Model Synchronization for Software Evolution

Software evolution refers to continuous change that a software system endures from inception to retirement. Each change must be efficiently and tractably propagated across models representing the system at different levels of abstraction. Model synchronization activities needed to support the systematic specification and analysis of evolution activities are still not adequately identified and formally defined. In our research, we first introduce a formal notation for the representation of domain models and model instances to form the theoretical basis for the proposed model synchronization framework. Besides conforming to a generic MOF metamodel, we consider that each software model also relates to an application domain context (e.g., operating systems, web services). Therefore, we are addressing the problems of model synchronization by focusing on domain-specific contexts. Secondly, we identify and formally define model dependencies that are needed to trace and propagate changes across system models at different levels of abstraction, such as from design to source code. The approach for extraction of these dependencies is based on Formal Concept Analysis (FCA) algorithms. We further model identified dependencies using Unified Modeling Language (UML) profiles and constraints, and utilize the extracted dependency relations in the context of coarse-grained model synchronization. Thirdly, we introduce modeling semantics that allow for more complex profile-based dependencies using Triple Graph Grammar (TGG) rules with corresponding Object Constraint Language (OCL) constraints. The TGG semantics provide for fine-grained model synchronization, and enable compliance with the Query/View/Transformation (QVT) standards. The introduced framework is assessed on a large, industrial case study of the IBM Commerce system. The dependency extraction framework is applied to repositories of business process models and related source code. The extracted dependencies were evaluated by IBM developers, and the corresponding precision and recall values calculated with results that match the scope and goals of the research. The grammar-based model synchronization and dependency modelling using profiles has also been applied to the IBM Commerce system, and evaluated by the developers and architects involved in development of the system. The results of this experiment have been found to be valuable by stakeholders, and a patent codifying the results has been filed by the IBM organization and has been granted. Finally, the results of this experiment have been formalized as TGG rules, and used in the context of fine-grained model synchronization

Bioreactor-Based Bone Tissue Engineering

The aim of this chapter is to describe the main issues of bone tissue engineering. Bone transplants are widely used in orthopedic, plastic and reconstructive surgery. Current technologies like autologous and allogenic transplantation have several disadvantages making them relatively unsatisfactory, like donor site morbidity, chronic pain, and immunogenicity and risk hazard from infectious disease. Therefore, regenerative orthopedics seeks to establish a successful protocol for the healing of severe bone damage using engineered bone grafts. The optimization of protocols for bone graft production using autologous mesenchymal stem cells loaded on appropriate scaffolds, exposed to osteogenic inducers and mechanical force in bioreactor, should be able to solve the current limitations in managing bone injuries. We discuss mesenchymal stem cells as the most suitable cell type for bone tissue engineering. They can be isolated from a variety of mesenchymal tissues and can differentiate into osteoblasts when given appropriate mechanical support and osteoinductive signal. Mechanical support can be provided by different cell scaffolds based on natural or synthetic biomaterials, as well as combined composite materials. Three-dimensional support is enabled by bioreactor systems providing several advantages as mechanical loading, homogeneous distribution of cells and adequate nutrients/waste exchange. We also discuss the variety of osteoinductive signals that can be applied in bone tissue engineering. The near future of bone healing and regeneration is closely related to advances in tissue engineering. The optimization of protocols of bone graft production using autologous mesenchymal stem cells loaded on appropriate scaffolds, exposed to osteogenic inducers and mechanical force in bioreactor, should be able to solve the current limitations in managing bone injuries

Expression of OCT-4 and SOX-2 in Bone Marrow-Derived Human Mesenchymal Stem Cells during Osteogenic Differentiation

AIM: Determine the levels of expression of pluripotency genes OCT-4 and SOX-2 before and after osteogenic differentiation of human mesenchymal stem cells (hMSCs).METHODS: Human MSCs were derived from the bone marrow and differentiated into osteoblasts. The analyses were performed on days 0 and 14 of the cell culture. In vitro differentiation was evaluated due to bone markers – alkaline phosphatase (AP) activity and the messenger RNA (mRNA) expression of AP and bone sialoprotein (BSP). The OCT-4 and SOX-2 expression was evaluated at mRNA level by real-time qPCR and at protein level by immunocytochemistry.RESULTS: In vitro cultures on day 14 showed an increase in AP activity and upregulation of AP and BSP gene expression. OCT-4 and SOX-2 in undifferentiated hMSCs on day 0 is detectable and very low compared to tumor cell lines as a positive control. Immunocytochemistry detected OCT-4 in the cell nuclei prior (day 0) and post differentiation (day 14). On the same time points, cultures were negative for SOX-2 protein.CONCLUSION: Messenger RNA for pluripotency markers OCT-4 and SOX-2 isolated from hMSCs was less present, while OCT-4 protein was detected in cell nuclei prior and post differentiation into osteoblast lineage

Rising rural body-mass index is the main driver of the global obesity epidemic in adults

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities(.)(1,2) This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity(3-6). Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55% of the global rise in mean BMI from 1985 to 2017-and more than 80% in some low- and middle-income regions-was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing-and in some countries reversal-of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories.Peer reviewe

Architecture Recovery of Dynamically Linked Applications: A Case Study

Most previously published case studies in architecture recovery have been performed on statically linked software systems. Due to the increase in use of middleware technologies, such as CORBA, and OOP concepts, such as polymorphism, there is an opportunity and a need to analyze architectures of these dynamically linked systems. This paper presents the results of software architecture extraction of the Nautilus file manager, which employs CORBA in its implementation. A combination of existing static analysis and use-case modeling architecture recovery techniques was used with the expectation of complex but complete architecture extraction of a system such as Nautilus. We have found that this combined approach named Dynamo-1 presented in this paper provided successful focused architecture recovery and guidance for the future work in complete architecture recovery of dynamically linked applications

c ○ World Scientific Publishing Company TOWARDS AUTOMATIC ESTABLISHMENT OF MODEL DEPENDENCIES USING FORMAL CONCEPT ANALYSIS

Software evolution is an iterative and incremental process that encompasses the modification and alteration of software models at different levels of abstraction. These modifications are usually performed independently, but the objects to which they are applied to, are in most cases mutually dependent. Inconsistencies and drift among related artifacts may be created if the effects of an alteration are not properly identified, recorded, and propagated in other dependent models. For large systems, it is possible that there is a considerable number of such model dependencies, for which manual extraction is not feasible. In this paper, we introduce an approach for automating the identification and encoding of dependence relations among software models and their elements. The proposed dependency extraction technique first uses association rules to map types between models at different levels of abstraction. Formal concept analysis is then used to identify clusters of model elements that pertain to similar or associated concepts. Model elements that cluster together are considered related by a dependency relation. The technique is used to synchronize business process specifications with the underlying J2EE source code models

Enhancing Domain-Specific Software Architecture Recovery

Performing software architecture analysis and recovery on a large software system is expensive and time consuming; when it is done at all, it is often performed within a narrow context, focused on a few areas of particular concern. However, for a long-lived system within a well understood application domain, the costs for performing detailed architecture recovery may be amortized over several generations of the system; the resulting models can also be broadened and put into context by incorporating information about the history and anticipated future evolution of both the application and its underlying domain. This paper proposes a systematic approach for organizing application domain knowledge into a unified structure called the Architectural Domain Assets Set (ADAS). The ADAS structure builds on previous research, as well as our experience in performing an architecture recovery of IBM's DB2. Our initial experiences in using ADAS suggest that it brings needed focus to the recovery process and provides assistance to domain-specific architecture recovery