Well-Formed and Scalable Invasive Software Composition

Software components provide essential means to structure and organize software effectively. However, frequently, required component abstractions are not available in a programming language or system, or are not adequately combinable with each other. Invasive software composition (ISC) is a general approach to software composition that unifies component-like abstractions such as templates, aspects and macros. ISC is based on fragment composition, and composes programs and other software artifacts at the level of syntax trees. Therefore, a unifying fragment component model is related to the context-free grammar of a language to identify extension and variation points in syntax trees as well as valid component types. By doing so, fragment components can be composed by transformations at respective extension and variation points so that always valid composition results regarding the underlying context-free grammar are yielded. However, given a language’s context-free grammar, the composition result may still be incorrect. Context-sensitive constraints such as type constraints may be violated so that the program cannot be compiled and/or interpreted correctly. While a compiler can detect such errors after composition, it is difficult to relate them back to the original transformation step in the composition system, especially in the case of complex compositions with several hundreds of such steps. To tackle this problem, this thesis proposes well-formed ISC—an extension to ISC that uses reference attribute grammars (RAGs) to specify fragment component models and fragment contracts to guard compositions with context-sensitive constraints. Additionally, well-formed ISC provides composition strategies as a means to configure composition algorithms and handle interferences between composition steps. Developing ISC systems for complex languages such as programming languages is a complex undertaking. Composition-system developers need to supply or develop adequate language and parser specifications that can be processed by an ISC composition engine. Moreover, the specifications may need to be extended with rules for the intended composition abstractions. Current approaches to ISC require complete grammars to be able to compose fragments in the respective languages. Hence, the specifications need to be developed exhaustively before any component model can be supplied. To tackle this problem, this thesis introduces scalable ISC—a variant of ISC that uses island component models as a means to define component models for partially specified languages while still the whole language is supported. Additionally, a scalable workflow for agile composition-system development is proposed which supports a development of ISC systems in small increments using modular extensions. All theoretical concepts introduced in this thesis are implemented in the Skeletons and Application Templates framework SkAT. It supports “classic”, well-formed and scalable ISC by leveraging RAGs as its main specification and implementation language. Moreover, several composition systems based on SkAT are discussed, e.g., a well-formed composition system for Java and a C preprocessor-like macro language. In turn, those composition systems are used as composers in several example applications such as a library of parallel algorithmic skeletons

Structured and flexible gray-box composition using invasive distributed patterns

ISBN = {ISSN: 1646-3692}International audienceThe evolution of complex distributed software systems often requires intricate composition operations in order to adapt or add functionalities, to react to unanticipated changes, or to apply performance improvements that cannot be modularized in terms of existing services and components. These evolutions often need controlled access to selected parts of the implementation, e.g., to manage exceptional situations and crosscutting within services and their compositions. However, existing composition techniques typically support only interface-level (black-box) composition or arbitrary access to the implementation (gray-box or white-box composition). In this paper, we present a structured approach to the composition of complex software systems that require invasive modifications. Concretely, we provide three contributions: (i) we present a small kernel composition language for structured gray-box composition using invasive distributed patterns; (ii) we motivate that gray-box composition approaches should be defined and evaluated in terms of the flexibility and control they provide, a notion of degrees of invasiveness is introduced to help assess this trade-off; (iii) we apply our approach to a new case study of evolution and evaluate it in the context of two previous studies involving two real-world software systems: benchmarking of grid algorithms with NASGrid and transactional replication with JBoss Cache. As a main result, we show that gray-box composition using invasive distributed patterns allows the declarative and modular definition of evolutions of real-world applications that need moderate to high degrees of invasive modifications

Structured and flexible gray-box composition: Application to task rescheduling for grid benchmarking

International audienceThe evolution of complex distributed software systems often requires intricate composition operations in order to adapt or add functionalities, react to unanticipated changes to security policies, or do performance improvements, which cannot be modularized in terms of existing services or components. They often need controlled access to selected parts of the implementation, e.g., to manage exceptional situations and crosscutting within services and their compositions. However, existing composition techniques typically support only interface-level (black-box) composition or arbitrary access to the implementation (gray-box or white-box composition). In this paper, we present a more structured approach to the composition of complex software systems that require invasive accesses. Concretely, we provide two contributions, we (i) present a small kernel composition language for structured gray-box composition with explicit control mechanisms and a corresponding aspect-based implementation; (ii) present and compare evolutions using this approach to gray-box composition in the context of two real-world software systems: benchmarking of grid algorithms with NASGrid and transactional replication with JBoss Cache

ENVIRONMENTAL VARIABLES ASSOCIATED WITH INVASIVE GLOSSY BUCKTHORN (FRANGULA ALNUS MILL.) AND INDIRECT CONTROL STRATEGIES FOR FOREST MANAGERS

Glossy buckthorn (Frangula alnus Mill.) is one of the most prominent non-native invasive plant species affecting New England forests. It quickly invades a forest and can create a dense understory effectively altering the species composition and dynamics of that forest. To gain a better understanding of the environmental variables associated with glossy buckthorn density we sampled forests across New Hampshire with varying degrees of buckthorn invasion. The effect on tree regeneration was analyzed with measurements of height and abundance of glossy buckthorn and native regeneration. Glossy buckthorn was found to be at its highest densities in disturbed softwood forests that were historically old fields, specifically eastern white pine (Pinus strobus L.), with a thin organic layer and low herbaceous cover on drained loam and clay soils. The data show there is direct competition between glossy buckthorn and forest tree regeneration, although no relationship with regeneration shade tolerance was found. This information was used to create a prescription risk tree to aid forest managers in assessing the risk of buckthorn invasion and inhibition of tree regeneration associated with harvesting and suggests how to adapt their silvicultural prescriptions

Do species differ in their ability to coexist with the dominant alien Lupinus polyphyllus? : A comparison between two distinct invaded ranges and a native range

The community-level impacts of invasive plants are likely to vary depending on the character of native species of the target communities and their ability to thrive within the stands of the dominant alien invader. Therefore, I examined the response of native species richness to the cover of the dominant alien Lupinus polyphyllus in two distinct invaded ranges: Czech Republic (Central Europe) and New Zealand. I compared the relation between native species richness and the cover of the dominant alien L. polyphyllus with that in its native range, Pacific Northwest, USA. In the native range, I found no response of native species richness to the cover of L. polyphyllus. In the Czech Republic (central Europe), the richness of native species related to it negativelly, but the relation was only marginally significant. Contrary to that, the richness of species native to New Zealand related to the cover of L. polyphyllus strongly negatively and the negative relation was significantly stronger than that of species native to Europe. Of the two invaded ranges, species native to New Zealand have been documented to be much more vulnerable to the conditions associated with the invasion and dominance of L. polyphyllus, compared to species native to central Europe. This principle has been shown both across these two invaded ranges and in New Zealand, where the aliens of european origin successfully coexist with the dominant invasive alien L. polyphyllus. Similarly, species in the native range of L. polyphyllus showed no relation to its cover, indicating their ability to thrive even in dense stands of this dominant species

Cadherin composition and multicellular aggregate invasion in organotypic models of epithelial ovarian cancer intraperitoneal metastasis.

During epithelial ovarian cancer (EOC) progression, intraperitoneally disseminating tumor cells and multicellular aggregates (MCAs) present in ascites fluid adhere to the peritoneum and induce retraction of the peritoneal mesothelial monolayer prior to invasion of the collagen-rich submesothelial matrix and proliferation into macro-metastases. Clinical studies have shown heterogeneity among EOC metastatic units with respect to cadherin expression profiles and invasive behavior; however, the impact of distinct cadherin profiles on peritoneal anchoring of metastatic lesions remains poorly understood. In the current study, we demonstrate that metastasis-associated behaviors of ovarian cancer cells and MCAs are influenced by cellular cadherin composition. Our results show that mesenchymal N-cadherin-expressing (Ncad+) cells and MCAs invade much more efficiently than E-cadherin-expressing (Ecad+) cells. Ncad+ MCAs exhibit rapid lateral dispersal prior to penetration of three-dimensional collagen matrices. When seeded as individual cells, lateral migration and cell-cell junction formation precede matrix invasion. Neutralizing the Ncad extracellular domain with the monoclonal antibody GC-4 suppresses lateral dispersal and cell penetration of collagen gels. In contrast, use of a broad-spectrum matrix metalloproteinase (MMP) inhibitor (GM6001) to block endogenous membrane type 1 matrix metalloproteinase (MT1-MMP) activity does not fully inhibit cell invasion. Using intact tissue explants, Ncad+ MCAs were also shown to efficiently rupture peritoneal mesothelial cells, exposing the submesothelial collagen matrix. Acquisition of Ncad by Ecad+ cells increased mesothelial clearance activity but was not sufficient to induce matrix invasion. Furthermore, co-culture of Ncad+ with Ecad+ cells did not promote a 'leader-follower' mode of collective cell invasion, demonstrating that matrix remodeling and creation of invasive micro-tracks are not sufficient for cell penetration of collagen matrices in the absence of Ncad. Collectively, our data emphasize the role of Ncad in intraperitoneal seeding of EOC and provide the rationale for future studies targeting Ncad in preclinical models of EOC metastasis

Formation of atypical podosomes in extravillous trophoblasts regulates extracellular matrix degradation

Throughout pregnancy the cytotrophoblast, the stem cell of the placenta, gives rise to the differentiated forms of trophoblasts. The two main cell lineages are the syncytiotrophoblast and the invading extravillous trophoblast. A successful pregnancy requires extravillous trophoblasts to migrate and invade through the decidua and then remodel the maternal spiral arteries. Many invasive cells use specialised cellular structures called invadopodia or podosomes in order to degrade extracellular matrix. Despite being highly invasive cells, the presence of invadapodia or podosomes has not previously been investigated in trophoblasts. In this study these structures have been identified and characterised in extravillous trophoblasts. The role of specialised invasive structures in trophoblasts in the degradation of the extracellular matrix was compared with well characterised podosomes and invadopodia in other invasive cells and the trophoblast specific structures were characterised by using a sensitive matrix degradation assay which enabled visualisation of the structures and their dynamics. We show trophoblasts form actin rich protrusive structures which have the ability to degrade the extracellular matrix during invasion. The degradation ability and dynamics of the structures closely resemble podosomes, but have unique characteristics that have not previously been described in other cell types. The composition of these structures does not conform to the classic podosome structure, with no distinct ring of plaque proteins such as paxillin or vinculin. In addition, trophoblast podosomes protrude more deeply into the extracellular matrix than established podosomes, resembling invadopodia in this regard. We also show several significant pathways such as Src kinase, MAPK kinase and PKC along with MMP-2 and 9 as key regulators of extracellular matrix degradation activity in trophoblasts, while podosome activity was regulated by the rigidity of the extracellular matrix

Five-Year Response of Spontaneous Vegetation to Removal of Invasive Amur Bush Honeysuckle Along an Urban Creek

Non-native invasive species have major impacts on landscapes worldwide, but their effects in urban areas are not well documented. We quantified the response of naturally regenerating vegetation along an urban creek to removal of the invasive shrub Lonicera maackii (Amur Bush Honeysuckle). Over the 5-year study, species richness more than doubled. Most new plants were native, disturbance-adapted, early successional species. Trend analysis of function traits revealed annuals that rely on seed dispersal by wind or externally on animals were significantly overrepresented among new plants in comparison to their proportion in the countywide species pool. Increased species richness did not result in improved habitat quality, as indicated by Floristic Quality Assessment. Eight new invasive species appeared over the course of the study. Active management of this site may be needed in perpetuit

Non-invasive investigations of a wall painting using optical coherence tomography and hyperspectral imaging

Multispectral and hyperspectral imaging are efficient methods of measuring spectral reflectance at high spatial resolution. This non-invasive technique has been applied to the imaging of paintings over the last 20 years. PRISMS (Portable Remote Imaging System for Multispectral Scanning) was designed specifically for imaging wall paintings. Optical Coherence Tomography (OCT) is a low coherence interferometric technique capable of fast non-invasive imaging of subsurface microstructure. This paper shows the first application of in situ OCT imaging of a wall painting. The combination of PRISMS and OCT gives information on the varnish and paint layer structure, pigment identification, the state of degradation of the paint and varnish layers and informing curators on the painting schemes and techniques

Remote multispectral imaging with PRISMS and XRF analysis of Tang Tomb paintings

PRISMS (Portable Remote Imaging System for Multispectral Scanning) is a multispectral/hyperspectral imaging system designed for flexible in situ imaging of wall paintings at high resolution (tens of microns) over a large range of distances (less than a meter to over ten meters). This paper demonstrates a trial run of the VIS/NIR (400-880nm) component of the instrument for non-invasive imaging of wall paintings in situ. Wall painting panels from excavated Tang dynasty (618-907AD) tombs near Xi’an were examined by PRISMS. Pigment identifications were carried out using the spectral reflectance obtained from multispectral imaging coupled with non-invasive elemental analysis using a portable XRF