The Invisible Web: A Quick Overview

This article provides a quick overview of recent literature published about the Invisible Web. In particular, this article covers such topics as what is the Invisible Web, weaknesses of popular search engines, types of information found on the Invisible Web, when to use the Invisible Web, search tools and search strategies

Root data with group actions

Suppose $k$ is a field, $G$ is a connected reductive algebraic $k$-group, $T$ is a maximal $k$-torus in $G$, and $\Gamma$ is a finite group that acts on $(G,T)$. From the above, one obtains a root datum $\Psi$ on which $\text{Gal}(k)\times\Gamma$ acts. Provided that $\Gamma$ preserves a positive system in $\Psi$, not necessarily invariant under $\text{Gal}(k)$, we construct an inverse to this process. That is, given a root datum on which $\text{Gal}(k)\times\Gamma$ acts appropriately, we show how to construct a pair $(G,T)$, on which $\Gamma$ acts as above. Although the pair $(G,T)$ and the action of $\Gamma$ are canonical only up to an equivalence relation, we construct a particular pair for which $G$ is $k$-quasisplit and $\Gamma$ fixes a $\text{Gal}(k)$-stable pinning of $G$. Using these choices, we can define a notion of taking "$\Gamma$-fixed points" at the level of equivalence classes, and this process is compatible with a general "restriction" process for root data with $\Gamma$-action.Comment: v2: one word inserted, one citation inserted, one reference updated, one misspelling correcte

Age-specific mortality during the 1918 influenza pandemic: unravelling the mystery of high young adult mortality.

The worldwide spread of a novel influenza A (H1N1) virus in 2009 showed that influenza remains a significant health threat, even for individuals in the prime of life. This paper focuses on the unusually high young adult mortality observed during the Spanish flu pandemic of 1918. Using historical records from Canada and the U.S., we report a peak of mortality at the exact age of 28 during the pandemic and argue that this increased mortality resulted from an early life exposure to influenza during the previous Russian flu pandemic of 1889-90. We posit that in specific instances, development of immunological memory to an influenza virus strain in early life may lead to a dysregulated immune response to antigenically novel strains encountered in later life, thereby increasing the risk of death. Exposure during critical periods of development could also create holes in the T cell repertoire and impair fetal maturation in general, thereby increasing mortality from infectious diseases later in life. Knowledge of the age-pattern of susceptibility to mortality from influenza could improve crisis management during future influenza pandemics

ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data

<p>Abstract</p> <p>Background</p> <p>Many high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data points, making data analysis a time consuming and painstaking process. Here we describe <it>ScreenMill</it>, a new software suite that automates image analysis and simplifies data review and analysis for high-throughput biological experiments.</p> <p>Results</p> <p>The <it>ScreenMill</it>, software suite includes three software tools or "engines": an open source <it>Colony Measurement Engine </it>(<it>CM Engine</it>) to quantitate colony growth data from plate images, a web-based <it>Data Review Engine </it>(<it>DR Engine</it>) to validate and analyze quantitative screen data, and a web-based <it>Statistics Visualization Engine </it>(<it>SV Engine</it>) to visualize screen data with statistical information overlaid. The methods and software described here can be applied to any screen in which growth is measured by colony size. In addition, the <it>DR Engine </it>and <it>SV Engine </it>can be used to visualize and analyze other types of quantitative high-throughput data.</p> <p>Conclusions</p> <p><it>ScreenMill </it>automates quantification, analysis and visualization of high-throughput screen data. The algorithms implemented in S<it>creenMill </it>are transparent allowing users to be confident about the results <it>ScreenMill </it>produces. Taken together, the tools of <it>ScreenMill </it>offer biologists a simple and flexible way of analyzing their data, without requiring programming skills.</p

How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae)

Manta rays and their relatives of the family Myliobatidae have pectoral fins that have been modified for underwater flight, as well as a pair of fleshy projections at the anterior of the body called cephalic lobes, which are specialized for feeding. As a unique trait with a dedicated function, cephalic lobes offer an excellent opportunity to elucidate the processes by which diverse body plans and features evolve. To shed light on the morphological development and genetic underpinnings of cephalic lobes, we examined paired fin development in cownose rays, which represent the sister taxon to manta rays in the genus Mobula. We find that cephalic lobes develop as anterior pectoral fin domains and lack independent posterior patterning by 5\u27 HoxD genes and Shh, indicating that cephalic lobes are not independent appendages but rather are modified pectoral fin domains. In addition, by leveraging interspecies comparative transcriptomics and domain-specific RNA-sequencing, we identify shared expression of anterior patterning genes, including Alx1, Alx4, Pax9, Hoxa13, Hoxa2, and Hoxd4, in the pectoral fins of cownose ray (Rhinoptera bonasus) and little skate (Leucoraja erinacea), providing evidence supporting homology between the cephalic lobes of myliobatids and the anterior pectoral fins of skates. We also suggest candidate genes that may be involved in development of myliobatid-specific features, including Omd, which is likely associated with development of thick anterior pectoral fin radials of myliobatids, and Dkk1, which may inhibit tissue outgrowth at the posterior boundary of the developing cephalic lobes. Finally, we observe that cephalic lobes share a surprising number of developmental similarities with another paired fin modification: the claspers of male cartilaginous fishes, including enrichment of Hand2, Hoxa13, and androgen receptor. These results suggest that cephalic lobes may have evolved by co-opting developmental pathways that specify novel domains in paired fins. Taken together, these data on morphological development and comparative gene expression patterns illustrate how distinct body plans and seemingly novel features can arise via subtle changes to existing developmental pathways

Determinants of Influenza Mortality Trends: Age-Period-Cohort Analysis of Influenza Mortality in the United States, 1959-2016.

This study examines the roles of age, period, and cohort in influenza mortality trends over the years 1959-2016 in the United States. First, we use Lexis surfaces based on Serfling models to highlight influenza mortality patterns as well as to identify lingering effects of early-life exposure to specific influenza virus subtypes (e.g., H1N1, H3N2). Second, we use age-period-cohort (APC) methods to explore APC linear trends and identify changes in the slope of these trends (contrasts). Our analyses reveal a series of breakpoints where the magnitude and direction of birth cohort trends significantly change, mostly corresponding to years in which important antigenic drifts or shifts took place (i.e., 1947, 1957, 1968, and 1978). Whereas child, youth, and adult influenza mortality appear to be influenced by a combination of cohort- and period-specific factors, reflecting the interaction between the antigenic experience of the population and the evolution of the influenza virus itself, mortality patterns of the elderly appear to be molded by broader cohort factors. The latter would reflect the processes of physiological capital improvement in successive birth cohorts through secular changes in early-life conditions. Antigenic imprinting, cohort morbidity phenotype, and other mechanisms that can generate the observed cohort effects, including the baby boom, are discussed

Ligand-based virtual screening using binary kernel discrimination

This paper discusses the use of a machine-learning technique called binary kernel discrimination (BKD) for virtual screening in drug- and pesticide-discovery programmes. BKD is compared with several other ligand-based tools for virtual screening in databases of 2D structures represented by fragment bit-strings, and is shown to provide an effective, and reasonably efficient, way of prioritising compounds for biological screening