Literature mining and network analysis in Biology

Η παρούσα διπλωματική παρουσιάζει το OnTheFly2.0, ένα διαδικτυακό εργαλείο που επικεντρώνεται στην εξαγωγή και επακόλουθη ανάλυση βιοϊατρικών όρων από μεμονωμένα αρχεία. Συγκεκριμένα, το OnTheFly2.0 υποστηρίζει πολλούς διαφορετικούς επιτρέποντας τον παράλληλο χειρισμό τους. Μέσω της ενσωμάτωσης της υπηρεσίας EXTRACT υλοποιείται η Αναγνώριση Ονοματικών Οντοτήτων (Named Entity Recognition) για γονίδια/πρωτεΐνες, χημικές ουσίες, οργανισμούς, ιστούς, περιβάλλοντα, ασθένειες, φαινοτύπους και όρους οντολογίας γονιδίων (Gene Ontology terms), καθώς και η δημιουργία αναδυόμενων παραθύρων που παρέχουν πληροφορίες για τον αναγνωρισμένο όρο, συνοδευόμενες από σύνδεσμο για διάφορες βάσεις δεδομένων. Οι αναγνωρισμένες πρωτεΐνες, τα γονίδια και οι χημικές ουσίες μπορούν να επεξεργαστούν περαιτέρω μέσω αναλύσεων εμπλουτισμού για τη λειτουργικότητα και τη βιβλιογραφία ή να συσχετιστούν με ασθένειες και πρωτεϊνικές δομές. Τέλος, είναι δυνατή η απεικόνιση αλληλεπιδράσεων μεταξύ πρωτεϊνών ή μεταξύ πρωτεϊνών και χημικών ουσιών μέσω της δημιουργίας διαδραστικών δικτύων από τις βάσεις STRING και STITCH αντίστοιχα. Το OnTheFly2.0 υποστηρίζει 197 διαφορετικά είδη οργανισμών και είναι διαθέσιμο στον παρακάτω σύνδεσμο: http://onthefly.pavlopouloslab.info.The particular thesis presents OnTheFly2.0, a web-based, versatile tool dedicated to the extraction and subsequent analysis of biomedical terms from individual files. More specifically, OnTheFly2.0 supports different file formats, enabling simultaneous file handling. The integration of the EXTRACT tagging service allows the implementation of Named Entity Recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and Gene Ontology terms, as well as the generation of popup windows which provide concise, context related information about the identified term, accompanied by links to various databases. Once named entities, such as proteins, genes and chemicals are identified, they can be further explored via functional and publication enrichment analysis or be associated with diseases and protein domains reporting from protein family databases. Finally, visualization of protein-protein and protein-chemical associations is possible through the generation of interactive networks from the STRING and STITCH services, respectively. OnTheFly2.0 currently supports 197 species and is available at http://onthefly.pavlopouloslab.info

Sex difference and intra-operative tidal volume: Insights from the LAS VEGAS study

BACKGROUND: One key element of lung-protective ventilation is the use of a low tidal volume (VT). A sex difference in use of low tidal volume ventilation (LTVV) has been described in critically ill ICU patients.OBJECTIVES: The aim of this study was to determine whether a sex difference in use of LTVV also exists in operating room patients, and if present what factors drive this difference.DESIGN, PATIENTS AND SETTING: This is a posthoc analysis of LAS VEGAS, a 1-week worldwide observational study in adults requiring intra-operative ventilation during general anaesthesia for surgery in 146 hospitals in 29 countries.MAIN OUTCOME MEASURES: Women and men were compared with respect to use of LTVV, defined as VT of 8 ml kg-1 or less predicted bodyweight (PBW). A VT was deemed 'default' if the set VT was a round number. A mediation analysis assessed which factors may explain the sex difference in use of LTVV during intra-operative ventilation.RESULTS: This analysis includes 9864 patients, of whom 5425 (55%) were women. A default VT was often set, both in women and men; mode VT was 500 ml. Median [IQR] VT was higher in women than in men (8.6 [7.7 to 9.6] vs. 7.6 [6.8 to 8.4] ml kg-1 PBW, P < 0.001). Compared with men, women were twice as likely not to receive LTVV [68.8 vs. 36.0%; relative risk ratio 2.1 (95% CI 1.9 to 2.1), P < 0.001]. In the mediation analysis, patients' height and actual body weight (ABW) explained 81 and 18% of the sex difference in use of LTVV, respectively; it was not explained by the use of a default VT.CONCLUSION: In this worldwide cohort of patients receiving intra-operative ventilation during general anaesthesia for surgery, women received a higher VT than men during intra-operative ventilation. The risk for a female not to receive LTVV during surgery was double that of males. Height and ABW were the two mediators of the sex difference in use of LTVV.TRIAL REGISTRATION: The study was registered at Clinicaltrials.gov, NCT01601223

A survey of soft cheeses in Greek retail outlets highlights a low prevalence of Listeria spp.

Recently, the European Food Safety Authority proposed that each EU member state should conduct a survey of Listeria monocytogenes in soft cheeses for sale in retail outlets. Hence, retail samples of soft cheeses in Greece (n = 137) were analyzed qualitatively and quantitatively for both L. monocytogenes and other Listeria spp., as well as for pH and a (w). None of the cheeses analyzed were found positive for L. monocytogenes (0%; 95% confidence interval (CI) = 0.0-2.2%). Three samples (2.2%; 95% CI = 0.5-6.3%) were positive for other Listeria spp., with populations ranging from < 5 to 4.5 x 10(2) CFU g(-1). Although soft cheeses are regarded as foods that permit the proliferation of L. monocytogenes, 15.4% of the whey cheeses tested had pH values a parts per thousand currency sign4.4 and 29% of the interior mold-ripened cheeses had a (w) values a parts per thousand currency sign0.92. Such low pH values for whey cheeses are unexpected, based on their manufacturing technology, and are associated with lower quality and reduced shelf life. Nonetheless, in the present survey, the percentage of whey cheeses in the Greek retail market exhibiting unusually low pH values or testing positive for Listeria spp. was much lower compared to the respective percentages reported from studies conducted in the 1990s. The absence of L. monocytogenes in the tested cheeses undoubtedly constitutes an encouraging result with respect to the safety of soft cheeses in the Greek retail market. However, the presence of other Listeria spp. in three of the tested samples implies that L. monocytogenes would, most likely, also be present in the food-processing or retail-handling environments of these products. Therefore, cheese manufacturers and retail handlers should continue or even intensify the application of all necessary measures with the aim of preventing food contamination

Biomolecule and Bioentity Interaction Databases in Systems Biology:A Comprehensive Review

Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology

OnTheFly(2.0): a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analyzing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly(2.0), a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images. OnTheFly(2.0) can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform named entity recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms. Multiple files can be analyzed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein-protein and protein-chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly(2.0) currently supports 197 species and is available at http://bib.fleming.gr:3838/OnTheFly/and http://onthefly.pavlopouloslab.info

Association between night-time surgery and occurrence of intraoperative adverse events and postoperative pulmonary complications

Background: The aim of this post hoc analysis of a large cohort study was to evaluate the association between night-time surgery and the occurrence of intraoperative adverse events (AEs) and postoperative pulmonary complications (PPCs). Methods: LAS VEGAS (Local Assessment of Ventilatory Management During General Anesthesia for Surgery) was a prospective international 1-week study that enrolled adult patients undergoing surgical procedures with general anaesthesia and mechanical ventilation in 146 hospitals across 29 countries. Surgeries were defined as occurring during 'daytime' when induction of anaesthesia was between 8: 00 AM and 7: 59 PM, and as 'night-time' when induction was between 8: 00 PM and 7: 59 AM. Results: Of 9861 included patients, 555 (5.6%) underwent surgery during night-time. The proportion of patients who developed intraoperative AEs was higher during night-time surgery in unmatched (43.6% vs 34.1%; P<0.001) and propensity-matched analyses (43.7% vs 36.8%; P = 0.029). PPCs also occurred more often in patients who underwent night-time surgery (14% vs 10%; P = 0.004) in an unmatched cohort analysis, although not in a propensity-matched analysis (13.8% vs 11.8%; P = 0.39). In a multivariable regression model, including patient characteristics and types of surgery and anaesthesia, night-time surgery was independently associated with a higher incidence of intraoperative AEs (odds ratio: 1.44; 95% confidence interval: 1.09-1.90; P = 0.01), but not with a higher incidence of PPCs (odds ratio: 1.32; 95% confidence interval: 0.89-1.90; P = 0.15). Conclusions: Intraoperative adverse events and postoperative pulmonary complications occurred more often in patients undergoing night-time surgery. Imbalances in patients' clinical characteristics, types of surgery, and intraoperative management at night-time partially explained the higher incidence of postoperative pulmonary complications, but not the higher incidence of adverse events