Metric suite to Evaluate Reusability of Software Product Line

Metrics have long been used to measure and evaluate  software products and processes. Software product line architecture is a field in which few metrics have been applied, a surprising fact given the important role of software product line architecture in software product line development. Recently, Some metrics have been developed to assess software product line architecture. These metrics are useful but have not been widely used in industry. In this paper, some new metrics are provided to assess reusability of Software product line architecture. Our metrics are evaluated in action.DOI:http://dx.doi.org/10.11591/ijece.v4i2.513

Extractability Effectiveness on Software Product Line

A software product line consists of a family of software systems. Most of quality attributes are defined for single systems. When we are facing a family of products instead of a single system, some aspects of architecture evaluation, such as cost, time, and reusability of available assets, become more highlighted. In this paper a new quality attribute for software product line, which we called it extractability, is introduced. Also extractability measuring method and relationship between extractability with some quality attributes is presented. At the end, Extractability Effectiveness on Software Product Line is evaluated in practice.DOI:http://dx.doi.org/10.11591/ijece.v4i1.410

A Systematic Method for Identification of Anti-patterns in Service Oriented System Development

Service-Oriented Architecture is one of the popular software architecture's patterns used for developing lots of modern systems. However, it has been involved in many failures. Anti-patterns are solutions which have good view, but in fact they are wrong solutions that cause failure of systems. There are a lot of anti-patterns for SOA and new anti-patterns are revealed every day. Anti-patterns have their own reasons for being formed and also they are appeared in special area of the problem. As human's mind is restricted and it can process a limited number of states (piece of information) therefore identification of anti-patterns will be difficult for architects. In this paper, we propose a systematic method based on repository of anti-patterns along with a check list to identify anti-patterns of SOA. This method will assist architects to easily detect and avoid anti-patterns in development process and so escape from risks which related to anti-patterns. Furthermore, in this paper, we present a repository of forty five general anti-patterns in SOA. Reviewing these anti-patterns will help developers to work with clear understanding of patterns in phases of software development and so avoid from many potential problems. Also, our method is evaluated in action.DOI:http://dx.doi.org/10.11591/ijece.v4i1.409

Multi-Agent Approach for facing challenges in Ultra-Large Scale systems

The primary characteristics of ULS systems are ultra-large size, number of lines of code (LOC); number of people employing the systems; amount of data stored, accessed, manipulated, and refined; number of connections and interdependencies among software components; number of hardware elements. These characteristics of ULS systems make it impossible to rely on our current knowledge and techniques of software development. We will face fundamental challenges in the design and evolution, orchestration and control, and monitoring and assessment of ULS systems. In this paper we try to make a combination between ULS systems and Multi Agent Systems and to use Multi Agent System strengths to help tackling some challenges found in ultra-large scale systems. Banking system is an instance of ULS systems. As a case study, in a real project we have designed Automated Teller Machine (ATM) combination with biometric sensors based on multi-agent architecture.DOI:http://dx.doi.org/10.11591/ijece.v4i2.4102

Architectural Approaches for Self-Healing Systems Based on Multi Agent Technologies

Self-healing systems are able to adapt themselves at runtime time in response to changing environmental or operational circumstances, shifting user requirements, and unanticipated faults without human intervention. Conceptually, a self-managing system is composed of four key capabilities; Monitoring, performing Analysis, Planning and Executing the plan. The preferred way to enable repair in a self-healing system is to use externalized repair/adaptation architecture. Adaptability, dynamicity, awareness, observability, autonomy, robustness, distributability, mobility and traceability are requirements that an architecture style for self-healing system should satisfy. In this paper we discuss Multi agent based self-healing system has a characteristics that can satisfy mentioned requirement. We define associations between architecture style requirements for self-healing system and MAS characteristics. As a case study in a real project we have designed Automated Teller Machine (ATM) combination with biometric sensors based on multi-agent architecture.DOI:http://dx.doi.org/10.11591/ijece.v3i6.395

Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300.

BackgroundCommunity-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease burden consists of skin and soft tissue infections (SSTI) not associated with significant morbidity; however, CA-MRSA also causes severe, invasive infections resulting in significant morbidity and mortality. The broad range of disease severity may be influenced by bacterial genetic variation.ResultsWe sequenced the complete genomes of 36 CA-MRSA clinical isolates from the predominant North American community acquired clonal type USA300 (18 SSTI and 18 severe infection-associated isolates). While all 36 isolates shared remarkable genetic similarity, we found greater overall time-dependent sequence diversity among SSTI isolates. In addition, pathway analysis of non-synonymous variations revealed increased sequence diversity in the putative virulence genes of SSTI isolates.ConclusionsHere we report the first whole genome survey of diverse clinical isolates of the USA300 lineage and describe the evolution of the pathogen over time within a defined geographic area. The results demonstrate the close relatedness of clinically independent CA-MRSA isolates, which carry implications for understanding CA-MRSA epidemiology and combating its spread

Reshaping Antibody Diversity

SummarySome species mount a robust antibody response despite having limited genome-encoded combinatorial diversity potential. Cows are unusual in having exceptionally long CDR H3 loops and few V regions, but the mechanism for creating diversity is not understood. Deep sequencing reveals that ultralong CDR H3s contain a remarkable complexity of cysteines, suggesting that disulfide-bonded minidomains may arise during repertoire development. Indeed, crystal structures of two cow antibodies reveal that these CDR H3s form a very unusual architecture composed of a β strand “stalk” that supports a structurally diverse, disulfide-bonded “knob” domain. Diversity arises from somatic hypermutation of an ultralong DH with a severe codon bias toward mutation to cysteine. These unusual antibodies can be elicited to recognize defined antigens through the knob domain. Thus, the bovine immune system produces an antibody repertoire composed of ultralong CDR H3s that fold into a diversity of minidomains generated through combinations of somatically generated disulfides

Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation

Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM

Combined accelerometer and genetic analysis to differentiate essential tremor from Parkinson’s disease

Essential tremor (ET) and Parkinson’s disease (PD) are among the most common adult-onset tremor disorders. Clinical and pathological studies suggest that misdiagnosis of PD for ET, and vice versa, occur in anywhere from 15% to 35% of cases. Complex diagnostic procedures, such as dopamine transporter imaging, can be powerful diagnostic aids but are lengthy and expensive procedures that are not widely available. Preliminary studies suggest that monitoring of tremor characteristics with consumer grade accelerometer devices could be a more accessible approach to the discrimination of PD from ET, but these studies have been performed in well-controlled clinical settings requiring multiple maneuvers and oversight from clinical or research staff, and thus may not be representative of at-home monitoring in the community setting. Therefore, we set out to determine whether discrimination of PD vs. ET diagnosis could be achieved by monitoring research subject movements at home using consumer grade devices, and whether discrimination could be improved with the addition of genetic profiling of the type that is readily available through direct-to-consumer genetic testing services. Forty subjects with PD and 27 patients with ET were genetically profiled and had their movements characterized three-times a day for two weeks through a simple procedure meant to induce rest tremors. We found that tremor characteristics could be used to predict diagnosis status (sensitivity = 76%, specificity = 65%, area under the curve (AUC) = 0.75), but that the addition of genetic risk information, via a PD polygenic risk score, did not improve discriminatory power (sensitivity = 80%, specificity = 65%, AUC = 0.73)

All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs

Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate (TDR = 1−FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in introns, and negative enrichment for intergenic SNPs. Stratified enrichment directly leads to increased TDR for a given p-value, mirrored by increased replication rates in independent samples. We show this in independent Crohn's disease GWAS, where we find a hundredfold variation in replication rate across genic categories. Applying a well-established sFDR methodology we demonstrate the utility of stratification for improving power of GWAS in complex phenotypes, with increased rejection rates from 20% in height to 300% in schizophrenia with traditional FDR and sFDR both fixed at 0.05. Our analyses demonstrate an inherent stratification among GWAS SNPs with important conceptual implications that can be leveraged by statistical methods to improve the discovery of loci