Software Product Line

The Software Product Line (SPL) is an emerging methodology for developing software products. Currently, there are two hot issues in the SPL: modelling and the analysis of the SPL. Variability modelling techniques have been developed to assist engineers in dealing with the complications of variability management. The principal goal of modelling variability techniques is to configure a successful software product by managing variability in domain-engineering. In other words, a good method for modelling variability is a prerequisite for a successful SPL. On the other hand, analysis of the SPL aids the extraction of useful information from the SPL and provides a control and planning strategy mechanism for engineers or experts. In addition, the analysis of the SPL provides a clear view for users. Moreover, it ensures the accuracy of the SPL. This book presents new techniques for modelling and new methods for SPL analysis

Integration of Quality Attributes in Software Product Line Development

Different approaches for building modern software systems in complex and open environments have been proposed in the last few years. Some efforts try to apply Software Product Line (SPL) approach to take advantage of the massive reuse for producing software systems that share a common set of features. In general quality assurance is a crucial activity for success in software industry, but it is even more important when talking about Software Product Lines since the intensive reuse of assets makes the quality attributes (a measurable physical or abstract property of an entity) of the assets to be transmitted to the whole SPL scope. However, despite the importance that quality has in software product line development, most of the methodologies being applied in Software Product Line Development focus only on managing the commonalities and variability within the product line and not giving support to the non--¿ functional requirements that the products must fit. The main goal of this master final work is to introduce quality attributes in early stages of software product line development processes by means of the definition of a production plan that, on one hand, integrates quality as an additional view for describing the extension of the software product line and, on the other hand introduces the quality attributes as a decision factor during product configuration and when selecting among design alternatives. Our approach has been defined following the Model--¿ Driven Software Development paradigm. Therefore all the software artifacts defined had its correspondent metamodels and the processes defined rely on automated model transformations. Finally in order to illustrate the feasibility of the approach we have integrated the quality view in an SPL example in the context of safety critical embedded systems on the automotive domain.González Huerta, J. (2011). Integration of Quality Attributes in Software Product Line Development. http://hdl.handle.net/10251/15835Archivo delegad

From forests to microbiomes : The mediation of plant-soil systems by root-symbiotic fungi

Plant-microbial symbioses play crucial roles in ecological and biogeochemical processes such as carbon and nutrient cycling, plant-soil feedback, and evolutionary dynamics. However, less is known about how these symbioses influence the broader soil microbial communities (microbiomes) that they interact with, which is essential to understanding the ecosystem processes they facilitate.In this thesis, I investigate the effect of mycorrhizal type and other root symbioses on the structure and potential function of belowground microbiomes, as well as leaf microbiomes and leaf element concentrations. To accomplish this, I used a variety of techniques, including metabarcoding and metagenomic analysis of microbial communities and their functional genes from field studies at various scales, from single vegetation communities to a European latitudinal gradient.Regionally, I found that sites dominated by arbuscular mycorrhizal (AM) vegetation had relatively more AM fungi, bacteria, fungal saprotrophs, and pathogens in their soils compared to ectomycorrhizal (EcM) vegetation, and that coniferous EcM vegetation was a particularly important determinant of soil conditions and microbiome features. I also found that root colonization by dark septate endophytic (DSE) fungi was strongly associated with the composition of microbial communities and functional genes, including a negative relationship with the relative abundance of fungal pathogens and bacteria across Europe. Lastly, I found that tree species with different root symbioses and levels of colonization and their leaf element profiles were a key factor shaping leaf microbial communities and diversity compared to climate, with contrasting relative abundances of bacterial and fungal guilds and taxa between and within tree species.Overall, my findings suggest that the biotic interactions between plants and their root symbionts are important factors determining the structure and function of microbiomes across vegetation communities and tree species, with implications for wider ecosystem processes

Diversity of wheat phyllosphere fungi in different agricultural production systems

Fusarium head blight (FHB) is a disease affecting cereals world-wide caused by Fusarium fungi. The disease is of great economic importance especially since it is associated with contamination by harmful mycotoxins produced by Fusarium spp. In recent years, several studies have reported lower mycotoxin contamination of organically produced cereals compared with those produced conventionally. An unexplored factor is differences in the microbial communities on cereal crops between the organic and conventional systems, which may exert a biocontrol effect on FHB. The aim of this thesis was to investigate the effect of different environmental and agricultural factors on Fusarium communities and fungal phyllosphere communities in wheat in different agricultural production systems. New primers for amplifying Fusarium communities, in conjunction with 454 se-quencing, were evaluated, and Fusarium communities associated with soil and wheat kernels were successfully characterised. Comparison of fungicide-treated and untreated wheat leaves from 18 fields in Sweden in 2011 revealed that fungicide use was associ-ated with decreased evenness of fungal communities. Furthermore, organic farming was associated with increased fungal species richness on wheat leaves when pairs of 22 organically and conventionally managed fields in Sweden were compared in 2012. There was no difference in the abundance of leaf pathogens between cropping systems. Several fungal species were consistently found regardless of geographical location, year and cropping system, while fungal abundance was highly variable between fields. Both Fusarium and fungal communities were affected by agricultural intensity. How-ever, there was no difference in Fusarium community composition in wheat kernels from organically and conventionally managed fields. The method evaluated in this thesis can be used to monitor Fusarium communities in the field, which is important in order to develop strategies for limiting FHB and mycotoxin contamination. The present thesis demonstrates that fungicide use and organic farming are associated with differen-tial fungal communities in the wheat phyllosphere. This indicates that there is an oppor-tunity for the farmer to manage these communities with the aim of enhancing their biocontrol potential against plant pathogens such as Fusarium

Proceedings, MSVSCC 2015

The Virginia Modeling, Analysis and Simulation Center (VMASC) of Old Dominion University hosted the 2015 Modeling, Simulation, & Visualization Student capstone Conference on April 16th. The Capstone Conference features students in Modeling and Simulation, undergraduates and graduate degree programs, and fields from many colleges and/or universities. Students present their research to an audience of fellow students, faculty, judges, and other distinguished guests. For the students, these presentations afford them the opportunity to impart their innovative research to members of the M&S community from academic, industry, and government backgrounds. Also participating in the conference are faculty and judges who have volunteered their time to impart direct support to their students’ research, facilitate the various conference tracks, serve as judges for each of the tracks, and provide overall assistance to this conference. 2015 marks the ninth year of the VMASC Capstone Conference for Modeling, Simulation and Visualization. This year our conference attracted a number of fine student written papers and presentations, resulting in a total of 51 research works that were presented. This year’s conference had record attendance thanks to the support from the various different departments at Old Dominion University, other local Universities, and the United States Military Academy, at West Point. We greatly appreciated all of the work and energy that has gone into this year’s conference, it truly was a highly collaborative effort that has resulted in a very successful symposium for the M&S community and all of those involved. Below you will find a brief summary of the best papers and best presentations with some simple statistics of the overall conference contribution. Followed by that is a table of contents that breaks down by conference track category with a copy of each included body of work. Thank you again for your time and your contribution as this conference is designed to continuously evolve and adapt to better suit the authors and M&S supporters. Dr.Yuzhong Shen Graduate Program Director, MSVE Capstone Conference Chair John ShullGraduate Student, MSVE Capstone Conference Student Chai

Physiologically based modelling of nanoparticle biodistribution and biokinetics

To predict the toxicity of nanoparticles (1-100 nm), it is crucial to understand their biokinetics i.e. how they are taken up, distributed, dissolved and removed from the body. Such information can be gained from biodistribution studies in animals. However, to make predictions for other types of nanoparticles, exposure conditions and species, including humans, extrapolations from such studies are required. Use of models, such as physiologically based pharmacokinetic (PBPK) models, makes extrapolations feasible, given that the models are sufficiently validated. In this thesis, a conceptual nanospecific PBPK model for intravenous administration to rats was developed and applied to different types of inert nanoparticles using experimental data from recent scientific publications (Papers I and II). The model represents systemic distribution and serves as a foundation for expansion to other species and other exposure routes (inhalation, dermal, oral). The PBPK simulations suggest that the model is able to describe the biokinetics of different types of inert nanoparticles given intravenously despite large differences in properties and exposure conditions. Our model is the first to include separate compartments for phagocytic cells and saturable phagocytosis. The simulations show that (1) phagocytosis needs to be incorporated in nano PBPK models, (2) the dose has a clear impact on biokinetics, but (3) further refinements are needed to better reflect processes such as agglomeration, corona formation and dissolution. The model was slightly modified to describe the biodistribution and biokinetics of nanoceria of different sizes and administered via other routes (Paper III). While the model could well predict the biokinetics after intravenous dosing, the predictions of inhalation, instillation and ingestion data were poor. The poor agreement may be partly due to low absorption via these routes, resulting in low nanoceria levels in tissues and organs, often close to or below the detection limit, in tissues. However, low absorption is hardly the only explanation, as the experimentally observed concentration time courses of nanoceria in tissues suggest that the biokinetics depend not only on the nanoparticle properties (size, coating) but also on the exposure conditions (dose, exposure route). The PBPK model was further developed to account for the complexity of inhalation exposure to nanoparticles (Paper IV). The modified model includes regional particle deposition in the respiratory tract, mucociliary clearance and phagocytosis in the lungs, olfactory uptake, and transport into the systemic circulation by alveolar wall translocation. The PBPK model described the biodistribution well and again suggested phagocytosis to be very important. The PBPK simulations were performed assuming that the nanoparticles are inert, i.e. do not dissolve or degrade in the body. However, when modelling the experimental data it seemed that the biokinetics might be better explained by introducing dissolution in the PBPK model. A related problem is that most experimental studies of metal nanoparticles use elemental analysis such as inductively coupled plasma mass spectrometry (ICP-MS). Such analyses do not discriminate between different forms of metal and therefore obscures the biokinetics. To test if gold nanoparticles dissolve in biological media, we developed an in vitro method to characterize dissolution of gold nanoparticles in contact with cell medium, macrophages and lipopolysaccharide (LPS)-triggered macrophages, simulating a disease state (Paper V). We demonstrated that gold nanoparticles are dissolved by cell medium and macrophages and even more so by LPS-triggered macrophages. The dissolution rate was higher for 5 nm than for 50 nm gold particles

Ecology and Molecular Phylogenetics of \u3ci\u3eHydnora\u3c/i\u3e (Hydnoraceae) in Southern Africa

The Hydnoraceae are a clade of root holoparasitic angiosperms that contain two small genera, Hydnora and Prosopanche. This study, focused on Hydnora, presents novel data regarding the pollination biology, germination ecology, parasite-host nutritional relationships, and the molecular systematics of this group. Experimental addition of the primary pollinator, Dermestes maculatus to Hydnora africana chamber flowers demonstrated beetle imprisonment during the carpellate stage. Changes in the inner surfaces of the androecial chamber allowed beetle escape after pollen release. Most beetles escaped, dusted with viable pollen, three days after pollen release. To investigate germination ecology, aqueous root extracts of host and non-host Euphorbia spp. were applied to seeds of Hydnora triceps which germinated only in response to root extracts of its exclusive host, Euphorbia dregeana, and not for co-occurring non-host Euphorbia spp. This pattern of host specific germination suggests that germination response to host-root cues may be responsible for host partitioning. There are large gaps in our understanding of holoparasitic plant-host nutrient relationships and the mechanisms of solute uptake. Transdermal water loss, parasite-host mineral relationships, and heterotrophy were evaluated for Hydnora . Transdermal water loss in Hydnora ranged from 0.14±.02 to 0.38±.04 mg cm-2 hr-1, comparable to transpiration rates recorded for xerophytes. Concentrations of P and K were higher in Hydnora relative to their CAM (Crassulacean acid metabolism) hosts; other mineral concentrations were significantly lower in the parasite or were not different. Stable isotope fractionation in host tissues dictated significant differences between parasite and host δ 13C signatures. A phylogeny of the Hydnoraceae was generated using plastid (rpoB) and nuclear ITS (internal transcribed spacer) DNA sequences. The analyses supported the monophyly of Hydnora and Prosopanche, their relationship as sister genera, and validated subgeneric sections of Hydnora. Optimization of the character of host preference suggests the Fabaceae as the ancestral state of Prosopanche and Hydnora. A well resolved Hydnora clade parasitizing Fabaceae was resolved as sister to a clade parasitizing exclusively Euphorbia, indicating a single host shift. In order to examine the specific limits of H. africana phylogenetic and morphological data were compared. In the section Euhydnora, floral morphometric data was congruent with phylogenetic data, revealing three cryptic taxa within Hydnora africana sensu lato, Hydnora africana, Hydnora longicollis, and a new Hydnora species