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

AnEnPi: Identification and annotation of analogous enzymes

Enzymes are responsible for the catalysis of the biochemical reactions in metabolic pathways. Analogous enzymes are able to catalyze the same reactions, but they present no significant sequence similarity at the primary level, and possibly different tertiary structures as well. They are thought to have arisen as the result of independent evolutionary events. A detailed study of analogous enzymes may reveal new catalytic mechanisms, add information about the origin and evolution of biochemical pathways and disclose potential targets for drug development. Results: In this work, we have constructed and implemented a new approach, AnEnPi (the Analogous Enzyme Pipeline), using a combination of bioinformatics tools like BLAST, HMMer, and in-house scripts, to assist in the identification, annotation, comparison and study of analogous and homologous enzymes. The algorithm for the detection of analogy is based i) on the construction of groups of homologous enzymes and ii) on the identification of cases where a given enzymatic activity is performed by two or more proteins without significant similarity between their primary structures. We applied this approach to a dataset obtained from KEGG Comprising all annotated enzymes, which resulted in the identification of 986 EC classes where putative analogy was detected (40.5% of all EC classes). AnEnPi is of considerable value in the construction of initial datasets that can be further curated, particularly in gene and genome annotation, in studies involving molecular evolution and metabolism and in the identification of new potential drug targets. Conclusion: AnEnPi is an efficient tool for detection and annotation of analogous enzymes and other enzymes in whole genomes

A two-step approach for the seismic assessment of masonry structures accounting for the actual masonry pattern

Seismic assessment of masonry structures is a pressing concern in the scientific community. Over the last few decades, significant progress has been made in developing numerical modelling strategies for masonry. However, due to the unique mechanics of masonry, which exhibit a quasi-brittle and anisotropic behaviour, there is no trade-off between accuracy and computational efficiency when conducting numerical simulations of masonry structures. This study proposes a new approach to conduct in-plane numerical simulations of masonry structures, which couple limit and pushover analyses considering the actual masonry pattern. The first step of the procedure involves a block-based limit analysis, which considers the actual masonry pattern. Macroblocks, i.e., the portions which compose the collapse mechanism, are then identified using an ad-hoc algorithm that searches for the pivot point of the obtained failure mechanisms. In the second step, a pushover analysis is conducted on the simplified structure composed of macroblocks, considered as continuum bodies, interacting via frictional interfaces. The proposed approach is preliminary tested on two structural-scale benchmarks made of dry-stack masonry, showing promising results.This research is partially funded by the School of Sustainability, Civil and Environmental Engineering, University of Surrey. This study is partly funded by the STAND4HERITAGE project (New Standards for Seismic Assessment of Built Cultural Heritage), which has received funding from the European Re search Council (ERC) under the European Union's Horizon 2020 research and innovation pro gram (Grant Agreement No. 833123) as an Advanced Grant. This work is also partly financed by MPP2030-FCT PhD Grants under the R&D Unit Institute for Sustainability and Innovation in Structural Engineering (ISISE), under reference PRT/BD/154348/2022. This project has received funding from the European Union's Horizon 2020 research and inno vation programme under the Marie Sklodowska-Curie grant agreement No 101029792 (HOLAHERIS project, "A holistic structural analysis method for cultural heritage structures conservation" https://site.unibo.it/holaheris/en)

Direito à poesia: círculos de leitura com pessoas em situação de privação de liberdade em Foz do Iguaçu e região

Este projeto desdobrou-se da experiência de extensão universitária que vem sendo desenvolvida há três anos em duas unidades prisionais de Foz do Iguaçu, o CRESF (Centro de Reintegração Social Feminino) e a PEF 2 (Penitenciária Estadual 2), ambas no bairro de Três Fronteiras. Pretendia-se imprimir a essa experiência já em andamento um desdobramento no presídio feminino de Ciudad del Leste. Em virtude de barreiras institucionais para a concretização deste objetivo, este projeto incorpourou-se às atividades da PEF 2. A atividade fundamental do projeto é a realização de Rodas de Leitura e Oficinas de Escrita com mulheres e homens privados de liberdade no interior das prisões. O objetivo mais geral deste texto é compartilhar introdutoriamente algumas das reflexões teóricas no campo da mediação de leitura que têm orientado a prática do grupo, além de compartilhar alguns dos resultados do trabalho na PEF

Electronic and Geometric Corrugation of Periodically Rippled, Self-nanostructured Graphene Epitaxially Grown on Ru(0001)

Graphene epitaxially grown on Ru(0001) displays a remarkably ordered pattern of hills and valleys in Scanning Tunneling Microscopy (STM) images. To which extent the observed "ripples" are structural or electronic in origin have been much disputed recently. A combination of ultrahigh resolution STM images and Helium Atom diffraction data shows that i) the graphene lattice is rotated with respect to the lattice of Ru and ii) the structural corrugation as determined from He diffraction is substantially smaller (0.015 nm) than predicted (0.15 nm) or reported from X-Ray Diffraction or Low Energy Electron Diffraction. The electronic corrugation, on the contrary, is strong enough to invert the contrast between hills and valleys above +2.6 V as new, spatially localized electronic states enter the energy window of the STM. The large electronic corrugation results in a nanostructured periodic landscape of electron and holes pockets.Comment: 16 pages, 6 figure

Parenting program versus telephone support for Mexican parents of children with acquired brain injury: A blind randomized controlled trial

Introduction: Acquired brain injury (ABI) during childhood typically causes behavior problems in the child and high levels of stress in the family. The aims of this study are: (1) to investigate the effectiveness and feasibility of a parenting intervention in improving behavior and self-regulation in Mexican children with ABI compared to telephone support; (2) to investigate the effectiveness and feasibility of a parenting intervention in improving parenting skills, parent self-efficacy and decreasing parental stress in parents of children with ABI compared to telephone support. Our secondary aims are (1) to explore the impact that parent characteristics have on the intervention outcomes; (2) to investi

Thermal monitoring of a Cryosol in a high marine terrace (Half Moon Island, Maritime Antarctica)

Abstract Active layer and permafrost are important indicators of climate changes in periglacial areas of Antarctica, and the soil thermal regime of Maritime Antarctica is sensitive to the current warming trend. This research aimed to characterize the active layer thermal regime of a patterned ground located at an upper marine terrace in Half Moon Island, during 2015-2018. Temperature and moisture sensors were installed at different soil depths, combined with air temperature, collecting hourly data. Statistical analysis was applied to describe the soil thermal regime and estimate active layer thickness. The thermal regime of the studied soil was typical of periglacial environment, with high variability in temperature and water content in the summer, resulting in frequent freeze-thaw cycles. We detected dominant freezing conditions, whereas soil temperatures increased, and the period of high soil moisture content lasted longer over the years. Active layer thickness varied between the years, reaching a maximum depth in 2018. Permafrost degradation affects soil drainage and triggers erosion in the upper marine terrace, where permafrost occurrence is unlikely. Longer monitoring periods are necessary for a detailed understanding on how current climatic and geomorphic conditions affect the unstable permafrost of low-lying areas of Antarctica (marine terraces)