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

Attachment and mother-infant interactions in dyads with infants born full-term, moderate-to-late preterm, and very-to-extreme preterm

Background: The impact of prematurity status on attachment quality remains indeterminate. Some studies found no differences between infants born preterm (PT) and infants born full-term (FT), while other investigations present opposite results. Aims: We aim to contribute to this body of research by studying mother-infant interactive behaviors and quality of attachment in 3 independent samples: Full-Term (FT), Moderate-to-Late Preterm (MLPT) and Very-to-Extreme Preterm (VEPT). Study design: This is a longitudinal laboratory study conducted from 3 to 12 months of age (corrected-age in the case of infants born PT). Subjects: The participants are 213 Portuguese infants (FT =105; MLPT =52; VEPT =56) and their mothers. Outcome measures: Mother-infant interactive behavior was observed in free-play at 3 and 9 months (corrected- age). Infant attachment was observed in Strange Situation at 12 months. Results: Secure attachment is more prevalent in infants born FT, and ambivalent attachment is more prevalent in infants born VEPT. Infants with a secure attachment have higher gestational age and weight at birth. Infant and maternal interactive behavior quality is associated with attachment patterns and varies according to infant prematurity status. Last, the results indicate changes in maternal sensitivity and infant difficult behavior from 3 to 9 months of infant’s age. Conclusions: Our findings indicate that prematurity status impacts attachment quality. Changes in maternal and infant behavior from 3 to 9 months suggest a period of rapid non-linear development, supporting a transactional multilayered approach to the study of mother-infant relationship.info:eu-repo/semantics/publishedVersio

Dentin bonding and SEM analysis of a new experimental universal adhesive system containing a dendrimer

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Due to their polymerization characteristics, hyper-branched dendrimers have lately shown to be promising candidates for use in dental materials. In this study, a new dental adhesive system was prepared, using a dendrimer derived from 2-isocyanatoethyl methacrylate (G-IEMA), and its adhesive properties were investigated. The exposed dentin was treated with four universal adhesives (UAs): SBU (Scotchbond Universal™), FUT (Futurabond M+™), AE1 (experimental adhesive with Bis-GMA) and AE2 (experimental adhesive with G-IEMA), using Etch & Rinse (ER) or Self Etch (SE) protocols. Composite build-ups were prepared and stored for 24 h at 37 °C in distilled water. Composite/dentin beams were prepared with cross-sectional areas of 1 ± 0.3 mm2 and µTBS (Micro-tensile bond strength) test was performed at 0.5 mm/min. Failures modes were evaluated by stereomicroscopy, and bonding interfaces were observed by scanning electron microscopy (SEM). Statistical analysis of µTBS data was performed using General Linear (GLM) and Linear Mixed Models (LMM). The effect of adhesive type on µTBS was significant (p = 0.010), with AE1 presenting significantly higher µTBS than SBU (p = 0.019). No other differences between adhesives were observed. ER showed significantly better results than SE (p = 0.019), and no significant interactions between the adhesives and protocols were determined. Results obtained so far pinpoint the emergence of a new paradigm in the dental materials field, as G-IEMA can be used successfully as an alternative to Bis-GMA.info:eu-repo/semantics/publishedVersio

Antibiotic consumption, illness, and maternal sensitivity in infants with a disorganized attachment

Prior research found an association between mother–infant attachment and antibiotic use. Ambivalent-attached infants are more likely to take antibiotics than other infants, and their mothers tend to be less sensitive to their needs than most. This finding is important because it shows the association between psychological processes, early relationships, and health outcomes. We aim to learn about children with high-risk attachment relationships, such as disorganized-attached infants. This study compares antibiotic use, infant–mother interactive behavior, and health indicators according to infant attachment patterns (including disorganized attachment). For this purpose, we observed mothers–infants’ interactive behavior in free play at nine months and infants’ attachment in the Ainsworth Strange Situation at twelve months. Participants included 77 girls and 104 boys (full-term and preterm) and their mothers. Paradoxically, mothers of disorganized-attached infants reported that their children were ill only 1.56 times on average, but 61% of their children used antibiotics in the first nine months. The other mothers reported that their children were sick 5.73 times on average, but only 54% of their children used antibiotics in the same period. Infants with disorganized attachment had mothers who were more literate and less sensitive. These results add to a body of research that shows that early high-risk relationships affect children’s lives at multiple levels.info:eu-repo/semantics/publishedVersio

Aplicação do sistema de avaliação SBToolPT-H na otimização da sustentabilidade de um caso de estudo em Guimarães

O contexto presente alerta para a necessidade de repensar o atual modelo de consumo: a escassez de alguns recursos naturais, nomeadamente combustíveis fósseis e matérias-primas, e a consequente escalada de preços, tornam-se insustentáveis tanto a nível ambiental, como económico e social. A prática de uma construção sustentável é um dos passos mais importantes para fazer face a esta situação. Neste sentido, torna-se essencial a utilização de ferramentas que, durante a fase de projeto, permitam compreender os impactes associados às diferentes alternativas de projeto. O sistema de avaliação SBToolPT-H é uma importante ferramenta para os projetistas no sentido de se projetar com base nos princípios do desenvolvimento sustentável. Neste artigo apresenta-se a aplicação do sistema SBToolPT-H na otimização da sustentabilidade de um caso de estudo

Design and technical validation of a wearable biofeedback system for robotic gait rehabilitation

Gait disabilities affect the human quality of life. Current directions for time-effective robotic gait rehabilitation require the inclusion of biofeedback systems (BSs) as a complementary robotic tool for efficient motor relearning. This work aims to present the user-centered design and validation of a wearable BS to foster users' active participation and enable therapists' effective participation during robotic gait rehabilitation driven by active orthoses. The multimodal BS comprises a development board to manage the activation of the stimuli (vibrotactile through the vibrotactile waist and shank bands, sonorous via single earphone, and visual using RGB LED) according to data tracked by orthosis embedded sensors. The BS's versatility allows its functioning as a modular and stand-alone system or integrated into the orthotic system. The system's operability was validated with four healthy subjects walking on a treadmill with the orthotic system and BS at 1 km/h. The results showed an operable system with good usability during robotic gait rehabilitation. This wearable BS has the potential to boost symmetric gait recovery and to effectively augment the user's active participation during robotic gait therapy; thus, contributing to accelerating the user's motor recovery.This work has been supported by the FEDER Funds through the Programa Operacional Regional do Norte and national funds from Fundacao para a Ciencia e Tecnologia with the project SmartOs under Grant NORTE-01-0145-FEDER-030386, and through the COMPETE 2020-Programa Operacional Competitividade e Internacionalizacao (POCI)-with the Reference Project under Grant POCI-01-0145-FEDER-006941

Building inclusive preschool classrooms: How desirable and feasible is a set of strategies that facilitate teacher-child relationships?

Positive teacher-child relationships promote children’s engagement, as children feel more secure to explore and participate in free or oriented activities. For children with disabilities, a context wherein they can receive the support to maintain a positive engagement in different activities is even more relevant. A scarcity of research exists on how to promote ECEC quality, namely, how to facilitate teacher-child interactions in inclusive environments. This study aims to evaluate preschool teachers’ opinions about the desirability and feasibility of a set of empirically validated strategies to improve teacher-child interactions in ECEC classrooms, for the group and children with disabilities. The participants were 89 Portuguese preschool teachers. Based on a non-systematic literature review, a questionnaire composed of 22 strategies to facilitate teacher-child interactions (in 4 dimensions: emotionally responsive interactions, classroom management, attend to children’s perspectives, and scaffolding learning) was developed. Along with the questionnaire, a set of socio-demographic variables was also collected. ECEC teachers scored significantly higher in the desirability subscale compared with the feasibility subscale in all dimensions and at both the child and the group level. This gap between teachers’ perceived desirability and feasibility provides important insights regarding the dimensions which are important to reinforce in ECEC teachers’ education and professional development. The mean difference between the desirability and feasibility subscales registered a higher effect size at the child’s level than at the group’s level, confirming that the inclusion of children with disabilities in preschool settings remains a challenge. Moreover, the effect size was small to moderate in the Emotionally Responsive Interactions dimension for both child and group levels. These results are aligned with previous studies stating that among different self-identified dimensions for improvement, emotional support is the less evoked by ECEC teachers. Across all dimensions, the main reason teachers give for difficulty in feasibility, both at the group and child’s level, is lack of knowledge. Overall, understanding the reasons teachers attribute to the difference between the strategies’ desirability and feasibility informs the assessment of teacher education needs and might be operationalized as a new observation instrument.info:eu-repo/semantics/publishedVersio

Author Correction: Human Sexual Cycles are Driven by Culture and Match Collective Moods

This deposit is composed simultaneously by the original published article and also by the "correction" for the published article (erratum).This deposit is composed by the main article plus the supplementary materials of the publication.The link for the original article: https://www.nature.com/articles/s41598-017-18262-5A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.Human reproduction does not happen uniformly throughout the year and what drives human sexual cycles is a long-standing question. The literature is mixed with respect to whether biological or cultural factors best explain these cycles. The biological hypothesis proposes that human reproductive cycles are an adaptation to the seasonal (hemisphere-dependent) cycles, while the cultural hypothesis proposes that conception dates vary mostly due to cultural factors, such as holidays. However, for many countries, common records used to investigate these hypotheses are incomplete or unavailable, biasing existing analysis towards Northern Hemisphere Christian countries. Here we show that interest in sex peaks sharply online during major cultural and religious celebrations, regardless of hemisphere location. This online interest, when shifted by nine months, corresponds to documented human births, even after adjusting for numerous factors such as language and amount of free time due to holidays. We further show that mood, measured independently on Twitter, contains distinct collective emotions associated with those cultural celebrations. Our results provide converging evidence that the cyclic sexual and reproductive behavior of human populations is mostly driven by culture and that this interest in sex is associated with specific emotions, characteristic of major cultural and religious celebrations.National Institutes of Health grant: (01LM011945-01); Fundação para a Ciência e a Tecnologia grant: (PTDC IVC ESCT 5337 2012); Welcome DFRH WIIA 60 2011; Marie Curie Actions; Defense Advanced Research Projects Agency (DARPA) - NGS2 program grant: (#D17AC00005); Economic Development Agency grant: (ED17HDQ3120040); NSF Award grant: (IIS-0811994).info:eu-repo/semantics/publishedVersio

Methacrylated gellan gum hydrogels for application in nucleus pulposus regeneration: in vitro and in vivo studies

Natural-based hydrogels have been attracting great deal of attention for tissue engineering of nucleus pulposus (NP). Gellan gum is an extracellular microbial polysaccharide from Sphingomonas elodea that forms a firm and transparent gel with interesting features for use as an in vitro 3D cell support, or as an in vivo injectable system. Recently, gellan gum-based hydrogels (ionic- and photocrosslinked methacrylated gellan gum) have been proposed as potential candidates for NP regeneration1. An important feature of these hydrogels will be their capacity to control blood vessel growth, since the NP is naturally avascular. Our aim was to investigate the biological performance of the developed hydrogels, in vitro. The angiogenic/anti-angiogenic potential of the GG-based hydrogels was also carried out in vivo, using an optimized adaptation of the chorioallantoic membrane (CAM) assay.(undefined