A multi-species functional embedding integrating sequence and network structure

A key challenge to transferring knowledge between species is that different species have fundamentally different genetic architectures. Initial computational approaches to transfer knowledge across species have relied on measures of heredity such as genetic homology, but these approaches suffer from limitations. First, only a small subset of genes have homologs, limiting the amount of knowledge that can be transferred, and second, genes change or repurpose functions, complicating the transfer of knowledge. Many approaches address this problem by expanding the notion of homology by leveraging high-throughput genomic and proteomic measurements, such as through network alignment. In this work, we take a new approach to transferring knowledge across species by expanding the notion of homology through explicit measures of functional similarity between proteins in different species. Specifically, our kernel-based method, HANDL (Homology Assessment across Networks using Diffusion and Landmarks), integrates sequence and network structure to create a functional embedding in which proteins from different species are embedded in the same vector space. We show that inner products in this space and the vectors themselves capture functional similarity across species, and are useful for a variety of functional tasks. We perform the first whole-genome method for predicting phenologs, generating many that were previously identified, but also predicting new phenologs supported from the biological literature. We also demonstrate the HANDL embedding captures pairwise gene function, in that gene pairs with synthetic lethal interactions are significantly separated in HANDL space, and the direction of separation is conserved across species. Software for the HANDL algorithm is available at http://bit.ly/lrgr-handl.Published versio

Molecular evidence for Anaplasma phagocytophilum in Israel

Sequences from the Anaplasma phagocytophilum 16S rRNA gene were detected in 5 ticks representing 3 species (Hyalomma marginatum, Rhipicephalus turanicus, and Boophilus kohlsi) collected from roe deer (Capreolus capreolus) in Mount Carmel, Israel. The sequences were all identical to those of Ap-variant 1 strain

Andean Land Use And Biodiversity: Humanized Landscapes In A Time Of Change

Some landscapes Cannot be understood without reference., to the kinds. degrees, kinds, degrees, and history of human-caused modifications to the Earth's surface. The tropical latitudes of the Andes represent one such place, with agricultural land-use systems appearing in the Early Holocene. Current land use includes both intensive and extensive grazing and crop- or tree-based agricultural systems found across virtually the, entire range of possible elevations and humidity regimes. Biodiversity found in or adjacent to such humanized landscapes will have been altered in abundance. composition, and distribution in relation to the resiliency of the native Species to harvest, hold cover modifications, and other deliberate or inadvertent human land uses. In addition, the geometries of land cover, resulting flout difference among the shapes, sizes, connectivities, and physical structures of the patches, corridors, and matrices that compose landscape mosaics, will constrain biodiversity, often in predictable ways. This article proposes a conceptual model that alter ins that the Continued persistence of native species may depend as much oil the shifting Of Andean landscape mosaics as on species characteristics, themselves. Furthermore, mountains such as the Andes display long gradients of environmental Conditions that after in relation to latitude, soil moisture, aspect, and elevation. Global environmental change will shift these, especially temperature and humidity regimes along elevational gradients, causing Changes outside the historical range of variation for some species. Both land-use systems and Conservation efforts will need to respond spatially to these shifts in the future, at both landscape and regional scales.Geography and the Environmen

Menstrual cycle phase does not predict political conservatism

Recent authors have reported a relationship between women's fertility status, as indexed by menstrual cycle phase, and conservatism in moral, social and political values. We conducted a survey to test for the existence of a relationship between menstrual cycle day and conservatism. 2213 women reporting regular menstrual cycles provided data about their political views. Of these women, 2208 provided information about their cycle date, 1260 provided additional evidence of reliability in self-reported cycle date, and of these, 750 also indicated an absence of hormonal disruptors such as recent hormonal contraception use, breastfeeding or pregnancy. Cycle day was used to estimate day-specific fertility rate (probability of conception); political conservatism was measured via direct self-report and via responses to the "Moral Foundations” questionnaire. We also recorded relationship status, which has been reported to interact with menstrual cycle phase in determining political preferences. We found no evidence of a relationship between estimated cyclical fertility changes and conservatism, and no evidence of an interaction between relationship status and cyclical fertility in determining political attitudes. Our findings were robust to multiple inclusion/exclusion criteria and to different methods of estimating fertility and measuring conservatism. In summary, the relationship between cycle-linked reproductive parameters and conservatism may be weaker or less reliable than previously thought

Effects of pressure on diffusion and vacancy formation in MgO from non-empirical free-energy integrations

The free energies of vacancy pair formation and migration in MgO were computed via molecular dynamics using free-energy integrations and a non-empirical ionic model with no adjustable parameters. The intrinsic diffusion constant for MgO was obtained at pressures from 0 to 140 GPa and temperatures from 1000 to 5000 K. Excellent agreement was found with the zero pressure diffusion data within experimental error. The homologous temperature model which relates diffusion to the melting curve describes well our high pressure results within our theoretical framework.Comment: 4 pages, latex, 1 figure, revtex, submitted to PR

Is the Relationship Between Pathogen Avoidance and Ideological Conservatism Explained by Sexual Strategies?

Multiple recent studies report that measures of pathogen avoidance (e.g., disgust sensitivity) correlate with political ideology. This relationship has been interpreted as suggesting that certain political views (specifically, those views that are categorized as socially conservative) function to mitigate the pathogen threats posed either by intergroup interactions or by departures from traditional societal norms, which sometimes evolve culturally for anti-pathogen functions. We propose and test the alternative hypothesis that pathogen avoidance relates to conservatism indirectly via sexual strategies (e.g., relatively monogamous versus relatively promiscuous). Specifically, we argue that individuals who are more invested in avoiding pathogens follow a more monogamous mating strategy to mitigate against pathogens transmitted during sexual contact, and individuals following a more monogamous mating strategy adopt socially conservative political ideologies to support their reproductive interests. Results from three studies ( N's = 819, 238, and 248) using multiple measures of pathogen avoidance, sexual strategies, and ideology support this account, with sexual strategies fully mediating the relationship between measures of pathogen avoidance and conservatism in each study

Comparison of the Electronic Structures and Energetics of Ferroelectric LiNbO3 and LiTaO3

This paper explains the origin of the ferroelectric instability in LiNbO3 and LiTaO3 and compares the electronic structures and energetics of the two materials.Comment: 31 pages, 11 Postscript figure

Ornamental plants: a summary of research, 1990

Physical facilities and capital requirements for establishing a three-acre perennial container nursery in Ohio -1989 / Reed D. Taylor, Elton M. Smith, George P. Pealer -- Production costs of operating a three-acre perennial container nursery in Ohio - 1989 / Reed D. Taylor, Elton M. Smith, George P. Pealer -- Comparative costs of producing alternative plants in a three-acre perennial container nursery in Ohio – 1989 / Reed D. Taylor, Elton M. Smith, George P. Pealer -- Marketing and sales strategies practiced by Ohio nurseries / Reed D. Taylor, Elton M. Smith, W. Timothy Rhodus -- Evaluation of flowering crabapple susceptibility to apple scab in Ohio - 1989 / Elton M. Smith and Sharon A. Treaster -- Fertilizing trees in the landscape: an 18-year evaluation / Elton M. Smith and Sharon A. Treaster -- The influence of irrigation water temperature upon leaf abscision in Ficus benjamina and Dracaena marginata / Julia A. O’Bryan and John C. Peterson -- A two-year tolerance study of narcissus cultivars to selected pre-emergence herbicides / Elton M. Smith and Sharon A. Treaster -- Tolerance of clematis and wisteria to Ronstar and Devrinol / Elton M. Smith and Sharon A. Treaster -- Increasing efficiency of slow-release herbicide tablets / Elton M. Smith and Sharon A. Treaster -- Developing biorational pesticides for the landscape industry / David G. Nielsen -- Interactions between subdue and slow-release fertilizers at high temperatures / Y. Inbar, H. A. J. Hoitink, M. E. Watson, K. D. Cochran, E. M. Smith -- Evaluation of powdery mildew severity on deciduous azaleas at the Secrest Arboretum - 1989 / Kenneth D. Cochran and C. Wayne Ellett -- Winter damage, regrowth and vigor of old garden roses / Gary A. Anderso

Hybridization in parasites: consequences for adaptive evolution, pathogenesis and public health in a changing world

[No abstract available

Foreign policy and globalization theory: The case of Israel

Since the early 1990s, international relations has witnessed a stimulating debate on globalization. This debate laid the foundations for globalization theory (GT), providing the tools for an empirical examination of the globalization of multiple activities: from politics and organized violence, to finance, trade and production, through culture and environmental degradation. However, examination of what appear to be the best-known works on globalization reveals that foreign policy has been virtually excluded from GT. In this context, based on what is described here as a synergistic transformationalist approach (STA) to globalization, I provide a critique of GT. The critique is geared towards examining why foreign policy hitherto has been overlooked by contemporary GT. I expose the problems this generates and address them by exploring how STA enables GT to incorporate foreign policy. I use the case of Israel heuristically to elicit how incorporating foreign policy into GT may provide a better understanding of the relationship between foreign policy and globalization. Three themes are highlighted: the role of foreign policy in inducing and reproducing globalization; determining the mutually constitutive relationship between globalization and the state; and shaping the interfacing between international politics and globalization