Optimism and pessimism analysis using deep learning on COVID-19 related twitter conversations

Financiado para publicación en acceso aberto: Universidade de Vigo/CISUGThis paper proposes a new deep learning approach to better understand how optimistic and pessimistic feelings are conveyed in Twitter conversations about COVID-19. A pre-trained transformer embedding is used to extract the semantic features and several network architectures are compared. Model performance is evaluated on two new, publicly available Twitter corpora of crisis-related posts. The best performing pessimism and optimism detection models are based on bidirectional long- and short-term memory networks. Experimental results on four periods of the COVID-19 pandemic show how the proposed approach can model optimism and pessimism in the context of a health crisis. There is a total of 150,503 tweets and 51,319 unique users. Conversations are characterised in terms of emotional signals and shifts to unravel empathy and support mechanisms. Conversations with stronger pessimistic signals denoted little emotional shift (i.e. 62.21% of these conversations experienced almost no change in emotion). In turn, only 10.42% of the conversations laying more on the optimistic side maintained the mood. User emotional volatility is further linked with social influence.Xunta de Galicia | Ref. ED431C2018/55-GRCMinisterio de Ciencia e Innovación | Ref. PID2020–113673RB-I00Xunta de Galicia y European Regional Development Fund | Ref. ED431G2019/06Fundação para a Ciência e a Tecnologia | Ref. UIDB/04469/202

Spanish Corpora of tweets about COVID-19 vaccination for automatic stance detection

The paper presents new annotated corpora for performing stance detection on Spanish Twitter data, most notably Health-related tweets. The objectives of this research are threefold: (1) to develop a manually annotated benchmark corpus for emotion recognition taking into account different variants of Spanish in social posts; (2) to evaluate the efficiency of semi-supervised models for extending such corpus with unlabelled posts; and (3) to describe such short text corpora via specialised topic modelling. A corpus of 2,801 tweets about COVID-19 vaccination was annotated by three native speakers to be in favour (904), against (674) or neither (1,223) with a 0.725 Fleiss’ kappa score. Results show that the self-training method with SVM base estimator can alleviate annotation work while ensuring high model performance. The self-training model outperformed the other approaches and produced a corpus of 11,204 tweets with a macro averaged f1 score of 0.94. The combination of sentence-level deep learning embeddings and density-based clustering was applied to explore the contents of both corpora. Topic quality was measured in terms of the trustworthiness and the validation index.Agencia Estatal de Investigación | Ref. PID2020–113673RB-I00Xunta de Galicia | Ref. ED431C2018/55Fundação para a Ciência e a Tecnologia | Ref. UIDB/04469/2020Financiado para publicación en acceso aberto: Universidade de Vigo/CISU

Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

Background: Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled textual data, regardless of efficiency and robustness of the underlying implementations. Due to the rapid growth of unstructured data collections, including patent databases and particularly the scientific literature, there is a pressing need to generate, assess and expose robust big data text mining solutions to semantically enrich documents in real time. To address this pressing need, a novel track called “Technical interoperability and performance of annotation servers” was launched under the umbrella of the BioCreative text mining evaluation effort. The aim of this track was to enable the continuous assessment of technical aspects of text annotation web servers, specifically of online biomedical named entity recognition systems of interest for medicinal chemistry applications. Results: A total of 15 out of 26 registered teams successfully implemented online annotation servers. They returned predictions during a two-month period in predefined formats and were evaluated through the BeCalm evaluation platform, specifically developed for this track. The track encompassed three levels of evaluation, i.e. data format considerations, technical metrics and functional specifications. Participating annotation servers were implemented in seven different programming languages and covered 12 general entity types. The continuous evaluation of server responses accounted for testing periods of low activity and moderate to high activity, encompassing overall 4,092,502 requests from three different document provider settings. The median response time was below 3.74 s, with a median of 10 annotations/document. Most of the servers showed great reliability and stability, being able to process over 100,000 requests in a 5-day period. Conclusions: The presented track was a novel experimental task that systematically evaluated the technical performance aspects of online entity recognition systems. It raised the interest of a significant number of participants. Future editions of the competition will address the ability to process documents in bulk as well as to annotate full-text documents.Portuguese Foundation for Science and Technology | Ref. UID/BIO/04469/2013Portuguese Foundation for Science and Technology | Ref. COMPETE 2020 (POCI-01-0145-FEDER-006684)Xunta de Galicia | Ref. ED431C2018/55-GRCEuropean Commission | Ref. H2020, n. 65402

The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohn’s Disease patients

Lactobacillus genus includes both probiotic and representative strains of the human gut microbiota. Independent studies have reported on the anti-inflammatory properties of different Lactobacillus strains, although we are far from understanding the underlying molecular interplay. In this work we show that a daily administration of Lactobacillus acidophilus DSM20079T (DSM20079) to healthy piglets resulted in plasmatic increases of the anti-inflammatory IL10, whilst IL12 and the pro-inflammatory ratio IL12+TNFα/IL10 decreased. The extracellular protein fraction of DSM20079 was identified as the responsible for the crosstalk interaction that elicited these tolerogenic effects. This strain was able to activate innate immune pathways in dendritic cells and to decrease the production of pro-inflammatory cytokines in both CD4+/CD8+ T cell subsets in healthy donors and in Crohn’s Disease patients. The tolerogenic effect exerted by the extracellular proteins of this strain suggests their potential use as coadjutant for therapeutic applications targeting chronic inflammatory illnesses.Asociación Española Contra el Cancer | Ref. PS-2016Fundação para a Ciência e a Tecnologia | | Ref. UID/BIO/04469/2013Agencia Estatal de Investigación | Ref. AGL2016-78311-RPrincipado de Asturias | Ref. PCTI 2018–2020Xunta de Galicia | Ref. ED431C2018/5

In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome

This work supports the massive presence of potential immunomodulatory peptides in the human gut metaproteome. These peptides were identified through the MAHMI database as potentially anti-inflammatory, and sixteen of them synthesized for characterize their mechanism of action. From them, peptide HM14 was encrypted in an extracellular protein produced by Bifidobacterium longum, a common member of the human microbiota, and displayed the highest anti-inflammatory capability. Molecular mechanism of action of HM14 pointed to a specific interaction between this immunomodulatory peptide and antigen presenting cells, which resulted in a higher formation of iTreg cells. Moreover, HM14 was effective in decreasing pro-inflammatory parameters in PBMCs isolated from a cohort of Crohn's patients. Finally, non-targeted metabolomics confirmed the ability of HM14 to modulate the metabolic activity of PBMCs to fulfil its energy and biosynthetic requirements. Overall, our combined in silico/multiomics approach supports the human gut metaproteome as a source for immunomodulatory peptides.Ministerio de Economía y Competitividad | Ref. AGL2013-44761-PAgencia Estatal de Investigación | Ref. AGL2016-78311-

P4P: a peptidome-based strain-level genome comparison web tool

Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny. P4P can be used to analyze different peptide datasets, i.e. bacteria, viruses, eukaryotic species or even metaproteomes. Also, it is able to work with whole proteome datasets and experimental mass-to-charge lists originated from mass spectrometers. The ultimate aim is to generate a valid and manageable list of peptides that have phylogenetic signal and are potentially sample-specific. Sample-to-sample comparison is based on a consensus peak set matrix, which can be further submitted to phylogenetic analysis. P4P holds great potential for improving phylogenetic analyses in challenging taxonomic groups, biomarker identification or epidemiologic studies. Notably, P4P can be of interest for applications handling large proteomic datasets, which it is able to reduce to small matrices while maintaining high phylogenetic resolution. The web server is available at http://sing-group.org/p4p.Ministerio de Economía y Competitividad | Ref. AGL2013-44039RFundação para a Ciência e a Tecnologia | Ref. UID/BIO/04469/201

BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results

Background: The wide range of potential applications has made the Basic Local Alignment Search Tool (BLAST) a ubiquitous tool in the field of Molecular Biology. Within this context, it is increasingly appealing to embed BLAST services within larger Web applications. Results: This work introduces BlasterJS viewer, a new JavaScript library for the lightweight development of Web-based applications supporting the visualisation of BLAST outputs. BlasterJS detaches from similar data viewers by focusing on the visual and interactive display of sequence similarity results and being completely independent of BLAST services. BlasterJS is compatible with the text outputs generated by the BLAST family of programs, namely BLASTp, BLASTn, BLASTx, tBLASTn, and tBLASTx, and works in all major Web browsers. Furthermore, BlasterJS is available through the EBI's BioJS registry 5, which extends its potential use to a wider scope of bioinformatics applications. Conclusions: BlasterJS is new Javascript library that enables easy and seamless integration of visual and interactive representations of BLAST outputs in Web-based applications supporting sequence similarity search. BlasterJS is free accessible at http://sing-group.org/blasterjs/Ministerio de Economía y Competitividadd | Ref. AGL2013-44039RFundação para a Ciência e a Tecnologia | Ref. UID/BIO/04469/2013Asociación Española Contra el Cánce

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome. Bioactivity prediction is based on the global alignment of the automatically processed peptides with experimentally validated immunomodulatory and antiproliferative peptides, in the reference section. MAHMI provides researchers with a comparative tool for inspecting the potential immunomodulatory or antiproliferative bioactivity of new amino acidic sequences and identifying promising peptides to be further investigated. Moreover, researchers are welcome to submit new experimental evidence on peptide bioactivity, namely, empiric and structural data, as a proactive, expert means to keep the database updated and improve the implemented bioactivity prediction method. Bioactive peptides identified by MAHMI have a huge biotechnological potential, including the manipulation of aberrant immune responses and the design of new functional ingredients/foods based on the genetic sequences of the human microbiome. Hopefully, the resources provided by MAHMI will be useful to those researching gastrointestinal disorders of autoimmune and inflammatory nature, such as Inflammatory Bowel Diseases. MAHMI database is routinely updated and is available free of charge.Ministerio de Economía y Competitividad | Ref. AGL2013-44039-RXunta de Galicia | Ref. EM2014/04