Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

Brain Radiation Information Data Exchange (BRIDE): Integration of experimental data from low-dose ionising radiation research for pathway discovery

Background: The underlying molecular processes representing stress responses to low-dose ionising radiation (LDIR) in mammals are just beginning to be understood. In particular, LDIR effects on the brain and their possible association with neurodegenerative disease are currently being explored using omics technologies. Results: We describe a light-weight approach for the storage, analysis and distribution of relevant LDIR omics datasets. The data integration platform, called BRIDE, contains information from the literature as well as experimental information from transcriptomics and proteomics studies. It deploys a hybrid, distributed solution using both local storage and cloud technology. Conclusions: BRIDE can act as a knowledge broker for LDIR researchers, to facilitate molecular research on the systems biology of LDIR response in mammals. Its flexible design can capture a range of experimental information for genomics, epigenomics, transcriptomics, and proteomics. The data collection is available at:

A Strong Seasonality Pattern for Covid-19 Incidence Rates Modulated by UV Radiation Levels

The Covid-19 pandemic has required nonpharmaceutical interventions, primarily physical distancing, personal hygiene and face mask use, to limit community transmission, irrespective of seasons. In fact, the seasonality attributes of this pandemic remain one of its biggest unknowns. Early studies based on past experience from respiratory diseases focused on temperature or humidity, with disappointing results. Our hypothesis that ultraviolet (UV) radiation levels might be a factor and a more appropriate parameter has emerged as an alternative to assess seasonality and exploit it for public health policies. Using geographical, socioeconomic and epidemiological criteria, we selected twelve North-equatorial-South countries with similar characteristics. We then obtained UV levels, mobility and Covid-19 daily incidence rates for nearly the entire 2020. Using machine learning, we demonstrated that UV radiation strongly associated with incidence rates, more so than mobility did, indicating that UV is a key seasonality indicator for Covid-19, irrespective of the initial conditions of the epidemic. Our findings can inform the implementation of public health emergency measures, partly based on seasons in the Northern and Southern Hemispheres, as the pandemic unfolds into 2021

BRIDE v2: A Validated Collection of Genes Involved in the Mammalian Brain Response to Low-Dose Ionizing Radiation

There is significant interest in the response of the mammalian brain to low-dose ionizing radiation (LDIR), mainly examined by gene or protein expression, with applications in radiation safety on Earth, the atmosphere and outer space. Potential associations of molecular-level responses with sensory or cognitive defects and neurodegenerative diseases are currently under investigation. Previously, we have described a light-weight approach for the storage, analysis and distribution of relevant datasets, with the platform BRIDE. We have re-implemented the platform as BRIDE v2 on the cloud, using the bioinformatics infrastructure ELIXIR. We connected the annotated list of 3174 unique gene records with modern omics resources for downstream computational analysis. BRIDE v2 is a cloud-based platform with capabilities that enable researchers to extract, analyze, visualize as well as export the gene collection. The resource is freely available online at

Learning Analytics on YouTube Educational Videos: Exploring Sentiment Analysis Methods and Topic Clustering

The popularity of social media is continuously growing, as it endeavors to bridge the gap in communication between individuals. YouTube, one of the most well-known social media platforms with millions of users, stands out due to its remarkable ability to facilitate communication through the exchange of video content. Despite its primary purpose being entertainment, YouTube also offers individuals the valuable opportunity to learn from its vast array of educational content. The primary objective of this study is to explore the sentiments of YouTube learners by analyzing their comments on educational YouTube videos. A total of 167,987 comments were extracted and processed from educational YouTube channels through the YouTube Data API and Google Sheets. Lexicon-based sentiment analysis was conducted using two different methods, VADER and TextBlob, with the aim of detecting the prevailing sentiment. The sentiment analysis results revealed that the dominant sentiment expressed in the comments was neutral, followed by positive sentiment, while negative sentiment was the least common. VADER and TextBlob algorithms produced comparable results. Nevertheless, TextBlob yielded higher scores in both positive and negative sentiments, whereas VADER detected a greater number of neutral statements. Furthermore, the Latent Dirichlet Allocation (LDA) topic clustering outcomes shed light on various video attributes that potentially influence viewers’ experiences. These attributes included animation, music, and the conveyed messages within the videos. These findings make a significant contribution to ongoing research efforts aimed at understanding the educational advantages of YouTube and discerning viewers’ preferences regarding video components and educational topics

CGG toolkit: Software components for computational genomics.

Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release

CGG toolkit: Software components for computational genomics.

Acknowledgements: We recognize multiple contributions by former members of the CGG and other colleagues who have contributed to the testing and use of the mentioned software. Most of the original development was by AJE and CAO (DifFuse, GeneRAGE, Tribe-MCL), AJE and VJP (GeneCAST) and AJE and CAO (CoGenT/++, TRIBES/OFAM). Other members of CGG who have contributed to additional components (BioLayout, MagicMatch) can be identified as co-authors in the original manuscripts. DA and PJJ have acted as curators and test-drivers for CoGenT and CoGenT++ frameworks. DV and CAO reimplemented and launched the GitHub versions as v1.0.1 and tested clustt_utils. IB with II (specifically GeneCAST, DifFuse) and CK with AC (specifically MagicMatch, cogent_utils) helped with testing and validation phases of the current versions.Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release

Information System for Symptom Diagnosis and Improvement of Attention Deficit Hyperactivity Disorder: Protocol for a Nonrandomized Controlled Pilot Study

BackgroundAttention deficit hyperactivity disorder (ADHD) is one of the most common neurodevelopmental disorders during childhood; however, the diagnosis procedure remains challenging, as it is nonstandardized, multiparametric, and highly dependent on subjective evaluation of the perceived behavior. ObjectiveTo address the challenges of existing procedures for ADHD diagnosis, the ADHD360 project aims to develop a platform for (1) early detection of ADHD by assessing the user’s likelihood of having ADHD characteristics and (2) providing complementary training for ADHD management. MethodsA 2-phase nonrandomized controlled pilot study was designed to evaluate the ADHD360 platform, including ADHD and non-ADHD participants aged 7 to 16 years. At the first stage, an initial neuropsychological evaluation along with an interaction with the serious game developed (“Pizza on Time”) for approximately 30-45 minutes is performed. Subsequently, a 2-week behavior monitoring of the participants through the mADHD360 app is planned after a telephone conversation between the participants’ parents and the psychologist, where the existence of any behaviors characteristic of ADHD that affect daily functioning is assessed. Once behavior monitoring is complete, the research team invites the participants to the second stage, where they play the game for a mean duration of 10 weeks (2 times per week). Once the serious game is finished, a second round of behavior monitoring is performed following the same procedures as the initial one. During the study, gameplay data were collected and preprocessed. The protocol of the pilot trials was initially designed for in-person participation, but after the COVID-19 outbreak, it was adjusted for remote participation. State-of-the-art machine learning (ML) algorithms were used to analyze labeled gameplay data aiming to detect discriminative gameplay patterns among the 2 groups (ADHD and non-ADHD) and estimate a player’s likelihood of having ADHD characteristics. A schema including a train-test splitting with a 75:25 split ratio, k-fold cross-validation with k=3, an ML pipeline, and data evaluation were designed. ResultsA total of 43 participants were recruited for this study, where 18 were diagnosed with ADHD and the remaining 25 were controls. Initial neuropsychological assessment confirmed that the participants in the ADHD group showed a deviation from the participants without ADHD characteristics. A preliminary analysis of collected data consisting of 30 gameplay sessions showed that the trained ML models achieve high performance (ie, accuracy up to 0.85) in correctly predicting the users’ labels (ADHD or non-ADHD) from their gameplay session on the ADHD360 platform. ConclusionsADHD360 is characterized by its notable capacity to discriminate player gameplay behavior as either ADHD or non-ADHD. Therefore, the ADHD360 platform could be a valuable complementary tool for early ADHD detection. Trial RegistrationClinicalTrials.gov NCT04362982; https://clinicaltrials.gov/ct2/show/NCT04362982 International Registered Report Identifier (IRRID)RR1-10.2196/4018