Οπτικοποίηση και ανάλυση τρισδιάστατων πολυεπίπεδων βιολογικών δικτύων με πολλαπλές ακμές

Η αποτελεσματική ενσωμάτωση και οπτικοποίηση ετερογενών πληροφοριών σε μία απεικόνιση αποτελεί βασική πρόκληση. Σε αυτή τη μελέτη, παρουσιάζουμε το εργαλείο Arena3D web, την πρώτη, πλήρως διαδραστική και χωρίς εξάρτηση από άλλα εργαλεία, διαδικτυακή εφαρμογή που επιτρέπει την οπτικοποίηση πολυεπίπεδων δικτύων στον 3D χώρο και τις καινούριες δυνατότητες της. Με την Arena3D web, οι χρήστες μπορούν να ενσωματώσουν πολλαπλά δίκτυα σε μία μόνο προβολή, μαζί με τις συνδέσεις τους, εντός και μεταξύ επιπέδων. Για σαφέστερες και πιο ενημερωτικές οπτικοποιήσεις, οι χρήστες μπορούν να επιλέξουν ανάμεσα σε μια πληθώρα αλγορίθμων διάταξης και ομαδοποίησης και να τις εφαρμόσουν σε ένα σύνολο επιλεγμένων επιπέδων, είτε μεμονωμένα, είτε σε συνδυασμό. Οι χρήστες μπορούν επίσης να ευθυγραμμίσουν τα δίκτυα και να επισημάνουν τοπολογικά χαρακτηριστικά κόμβων, ενώ κάθε επίπεδο, καθώς και ολόκληρη η σκηνή, μπορούν να περιστραφούν και να τοποθετηθούν οπουδήποτε στον 3D χώρο. Ο χρήστης μπορεί να επιλέξει χρώματα, τόσο για τις ακμές και τα διαφορετικά κανάλια σε περίπτωση πολλαπλών ακμών, όσο και για τους κόμβους, ενώ χρώματα μπορούν επίσης να χρησιμοποιηθούν για την επισήμανση σημαντικών διαδρομών και μονοπατιών. Στην τρέχουσα έκδοση, η Arena3D web υποστηρίζει κατευθυνόμενους ή μη κατευθυνόμενους, βεβαρημένους ή βεβαρημένους μη γράφους, με πολλαπλές ακμές. Η εφαρμογή είναι γραμμένη σε R, Shiny και JavaScript. Κάνουμε μια εισαγωγή στην θεωρία των γράφων, στα διάφορα μοντέλα και αλγορίθμους, καθώς και σε ανταγωνιστικά εργαλεία και αναλύουμε την υπάρχουσα και νέα λειτουργικότητα της Arena3D web χρησιμοποιώντας διαφορετικά σενάρια χρήσης.Εfficient integration and visualization of heterogeneous biomedical information in a single view is a key challenge. In this study, we present Arena3Dweb, the first, fully interactive and dependencyfree, web application which allows the visualization of multilayered graphs in 3D space, as well as its new features. With Arena3Dweb, users can integrate multiple networks in a single view along with their intra- and inter-layer connections. For clearer and more informative views, users can choose between a plethora of layout and clustering algorithms and apply them to a set of selected layers either individually or in combination. Users can align networks and highlight node topological features, whereas each layer, as well as the whole scene, can be translated, rotated, and scaled in 3D space. User-selected edge colors can be used to highlight important paths, while node positioning, coloring, and resizing can be adjusted on-the-fly. In its current version, Arena3Dweb supports weighted and unweighted, directed and undirected multi-edge networks. The application is written in R, Shiny, and JavaScript. We demonstrate the old and new functionality of Arena3Dweb using different use-case scenarios

Trauma and Repair in the Museum: An Introduction

This introduction to the special issue on ‘Trauma and Repair in the Museum’ outlines the issues around reparation that surround the modern museum due to the traumatic legacies of coloniality. Timothy P. Brown’s notion of how the trauma of displacement and dissociation effects both objects and communities is key to our consideration of the museum as symptomatic of trauma, as is Cathy Caruth’s reading of history as trauma. Referring to several artists’ practices, such as Lisa Reihana, Erika Tan, and especially Kader Attia’s concept of repair, as well as a number of museological approaches to restitution, we expand on the complexities of on-going coloniality and its implication with museum as institutions, practices of collection and display, and highly charged psychoactive spaces. Eve Sedgwick Kosofsky’s re-reading of Melanie Klein’s notion of reparation allows us to posit a form of decolonial repair that involves the assembling of damaged part-objects into ‘something like a whole [but] not necessarily like any preexisting whole ’ (2002:128, original emphasis). This approach enables a reckoning with trauma and its legacies that keeps them visible without out-ruling processes of reparation

Four-Year Overview of Winter Colony Losses in Greece: Citizen Science Evidence That Transitioning to Organic Beekeeping Practices Reduces Colony Losses

The honey bee is one of the most important pollinators with a close relationship to humans. The questionnaire from the non-governmental association “COLOSS”, answered by beekeepers around the world, is a valuable tool for monitoring and analyzing factors involved in overwintering losses, as well as for understanding the evolution of the beekeeping sector over the years. Between 2018–2021, Greece’s participation in this survey involved collecting data from 752 beekeepers and 81,903 hives, from almost the whole country, with a stable balance between professional/non-professional participants and hives, providing a solid representation of the beekeeping practices and winter losses during this period. The results of this study identify a transition towards more natural beekeeping practices concomitant with a significant decrease in winter losses (average losses in 2018: 22.3% and 2019: 24%, dropped in 2020: 14.4% and 2021: 15.3%). Indeed, some factors, such as the increased use of natural landscapes for honey production (from 66.7% usage in 2018 to 76.3% in 2021) and the reduction in the exclusive use of synthetic acaricides (from 24.7% usage in 2018 to 6.7% in 2021) seem to have a significant impact on hive survival. Although these correlations remain to be confirmed experimentally, our study shows that Greek beekeepers follow recommendations and policies toward more sustainable practices. In the future, these trends could be further analyzed and integrated into training programs to strengthen the cooperation and information exchange between citizens and science

Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration.

Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3Dweb supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection), while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape app has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org

Visualizing metagenomic and metatranscriptomic data: A comprehensive review.

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively

Assessment of DNA Topoisomerase I Unwinding Activity, Radical Scavenging Capacity, and Inhibition of Breast Cancer Cell Viability of <i>N</i>-alkyl-acridones and <i>N</i>,<i>N′</i>-dialkyl-9,9′-biacridylidenes

The anticancer activity of acridone derivatives has attracted increasing interest, therefore, a variety of substituted analogs belonging to this family have been developed and evaluated for their anti-cancer properties. A series of N-alkyl-acridones 1&#8722;6 and N,N&#8242;-dialkyl-9,9&#8242;-biacridylidenes 7&#8722;12 with variable alkyl chains were examined for their topoisomerase I activity at neutral and acidic conditions as well as for their binding capacity to calf thymus and possible radical trapping antioxidant activity. It was found that at a neutral pH, topoisomerase I activity of both classes of compounds was similar, while under acidic conditions, enhanced intercalation was observed. N-alkyl-acridone derivatives 1&#8722;6 exhibited stronger, dose-dependent, cytotoxic activity against MCF-7 human breast epithelial cancer cells than N,N&#8242;-dialkyl-9,9&#8242;-biacridylidenes 7&#8722;12, revealing that conjugation of the heteroaromatic system plays a significant role on the effective distribution of the compound in the intracellular environment. Cellular investigation of long alkyl derivatives against cell migration exhibited 40&#8722;50% wound healing effects and cytoplasm diffusion, while compounds with shorter alkyl chains were accumulated both in the nucleus and cytoplasm. All N,N&#8242;-dialkyl-9,9&#8242;-biacridylidenes showed unexpected high scavenging activity towards DPPH or ABTS radicals which may be explained by higher stabilization of radical cations by the extended conjugation of heteroaromatic ring system