Non-linear Pattern Matching with Backtracking for Non-free Data Types

Non-free data types are data types whose data have no canonical forms. For example, multisets are non-free data types because the multiset $\{a,b,b\}$ has two other equivalent but literally different forms $\{b,a,b\}$ and $\{b,b,a\}$. Pattern matching is known to provide a handy tool set to treat such data types. Although many studies on pattern matching and implementations for practical programming languages have been proposed so far, we observe that none of these studies satisfy all the criteria of practical pattern matching, which are as follows: i) efficiency of the backtracking algorithm for non-linear patterns, ii) extensibility of matching process, and iii) polymorphism in patterns. This paper aims to design a new pattern-matching-oriented programming language that satisfies all the above three criteria. The proposed language features clean Scheme-like syntax and efficient and extensible pattern matching semantics. This programming language is especially useful for the processing of complex non-free data types that not only include multisets and sets but also graphs and symbolic mathematical expressions. We discuss the importance of our criteria of practical pattern matching and how our language design naturally arises from the criteria. The proposed language has been already implemented and open-sourced as the Egison programming language

Rab14 regulates the maturation of macrophage phagosomes containing the fungal pathogen Candida albicans and the outcome of the host-pathogen interaction

Date of Acceptance: 02/02/2015 Copyright © 2015, American Society for Microbiology. All Rights Reserved.Peer reviewedPublisher PD

Macrophage Migration Is Impaired within Candida albicans Biofilms

Acknowledgments: We thank the Microscopy and Histology Core Facility at the University of Aberdeen. This work was funded by NHS Grampian Endowments (grant RG10191); the Wellcome Trust Strategic Award in Medical Mycology and Fungal Immunology (grant 097377); the Wellcome Trust Investigator award (grants 101873, 086827, 075470, & 200208) and the Medical Research Council Centre for Medical Mycology (grant MR/N006364/1).Peer reviewedPublisher PD

Hyphal growth of phagocytosed fusarium oxysporum causes cell lysis and death of murine macrophages

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Kinetic studies of Candida parapsilosis phagocytosis by macrophages and detection of intracellular survival mechanisms

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Blocking two-component signalling enhances Candida albicans virulence and reveals adaptive mechanisms that counteract sustained SAPK activation

This work was funded by the UK Biotechnology and Biological Research Council [www.bbsrc.ac.uk] JQ (BB/K016393/1); AJPB (BB/K017365/1). The work was also supported by the Wellcome Trust [www.wellcome.ac.uk], JQ (086048, 097377); AJPB (097377)); LPE (097377). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Differential Kinetics of Aspergillus nidulans and Aspergillus fumigatus Phagocytosis

Acknowledgements: The authors would like to acknowledge Fraser P. Coxon and Ian Ganley for providing LC3-GFP-mCherry BMDMs. M.S.G. was supported by an FEMS research grant and F.L.v.d.V. was supported by ZonMW under the name EURO-CMC frame of E-Rare-2, the ERA-Net for Research on Rare Diseases.Peer reviewedPublisher PD

Targeted inactivation of the Septin2 and Septin9 genes in myelinating Schwann cells of mice

The formation of axon-enwrapping myelin sheaths by oligodendrocytes in the central nervous system (CNS) involves the assembly of a scaffolding septin filament comprised of the subunits SEPTIN2, SEPTIN4, SEPTIN7 and SEPTIN8. Conversely, in the peripheral nervous system (PNS) myelin is synthesized by a different cell type termed Schwann cells, and it remained unknown if septins also assemble as a multimer in PNS myelin. According to prior proteome analysis, PNS myelin comprises the subunits SEPTIN2, SEPTIN7, SEPTIN8, SEPTIN9 and SEPTIN11, which localize to the paranodal and abaxonal myelin sub-compartments. Here we use the Cre/loxP-system to delete the Septin9-gene specifically in Schwann cells, causing a markedly reduced abundance of SEPTIN9 in sciatic nerves, implying that Schwann cells are the main cell type expressing SEPTIN9 in the nerve. However, Septin9-deficiency in Schwann cells did not affect the abundance or localization of other septin subunits. In contrast, when deleting the Septin2-gene in Schwann cells the abundance of all relevant septin subunits was markedly reduced, including SEPTIN9. Notably, we did not find evidence that deleting Septin2 or Septin9 in Schwann cells impairs myelin biogenesis, nerve conduction velocity or motor/sensory capabilities, at least at the assessed timepoints. Our data thus show that SEPTIN2 but not SEPTIN9 is required for the formation or stabilization of a septin multimer in PNS myelin in vivo; however, its functional relevance remains to be established

SOCS3 is a modulator of human macrophage phagocytosis

ACKNOWLEDGMENTS This work was supported by Kidney Research UK (Grant Number RP1/2012). The authors thank the staff of the Aberdeen Microscopy and Histology Core Facility for advice and technical assistance. The authors acknowledge and are grateful to all volunteers for donating blood for macrophage and neutrophil isolation.Peer reviewedPublisher PD

Model inference for spreadsheets

Many errors in spreadsheet formulas can be avoided if spreadsheets are built automati- cally from higher-level models that can encode and enforce consistency constraints in the generated spreadsheets. Employing this strategy for legacy spreadsheets is dificult, because the model has to be reverse engineered from an existing spreadsheet and existing data must be transferred into the new model-generated spreadsheet. We have developed and implemented a technique that automatically infers relational schemas from spreadsheets. This technique uses particularities from the spreadsheet realm to create better schemas. We have evaluated this technique in two ways: First, we have demonstrated its appli- cability by using it on a set of real-world spreadsheets. Second, we have run an empirical study with users. The study has shown that the results produced by our technique are comparable to the ones developed by experts starting from the same (legacy) spreadsheet data. Although relational schemas are very useful to model data, they do not t well spreadsheets as they do not allow to express layout. Thus, we have also introduced a mapping between relational schemas and ClassSheets. A ClassSheet controls further changes to the spreadsheet and safeguards it against a large class of formula errors. The developed tool is a contribution to spreadsheet (reverse) engineering, because it lls an important gap and allows a promising design method (ClassSheets) to be applied to a huge collection of legacy spreadsheets with minimal effort.We would like to thank Orlando Belo for his help on running and analyzing the empirical study. We would also like to thank Paulo Azevedo for his help in conducting the statistical analysis of our empirical study. We would also like to thank the anonymous reviewers for their suggestions which helped us to improve the paper. This work is funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundacao para a Ciencia e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-010048. The first author was also supported by FCT grant SFRH/BPD/73358/2010