Nikolas Dovrolis

• Computer Science
• PostDoc Position at Democritus University of Thrace

Peptides, either as protein fragments or as naturally occurring entities are characterized by their sequence and function features. Many times the researchers need to massively manage peptide lists concerning protein identification, biomarker discovery, bioactivity, immune response or other functionalities. We present a web server that manages pept...

Reusable educational resources became increasingly important for enhancing learning and teaching experiences, particularly in the medical domain where resources are particularly expensive to produce. While interoperability across educational resources metadata repositories is yet limited to the heterogeneity of metadata standards and interface mech...

Research in technology-enhanced learning (TEL) throughout the last decade has largely focused on sharing and reusing educational resources and data. This effort has led to a fragmented landscape of competing metadata schemas, such as IEEE LOM or ADL SCORM, and interface mechanisms, such as OAI-PMH, SQI and REST-ful services in general. More recentl...

Educational content is often shared among different educators and is enriched, adapted and in general repurposed so that it can be re-used in different contexts. This paper presents the MetaMorphosis+ environment for publishing, sharing and repurposing educational content in medical education. The environment meshes the paradigms of social Web and...

Background Sphingosine-1-phosphate (S1P) receptor (S1PR) modulators (S1PRMs) block chemotaxis of cells of immunity to the locus of inflammation. S1PRM effectiveness depends on the extent of the pathway activation. We explored the contribution of colonic stromal cells (CSC) to S1P production in patients with ulcerative colitis (UC) and healthy contr...

Background Ustekinumab, a monoclonal antibody targeting the p40 subunit of interleukin (IL)-12 and IL-23, is a promising therapeutic approach in patients with ulcerative colitis (UC), but predicting treatment response remains a challenge. In the present study, we focused to identify prognostic response markers to ustekinumab in patients with active...

Background/Objectives: The role of the gut microbiome in cancer biology has become an increasingly prominent area of research, particularly regarding the role of microbial metabolites and their receptors (MMRs). These metabolites, through the various gut–organ axes, have been proven to influence several pathogenetic mechanisms. This study conducted...

Alcohol use disorder’s complexity arises from genetic and environmental factors, with alcohol metabolism genes and neurotransmitter pathways being critical. This study aims to analyze synaptic plasticity gene expression changes in individuals with AUD in order to study their contribution to AUD development and to identify potential biomarkers of tr...

Background Ulcerative colitis (UC) increases the risk for venous thromboembolism. Tissue factor (TF) initiates the extrinsic coagulation pathway (ECP). Aims To investigate the correlation of UC severity with latent ECP activation and TF expression in primary colonic stromal cells (PCSC). Methods In plasma of 38 UC patients (31 males, disease dura...

Background and aims: Monocyte recruitment in the lamina propria and inflammatory phenotype driven by the mucosal microenvironment is critical for the pathogenesis of inflammatory bowel disease. However, the stimuli responsible remain largely unknown. Recent works have focused on stromal cells, the main steady-state cellular component in tissue, as...

It has recently been proposed that the study of microbial dynamics in humans may gain insights from island biogeographical theory. Here, we test whether the diversity of the intratumoral microbiota of colorectal cancer tumors (CRC) follows a power law with tumor size akin to the island species-area relationship. We confirm a direct correlation betw...

Subgenomic flaviviral RNAs (sfRNAs) are small non-coding products of the incomplete degradation of viral genomic RNA. They accumulate during flaviviral infection and have been associated with many functional roles inside the host cell. Studies so far have demonstrated that sfRNA plays a crucial role in determining West Nile virus (WNV) pathogenicit...

Introduction: Optimizing treatment with biological agents is an ideal goal for patients with ulcerative colitis (UC). Recent data suggest that mucosal inflammation patterns and serum cytokine profiles differ between patients who respond and those who do not. Ustekinumab, a monoclonal antibody targeting the p40 subunit of interleukin (IL)-12 and IL-...

Background Oncostatin-M (OSM) is associated with antitumor necrosis factor (anti-TNF)-α resistance in inflammatory bowel disease (IBD) and fibrosis in inflammatory diseases. We studied the expression of OSM and its receptors (OSMR, gp130) on intestinal subepithelial myofibroblasts (SEMFs) and the effect of OSM stimulation on SEMFs. Methods The mRN...

Pancreatic cancer (PC) ranks as the seventh leading cause of cancer-related deaths, with approximately 500,000 new cases reported in 2020. Existing strategies for early PC detection primarily target individuals at high risk of developing the disease. Nevertheless, there is a pressing need to identify innovative clinical approaches and personalized...

Metabolites produced by dysbiotic intestinal microbiota can influence disease pathophysiology by participating in ligand–receptor interactions. Our aim was to investigate the differential expression of metabolite receptor (MR) genes between inflammatory bowel disease (IBD), healthy individuals (HIs), and disease controls in order to identify possib...

Background Ulcerative colitis (UC) is associated with an increased risk of venous thromboembolism. We investigated the correlation of UC severity with latent activation of the extrinsic coagulation pathway and colonic stromal tissue factor (TF) expression. Methods Plasma exosomes, microparticles (EM), TF protein, activities of EM-bound TF (EM-TF)...

Background The rise of microbiome-focused research, reveals that the intrafamilial microbiome can be linked to specific genetic traits and be studied for its behavior during dysbiosis. It has been reported that microbiota composition is shared between cohabitating individualsand displays patterns of similarity that differ between families. Based on...

Simple Summary Clear cell renal cell carcinoma (ccRCC) is the most common form of renal cancer. Currently, treatment of metastatic ccRCC (mccRCC) is challenging despite the use of modern immunotherapy options. In order for the patient to receive the most effective treatment among the available pharmaceutical agents, there is a constant need for bio...

The role of probiotic supplementation in type 2 diabetes (T2D) treatment is controversial. The present study aimed to assess the effects of a multi-strain probiotic supplement (LactoLevureR (containing Lactobacillus acidophilus, Lactobacillus plantarum, Bifidobacterium lactis, and Saccharomyces boulardii)) over 6 months, primarily on glycemic contr...

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia worldwide and is characterized by a high risk of thromboembolism, ischemic stroke, and fatality. The precise molecular mechanisms of AF pathogenesis remain unclear. The purpose of this study was to use bioinformatics tools to identify novel key genes in AF, provide deeper insights into the...

Background: Pediatric inflammatory bowel disease (IBD) is a chronic inflammatory intestinal disease that affects both children and adolescents. Symptoms can significantly affect a child's growth, development, and quality of life, making early diagnosis and effective management crucial. This study focuses on treatment-naïve pediatric IBD patients a...

IntroductionHeart failure (HF) is a complex clinical syndrome leading to high morbidity. In this study, we aimed to identify the gene expression and protein signature of HF main causes, namely dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM).Methods Omics data were accessed through GEO repository for transcriptomic and PRIDE repositor...

Background Inflammatory Bowel Disease (IBD) is a chronic inflammatory condition of the alimentary tract, primarily manifested as Crohn’s disease and Ulcerative colitis. Dysbiosis of the intestinal microbial microflora is a well-established characteristic of IBD. The microbiota metabolism ends in the production of several metabolites that participat...

Alterations of the gut microbiome in cases of colorectal cancer (CRC) hint at the involvement of host–microbe interactions in the onset and progression of CRC and also, possibly, provide novel ways to detect and prevent CRC early. The aim of the present study was to evaluate whether the oral and fecal microbiomes of an individual can be suitable fo...

Introduction Extracellular matrix turnover, a ubiquitous dynamic biological process, can be diverted to fibrosis. The latter can affect the intestine as a serious complication of Inflammatory Bowel Diseases (IBD) and is resistant to current pharmacological interventions. It embosses the need for out-of-the-box approaches to identify and target mole...

Colorectal cancer represents a leading cause of cancer-related morbidity and mortality. Despite improvements, chemotherapy remains the backbone of colorectal cancer treatment. The aim of this study is to investigate the variation of circulating microRNA expression profiles and the response to irinotecan-based treatment in metastatic colorectal canc...

Hepatitis C virus (HCV) core protein is a multifunctional protein that is involved in the proliferation, inflammation, and apoptosis mechanism of hepatocytes. HCV core protein genetic variability has been implicated in various outcomes of HCV pathology and treatment. In the present study, we aimed to analyze the role of the HCV core protein in tumo...

Background/aim: Breast cancer is a leading worldwide cause of female cancer-related morbidity and mortality. Since molecular characteristics increasingly guide disease management, demystifying breast tumor miRNA signature emerges as an essential step toward personalized care. This study aimed to investigate the variations in circulating miRNA expr...

COVID-19 is a systemic disease affecting tissues and organs, including and beyond the lung. Apart from the current pandemic context, we also have vastly inadequate knowledge of consequences of repeated exposures to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, in multiple organ systems and the whole organ...

Background Clinical classification of autistic patients based on current WHO criteria provides a valuable but simplified depiction of the true nature of the disorder. Our goal is to determine the biology of the disorder and the ASD-associated genes that lead to differences in the severity and variability of clinical features, which can enhance the...

Hepatitis C virus (HCV) core protein is a multifunctional protein that is involved in proliferation, inflammation and apoptosis mechanism of hepatocytes. HCV core protein genetic variability has been implicated in various outcomes of HCV pathology and treatment. In the present study, we aimed to analyze the role of HCV core protein in tumor necrosi...

Mosquitoes are the most important vectors of emerging infectious diseases. During the past decade, our understanding of the diversity of viruses they carry has greatly expanded. Most of these viruses are considered mosquito-specific but there is increasing evidence that these viruses may affect the vector competence of mosquitoes. Metagenomics appr...

Background: Gatrointestinal stromal tumors (GISTs) are the main mesenchymal tumors found in the gastrointestinal system. GISTs clinical phenotypes differ significantly and their molecular basis is not yet completely known. microRNAs (miRNAs) have been involved in carcinogenesis pathways by regulating gene expression at post-transcriptional level....

Alzheimer’s Disease (AD) is a neurodegenerative disorder characterized by a progressive loss of memory and a general cognitive decline leading to dementia. AD is characterized by changes in the behavior of the genome and can be traced across multiple brain regions and cell types. It is mainly associated with β-amyloid deposits and tau protein misfo...

Biting midges (Culicoides) are vectors of arboviruses of both veterinary and medical importance. The surge of emerging and re-emerging vector borne-diseases and their expansion in geographical areas affected by climate change has increased the importance of understanding their capacity to contribute to novel and emerging infectious diseases. The st...

Background The inflammatory bowel disease (iBD) etiology remain elusive and both genetic and environmental factors have been implicated in the establishment of systemic inflammatory reactions that typify IBD. A basic, modifiable environmental factor is the gut microbiota and dysbiosis seems to be a key factor in IBD pathogenesis. Nowadays, it is we...

Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and pipelines have been developed, to date, for the identification and assembly of viral genomes. Assembly pipeline...

Background Improving treatment outcomes with biological therapy is a demanding current need for patients with inflammatory bowel disease. Discovery of pretreatment prognostic indicators of response may facilitate patient selection and increase long-term remission rates. We aimed to identify baseline mucosal gene expression profiles with predictive...

The field of metagenomics (study of a system’s microbiome) comes with various questions researchers are called to answer. Questions about the microbiota’s identity, the interactions of the participating bacteria, fungi, and viruses and their associations with health and disease. Nowadays, the answers to these questions are revealed via next-generat...

In the present study, the course of SARS‐CoV‐2 natural infection in two asymptomatic cats, which were negative for immunosuppressive retroviral infections, is investigated. The source of the virus for the cats was their COVID‐19‐affected owner, with whom they were in continuous proximity in a small household setting. The owner’s signs included fati...

In the present study, the course of SARS-CoV-2 natural infection in two asymptomatic cats is investigated. The source of the virus for the cats was their COVID-19-affected owner, with whom they were in continuous proximity, in a small household setting. Oropharyngeal and fecal swabs were collected to investigate the course of SARS-CoV-2 RNA concent...

Background Mosquitoes are the most important vectors of emerging infectious diseases. During the past decade, our understanding of the diversity of viruses they carry has greatly expanded. Most of these viruses are considered mosquito-specific, while there is increasing evidence that these viruses may affect mosquito vector potential. Metagenomics...

SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus 2) is a novel Coronavirus responsible for the Coronavirus Disease‐2019 (COVID‐19) pandemic. Chains of infections starting from various countries worldwide seeded the outbreak of COVID‐19 in Athens, capital city of Greece. Full‐genome analysis of isolates from Athens’ hospitals and other heal...

Irritable bowel syndrome (IBS) is a functional gut brain gastrointestinal (GI) disorder, typically accompanied by constipation or diarrhea, usually without any organic evidence. The prevalence of IBS is rather high of about 10-15% (10, 1 % according to Rome III and 4, 1% according to Rome IV, Enck P. et al 2016, Sperber A.D. et al 2020, Black C.J....

Background Several studies correlated elevated B-cell activating factor (BAFF) levels and its polymorphisms (SNPs) in patients with autoimmunity. Limited data existed regarding the role of BAFF in Crohn's Disease (CD) susceptibility and/or treatment response to infliximab. Aim This study aims to evaluate BAFF expression in CD patients, investigate...

In the era of emergence and re-emergence of vector-borne diseases, a high throughput trap-based insect monitoring is essential for the identification of invasive species, study of mosquito populations and risk assessment of disease outbreaks. Insect DNA metabarcoding technology has emerged as a highly promising methodology for unbiased and large-sc...

Background Anti-TNF agents have been a cornerstone of IBD therapy; however, response to treatment has been variable, and clinically applicable biomarkers are urgently needed. We hypothesized that the type I and type II interferon (IFN) signatures may be a confounding factor for response to antitumor necrosis factor (TNF) treatment via interactions...

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel Coronavirus responsible for the Coronavirus Disease-2019 (COVID-19) pandemic. Since the beginning of the pandemic, the virus has spread in almost the entire world. Tracing and tracking virus international and local transmission has been an enormous challenge. Chains of infectio...

Even though anti-TNF therapy significantly improves the rates of remission in inflammatory bowel disease (IBD) patients, there is a noticeable subgroup of patients who do not respond to treatment. Dysbiosis emerges as a key factor in IBD pathogenesis. The aim of the present study is to profile changes in the gut microbiome and transcriptome before...

Background: Crohn's disease (CD) and Ulcerative colitis (UC) are the two main entities of inflammatory bowel disease (IBD). Previous works have identified more than 200 risk factors (including loci and signaling pathways) in populations of predominantly European ancestry. Our study was conducted on an extended population-specific cohort of 573 Gre...

Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining...

Background Crohn’s disease (CD) and Ulcerative colitis (UC) are the two main entities of inflammatory bowel disease (IBD). Genome-wide association studies (GWAS) identified more than 200 risk loci in populations of predominantly European ancestry. Methods Here we report the GWAS study of IBD data from an extended cohort of 573 Greek IBD patients (...

Microflora dysbiosis is implicated in the pathophysiology of Crohn’s disease. This work analyzes differences in microbial communities and relevant metabolic pathways among the nonstricturing nonpenetrating (B1), stricturing (B2), and penetrating (B3) subphenotypes of Crohn’s disease vs healthy controls. We conducted a bioinformatics analysis using...

Background Crohn’s disease (CD) is an inflammatory bowel disease (IBD) of idiopathic nature with a heavy burden on the quality of patient life. In 2005 the Montreal World Congress of Gastroenterology introduced the behavioural B1 non‐stricturing non‐penetrating, B2 stricturing and B3 penetrating phenotypes. Today these phenotypes have been properly...

Almost 2500 years after Hippocrates' observations on health and its direct association to the gastrointestinal tract, a paradigm shift has recently occurred, making the gut and its symbionts (bacteria, fungi, archaea and viruses) a point of convergence for studies. It is nowadays well established that the gut microflora's compositional diversity re...

When faced with time- and money-consuming problems, new practices in pharmaceutical R&D arose when trying to alleviate them. Drug repositioning has great promise and when combined with today's computational power and intelligence it becomes more precise and potent. This work showcases current approaches of creating a computational pipeline for drug...

This paper presents work towards constructing a generic information model for comorbidities management. This involves the following conceptual steps: (a) develop an information model and ontology of the management of disease and comorbidities based on ground medical knowledge; (b) enrich the generic model to reflect current-state-of-the-art medical...

An important aspect of integrated care is the provision of personalized patient empowerment and decision support services, especially in case of the chronic patient with comorbidities. The paper discusses a blending of notions of social networks and semantic technologies in order to develop comprehensive personalized and dynamic models of the chron...

The accelerated development of the networked society throughout the last few years had a strong impact on the teaching and learning activities from the medical related domains. E-learning applications have become very popular and encouraged the shift from traditional training activities - having the teacher as a mediator, towards self-guided ones w...

mEducator 3.0 is a content sharing approach for medical education, based on Linked Data principles. Through standardization, it enables sharing and discovery of medical information. Overall the mEducator project seeks to address the following two different approaches, mEducator 2.0, based on web 2.0 and ad-hoc Application Programmers Interfaces (AP...

Research on interoperability of technology-enhanced learning (TEL) repositories throughout the last decade has led to a fragmented landscape of competing approaches, such as metadata schemas and interface mechanisms. However, so far Web-scale integration of resources is not facilitated, mainly due to the lack of take-up of shared principles, datase...

The development of new, high quality e-Learning resources has become increasingly important in medicine, as the online learning approach is used in most of the disciplines, specialities and teaching levels. Either a theoretical presentation or a clinical case, the creation process of any valuable didactical material involves a lot of effort and usu...

Past research aiming at interoperability within the Technology- Enhanced Learning (TEL) field has led to a fragmented landscape of competing metadata schemas and interface mechanisms. So far, Web-scale integration of resources is not facilitated, mainly due to the lack of take-up of shared principles, datasets and schemas. On the other hand, the Li...

The social Web has become an important trend during the last few years with a thriving number of social networking sites that currently address a variety of information needs. Following a first generation of human centered social networks, the notion of object-centered sociality has been introduced to describe the fact that strong social relationsh...

Educational content is often shared among different educators and is enriched, adapted and in general repurposed so that it can be re-used in different contexts. This paper exploits the various aspects of object-centered sociality that the educational resource can manifest in a participatory virtual community of authors and learners These social fa...

The two fundamental aims of managing educational resources are to enable resources to be reusable and interoperable and to enable Web-scale sharing of resources across learning communities. Currently, a variety of approaches have been proposed to expose and manage educational resources and their metadata on the Web. These are usually based on heter...

Educational content is often shared among different educators and is enriched, adapted, and, in general, repurposed so that it can be reused in different contexts. This paper discusses educational content and content repurposing in medical education, presenting different repurposing contexts. Finally, it proposes a novel approach to content repurpo...

Biomedical Engineering and Medical Informatics complete educational programs are offered throughout european institutions. Common curriculum and level of provided knowledge is trying to be reached through protocols and guidelines from international and European organizations. Educational material that used, shared and repurposed across institutions...

Educational content is often shared among different educators and is enriched, adapted and in general repurposed so that it can be re-used in different contexts. This paper discusses educational content and content repurposing in medical education, presenting different repurposing contexts. Finally, it proposes a novel approach to content repurposi...

Today there is an abundance of up-to-date highly specialised medical educational content created by medical and health related academic institutions and available in digital format on the internet. Such educational content includes learning objects of conventional types, content unique in medical education and a variety of alternative educational c...