Model-based probabilistic frequent itemset mining

Data uncertainty is inherent in emerging applications such as location-based services, sensor monitoring systems, and data integration. To handle a large amount of imprecise information, uncertain databases have been recently developed. In this paper, we study how to efficiently discover frequent itemsets from large uncertain databases, interpreted under the Possible World Semantics. This is technically challenging, since an uncertain database induces an exponential number of possible worlds. To tackle this problem, we propose a novel methods to capture the itemset mining process as a probability distribution function taking two models into account: the Poisson distribution and the normal distribution. These model-based approaches extract frequent itemsets with a high degree of accuracy and support large databases. We apply our techniques to improve the performance of the algorithms for (1) finding itemsets whose frequentness probabilities are larger than some threshold and (2) mining itemsets with the {Mathematical expression} highest frequentness probabilities. Our approaches support both tuple and attribute uncertainty models, which are commonly used to represent uncertain databases. Extensive evaluation on real and synthetic datasets shows that our methods are highly accurate and four orders of magnitudes faster than previous approaches. In further theoretical and experimental studies, we give an intuition which model-based approach fits best to different types of data sets. © 2012 The Author(s).published_or_final_versio

Determinants of host susceptibility to murine respiratory syncytial virus (RSV) disease identify a role for the innate immunity scavenger receptor MARCO gene in human infants

AbstractBackgroundRespiratory syncytial virus (RSV) is the global leading cause of lower respiratory tract infection in infants. Nearly 30% of all infected infants develop severe disease including bronchiolitis, but susceptibility mechanisms remain unclear.MethodsWe infected a panel of 30 inbred strains of mice with RSV and measured changes in lung disease parameters 1 and 5days post-infection and they were used in genome-wide association (GWA) studies to identify quantitative trait loci (QTL) and susceptibility gene candidates.FindingsGWA identified QTLs for RSV disease phenotypes, and the innate immunity scavenger receptor Marco was a candidate susceptibility gene; targeted deletion of Marco worsened murine RSV disease. We characterized a human MARCO promoter SNP that caused loss of gene expression, increased in vitro cellular response to RSV infection, and associated with increased risk of disease severity in two independent populations of children infected with RSV.InterpretationTranslational integration of a genetic animal model and in vitro human studies identified a role for MARCO in human RSV disease severity. Because no RSV vaccines are approved for clinical use, genetic studies have implications for diagnosing individuals who are at risk for severe RSV disease, and disease prevention strategies (e.g. RSV antibodies)

Egg Formation in Lepidoptera

Reproductive biology in the Twentieth Century produced comprehensive descriptions of the mechanisms of egg formation in most of the major orders of insects. While many general principles of ovarian development and physiology emerged, every order turned out to have a set of its own special motifs. Discovery of the lepidopteran motifs is summarized in this essay. The emphasis is on developmental mechanisms, beginning with the early growth and differentiation of female germ cells and ending, after many turns in morphogenesis, physiology and biosynthesis, with eggs that are filled with yolk and encased in chorions. Examples of uniquely lepidopteran traits include the cellular composition of ovarian follicles, the number of tubular ovarioles in which they mature, the functions of cell-to-cell junctional complexes in their maturation, their use of glycosaminoglycans to maintain intercellular patency during vitellogenesis, the role of proton and calcium pumps in their ion physiology, a separate postvitellogenic period of water and inorganic ion uptake, and the fine structure and protein composition of their chorions. Discovery of this combination of idiosyncracies was based on advances in the general concepts and techniques of cell and molecular biology and on insights borrowed from studies on other insects. The lepidopteran ovary in turn has contributed much to the understanding of egg formation in insects generally

H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases

Nucleosomes in heterochromatic regions bear histone modifications that distinguish them from euchromatic nucleosomes. Among those, histone H3 lysine 9 methylation (H3K9me) and hypoacetylation have been evolutionarily conserved and are found in both multicellular eukaryotes and single-cell model organisms such as fission yeast. In spite of numerous studies, the relative contributions of the various heterochromatic histone marks to the properties of heterochromatin remain largely undefined. Here, we report that silencing of the fission yeast mating-type cassettes, which are located in a well-characterized heterochromatic region, is hardly affected in cells lacking the H3K9 methyltransferase Clr4. We document the existence of a pathway parallel to H3K9me ensuring gene repression in the absence of Clr4 and identify a silencing factor central to this pathway, Clr5. We find that Clr5 controls gene expression at multiple chromosomal locations in addition to affecting the mating-type region. The histone deacetylase Clr6 acts in the same pathway as Clr5, at least for its effects in the mating-type region, and on a subset of other targets, notably a region recently found to be prone to neo-centromere formation. The genomic targets of Clr5 also include Ste11, a master regulator of sexual differentiation. Hence Clr5, like the multi-functional Atf1 transcription factor which also modulates chromatin structure in the mating-type region, controls sexual differentiation and genome integrity at several levels. Globally, our results point to histone deacetylases as prominent repressors of gene expression in fission yeast heterochromatin. These deacetylases can act in concert with, or independently of, the widely studied H3K9me mark to influence gene silencing at heterochromatic loci