The radiative transport equation with heterogeneous cross-sections

We consider the classical integral equation reformulation of the radiative transport equation (RTE) in a heterogeneous medium, assuming isotropic scattering. We prove an estimate for the norm of the integral operator in this formulation which is explicit in the (variable) coefficients of the problem (also known as the cross-sections). This result uses only elementary properties of the transport operator and some classical functional analysis. As a corollary, we obtain a bound on the convergence rate of source iteration (a classical stationary iterative method for solving the RTE). We also obtain an estimate for the solution of the RTE which is explicit in its dependence on the cross-sections. The latter can be used to estimate the solution in certain Bochner norms when the cross-sections are random fields. Finally we use our results to give an elementary proof that the generalised eigenvalue problem arising in nuclear reactor safety has only real and positive eigenvalues

Using theorem provers to increase the precision of dependence analysis for information flow control

Information flow control (IFC) is a category of techniques for enforcing information flow properties. In this paper we present the Combined Approach, a novel IFC technique that combines a scalable system-dependence-graph-based (SDG-based) approach with a precise logic-based approach based on a theorem prover. The Combined Approach has an increased precision compared with the SDG-based approach on its own, without sacrificing its scalability. For every potential illegal information flow reported by the SDG-based approach, the Combined Approach automatically generates proof obligations that, if valid, prove that there is no program path for which the reported information flow can happen. These proof obligations are then relayed to the logic-based approach. We also show how the SDG-based approach can provide additional information to the theorem prover that helps decrease the verification effort. Moreover, we present a prototypical implementation of the Combined Approach that uses the tools JOANA and KeY as the SDG-based and logic-based approach respectively

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species

[EN] Background The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 euro/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted fromSolanum elaeagnifoliumusing this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.This research has been funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No 677379 (Linking genetic resources, genomes and phenotypes of Solanaceous crops; G2P-SOL). David Alonso is grateful to Universitat Politecnica de Valencia for a predoctoral (PAID-01-16) contract under the Programa de Ayudas de Investigacion y Desarrollo initiative. Mariola Plazas is grateful to Generalitat Valenciana and Fondo Social Europeo for a postdoctoral grant (APOSTD/2018/014). Pietro Gramazio is grateful to Japan Society for the Promotion of Science for a Postdoctoral Grant (P19105, FY2019 JSPS Postdoctoral Fellowship for Research in Japan (Standard)). The Spanish Ministerio de Educacion, Cultura y Deporte funded a predoctoral fellowship granted to Edgar Garcia-Fortea (FPU17/02389).Vilanova Navarro, S.; Alonso-Martín, D.; Gramazio, P.; Plazas Ávila, MDLO.; García-Fortea, E.; Ferrante, P.; Schmidt, M.... (2020). SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species. Plant Methods. 16(1):1-11. https://doi.org/10.1186/s13007-020-00652-yS111161Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J. 2017;15:149–61.Jung H, Winefield C, Bombarely A, Prentis P, Waterhouse P. Tools and strategies for long-read sequencing and de novo assembly of plant genomes. 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Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

[EN] Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers are amongst the most common markers of choice for studies of diversity and relationships in horticultural species. We have used 11 SSR and 35 SNP markers derived from transcriptome sequencing projects to fingerprint 48 accessions of a collection of brinjal (Solanum melongena), gboma (S. macrocarpon) and scarlet (S. aethiopicum) eggplant complexes, which also include their respective wild relatives S. incanum, S. dasyphyllum and S. anguivi. All SSR and SNP markers were polymorphic and 34 and 36 different genetic fingerprints were obtained with SSRs and SNPs, respectively. When combining both markers all accessions but two had different genetic profiles. Although on average SSRs were more informative than SNPs, with a higher number of alleles, genotypes and polymorphic information content (PIC), and expected heterozygosity (He) values, SNPs have proved highly informative in our materials. Low observed heterozygosity (Ho) and high fixation index (f) values confirm the high degree of homozygosity of eggplants. Genetic identities within groups of each complex were higher than with groups of other complexes, although differences in the ranks of genetic identity values among groups were observed between SSR and SNP markers. For low and intermediate values of pair-wise SNP genetic distances, a moderate correlation between SSR and SNP genetic distances was observed (r(2) = 0.592), but for high SNP genetic distances the correlation was low (r(2) = 0.080). The differences among markers resulted in different phenogram topologies, with a different eggplant complex being basal (gboma eggplant for SSRs and brinjal eggplant for SNPs) to the two others. Overall the results reveal that both types of markers are complementary for eggplant fingerprinting and that interpretation of relationships among groups may be greatly affected by the type of marker used.This work has been funded by European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia y Competitividad and Fondo Europeo de Desarrollo Regional (Grant AGL2015-64755-R from MINECO/FEDER). Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral contract (Programa FPI de la UPV-Subprograma 1/2013 call). Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Juan de la Cierva-Formacion programme (FJCI-2015-24835).Gramazio, P.; Prohens Tomás, J.; Borras, D.; Plazas Ávila, MDLO.; Herraiz García, FJ.; Vilanova Navarro, S. 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Human processor modelling language (HPML): Estimate working memory load through interaction

To operate machines over their user interface may cause high load on human's working memory. This load can decrease performance in the working task significantly if this task is a cognitive challenging one, e. g. diagnosis. With the »Human Processor Modelling Language« (HPML) the interaction activity can be modelled with a directed graph. From such models a condensed indicator value for working memory load can be estimated. Thus different user interface solutions can get compared with respect to their relative demand on working memory resource

The KeY platform for verification and analysis of java programs

The KeY system offers a platform of software analysis tools for sequential Java. Foremost, this includes full functional verification against contracts written in the Java Modeling Language. But the approach is general enough to provide a basis for other methods and purposes: (i) complementary validation techniques to formal verification such as testing and debugging, (ii) methods that reduce the complexity of verification such as modularization and abstract interpretation, (iii) analyses of non-functional properties such as information flowsecurity, and (iv) sound program transformation and code generation. We show that deductive technology that has been developed for full functional verification can be used as a basis and framework for other purposes than pure functional verification. We use the current release of the KeY system as an example to explain and prove this claim

The KeY Platform for Verification and Analysis of Java Programs

The KeY system offers a platform of software analysis tools for sequential Java. Foremost, this includes full functional verification against contracts written in the Java Modeling Language. But the approach is general enough to provide a basis for other methods and purposes: (i) complementary validation techniques to formal verification such as testing and debugging, (ii) methods that reduce the complexity of verification such as modularization and abstract interpretation, (iii) analyses of non-functional properties such as information flow security, and (iv) sound program transformation and code generation. We show that deductive technology that has been developed for full functional verification can be used as a basis and framework for other purposes than pure functional verification. We use the current release of the KeY system as an example to explain and prove this claim