La exploración del litoral atlántico norteafricano según el periplo de Hannón de Cartago

El periplo de Hannón, frente a las propuestas que lo interpretan como una obra literaria, creemos que recoge un periplo auténtico, que sólo alcanzó cabo Juby y algunas de las Islas Canarias. Las refundaciones cartaginesas fueron todas en la Mauretania fértil, en los 7 primeros días de la expedición. Desde el islote de Kérne, en la expedición primó una primera exploración de evaluación, indicativo de que se trataba de apenas 2 o 3 barcos, con una tripulación limitada, que evitaban enfrentamientos con la población local. Los intérpretes Lixítai parecen conocer todos los puntos explorados, el río Chrétes, los etíopes del Alto Atlas costero, el gran golfo caluroso que finalizaba en el Hespérou Kéras, el volcán Theôn Óchema, o las gentes salvajes que denominaban Goríllai. Probablemente la mayor sorpresa fuese encontrar un volcán activo, emitiendo lava, que pudo ser la razón última para redactar este periplo. La falta de agua, alimentos y caza como razón para finalizar la expedición exploratoria sólo es comprensible en un trayecto corto que alcanzó hasta el inicio del desierto del Sahara. Otro tanto sucede con la ausencia de ríos importantes al Sur del río Chrétes, una clara prueba de que no se alcanzaron latitudes ecuatoriales y que los barcos se fueron alejando de la costa norteafricana.

Grammar in dictionaries revisited: the case of verbs with se

This paper is a study about the way in which se structures are represented in 20 verb entries of nine dictionaries of Spanish language. There is a large number of these structures and they are problematic for native and non native speakers. Verbs of the analysis are middle-high frequency and, in the most part of the cases, very polysemous, and this allows to observe interconnections between the different se structures and the different meanings of each verb. Data of the lexicographic analysis are cross-checked with corpus analysis of the same units. As a result, it is observed that there is a large variety in the data which are offered in each dictionary and in the way they are offered, inter and intradictionary. The reasons range from the theoretical overall of each Project to practical performance. This leads to the conclusion that it is necessary to further progress in the dictionary model it is being handled, in order to offer lexico-grammatical phenomenon such as se verbs in an accurate, clear and exhaustive way.

Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis

Background: Esophageal adenocarcinoma (EA) is one of the fastest rising cancers in western countries. Barrett’s Esophagus (BE) is the premalignant precursor of EA. However, only a subset of BE patients develop EA, which complicates the clinical management in the absence of valid predictors. Genetic risk factors for BE and EA are incompletely understood. This study aimed to identify novel genetic risk factors for BE and EA.Methods: Within an international consortium of groups involved in the genetics of BE/EA, we performed the first meta-analysis of all genome-wide association studies (GWAS) available, involving 6,167 BE patients, 4,112 EA patients, and 17,159 representative controls, all of European ancestry, genotyped on Illumina high-density SNP-arrays, collected from four separate studies within North America, Europe, and Australia. Meta-analysis was conducted using the fixed-effects inverse variance-weighting approach. We used the standard genome-wide significant threshold of 5×10-8 for this study. We also conducted an association analysis following reweighting of loci using an approach that investigates annotation enrichment among the genome-wide significant loci. The entire GWAS-data set was also analyzed using bioinformatics approaches including functional annotation databases as well as gene-based and pathway-based methods in order to identify pathophysiologically relevant cellular pathways.Findings: We identified eight new associated risk loci for BE and EA, within or near the CFTR (rs17451754, P=4·8×10-10), MSRA (rs17749155, P=5·2×10-10), BLK (rs10108511, P=2·1×10-9), KHDRBS2 (rs62423175, P=3·0×10-9), TPPP/CEP72 (rs9918259, P=3·2×10-9), TMOD1 (rs7852462, P=1·5×10-8), SATB2 (rs139606545, P=2·0×10-8), and HTR3C/ABCC5 genes (rs9823696, P=1·6×10-8). A further novel risk locus at LPA (rs12207195, posteriori probability=0·925) was identified after re-weighting using significantly enriched annotations. This study thereby doubled the number of known risk loci. The strongest disease pathways identified (P<10-6) belong to muscle cell differentiation and to mesenchyme development/differentiation, which fit with current pathophysiological BE/EA concepts. To our knowledge, this study identified for the first time an EA-specific association (rs9823696, P=1·6×10-8) near HTR3C/ABCC5 which is independent of BE development (P=0·45).Interpretation: The identified disease loci and pathways reveal new insights into the etiology of BE and EA. Furthermore, the EA-specific association at HTR3C/ABCC5 may constitute a novel genetic marker for the prediction of transition from BE to EA. Mutations in CFTR, one of the new risk loci identified in this study, cause cystic fibrosis (CF), the most common recessive disorder in Europeans. Gastroesophageal reflux (GER) belongs to the phenotypic CF-spectrum and represents the main risk factor for BE/EA. Thus, the CFTR locus may trigger a common GER-mediated pathophysiology.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Automated Equation Formulation for Causal Loop Diagrams

The annotation of Business Dynamics models with parameters and equations, to simulate the system under study and further evaluate its simulation output, typically involves a lot of manual work. In this paper we present an approach for automated equation formulation of a given Causal Loop Diagram (CLD) and a set of associated time series with the help of neural network evolution (NEvo). NEvo enables the automated retrieval of surrogate equations for each quantity in the given CLD, hence it produces a fully annotated CLD that can be used for later simulations to predict future KPI development. In the end of the paper, we provide a detailed evaluation of NEvo on a business use-case to demonstrate its single step prediction capabilities.

Trans-ethnic fine mapping highlights kidney-function genes linked to salt sensitivity

We analyzed genome-wide association studies (GWASs), including data from 71,638 individuals from four ancestries, for estimated glomerular filtration rate (eGFR), a measure of kidney function used to define chronic kidney disease (CKD). We identified 20 loci attaining genome-wide-significant evidence of association (p < 5 × 10(-8)) with kidney function and highlighted that allelic effects on eGFR at lead SNPs are homogeneous across ancestries. We leveraged differences in the pattern of linkage disequilibrium between diverse populations to fine-map the 20 loci through construction of "credible sets" of variants driving eGFR association signals. Credible variants at the 20 eGFR loci were enriched for DNase I hypersensitivity sites (DHSs) in human kidney cells. DHS credible variants were expression quantitative trait loci for NFATC1 and RGS14 (at the SLC34A1 locus) in multiple tissues. Loss-of-function mutations in ancestral orthologs of both genes in Drosophila melanogaster were associated with altered sensitivity to salt stress. Renal mRNA expression of Nfatc1 and Rgs14 in a salt-sensitive mouse model was also reduced after exposure to a high-salt diet or induced CKD. Our study (1) demonstrates the utility of trans-ethnic fine mapping through integration of GWASs involving diverse populations with genomic annotation from relevant tissues to define molecular mechanisms by which association signals exert their effect and (2) suggests that salt sensitivity might be an important marker for biological processes that affect kidney function and CKD in humans.

Learning to Interpret and Generate Instructional Recipes

Thesis (Ph.D.)--University of Washington, 2016-08

La traducción al latín de algunos términos griegos y su repercusión en los comentarios a los "Aphthonii Progymnasmata"

En este trabajo hemos examinado comentarios a la traducción al latín del ejercicio de la Fábula de los Progymnasmata de Aftonio para ver cómo afecta la traducción de algunos términos al comentario. Dado que, al traducir de una lengua a otra, difícilmente hay correspondencia exacta, el traductor opta por la solución que estima más adecuada, primando ciertos matices sobre otros y, con frecuencia, llega, incluso, a dotar al término de acepciones en la lengua meta que no existían en la lengua origen. La elección realizada no parece obedecer a otra razón que a preferencias del traductor, pero tiene consecuencias e influye en los comentaristas. Por otra parte, la existencia de un término acuñado no impide que tanto los traductores como los escoliastas creen otros nuevos, tal vez por deseo de mostrar originalidad. Finalmente, la traducción tiene una doble vertiente: de un lado, influye en el entendimiento del concepto y en el comentario, y, de otro, refleja la concepción que de la realidad tiene el traductor.

Transactions and schema evolution in a persistent object-oriented programming system

Applications are subject of a continuous evolution process with a profound impact on their underlining data model, hence requiring frequent updates in the applications' class structure and database structure as well. This twofold problem, schema evolution and instance adaptation, usually known as database evolution, is addressed in this thesis. Additionally, we address concurrency and error recovery problems with a novel meta-model and its aspect-oriented implementation. Modern object-oriented databases provide features that help programmers deal with object persistence, as well as all related problems such as database evolution, concurrency and error handling. In most systems there are transparent mechanisms to address these problems, nonetheless the database evolution problem still requires some human intervention, which consumes much of programmers' and database administrators' work effort. Earlier research works have demonstrated that aspect-oriented programming (AOP) techniques enable the development of flexible and pluggable systems. In these earlier works, the schema evolution and the instance adaptation problems were addressed as database management concerns. However, none of this research was focused on orthogonal persistent systems. We argue that AOP techniques are well suited to address these problems in orthogonal persistent systems. Regarding the concurrency and error recovery, earlier research showed that only syntactic obliviousness between the base program and aspects is possible. Our meta-model and framework follow an aspect-oriented approach focused on the object-oriented orthogonal persistent context. The proposed meta-model is characterized by its simplicity in order to achieve efficient and transparent database evolution mechanisms. Our meta-model supports multiple versions of a class structure by applying a class versioning strategy. Thus, enabling bidirectional application compatibility among versions of each class structure. That is to say, the database structure can be updated because earlier applications continue to work, as well as later applications that have only known the updated class structure. The specific characteristics of orthogonal persistent systems, as well as a metadata enrichment strategy within the application's source code, complete the inception of the meta-model and have motivated our research work. To test the feasibility of the approach, a prototype was developed. Our prototype is a framework that mediates the interaction between applications and the database, providing them with orthogonal persistence mechanisms. These mechanisms are introduced into applications as an {\it aspect} in the aspect-oriented sense. Objects do not require the extension of any super class, the implementation of an interface nor contain a particular annotation. Parametric type classes are also correctly handled by our framework. However, classes that belong to the programming environment must not be handled as versionable due to restrictions imposed by the Java Virtual Machine. Regarding concurrency support, the framework provides the applications with a multithreaded environment which supports database transactions and error recovery. The framework keeps applications oblivious to the database evolution problem, as well as persistence. Programmers can update the applications' class structure because the framework will produce a new version for it at the database metadata layer. Using our XML based pointcut/advice constructs, the framework's instance adaptation mechanism is extended, hence keeping the framework also oblivious to this problem. The potential developing gains provided by the prototype were benchmarked. In our case study, the results confirm that mechanisms' transparency has positive repercussions on the programmer's productivity, simplifying the entire evolution process at application and database levels. The meta-model itself also was benchmarked in terms of complexity and agility. Compared with other meta-models, it requires less meta-object modifications in each schema evolution step. Other types of tests were carried out in order to validate prototype and meta-model robustness. In order to perform these tests, we used an OO7 small size database due to its data model complexity. Since the developed prototype offers some features that were not observed in other known systems, performance benchmarks were not possible. However, the developed benchmark is now available to perform future performance comparisons with equivalent systems. In order to test our approach in a real world scenario, we developed a proof-of-concept application. This application was developed without any persistence mechanisms. Using our framework and minor changes applied to the application's source code, we added these mechanisms. Furthermore, we tested the application in a schema evolution scenario. This real world experience using our framework showed that applications remains oblivious to persistence and database evolution. In this case study, our framework proved to be a useful tool for programmers and database administrators. Performance issues and the single Java Virtual Machine concurrent model are the major limitations found in the framework.

Top-K Query Processing in Edge-Labeled Graph Data

Edge-labeled graphs have proliferated rapidly over the last decade due to the increased popularity of social networks and the Semantic Web. In social networks, relationships between people are represented by edges and each edge is labeled with a semantic annotation. Hence, a huge single graph can express many different relationships between entities. The Semantic Web represents each single fragment of knowledge as a triple (subject, predicate, object), which is conceptually identical to an edge from subject to object labeled with predicates. A set of triples constitutes an edge-labeled graph on which knowledge inference is performed. Subgraph matching has been extensively used as a query language for patterns in the context of edge-labeled graphs. For example, in social networks, users can specify a subgraph matching query to find all people that have certain neighborhood relationships. Heavily used fragments of the SPARQL query language for the Semantic Web and graph queries of other graph DBMS can also be viewed as subgraph matching over large graphs. Though subgraph matching has been extensively studied as a query paradigm in the Semantic Web and in social networks, a user can get a large number of answers in response to a query. These answers can be shown to the user in accordance with an importance ranking. In this thesis proposal, we present four different scoring models along with scalable algorithms to find the top-k answers via a suite of intelligent pruning techniques. The suggested models consist of a practically important subset of the SPARQL query language augmented with some additional useful features. The first model called Substitution Importance Query (SIQ) identifies the top-k answers whose scores are calculated from matched vertices' properties in each answer in accordance with a user-specified notion of importance. The second model called Vertex Importance Query (VIQ) identifies important vertices in accordance with a user-defined scoring method that builds on top of various subgraphs articulated by the user. Approximate Importance Query (AIQ), our third model, allows partial and inexact matchings and returns top-k of them with a user-specified approximation terms and scoring functions. In the fourth model called Probabilistic Importance Query (PIQ), a query consists of several sub-blocks: one mandatory block that must be mapped and other blocks that can be opportunistically mapped. The probability is calculated from various aspects of answers such as the number of mapped blocks, vertices' properties in each block and so on and the most top-k probable answers are returned. An important distinguishing feature of our work is that we allow the user a huge amount of freedom in specifying: (i) what pattern and approximation he considers important, (ii) how to score answers - irrespective of whether they are vertices or substitution, and (iii) how to combine and aggregate scores generated by multiple patterns and/or multiple substitutions. Because so much power is given to the user, indexing is more challenging than in situations where additional restrictions are imposed on the queries the user can ask. The proposed algorithms for the first model can also be used for answering SPARQL queries with ORDER BY and LIMIT, and the method for the second model also works for SPARQL queries with GROUP BY, ORDER BY and LIMIT. We test our algorithms on multiple real-world graph databases, showing that our algorithms are far more efficient than popular triple stores.

Suite du theatre de la guerre dans l'Amérique Septentrionale y compris le Golfe du Méxique /

Relief shown pictorially.

A contribution to semantic description of images and videos: an application of soft biometrics

Humans have a high ability to extract visual data information acquired by sight. Trought a learning process, which starts at birth and continues throughout life, image interpretation becomes almost instinctively. At a glance, one can easily describe a scene with reasonable precision, naming its main components. Usually, this is done by extracting low-level features such as edges, shapes and textures, and associanting them to high level meanings. In this way, a semantic description of the scene is done. An example of this, is the human capacity to recognize and describe other people physical and behavioral characteristics, or biometrics. Soft-biometrics also represents inherent characteristics of human body and behaviour, but do not allow unique person identification. Computer vision area aims to develop methods capable of performing visual interpretation with performance similar to humans. This thesis aims to propose computer vison methods which allows high level information extraction from images in the form of soft biometrics. This problem is approached in two ways, unsupervised and supervised learning methods. The first seeks to group images via an automatic feature extraction learning , using both convolution techniques, evolutionary computing and clustering. In this approach employed images contains faces and people. Second approach employs convolutional neural networks, which have the ability to operate on raw images, learning both feature extraction and classification processes. Here, images are classified according to gender and clothes, divided into upper and lower parts of human body. First approach, when tested with different image datasets obtained an accuracy of approximately 80% for faces and non-faces and 70% for people and non-person. The second tested using images and videos, obtained an accuracy of about 70% for gender, 80% to the upper clothes and 90% to lower clothes. The results of these case studies, show that proposed methods are promising, allowing the realization of automatic high level information image annotation. This opens possibilities for development of applications in diverse areas such as content-based image and video search and automatica video survaillance, reducing human effort in the task of manual annotation and monitoring.

Évaluation formative et TIC pour une meilleure intégration des apprentissages en biochimie clinique

Dans cette recherche, l’enseignante-chercheuse analyse la méthode d’enseignement, les activités d’apprentissage et les modalités d’évaluation de la portion théorique du cours de stage en biochimie clinique dans le cadre du programme Technologie d’analyses biomédicales (140.BO) offert au Collège de Rosemont. Dans les années précédant la recherche, les stagiaires avaient formulé certains problèmes dont: un contenu trop lourd et le manque d’interactivité. Ces contraintes ont obligé l’enseignante-chercheuse à se questionner sur le processus pédagogique et sur la relation d’apprentissage. De plus, le manque d’intégration des connaissances des stagiaires mis en évidence lors de la préparation de l’examen national de la SCSLM et la baisse de performance à ces mêmes examens ont été les éléments déclencheurs de la recherche. Trois approches pédagogiques ont été utilisées afin de favoriser l’intégration des apprentissages et faire progresser les étudiantes et les étudiants vers un résultat acceptable en fin de stage. Premièrement, il a fallu passer par une réorganisation de contenu. Deuxièmement, nous avons mis en place un environnement plus interactif favorisant l’évaluation formative à l’aide de la plate-forme pédagogique Moodle. Troisièmement, nous avons introduit un mode d’évaluation formative qui s’harmonise à l’évaluation sommative. Toutes ces étapes ont été effectuées afin de faire progresser l’étudiante et l’étudiant et de l’informer clairement de ses performances pour qu’elle ou qu’il en arrive à intégrer les nombreuses notions théoriques en biochimie. Il est important de préciser que c’est à partir des assises du cadre de référence de cette recherche qu’il a été possible de dégager des actions pour innover notre pratique pédagogique. C’est par l’évaluation formative s’inscrivant dans diverses modalités de régulation ou d’autorégulation de l’apprentissage, permettant l’accès à la reprise à l’aide des questionnaires interactifs de la plate-forme pédagogique Moodle que nous avons mis en place une première solution. Comme deuxième solution, l’enseignante-chercheuse a présenté à chaque étape, par sujet de révision, une évaluation formative à des fins sommatives avec la possibilité d’une deuxième tentative. Les performances qui y ont été évaluées, ont été modifiables et ont contribué à la note de fin d’étape. Le but de notre démarche était de trouver des réponses à la question de recherche: L’évaluation formative par l’utilisation des technologies améliorera-t-elle les apprentissages des étudiantes et des étudiants en biochimie à la fin du programme d’étude en Techniques d’analyses biomédicales? La conception du scénario pédagogique ainsi que la mise à l’essai du matériel servant à l’évaluation formative à travers les outils interactifs de la plate-forme Moodle, ont tous été aussi importants. Dans le cadre du choix méthodologique, les trois objectifs spécifiques de la recherche ont été respectés, c’est-à-dire: 1. Concevoir le matériel servant à l’évaluation formative et le générer sur la plate-forme informatisée; 2. Mettre en application l’utilisation des nouveaux éléments d’apprentissage et des processus d’évaluation; 3. Vérifier si l’évaluation formative influencera l’apprentissage qui aura pour but une meilleure intégration des connaissances. Par le volet qualitatif de l’étude, l’enseignante-chercheuse vise à comprendre ce qui a été formulé par les étudiantes et les étudiants relativement à une démarche d’évaluation formative, interactive et continue générée par l’usage de l’outil informatisé Moodle. Cette démarche d’apprentissage assisté par ordinateur comprenait des applications d’évaluation formative élaborées sur la plate-forme pédagogique Moodle pour que les étudiantes et les étudiants en arrivent à cibler plus facilement leurs lacunes. Ainsi, les étudiantes et les étudiants étaient en mesure d’y remédier immédiatement par la fonction régulatrice propre à l’évaluation formative à l’aide des TIC. Ce qui situe la recherche dans le pôle de l’innovation, c’est l’intégration des TIC qui a permis d’établir les modalités d’évaluation formative à des fins sommatives, une reprise en deux temps, dans une perspective d’intégration des apprentissages. Par la collecte de données, se rangeant sous le paradigme interprétatif, la grille d’appréciation et l’entrevue semi-dirigée ont permis de faire ressortir ce que les étudiantes et les étudiants ont noté comme éléments d’approbation ou de valorisation de l’enseignement et de l’apprentissage. Dans le volet quantitatif de l’étude, l’enseignante-chercheuse a analysé les résultats des examens du parcours de stage dans l’intérêt de savoir s’il y a eu amélioration des apprentissages des étudiantes et des étudiants en stage à la fin du programme. De ces étapes, l’interprétation des données recueillies a permis d’alimenter la réflexion sur les principales approches mises en place dans les cours théoriques du stage en biochimie clinique. Cette étape a contribué à supporter l’objectivation du sens produit de cette recherche. Les résultats obtenus et l’interprétation qui en résulte présente que l’ensemble des stagiaires s’accorde à dire que les tests formatifs, le processus d’évaluation formative à des fins sommatives, une reprise en deux temps et le contenu interactif sur la plate-forme Moodle, permettent de faire des liens entre les connaissances déjà acquises, d’intégrer la matière et contribue à stimuler leur motivation à fournir un effort soutenu. L’utilisation des ressources du système de gestion de l’apprentissage Moodle a permis d’établir des modes d’évaluation formative dans une perspective d’intégration des apprentissages. Ces résultats sont intéressants puisqu’il a été possible de constater les difficultés des stagiaires aux examens, de relier des questions à des objectifs moins bien réussis et pour lesquels les étudiantes et les étudiants affirment ne pas avoir assez de temps d’enseignement à propos de ces notions théoriques. L’enseignante-chercheuse a alors entrepris une démarche d’amélioration continue de sa pratique pédagogique et de l’environnement numérique d’apprentissage. Entre 2012 et 2015, elle a utilisé une grille d’évaluation et a analysé les résultats des examens lui permettant de mieux cibler les ressources à améliorer pour favoriser la réussite de ses étudiantes et de ses étudiants. Elle poursuit sa réflexion à propos des conditions d’appropriation des connaissances théoriques en biochimie et aux interventions les plus susceptibles d’assurer l’intégration des apprentissages.

EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data

Background: Understanding transcriptional regulation by genome-wide microarray studies can contribute to unravel complex relationships between genes. Attempts to standardize the annotation of microarray data include the Minimum Information About a Microarray Experiment (MIAME) recommendations, the MAGE-ML format for data interchange, and the use of controlled vocabularies or ontologies. The existing software systems for microarray data analysis implement the mentioned standards only partially and are often hard to use and extend. Integration of genomic annotation data and other sources of external knowledge using open standards is therefore a key requirement for future integrated analysis systems. Results: The EMMA 2 software has been designed to resolve shortcomings with respect to full MAGE-ML and ontology support and makes use of modern data integration techniques. We present a software system that features comprehensive data analysis functions for spotted arrays, and for the most common synthesized oligo arrays such as Agilent, Affymetrix and NimbleGen. The system is based on the full MAGE object model. Analysis functionality is based on R and Bioconductor packages and can make use of a compute cluster for distributed services. Conclusion: Our model-driven approach for automatically implementing a full MAGE object model provides high flexibility and compatibility. Data integration via SOAP-based web-services is advantageous in a distributed client-server environment as the collaborative analysis of microarray data is gaining more and more relevance in international research consortia. The adequacy of the EMMA 2 software design and implementation has been proven by its application in many distributed functional genomics projects. Its scalability makes the current architecture suited for extensions towards future transcriptomics methods based on high-throughput sequencing approaches which have much higher computational requirements than microarrays.