Global Consequences of Liver Ischemia/Reperfusion Injury

Liver ischemia/reperfusion injury has been extensively studied during the last decades and has been implicated in the pathophysiology of many clinical entities following hepatic surgery and transplantation. Apart from its pivotal role in the pathogenesis of the organ’s post reperfusion injury, it has also been proposed as an underlying mechanism responsible for the dysfunction and injury of other organs as well. It seems that liver ischemia and reperfusion represent an event with “global” consequences that influence the function of many remote organs including the lung, kidney, intestine, pancreas, adrenals, and myocardium among others. The molecular and clinical manifestation of these remote organs injury may lead to the multiple organ dysfunction syndrome, frequently encountered in these patients. Remote organ injury seems to be in part the result of the oxidative burst and the inflammatory response following reperfusion. The present paper aims to review the existing literature regarding the proposed mechanisms of remote organ injury after liver ischemia and reperfusion

The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets

Cellular life depends on a complex web of functional associations between biomolecules. Among these associations, protein-protein interactions are particularly important due to their versatility, specificity and adaptability. The STRING database aims to integrate all known and predicted associations between proteins, including both physical interactions as well as functional associations. To achieve this, STRING collects and scores evidence from a number of sources: (i) automated text mining of the scientific literature, (ii) databases of interaction experiments and annotated complexes/pathways, (iii) computational interaction predictions from co-expression and from conserved genomic context and (iv) systematic transfers of interaction evidence from one organism to another. STRING aims for wide coverage; the upcoming version 11.5 of the resource will contain more than 14 000 organisms. In this update paper, we describe changes to the text-mining system, a new scoring-mode for physical interactions, as well as extensive user interface features for customizing, extending and sharing protein networks. In addition, we describe how to query STRING with genome-wide, experimental data, including the automated detection of enriched functionalities and potential biases in the user's query data. The STRING resource is available online, at https://string-db.org/

The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest

Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scattered across different database resources, experimental modalities and levels of mechanistic detail. The STRING database (https://string-db.org/) systematically collects and integrates protein-protein interactions-both physical interactions as well as functional associations. The data originate from a number of sources: automated text mining of the scientific literature, computational interaction predictions from co-expression, conserved genomic context, databases of interaction experiments and known complexes/pathways from curated sources. All of these interactions are critically assessed, scored, and subsequently automatically transferred to less well-studied organisms using hierarchical orthology information. The data can be accessed via the website, but also programmatically and via bulk downloads. The most recent developments in STRING (version 12.0) are: (i) it is now possible to create, browse and analyze a full interaction network for any novel genome of interest, by submitting its complement of encoded proteins, (ii) the co-expression channel now uses variational auto-encoders to predict interactions, and it covers two new sources, single-cell RNA-seq and experimental proteomics data and (iii) the confidence in each experimentally derived interaction is now estimated based on the detection method used, and communicated to the user in the web-interface. Furthermore, STRING continues to enhance its facilities for functional enrichment analysis, which are now fully available also for user-submitted genomes

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Handedness in ADHD: Meta-Analyses

Meta-analyses have shown that several neurodevelopmental and psychiatric disorders, such as autism spectrum disorder and schizophrenia, are associated with a higher prevalence of atypical (left-, non-right-, or mixed-) handedness. One neurodevelopmental disorder for which this association is unclear is attention deficit hyperactivity disorder (ADHD). Here, some empirical studies have found evidence for a higher prevalence of atypical handedness in individuals with ADHD compared to neurotypical individuals. However, other studies failed to establish such an association. Therefore, meta-analytic integration is critical to estimate whether or not there is an association between handedness and ADHD. We report the results of three meta-analyses (left-, mixed-, and non-right-handedness) comparing handedness in individuals with ADHD to controls (typically developing individuals). The results show evidence of a trend towards elevated levels of atypical handedness when it comes to differences in left- and mixed-handedness (p = 0.09 and p = 0.07, respectively), but do show clear evidence of elevated levels of non-right-handedness between individuals with ADHD and controls (p = 0.02). These findings are discussed in the context of the hypothesis that ADHD is a disorder in which mostly right-hemispheric brain networks are affected. Since right-handedness represents a dominance of the left motor cortex for fine motor behavior, such as writing, as well as a left-hemispheric dominance for language functions, and about 90% of individuals are right-handers, this hypothesis might explain why there is not stronger evidence for an association of left-handedness with ADHD. We suggest that the mechanisms involved in the pathogenesis of ADHD might show an overlap with the mechanisms involved in handedness strength, but not handedness direction. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature

Development of analytical strategies for the determination of olive fruit bioactive compounds using UPLC-HRMS and HPLC-DAD. Chemical characterization of kolovi lesvos variety as a case study

In this study, an overall survey regarding the determination of several bioactive compounds in olive fruit is presented. Two methodologies were developed, one UPLC-Q-TOF-MS method for the determination of olive fruit phenolic compounds and one HPLC-DAD methodology targeting the determination of pigments (chlorophylls and carotenoids), tocopherols (α-, β,-γ, δ-) and squalene. Target and suspect screening workflows were developed for the thorough fingerprinting of the phenolic fraction of olives. Both methods were validated, presenting excellent performance characteristics, and can be used as reliable tools for the monitoring of bioactive compounds in olive fruit samples. The developed methodologies were utilized to chemical characterize the fruits of the Kolovi olive variety, originating from the island of Lesvos, North Aegean Region, Greece. Twenty-five phenolic compounds were identified and quantified in Kolovi olives with verbascoside, hydroxytyrosol, oleacein and oleomissional found in significantly high concentrations. Moreover, 12 new bioactive compounds were identified in the samples using an in-house suspect database. The results of pigments analysis suggested that Kolovi variety should be characterized as low pigmentation, while the tocopherol and squalene content was relatively high compared to other olive varieties. The characterization of Kolovi olive bioactive content highlighted the high nutritional and possible economic value of the Kolovi olive fruit. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Global consequences of liver ischemia/reperfusion injury

Liver ischemia/reperfusion injury has been extensively studied during the last decades and has been implicated in the pathophysiology of many clinical entities following hepatic surgery and transplantation. Apart from its pivotal role in the pathogenesis of the organ's post reperfusion injury, it has also been proposed as an underlying mechanism responsible for the dysfunction and injury of other organs as well. It seems that liver ischemia and reperfusion represent an event with "global" consequences that influence the function of many remote organs including the lung, kidney, intestine, pancreas, adrenals, and myocardium among others. The molecular and clinical manifestation of these remote organs injury may lead to the multiple organ dysfunction syndrome, frequently encountered in these patients. Remote organ injury seems to be in part the result of the oxidative burst and the inflammatory response following reperfusion. The present paper aims to review the existing literature regarding the proposed mechanisms of remote organ injury after liver ischemia and reperfusion. © 2014 Constantinos Nastos et al

Result disambiguation in web people search

We study the problem of disambiguating the results of a web people search engine: given a query consisting of a person name plus the result pages for this query, find correct referents for all mentions by clustering the pages according to the different people sharing the name. While the problem has been studied extensively, we discover that the increasing availability of results retrieved from social media platforms causes state-of-the-art methods to break down. We analyze the problem and propose a dual strategy where we distinguish between results obtained from social media platforms and those obtained from other sources. In our dual strategy, the two types of documents are disambiguated separately, using different strategies, and their results are then merged. We study several instantiations for the different stages in our proposed strategy and manage to achieve state-of-the-art performance