Analysis and clustering of model clones: An automotive industrial experience

Abstract—In this paper we present our early experience analyzing subsystem similarity in industrial automotive models. We apply our model clone detection tool, SIMONE, to identify identical and near-miss Simulink subsystem clones and cluster them into classes based on clone size and similarity threshold. We then analyze clone detection results using graph visualizations generated by the SIMGraph, a SIMONE extension, to identify subsystem patterns. SIMGraph provides us and our industrial partners with new interesting and useful insights that improves our understanding of the analyzed models and suggests better ways to maintain them. I

Towards a Taxonomy for Simulink Model Mutations

Abstract—A relatively new and important branch of Mutation Analysis involves model mutations. In our attempts to realize model-clone detector testing, we found that there was little mutation research on Simulink, which is a fairly prevalent modeling language, especially in embedded domains. Because Simulink model mutations are the crux of our model-clone detector testing framework, we want to ensure that we are selecting the appropriate mutations. In this paper, we propose a taxonomy of Simulink model mutations, which is based on our experiences thus far with Simulink, that aims to inject model clones of various types and is fairly representative of realistic Simulink edit operations. We organize the mutations by categories based on the types of model clones they will inject, and further break them down into mutation classes. For each class, we define the characteristics of mutation operators belonging to that class and demonstrate an example operator. Lastly, in an attempt to validate our taxonomy, we perform a case study on multiple versions of three Simulink projects, including an industrial project, to ascertain if the actual subsystem edit operations observed across versions can be classified using our taxonomy and present any interesting cases. While we developed the taxonomy with the specific goal of facilitating and guiding the injection of mutants for model clones, we believe it is fairly general and a solid foundation for future Simulink model mutation work. I

SimNav: Simulink navigation of model clone classes

SimNav is a GUI designed for displaying and navigating clone classes of Simulink models detected by the model clone detector Simone. As an embedded Simulink interface tool, SimNav allows model developers to explore detected clones directly in their own model development environment rather than a separate research tool interface. SimNav allows users to open selected models for side-by-side comparison, in order to visually explore clone classes and view the differences in the clone instances, as well as to explore the context in which the clones exist. This tool paper describes the motivation, implementation, and use cases for SimNav

Formal verification techniques for model transformations: A tridimensional classification

In Model Driven Engineering (Mde), models are first-class citizens, and model transformation is Mde's "heart and soul". Since model transformations are executed for a family of (conforming) models, their validity becomes a crucial issue. This paper proposes to explore the question of the formal verification of model transformation properties through a tridimensional approach: the transformation involved, the properties of interest addressed, and the formal verification techniques used to establish the properties. This work is intended for a double audience. For newcomers, it provides a tutorial introduction to the field of formal verification of model transformations. For readers more familiar with formal methods and model transformations, it proposes a literature review (although not systematic) of the contributions of the field. Overall, this work allows to better understand the evolution, trends and current practice in the domain of model transformation verification. This work opens an interesting research line for building an engineering of model transformation verification guided by the notion of model transformation intent

RETRACTED ARTICLE: Age-dependent Increase in Desmosterol Restores DRM Formation and Membrane-related Functions in Cholesterol-free DHCR24−/− Mice

Cholesterol is a prominent modulator of the integrity and functional activity of physiological membranes and the most abundant sterol in the mammalian brain. DHCR24-knock-out mice lack cholesterol and accumulate desmosterol with age. Here we demonstrate that brain cholesterol deficiency in 3-week-old DHCR24−/− mice was associated with altered membrane composition including disrupted detergent-resistant membrane domain (DRM) structure. Furthermore, membrane-related functions differed extensively in the brains of these mice, resulting in lower plasmin activity, decreased β-secretase activity and diminished Aβ generation. Age-dependent accumulation and integration of desmosterol in brain membranes of 16-week-old DHCR24−/− mice led to the formation of desmosterol-containing DRMs and rescued the observed membrane-related functional deficits. Our data provide evidence that an alternate sterol, desmosterol, can facilitate processes that are normally cholesterol-dependent including formation of DRMs from mouse brain extracts, membrane receptor ligand binding and activation, and regulation of membrane protein proteolytic activity. These data indicate that desmosterol can replace cholesterol in membrane-related functions in the DHCR24−/− mouse

The Oldest Case of Decapitation in the New World (Lapa do Santo, East-Central Brazil)

We present here evidence for an early Holocene case of decapitation in the New World (Burial 26), found in the rock shelter of Lapa do Santo in 2007. Lapa do Santo is an archaeological site located in the Lagoa Santa karst in east-central Brazil with evidence of human occupation dating as far back as 11.7-12.7 cal kyBP (95.4% interval). An ultra-filtered AMS age determination on a fragment of the sphenoid provided an age range of 9.1-9.4 cal kyBP (95.4% interval) for Burial 26. The interment was composed of an articulated cranium, mandible and first six cervical vertebrae. Cut marks with a v-shaped profile were observed in the mandible and sixth cervical vertebra. The right hand was amputated and laid over the left side of the face with distal phalanges pointing to the chin and the left hand was amputated and laid over the right side of the face with distal phalanges pointing to the forehead. Strontium analysis comparing Burial 26's isotopic signature to other specimens from Lapa do Santo suggests this was a local member of the group. Therefore, we suggest a ritualized decapitation instead of trophy-taking, testifying for the sophistication of mortuary rituals among hunter-gatherers in the Americas during the early Archaic period. In the apparent absence of wealth goods or elaborated architecture, Lapa do Santo's inhabitants seemed to use the human body to express their cosmological principles regarding death

Vacuolar ATPase Regulates Surfactant Secretion in Rat Alveolar Type II Cells by Modulating Lamellar Body Calcium

Lung surfactant reduces surface tension and maintains the stability of alveoli. How surfactant is released from alveolar epithelial type II cells is not fully understood. Vacuolar ATPase (V-ATPase) is the enzyme responsible for pumping H+ into lamellar bodies and is required for the processing of surfactant proteins and the packaging of surfactant lipids. However, its role in lung surfactant secretion is unknown. Proteomic analysis revealed that vacuolar ATPase (V-ATPase) dominated the alveolar type II cell lipid raft proteome. Western blotting confirmed the association of V-ATPase a1 and B1/2 subunits with lipid rafts and their enrichment in lamellar bodies. The dissipation of lamellar body pH gradient by Bafilomycin A1 (Baf A1), an inhibitor of V-ATPase, increased surfactant secretion. Baf A1-stimulated secretion was blocked by the intracellular Ca2+ chelator, BAPTA-AM, the protein kinase C (PKC) inhibitor, staurosporine, and the Ca2+/calmodulin-dependent protein kinase II (CaMKII), KN-62. Baf A1 induced Ca2+ release from isolated lamellar bodies. Thapsigargin reduced the Baf A1-induced secretion, indicating cross-talk between lamellar body and endoplasmic reticulum Ca2+ pools. Stimulation of type II cells with surfactant secretagogues dissipated the pH gradient across lamellar bodies and disassembled the V-ATPase complex, indicating the physiological relevance of the V-ATPase-mediated surfactant secretion. Finally, silencing of V-ATPase a1 and B2 subunits decreased stimulated surfactant secretion, indicating that these subunits were crucial for surfactant secretion. We conclude that V-ATPase regulates surfactant secretion via an increased Ca2+ mobilization from lamellar bodies and endoplasmic reticulum, and the activation of PKC and CaMKII. Our finding revealed a previously unrealized role of V-ATPase in surfactant secretion