Inflation in R2R^2 supergravity with non-minimal superpotentials

We investigate the cosmological inflation in a class of supergravity models that are generalizations of non-supersymmetric $R^2$ models. Although such models have been extensively studied recently, especially after the launch of the PLANCK and BICEP2 data, the class of models that can be constructed has not been exhausted. In this note, working in a supergravity model that is a generalization of Cecotti's model, we show that the appearance of new superpotential terms, which are quadratic in the superfield $\, \Lambda$ that couples to the Ricci supermultiplet, alters substantially the form of the scalar potential. The arising potential has the form of the Starobinsky potential times a factor that is exponential in the inflaton field and dominates for large inflaton values. We show that the well-known Starobinsky inflation scenario is maintained only for unnaturally small fine-tuned values of the coupling describing the $\Lambda^2$ superpotential terms. A welcome feature is the possible increase of the tensor to scalar ratio $r$, within the limits set by the new Planck and BICEP2 data.Comment: 13 pages, 9 figures, text and references added, version submitted to Phys. Lett.

Geomorphological mapping of Messogia plain (East Attica, Greece).

Η παρούσα μελέτη αφορά τη γεωμορφολογική χαρτογράφηση της περιοχής που περιλαμβάνεται στα φύλλα χάρτη Κορωπί και Πλάκα της διανομής της Γ.Υ.Σ. σε κλίμακα 1:50.000 . Πρόκειται για μια εκτεταμένη περιοχή της Ανατολικής Αττικής η οποία παρουσιάζει σύνθετο ανάγλυφο και μεγάλη ποικιλία γεωμορφών, λόγω του έντονου τεκτονισμού της και των φυσικών διεργασιών που διαμόρφωσαν τη μορφολογία της. Για τη δημιουργία του χάρτη χρησιμοποιήθηκαν κυρίως γεωλογικοί και τοπογραφικοί χάρτες, από τους οποίους κατασκευάστηκαν μέσω Γεωγραφικών Συστημάτων Πληροφοριών τα θεματικά επίπεδα της τοπογραφίας, της υδρογραφίας και της γεωλογίας, ενώ κατασκευάστηκε επίσης και το Ψηφιακό Μοντέλο Εδάφους, από το οποίο προέκυψαν οι χάρτες κλίσεων και έκθεσης. Οι θεματικοί χάρτες των κλίσεων και της λιθολογίας ταξινομήθηκαν σε κατηγορίες οι οποίες συνδυάστηκαν αποτελώντας κριτήρια εντοπισμού γεωμορφών. Στη χαρτογράφηση συνέβαλλαν καθοριστικά οι διαθέσιμοι ορθοφωτοχάρτες και αεροφωτογραφίες, όπως επίσης η εργασία πεδίου. Στη συνέχεια, με τον κατάλληλο συνδυασμό χρωμάτων και συμβολισμών δημιουργήθηκε ο γεωμορφολογικός χάρτης της περιοχής μελέτης, η οποία αποτελείται από τμήματα διαφοροποιημένων μορφολογικών χαρακτηριστικών του αναγλύφου.This study concerns the geomorphological mapping of the area included in the map sheets Koropi and Plaka of the Hellenic Military Geographical Service map distribution in scale 1:50.000. This is an extensive area of East Attica which presents a complex terrain and a wide variety of landforms, due to its intense tectonism and the natural processes that shaped its morphology. The primary data that were used in the creation of the map mainly included geological and topographic maps, from which thematic layers of the topography, hydrography and geology were constructed through GIS processes. A Digital Elevation Model was also constructed, from which the slope and aspect maps were created. The thematic maps of slοpe and lithology were classified into categories, which were combined to constitute detection criteria of landforms. Decisive contribution in mapping was provided by the available orthophotomaps and aerial photographs, as well as the field work. Finally, with the appropriate combination of colors and symbols the geomorphological map of the study area was produced

Lost in translation: data integration tools meet the Semantic Web (experiences from the Ondex project)

More information is now being published in machine processable form on the web and, as de-facto distributed knowledge bases are materializing, partly encouraged by the vision of the Semantic Web, the focus is shifting from the publication of this information to its consumption. Platforms for data integration, visualization and analysis that are based on a graph representation of information appear first candidates to be consumers of web-based information that is readily expressible as graphs. The question is whether the adoption of these platforms to information available on the Semantic Web requires some adaptation of their data structures and semantics. Ondex is a network-based data integration, analysis and visualization platform which has been developed in a Life Sciences context. A number of features, including semantic annotation via ontologies and an attention to provenance and evidence, make this an ideal candidate to consume Semantic Web information, as well as a prototype for the application of network analysis tools in this context. By analyzing the Ondex data structure and its usage, we have found a set of discrepancies and errors arising from the semantic mismatch between a procedural approach to network analysis and the implications of a web-based representation of information. We report in the paper on the simple methodology that we have adopted to conduct such analysis, and on issues that we have found which may be relevant for a range of similar platformsComment: Presented at DEIT, Data Engineering and Internet Technology, 2011 IEEE: CFP1113L-CD

GIS as an educational tool: Mapping cultural sites in greek space-time

Το θέμα της παρούσας εργασίας είναι η χαρτογραφική παρουσίαση της πολιτιστικής διαδοχής στον ελληνικό χωρο-χρόνο που σχετίζεται με βασικές έννοιες της γεωγραφικής και ιστορικής εκπαίδευσης. Η παιδαγωγική αξία της μελέτης είναι η ανάπτυξη πέντε διακριτών δεξιότητων: της έννοιας του χρόνου-κλίμακας, της ιστορικής και γεωγραφικής κατανόησης, της χωρικής ανάλυσης και ερμηνείας, της ικανότητας διεξαγωγής γεω-ιστορικής έρευνας, και της γεω-ιστορικής διαδικασίας λήψης αποφάσεων. Η μεθοδολογία βασίζεται στη βαθμονόμηση μιας σειράς κριτηρίων για κάθε πολιτιστική περιοχή που καλύπτει τα θέματα της οικονομίας, της γεωμορφολογίας, της κοινωνίας των πολιτών, της θρησκείας, της τέχνης και της επιστήμης. Η περαιτέρω ανάλυση αυτών των δεδομένων οδηγεί στη δημιουργία μιας γεω-βάσης. Οι παλαιογεωγραφικοί και ιστορικοί χάρτες των πολιτιστικών χώρων που προέρχονται από την γεωβάση παρέχουν πληροφορίες σχετικά με τις χρονικές και χωρικές μεταβολές. Ως αποτέλεσμα, οι μαθητές θα είναι σε θέση να αναπτύξουν μια πολυδιάστατη και διεπιστημονική προσέγγιση, προκειμένου να ανακατασκευάσουν την εξέλιξη του τόπου.This paper deals with the cartographical presentation of cultural succession in Greek space-time associated with core concepts of geographic and historical education. The pedagogic value of this study is to develop five distinct skills: sense of time-scale, historical and geographic comprehension, spatial analysis and interpretation, ability to perform geo-historical research, and procedure of geohistorical decision-making. The methodology is based on the calibration of a set of criteria for each cultural site that covers the topics of economy, geomorphology, society, religion, art and science. Further analysis of these data forms a geodatabase. In addition, palaeogeographic and historical maps of the cultural sites derived by the geodatabase provide information about temporal and spatial changes. As result, students will be able to develop a multidimensional and interdisciplinary approach, in order to reconstruct the evolution of the site

OnTheFly: a tool for automated document-based text annotation, data linking and network generation

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

"Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further

Metagenomics : tools and insights for analyzing next-generation sequencing data derived from biodiversity studies

Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of “metagenomics”, often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards

Arena3D: visualization of biological networks in 3D

<p>Abstract</p> <p>Background</p> <p>Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance.</p> <p>Results</p> <p>We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease.</p> <p>Conclusion</p> <p>Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from <url>http://arena3d.org</url>. Java3D library and Java 1.5 need to be pre-installed for the software to run.</p