Ontological View-driven Semantic Integration in Open Environments

In an open computing environment, such as the World Wide Web or an enterprise Intranet, various information systems are expected to work together to support information exchange, processing, and integration. However, information systems are usually built by different people, at different times, to fulfil different requirements and goals. Consequently, in the absence of an architectural framework for information integration geared toward semantic integration, there are widely varying viewpoints and assumptions regarding what is essentially the same subject. Therefore, communication among the components supporting various applications is not possible without at least some translation. This problem, however, is much more than a simple agreement on tags or mappings between roughly equivalent sets of tags in related standards. Industry-wide initiatives and academic studies have shown that complex representation issues can arise. To deal with these issues, a deep understanding and appropriate treatment of semantic integration is needed. Ontology is an important and widely accepted approach for semantic integration. However, usually there are no explicit ontologies with information systems. Rather, the associated semantics are implied within the supporting information model. It reflects a specific view of the conceptualization that is implicitly defining an ontological view. This research proposes to adopt ontological views to facilitate semantic integration for information systems in open environments. It proposes a theoretical foundation of ontological views, practical assumptions, and related solutions for research issues. The proposed solutions mainly focus on three aspects: the architecture of a semantic integration enabled environment, ontological view modeling and representation, and semantic equivalence relationship discovery. The solutions are applied to the collaborative intelligence project for the collaborative promotion / advertisement domain. Various quality aspects of the solutions are evaluated and future directions of the research are discussed

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Frame-based ontological view for semantic integration

Semantic integration is crucial for successful collaboration between heterogeneous information systems. Traditional ontology-driven approaches rely on the availability of explicit ontologies. However, in most application domains, this prerequisite cannot be met. In order to address this issue, this paper investigates the theoretical foundation of ontologies and extends the traditional ontology concept to an ontologicalview concept. To explicitly and formally specify the ontologicalviews, a Frame-basedOntologicalview Specification Language (FOSL) is proposed. This language is based on the frame knowledge representation paradigm and uses XML as the encoding. The ontologicalview driven semanticintegration can be achieved based on the specifications. A proof-of-concept prototype environment has been implemented to achieve semanticintegrationbased on ontologicalviews specified with FOSL.Peer reviewed: YesNRC publication: Ye

A service-oriented system integration framework for community-based independent living spaces

Budget constraints, technological advances, and a growing elderly population are calling for major reforms in healthcare systems. The publicly managed and community-based independent living service provided for the elderly outside hospitals or long-term care institutions is a trend all over the world so that the healthcare systems would be sustainable in the future. We have started a long term initiative to integrate and develop innovative ICT solutions and construction technologies to provide quality and yet affordable supports for seniors to live safely and independently at their own homes. This paper presents some preliminary results on the development of a service-oriented system integration framework for community-based independent living spaces.Peer reviewed: YesNRC publication: Ye

A Computer Aided Grading System for Subjective Tests

Computer aided tests replace traditional written answers on paper sheets with electronic records. For subjective tests, computers are not able to do all grading jobs, due to limited comprehensive ability of computers. Subjective answers need be reviewed by different graders in order to improve justice. We propose a distributed computational model for grading electronic subjective answers. Answer data are divided into numerous independent data cells. Computational resources are automatically allocated by the system to do grading jobs and independently report grading results to the system. Since the grading results may vary slightly or magnificently, we assign computational factors to data cells and computational resources to minimize the variation. In addition, rules are defined to obtain a final result. We successfully apply the proposed model in our grading system in computer aided spoken English tests. 1

A frame-based ontological view specification language

Semantic integration is crucial for successful collaboration between heterogeneous information systems in an open environment. Traditional ontologydriven approaches rely on the availability of explicit ontologies. However, in many domains, this prerequisite cannot be met. In order to address this issue, this paper investigates the theoretical foundation of ontologies and extends the traditional ontology concept to an ontological view concept. To explicitly and formally specify the ontological views, a Framebased Ontological view Specification Language (FOSL) is proposed. This language is based on the Frame knowledge representation paradigm and uses XML as the encoding. A prototype environment that supports semantic integration, based on ontological views specified with FOSL is introduced.L?int\ue9gration s\ue9mantique est une composante essentielle du succ\ue8s de la collaboration entre les syst\ue8mes d'information h\ue9t\ue9rog\ue8nes en milieu ouvert. Les approches classiques ax\ue9es sur l'ontologie reposent sur la disponibilit\ue9 d'ontologies explicites. Toutefois, dans de nombreux domaines, cette condition pr\ue9alable ne peut \ueatre remplie. En r\ue9ponse \ue0 cette probl\ue9matique, ce document examine le fondement th\ue9orique des ontologies et \ue9largit la d\ue9finition traditionnelle de l'ontologie \ue0 la notion de vue ontologique. Aux fins d'une sp\ue9cification explicite et formelle des vues ontologiques, nous proposons ici un langage de sp\ue9cification de vue ontologique bas\ue9 sur des cadres (LSOC). Ce langage est fond\ue9 sur le paradigme de la repr\ue9sentation de la connaissance du cadre et utilise l'encodage XML. Nous pr\ue9sentons un environnement prototype qui supporte l'int\ue9gration s\ue9mantique, fond\ue9 sur les vues ontologiques sp\ue9cifi\ue9es avec le LSOC.NRC publication: Ye

Performance evaluation of ns-2 simulator for wireless sensor networks

Abstract—Simulation for wireless sensor networks has become a challenging exercise due to the hardware design, energy constraints, and deployment of large number of nodes. NS-2 has been widely used in network simulations but does not perform well for wireless sensor networks. This paper provides a comprehensive analysis of the NS-2 simulator based on performance evaluation of simulation results, and proposes some improvements needed in NS-2 to cope up with wireless sensor network simulations. Keywords-performance evaluation; NS-2; wireless sensor network; simulation I

Different gut microbial types were found in captive striped hamsters

Background Typing analysis has become a popular approach to categorize individual differences in studies of animal gut microbial communities. However, previous definitions of gut microbial types were more understood as a passive reaction process to different external interferences, as most studies involve diverse environmental variables. We wondered whether distinct gut microbial types can also occur in animals under the same external environment. Moreover, the role of host sex in shaping gut microbiota has been widely reported; thus, the current study preliminarily explores the effects of sex on potential different microbial types. Methods Here, adult striped hamsters Cricetulus barabensis of different sexes were housed under the same controlled laboratory conditions, and their fecal samples were collected after two months to assess the gut microbiota by 16S rRNA sequencing. Results The gut microbiota of captive striped hamsters naturally separated into two types at the amplicon sequence variant (ASV) level. There was a significant difference in the Shannon index among these two types. A receiver operating characteristic (ROC) curve showed that the top 30 ASVs could effectively distinguish each type. Linear discriminant analysis of effect size (LEfSe) showed enrichment of the genera Lactobacillus, Treponema and Pygmaiobacter in one gut microbial type and enrichment of the genera Turicibacter and Ruminiclostridium in the other. The former type had higher carbohydrate metabolism ability, while the latter harbored a more complex co-occurrence network and higher amino acid metabolism ability. The gut microbial types were not associated with sex; however, we did find sex differences in the relative abundances of certain bacterial taxa, including some type-specific sex variations. Conclusions Although captive animals live in a unified environment, their gut bacteria can still differentiate into distinct types, but the sex of the hosts may not play an important role in the typing process of small-scale captive animal communities. The relevant driving factors as well as other potential types need to be further investigated to better understand host-microbe interactions

Genome of lethal Lepiota venenata and insights into the evolution of toxin-biosynthetic genes

Abstract Background Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushroom poisoning case in China has led to acquisition of fresh L. venenata fruiting bodies, based on which a draft genome was obtained through PacBio and Illumina sequencing platforms. Toxin-biosynthetic MSDIN family and Porlyl oligopeptidase B (POPB) genes were mined from the genome and used for phylogenetic and statistical studies to gain insights into the evolution of the biosynthetic pathway. Results The analysis of the genome data illustrated that only one MSDIN, named LvAMA1, exits in the genome, along with a POPB gene. No POPA homolog was identified by direct homology searching, however, one additional POP gene, named LvPOPC, was cloned and the gene structure determined. Similar to ApAMA1 in A. phalloides and GmAMA1 in G. marginata, LvAMA1 directly encodes α-amanitin. The two toxin genes were mapped to the draft genome, and the structures analyzed. Furthermore, phylogenetic and statistical analyses were conducted to study the evolution history of the POPB genes. Compared to our previous report, the phylogenetic trees unambiguously showed that a monophyletic POPB lineage clearly conflicted with the species phylogeny. In contrast, phylogeny of POPA genes resembled the species phylogeny. Topology and divergence tests showed that the POPB lineage was robust and these genes exhibited significantly shorter genetic distances than those of the house-keeping rbp2, a characteristic feature of genes with horizontal gene transfer (HGT) background. Consistently, same scenario applied to the only MSDIN, LvAMA1, in the genome. Conclusions To the best of our knowledge, this is the first reported genome of Lepiota. The analyses of the toxin genes indicate that the cyclic peptides are synthesized through a ribosomal mechanism. The toxin genes, LvAMA1 and LvPOPB, are not in the vicinity of each other. Phylogenetic and evolutionary studies suggest that HGT is the underlining cause for the occurrence of POPB and MSDIN in Amanita, Galerina and Lepiota, which are allocated in three distantly-related families