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BackgroundAllergy disorders caused by biological particles, such as the proteins in some airborne pollen grains, are currently considered one of the most common chronic diseases, and European Academy of Allergy and Clinical Immunology forecasts indicate that within 15 years 50% of Europeans will have some kind of allergy as a consequence of urbanization, industrialization, pollution, and climate change. ObjectiveThe aim of this study was to monitor and analyze the dissemination of information about pollen symptoms from December 2006 to January 2022. By conducting a comprehensive evaluation of public comments and trends on Twitter, the research sought to provide valuable insights into the impact of pollen on sensitive individuals, ultimately enhancing our understanding of how pollen-related information spreads and its implications for public health awareness. MethodsUsing a blend of large language models, dimensionality reduction, unsupervised clustering, and term frequency–inverse document frequency, alongside visual representations such as word clouds and semantic interaction graphs, our study analyzed Twitter data to uncover insights on respiratory allergies. This concise methodology enabled the extraction of significant themes and patterns, offering a deep dive into public knowledge and discussions surrounding respiratory allergies on Twitter. ResultsThe months between March and August had the highest volume of messages. The percentage of patient tweets appeared to increase notably during the later years, and there was also a potential increase in the prevalence of symptoms, mainly in the morning hours, indicating a potential rise in pollen allergies and related discussions on social media. While pollen allergy is a global issue, specific sociocultural, political, and economic contexts mean that patients experience symptomatology at a localized level, needing appropriate localized responses. ConclusionsThe interpretation of tweet information represents a valuable tool to take preventive measures to mitigate the impact of pollen allergy on sensitive patients to achieve equity in living conditions and enhance access to health information and services.

BackgroundPolyDeep is a computer-aided detection and classification (CADe/x) system trained to detect and classify polyps. During colonoscopy, CADe/x systems help endoscopists to predict the histology of colonic lesions.ObjectiveTo compare the diagnostic performance of PolyDeep and expert endoscopists for the optical diagnosis of colorectal polyps on still images.MethodsPolyDeep Image Classification (PIC) is an in vitro diagnostic test study. The PIC database contains NBI images of 491 colorectal polyps with histological diagnosis. We evaluated the diagnostic performance of PolyDeep and four expert endoscopists for neoplasia (adenoma, sessile serrated lesion, traditional serrated adenoma) and adenoma characterization and compared them with the McNemar test. Receiver operating characteristic curves were constructed to assess the overall discriminatory ability, comparing the area under the curve of endoscopists and PolyDeep with the chi- square homogeneity areas test.ResultsThe diagnostic performance of the endoscopists and PolyDeep in the characterization of neoplasia is similar in terms of sensitivity (PolyDeep: 89.05%; E1: 91.23%, p=0.5; E2: 96.11%, p

This article explores the intertwining connections among artificial intelligence, machine learning, digital transformation, and computational sustainability, detailing how these elements jointly empower citizens within a smart city framework. As technological advancement accelerates, smart cities harness these innovations to improve residents’ quality of life. Artificial intelligence and machine learning act as data analysis powerhouses, making urban living more personalized, efficient, and automated, and are pivotal in managing complex urban infrastructures, anticipating societal requirements, and averting potential crises. Digital transformation transforms city operations by weaving digital technology into every facet of urban life, enhancing value delivery to citizens. Computational sustainability, a fundamental goal for smart cities, harnesses artificial intelligence, machine learning, and digital resources to forge more environmentally responsible cities, minimize ecological impact, and nurture sustainable development. The synergy of these technologies empowers residents to make well-informed choices, actively engage in their communities, and adopt sustainable lifestyles. This discussion illuminates the mechanisms and implications of these interconnections for future urban existence, ultimately focusing on empowering citizens in smart cities.

ABSTRACT The pks island is one of the most prevalent pathogenicity islands among the Escherichia coli strains that colonize the colon of colorectal carcinoma (CRC) patients. This pathogenic island encodes the production of a nonribosomal polyketide-peptide named colibactin, which induces double-strand breaks in DNA molecules. Detection or even depletion of this pks-producing bacteria could help to understand the role of these strains in the context of CRC. In this work, we performed a large-scale in silico screening of the pks cluster in more than 6,000 isolates of E. coli. The results obtained reveal that not all the pks-detected strains could produce a functional genotoxin and, using antibodies against pks-specific peptides from surface cell proteins, a methodology for detection and depletion of pks+ bacteria in gut microbiotas was proposed. With our method, we were able to deplete a human gut microbiota of this pks+ strains, opening the door to strain-directed microbiota modification and intervention studies that allow us to understand the relation between these genotoxic strains and some gastrointestinal diseases. IMPORTANCE The human gut microbiome has also been hypothesized to play a crucial role in the development and progression of colorectal carcinoma (CRC). Between the microorganisms of this community, the Escherichia coli strains carrying the pks genomic island were shown to be capable of promoting colon tumorigenesis in a colorectal cancer mouse model, and their presence seems to be directly related to a distinct mutational signature in patients suffering CRC. This work proposes a novel method for the detection and depletion of pks-carrying bacteria in human gut microbiotas. In contrast to methods based on probes, this methodology allows the depletion of low-abundance bacterial strains maintaining the viability of both targeted and non-targeted fractions of the microbiota, allowing the study of the contribution of these pks-carrying strains to different diseases, such as CRC, and their role in other physiological, metabolic or immune processes.

Motivated by the pervasiveness of artificial intelligence (AI) and the Internet of Things (IoT) in the current “smart everything” scenario, this article provides a comprehensive overview of the most recent research at the intersection of both domains, focusing on the design and development of specific mechanisms for enabling a collaborative inference across edge devices towards the in situ execution of highly complex state-of-the-art deep neural networks (DNNs), despite the resource-constrained nature of such infrastructures. In particular, the review discusses the most salient approaches conceived along those lines, elaborating on the specificities of the partitioning schemes and the parallelism paradigms explored, providing an organized and schematic discussion of the underlying workflows and associated communication patterns, as well as the architectural aspects of the DNNs that have driven the design of such techniques, while also highlighting both the primary challenges encountered at the design and operational levels and the specific adjustments or enhancements explored in response to them.

Developing models able to predict interactions between drugs and enzymes is a primary goal in computational biology since these models may be used for predicting both new active drugs and the interactions between known drugs on untested targets. With the compilation of a large dataset of drug–enzyme pairs (62,524), we recognized a unique opportunity to attempt to build a novel multi-target machine learning (MTML) quantitative structure-activity relationship (QSAR) model for probing interactions among different drugs and enzyme targets. To this end, this paper presents an MTML-QSAR model based on using the features of topological drugs together with the artificial neural network (ANN) multi-layer perceptron (MLP). Validation of the final best model found was carried out by internal cross-validation statistics and other relevant diagnostic statistical parameters. The overall accuracy of the derived model was found to be higher than 96%. Finally, to maximize the diffusion of this model, a public and accessible tool has been developed to allow users to perform their own predictions. The developed web-based tool is public accessible and can be downloaded as free open-source software.

Abstract Background Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebellar ataxia type 1 (SCA1), results in abnormal PPI. For ATXN1 a larger number of interactors has been reported for the expanded (82Q) than the wt (29Q) protein. Methods To understand how the expanded polyQ affects PPI, protein structures were predicted for wt and expanded ATXN1, as well as, for 71 ATXN1 interactors. Then, the binding surfaces of wt and expanded ATXN1 with the reported interactors were inferred. Results Our data supports that the polyQ expansion alters the ATXN1 conformation and that it enhances the strength of interaction with ATXN1 partners. For both ATXN1 variants, the number of residues at the predicted binding interface are greater after the polyQ, mainly due to the AXH domain. Moreover, the difference in the interaction strength of the ATXN1 variants was due to an increase in the number of interactions at the N-terminal region, before the polyQ, for the expanded form. Conclusions There are three regions at the AXH domain that are essential for ATXN1 PPI. The N-terminal region is responsible for the strength of the PPI with the ATXN1 variants. How the predicted motifs in this region affect PPI is discussed, in the context of ATXN1 post-transcriptional modifications.

Abstract Background L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C. Results By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans. Conclusions Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.

Abstract 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.

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.

A better understanding of the response against Tuberculosis (TB) infection is required to accurately identify the individuals with an active or a latent TB infection (LTBI) and also those LTBI patients at higher risk of developing active TB. In this work, we have used the information obtained from studying the gene expression profile of active TB patients and their infected –LTBI- or uninfected –NoTBI- contacts, recruited in Spain and Mozambique, to build a class-prediction model that identifies individuals with a TB infection profile. Following this approach, we have identified several genes and metabolic pathways that provide important information of the immune mechanisms triggered against TB infection. As a novelty of our work, a combination of this class-prediction model and the direct measurement of different immunological parameters, was used to identify a subset of LTBI contacts (called TB-like) whose transcriptional and immunological profiles are suggestive of infection with a higher probability of developing active TB. Validation of this novel approach to identifying LTBI individuals with the highest risk of active TB disease merits further longitudinal studies on larger cohorts in TB endemic areas.

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.

Ambient Intelligence (AmI) encompasses technological infrastructures capable of sensing data from environments and extracting high-level knowledge to detect or recognize users’ features and actions, as well as entities or events in their surroundings. Visual perception, particularly object detection, has become one of the most relevant enabling factors for this context-aware user-centered intelligence, being the cornerstone of relevant but complex tasks, such as object tracking or human action recognition. In this context, convolutional neural networks have proven to achieve state-of-the-art accuracy levels. However, they typically result in large and highly complex models that typically demand computation offloading onto remote cloud platforms. Such an approach has security- and latency-related limitations and may not be appropriate for some AmI use cases where the system response time must be as short as possible, and data privacy must be guaranteed. In the last few years, the on-device paradigm has emerged in response to those limitations, yielding more compact and efficient neural networks able to address inference directly on client machines, thus providing users with a smoother and better-tailored experience, with no need of sharing their data with an outsourced service. Framed in that novel paradigm, this work presents a review of the recent advances made along those lines in object detection, providing a comprehensive study of the most relevant lightweight CNN-based detection frameworks, discussing the most paradigmatic AmI domains where such an approach has been successfully applied, the different challenges arisen, the key strategies and techniques adopted to create visual solutions for image-based object classification and localization, as well as the most relevant factors to bear in mind when assessing or comparing those techniques, such as the evaluation metrics or the hardware setups used.

Non-self gametophytic self-incompatibility (GSI) recognition system is characterized by the presence of multiple F-box genes tandemly located in the S-locus, that regulate pollen specificity. This reproductive barrier is present in Solanaceae, Plantaginacea and Maleae (Rosaceae), but only in Petunia functional assays have been performed to get insight on how this recognition mechanism works. In this system, each of the encoded S-pollen proteins (called SLFs in Solanaceae and Plantaginaceae /SFBBs in Maleae) recognizes and interacts with a sub-set of non-self S-pistil proteins, called S-RNases, mediating their ubiquitination and degradation. In Petunia there are 17 SLF genes per S-haplotype, making impossible to determine experimentally each SLF specificity. Moreover, domain –swapping experiments are unlikely to be performed in large scale to determine S-pollen and S-pistil specificities. Phylogenetic analyses of the Petunia SLFs and those from two Solanum genomes, suggest that diversification of SLFs predate the two genera separation. Here we first identify putative SLF genes from nine Solanum and 10 Nicotiana genomes to determine how many gene lineages are present in the three genera, and the rate of origin of new SLF gene lineages. The use of multiple genomes per genera precludes the effect of incompleteness of the genome at the S-locus. The similar number of gene lineages in the three genera implies a comparable effective population size for these species, and number of specificities. The rate of origin of new specificities is one per 10 million years. Moreover, here we determine the amino acids positions under positive selection, those involved in SLF specificity recognition, using 10 Petunia S-haplotypes with more than 11 SLF genes. These 16 amino acid positions account for the differences of self-incompatible (SI) behavior described in the literature. When SLF and S-RNase proteins are divided according to the SI behavior, and the positively selected amino acids classified according to hydrophobicity, charge, polarity and size, we identified fixed differences between SI groups. According to the in silico 3D structure of the two proteins these amino acid positions interact. Therefore, this methodology can be used to infer SLF/S-RNase specificity recognition.

This work presents a novel in silico approach to the prediction and characterization of the glycolytic capacities of the beneficial intestinal bacterium Faecalibacterium prausnitzii. Available F. prausnitzii genomes were explored taking the glycolytic capacities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as reference. The comparison of the generated glycolytic profiles offered insights into the particular capabilities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as well as the potential of the rest of strains. Glycoside hydrolases were mostly detected in the pathways responsible for the starch and sucrose metabolism and the biosynthesis of secondary metabolites, but this analysis also identified some other potentially interesting, but still uncharacterized activities, such as several hexosyltransferases and some hydrolases. Gene neighborhood maps offered additional understanding of the genes coding for relevant glycoside hydrolases. Although information about the carbohydrate preferences of F. prausnitzii is scarce, the in silico metabolic predictions were consistent with previous knowledge about the impact of fermentable sugars on the growth promotion and metabolism of F. prausnitzii. So, while the predictions still need to be validated using culturing methods, the approach holds the potential to be reproduced and scaled to accommodate the analysis of other strains (or even families and genus) as well as other metabolic activities. This will allow the exploration of novel methodologies to design or obtain targeted probiotics for F. prausnitzii and other strains of interest.

In recent years, natural thermal mineral waters have been gaining the special attention of the scientific community, namely in the prevention and treatment of some diseases, due to the microbial properties that exist in these habitats. The aim of this work was to characterize the physicochemical composition and the microbial taxonomic communities present in three thermal waters of the Galician region in Spain and two samples of the northern region in Portugal. These collected water samples were analyzed for physicochemical characterization and the respective hydrogenome of the waters using next generation sequencing together with 16S rRNA gene sequencing. The sequencing showed a high diversity of microorganisms in all analyzed waters; however, there is a clear bacterial predominance of Proteobacteria phylum, followed by Firmicutes, Deinococcus-Thermus, Aquificae and Nitrospira. The main physicochemical parameters responsible for the clustering within the Spanish waters were sulfur compounds (SO32− and S2−), CO32− and neutral pH, and in the Portuguese waters were Mg, Ca and Sr, nitrogen compounds (NO3− and NH4+), Na, Rb, conductivity and dry residue. This work will allow for a better understanding of the microbial community’s composition and how these microorganisms interfere in the physicochemical constitution of these waters often associated with medicinal properties. Furthermore, the hydrogenome may be used as an auxiliary tool in the practice of medical hydrology, increasing the likelihood of safe use of these unique water types.

Last decade, biomedical and bioinformatics researchers have been demanding advanced and user-friendly applications for real use in practice. In this context, the Artificial Intelligence Workbench, an open-source Java desktop application framework for scientific software development, emerged with the goal of provid-ing support to both fundamental and applied research in the domain of transla-tional biomedicine and bioinformatics. AIBench automatically provides function-alities that are common to scientific applications, such as user parameter defini-tion, logging facilities, multi-threading execution, experiment repeatability, work-flow management, and fast user interface development, among others. Moreover, AIBench promotes a reusable component based architecture, which also allows assembling new applications by the reuse of libraries from existing projects or third-party software. Ten years have passed since the first release of AIBench, so it is time to look back and check if it has fulfilled the purposes for which it was conceived to and how it evolved over time.

Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4s.

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/.

La evaluación representa un aspecto determinante en la elaboración de estrategias de éxito durante el aprendizaje. En un contexto presencial, el docente puede observar el comportamiento de sus alumnos e identificar diferentes vías que faciliten la evaluación sin inducir al estrés, evitando las consecuencias negativas de éste en el resultado del aprendizaje. Sin embargo, en entornos de aprendizaje con e-Learning el contacto directo resulta imposible y, por lo tanto, deben existir formas alternativas que faciliten tanto la detección como la prevención de situaciones de estrés durante la evaluación. Resulta por tanto conveniente el análisis del estrés y la determinación de estrategias para la resolución de problemas derivados de su aparición. En este trabajo se propone un módulo de análisis de estrés para su aplicación durante la evaluación on-line de los alumnos, que es capaz de indicar al docente los instantes de tiempo más propicios para intervenir así como los contenidos que causan mayores dificultades. De esta forma, el educador podrá asistir de forma eficaz a aquellos alumnos que más lo necesiten.

Scientific studies focused on the role of the human microbiome over human health have generated billions of gigabits of genetic information during the last decade. Nowadays integration of all this information in public databases and development of pipelines allowing us to biotechnologically exploit this information are urgently needed. Prediction of the potential bioactivity of the products encoded by the human gut microbiome, or metaproteome, is the first step for identifying proteins responsible for the molecular interaction between microorganisms and the immune system. We have recently published the Mechanism of Action of the Human Microbiome (MAHMI) database (http://www.mahmi.org), conceived as a resource compiling peptide sequences with a potential immunomodulatory activity. Fifteen out of the 300 hundred million peptides contained in the MAHMI database were synthesized. These peptides were identified as being encrypted in proteins produced by gut microbiota members, they do not contain cleavage points for the major intestinal endoproteases and displayed high probability to have immunomodulatory bioactivity. The bacterial peptides FR-16 and LR-17 encrypted in proteins from Bifidobacterium longum DJ010A and Bifidobacterium fragilis YCH46 respectively, showed the higher immune modulation capability over human peripheral blood mononuclear cells. Both peptides modulated the immune response toward increases in the Th17 and decreases in the Th1 cell response, together with an induction of IL-22 production. These results strongly suggest the combined use of bioinformatics and in vitro tools as a first stage in the screening of bioactive peptides encrypted in the human gut metaproteome.

Ambient Intelligence promises to transform current spaces into electronic environments that are responsive, assistive and sensitive to human presence. Those electronic environments will be fully populated with dozens, hundreds or even thousands of connected devices that share information and thus become intelligent. That massive wave of electronic devices will also invade everyday objects, turning them into smart entities, keeping their native features and characteristics while seamlessly promoting them to a new class of thinking and reasoning everyday objects. Although there are strong expectations that most of the users’ needs can be fulfilled without their intervention, there are still situations where interaction is required. This paper presents work being done in the field of human-computer interaction, focusing on smart home environments, while being a part of a larger project called Aging Inside a Smart Home. This initiative arose as a way to deal with a large scourge of our country, where lots of elderly persons live alone in their homes, often with limited or no physical mobility. The project relies on the mobile agent computing paradigm in order to create a Virtual Butler that provides the interface between the elderly and the smart home infrastructure. The Virtual Butler is receptive to user questions, answering them according to the context and knowledge of the AISH. It is also capable of interacting with the user whenever it senses that something has gone wrong, notifying next of kin and/or medical services, etc. The Virtual Butler is aware of the user location and moves to the computing device which is closest to the user, in order to be always present. Its avatar can also run in handheld devices keeping its main functionality in order to track user when s/he goes out. According to the evaluation carried out, the Virtual Butler is assessed as a very interesting and loved digital friend, filling the gap between the user and the smart home. The evaluation also showed that the Virtual Butler concept can be easily ported to other types of possible smart and assistive environments like airports, hospitals, shopping malls, offices, etc.

Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains. To address this problem, we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides. These can be further investigated using in vitro approaches, laying a foundation for the development of biomarker detection and application-specific methods. This novel method aims at reducing large amounts of comparative peptide data to binary matrices while maintaining a high phylogenetic resolution. The underlying case study concerns the Bacillus cereus group, namely the differentiation of Bacillus thuringiensis, Bacillus anthracis and Bacillus cereus strains. Results show that trees based on cytoplasmic and extracellular peptidomes are only marginally in conflict with those based on whole proteomes, as inferred by the established Genome-BLAST Distance Phylogeny (GBDP) method. Hence, these results indicate that the two approaches can most likely be used complementarily even in other organismal groups. The obtained results confirm previous reports about the misclassification of many strains within the B. cereus group. Moreover, our method was able to separate the B. anthracis strains with high resolution, similarly to the GBDP results as benchmarked via Bayesian inference and both Maximum Likelihood and Maximum Parsimony. In addition to the presented phylogenomic applications, whole-peptide fingerprinting might also become a valuable complementary technique to digital DNA-DNA hybridization, notably for bacterial classification at the species and subspecies level in the future.

E-learning platforms are becoming more and more common in education and with organisations. They are seen as a complementary tool to support learning or, as in many cases, as the primary tool to do it (possibly the only one). In traditional learning, teachers can easily get an insight into how their students work and learn, and how they interact in the classroom. However, in online learning, it is more difficult for teachers to see how individual students behave. Affective states and learning styles are determinant in students’ performance. Together with stress, these are crucial factor to success. It is believed that the sole use of an E-learning platform can in itself be a cause of stress for students. Estimating, in a non-invasive way, such parameters, and taking measures to deal with them, are then the goal of this paper. We do not consider the use of dedicated sensors (invasive) such as special gloves or wrist bracelets since we intend not to be dependent on specific hardware and also because we believe that such specific hardware can induce for itself some alteration in the parameters being analysed. Our work focuses on the development of a new module (Dynamic Recognition Module) to incorporate in Moodle E-learning platform, to accommodate individualized support to E-learning students.

E-learning platforms are becoming more and more common in education and with organisations. They are seen as a complementary tool to support learning or, as in many cases, as the primary tool to do it (possibly the only one). In traditional learning, teachers can easily get an insight into how their students work and learn, and how they interact in the classroom. However, in online learning, it is more difficult for teachers to see how individual students behave. Affective states and learning styles are determinant in students’ performance. Together with stress, these are crucial factor to success. It is believed that the sole use of an E-learning platform can in itself be a cause of stress for students. Estimating, in a non-invasive way, such parameters, and taking measures to deal with them, are then the goal of this paper. We do not consider the use of dedicated sensors (invasive) such as special gloves or wrist bracelets since we intend not to be dependent on specific hardware and also because we believe that such specific hardware can induce for itself some alteration in the parameters being analysed. Our work focuses on the development of a new module (Dynamic Recognition Module) to incorporate in Moodle E-learning platform, to accommodate individualized support to E-learning students.

The technological advances in medical sensors, low-power microelectronics and miniaturization, wireless communications and networks have enabled the appearance of a new generation of wireless sensor networks: the so-called wireless body area networks (WBAN). These networks can be used for continuous monitoring of vital parameters, movement, and the surrounding environment. The data gathered by these networks contributes to improve users’ quality of life and allows the creation of a knowledge database by using learning techniques, useful to infer abnormal behaviour. In this paper we present a wireless body area network architecture to recognize human movement, identify human postures and detect harmful activities in order to prevent risk situations. The WBAN was created using tiny, cheap and low-power nodes with inertial and physiological sensors, strategically placed on the human body. Doing so, in an as ubiquitous as possible way, ensures that its impact on the users’ daily actions is minimum. The information collected by these sensors is transmitted to a central server capable of analysing and processing their data. The proposed system creates movement profiles based on the data sent by the WBAN’s nodes, and is able to detect in real time any abnormal movement and allows for a monitored rehabilitation of the user.

A novel ecosystem to promote the physical, emotional and psychic health and well-being of the elderly is presented. Our proposal was designed to add several services developed to meet the needs of the senior population, namely services to improve social inclusion and increase contribution to society. Moreover, the solution monitors the vital signs of elderly individuals, as well as environmental parameters and behavior patterns, in order to seek eminent danger situations and predict potential hazardous issues, acting in accordance with the various alert levels specified for each individual. The platform was tested by seniors in a real scenario. The experimental results demonstrated that the proposed ecosystem was well accepted and is easy to use by seniors.

In this work we present the design and implementation of WARCProcessor, a novel multiplatform integrative tool aimed to build scientific datasets to facilitate experimentation in web spam research. The developed application allows the user to specify multiple criteria that change the way in which new corpora are generated whilst reducing the number of repetitive and error prone tasks related with existing corpus maintenance. For this goal, WARCProcessor supports up to six commonly used data sources for web spam research, being able to store output corpus in standard WARC format together with complementary metadata files. Additionally, the application facilitates the automatic and concurrent download of web sites from Internet, giving the possibility of configuring the deep of the links to be followed as well as the behaviour when redirected URLs appear. WARCProcessor supports both an interactive GUI interface and a command line utility for being executed in background.

Smartphones and tablets proliferation enabled by accessible prices and also by the inclusion of sensing abilities promotes their use in several areas, such as healthcare. It opens new horizons in the field of continuous and noninvasive monitoring and support to population, namely, to seniors. Despite the great benefits that mobile sensing and social computing could provide to increase elderly's quality of life, many studies have shown that elderlies deal with difficulty with Information and Communication Technology (ICT). In this paper we present a solution to overcome barriers between elderlies and their ICT usage in order to potentiate all the benefits provided from mobile sensing and social computing. A survey on guidelines, standards, and advice regarding usability and accessibility issues when developing solutions for elderly people was carried out. This survey was made having in mind that senior population have singular requirements due to age related changes and also frequently technological illiteracy. We have identified and applied the most important guidelines to our solution. A prototype was made using responsive design in order to be adaptable to any type of devices. Regarding evaluation, usability tests and semistructured interviews were conducted in real scenario.

Wireless Body Area Networks (WBANs) supporting healthcare applications are in early development stage but offer valuable contributions at monitoring, diagnostic, or therapeutic levels. They cover real-time medical information gathering obtained from different sensors with secure data communication and low power consumption. As a consequence of the increasing interest in the application of this type of networks, several articles dealing with different aspects of such systems have been published recently. In this paper, we compile and compare technologies and protocols published in the most recent researches, seeking WBAN issues for medical monitoring purposes to select the most useful solutions for this area of networking. The most important features under consideration in our analysis include wireless communication protocols, frequency bands, data bandwidth, transmission distance, encryption, authentication methods, power consumption, and mobility. Our study demonstrates that some characteristics of surveyed protocols are very useful to medical appliances and patients in a WBAN domain.

The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila), a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.