Environmental data mining and modeling based on machine learning algorithms and geostatistics

The paper presents some contemporary approaches to spatial environmental data analysis. The main topics are concentrated on the decision-oriented problems of environmental spatial data mining and modeling: valorization and representativity of data with the help of exploratory data analysis, spatial predictions, probabilistic and risk mapping, development and application of conditional stochastic simulation models. The innovative part of the paper presents integrated/hybrid model-machine learning (ML) residuals sequential simulations-MLRSS. The models are based on multilayer perceptron and support vector regression ML algorithms used for modeling long-range spatial trends and sequential simulations of the residuals. NIL algorithms deliver non-linear solution for the spatial non-stationary problems, which are difficult for geostatistical approach. Geostatistical tools (variography) are used to characterize performance of ML algorithms, by analyzing quality and quantity of the spatially structured information extracted from data with ML algorithms. Sequential simulations provide efficient assessment of uncertainty and spatial variability. Case study from the Chernobyl fallouts illustrates the performance of the proposed model. It is shown that probability mapping, provided by the combination of ML data driven and geostatistical model based approaches, can be efficiently used in decision-making process. (C) 2003 Elsevier Ltd. All rights reserved.

Multi-scale systems analysis of plant development : beyond cellular signaling and tissue morphodynamics

Les plantes sont essentielles pour les sociétés humaines. Notre alimentation quotidienne, les matériaux de constructions et les sources énergétiques dérivent de la biomasse végétale. En revanche, la compréhension des multiples aspects développementaux des plantes est encore peu exploitée et représente un sujet de recherche majeur pour la science. L'émergence des technologies à haut débit pour le séquençage de génome à grande échelle ou l'imagerie de haute résolution permet à présent de produire des quantités énormes d'information. L'analyse informatique est une façon d'intégrer ces données et de réduire la complexité apparente vers une échelle d'abstraction appropriée, dont la finalité est de fournir des perspectives de recherches ciblées. Ceci représente la raison première de cette thèse. En d'autres termes, nous appliquons des méthodes descriptives et prédictives combinées à des simulations numériques afin d'apporter des solutions originales à des problèmes relatifs à la morphogénèse à l'échelle de la cellule et de l'organe. Nous nous sommes fixés parmi les objectifs principaux de cette thèse d'élucider de quelle manière l'interaction croisée des phytohormones auxine et brassinosteroïdes (BRs) détermine la croissance de la cellule dans la racine du méristème apical d'Arabidopsis thaliana, l'organisme modèle de référence pour les études moléculaires en plantes. Pour reconstruire le réseau de signalement cellulaire, nous avons extrait de la littérature les informations pertinentes concernant les relations entre les protéines impliquées dans la transduction des signaux hormonaux. Le réseau a ensuite été modélisé en utilisant un formalisme logique et qualitatif pour pallier l'absence de données quantitatives. Tout d'abord, Les résultats ont permis de confirmer que l'auxine et les BRs agissent en synergie pour contrôler la croissance de la cellule, puis, d'expliquer des observations phénotypiques paradoxales et au final, de mettre à jour une interaction clef entre deux protéines dans la maintenance du méristème de la racine. Une étude ultérieure chez la plante modèle Brachypodium dystachion (Brachypo- dium) a révélé l'ajustement du réseau d'interaction croisée entre auxine et éthylène par rapport à Arabidopsis. Chez ce dernier, interférer avec la biosynthèse de l'auxine mène à la formation d'une racine courte. Néanmoins, nous avons isolé chez Brachypodium un mutant hypomorphique dans la biosynthèse de l'auxine qui affiche une racine plus longue. Nous avons alors conduit une analyse morphométrique qui a confirmé que des cellules plus anisotropique (plus fines et longues) sont à l'origine de ce phénotype racinaire. Des analyses plus approfondies ont démontré que la différence phénotypique entre Brachypodium et Arabidopsis s'explique par une inversion de la fonction régulatrice dans la relation entre le réseau de signalisation par l'éthylène et la biosynthèse de l'auxine. L'analyse morphométrique utilisée dans l'étude précédente exploite le pipeline de traitement d'image de notre méthode d'histologie quantitative. Pendant la croissance secondaire, la symétrie bilatérale de l'hypocotyle est remplacée par une symétrie radiale et une organisation concentrique des tissus constitutifs. Ces tissus sont initialement composés d'une douzaine de cellules mais peuvent aisément atteindre des dizaines de milliers dans les derniers stades du développement. Cette échelle dépasse largement le seuil d'investigation par les moyens dits 'traditionnels' comme l'imagerie directe de tissus en profondeur. L'étude de ce système pendant cette phase de développement ne peut se faire qu'en réalisant des coupes fines de l'organe, ce qui empêche une compréhension des phénomènes cellulaires dynamiques sous-jacents. Nous y avons remédié en proposant une stratégie originale nommée, histologie quantitative. De fait, nous avons extrait l'information contenue dans des images de très haute résolution de sections transverses d'hypocotyles en utilisant un pipeline d'analyse et de segmentation d'image à grande échelle. Nous l'avons ensuite combiné avec un algorithme de reconnaissance automatique des cellules. Cet outil nous a permis de réaliser une description quantitative de la progression de la croissance secondaire révélant des schémas développementales non-apparents avec une inspection visuelle classique. La formation de pôle de phloèmes en structure répétée et espacée entre eux d'une longueur constante illustre les bénéfices de notre approche. Par ailleurs, l'exploitation approfondie de ces résultats a montré un changement de croissance anisotropique des cellules du cambium et du phloème qui semble en phase avec l'expansion du xylème. Combinant des outils génétiques et de la modélisation biomécanique, nous avons démontré que seule la croissance plus rapide des tissus internes peut produire une réorientation de l'axe de croissance anisotropique des tissus périphériques. Cette prédiction a été confirmée par le calcul du ratio des taux de croissance du xylème et du phloème au cours de développement secondaire ; des ratios élevés sont effectivement observés et concomitant à l'établissement progressif et tangentiel du cambium. Ces résultats suggèrent un mécanisme d'auto-organisation établi par un gradient de division méristématique qui génèrent une distribution de contraintes mécaniques. Ceci réoriente la croissance anisotropique des tissus périphériques pour supporter la croissance secondaire. - Plants are essential for human society, because our daily food, construction materials and sustainable energy are derived from plant biomass. Yet, despite this importance, the multiple developmental aspects of plants are still poorly understood and represent a major challenge for science. With the emergence of high throughput devices for genome sequencing and high-resolution imaging, data has never been so easy to collect, generating huge amounts of information. Computational analysis is one way to integrate those data and to decrease the apparent complexity towards an appropriate scale of abstraction with the aim to eventually provide new answers and direct further research perspectives. This is the motivation behind this thesis work, i.e. the application of descriptive and predictive analytics combined with computational modeling to answer problems that revolve around morphogenesis at the subcellular and organ scale. One of the goals of this thesis is to elucidate how the auxin-brassinosteroid phytohormone interaction determines the cell growth in the root apical meristem of Arabidopsis thaliana (Arabidopsis), the plant model of reference for molecular studies. The pertinent information about signaling protein relationships was obtained through the literature to reconstruct the entire hormonal crosstalk. Due to a lack of quantitative information, we employed a qualitative modeling formalism. This work permitted to confirm the synergistic effect of the hormonal crosstalk on cell elongation, to explain some of our paradoxical mutant phenotypes and to predict a novel interaction between the BREVIS RADIX (BRX) protein and the transcription factor MONOPTEROS (MP),which turned out to be critical for the maintenance of the root meristem. On the same subcellular scale, another study in the monocot model Brachypodium dystachion (Brachypodium) revealed an alternative wiring of auxin-ethylene crosstalk as compared to Arabidopsis. In the latter, increasing interference with auxin biosynthesis results in progressively shorter roots. By contrast, a hypomorphic Brachypodium mutant isolated in this study in an enzyme of the auxin biosynthesis pathway displayed a dramatically longer seminal root. Our morphometric analysis confirmed that more anisotropic cells (thinner and longer) are principally responsible for the mutant root phenotype. Further characterization pointed towards an inverted regulatory logic in the relation between ethylene signaling and auxin biosynthesis in Brachypodium as compared to Arabidopsis, which explains the phenotypic discrepancy. Finally, the morphometric analysis of hypocotyl secondary growth that we applied in this study was performed with the image-processing pipeline of our quantitative histology method. During its secondary growth, the hypocotyl reorganizes its primary bilateral symmetry to a radial symmetry of highly specialized tissues comprising several thousand cells, starting with a few dozens. However, such a scale only permits observations in thin cross-sections, severely hampering a comprehensive analysis of the morphodynamics involved. Our quantitative histology strategy overcomes this limitation. We acquired hypocotyl cross-sections from tiled high-resolution images and extracted their information content using custom high-throughput image processing and segmentation. Coupled with an automated cell type recognition algorithm, it allows precise quantitative characterization of vascular development and reveals developmental patterns that were not evident from visual inspection, for example the steady interspace distance of the phloem poles. Further analyses indicated a change in growth anisotropy of cambial and phloem cells, which appeared in phase with the expansion of xylem. Combining genetic tools and computational modeling, we showed that the reorientation of growth anisotropy axis of peripheral tissue layers only occurs when the growth rate of central tissue is higher than the peripheral one. This was confirmed by the calculation of the ratio of the growth rate xylem to phloem throughout secondary growth. High ratios are indeed observed and concomitant with the homogenization of cambium anisotropy. These results suggest a self-organization mechanism, promoted by a gradient of division in the cambium that generates a pattern of mechanical constraints. This, in turn, reorients the growth anisotropy of peripheral tissues to sustain the secondary growth.

Learning-induced gene expression in the heads of two Nasonia species that differ in long-term memory formation.

BACKGROUND: Cellular processes underlying memory formation are evolutionary conserved, but natural variation in memory dynamics between animal species or populations is common. The genetic basis of this fascinating phenomenon is poorly understood. Closely related species of Nasonia parasitic wasps differ in long-term memory (LTM) formation: N. vitripennis will form transcription-dependent LTM after a single conditioning trial, whereas the closely-related species N. giraulti will not. Genes that were differentially expressed (DE) after conditioning in N. vitripennis, but not in N. giraulti, were identified as candidate genes that may regulate LTM formation. RESULTS: RNA was collected from heads of both species before and immediately, 4 or 24 hours after conditioning, with 3 replicates per time point. It was sequenced strand-specifically, which allows distinguishing sense from antisense transcripts and improves the quality of expression analyses. We determined conditioning-induced DE compared to naïve controls for both species. These expression patterns were then analysed with GO enrichment analyses for each species and time point, which demonstrated an enrichment of signalling-related genes immediately after conditioning in N. vitripennis only. Analyses of known LTM genes and genes with an opposing expression pattern between the two species revealed additional candidate genes for the difference in LTM formation. These include genes from various signalling cascades, including several members of the Ras and PI3 kinase signalling pathways, and glutamate receptors. Interestingly, several other known LTM genes were exclusively differentially expressed in N. giraulti, which may indicate an LTM-inhibitory mechanism. Among the DE transcripts were also antisense transcripts. Furthermore, antisense transcripts aligning to a number of known memory genes were detected, which may have a role in regulating these genes. CONCLUSION: This study is the first to describe and compare expression patterns of both protein-coding and antisense transcripts, at different time points after conditioning, of two closely related animal species that differ in LTM formation. Several candidate genes that may regulate differences in LTM have been identified. This transcriptome analysis is a valuable resource for future in-depth studies to elucidate the role of candidate genes and antisense transcription in natural variation in LTM formation.

The determinants of CAP reform: learning from the European financial crisis and CAP 2013

There is an ongoing debate on which are the determinants of CAP reform. The economic environment has not been contemplated as a direct determinant of CAP reform but its proxy, the budget, has not only been looked at as such but underlined as a key cause of CAP reform. This paper argues, however, that the budget does not affect the modus operandi of the CAP. It affects the quantity of support each farmer is going to get and sometimes even the timing of the reform, but not the form it is going to receive it. Other CAP determinants and international negotiations in particular, have an impact on the substance of CAP reform. This hypothesis is not contradicted by an analysis of CAP 2013 changes.

From bird to sparrow: Learning-induced modulations in fine-grained semantic discrimination.

Recognition of environmental sounds is believed to proceed through discrimination steps from broad to more narrow categories. Very little is known about the neural processes that underlie fine-grained discrimination within narrow categories or about their plasticity in relation to newly acquired expertise. We investigated how the cortical representation of birdsongs is modulated by brief training to recognize individual species. During a 60-minute session, participants learned to recognize a set of birdsongs; they improved significantly their performance for trained (T) but not control species (C), which were counterbalanced across participants. Auditory evoked potentials (AEPs) were recorded during pre- and post-training sessions. Pre vs. post changes in AEPs were significantly different between T and C i) at 206-232ms post stimulus onset within a cluster on the anterior part of the left superior temporal gyrus; ii) at 246-291ms in the left middle frontal gyrus; and iii) 512-545ms in the left middle temporal gyrus as well as bilaterally in the cingulate cortex. All effects were driven by weaker activity for T than C species. Thus, expertise in discriminating T species modulated early stages of semantic processing, during and immediately after the time window that sustains the discrimination between human vs. animal vocalizations. Moreover, the training-induced plasticity is reflected by the sharpening of a left lateralized semantic network, including the anterior part of the temporal convexity and the frontal cortex. Training to identify birdsongs influenced, however, also the processing of C species, but at a much later stage. Correct discrimination of untrained sounds seems to require an additional step which results from lower-level features analysis such as apperception. We therefore suggest that the access to objects within an auditory semantic category is different and depends on subject's level of expertise. More specifically, correct intra-categorical auditory discrimination for untrained items follows the temporal hierarchy and transpires in a late stage of semantic processing. On the other hand, correct categorization of individually trained stimuli occurs earlier, during a period contemporaneous with human vs. animal vocalization discrimination, and involves a parallel semantic pathway requiring expertise.

Los enfoques de aprendizaje en estudiantes universitarios Catalanes mediante el approaches and study skills inventory for students (ASSIST) = Learning Approaches of Catalan University Students Measured with the Approaches and Study Skills Inventory for Students (ASSIST)

The aim of this study is to measure the psychometric properties of a Catalan translation of the Approaches and Study Skills Inventory for Students (ASSIST), and to analyse the different learning styles used by university students, considering the influence of gender and type of studies. The instrument was administered to 834 students at the University of Girona. The results showed that most students interviewed had a deep approach to learning, although the analysis by gender showed that females tended to use a more strategic approach, while males used a deep approach predominantly. As to whether the type of studies influenced learning styles, a prevalence of deep approach was found among Science and Technology students, while a more strategic approach was found among Humanities and Education students

Gestión de la actividad no presencial y autoevaluación de competencias = Management of Student Learning Outside the Classroom and the Self-evaluation of Competences

Psychological Assessment is a core subject of Psychology studies, and of the university degree Human development, at the University of Girona and according to the University regulations, had 12 credits. Until the 2005-06 academic years, the student work conducted outside the classroom consisted of undertaking a psychological assessment that was written and handed in at the end of the course. From this the student obtained a qualification and a review if they applied for it In accordance with the European Credits for Higher Education, this subject was reduced to 9 credits, which is the equivalent of a total of 255 hours of in-class work and outside the classroom. In the 2006-07 academic year we created a guide to manage the student’s experiences outside the classroom, with the objective of encouraging the application of problem solving/critical thinking (Bloom, 1975), in line with the recommendations of the Catalonia Agency for University System Quality (2005). The guide includes: learning objectives, evaluation criterions, a description of activities, work week timetable for the whole course, programmed tutorials to review all steps of the psychological assessment process, and the use of a web-based virtual forum for the transfer of knowledge, analysis and constructive critiques of the assessment done by themselves and their colleagues

Undergraduate palliative care teaching in Swiss medical faculties: a nationwide survey and improved learning objectives.

BACKGROUND: In 2007, a first survey on undergraduate palliative care teaching in Switzerland has revealed major heterogeneity of palliative care content, allocation of hours and distribution throughout the 6 year curriculum in Swiss medical faculties. This second survey in 2012/13 has been initiated as part of the current Swiss national strategy in palliative care (2010 - 2015) to serve as a longitudinal monitoring instrument and as a basis for redefinition of palliative care learning objectives and curriculum planning in our country. METHODS: As in 2007, a questionnaire was sent to the deans of all five medical faculties in Switzerland in 2012. It consisted of eight sections: basic background information, current content and hours in dedicated palliative care blocks, current palliative care content in other courses, topics related to palliative care presented in other courses, recent attempts at improving palliative care content, palliative care content in examinations, challenges, and overall summary. Content analysis was performed and the results matched with recommendations from the EAPC for undergraduate training in palliative medicine as well as with recommendations from overseas countries. RESULTS: There is a considerable increase in palliative care content, academic teaching staff and hours in all medical faculties compared to 2007. No Swiss medical faculty reaches the range of 40 h dedicated specifically to palliative care as recommended by the EAPC. Topics, teaching methods, distribution throughout different years and compulsory attendance still differ widely. Based on these results, the official Swiss Catalogue of Learning Objectives (SCLO) was complemented with 12 new learning objectives for palliative and end of life care (2013), and a national basic script for palliative care was published (2015). CONCLUSION: Performing periodic surveys of palliative care teaching at national medical faculties has proven to be a useful tool to adapt the national teaching framework and to improve the recognition of palliative medicine as an integral part of medical training.

Language Learning in Task Management and Task Accomplishment

In this paper we study student interaction in English and Swedish courses at a Finnish university. We focus on language choices made in task-related activities in small group interaction. Our research interests arose from the change in the teaching curriculum, in which content and language courses were integrated at Tampere University of Technology in 2013. Using conversation analysis, we analysed groups of 4-5 students who worked collaboratively on a task via a video conference programme. The results show how language alternation has different functions in 1) situations where students orient to managing the task, e.g., in transitions into task, or where they orient to technical problems, and 2) situations where students accomplish the task. With the results, we aim to show how language alternation can provide interactional opportunities for language learning. The findings will be useful in designing tasks in the future.

A framework for the analysis of CLIL lecturers’ discourse from a genre perspective

Internationalization strategies and the European Space of Higher Education are causing a growing interest in English medium instruction (EMI). University linguistic and internationalization policies are attempting to provide lectures with the required training and education. Linguists can supply not only the knowledge of the language but the knowledge about language which may enable lecturers to increase their academic language competence autonomously. This paper presents a framework for the analysis of lecturers’ discourse to trigger reflection about the linguistic needs in CLIL/EMI contexts.

The learning about imaging diagnosis technology

Objective To investigate the learning about management of the technology (efficient use, acquisition and maintenance of imaging diagnosis equipment) in the radiology residency program of Escola Paulista de Medicina - Universidade Federal de São Paulo, with a view to improving the education of radiologists. Materials and Methods Exploratory research where residents, faculty staff and tutors of the program were quantitative and qualitatively approached with Likert scale questionnaires (46), and deepening with recorded interviews (18) and categorization based upon meaning units (thematic analysis). Results Among the participants, 66% agreed that they had the opportunity of learning about the use of radiological equipment; for 61% the program should include knowledge on the importance of acquiring equipment; and 72% emphasized the lack of learning about equipment management and maintenance. Conclusion As the major moment in the education of specialists, the medical residency program provides residents with a favorable environment to the learning of the skills required to the future of their professional practice, but with limited emphasis on the management of the technology: efficient use, acquisition and mainly maintenance of equipment, still poorly explored. Both the investigated program and the medical residency in radiology should incorporate, whenever possible, the commitment with the training in supplementary skills related to equipment management, developing the competence of the future radiologists.

Learning on human resources management in the radiology residency program

Objective To investigate the process of learning on human resource management in the radiology residency program at Escola Paulista de Medicina – Universidade Federal de São Paulo, aiming at improving radiologists' education. Materials and Methods Exploratory study with a quantitative and qualitative approach developed with the faculty staff, preceptors and residents of the program, utilizing a Likert questionnaire (46), taped interviews (18), and categorization based on thematic analysis. Results According to 71% of the participants, residents have clarity about their role in the development of their activities, and 48% said that residents have no opportunity to learn how to manage their work in a multidisciplinary team. Conclusion Isolation at medical records room, little interactivity between sectors with diversified and fixed activities, absence of a previous culture and lack of a training program on human resources management may interfere in the development of skills for the residents' practice. There is a need to review objectives of the medical residency in the field of radiology, incorporating, whenever possible, the commitment to the training of skills related to human resources management thus widening the scope of abilities of the future radiologists.

La Incidencia de las nuevas tecnologías en los hábitos formativos de los estudiantes de magisterio = The Impact of new technologies in the learning habits of teacher students

Este trabajo persigue dos objetivos: el primero es analizar el uso de las TIC en un grupo de estudiantes de segundo curso de Magisterio de la Universidad de Girona; el segundo es analizar los documentos normativos legales que establecen el currículum de educación primaria en Cataluña para observar qué tipo de papel juegan las TIC en las nuevas programaciones educativas. La primera parte se ha llevado a cabo mediante una encuesta, cuyos resultados permiten observar tres aspectos distintos: el primero, que una parte considerable del grupo considera las TIC más como un complemento para el aprendizaje que como una forma de aprendizaje; el segundo, que a pesar de hacer un uso considerable de las TIC, el conocimiento que tienen de ellas es muy básico y utilizan aplicaciones muy genéricas; y el tercero es que una parte de sus propuestas didácticas para el uso de las TIC son propuestas tradicionales simplemente adaptadas a un nuevo instrumento, sin buscar realmente la innovación que puede suponer la incorporación de las TIC. En la segunda parte del artículo, a partir del análisis e interpretación de los documentos legales que establecen el currículum de Educación Primaria, se observa que en un mismo documento conviven aserciones sobre las TIC como complemento al aprendizaje de contenidos con otras formulaciones que consideran las TIC como constructoras de conocimiento. A partir del perfil de los estudiantes y del estado de los documentos legales, al final del artículo se hacen propuestas para formar al futuro maestro teniendo en cuenta las TIC como herramientas básicas de conocimiento