ReverCSP: Time-Travelling in CSP Computations

[EN] This paper presents reverCSP, a tool to animate both forward and backward CSP computations. This ability to reverse computations can be done step by step or backtracking to a given desired state of interest. reverCSP allows us to reverse computations exactly in the same order in which they happened, or also in a causally-consistent way. Therefore, reverCSP is a tool that can be especially useful to comprehend, analyze, and debug computations. reverCSP is an open-source project publicly available for the community. We describe the tool and its functionality, and we provide implementation details so that it can be reimplemented for other languages.This work has been partially supported by the EU (FEDER) and the Spanish MCI/AEI under grants TIN2016-76843-C4-1-R and PID2019- 104735RB-C41, and by the Generalitat Valenciana under grant Prometeo/2019/098 (DeepTrust).Galindo-Jiménez, CS.; Nishida, N.; Silva, J.; Tamarit, S. (2020). ReverCSP: Time-Travelling in CSP Computations. Springer. 239-245. https://doi.org/10.1007/978-3-030-52482-1_14S239245Bernadet, A., Lanese, I.: A modular formalization of reversibility for concurrent models and languages. In: Proceedings of ICE 2016, EPTCS (2016)Brown, G., Sabry, A.: Reversible communicating processes. Electron. Proc. Theor. Comput. Sci. 203, 45–59 (2016)Conserva Filhoa, M., Oliveira, M., Sampaio, A., Cavalcanti, A.: Compositional and local livelock analysis for CSP. Inf. Process. Lett 133, 21–25 (2018)Danos, V., Krivine, J.: Reversible communicating systems. In: Gardner, P., Yoshida, N. (eds.) CONCUR 2004. LNCS, vol. 3170, pp. 292–307. Springer, Heidelberg (2004). https://doi.org/10.1007/978-3-540-28644-8_19Elnozahy, E.N.M., Alvisi, L., Wang, Y.-M., Johnson, D.B.: A survey of rollback- recovery protocols in message-passing systems. ACM Comput. Surv. 34(3), 375–408 (2002)Fang, Y., Zhu, H., Zeyda, F., Fei, Y.: Modeling and analysis of the disruptor framework in csp. In: Proceedings of CCWC 2018. IEEE Computer Society (2018)Ladkin, P.B., Simons, B.B.: Static deadlock analysis for CSP-type communications. In: Fussell, D.S., Malek, M. (eds.) Responsive Computer Systems: Steps Toward Fault-Tolerant Real-Time Systems. The Springer International Series in Engineering and Computer Science, vol. 297, pp. 89–102. Springer, Boston (1995). https://doi.org/10.1007/978-1-4615-2271-3_5Landauer, R.: Irreversibility and heat generation in the computing process. IBM J. Res. Dev. 5, 183–191 (1961)Lanese, I., Antares Mezzina, C., Tiezzi, F.: Causal-consistent reversibility. Bull. EATCS 114, 17 (2014)Lanese, I., Nishida, N., Palacios, A., Vidal, G.: CauDEr: a causal-consistent reversible debugger for erlang. In: Gallagher, J.P., Sulzmann, M. (eds.) FLOPS 2018. LNCS, vol. 10818, pp. 247–263. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-90686-7_16Lanese, I., Palacios, A., Vidal, G.: Causal-consistent replay debugging for message passing programs. In: Pérez, J.A., Yoshida, N. (eds.) FORTE 2019. LNCS, vol. 11535, pp. 167–184. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-21759-4_10Llorens, M., Oliver, J., Silva, J., Tamarit, S.: Dynamic slicing of concurrent specification languages. Parallel Comput. 53, 1–22 (2016)Llorens, M., Oliver, J., Silva, J., Tamarit, S.: Tracking CSP computations. J. Log. Algebr. Meth. Program. 102, 138–175 (2019)Perera, R., Garg, D., Cheney, J.: Causally consistent dynamic slicing. In Proceedings of CONCUR 2016, LIPIcs, vol. 59, pp. 18:1–18:15 (2016)Phillips, I., Ulidowski, I., Yuen, S.: A reversible process calculus and the modelling of the ERK signalling pathway. In: Glück, R., Yokoyama, T. (eds.) RC 2012. LNCS, vol. 7581, pp. 218–232. Springer, Heidelberg (2013). https://doi.org/10.1007/978-3-642-36315-3_18Roscoe, A.W.: The Theory and Practice of Concurrency. Prentice Hall PTR, Upper Saddle River (1997)Zhao, H., Zhu, H., Yucheng, F., Xiao, L.: Modeling and verifying storm using CSP. In: Proceedings of HASE 2019. IEEE Computer Society (2019

Cómo motivar a los estudiantes de secundaria mediante actividades de ciencias atractivas y divertidas

Se presenta una propuesta de formación del profesorado llevada a cabo durante dos cursos académicos (2006/08) con la finalidad de mejorar la motivación e interés de los estudiantes hacia el aprendizaje de las ciencias. Se diseñó e implementó un curso desde la perspectiva de una ciencia comprometida, pero también amena, creativa y divertida, incluyendo actividades interactivas realizadas en colaboración con el Museo de Ciencias Príncipe Felipe, experimentos de laboratorio, textos divulgativos con enfoques CTSA (Ciencia-Tecnología-Sociedad-Ambiente), juguetes científicos, así como el aporte de experiencias provenientes de otros países europeos (Alemania, Francia y Reino Unido). Esta iniciativa, en la que han participado 80 profesores ha sido un instrumento eficaz tanto para la mejora de la motivación como para promover la formación de comunidades de práctica

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org

Endovascular Treatment for Pseudoaneurysms after Surgical Correction of Aortic Coarctation

Late complications after surgical repair of aortic coarctation are not uncommon. Among these complications pseudoaneurysms are the most frequent complications, occurring between 3 and 38%. Reoperation in these patients is associated with high morbidity and mortality. In the last decade, endovascular techniques emerged as an alternative to conventional surgery with excellent results. We report the case of two patients who presented with pseudoaneurysms after surgical correction for aortic coarctation, which were treated by endovascular means

Genome-Wide Transcription Factor Binding in Leaves from C3 and C4 Grasses.

The majority of plants use C3 photosynthesis, but over 60 independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle-sheath cells. We performed DNaseI sequencing to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor, and Setaria italica as well as C3 Brachypodium distachyon In C4 species, while bundle-sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that influence gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.BBSRC ERC CONACy

Valorization of Ferulic Acid from Agro-Industrial by-Products for Application in Agriculture

The use of bioplastic mulch in agriculture has increased dramatically in the last years throughout the world. Nowadays, biodegradable materials for mulching films strive to constitute a reliable and more sustainable alternative to classical materials such as polyethylene (PE). The main challenge is to improve their durability in the soil to meet the required service length for crop farming by using benign and sustainable antioxidant systems. Here, we report the design and fabrication of biodegradable materials based on polybutylene (succinate adipate) (PBSA) for mulching applications, incorporating a fully biobased polymeric antioxidant deriving from ferulic acid, which can be extracted from an industrial by-product. Poly-dihydro (ethylene ferulate) (PHEF) from ferulic acid was synthesized by a two-step polymerization process. It is characterized by improved thermal stability in comparison with ferulic acid monomer and therefore suitable for common industrial processing conditions. Different blends of PBSA and PHEF obtained by melt mixing or by reactive extrusion were prepared and analyzed to understand the effect of the presence of PHEF. The results demonstrate that PHEF, when processed by reactive extrusion, presents a remarkable antioxidant effect, even in comparison with commercial additives, preserving a high level of the mechanical properties of the PBSA matrix without affecting the biodegradable character of the blend

Droplet-based microfluidic analysis and screening of single plant cells.

Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 cells per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate its potential for assessing gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics to selection of rare plant phenotypes.BBSRC and EPSRC OpenPlant BB/L014130/