Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement

Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models

Caracterização de revestimentos de edifícios antigos

Como é de conhecimento geral as argamassas de revestimento antigas diferem das argamassas atuais, tanto na sua produção, como nos seus constituintes e até na sua resistência e durabilidade. O presente trabalho surge com o principal intuito de dissertar sobre a caraterização de algumas argamassas de revestimento e de enchimento antigas na Região Autónoma da Madeira. Desta forma foram realizados vários ensaios como a difração de raios X, a análise termogravimétrica, a determinação da percentagem do resíduo insolúvel com ataque àcido e a análise granulométrica, podendo assim ficar-se com uma ideia dos seus minerais, a quantidade de carbonato de cálcio utilizada, a quantidade de material insolúvel no ácido clorídrico e a granulometria (tamanho/dimensões) das areias. A escolha das amostras baseou-se nos critérios de maior longevidade dos edifícios, a não reabilitação destes e a possibilidade da realização do estudo dessas habitações (i.e. acessibilidade física e legal). Quanto aos ensaios efetuados, a opção de os ter utilizado prende-se com as técnicas disponíveis no Laboratório Regional de Engenharia Civil (LREC)

Bond behaviour of concrete elements strengthened with NSM CFRP laminate strips under wet-dry cycles

In the last years, the near-surface mounted (NSM) technique has been adopted to increase the load carrying capacity of concrete members. Up to now, research was mainly focused on the structural aspects of NSM strengthening of concrete structures. From an extensive bibliographic search performed, no significant information was found concerning to the NSM long-term performance. The present work has the main objective to contribute for the knowledge on durability performance of the NSM technique with CFRP lami-nates submitted to wet-dry cycles by means of direct pullout tests. The influence of the bond length, the groove width and depth, and the number of wet-dry cycles on the bond performance were the main parame-ters analyzed. Thirty five cubic specimens were tested. Digital image correlation method was used, as a com-plementary tool for monitoring the NSM pullout tests. The tests are described, and the obtained results are presented and discussed

Diferentes métodos de avaliação do comportamento da ligação de laminados de CFRP ao betão de acordo com a técnica NSM

O presente trabalho pretende contribuir para o conhecimento da durabilidade da técnica baseada na inserção de laminados de CFRP (Carbon Fiber Reinforced Polymer) no betão de recobrimento (NSM, Near-Surface Mounted). Para isso, foram realizados trinta e cinco ensaios de arrancamento direto em provetes cúbicos previamente submetidos a ciclos de molhagem e secagem na presença de cloretos (NaCl). A monitorização dos ensaios realizou-se com recurso a equipamentos tradicionais (e.g. células de carga e LVDT) e ainda ao método de correlação digital de imagem. No presente trabalho, os ensaios realizados são descritos e os resultados mais significativos, experimentais e numéricos, são apresentados e analisados

Effects of different environmental conditions on the mechanical characteristics of a structural epoxy

With the aim of characterising a commercially available epoxy adhesive used for fibre-reinforced polymers strengthening applications, when submitted to different environmental conditions, mainly thermal (TC), freeze-thaw (FT), and wet-dry (WD) cycles and immersion in pure (PW) and water with chlorides (CW) for periods of exposure that lasted up to 16 months, an experimental program was carried out. Several methodologies were used in its characterization, mainly the scanning electron microscope (SEM), dynamic mechanical analysis (DMA), standard tensile tests (STT) coupled with digital image correlation (DIC). In general the results revealed that the chemical composition was not affected by the environmental conditions. Nevertheless, it was verified through DMA and STT that the modulus of elasticity and tensile strength of the epoxy adhesive increased in the TC, while the specimens submitted to PW and CW faced a high degradation in terms of its mechanical properties. Eventually, the glass transition temperature (Tg) was not affected by the environmental conditions, apart from the specimens subjected to TC and FT, presenting a higher and lower Tg, respectively, when compared with the reference specimens.This work is supported by FEDER funds through the Operational Program for Competitiveness Factors - COMPETE and National Funds through FCT - Portuguese Foundation for Science and Technology under the project FPReDur PTDC/ECM-EST/2424/2012. The first and second authors wishes also to acknowledge the grants SFRH/BD/89768/2012 and SFRH/BD/80338/2011, respectively, provided by FCT

Durability of bond in NSM CFRP-concrete systems under different environmental conditions

This paper addresses the durability of bond between concrete and carbon fibre reinforced polymer (CFRP) strips installed according to the near-surface mounted (NSM) technique (NSM CFRP-concrete systems) under the effects of two main groups of environmental conditions: (i) laboratory-based ageing conditions; (ii) real outdoor ageing conditions. The bond degradation was evaluated by carrying out direct pullout tests on aged specimens that were previously subjected to distinct environmental conditions for different periods of exposure. Moreover, the degradation of the mechanical properties of the involved materials was investigated. The digital image correlation (DIC) method was used to document the evolution of the deformation fields at the surface over the whole region of interest consisting of concrete and epoxy adhesive at the ligament region. This information supported the discussion about the evolution of the bond resistant mechanism developed in NSM CFRP-concrete specimens during testing, as well as the assessment of the bond quality of the system. In general, the results obtained from the durability tests conducted have shown that the different exposure environments, which may be considered as quite severe, did not result in significant damage on NSM CFRP-concrete system. The maximum decrease of about 12% on bond strength was obtained for real outdoor environments. Conversely, a maximum increase of 8% on bond strength was obtained on the specimens exposed to the temperature cycles between –15 °C and +60 °C. DIC allowed to document the stress transfer mechanisms established between the CFRP and the concrete substrate, revealing the crack patterns and the influence widths of the CFRP reinforcement strips, which were shown to be important for avoiding group effect when using multiple parallel strengthening CFRP strips.FEDER funds through the Operational Program for Competitiveness Factors - COMPETE and National Funds through FCT - Portuguese Foundation for Science and Technology under the projects CutInDur FCOMP-01-0124-FEDER-014811 (PTDC/ECM/112396/2009), FRPLongDur POCI-01-0145-FEDER-016900 (PTDC/ECM-EST/1282/2014) and partly financed by the project POCI-01-0145-FEDER-007633. The authors also like to thank all the companies that have been involved supporting and contributing for the development of this study, mainly: S&P Clever Reinforcement Ibérica Lda., Artecanter - Indústria de Transformação de Granitos, Lda., Vialam – Indústrias Metalúrgicas e Metalomecânicas, Lda.info:eu-repo/semantics/publishedVersio

Durabilidade da ligação entre o betão e laminados de CFRP aplicados de acordo com a técnica NSM

Nos últimos anos, considerável investigação tem sido desenvolvida no reforço de estruturas de betão armado com a técnica NSM. Esta técnica consiste na introdução de laminados ou varões de FRP em ranhuras pré-executadas no betão de recobrimento do elemento a reforçar. Normalmente, são utilizados adesivos epoxídicos na ligação entre FRP e betão O presente trabalho procura contribuir para o conhecimento da durabilidade do comportamento da aderência entre o betão e laminados de fibra de carbono (CFRP) aplicados de acordo com a técnica NSM, de modo a colmatar algumas lacunas relevantes que existem sobre este assunto. Com esse propósito, foi realizado um extenso programa experimental através de ensaios de arranque direto em provetes cúbicos de betão reforçados com laminados de CFRP aplicando a técnica NSM (sistema NSM CFRP). A geometria da ranhura, o comprimento de amarração e a classe de resistência do betão foram considerados parâmetros fixos. Os provetes foram inicialmente submetidos a ações ambientais de envelhecimento acelerado e posteriormente ensaiados até à rotura de forma a ser avaliado o respetivo comportamento da ligação entre CFRP e betão. O efeito das seguintes condições ambientais no comportamento da ligação foi estudado: (i) imersão em água pura; (ii) imersão em água com cloretos; (iii) ciclos de molhagem/secagem em água com cloretos; (iv) ciclos térmicos; e, (v) ciclos de gelo/degelo. O período de exposição variou entre 240 a 480 dias. Após terem sido submetidos às respetivas condições ambientais, os provetes foram monotonicamente ensaiados até à rotura, monitorizando-se a força de arranque aplicada e o deslizamento do laminado na extremidade carregada da ligação. As ações ambientais investigadas não conduziram a níveis de degradação significativos no desempenho global da ligação do sistema NSM CFRP-betão, sendo que a máxima redução da resistência da ligação obtida foi cerca de 5% e ocorreu nos provetes que estiveram expostos a 240 ciclos de gelo-degelo.FEDER através do Programa Operacional para Fatores de Competitividade – COMPETE e fundos nacionais através da FCT- Fundação Portuguesa para a Ciência e a Tecnologia, no âmbito do projeto de investigação CutInDur FCOMP-01-0124-FEDER-014811 (FCT PTDC/ECM/112396/2009), FRPLongDur POCI-01-0145-FEDER-016900 (FCT PTDC/ECM- EST/1282/2014) e em parte financiado pelo projeto POCI-01-0145-FEDER-007633. Os autores também gostariam de agradecer à empresa S&P Clever Reinforcement Ibérica Lda, que esteve envolvida, apoiando e contribuindo para o desenvolvimento deste estudo

Implementação em Portugal de um estudo de prevalência da demência e da depressão geriátrica: a metodologia do 10/66 Dementia Research Group

ResumoIntroduçãoA demência e a depressão têm um impacto social muito significativo. Em Portugal, escasseiam dados epidemiológicos em pessoas idosas na comunidade. Em países em desenvolvimento, o 10/66 Dementia Research Group (DRG) conduziu múltiplos estudos sobre a prevalência e a incidência destes quadros. Os protocolos de avaliação 10/66‐DRG foram validados extensivamente nesses países, havendo vantagens potenciais na aplicação em regiões europeias com populações idosas de baixa escolaridade. Neste estudo, fundamentamos e descrevemos a implementação em Portugal da metodologia 10/66‐DRG para estudo da prevalência da demência e da depressão geriátrica.Materiais e métodosO trabalho de campo desenrola‐se numa fase única, em áreas geográficas definidas, sendo avaliados detalhadamente e de forma sistemática todos os residentes de 65 anos ou mais. A informação é recolhida dos participantes e de informadores próximos (www.alz.co.uk/1066/).ResultadosSelecionámos e mapeámos uma área urbana (em Fernão Ferro) e outra rural (em Mora), definindo amostras finais de 702 e 779 pessoas, respetivamente. Os instrumentos de avaliação foram cuidadosamente traduzidos e adaptados ao contexto português. Teve lugar um treino rigoroso dos entrevistadores, assegurando a fiabilidade de cotação interobservadores.Discussão e conclusãoA aplicação dos protocolos 10/66‐DRG permitirá obter dados robustos de prevalência de demência e de depressão, com amostras comunitárias de pessoas idosas em Portugal. Dada a validade internacional da metodologia utilizada, estes resultados serão comparáveis com os de outros centros 10/66, à escala mundial.AbstractIntroductionDementia and depression have a huge social impact. In Portugal, epidemiological data is scarce regarding community dwelling elderly people with these conditions. In developing countries, the 10/66 Dementia Research Group‐DRG has conducted multiple studies on the corresponding prevalence and incidence. The 10/66‐DRG protocols for population‐based studies were extensively validated in those countries, and there is a rationale to apply them in low literacy elderly populations in Europe. We describe the implementation of the protocols related to the prevalence study (on dementia and geriatric depression) in Portuguese settings.Materials and methodsThis is a one‐phase survey, in which all people 65+ years living in defined catchment areas are comprehensively evaluated. Information is collected directly from participants and from a related informant (www.alz.co.uk/1066/).ResultsWe selected and mapped an urban area (in Fernão Ferro) and a rural one (in Mora). The final samples were n=702 and n=779 respectively. Questionnaires were carefully translated and culturally adapted. Rigorous training procedures took place to ensure inter‐rater reliability.Discussion and conclusionsThe implementation of the 10/66‐DRG protocols will lead to robust data on the prevalence of dementia and depression in community samples of elderly people in Portugal. Given the international validity of our methodology, these results will be comparable with those from other 10/66 centres around the world

Bond strength of resin cements to leucite-reinforced ceramics: part 2 – after one-year aging in water

The aim of this study was to compare the shear bond strength (SBS) of two resin cements bonded to four leucite-reinforced ceramics after one week and one year of aging. Material and methods: Forty ceramic blocks (4 mm wide, 14 mm length, and 2 mm thick) were used (1 week) and reused at the back side (1 year). The blocks were abraded with aluminum oxide (90 µm) and randomly divided into eight groups for each time. Two dual resin cements (RelyX ARC and RelyX U200 self-adhesive, 3M ESPE) were bonded to ceramics Creapress (CRE – Creation / Klema), Finesse All-Ceramic (FIN – Dentsply / Ceramco), IPS Empress Esthetic (IEE – Ivoclar Vivadent) and Vita PM9 (PM9-Vita). For each resin, time, and ceramic block, after applications of the 10% hydrofluoric acid (for 1 min) and silane, 3 Tygon cut tubes were positioned over each block and filled in with the resin cements (light-cured for 40 s). The tubing molds were removed to expose the bond specimens as cylinders (area=0.38 mm2) stored in relative humidity at 24±2°C for one week and at 37±2°C for one year. All bonds were tested in an Instron in shear (applied of the base cylinder with a thin wire - 0.25 mm) at speed of 0.5 mm/min, until failure. Results: The results were analyzed by ANOVA (resin cements, ceramic systems, and time) and Tukey test (p<0.05) for rank ordering of SBS. The FIN and IEE ceramics did not show significant SBS decreasing on aging with U200. The mean SBS decreasing for all the ceramics was 36% with ARC and 14% with U200 cement. Conclusion: The SBS of ARC cement were significantly lower for all ceramics with aging than that of U200 cement. The SBS of ARC cement was also weakened by aging. FIN ceramic + U200 cement proved to be the most stable and strongest bond strength, and PM9+ARC cement proved to be the weakest bond strength with low stability.The aim of this study was to compare the shear bond strength (SBS) of two resin cements bonded to four leucite-reinforced ceramics after one week and one year of aging. Material and methods: Forty ceramic blocks (4 mm wide, 14 mm length, and 2 mm thick) were used (1 week) and reused at the back side (1 year). The blocks were abraded with aluminum oxide (90 µm) and randomly divided into eight groups for each time. Two dual resin cements (RelyX ARC and RelyX U200 self-adhesive, 3M ESPE) were bonded to ceramics Creapress (CRE – Creation / Klema), Finesse All-Ceramic (FIN – Dentsply / Ceramco), IPS Empress Esthetic (IEE – Ivoclar Vivadent) and Vita PM9 (PM9-Vita). For each resin, time, and ceramic block, after applications of the 10% hydrofluoric acid (for 1 min) and silane, 3 Tygon cut tubes were positioned over each block and filled in with the resin cements (light-cured for 40 s). The tubing molds were removed to expose the bond specimens as cylinders (area=0.38 mm2) stored in relative humidity at 24±2°C for one week and at 37±2°C for one year. All bonds were tested in an Instron in shear (applied of the base cylinder with a thin wire - 0.25 mm) at speed of 0.5 mm/min, until failure. Results: The results were analyzed by ANOVA (resin cements, ceramic systems, and time) and Tukey test (p<0.05) for rank ordering of SBS. The FIN and IEE ceramics did not show significant SBS decreasing on aging with U200. The mean SBS decreasing for all the ceramics was 36% with ARC and 14% with U200 cement. Conclusion: The SBS of ARC cement were significantly lower for all ceramics with aging than that of U200 cement. The SBS of ARC cement was also weakened by aging. FIN ceramic + U200 cement proved to be the most stable and strongest bond strength, and PM9+ARC cement proved to be the weakest bond strength with low stability

Show your beaks and we tell you what you eat: Different ecology in sympatric Antarctic benthic octopods under a climate change context

Sympatry can lead to higher competition under climate change and other environmental pressures, including in South Georgia, Antarctica, where the two most common octopod species, Adelieledone polymorpha and Pareledone turqueti, occur side by side. Since cephalopods are typically elusive animals, the ecology of both species is poorly known. As beaks of cephalopods are recurrently found in top predator's stomachs, we studied the feeding ecology of both octopods through the evaluation of niche overlapping and specific beak adaptations that both species present. A multidisciplinary approach combining carbon (δ13C) and nitrogen (δ15N) stable isotope signatures, mercury (Hg) analysis and biomaterials' engineering techniques was applied to investigate the beaks. An isotopic niche overlap of 95.6% was recorded for the juvenile stages of both octopod species, dropping to 19.2% for the adult stages. Both A. polymorpha and P. turqueti inhabit benthic ecosystems around South Georgia throughout their lifecycles (δ13C: −19.21 ± 1.87‰, mean ± SD for both species) but explore trophic niches partially different during adult life stages (δ15N: 7.01 ± 0.40‰, in A. polymorpha, and 7.84 ± 0.65‰, in P. turqueti). The beaks of A. polymorpha are less dense and significantly less stiff than in P. turqueti. Beaks showed lower mercury concentration relative to muscle (A. polymorpha - beaks: 0.052 ± 0.009  μg g−1, muscle: 0.322 ± 0.088  μg g−1; P. turqueti - beaks: 0.038 ± 0.009  μg g−1; muscle: 0.434 ± 0.128  μg g−1). Overall, both octopods exhibit similar habitats but different trophic niches, related to morphology/function of beaks. The high Hg concentrations in both octopods can have negative consequences on their top predators and may increase under the present climate change context.British Antarctic Survey for assisting in the collection of the specimens for this work. Many thanks to 3B's Research Group (University of Minho) and MAREFOZ who were responsible for analysing the physical properties of beaks and stable isotope signatures. A special thank you to our colleague José Queirós from MARE-UC (Coimbra, Portugal) for his suggestions and guidance. A debt of gratitude is also owed to Dr. A. Louise Allcock (NUI Galway) for her useful guidelines. This work is an international effort under the Scientific Committee on Antarctic Research (SCAR) associated programs, expert and action groups, namely SCAR AnT-ERA, SCAR EGBAMM and ICED. J.C. Xavier was supported by the Investigator Programme (IF/00616/2013) of the Foundation for Science and Technology (FCT-Portugal) and PROPOLAR, and F.R. Ceia was supported by a postdoctoral fellowship (SFRH/BPD/95372/2013) attributed by FCT-Portugal and the European Social Fund (POPH, EU). This study benefited from the strategic program of MARE, financed by FCT-Portugal (MARE- UID/MAR/04292/2019). We also acknowledge FCT-Portugal through a PhD grant to J. Seco (SRFH/PD/BD/113487