Derivation of scientific software from mathematical specifications

Often the modification and enhancement of large scientific software systems are severely hampered because many components of the system are written in an implementation dependent fashion, they are inadequately documented, and their functionalities are not precisely known. In this paper we consider how mathematics may be employed to alleviate some of these problems. In particular, we illustrate how the formal specification notation VDM-SL is being used to specify precisely abstract data types for use in the development of scientific software.

Elements of A New Framework for the principle of Equal Treatment of persons in EC Law

In June and November 2000, the European Parliament and the Council adopted two Directives referring to ‘the principle of equal treatment irrespective of’ in their title, one relating to racial and ethnic origin, the other to disability, age, religion and belief or sexual orientation. A thorough reform of Directive 76/207/EEC on the principle of equal treatment for women and men in employment matters is pending between the European Parliament's second reading and adoption while this is written. Community secondary legislation on equal treatment of persons has thus expanded in scope and number of reasons which must not serve as starting points for differentiation. Does this signify progress in legal protection against personal discrimination? While not providing a ready answer, this article proposes an analytical framework to answer this question, concentrating on conceptions of equality in general and in particular on the problems multi-dimensional discrimination might pose for the law.

Current-induced forces: a simple derivation

We revisit the problem of forces on atoms under current in nanoscale conductors. We derive and discuss the five principal kinds of force under steady-state conditions from a simple standpoint that—with the help of background literature—should be accessible to physics undergraduates. The discussion aims at combining methodology with an emphasis on the underlying physics through examples. We discuss and compare two forces present only under current—the non-conservative electron wind force and a Lorentz-like velocity-dependent force. It is shown that in metallic nanowires both display significant features at the wire surface, making it a candidate for the nucleation of current-driven structural transformations and failure. Finally we discuss the problem of force noise and the limitations of Ehrenfest dynamics

Landauer’s Principle in Multipartite Open Quantum System Dynamics

We investigate the link between information and thermodynamics embodied by Landauer’s principle in the open dynamics of a multipartite quantum system. Such irreversible dynamics is described in terms of a collisional model with a finite temperature reservoir. We demonstrate that Landauer’s principle holds, for such a configuration, in a form that involves the flow of heat dissipated into the environment and the rate of change of the entropy of the system. Quite remarkably, such a principle for heat and entropy power can be explicitly linked to the rate of creation of correlations among the elements of the multipartite system and, in turn, the non-Markovian nature of their reduced evolution. Such features are illustrated in two exemplary cases.

‘Harmonising the precaution out of the precautionary principle? The need for maintaining flexibility and an interpretative role’

The precautionary principle has the potential to act as a valuable tool in food law. It operates in areas of scientific uncertainty, calling for protective measures where there are potential threats to human health (or the environment). However, the manner of the principle’s incorporation and implementation within legislation are key to its effectiveness and general legitimacy. Specific considerations include the role and nature of risk assessments, assessors, sources of evidence, divergent opinions, risk communication, other legitimate factors and the weighting of interests. However, more fundamentally, the crystallisation of approaches and removal of all flexibility would undermine the principle’s central tenets. Firstly, principles crucially play a guiding and interpretative role. Secondly, reflexive modernisation and continuing scientific uncertainty call for the precautionary principle’s continued application – precautionary measures do not end the precautionary principle’s relevance. This can be partially achieved through the legislation so as to facilitate later precautionary measures, e.g. through temporary authorisations, derogations and safeguard clauses. However, crucially, it requires that the legislation also be interpreted in light of the precautionary principle. This paper investigates the logic behind the Court of Justice of the EU’s judgments and the circumstances that enable or deter the Court in taking, or permitting, stronger precautionary approaches. Although apparently inconsistent, a number of contextual factors including the legislative provisions and actors involved influence the judgments substantially. The analysis provides insight into improving the principle’s incorporation to facilitate its continued application and maintenance of flexibility, whilst bearing in mind the general desirability of objectivity and legal certainty.

Derivation of soil screening values for metals in Portuguese natural soil

The increasing human activity has been responsible by profound changes and a constinuos degradation of the soil compartment in all the European territory. Some European policies are appearing focusing soil’s protection and the management of contaminated sites, in order to recover land for other uses. To regulate the risk assessment and the management of contaminated soils, many European member states adopted soil guideline values, as for example soil screnning values (SSV).These values are particularly useful for the the first tier of the Ecological Risk Assessment (ERA) processes of contaminated sites,especially for a first screening of sites requiring a more site-specific evaluation. Hence, the approriate definition of regional SSVs will have relevant economic impacts in the management of contaminated sites. Portugal is one of European Member States that still lack these soil guideline values. In this context, this study gaves a remarkable contribution in the generation of ecotoxicological data for soil microbiological parameters, terrestrial plants and invertebrates for the derivation of SSVs for uranium (U), cadmium (Cd) and copper (Cu), using a Portuguese natural soil, representative of a dominant type of soil in the Portuguese territory. SSVs were derived based on two methods proposed by the the Technical Guidance Document for Risk Assessment of the European Commission; namely the assessment factor method (AF) and the species sensitivity distribution (SSD) method (with some adaptations). The outputs of both methods were compared and discussed. Further, this study laid the foundation for a deeper reflection about the cut-off (hazard concentration for a given percentage of species - HCps) to be estimated from the SSDs, and to be selected for the derivation of SSVs, with the adequate level of protection. It was proven that this selection may vary for different contaminants, however a clear justification should be given, in each case. The SSvs proposed in this study were for: U (151.4 mg U kg-1dw), Cd (5.6 mg Cd kg-1dw), and Cu (58.5 mg Cu kg-1dw) These values should now be tested for their descriminating power of soils with different levels of contamination. However, this studies clarifies the approach that should be followed for the derivation of SSVs for other metals and organic contaminants, and for other dominant types of Portuguese natural soils.

Development of a Piggybac based direct reprogramming system for derivation of integration free induced pluripotent stem cells

Induced pluripotent stem cells (iPSc) have great potential for applications in regenerative medicine, disease modeling and basic research. Several methods have been developed for their derivation. The original method of Takahashi and Yamanaka involved the use of retroviral vectors which result in insertional mutagenesis, presence in the genome of potential oncogenes and effects of residual transgene expression on differentiation bias of each particular iPSc line. Other methods have been developed, using different viral vectors (adenovirus and Sendai virus), transient plasmid transfection, mRNA transduction, protein transduction and use of small molecules. However, these methods suffer from low efficiencies; can be extremely labor intensive, or both. An additional method makes use of the piggybac transposon, which has the advantage of inserting its payload into the host genome and being perfectly excised upon re-expression of the transposon transposase. Briefly, a policistronic cassette expressing Oct4, Sox2, Klf4 and C-Myc flanked by piggybac terminal repeats is delivered to the cells along with a plasmid transiently expressing piggybac transposase. Once reprogramming occurs, the cells are re-transfected with transposase and subclones free of tranposon integrations screened for. The procedure is therefore very labor intensive, requiring multiple manipulations and successive rounds of cloning and screening. The original method for reprogramming with the the PiggyBac transposon was created by Woltjen et al in 2009 (schematized here) and describes a process with which it is possible to obtain insert-free iPSc. Insert-free iPSc enables the establishment of better cellular models of iPS and adds a new level of security to the use of these cells in regenerative medicine. Due to the fact that it was based on several low efficiency steps, the overall efficiency of the method is very low (<1%). Moreover, the stochastic transfection, integration, excision and the inexistence of an active way of selection leaves this method in need of extensive characterization and screening of the final clones. In this work we aime to develop a non-integrative iPSc derivation system in which integration and excision of the transgenes can be controlled by simple media manipulations, avoiding labor intensive and potentially mutagenic procedures. To reach our goal we developed a two vector system which is simultaneously delivered to original population of fibroblasts. The first vector, Remo I, carries the reprogramming cassette and GFP under the regulation of a constitutive promoter (CAG). The second vector, Eneas, carries the piggybac transposase associated with an estrogen receptor fragment (ERT2), regulated in a TET-OFF fashion, and its equivalent reverse trans-activator associated with a positive-negative selection cassette under a constitutive promoter. We tested its functionality in HEK 293T cells. The protocol is divided in two the following steps: 1) Obtaining acceptable transfection efficiency into human fibroblasts. 2) Testing the functionality of the construct 3) Determining the ideal concentration of DOX for repressing mPB-ERT2 expression 4) Determining the ideal concentration of TM for transposition into the genome 5) Determining the ideal Windows of no DOX/TM pulse for transposition into the genome 6) 3, 4 and 5) for transposition out of the genome 7) Determination of the ideal concentration of GCV for negative selection We successfully demonstrated that ENEAS behaved as expected in terms of DOX regulation of the expression of mPB-ERT2. We also demonstrated that by delivering the plasmid into 293T HEK cells and manipulating the levels of DOX and TM in the medium, we could obtain puromycin resistant lines. The number of puromycin resistant colonies obtained was significantly higher when DOX as absent, suggesting that the colonies resulted from transposition events. Presence of TM added an extra layer of regulation, albeit weaker. Our PCR analysis, while not a clean as would be desired, suggested that transposition was indeed occurring, although a background level of random integration could not be ruled out. Finally, our attempt to determine whether we could use GVC to select clones that had successfully mobilized PB out of the genome was unsuccessful. Unexpectedly, 293T HEK cells that had been transfected with ENEAS and selected for puromycin resistance were insensitive to GCV.

Self-similarity principle: the reduced description of randomness

A new general fitting method based on the Self-Similar (SS) organization of random sequences is presented. The proposed analytical function helps to fit the response of many complex systems when their recorded data form a self-similar curve. The verified SS principle opens new possibilities for the fitting of economical, meteorological and other complex data when the mathematical model is absent but the reduced description in terms of some universal set of the fitting parameters is necessary. This fitting function is verified on economical (price of a commodity versus time) and weather (the Earth’s mean temperature surface data versus time) and for these nontrivial cases it becomes possible to receive a very good fit of initial data set. The general conditions of application of this fitting method describing the response of many complex systems and the forecast possibilities are discussed.