FE - Contribuições em Revistas Científicas / Contribution to Journals
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- An experimental investigation of residual stresses in hard machining of AISI 52100 steelPublication . Caruso, S.; Umbrello, D.; Outeiro, J. C.; Filice, L.; Micari, F.In this paper an experimental investigation was conducted to determine the effects of the tool cutting-edge geometry, workpiece hardness, cutting speed, and microstructural changes (white and dark layers) on the residual stresses in dry orthogonal hard machining of AISI 52100 steel. X-ray diffraction technique was used to obtain in-depth residual stresses profiles in both axial and circumferential directions. The results show that tool geometry, workpiece hardness and cutting parameters significantly affect the surface residual stress, maximum compressive residual stress below the machined surface and its location. Moreover, microstructural analysis shows that thermally-induced phase transformations have a significant impact on the magnitude and location of this maximum compressive residual stress peak.
- Dynamic transitions in RNA polymerase II density profiles during transcription terminationPublication . Grosso, Ana Rita; Almeida, Sérgio Fernandes de; Braga, José; Carmo-Fonseca, MariaEukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3′-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for "metagene" analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3′-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3′-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3′-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.
- Formal extension of the Whitney functor and dualityPublication . Martins, Ana Rita; Fernandes, Teresa MonteiroOn a complex manifold we introduce the formal extension of the Whitney functor and the algebraic extension of the tempered cohomology functor, and prove a natural topological duality between them.
- Genome sequencing reveals a phage in Helicobacter pyloriPublication . Lehours, Philippe; Vale, Filipa F.; Bjursell, Magnus K.; Melefors, Ojar; Advani, Reza; Glavas, Steve; Guegueniat, Julia; Gontier, Etienne; Lacomme, Sabrina; Matos, António Alves; Menard, Armelle; Mégraud, Francis; Engstrand, Lars; Andersson, Anders F.Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensive H pylori pan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26× mean coverage) of H pylori strain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed in H pylori cells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341 H pylori strains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution of H pylori.
- Geographic distribution of methyltransferases of Helicobacter pylori: evidence of human host population isolation and migrationPublication . Vale, Filipa F.; Mégraud, Francis; Vítor, Jorge M.Background. Helicobacter pylori colonizes the human stomach and is associated with gastritis, peptic ulcer, and gastric cancer. This ubiquitous association between H. pylori and humans is thought to be present since the origin of modern humans. The H. pylori genome encodes for an exceptional number of restriction and modifications (R-M) systems. To evaluate if R-M systems are an adequate tool to determine the geographic distribution of H. pylori strains, we typed 221 strains from Africa, America, Asia, and Europe, and evaluated the expression of different 29 methyltransferases. Results. Independence tests and logistic regression models revealed that ten R-M systems correlate with geographical localization. The distribution pattern of these methyltransferases may have been originated by co-divergence of regional H. pylori after its human host migrated out of Africa. The expression of specific methyltransferases in the H. pylori population may also reflect the genetic and cultural background of its human host. Methyltransferases common to all strains, M. HhaI and M. NaeI, are likely conserved in H. pylori, and may have been present in the bacteria genome since the human diaspora out of Africa. Conclusion. This study indicates that some methyltransferases are useful geomarkers, which allow discrimination of bacterial populations, and that can be added to our tools to investigate human migrations.
- Mechanical construction and installation of the ATLAS tile calorimeterPublication . CERN 2013 for the benefit of the ATLAS collaboration; Abdallah, J.This paper summarises the mechanical construction and installation of the Tile Calorimeter for the ATLAS experiment at the Large Hadron Collider in CERN, Switzerland. The Tile Calorimeter is a sampling calorimeter using scintillator as the sensitive detector and steel as the absorber and covers the central region of the ATLAS experiment up to pseudorapidities ±1.7. The mechanical construction of the Tile Calorimeter occurred over a period of about 10 years beginning in 1995 with the completion of the Technical Design Report and ending in 2006 with the installation of the final module in the ATLAS cavern. During this period approximately 2600 metric tons of steel were transformed into a laminated structure to form the absorber of the sampling calorimeter. Following instrumentation and testing, which is described elsewhere, the modules were installed in the ATLAS cavern with a remarkable accuracy for a structure of this size and weight.
- Neural-network approach to modeling liquid crystals in complex confinementPublication . Santos-Silva, T.; Teixeira, P. I. C.; Anquetil-Deck, C.; Cleaver, D. J.Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.
- New NCI-N87-derived human gastric epithelial line after human telomerase catalytic subunit over-expressionPublication . Saraiva-Pava, Kathy; Navabi, Nazanin; Skoog, Emma C.; Lindén, Sara K.; Oleastro, Mónica; Roxo-Rosa, MónicaAIM: To establish a cellular model correctly mimicking the gastric epithelium to overcome the limitation in the study of Helicobacter pylori (H. pylori ) infection. METHODS: Aiming to overcome this limitation, clones of the heterogenic cancer-derived NCI-N87 cell line were isolated, by stably-transducing it with the human telomerase reverse-transcriptase (hTERT) catalytic subunit gene. The clones were first characterized regarding their cell growth pattern and phenotype. For that we measured the clones' adherence properties, expression of cell-cell junctions' markers (ZO-1 and E-cadherin) and ability to generate a sustained transepithelial electrical resistance. The gastric properties of the clones, concerning expression of mucins, zymogens and glycan contents, were then evaluated by haematoxylin and eosin staining, Periodic acid Schiff (PAS) and PAS/Alcian Blue-staining, immunocytochemistry and Western blot. In addition, we assessed the usefulness of the hTERT-expressing gastric cell line for H. pylori research, by performing co-culture assays and measuring the IL-8 secretion, by ELISA, upon infection with two H. pylori strains differing in virulence. RESULTS: Compared with the parental cell line, the most promising NCI-hTERT-derived clones (CL5 and CL6) were composed of cells with homogenous phenotype, presented higher relative telomerase activities, better adhesion properties, ability to be maintained in culture for longer periods after confluency, and were more efficient in PAS-reactive mucins secretion. Both clones were shown to produce high amounts of MUC1, MUC2 and MUC13. NCI-hTERT-CL5 mucins were shown to be decorated with blood group H type 2 (BG-H), Lewis-x (Lex), Ley and Lea and, in a less extent, with BG-A antigens, but the former two antigens were not detected in the NCI-hTERT-CL6. None of the clones exhibited detectable levels of MUC6 nor sialylated Lex and Lea glycans. Entailing good gastric properties, both NCIhTERT- clones were found to produce pepsinogen-5 and human gastric lipase. The progenitor-like phenotype of NCI-hTERT-CL6 cells was highlighted by large nuclei and by the apical vesicular-like distribution of mucin 5AC and Pg5, supporting the accumulation of mucus-secreting and zymogens-chief mature cells functions. CONCLUSION: These traits, in addition to resistance to microaerobic conditions and good responsiveness to H. pylori co-culture, in a strain virulence-dependent manner, make the NCI-hTERT-CL6 a promising model for future in vitro studies.
- Optimization of the culture medium composition using response surface methodology for new recombinant cyprosin B production in bioreactor for cheese productionPublication . Sampaio, Pedro N.; Calado, Cecília R. C.; Sousa, Lisete; Bressler, David C.; Pais, Maria Salomé; Fonseca, Luís PinaThe optimization of culture medium compositionwas carried out for improvement the recombinantcyprosin B production, an enzyme with high milk-clottingactivity. Response surface methodology (RSM) wasapplied to evaluate the effect of variables namely glucose,yeast extract (YE) and bactopeptone present in the culturemedium, used for recombinant cyprosin B production bytransformed Saccharomyces cerevisiae BJ1991 strain inshake-flask and bioreactor culture conditions. The centracomposite experimental design (CCD) was adopted toderive a statistical model for optimizing the composition ofthe fermentation medium. The optimal concentration estimatedfor each variable related to a theoretical maximumof cyprosin B activity (488 U mL-1) was 30 g L-1 glucose,15 g L-1 YE and 27 g L-1 bactopeptone. The optimizedmedium composition, based on empirical model, ledto a cyprosin B activity of 519 U mL-1, which correspondsto an increase of 46%. The fermentation using optimizedculture medium in a 5-L bioreactor allowed a significantincrease in biomass (82%) and recombinant cyprosin Bproduction (139%). The improvement in the recombinantcyprosin B production after optimization process can beconsidered adequate for large-scale applications, and theclotting activity of cyprosin B account for their use inindustrial cheese making.
- Overview of the radiographers’ practice in 65 healthcare centers using digital mammography systems in PortugalPublication . Reis, Cláudia Sá dos; Pascoal, Ana; Radu, Lucian; Oliveira, Mário Fartaria de; Alves, JoãoPurpose: To assess current practices in digital mammography (DM) in Portuguese healthcare providers using digital systems. To investigate compliance with European standards regarding mean glandular dose and quality control practice and to identify optimisation needs. Methods: Two questionnaires, targeted at breast radiographers and chief radiographers, were designed and applied in 65 imaging departments offering DM. Questions fielded were focused on the staff profile and technical/clinical practice. Results: Prior to starting their activity in DM, 70% (82 out of 118) of the respondents received training in DM. The practice in 29 out of 59 providers was established by the manufacturers’ recommendations for image acquisition. Variations were observed between radiographers who belong to the same provider namely the selection of exposure parameters such as the target-filter combination and automatic mode. The use of the manual exposure mode was reported for imaging breast implants (44%) and surgical specimens (22%). The main causes of repeat examinations were skin folding (21%) and absence of pectoral muscle (PM) (20%). Conclusions: The study revealed opportunities to optimise radiographers’ practice in DM regarding the selection of exposure parameters. A robust and consistent training programme in DM and established local protocols can help to reduce the variations observed and improve clinical practice. Main Messages: • Radiographers adopted different practices selecting AEC modes and T/F combinations. • Radiographer practice is more consistent using DR than using CR systems. • The main causes for rejecting images were the visibility of skin folding and PM absence. • Radiographers were partly unaware of the dose indicator. • Radiographers’ training needs: QC, interventional procedures and breast dose optimisation.