medical records