Modelling Cell Cycle using Different Levels of Representation

Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform computerised simulations of biological systems, which are called in silico experiments, to attain important insights and predictions about the system behaviour with a considerably lower cost. Computer visualisation is an important part of this approach, since it provides a realistic representation of the system behaviour. We define a formal methodology to model biological systems using different levels of representation: a purely formal representation, which we call molecular level, models the biochemical dynamics of the system; visualisation-oriented representations, which we call visual levels, provide views of the biological system at a higher level of organisation and are equipped with the necessary spatial information to generate the appropriate visualisation. We choose Spatial CLS, a formal language belonging to the class of Calculi of Looping Sequences, as the formalism for modelling all representation levels. We illustrate our approach using the budding yeast cell cycle as a case study

Squid – a simple bioinformatics grid

BACKGROUND: BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. RESULTS: Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. CONCLUSION: Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example

Euclid: Superluminous supernovae in the Deep Survey

Context. In the last decade, astronomers have found a new type of supernova called superluminous supernovae (SLSNe) due to their high peak luminosity and long light-curves. These hydrogen-free explosions (SLSNe-I) can be seen to z ~ 4 and therefore, offer the possibility of probing the distant Universe. Aims. We aim to investigate the possibility of detecting SLSNe-I using ESA’s Euclid satellite, scheduled for launch in 2020. In particular, we study the Euclid Deep Survey (EDS) which will provide a unique combination of area, depth and cadence over the mission. Methods. We estimated the redshift distribution of Euclid SLSNe-I using the latest information on their rates and spectral energy distribution, as well as known Euclid instrument and survey parameters, including the cadence and depth of the EDS. To estimate the uncertainties, we calculated their distribution with two different set-ups, namely optimistic and pessimistic, adopting different star formation densities and rates. We also applied a standardization method to the peak magnitudes to create a simulated Hubble diagram to explore possible cosmological constraints. Results. We show that Euclid should detect approximately 140 high-quality SLSNe-I to z ~ 3.5 over the first five years of the mission (with an additional 70 if we lower our photometric classification criteria). This sample could revolutionize the study of SLSNe-I at z > 1 and open up their use as probes of star-formation rates, galaxy populations, the interstellar and intergalactic medium. In addition, a sample of such SLSNe-I could improve constraints on a time-dependent dark energy equation-of-state, namely w(a), when combined with local SLSNe-I and the expected SN Ia sample from the Dark Energy Survey. Conclusions. We show that Euclid will observe hundreds of SLSNe-I for free. These luminous transients will be in the Euclid data-stream and we should prepare now to identify them as they offer a new probe of the high-redshift Universe for both astrophysics and cosmology.Acknowledgements. We thank the internal EC referees (P. Nugent and J. Brichmann) as well as the many comments from our EC colleagues and friends. C.I. thanks Chris Frohmaier and Szymon Prajs for useful discussions about supernova rates. C.I. and R.C.N. thank Mark Cropper for helpful information about the V IS instrument. C.I. thanks the organisers and participants of the Munich Institute for Astro- and Particle Physics (MIAPP) workshop “Superluminous supernovae in the next decade” for stimulating discussions and the provided online material. The Euclid Consortium acknowledges the European Space Agency and the support of a number of agencies and institutes that have supported the development of Euclid. A detailed complete list is available on the Euclid web site (http://www.euclid-ec.org). In particular the Agenzia Spaziale Italiana, the Centre National dEtudes Spatiales, the Deutsches Zentrum für Luft- and Raumfahrt, the Danish Space Research Institute, the Fundação para a Ciênca e a Tecnologia, the Ministerio de Economia y Competitividad, the National Aeronautics and Space Administration, The Netherlandse Onderzoekschool Voor Astronomie, the Norvegian Space Center, the Romanian Space Agency, the State Secretariat for Education, Research and Innovation (SERI) at the Swiss Space Office (SSO), the United Kingdom Space Agency, and the University of Helsinki. R.C.N. acknowledges partial support from the UK Space Agency. D.S. acknowledges the Faculty of Technology of the University of Portsmouth for support during his PhD studies. C.I. and S.J.S. acknowledge funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant agreement No. [291222]. C.I. and M.S. acknowledge support from EU/FP7-ERC grant No. [615929]. E.C. acknowledge financial contribution from the agreement ASI/INAF/I/023/12/0. The work by KJ and others at MPIA on NISP was supported by the Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR) under grant 50QE1202. M.B. and S.C. acknowledge financial contribution from the agreement ASI/INAF I/023/12/1. R.T. acknowledges funding from the Spanish Ministerio de Economía y Competitividad under the grant ESP2015-69020-C2- 2-R. I.T. acknowledges support from Fundação para a Ciência e a Tecnologia (FCT) through the research grant UID/FIS/04434/2013 and IF/01518/2014. J.R. was supported by JPL, which is run under a contract for NASA by Caltech and by NASA ROSES grant 12-EUCLID12-0004

A study on the immunological basis of the dissociation between type I-hypersensitivity skin reactions to Blomia tropicalis antigens and serum anti-B. tropicalis IgE antibodies

<p>Abstract</p> <p>Background</p> <p>Two conditions are used as markers of atopy: the presence of circulating anti-allergen IgE antibodies and the presence of positive skin prick test (SPT) reactions to allergenic extracts. The correlation between these conditions is not absolute. This study aimed at investigating immunological parameters that may mediate this lack of correlation. Individuals whose sera contained anti-<it>B. tropicalis </it>extract IgE antibodies (α<it>-Bt</it>E IgE) were divided into two groups, according to the presence or absence of skin reactivity to <it>B. tropicalis </it>extract (<it>Bt</it>E). The following parameters were investigated: total IgE levels; α<it>-Bt</it>E IgE levels; an arbitrary α<it>-Bt</it>E IgE/total IgE ratio; the proportion of carbohydrate-reactive α<it>-Bt</it>E IgE; the proportion of α<it>-Bt</it>E IgE that reacted with <it>Ascaris lumbricoides </it>extract (<it>Al</it>E); the production of IL-10 by <it>Bt</it>E- and <it>Al</it>E-stimulated peripheral blood cells (PBMC).</p> <p>Results</p> <p>Total IgE levels were similar in the two groups, but α<it>-Bt</it>E IgE was significantly higher in the SPT-positive group (SPT<b>+</b>). A large overlap of α<it>-Bt</it>E IgE levels was found in individuals of both groups, indicating that these levels alone cannot account for the differences in SPT outcome. Individuals of the two groups did not differ, statistically, in the proportion of α-<it>Bt</it>E IgE that reacted with carbohydrate and in the production of IL-10 by <it>Bt</it>E- and <it>Al</it>E-stimulated PBMC. Both groups had part of α-<it>Bt</it>E IgE activity absorbed out by <it>Al</it>E, indicating the existence of cross-reactive IgE antibodies. However, the α-<it>Bt</it>E IgE from the SPT-negative individuals (SPT-) was more absorbed with <it>AlE </it>than the α-<it>Bt</it>E IgE from the SPT+ individuals. This finding may be ascribed to avidity differences of the α-<it>Bt</it>E IgE that is present in the two groups of individuals, and could occur if at least part of the α-<it>Bt</it>E IgE from the SPT- individuals were elicited by <it>A. lumbricoides </it>infection.</p> <p>Conclusion</p> <p>The present results suggest that a low ratio of specific IgE to total IgE levels (in a minority of individuals), and differences in α-<it>Bt</it>E IgE avidities (which would have high affinities for <it>A. lumbricoides </it>antigens in SPT- than in SPT<b>+ </b>individuals) may play a role in the down-modulation of type-I hypersensitivity reaction against aeroallergens described in helminth-infected individuals.</p

Laser printing of micro-electronic communication systems for smart implants applications

Endow the implant with intrinsic communication system between sensors and actuators or between implant and patient is a key factor for its long-term success. The capacity of early diagnosis of failures and the ability to remedy them are necessary to minimize expensive complications and reducing revision procedures. Ti6Al4V is the most used titanium alloy for implant’s fabrication. In this sense, this work presents a promising approach to print communication systems by using laser technology, aiming integrate the smart components on titanium implants. Laser has been employed as a versatile tool to modify the surface in different ways, such as texturing, oxidizing and sintering. Silver wires have been printed on Ti6Al4V surface in order to conduct electrical current. To minimize current loss for the substrate, titanium oxide layer has been produced by different methods (laser and anodization). Laser sintering (LS) has been also compared to a conventional method (Hot-pressing- HP) to consolidate the silver powder into the cavities. In comparison to the conventional techniques, laser demonstrated to be a competitive approach to oxidizing the surface and also for consolidating the micro-wires on Ti6Al4V surface. Consequently, the micro-wires printed by laser approach presented satisfactory results in terms of electrical resistance, actuating as the conductor path for electrical current, with values of 0.0131 Ω, which is similar to the resistance of the wire printed in an insulator substrate.This work has been supported by FCT (Fundação para a Ciência e Tecnologia -Portugal) in the scope of the projects UID/EEA/04436/ 2019 and NORTE-01-0145-FEDER-000018-HAMaBICo and Add.Additive_Manufacturing to Portuguese Industry_POCI-01-0247- FEDER-024533. I wish to thank the CNPq (205791/2014-0)

Galacto-oligosaccharides production during lactose hydrolysis by free Aspergillus oryzae β-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol

The synthesis of galacto-oligosaccharides (GOS) by the action of Aspergillus oryzae β-galactosidase free and immobilized on magnetic polysiloxane-polyvinyl alcohol (mPOS-PVA) was studied. A maximum GOS concentration of 26% (w/v) of total sugars was achieved at near 55% lactose conversion from 50%, w/v lactose solution at pH 4.5 and 40 °C. Trisaccharides accounted for more than 81% of the total GOS produced. GOS formation was not considerably affected by pH and temperature. The concentrations of glucose and galactose encountered near maximum GOS concentration greatly inhibited the reactions and reduced GOS yield. GOS formation was not affected by enzyme immobilization in the mPOS-PVA matrix, indicating the absence of diffusional limitations in the enzyme carrier. Furthermore, this water insoluble magnetic derivative was reutilized 10-times and retained about 84% of the initial activity. In addition, the kinetic parameters for various initial lactose concentrations were determined and compared for the free and immobilized enzyme.David F. M. Neri gratefully acknowledges support by the Programme Alpan, the European Union Programme of High Level Scholarships for Latin America (Scholarship No. E05D057787BR). Luiz B. Carvalho Jr. is recipient of a scholarship of the Brazilian National Research Council (CNPq)