An integrated formal methods tool-chain and its application to verifying a file system model

Tool interoperability as a mean to achieve integration is among the main goals of the international Grand Challenge initiative. In the context of the Verifiable file system mini-challenge put forward by Rajeev Joshi and Gerard Holzmann, this paper focuses on the integration of different formal methods and tools in modelling and verifying an abstract file system inspired by the Intel (R) Flash File System Core. We combine high-level manual specification and proofs with current state of the art mechanical verification tools into a tool-chain which involves Alloy, VDM++ and HOL. The use of (pointfree) relation modelling provides the glue which binds these tools together.Mondrian Project funded by the Portuguese NSF under contract PTDC/EIA-CCO/108302/200

Alloy meets the algebra of programming: a case study

Relational algebra offers to software engineering the same degree of conciseness and calculational power as linear algebra in other engineering disciplines. Binary relations play the role of matrices with similar emphasis on multiplication and transposition. This matches with Alloy’s lemma “everything is a relation” and with the relational basis of the Algebra of Programming (AoP). Altogether, it provides a simple and coherent approach to checking and calculating programs from abstract models. In this paper, we put Alloy and the Algebra of Programming together in a case study originating from the Verifiable File System mini-challenge put forward by Joshi and Holzmann: verifying the refinement of an abstract file store model into a journaled (FLASH) data model catering to wear leveling and recovery from power loss. Our approach relies on diagrams to graphically express typed assertions. It interweaves model checking (in Alloy) with calculational proofs in a way which offers the best of both worlds. This provides ample evidence of the positive impact in software verification of Alloy’s focus on relations, complemented by induction-free proofs about data structures such as stores and lists.Fundação para a Ciência e a Tecnologia (FCT

LogCHEM: interactive discriminative mining of chemical structure

One of the most well known successes of Inductive Logic Programming (ILP) is on Structure-Activity Relationship (SAR) problems. In such problems, ILP has proved several times to be capable of constructing expert comprehensible models that hell) to explain the activity of chemical compounds based on their structure and properties. However, despite its successes on SAR problems, ILP has severe scalability problems that prevent its application oil larger datasets. In this paper we present LogCHEM, an ILP based tool for discriminative interactive mining of chemical fragments. LogCHEM tackles ILP's scalability issues in the context of SAR applications. We show that LogCHEM benefits from the flexibility of ILP both by its ability to quickly extend the original mining model, and by its ability, to interface with external tools. Furthermore, We demonstrate that LogCHEM can be used to mine effectively large chemoinformatics datasets, namely, several datasets from EPA's DSSTox database and on a dataset based on the DTP AIDS anti-viral screen

From algebras to objects : generation and composition

This paper addresses objectification, a formal specification technique which inspects the potential for object-orientation of a declarative model and brings the 'implicit objects' explicit. Criteria for such objectification are formalized and implemented in a runnable prototype tool which embeds Vdm-sl into Vdm++. The paper also includes a quick presentation of a (coinductive) calculus of such generated objects, framed as generalised Moore machines.Fundação para a Ciência e a Tecnologia (FCT

Biomass Valorization to Produce Porous Carbons: Applications in CO2 Capture and Biogas Upgrading to Biomethane—A Mini-Review

UIDB/50006/2020 UIDP/50006/2020 LA/P/0008/2020Porous carbon materials, derived from biomass wastes and/or as by-products, are considered versatile, economical and environmentally sustainable. Recently, their high adsorption capacity has led to an increased interest in several environmental applications related to separation/purification both in liquid- and gas-phases. Specifically, their use in carbon dioxide (CO2) capture/sequestration has been a hot topic in the framework of gas adsorption applications. Cost effective biomass porous carbons with enhanced textural properties and high CO2 uptakes present themselves as attractive alternative adsorbents with potential to be used in CO2 capture/separation, apart from zeolites, commercial activated carbons and metal-organic frameworks (MOFs). The renewable and sustainable character of the precursor of these bioadsorbents must be highlighted in the context of a circular-economy and emergent renewable energy market to reach the EU climate and energy goals. This mini-review summarizes the current understandings and discussions about the development of porous carbons derived from bio-wastes, focusing their application to capture CO2 and upgrade biogas to biomethane by adsorption-based processes. Biogas is composed by 55–65 v/v% of methane (CH4) mainly in 35–45 v/v% of CO2. The biogas upgraded to bio-CH4 (97%v/v) through an adsorption process yields after proper conditioning to high quality biomethane and replaces natural gas of fossil source. The circular-economy impact of bio-CH4 production is further enhanced by the use of biomass-derived porous carbons employed in the production process.publishersversionpublishe

Protein evolution of ANTP and PRD homeobox genes

<p>Abstract</p> <p>Background</p> <p>Although homeobox genes have been the subject of many studies, little is known about the main amino acid changes that occurred early in the evolution of genes belonging to different classes.</p> <p>Results</p> <p>In this study, we report a method for the fast and efficient retrieval of sequences belonging to the ANTP (HOXL and NKL) and PRD classes. Furthermore, we look for diagnostic amino acid residues that can be used to distinguish HOXL, NKL and PRD genes.</p> <p>Conclusion</p> <p>The reported protein features will facilitate the robust classification of homeobox genes from newly sequenced bilaterian genomes. Nevertheless, in non-bilaterian genomes our findings must be cautiously applied. In principle, as long as a good manually curated data set is available the approach here described can be applied to non-bilaterian organisms as well. Our results help focus experimental studies onto investigating the biochemical functions of key homeodomain residues in different gene classes.</p

The generation of magnetic fields by the Biermann battery and the interplay with the Weibel instability

An investigation of magnetic fields generated in an expanding bubble of plasma with misaligned temperature and density gradients (driving the Biermann battery mechanism) is performed. With gradient scales L, large-scale magnetic fields are generated by the Biermann battery mechanism with plasma 1, as long as L is comparable to the ion inertial length di. For larger system sizes, L/de 100 (where deis the electron inertial length), the Weibel instability generates magnetic fields of similar magnitude but with wavenumber kde0.2. In both cases, the growth and saturation of these fields have a weak dependence on mass ratio mi/me, indicating electron mediated physics. A scan in system size is performed at mi/me= 2000, showing agreement with previous results with mi/me= 25. In addition, the instability found at large system sizes is quantitatively demonstrated to be the Weibel instability. Furthermore, magnetic and electric energy spectra at scales below the electron Larmor radius are found to exhibit power law behavior with spectral indices -16/3 and -4/3, respectively

Inoculated cell density as a determinant factor of the growth dynamics and metastatic efficiency of a breast cancer murine model

Copyright: © 2016 Gregório et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.4T1 metastatic breast cancer model have been widely used to study stage IV human breast cancer. However, the frequent inoculation of a large number of cells, gives rise to fast growing tumors, as well as to a surprisingly low metastatic take rate. The present work aimed at establishing the conditions enabling high metastatic take rate of the triple-negative murine 4T1 syngeneic breast cancer model. An 87% 4T1 tumor incidence was observed when as few as 500 cancer cells were implanted. 4T1 cancer cells colonized primarily the lungs with 100% efficiency, and distant lesions were also commonly identified in the mesentery and pancreas. The drastic reduction of the number of inoculated cells resulted in increased tumor doubling times and decreased specific growth rates, following a Gompertzian tumor expansion. The established conditions for the 4T1 mouse model were further validated in a therapeutic study with peguilated liposomal doxorubicin, in clinical used in the setting of metastatic breast cancer. Inoculated cell density was proven to be a key methodological aspect towards the reproducible development of macrometastases in the 4T1 mouse model and a more reliable pre-clinical assessment of antimetastatic therapies.Ana Cristina Gregório is a student of the international PhD program in Experimental Biology and Biomedicine (PDBEB) from the Institute for Interdisciplinary Research, University of Coimbra and recipient of the fellowship SFRH/BD/51190/2010 from the Portuguese Foundation for Science and Technology (FCT). The work was supported by the grants PTDC/SAU-BMA/121028/2010 (FCT) and UID/NEU/04539/2013 (FEDER/COMPETE 2020/FCT).info:eu-repo/semantics/publishedVersio

Fully kinetic large scale simulations of the collisionless Magnetorotational instability

We present two-dimensional particle-in-cell (PIC) simulations of the fully kinetic collisionless magnetorotational instability (MRI) in weakly magnetized (high $\beta$) pair plasma. The central result of this numerical analysis is the emergence of a self-induced turbulent regime in the saturation state of the collisionless MRI, which can only be captured for large enough simulation domains. One of the underlying mechanisms for the development of this turbulent state is the drift-kink instability (DKI) of the current sheets resulting from the nonlinear evolution of the channel modes. The onset of the DKI can only be observed for simulation domain sizes exceeding several linear MRI wavelengths. The DKI, together with ensuing magnetic reconnection, activate the turbulent motion of the plasma in the late stage of the nonlinear evolution of the MRI. At steady state, the magnetic energy has an MHD-like spectrum with a slope of $k^{-5/3}$ for $k\rho1$). We also examine the role of the collisionless MRI and associated magnetic reconnection in the development of pressure anisotropy. We study the stability of the system due to this pressure anisotropy, observing the development of mirror instability during the early-stage of the MRI. We further discuss the importance of magnetic reconnection for particle acceleration during the turbulence regime. In particular, consistent with reconnection studies, we show that at late times the kinetic energy presents a characteristic slope of $\epsilon^{-2}$ in the high-energy region.Comment: 13 pages, 9 figures, accepted to Astrophysical Journa

Application of the response surface method to optimize alkali activated cements based on low-reactivity ladle furnace slag

Steel-making slags, resulting from basic oxygen furnaces or electric arc furnaces are heavily applied in the construction industry, as an aggregate for pavements or concrete. Although possessing a significant crystalline content, it is expected that, if properly milled, the reactivity of these slags can increase up to a point when they are viable to produce alkaline cements. The aim of this study was the application of a response surface method to design the experimental work required to optimise the composition of an alkaline cement based on ladle furnace slag, a specific type of steel slag (SG). Fly ash (FA) was also added, in a precursor role, and the activation was achieved with an alkaline solution prepared with sodium silicate (SS) and sodium hydroxide (SH). The factors/variables considered were the activator index X = SS/(SS + SH), the precursor index Y = SG/(SG + FA) and the SH concentration (Z). The output variables were the unconfined compression strength and the flexural strength, after 7 and 28 days curing. Results indicate that the activator index (X) was the most influential variable, followed by the precursor index (Y). Microstructural analysis of selected pastes was also performed, using scanning electron microscopy and energy dispersive spectroscopy. The ideal composition obtained for the alkaline cement was the mixture constituted by X = 0.75, Y = 0.5 and Z = 10 (activator: 75% SS and 25% SH; precursor: 50% SG and 50% FA; SH concentration = 10 molal). This mixture achieved 8.70 MPa of flexural strength and 44.25 MPa of compressive strength which is reasonable for the required application (soil stabilisation)