BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

<p>Abstract</p> <p>Background</p> <p>The ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using expression time series, is critical to advance our understanding of complex biological processes. Biclustering has been recognized as an effective method for discovering local temporal expression patterns and unraveling potential regulatory mechanisms. The general biclustering problem is NP-hard. In the case of time series this problem is tractable, and efficient algorithms can be used. However, there is still a need for specialized applications able to take advantage of the temporal properties inherent to expression time series, both from a computational and a biological perspective.</p> <p>Findings</p> <p>BiGGEsTS makes available state-of-the-art biclustering algorithms for analyzing expression time series. Gene Ontology (GO) annotations are used to assess the biological relevance of the biclusters. Methods for preprocessing expression time series and post-processing results are also included. The analysis is additionally supported by a visualization module capable of displaying informative representations of the data, including heatmaps, dendrograms, expression charts and graphs of enriched GO terms.</p> <p>Conclusion</p> <p>BiGGEsTS is a free open source graphical software tool for revealing local coexpression of genes in specific intervals of time, while integrating meaningful information on gene annotations. It is freely available at: <url>http://kdbio.inesc-id.pt/software/biggests</url>. We present a case study on the discovery of transcriptional regulatory modules in the response of <it>Saccharomyces cerevisiae </it>to heat stress.</p

The Portuguese version of the body investment scale: psychometric properties and relationships with disordered eating and emotion dysregulation

Background This study aimed to examine the psychometric properties of the Portuguese version of the Body Investment Scale (BIS) in a nonclinical sample of students and a clinical sample of outpatients with eating disorders, to analyse the differences in the BIS factors between the samples and to explore the relationships among body investment, eating disorder symptoms and difficulties in emotion regulation. Methods The clinical (n = 93) and nonclinical (n = 448) samples completed self-report measures. Results In contrast to the nonclinical sample, confirmatory factor analysis showed an acceptable fit for the original four-factor solution of the BIS in the clinical sample. This scale also demonstrated adequate internal consistency in both samples. Significant differences in BIS factors were found between the samples; outpatients with eating disorders presented more negative feelings about the body, less comfort with touch and lower levels of body protection than those of the students. In the clinical sample, significant relationships were found between these factors and a higher severity of disordered eating, as well as between these factors and higher difficulties in emotion regulation. Conclusions The Portuguese version of the BIS is a psychometrically sound measure for the assessment of body investment, and it is especially appropriate in a clinical setting of outpatients with eating disorders.- This work was supported by the Foundation for Science and Technology under Grant [SFRH/BD/116974/2016]

Going beyond good intentions for the sustainable conservation of built heritage: a systematic literature review

This research addresses the performance gap between intentions towards a sustainable conservation of built heritage and its actual implementation. Socio-psychological models of human behaviour, such as the theory of planned behaviour (TPB), have been studying this dissonance between intention and behaviour, and allow to recognise latent critical factors. This paper provides a systematic literature review of research publications on the intersection of the topics of human behaviour, heritage, and sustainability. It aims to analyse how the TPB has been used in the field of sustainable conservation of built heritage. The studies are categorised according to the type of heritage, main actors targeted, aims, and methodology. A total of 140 publications were analysed. The results show a recent field of research. In the domain of built heritage conservation, behaviour is commonly addressed as a synonym of performance, targeting the building itself. Most publications relating socio-psychological constructs of behaviour and heritage sustainability can be found in the tourism and hospitality field, focusing on tourists’ and residents’ behaviours. The review shows that practitioners are still absent from the literature. However, research addressing other stakeholders shows that the theoretical framework can play an important role in the implementation of sustainable conservation practices in the built heritage.This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the scope of the Doctoral Program Eco-Construction and Rehabilitation (EcoCoRe), to the PhD scholarship with the reference PD/BD/127853/201

Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks

Explaining regulatory mechanisms is crucial to understand complex cellular responses leading to system perturbations. Some strategies reverse engineer regulatory interactions from experimental data, while others identify functional regulatory units (modules) under the assumption that biological systems yield a modular organization. Most modular studies focus on network structure and static properties, ignoring that gene regulation is largely driven by stimulus-response behavior. Expression time series are key to gain insight into dynamics, but have been insufficiently explored by current methods, which often (1) apply generic algorithms unsuited for expression analysis over time, due to inability to maintain the chronology of events or incorporate time dependency; (2) ignore local patterns, abundant in most interesting cases of transcriptional activity; (3) neglect physical binding or lack automatic association of regulators, focusing mainly on expression patterns; or (4) limit the discovery to a predefined number of modules. We propose Regulatory Snapshots, an integrative mining approach to identify regulatory modules over time by combining transcriptional control with response, while overcoming the above challenges. Temporal biclustering is first used to reveal transcriptional modules composed of genes showing coherent expression profiles over time. Personalized ranking is then applied to prioritize prominent regulators targeting the modules at each time point using a network of documented regulatory associations and the expression data. Custom graphics are finally depicted to expose the regulatory activity in a module at consecutive time points (snapshots). Regulatory Snapshots successfully unraveled modules underlying yeast response to heat shock and human epithelial-to-mesenchymal transition, based on regulations documented in the YEASTRACT and JASPAR databases, respectively, and available expression data. Regulatory players involved in functionally enriched processes related to these biological events were identified. Ranking scores further suggested ability to discern the primary role of a gene (target or regulator). Prototype is available at: http://kdbio.inesc-id.pt/software/regulatorysnapshots

Evaluation of Respiratory, Genotoxic and Cytotoxic Effects from Occupational Exposure to Typography Activities

This cross-sectional study was structured to allow the evaluation of the respiratory, genotoxic, and cytotoxic effects of occupational exposure to products resulting from the activity of printers in typographies and, to determine the risk of genotoxicity associated with such exposure. This study comprised 69 subjects, 25 individuals occupationally exposed to the products of typographies (study group), and 44 individuals non-exposed to the environment studied (reference group). The frequency of micronucleated cells and other nuclear anomalies (binucleated, karyolitic, pyknotic, and karyorrhectic cells) in the oral epithelia of each subject were analyzed. The frequency of micronucleated cells was significantly higher in the study group when compared to the reference one (12.96 MN/2000 cells vs. 4 MN/2000 cells, respectively). Occupational exposure to products of typography is a risk factor for the occurrence of micronucleated cells in the study group (RR = 3.2; 95% CI, 2.7–3.9; p < 0.001). The results of the spirometry test did not reveal significant respiratory effects between the reference and study groups.FUNDING: This work was financially supported by Azores DRCT Plurianual Funding (M1.1.A/ Func.UI&D/010/2021-2024) and by the Fundo Regional da Ciência (Regional Government of the Azores) (Diana Linhares post-doc fellowship-M3.1.a/F/004/2018).info:eu-repo/semantics/publishedVersio

Distribution of herpetofauna in caves of Portuguese karst massifs

Amphibians are frequently found exploring subterranean environments. Even though in Europe there are already some reports of amphibians present in subterranean habitats, in Portugal there is a major lack of knowledge of these ecosystems, namely in the karst region. Considering the relevance of amphibians and their current conservational status, it is important to assess their presence in every potential habitat. In order to provide further knowledge over this subject a preliminary survey was carried out in two Portuguese karst massifs, Estremenho and Sicó. A total of 24 caves were surveyed and as result three species (Tarentola mauritanica; Salamandra salamandra and Pleorodeles waltl) were found in Estremenho karst massif, and two species (Triturus marmoratus and Bufo bufo) were observed in Sicó karst massif. Furthermore, evidences were found that P. waltl uses caves for reproduction, which had only been reported once in Spain. This allowed perceiving that herpetofauna species occupy caves of Portuguese karst massifs and are also using them as reproduction sites

Oxidação electroquímica de compostos lipídicos como precursora do tratamento anaeróbio

A digestão anaeróbia é um processo de tratamento de efluentes e simultaneamente uma fonte de energia, através da produção de biogás. A presença de compostos lipídicos nos efluentes não só causa problemas de inibição dos microorganismos como pode levar à lavagem do sistema, sendo frequente a aplicação de pré-tratamentos. Os tratamentos físico-químicos mostram-se, por vezes, insuficientes e originam lamas indesejáveis. Em alternativa, a oxidação electroquímica deste tipo de compostos orgânicos apresenta-se como um processo prometedor na medida em que proporciona a alteração dos lípidos e promove a respectiva conversão em biogás. No presente trabalho, as transformações electroquímicas do ácido oleico, em solução aquosa com eléctrodos de platina (Pt), chumbo (Pb) e grafite, são analisadas numa vasta gama de potenciais. Os dados obtidos permitem estabelecer as condições operativas para proceder à electrooxidação do lípido sob controlo potenciostático. Os rendimentos da oxidação electroquímica do composto lipídico sobre os diferentes substratos e de acordo com os parâmetros electroquímicos empregues são discutidos.Fundação para a Ciência e a Tecnologia (FCT

Unraveling the ecotoxicity of deep eutectic solvents using the mixture toxicity theory

The interest on deep eutectic solvents (DES) has been increasing. However, the ecotoxicological profile of DES is scarcely known. Also, despite previous studies showed that DES components dissociate in water, none assessed DES toxicity using the classical and adequate models for mixture toxicity prediction - concentration addition (CA) and independent action (IA). This study evaluates the ecotoxicological profile of DES based on [N1111]Cl, [N2222]Cl and [N3333]Cl as hydrogen bond acceptors (HBA) combined with hydrogen-bond donors (HBD) vis. ethylene glycol and 1-propanol, through the Microtox® Acute Toxicity Test. CA and IA with deviations describing synergism/antagonism, dose-ratio and dose-level effects were fitted to the toxicity data. Neither the starting materials nor DES were found hazardous to Aliivibrio fischeri, in this specific case agreeing with the claimed "green character" of DES. Among the starting materials, ethylene glycol was the least toxic, whereas [N3333]Cl was the most toxic (30 min-EC50 = 96.49 g L-1 and 0.5456 g L-1, respectively). DES toxicity followed the same trend as observed for the salts: [N1111]Cl-based DES < [N2222]Cl-based DES < [N3333]Cl-based DES. The IA model, with specific deviations, adjusted better in 5 out of 6 DES. Antagonism was observed for [N1111]Cl-based DES, and synergism for [N3333]Cl-based DES and for 1-propanol:[N2222]Cl. The application of the mixture toxicity models represents a breakthrough in the problematic of assessing the toxicity of the countless number of DES that can be created with the same starting materials, since they provide the expected toxicity of any virtual combination between HBA and HBD.publishe

Editorial: Occupational health psychology: From burnout to well-being at work

This Research Topic entitled Occupational Health Psychology (OHP): From Burnout to Well-being at Work tried to bring together two applied disciplines within psychology: health psychology and industrial/organizational psychologyinfo:eu-repo/semantics/publishedVersio

Potential of Coccolithophore microalgae as fillers in starch-based films for active and sustainable food packaging

Coccolithophore microalgae, such as Emiliania huxleyi (EHUX) and Chrysotila pseudoroscoffensis (CP), are composed of calcium carbonate (CaCO3) and contain bioactive compounds that can be explored to produce sustainable food packaging. In this study, for the first time, these microalgae were incorporated as fillers in starch-based films, envisioning the development of biodegradable and bioactive materials for food packaging applications. The films were obtained by solvent casting using different proportions of the filler (2.5, 5, 10, and 20%, w/w). For comparison, commercial CaCO3, used as filler in the plastic industry, was also tested. The incorporation of CaCO3 and microalgae (EHUX or CP) made the films significantly less rigid, decreasing Young’s modulus up to 4.7-fold. Moreover, the incorporation of microalgae hydrophobic compounds as lipids turned the surface hydrophobic (water contact angles > 90°). Contrary to what was observed with commercial CaCO3, the films prepared with microalgae exhibited antioxidant activity, increasing from 0.9% (control) up to 60.4% (EHUX 20%) of ABTS radical inhibition. Overall, the introduction of microalgae biomass improved hydrophobicity and antioxidant capacity of starch-based films. These findings should be considered for further research using coccolithophores to produce active and sustainable food packaging material.info:eu-repo/semantics/publishedVersio