Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Effect of short chain fructooligosaccharides (scFOS) on immunological status and gut microbiota of gilthead sea bream (Sparus aurata) reared at two temperatures

The effects of dietary short chain fructooligosaccharides (scFOS) incorporation on hematology, fish immune status, gut microbiota composition, digestive enzymes activities, and gut morphology, was evaluated in gilthead sea bream (Sparus aurata) juveniles reared at 18 °C and 25 °C. For that purpose, fish with 32 g were fed diets including 0, 0.1, 0.25 and 0.5% scFOS during 8 weeks. Overall, scFOS had only minor effects on gilthead sea bream immune status. Lymphocytes decreased in fish fed the 0.1% scFOS diet. Fish fed the 0.5% scFOS diet presented increased nitric oxide (NO) production, while total immunoglobulins (Ig) dropped in those fish, but only in the ones reared at 25 °C. Red blood cells, hemoglobin, bactericidal activity and NO were higher at 25 °C, whereas total white blood cells, circulating thrombocytes, monocytes and neutrophils were higher at 18 °C. In fish fed scFOS, lymphocytes were higher at 18 °C. Total Ig were also higher at 18 °C but only in fish fed 0.1% and 0.5% scFOS diets. No differences in gut bacterial profiles were detected by PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) between dietary treatments. However, group's similarity was higher at 25 °C. Digestive enzymes activities were higher at 25 °C but were unaffected by prebiotics incorporation. Gut morphology was also unaffected by dietary prebiotic incorporation. Overall, gut microbiota composition, digestive enzymes activities and immunity parameters were affected by rearing temperature whereas dietary scFOS incorporation had only minor effects on these parameters. In conclusion, at the tested levels scFOS does not seem worthy of including it in gilthead sea bream juveniles diets.

Curry-Howard for sequent calculus at last!

This paper tries to remove what seems to be the remaining stumbling blocks in the way to a full understanding of the Curry-Howard isomorphism for sequent calculus, namely the questions: What do variables in proof terms stand for? What is co-control and a co-continuation? How to define the dual of Parigot's mu-operator so that it is a co-control operator? Answering these questions leads to the interpretation that sequent calculus is a formal vector notation with first-class co-control. But this is just the "internal" interpretation, which has to be developed simultaneously with, and is justified by, an "external" one, offered by natural deduction: the sequent calculus corresponds to a bi-directional, agnostic (w.r.t. the call strategy), computational lambda-calculus. Next, the duality between control and co-control is studied and proved in the context of classical logic, where one discovers that the classical sequent calculus has a distortion towards control, and that sequent calculus is the de Morgan dual of natural deduction.

A Gß protein and the TupA Co-Regulator bind to protein kinase A Tpk2 to act as antagonistic molecular switches of fungal morphological changes

A Gß protein and the TupA Co-Regulator Bind to Protein Kinase A Tpk2 to Act as Antagonistic Molecular Switches of Fungal Morphological Changes

NF-kB pathway controls mitochondrial dynamics

The Optic atrophy 1 protein (OPA1) is a key element in the dynamics and morphology of mitochondria. We demonstrated that the absence of I?B kinase-a, which is a key element of the nonclassical NF-?B pathway, has an impact on the mitochondrial network morphology and OPA1 expression. In contrast, the absence of NF-?B essential modulator (NEMO) or I?B kinase-ß, both of which are essential for the canonical NF-?B pathway, has no impact on mitochondrial dynamics. Whereas Parkin has been reported to positively regulate the expression of OPA1 through NEMO, herein we found that PARK2 overexpression did not modify the expression of OPA1. PARK2 expression reduced the levels of Bax, and it prevented stress-induced cell death only in Bak-deficient mouse embryonic fibroblast cells. Collectively, our results point out a role of the nonclassical NF-?B pathway in the regulation of mitochondrial dynamics and OPA1 expression.

Puberty in male collared peccary (Pecari tajacu) determined by quantitative analysis of spermatogenic cells

Biological studies are necessary for the management of wildlife in captivity, and knowledge of reproduction is one of the important features for increasing production. The objective of the research was to determine the age at which male collared peccaries reach puberty. Testicular samples of 15 animals, aged 7 to 16 months, distributed into five groups (G1, G2, G3, G4 and G5) were used. The testes showed considerably increased weight, length and width (p < 0.05) from G1 to G3, whereas, from this group onward, the development of this organ was slower. There was positive correlation (p < 0.001) between the following testicular parameters: weight and length (r = 0.97), weight and width (r = 0.88), length and width (r = 0.92). Regarding the diameter of seminiferous tubules, an increase was observed (p < 0.05) from G1 to G4. The total number of spermatogenic cells increased significantly (p < 0.05) until G3 and then it stabilized. There was also positive correlation between testis weight and tubular diameter (r = 0.99, p < 0.001), and testis weight and spermatogenic cells (r = 0.98, p < 0.001). The number of Sertoli cells decreased significantly (p < 0.05) from G1, when they were undifferentiated as support cells, to G5, when they occurred together with the complete line of spermatic cells. The results demonstrate that the reproductive development of peccaries can be classified into the following stages: impuberty (G1, 7-8 months); pre-pubertal (G2, 9-10 months); pubertal (G3, 11-12 months); post-pubertal 1 (G4, 13-14 months); and post-pubertal 2 (G5, 15-16 months). Based on the histological analyses, puberty in the male collared peccary was determined to occur between 11 and 12 months of age.

Relation between oral health and socioeconomic variables among schoolchildren aged 12 in the City of Manaus - AM

Studies have shown that the age of 12 was determined as the age of global monitoring of caries for international comparisons and monitoring of disease trends. The aimed was to evaluate the prevalence of dental caries, fluorosis and periodontal condition and their relation with socioeconomic factors among schoolchildren aged twelve in the city of Manaus, AM. This study with a probabilistic sample of 661 children was conducted, 609 from public and 52 from private schools, in 2008. Dental caries, periodontal condition and dental fluorosis were evaluated. In order to obtain the socioeconomic classification of each child (high, upper middle, middle, lower middle, low and lower low socioeconomic classes), the guardians were given a questionnaire. The mean decayed teeth, missing teeth, and filled teeth (DMFT) found at age twelve was 1.89. It was observed that the presence of dental calculus was the most severe periodontal condition detected in 39.48%. In relation to dental fluorosis, there was a low prevalence in the children examined, i.e., the more pronounced lines of opacity only occasionally merge, forming small white areas. The study showed a significant association of 5% among social class with dental caries and periodontal condition. In schoolchildren of Manaus there are low mean of DMFT and fluorosis, but a high occurrence of gingival bleeding.

Evolving hallmarks in urothelial bladder cancer: unveiling potential biomarkers

Urothelial bladder carcinoma (UBC), the most frequent type (90%) of bladder cancer and the second most common malignancy of the urogenital region, is a relatively well understood type of cancer, with numerous studies concerning pathogenetic pathways, natural history and bladder tumor biology being reported. Despite this, it continues to remain a challenge in the oncology field, mostly due to its relapsing and progressive nature, and to the heterogeneity in the response to cisplatin-containing regimens. Although the formulae based on clinical staging and histopathological parameters are classically used as diagnostic and prognostic tools, they have proven insufficient to characterize the individual biological features and clinical behaviour of the tumours. Understanding the pathobiology of the disease can add important information to these classical criteria, and contribute to accurately predict outcome and individualize therapy for UBC patients. In this line of investigation, we found that tumour angiogenesis and lymphangiogenesis, the process of invasion and metastasis and the energy metabolism reprogramming/tumour microenvironment encompass several potential biomarkers that seem to infl bladder cancer aggressiveness and chemoresistance. We particularly highlight the roles of lymphovascular invasion, and of RKIP, CD147 and MCT1 immunoexpressions, as relevant prognostic and/or predictive biomarkers, and as promising areas of therapeutic intervention, eliciting for the development of additional studies that can validate and further explore these biomarkers.

Urothelial bladder cancer progression: lessons learned from the bench

Urothelial bladder carcinoma (UBC) is an intricate malignancy with a variable natural history and clinical behavior. Despite developments in diagnosis/prognosis refinement and treatment modalities, the recurrence rate is high, and progression from non-muscle to muscle invasive UBC commonly leads to metastasis. Moreover, patients with muscle-invasive or extra-vesical disease often fail the standard chemotherapy treatment, and overall survival rates are poor. Thus, UBC remains a challenge in the oncology field, representing an ideal candidate for research on biomarkers that could identify patients at increased risk of recurrence, progression, and chemo-refractoriness. However, progress toward personalized medicine has been hampered by the unique genetic complexity of UBC. Recent genome-wide expression and sequencing studies have brought new insights into its molecular features, pathogenesis and clinical diversity, revealing a landscape where classical pathology is intersected by the novel and heterogeneous molecular groups. Hence, it seems plausible to postulate that only an integrated signature of prognostic/predictive biomarkers inherent in different cancer hallmarks will reach clinical validation. In this review, we have summarized ours and others' research into novel putative biomarkers of progression and chemoresistance that encompass several hallmarks of cancer: tumor neovascularization, invasion and metastasis, and energy metabolism reprogramming of the tumor microenvironment.

Eco-friendly luminescent hybrid materials based on EuIII and LiI co-doped chitosan

Biopolymer-based materials have been of particular interest as alternatives do synthetic polymers due to their low toxicity, biodegradability and biocompatibility. Among them, chitosan is one of the most studied ones and has recently been investigated for the application as solid state polymer electrolytes. Furthermore, it can serve as a host for luminescent species such as rare earth ions, giving rise to materials with increased functionality, of particular interest for electrochemical devices. In this study, we investigate chitosan based luminescent materials doped wit Eu3+ and Li+ triflate salts from the structural, photophysical and conductivity points of view. Because the host presents a broad emission band in the blue to green, while Eu3+ emits in the red, fine tuning of emission colour and/or generation of white light is possible by optimizing composition and excitation scheme. Europium lifetimes (5D0) are in the range 270 – 350 µs and quantum yields are as high as 2%. Although Li+ does not interfere with the luminescent properties, it grants ion-conducting properties to the material suggesting that a combination of both properties could be further explored in multifunctional device.

Biomimetic strategies to engineer mineralised human tissues

In the last few years, many reports have been describing promising biocompatible and biodegradable materials that can mimic in a certain extent the multidimensional hierarchical structure of bone, while are also capable of releasing bioactive agents or drugs in a controlled manner. Despite these great advances, new developments in the design and fabrication technologies are required to address the need to engineer suitable biomimetic materials in order tune cells functions, i.e. enhance cell-biomaterial interactions, and promote cell adhesion, proliferation, and differentiation ability. Scaffolds, hydrogels, fibres and composite materials are the most commonly used as biomimetics for bone tissue engineering. Dynamic systems such as bioreactors have also been attracting great deal of attention as it allows developing a wide range of novel in vitro strategies for the homogeneous coating of scaffolds and prosthesis with ceramics, and production of biomimetic constructs, prior its implantation in the body. Herein, it is overviewed the biomimetic strategies for bone tissue engineering, recent developments and future trends. Conventional and more recent processing methodologies are also described.

Smart interior design of buildings and its relationship to land use

Architectural design is often associated with aesthetics and style, but it is also very important to building performance and sustainability. There are some studies associating architectural design to the choice for materials from sustainable sources, to indoor air quality, to energy efficiency and productivity. This article takes a step further to analyse how the use of efficient interior design techniques can impact the habitable space in order to improve building sustainability in land use. Smart interior design, a current trend related to the use of efficient and flexible furniture and movable walls in tiny or compact apartments, is analysed. A building with a standard design is used as a case study reference building and compared to a proposed theoretical design alternative using smart interior design techniques. In order to correctly assess sustainability performance, a quantifiable and verified method is used. Results showed that the use of smart interior design techniques can greatly reduce buildingsâ impact on the environment.

Biomaterials for cartilage tissue engineering under mechanical stimulus

Tese de Doutoramento em Ciências (Especialidade de Física)

Aplicação da metodologia ROC na avaliação de desempenho de índices de gravidade clínica em unidades de neonatologia de Portugal

Tese de Doutoramento em Engenharia Industrial e de Sistemas

Synthesis of new peptide derivatives that self-assemble into nanostructured hydrogels for biomedical applications

Tese de Doutoramento em Ciências (área de especialização em Química)