Exploiting Term Hiding to Reduce Run-time Checking Overhead

One of the most attractive features of untyped languages is the flexibility in term creation and manipulation. However, with such power comes the responsibility of ensuring the correctness of these operations. A solution is adding run-time checks to the program via assertions, but this can introduce overheads that are in many cases impractical. While static analysis can greatly reduce such overheads, the gains depend strongly on the quality of the information inferred. Reusable libraries, i.e., library modules that are pre-compiled independently of the client, pose special challenges in this context. We propose a technique which takes advantage of module systems which can hide a selected set of functor symbols to significantly enrich the shape information that can be inferred for reusable libraries, as well as an improved run-time checking approach that leverages the proposed mechanisms to achieve large reductions in overhead, closer to those of static languages, even in the reusable-library context. While the approach is general and system-independent, we present it for concreteness in the context of the Ciao assertion language and combined static/dynamic checking framework. Our method maintains the full expressiveness of the assertion language in this context. In contrast to other approaches it does not introduce the need to switch the language to a (static) type system, which is known to change the semantics in languages like Prolog. We also study the approach experimentally and evaluate the overhead reduction achieved in the run-time checks.Comment: 26 pages, 10 figures, 2 tables; an extension of the paper version accepted to PADL'18 (includes proofs, extra figures and examples omitted due to space reasons

Catalysis at the Heart of Success!

Bornscheuer, UT.; Hashmi, ASK.; García Gómez, H.; Rowan, MA. (2017). Catalysis at the Heart of Success!. ChemCatChem. 9(1):6-9. doi:10.1002/cctc.201601553S6991Bornscheuer, U. T. (2015). Biocatalysis: Successfully Crossing Boundaries. Angewandte Chemie International Edition, 55(14), 4372-4373. doi:10.1002/anie.201510042Bornscheuer, U. T. (2015). Biokatalyse: ein erfolgreicher Blick über den Tellerrand. Angewandte Chemie, 128(14), 4446-4447. doi:10.1002/ange.201510042Bornscheuer, U. T. (2009). Combined Success for Efficient Catalysis. ChemCatChem, 1(1), 5-5. doi:10.1002/cctc.200900144Weckhuysen, B. M. (2009). Crossing the Interfaces of Catalysis. ChemCatChem, 1(1), 7-7. doi:10.1002/cctc.200900146Kan, S. B. J., Lewis, R. D., Chen, K., & Arnold, F. H. (2016). Directed evolution of cytochrome c for carbon–silicon bond formation: Bringing silicon to life. Science, 354(6315), 1048-1051. doi:10.1126/science.aah621

Implementing Groundness Analysis with Definite Boolean Functions

The domain of definite Boolean functions, Def, can be used to express the groundness of, and trace grounding dependencies between, program variables in (constraint) logic programs. In this paper, previously unexploited computational properties of Def are utilised to develop an efficient and succinct groundness analyser that can be coded in Prolog. In particular, entailment checking is used to prevent unnecessary least upper bound calculations. It is also demonstrated that join can be defined in terms of other operations, thereby eliminating code and removing the need for preprocessing formulae to a normal form. This saves space and time. Furthermore, the join can be adapted to straightforwardly implement the downward closure operator that arises in set sharing analyses. Experimental results indicate that the new Def implementation gives favourable results in comparison with BDD-based groundness analyses

Interaction of new fluorescent 2-quinolinone and coumarin derivatives with phospholipid monolayers and lipid vesicles

RICI4 - Book of AbstractsFCT-Portugal, QREN and FEDER/COMPETE through CFUM, CQ-UM, Project PTDC/QUI/81238/2006 and Post-doc. grant of Ana S. Abreu (SFRH/BPD/24548/2005

Fluorescence studies of 3-amino-4-phenylquinolin-2-one in solution and in lipid membranes

Book of Abstracts - QO-CP 090FCT-Portugal and FEDER/COMPETE through CFUM, CQ/UM, Project PTDC/QUI/81238/2006. A.S. Abreu also thanks her post-doctoral grant (SFRH/BPD/24548/2005) to FCT, POPH-QREN, FSE

Phenanthrenyl-indole as a fluorescent probe for peptides and lipid membranes

Prova tipográficaA 3-(phenanthren-9-yl)-1H-indole-2-carboxylic acid (2) obtained from the cleavage of the methyl ester of the methyl 3-(phenanthren-9-yl)-1H-indole-2-carboxylate (1) was inserted into a peptide containing the RGD sequence. The GGRGDG peptide sequence was prepared by solid phase synthesis and coupled to compound (2), using diisopropylcarbodiimide (DIC) and 1-hydroxybenzotriazole (HOBt) in DMF. The peptide (3) labelled with the phenanthrenylindole moiety was obtained in 31% yield. The photophysical properties of the phenanthrenyl-indole derivatives were studied in several solvents of different polarity. Compounds 1 and 2 have reasonably high fluorescence quantum yields (between 27% and 85%) in non-protic solvents, the methyl phenanthrenyl-indole-2-carboxylate 1 being the more fluorescent compound. The fluorescence emission of both compounds is sensitive to solvent, indicating that they are good candidates for fluorescent probes. Fluorescence emission measurements of the labelled peptide in solution showed a strong decrease of fluorescence quantum yield value caused by the attachment of the Gly-Gly-Arg-Gly-Asp-Gly chain. The phenanthrenyl-indoles 1 and 2 and the labelled peptide 3 were incorporated in liposomes of dipalmitoyl phosphatidylcholine (DPPC) and dipalmitoyl phosphatidylglycerol (DPPG) and mixtures of both lipids. Steady-state anisotropy measurements showed that compounds 1 and 2 are located inside the lipid bilayers and are able to report the transition between the gel and liquid-crystalline phases. The RGD labelled peptide locates mainly in the outer part of the vesicle interface. These results indicate that the phenanthrenyl-indole moiety may be used as a fluorescent probe for peptides and lipid membranes.Fundação para a Ciência e a Tecnologia (FCT) - projeto de investigação PTDC/QUI/81238/2006, Bolsa de doutoramento SFRH/BD/38766/2007, pós-doutoramento SFRH/BPD/24548/2005, "spectrometer Bruker Avance III 400" Portuguese NMR Network (Rede/1517/RMN/2005)Programa FEDER/COMPETE - FCOMP-01-0124- FEDER-007467Universidade do Minho. Centro de Física (CFUM)Universidade do Minho. Centro de Química (CQ-UM

Graphenes as Metal-Free Catalysts with Engineered Active Sites

[EN] This Perspective article highlights how recent discoveries on the activity of defective graphene to promote different organic reactions as metal-free catalysts has led to propose certain substructures present on these defective graphenes as active sites. The sustainability of using as catalysts graphenes obtained from biomass and the possibility to generate active sites by introducing defects on the sheet are the two main characteristics triggering research in this area. Emphasis is made in the need to gain understanding on the nature of the active sites and how this understanding requires the combination of conventional kinetic experiments as well as advanced characterization tools. The relationship between catalysis by graphene and that by organocatalysis has also been remarked.Financial support by the Spanish Ministry of Economy and Competitiveness (Severo Ochoa, Grapas, and CTQ2015-69153-CO2-1) and Generalitat Valenciana (Prometo 2013-014) is gratefully acknowledged. A.P. also thanks the Spanish Ministry of Economy and Competitiveness for a Ramon y Cajal research associate contract.Primo Arnau, AM.; Parvulescu, V.; García Gómez, H. (2017). Graphenes as Metal-Free Catalysts with Engineered Active Sites. The Journal of Physical Chemistry Letters. 8(1):264-278. https://doi.org/10.1021/acs.jpclett.6b01996S2642788

A model for inter-module analysis and optimizing compilation

Recent research into the implementation of logic programming languages has demonstrated that global program analysis can be used to speed up execution by an order of magnitude. However, currently such global program analysis requires the program to be analysed as a whole: sepárate compilation of modules is not supported. We describe and empirically evalúate a simple model for extending global program analysis to support sepárate compilation of modules. Importantly, our model supports context-sensitive program analysis and multi-variant specialization of procedures in the modules

Biocompatible peptide-based hydrogels as nanocarriers for a new antitumoral drug

In this work, several new hydrogelators were developed, containing a Naproxen or a Naphthalene group. The ability of these hydrogels to act as nanocarriers for an antitumoral drug was investigated.Foundation for the Science and Technology (FCT, Portugal), FEDER and QREN for financial support to the Research Centers, CFUM [Strategic Project Pest-C/FIS/UI0607/2013 (FCOMP-01-0124-FEDER-037291)] and CQ/UM [Strategic Project PEst-C/QUI/UI0686/2013 (FCOMP-01-0124-FEDER-037302)]. FCT is also acknowledged for the PhD grant of H. Vilaça (SFRH/BD/7265/2010)