Automated metamorphic testing on the analyses of feature models

Copyright © 2010 Elsevier B.V. All rights reserved.Context: A feature model (FM) represents the valid combinations of features in a domain. The automated extraction of information from FMs is a complex task that involves numerous analysis operations, techniques and tools. Current testing methods in this context are manual and rely on the ability of the tester to decide whether the output of an analysis is correct. However, this is acknowledged to be time-consuming, error-prone and in most cases infeasible due to the combinatorial complexity of the analyses, this is known as the oracle problem.Objective: In this paper, we propose using metamorphic testing to automate the generation of test data for feature model analysis tools overcoming the oracle problem. An automated test data generator is presented and evaluated to show the feasibility of our approach.Method: We present a set of relations (so-called metamorphic relations) between input FMs and the set of products they represent. Based on these relations and given a FM and its known set of products, a set of neighbouring FMs together with their corresponding set of products are automatically generated and used for testing multiple analyses. Complex FMs representing millions of products can be efficiently created by applying this process iteratively.Results: Our evaluation results using mutation testing and real faults reveal that most faults can be automatically detected within a few seconds. Two defects were found in FaMa and another two in SPLOT, two real tools for the automated analysis of feature models. Also, we show how our generator outperforms a related manual suite for the automated analysis of feature models and how this suite can be used to guide the automated generation of test cases obtaining important gains in efficiency.Conclusion: Our results show that the application of metamorphic testing in the domain of automated analysis of feature models is efficient and effective in detecting most faults in a few seconds without the need for a human oracle.This work has been partially supported by the European Commission(FEDER)and Spanish Government under CICYT project SETI(TIN2009-07366)and the Andalusian Government project ISABEL(TIC-2533)

Genome-wide approaches for identifying genes involved in the maintenance of genomic stability

The maintenance of genomic stability and the repair of DNA damage are essential for the survival of all cells. Despite diverse pathways for repair of DNA lesions, different mutations can arise, ranging from Single Nucleotide Variants (SNVs) to larger Structu- ral Variants (SVs). The processes that play a role in the formation of these alterations are not fully understood. In this thesis, I present two complementary approaches for accumulating genomic variants and for identifying pathways involved in the suppression of mutation formation using Saccharomyces cerevisiae (budding yeast) gene knockout strains. First, using next-generation sequencing, I studied neutral variants through a mutation accumulation assay for up to 1800 generations. I used 47 yeast strains with known defects in DNA replication, repair and recombination pathways. In all strains, small insertions and deletions (indels) were more common than larger SVs (>50bp). Most mutations occurred in repetitive sequences, implicating replication based mechanisms and homologous recombination in the formation of genomic variants. Furthermore, the knockout of MSH2 produced a hypermutable strain that acquired the highest number of indels. Moreover, the knockout of the genes SWR1 and ISW1, involved in chromatin remodeling, resulted in strains with high number of deletions. These results suggest that defects in establishing a correct chromatin architecture may play a role in the formation of genomic variants. I further performed a genome-wide screen for genes that suppress deletion formation under different drug treatments in the presence or absence of homologous repeats by using designed constructs. As expected, deletions occurred more often between repeats, in support of the frequent involvement of homologous recombination in the formation of chromosome rearrangements. In addition, I identified genes whose knockout led to incre- ased levels of deletions. Among these, IOC4 is of particular interest given that it belongs to the same chromatin remodeling complex as ISW1, identified in the neutral mutati- on accumulation assay. This provides further evidence that chromatin remodeling may be involved in preventing the occurrence of SVs. Furthermore, several meiosis-related mutants also showed increased levels of deletions, suggesting that meiosis proteins may have additional roles in the maintenance of genomic stability during vegetative growth. By performing additional experimental validations, I verified the higher vulnerability of meiosis gene knockouts to acquire deletions, especially in their diploid stages. In the last chapter, I briefly describe the results of several side projects in which I applied computational methods learned through the above mentioned projects, to identify and characterize genomic rearrangements in different human cancers. In summary, I have found that genome-wide approaches can provide interesting insights into the understanding of genomic variants in yeast and human cancers. In particular, given the evolutionary conservation of the ISWI chromatin remodeling complex and meiosis-related genes, the results presented here point to potentially novel functions of these proteins in the maintenance of genomic stability

Water IoT monitoring system for aquaponics health and fishery applications

Aquaponic health is a very important in the food industry field, as currently there is a huge amount of fishing farms, and the demands are growing in the whole world. This work examines the process of developing an innovative aquaponics health monitoring system that incorporates high-tech back-end innovation sensors to examine fish and crop health and a data analytics framework with a low-tech front-end approach to feedback actions to farmers. The developed system improves the state-of-the-art in terms of aquaponics life cycle monitoring metrics and communication technologies, and the energy consumption has been reduced to make a sustainable system

Spectral signatures of photosynthesis II: coevolution with other stars and the atmosphere on extrasolar worlds

As photosynthesis on Earth produces the primary signatures of life that can be detected astronomically at the global scale, a strong focus of the search for extrasolar life will be photosynthesis, particularly photosynthesis that has evolved with a different parent star. We take planetary atmospheric compositions simulated by Segura, et al. (2003, 2005) for Earth-like planets around observed F2V and K2V stars, modeled M1V and M5V stars, and around the active M4.5V star AD Leo; our scenarios use Earth's atmospheric composition as well as very low O2 content in case anoxygenic photosynthesis dominates. We calculate the incident spectral photon flux densities at the surface of the planet and under water. We identify bands of available photosynthetically relevant radiation and find that photosynthetic pigments on planets around F2V stars may peak in absorbance in the blue, K2V in the red-orange, and M stars in the NIR, in bands at 0.93-1.1 microns, 1.1-1.4 microns, 1.5-1.8 microns, and 1.8-2.5 microns. In addition, we calculate wavelength restrictions for underwater organisms and depths of water at which they would be protected from UV flares in the early life of M stars. We estimate the potential productivity for both surface and underwater photosynthesis, for both oxygenic and anoxygenic photosynthesis, and for hypothetical photosynthesis in which longer wavelength, multi-photosystem series are used.Comment: 59 pages, 4 figures, 4 tables, forthcoming in Astrobiology ~March 200

Automated metamorphic testing of variability analysis tools

Variability determines the capability of software applications to be configured and customized. A common need during the development of variability–intensive systems is the automated analysis of their underlying variability models, e.g. detecting contradictory configuration options. The analysis operations that are performed on variability models are often very complex, which hinders the testing of the corresponding analysis tools and makes difficult, often infeasible, to determine the correctness of their outputs, i.e. the well–known oracle problem in software testing. In this article, we present a generic approach for the automated detection of faults in variability analysis tools overcoming the oracle problem. Our work enables the generation of random variability models together with the exact set of valid configurations represented by these models. These test data are generated from scratch using step–wise transformations and assuring that certain constraints (a.k.a. metamorphic relations) hold at each step. To show the feasibility and generalizability of our approach, it has been used to automatically test several analysis tools in three variability domains: feature models, CUDF documents and Boolean formulas. Among other results, we detected 19 real bugs in 7 out of the 15 tools under test.CICYT TIN2012-32273CICYT IPT-2012- 0890-390000Junta de Andalucía TIC-5906Junta de Andalucía P12-TIC- 186

Transcriptional analysis of PRRSV-infected porcine dendritic cell response to Streptococcus suis infection reveals up-regulation of inflammatory-related genes expression

The porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important swine pathogens and often serves as an entry door for other viral or bacterial pathogens, of which Streptococcus suis is one of the most common. Pre-infection with PRRSV leads to exacerbated disease caused by S. suis infection. Very few studies have assessed the immunological mechanisms underlying this higher susceptibility. Since antigen presenting cells play a major role in the initiation of the immune response, the in vitro transcriptional response of bone marrow-derived dendritic cells (BMDCs) and monocytes in the context of PRRSV and S. suis co-infection was investigated. BMDCs were found to be more permissive than monocytes to PRRSV infection; S. suis phagocytosis by PRRSV-infected BMDCs was found to be impaired, whereas no effect was found on bacterial intracellular survival. Transcription profile analysis, with a major focus on inflammatory genes, following S. suis infection, with and without pre-infection with PRRSV, was then performed. While PRRSV pre-infection had little effect on monocytes response to S. suis infection, a significant expression of several pro-inflammatory molecules was observed in BMDCs pre-infected with PRRSV after a subsequent infection with S. suis. While an additive effect could be observed for CCL4, CCL14, CCL20, and IL-15, a distinct synergistic up-regulatory effect was observed for IL-6, CCL5 and TNF-α after co-infection. This increased pro-inflammatory response by DCs could participate in the exacerbation of the disease observed during PRRSV and S. suis co-infection

Annihilation emission from young supernova remnants

A promising source of the positrons that contribute through annihilation to the diffuse Galactic 511keV emission is the beta-decay of unstable nuclei like 56Ni and 44Ti synthesised by massive stars and supernovae. Although a large fraction of these positrons annihilate in the ejecta of SNe/SNRs, no point-source of annihilation radiation appears in the INTEGRAL/SPI map of the 511keV emission. We exploit the absence of detectable annihilation emission from young local SNe/SNRs to derive constraints on the transport of MeV positrons inside SN/SNR ejecta and their escape into the CSM/ISM, both aspects being crucial to the understanding of the observed Galactic 511keV emission. We simulated 511keV lightcurves resulting from the annihilation of the decay positrons of 56Ni and 44Ti in SNe/SNRs and their surroundings using a simple model. We computed specific 511keV lightcurves for Cas A, Tycho, Kepler, SN1006, G1.9+0.3 and SN1987A, and compared these to the upper-limits derived from INTEGRAL/SPI observations. The predicted 511keV signals from positrons annihilating in the ejecta are below the sensitivity of the SPI instrument by several orders of magnitude, but the predicted 511keV signals for positrons escaping the ejecta and annihilating in the surrounding medium allowed to derive upper-limits on the positron escape fraction of ~13% for Cas A, ~12% for Tycho, ~30% for Kepler and ~33% for SN1006. The transport of ~MeV positrons inside SNe/SNRs cannot be constrained from current observations of the 511keV emission from these objects, but the limits obtained on their escape fraction are consistent with a nucleosynthesis origin of the positrons that give rise to the diffuse Galactic 511keV emission.Comment: 15 pages, 11 figures, accepted for publication in A&

Transcriptional approach to study porcine tracheal epithelial cells individually or dually infected with swine influenza virus and Streptococcus suis

Background: Swine influenza is a highly contagious viral infection in pigs affecting the respiratory tract that can have significant economic impacts. Streptococcus suis serotype 2 is one of the most important post-weaning bacterial pathogens in swine causing different infections, including pneumonia. Both pathogens are important contributors to the porcine respiratory disease complex. Outbreaks of swine influenza virus with a significant level of co-infections due to S. suis have lately been reported. In order to analyze, for the first time, the transcriptional host response of swine tracheal epithelial (NPTr) cells to H1N1 swine influenza virus (swH1N1) infection, S. suis serotype 2 infection and a dual infection, we carried out a comprehensive gene expression profiling using a microarray approach. Results: Gene clustering showed that the swH1N1 and swH1N1/S. suis infections modified the expression of genes in a similar manner. Additionally, infection of NPTr cells by S. suis alone resulted in fewer differentially expressed genes compared to mock-infected cells. However, some important genes coding for inflammatory mediators such as chemokines, interleukins, cell adhesion molecules, and eicosanoids were significantly upregulated in the presence of both pathogens compared to infection with each pathogen individually. This synergy may be the consequence, at least in part, of an increased bacterial adhesion/invasion of epithelial cells previously infected by swH1N1, as recently reported. Conclusion: Influenza virus would replicate in the respiratory epithelium and induce an inflammatory infiltrate comprised of mononuclear cells and neutrophils. In a co-infection situation, although these cells would be unable to phagocyte and kill S. suis, they are highly activated by this pathogen. S. suis is not considered a primary pulmonary pathogen, but an exacerbated production of proinflammatory mediators during a co-infection with influenza virus may be important in the pathogenesis and clinical outcome of S. suis-induced respiratory diseases

A slip-based model for the size-dependent effective thermal conductivity of nanowires

The heat flux across a nanowire is computed based on the Guyer-Krumhansl equation. Slip conditions with a slip length depending on both temperature and nanowire radius are introduced at the outer boundary. An explicit expression for the effective thermal conductivity is derived and compared to existing models across a given temperature range, providing excellent agreement with experimental data for Si nanowires

A synthetic biology approach for consistent production of plant-made recombinant polyclonal antibodies against snake venom toxins

Antivenoms developed from the plasma of hyperimmunized animals are the only effective treatment available against snakebite envenomation but shortage of supply contributes to the high morbidity and mortality toll of this tropical disease. We describe a synthetic biology approach to affordable and cost-effective antivenom production based on plant-made recombinant polyclonal antibodies (termed pluribodies). The strategy takes advantage of virus superinfection exclusion to induce the formation of somatic expression mosaics in agroinfiltrated plants, which enables the expression of complex antibody repertoires in a highly reproducible manner. Pluribodies developed using toxin-binding genetic information captured from peripheral blood lymphocytes of hyperimmunized camels recapitulated the overall binding activity of the immune response. Furthermore, an improved plant-made antivenom (plantivenom) was formulated using an in vitro selected pluribody against Bothrops asper snake venom toxins and has been shown to neutralize a wide range of toxin activities and provide protection against lethal venom doses in mice.Fil: Julve Parreño, Jose Manuel. Universidad Politécnica de Valencia; EspañaFil: Huet, Estefanía. Universidad Politécnica de Valencia; EspañaFil: Fernández del Carmen, Asun. Universidad Politécnica de Valencia; EspañaFil: Segura, Alvaro. Universidad de Costa Rica; Costa RicaFil: Venturi, Micol. Universidad Politécnica de Valencia; EspañaFil: Gandía, Antoni. Universidad Politécnica de Valencia; EspañaFil: Pan, Wei-Song. Universidad Politécnica de Valencia; EspañaFil: Albaladejo, Irene. Universidad Politécnica de Valencia; EspañaFil: Forment, Javier. Universidad Politécnica de Valencia; EspañaFil: Pla, Davinia. Instituto de Biomedicina de Valencia; EspañaFil: Wigdorovitz, Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; ArgentinaFil: Calvete, Juan J.. Instituto de Biomedicina de Valencia; EspañaFil: Gutiérrez, Carlos. Universidad de Las Palmas de Gran Canaria; EspañaFil: Gutiérrez, José María. Universidad de Costa Rica; Costa RicaFil: Granell, Antonio. Universidad Politécnica de Valencia; EspañaFil: Orzáez, Diego. Universidad Politécnica de Valencia; Españ