microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites.

microRNAs (miRNAs) are central post-transcriptional gene expression regulators in healthy and diseased states. Despite decades of effort, deciphering miRNA targets remains challenging, leading to an incomplete miRNA interactome and partially elucidated miRNA functions. Here, we introduce microT-CNN, an avant-garde deep convolutional neural network model that moves the needle by integrating hundreds of tissue-matched (in-)direct experiments from 26 distinct cell types, corresponding to a unique training and evaluation set of >60 000 miRNA binding events and ~30 000 unique miRNA-gene target pairs.

Implementing the Global Leadership Initiative on Malnutrition (GLIM) criteria in Crohn's disease: Prevalence of malnutrition and association with clinical outcomes.

Background & Aims: Limited data exist regarding the implementation of the Global Leadership Initiative on Malnutrition (GLIM) criteria for diagnosing malnutrition in Crohn's disease (CD), and its association with CD prognosis. In the present study eighteen GLIM combinations and a combined one were implemented to identify differences in the prevalence of malnutrition and to investigate potential associations with clinical outcomes at 6 months.

Methods: Different methodologies to diagnose malnutrition were used at baseline, namely the Subjective Global Assessment (SGA), eighteen different combinations of phenotypic and etiologic GLIM criteria and a combined version based on all GLIM combinations (GLIMcv) to test differences in the estimated prevalence and outcomes' prognosis.

TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs.

TarBase is a reference database dedicated to produce, curate and deliver high quality experimentally-supported microRNA (miRNA) targets on protein-coding transcripts. In its latest version (v9.0, https://dianalab.

DIANA-microT 2023: including predicted targets of virally encoded miRNAs.

DIANA-microT-CDS is a state-of-the-art miRNA target prediction algorithm catering the scientific community since 2009. It is one of the first algorithms to predict miRNA binding sites in both the 3' Untranslated Region (3'-UTR) and the coding sequence (CDS) of transcripts, with increased performance. Its current version, DIANA-microT 2023 (www.

The natural history of COVID-19 in vaccinated inflammatory bowel disease patients.

Aim: Assess the characteristics of break through COVID-19 in Inflammatory Bowel Disease (IBD) patients, despite complete vaccination.

Methods: Patients who reported a COVID-19 at least 3 weeks after complete vaccination were asked to answer an on-line anonymous questionnaire which included patient and disease characteristics, vaccination history, and the evolution of COVID-19.

Results: Among 3240 IBD patients who reported complete vaccination between 1st May 2021 and 30thJune 2022, 402 (12.

Patients With Inflammatory Bowel Diseases Have Impaired Antibody Production After Anti-SARS-CoV-2 Vaccination: Results From a Panhellenic Registry.

Background: Four EMA-approved vaccines against SARS-CoV-2 are currently available. Data regarding antibody responses to initial vaccination regimens in patients with inflammatory bowel diseases (IBD) are limited.

Methods: We conducted a prospective, controlled, multicenter study in tertiary Greek IBD centers.

Poor performance of predictive equations to estimate resting energy expenditure in patients with Crohn's disease.

Studies exploring the accuracy of equations calculating Resting Energy Expenditure (REE) in patients with Crohn's disease are lacking. The aim of this study was to investigate the accuracy of REE predictive equations against indirect calorimetry in Crohn's disease patients. REE was measured using indirect calorimetry (mREE) after an overnight fasting.

Real-World Use and Adverse Events of SARS-CoV-2 Vaccination in Greek Patients with Inflammatory Bowel Disease.

Since inflammatory bowel disease (IBD) patients were excluded from vaccine authorization studies, limited knowledge exists regarding perceptions and unfavorable effects of COVID-19 vaccination in this group. We aimed to investigate the real-world use and adverse events (AEs) of COVID-19 vaccines in Greek IBD patients. Fully vaccinated IBD patients followed in Greek centers were invited to participate.

The natural history of COVID-19 in patients with inflammatory bowel disease: a nationwide study by the Hellenic Society for the study of IBD.

Objectives: COVID-19 has evolved into a global health crisis, variably affecting the management of patients with chronic illnesses. Patients with inflammatory bowel disease (IBD) may represent a vulnerable population due to frequent administration of immune-modifying treatments. We aimed to depict the natural history of COVID-19 infection in Greek patients with IBD at a nationwide level via unbiased reporting of all cases that were registered during the sequential waves of the pandemic.

Response to Anti-α4β7 Blockade in Patients With Ulcerative Colitis Is Associated With Distinct Mucosal Gene Expression Profiles at Baseline.

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 value for subsequent response to or failure of treatment with the monoclonal antibody against integrin α4β7, vedolizumab, in patients with active ulcerative colitis (UC).

Predictors of Response to Vedolizumab in Patients with Ulcerative Colitis: Results from the Greek VEDO-IBD Cohort.

Background: Optimization of treatment with biologics is currently an unmet need for patients with ulcerative colitis (UC). Real-world studies provide neutral estimates of drug efficacy and safety within unselected patient populations and allow for the recognition of specific characteristics that affect response to therapy.

Aims: We aimed to depict the efficacy of vedolizumab in patients with UC in a real-world setting and identify prognosticators of improved outcomes.

TL1A: A New Potential Target in the Treatment of Inflammatory Bowel Disease.

Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are chronic inflammatory diseases of the gastrointestinal tract. In the last few years, the development of biological agents targeting cytokines and receptors involved in IBD pathogenesis has led to better outcomes and has improved the course of the disease. Despite their effectiveness, drugs such as tumor necrosis factor (TNF) inhibitors, anti-Interleukin-12/23 and anti-integrins, do not induce a response in about one-third of patients, and 40% of patients lose response over time.

Application of Ultrasound Elastography for Assessing Intestinal Fibrosis in Inflammatory Bowel Disease: Fiction or Reality?

Background: Intestinal fibrosis and subsequent strictures represent an important burden in inflammatory bowel disease (IBD). Both the detection and evaluation of the degree of fibrosis in stricturing Crohn's disease (CD) are important when deciding the best therapeutic strategy (medical anti-inflammatory therapy, endoscopic dilation, surgery). Ultrasound elastography (USE) is a non-invasive technique that has been proposed in the field of IBD for evaluating intestinal stiffness as a biomarker of intestinal fibrosis.

Patients with Inflammatory Bowel Disease Are Not at Increased Risk of COVID-19: A Large Multinational Cohort Study.

The impact of COVID-19 on inflammatory bowel disease (IBD) patients under pharmacological immunosuppression is still not clearly understood. We investigated the incidence of COVID-19 and the impact of immunosuppression and containment measures on the risk of SARS-CoV-2 infection in a large IBD cohort, from a multicenter cohort from 21st of February to 30th of June, 2020. Ninety-seven patients with IBD (43 UC, 53 CD, one unclassified IBD) and concomitant COVID-19 over a total of 23,879 patients with IBD were enrolled in the study.

Early Intervention in Ulcerative Colitis: Ready for Prime Time?

Growing evidence shows that ulcerative colitis (UC) is a progressive disease similar to Crohn's disease (CD). The UC-related burden is often underestimated by physicians and a standard step-up therapeutic approach is preferred. However, in many patients with UC the disease activity is not adequately controlled by current management, leading to poor long-term prognosis.

Treat to target or 'treat to clear' in inflammatory bowel diseases: one step further?

Introduction: Inflammatory bowel diseases (IBD) are chronic and progressive diseases. Long-term complications are demolitive surgery and colon-rectal cancer. A 'treat to target' strategy, in which the treatment aims to achieve objective outcomes, has already been introduced in the management of chronic conditions as rheumatic diseases.

Endoscopy after surgery in inflammatory bowel disease: Crohn's disease recurrence and pouch surveillance.

Introduction: Crohn's disease (CD) and ulcerative colitis (UC) are immune-mediated disorders characterized by a chronic inflammation, with intermittent exacerbations of symptoms and inflammation. In both diseases, medical treatment has made revolutionary steps forward. Nevertheless, surgery is still required in many cases due to inefficacy of multiple medical therapies.

Targeting the gut layers in Crohn's disease: mucosal or transmural healing?

Introduction: Although the landmark of Crohn's Disease (CD) is the transmural inflammation, mucosal healing (MH), which is assessed by colonoscopy, is currently the gold standard of CD management. Transmural healing (TH) is a new concept evaluated by cross-sectional imaging (CSI) techniques, such as bowel ultrasound (US), computed tomography enterography (CTE), and magnetic resonance enterography (MRE). Little is known about the clinical significance of persisting mural disease and the predictive value of complete TH.

DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts.

DIANA-LncBase v3.0 (www.microrna.

Genetic analysis and clinical description of Greek patients with Peutz-Jeghers syndrome: Creation of a National Registry.

Peutz-Jeghers syndrome (PJS) is a rare autosomal dominant disorder caused by germline mutations in the STK11 tumor suppressor gene. PJS patients face a cumulative cancer risk as high as 93% for all sites combined. The present study reports the spectrum of STK11 mutations in eight families with clinical diagnosis of PJS, summarizes the clinical characteristics of sixteen mutation carriers and launches a National Registry for PJS in Greece.