ModelDB in Computational Neuroscience Education - A research tool as interactive educational media

ModelDB's mission is to link computational models and publications, supporting the field of computational neuroscience (CNS) by making model source code readily available. It is continually expanding, and currently contains source code for more than 300 models that cover more than 41 topics. Investigators, educators, and students can use it to obtain working models that reproduce published results and can be modified to test for new domains of applicability. Users can browse ModelDB to survey the field of computational neuroscience, or pursue more focused explorations of specific topics. Here we describe tutorials and initial experiences with ModelDB as an interactive educational tool.

International cooperation in ambient computing education

Funded by the US-EU Atlantis Program, the International Cooperation in Ambient Computing Education Project is establishing an international knowledge-building community for developing a broader computer science curriculum aimed at preparing students for real-world problems in a multidisciplinary, global world. The project is collaboration among Troy University (USA), University of Sunderland (UK), FernUniversität in Hagen (Germany), Universidade do Algarve (Portugal), University of Arkansas at Little Rock (USA) and San Diego State University (USA). The curriculum will include aspects of social science, cognitive science, human-computer interaction, organizational studies, global studies, and particular application areas as well as core computer science subjects. Programs offered at partner institutions will form trajectories through the curriculum. A degree will be defined in terms of combinations of trajectories which will satisfy degree requirements set by accreditation organizations. This is expected to lead to joint- or dual-degree programs among the partner institutions in the future. This paper describes the goals and activities of the project and discusses implementation issues.

Intransitive competition is widespread in plant communities and maintains their species richness

Intransitive competition networks, those in which there is no single best competitor, may ensure species coexistence. However, their frequency and importance in maintaining diversity in real-world ecosystems remain unclear. We used two large data sets from drylands and agricultural grasslands to assess: (1) the generality of intransitive competition, (2) intransitivity–richness relationships and (3) effects of two major drivers of biodiversity loss (aridity and land-use intensification) on intransitivity and species richness. Intransitive competition occurred in > 65% of sites and was associated with higher species richness. Intransitivity increased with aridity, partly buffering its negative effects on diversity, but was decreased by intensive land use, enhancing its negative effects on diversity. These contrasting responses likely arise because intransitivity is promoted by temporal heterogeneity, which is enhanced by aridity but may decline with land-use intensity. We show that intransitivity is widespread in nature and increases diversity, but it can be lost with environmental homogenisation.

Metabolomics in plant-herbivore interactions: challenges and applications

Metabolomics as the study of the entire set of metabolites of a given organism is an important frontier in life sciences. As a tool that captures the ‘front end’ of cellular machineries, metabolomics is particularly suited to investigate biotic interactions, including for instance the interplay between plants and insects. In this review, we discuss the opportunities and challenges of metabolomics to study plant–herbivore interactions. We first present a brief overview of the typical analytical workflows used in metabolomics and their associated issues, in particular those related to metabolome coverage and compound identification. Second, recent advances in the field of plant–herbivore relationships that are promoted by non-targeted approaches are reviewed, with examples ranging from classical herbivore resistance patterns to plant-mediated interactions across different spatial scales and volatile-mediated tritrophic interactions. Through general considerations and the discussion of a few selected case studies, our review highlights the potential and challenges of metabolomics as a research approach to understand biological interfaces.

Search for Low-Molecular-Weight Biomarkers in Plant Tissues and Seeds Using Metabolomics: Tools, Strategies, and Applications

This chapter summarises the metabolomic strategies currently in force used in plant science and describes the methods used. The metabolite profiling and fingerprinting of plant tissues through MS- and/or NMR-based approaches and the subsequent identification of biomarkers is detailed. Strategies for the microisolation and de novo identification of unknown biomarkers are also discussed. The various approaches are illustrated by a metabolomic study of the maize response to herbivory. A review of recent metabolomic studies performed on seed and crop plant tissues involving various analytical strategies is provided.

The Role of Roots in Plant Defence

Roots play an important role for plant defence and resistance against pathogens and insect herbivores: They act as environmental sensors for space, nutrients and water, they are important biosynthetic sites of plant toxins, they can store assimilates for future regrowth, and they possess themselves a potent defensive system to fend off belowground attackers. Although roots are often seen as passive tissue that only delivers services to the rest of the plant, it is becoming increasingly evident that roots actively respond to environmental conditions and are a vital part of the plant’s signaling and perception machinery. This chapter summarizes what is known about roots as constituents of plant resistance and defense mechanisms, with a particular emphasis on signaling aspects. It also discusses how the increasing knowledge about roots can be used to help protect plants from harmful pests.

Virtual Patients in continuing medical education and residency training: a pilot project for acceptance analysis in the framework of a residency revision course in pediatrics.

AIM Virtual patients (VPs) are a one-of-a-kind e-learning resource, fostering clinical reasoning skills through clinical case examples. The combination with face-to-face teaching is important for their successful integration, which is referred to as "blended learning". So far little is known about the use of VPs in the field of continuing medical education and residency training. The pilot study presented here inquired the application of VPs in the framework of a pediatric residency revision course. METHODS Around 200 participants of a pediatric nephology lecture ('nephrotic and nephritic syndrome in children') were offered two VPs as a wrap-up session at the revision course of the German Society for Pediatrics and Adolescent Medicine (DGKJ) 2009 in Heidelberg, Germany. Using a web-based survey form, different aspects were evaluated concerning the learning experiences with VPs, the combination with the lecture, and the use of VPs for residency training in general. RESULTS N=40 evaluable survey forms were returned (approximately 21%). The return rate was impaired by a technical problem with the local Wi-Fi firewall. The participants perceived the work-up of the VPs as a worthwhile learning experience, with proper preparation for diagnosing and treating real patients with similar complaints. Case presentations, interactivity, and locally and timely independent repetitive practices were, in particular, pointed out. On being asked about the use of VPs in general for residency training, there was a distinct demand for more such offers. CONCLUSION VPs may reasonably complement existing learning activities in residency training.

A conserved pattern in plant-mediated interactions between herbivores

Plant‐mediated interactions between herbivores are important determinants of community structure and plant performance in natural and agricultural systems. Current research suggests that the outcome of the interactions is determined by herbivore and plant identity, which may result in stochastic patterns that impede adaptive evolution and agricultural exploitation. However, few studies have systemically investigated specificity versus general patterns in a given plant system by varying the identity of all involved players. We investigated the influence of herbivore identity and plant genotype on the interaction between leaf‐chewing and root‐feeding herbivores in maize using a partial factorial design. We assessed the influence of leaf induction by oral secretions of six different chewing herbivores on the response of nine different maize genotypes and three different root feeders. Contrary to our expectations, we found a highly conserved pattern across all three dimensions of specificity: The majority of leaf herbivores elicited a negative behavioral response from the different root feeders in the large majority of tested plant genotypes. No facilitation was observed in any of the treatment combinations. However, the oral secretions of one leaf feeder and the responses of two maize genotypes did not elicit a response from a root‐feeding herbivore. Together, these results suggest that plant‐mediated interactions in the investigated system follow a general pattern, but that a degree of specificity is nevertheless present. Our study shows that within a given plant species, plant‐mediated interactions between herbivores of the same feeding guild can be stable. This stability opens up the possibility of adaptations by associated organisms and suggests that plant‐mediated interactions may contribute more strongly to evolutionary dynamics in terrestrial (agro)ecosystems than previously assumed.

Alternative Assessment in Engineering Language Education: The case of the Technical University of Madrid

This article describes a research project involving students from nine different engineering degrees at the Technical university of Madrid. The purpose of the project was to analyze the use of peer and self assessment and the students? attitudes toward alternative assessment procedures.

Knowledge Management and Leadership in the Higher Education: A First Approach

Today, it is more and more important to develop competences in the learning process of the university students (that is to say, to acquire knowledge but also skills, abilities, attitudes and values). This is because professional practice requires that the future graduates design and market products, defend the interests of their clients, be introduced in the Administration or, even, in the Politics. Universities must form professionals that become social and opinion leaders, consultants, advisory, entrepreneurs and, in short, people with capacity to solve problems. This paper offers a tool to evaluate the application for the professor of different styles of management in the process of the student’s learning. Its main contribution consists on advancing toward the setting in practice of a model that overcomes the limitations of the traditional practices based on the masterful class, and that it has been applied in Portugal and Spain.

Virtual Learning Environments In Faculties Of Education In Spain: Changes On Student Attitude

This paper presents some results of a R+D project entitled “e-Learning system for Practical Training of University students in Education Faculties (ForELearn)”, developed in Spain by the Universidad de Granada and the Universidad Politécnica de Madrid and funded by the Spanish Ministry of Education. In a first phase, through the use of AulaWeb Learning Management System, a set of adaptations and improvements of this software application have been done for the design and development of an experimental course of Practicum supervision. Next, the implementation of this course by means of a group of face to face and online seminars provides experimental data for the analysis and discussion about the point of view of users (preservice teachers) that have tracked their practice supervision with AulaWeb.

The involvement of thaumatin-like proteins in plant food cross-reactivity: a multicenter study using a specific protein microarray.

Cross-reactivity of plant foods is an important phenomenon in allergy, with geographical variations with respect to the number and prevalence of the allergens involved in this process, whose complexity requires detailed studies. We have addressed the role of thaumatin-like proteins (TLPs) in cross-reactivity between fruit and pollen allergies. A representative panel of 16 purified TLPs was printed onto an allergen microarray. The proteins selected belonged to the sources most frequently associated with peach allergy in representative regions of Spain. Sera from two groups of well characterized patients, one with allergy to Rosaceae fruit (FAG) and another against pollens but tolerant to food-plant allergens (PAG), were obtained from seven geographical areas with different environmental pollen profiles. Cross-reactivity between members of this family was demonstrated by inhibition assays. Only 6 out of 16 purified TLPs showed noticeable allergenic activity in the studied populations. Pru p 2.0201, the peach TLP (41%), chestnut TLP (24%) and plane pollen TLP (22%) proved to be allergens of probable relevance to fruit allergy, being mainly associated with pollen sensitization, and strongly linked to specific geographical areas such as Barcelona, Bilbao, the Canary Islands and Madrid. The patients exhibited mayor que50% positive response to Pru p 2.0201 and to chestnut TLP in these specific areas. Therefore, their recognition patterns were associated with the geographical area, suggesting a role for pollen in the sensitization of these allergens. Finally, the co-sensitizations of patients considering pairs of TLP allergens were analyzed by using the co-sensitization graph associated with an allergen microarray immunoassay. Our data indicate that TLPs are significant allergens in plant food allergy and should be considered when diagnosing and treating pollen-food allergy.

Estudios termodinámicos de los procesos de vitrificación en la crioconservación de germoplasma vegetal=Thermodynamic studies of vitrification processes in plant germplasm cryopreservation

En la actualidad, las técnicas de crioconservación poseen una importancia creciente para el almacenamiento a largo plazo de germoplasma vegetal. En las dos últimas décadas, estos métodos experimentaron un gran desarrollo y se han elaborado protocolos adecuados a diferentes sistemas vegetales, utilizando diversas estrategias como la vitrificación, la encapsulación-desecación con cuentas de alginato y el método de “droplet”-vitrificación. La presente tesis doctoral tiene como objetivo aumentar el conocimiento sobre los procesos implicados en los distintos pasos de un protocolo de crioconservación, en relación con el estado del agua presente en los tejidos y sus cambios, abordado mediante diversas técnicas biofísicas, principalmente calorimetría diferencial de barrido (DSC) y microscopía electrónica de barrido a baja temperatura (crio-SEM). En un primer estudio sobre estos métodos de crioconservación, se describen las fases de enfriamiento hasta la temperatura del nitrógeno líquido y de calentamiento hasta temperatura ambiente, al final del periodo de almacenamiento, que son críticas para la supervivencia del material crioconservado. Tanto enfriamiento como calentamiento deben ser realizados lo más rápidamente posible pues, aunque los bajos contenidos en agua logrados en etapas previas de los protocolos reducen significativamente las probabilidades de formación de hielo, éstas no son del todo nulas. En ese contexto, se analiza también la influencia de las velocidades de enfriamiento y calentamiento de las soluciones de crioconservación de plantas en sus parámetros termofísicos referente a la vitrificación, en relación su composición y concentración de compuestos. Estas soluciones son empleadas en la mayor parte de los protocolos actualmente utilizados para la crioconservación de material vegetal. Además, se estudia la influencia de otros factores que pueden determinar la estabilidad del material vitrificado, tales como en envejecimiento del vidrio. Se ha llevado a cabo una investigación experimental en el empleo del crio-SEM como una herramienta para visualizar el estado vítreo de las células y tejidos sometidos a los procesos de crioconservación. Se ha comparado con la más conocida técnica de calorimetría diferencial de barrido, obteniéndose resultados muy concordantes y complementarios. Se exploró también por estas técnicas el efecto sobre tejidos vegetales de la adaptación a bajas temperaturas y de la deshidratación inducida por los diferentes tratamientos utilizados en los protocolos. Este estudio permite observar la evolución biofísica de los sistemas en el proceso de crioconservación. Por último, se estudió la aplicación de películas de quitosano en las cuentas de alginato utilizadas en el protocolo de encapsulación. No se observaron cambios significativos en su comportamiento frente a la deshidratación, en sus parámetros calorimétricos y en la superficie de las cuentas. Su aplicación puede conferir propiedades adicionales prometedoras. ABSTRACT Currently, cryopreservation techniques have a growing importance for long term plant germplasm storage. These methods have undergone great progress during the last two decades, and adequate protocols for different plant systems have been developed, making use of diverse strategies, such as vitrification, encapsulation-dehydration with alginate beads and the dropletvitrification method. This PhD thesis has the goal of increasing the knowledge on the processes underlying the different steps of cryopreservation protocols, in relation with the state of water on tissues and its changes, approached through diverse biophysical techniques, especially differential scanning calorimetry (DSC) and low-temperature scanning electron microscopy (cryo-SEM). The processes of cooling to liquid nitrogen temperature and warming to room temperature, at the end of the storage period, critical for the survival of the cryopreserved material, are described in a first study on these cryopreservation methods. Both cooling and warming must be carried out as quickly as possible because, although the low water content achieved during previous protocol steps significantly reduces ice formation probability, it does not completely disappear. Within this context, the influence of plant vitrification solutions cooling and warming rate on their vitrification related thermophysical parameters is also analyzed, in relation to its composition and component concentration. These solutions are used in most of the currently employed plant material cryopreservation protocols. Additionally, the influence of other factors determining the stability of vitrified material is studied, such as glass aging. An experimental research work has been carried out on the use of cryo-SEM as a tool for visualizing the glassy state in cells and tissues, submitted to cryopreservation processes. It has been compared with the better known differential scanning calorimetry technique, and results in good agreement and complementary have been obtained. The effect on plant tissues of adaptation to low temperature and of the dehydration induced by the different treatments used in the protocols was explored also by these techniques. This study allows observation of the system biophysical evolution in the cryopreservation process. Lastly, the potential use of an additional chitosan film over the alginate beads used in encapsulation protocols was examined. No significant changes could be observed in its dehydration and calorimetric behavior, as well as in its surface aspect; its application for conferring additional properties to gel beads is promising.

Simplifying data acquisition in plant canopies- Measurements of leaf angles with a cell phone

1. Canopies are complex multilayered structures comprising individual plant crowns exposing a multifaceted surface area to sunlight. Foliage arrangement and properties are the main mediators of canopy functions. The leaves act as light traps whose exposure to sunlight varies with time of the day, date and latitude in a trade-off between photosynthetic light harvesting and excessive or photoinhibitory light avoidance. To date, ecological research based upon leaf sampling has been limited by the available echnology, with which data acquisition becomes labour intensive and time-consuming, given the verwhelming number of leaves involved. 2. In the present study, our goal involved developing a tool capable of easuring a sufficient number of leaves to enable analysis of leaf populations, tree crowns and canopies.We specifically tested whether a cell phone working as a 3Dpointer could yield reliable, repeatable and valid leaf anglemeasurements with a simple gesture. We evaluated the accuracy of this method under controlled conditions, using a 3D digitizer, and we compared performance in the field with the methods commonly used. We presented an equation to estimate the potential proportion of the leaf exposed to direct sunlight (SAL) at any given time and compared the results with those obtained bymeans of a graphicalmethod. 3. We found a strong and highly significant correlation between the graphical methods and the equation presented. The calibration process showed a strong correlation between the results derived from the two methods with amean relative difference below 10%. Themean relative difference in calculation of instantaneous exposure was below 5%. Our device performed equally well in diverse locations, in which we characterized over 700 leaves in a single day. 4. The newmethod, involving the use of a cell phone, ismuchmore effective than the traditionalmethods or digitizers when the goal is to scale up from leaf position to performance of leaf populations, tree crowns or canopies. Our methodology constitutes an affordable and valuable tool within which to frame a wide range of ecological hypotheses and to support canopy modelling approaches.