Novel phylogenetic algorithm to monitor human tropism in Egyptian H5N1-HPAIV reveals evolution toward efficient human-to-human transmission

Years of endemic infections with highly pathogenic avian influenza (HPAI) A subtype H5N1 virus in poultry and high numbers of infections in humans provide ample opportunity in Egypt for H5N1-HPAIV to develop pandemic potential. In an effort to better understand the viral determinants that facilitate human infections of the Egyptian H5N1-HPAIVvirus, we developed a new phylogenetic algorithm based on a new distance measure derived from the informational spectrum method (ISM). This new approach, which describes functional aspects of the evolution of the hemagglutinin subunit 1 (HA1), revealed a growing group G2 of H5N1-HPAIV in Egypt after 2009 that acquired new informational spectrum (IS) properties suggestive of an increased human tropism and pandemic potential. While in 2006 all viruses in Egypt belonged to the G1 group, by 2011 these viruses were virtually replaced by G2 viruses. All of the G2 viruses displayed four characteristic mutations (D43N, S120(D,N), (S,L)129Δ and I151T), three of which were previously reported to increase binding to the human receptor. Already in 2006–2008 G2 viruses were significantly (p<0.02) more often found in humans than expected from their overall prevalence and this further increased in 2009–2011 (p<0.007). Our approach also identified viruses that acquired additional mutations that we predict to further enhance their human tropism. The extensive evolution of Egyptian H5N1-HPAIV towards a preferential human tropism underlines an urgent need to closely monitor these viruses with respect to molecular determinants of virulence

Contract Aware Components, 10 years after

The notion of contract aware components has been published roughly ten years ago and is now becoming mainstream in several fields where the usage of software components is seen as critical. The goal of this paper is to survey domains such as Embedded Systems or Service Oriented Architecture where the notion of contract aware components has been influential. For each of these domains we briefly describe what has been done with this idea and we discuss the remaining challenges.Comment: In Proceedings WCSI 2010, arXiv:1010.233

A global view of the nonprotein-coding transcriptome in Plasmodium falciparum

Nonprotein-coding RNAs (npcRNAs) represent an important class of regulatory molecules that act in many cellular pathways. Here, we describe the experimental identification and validation of the small npcRNA transcriptome of the human malaria parasite Plasmodium falciparum. We identified 630 novel npcRNA candidates. Based on sequence and structural motifs, 43 of them belong to the C/D and H/ACA-box subclasses of small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). We further observed the exonization of a functional H/ACA snoRNA gene, which might contribute to the regulation of ribosomal protein L7a gene expression. Some of the small npcRNA candidates are from telomeric and subtelomeric repetitive regions, suggesting their potential involvement in maintaining telomeric integrity and subtelomeric gene silencing. We also detected 328 cis-encoded antisense npcRNAs (asRNAs) complementary to P. falciparum protein-coding genes of a wide range of biochemical pathways, including determinants of virulence and pathology. All cis-encoded asRNA genes tested exhibit lifecycle-specific expression profiles. For all but one of the respective sense–antisense pairs, we deduced concordant patterns of expression. Our findings have important implications for a better understanding of gene regulatory mechanisms in P. falciparum, revealing an extended and sophisticated npcRNA network that may control the expression of housekeeping genes and virulence factors

On comprehensive contractual descriptions of Web services

Comprehensive contractual description of Web Services and Web Service compositions is needed for selection of appropriate Web Services and their service and quality of service (QoS) levels, for monitoring of operation of Web Services, and for management of Web Services and Web Service compositions. We systematically examined what types of technical contracts are useful for Web Services and Web Service compositions and classified them into three categories: functional, quality, and infrastructure contracts. Functional contracts include syntactic, behavioral, synchronization, and compositional contracts; quality contracts include QoS and pricing contracts; while infrastructure contracts include communication, security, and management contracts. Our study of how prominent Web Service languages can or cannot be used for specification of these contract types shows that they enable specification of only particular types of contracts, sometimes even in incompatible ways. Consequently, we advocate a unified framework for comprehensive contractual description of Web Services and Web Service compositions. We suggest that principles for such framework should be: modularity, unification and standardization of common contract elements, extensibility, use of only few contract languages, reuse and extension of the widely accepted Web Service languages, specification of relationships between contracts, and standardization of quality contracts. At the end, we outline one possible approach to comprehensive contractual description, based on extending existing Web Service technologies. 1

Support for Concurrent Adaptation of Multiple Web Service Compositions to Maximize Business Metrics

Runtime adaptation of Web service compositions can often be done in several ways, so it is necessary to decide which adaptation approach to take. While many research projects studied runtime adaptation of Web service compositions or business processes, this paper presents our unique solutions that maximize business metrics, in cases when several Web service composition instances should be adapted at the same time. We specify all necessary information about possible adaptations and their business metrics as policies in our WS-Policy4MASC language and model the optimization problem in the powerful constraint programming language MiniZinc. Into our MiniZnMASC middleware we integrated new algorithms that determine how to adapt each Web service composition instance so the total business value is maximized, while satisfying all given constraints (e.g., about resource limitations). Experiments with the MiniZnMASC prototype showed that our solutions are feasible, functionally correct, business beneficial, with low performance overhead, and with linear scalability

MiniMASC: A Framework for Diverse Autonomic Adaptations of Web Service Compositions

Abstract—When various technical and business changes related to Web service compositions occur, there is often a need for runtime adaptation with minimal human intervention. While many research projects work on particular types of such adaptation, much more research is needed on decision making for diverse autonomic adaptations, particularly to maximize business (as opposed to technical) metrics. Our MiniMASC middleware is a framework for diverse autonomic adaptations of Web service compositions, focusing on supporting such advanced decision-making algorithms. MiniMASC is relatively simple, light weight, modular, and extensible. It uses the WS-Policy4MASC policy language that can describe all information necessary for different types of adaptation. After presenting our classification of different types of decision making in adaptation of Web service compositions, this paper discusses how MiniMASC (with WS

Using MiniZnMASC Middleware with Different Algorithms for Business-Driven Adaptation of Business Processes

Abstract—Runtime adaptation of business processes and their IT system implementations to changes can usually be done in several ways. MiniZnMASC middleware makes adaptation decisions that maximize business value while satisfying all given constraints. All necessary information about alternative adaptations and their business metrics are specified as policies in WS-Policy4MASC. Using an example loan application business process, we demonstrate how MiniZnMASC supports 4 different autonomic business-driven decision making algorithms for adaptation. Keywords- business-driven IT management; autonomic computing; dynamic adaptation; decision making; business process management; constraint programming; REST I