Analysis of genotype effects for the immunosuppression via two-step method

This paper studies the main effects and interactive effects between genes on immunosuppression susceptibility caused by ultraviolet radiation in population of mice. We present a two-step strategy, i.e., we first establish one full linear model based on all main effects and interactive effects, and use the Dantzig selector method to screen the genotype effects preliminary; then via the idea of stepwise regression, under the other model we further detect the significant main effects and interactive effects for the UV-induced immunosuppression susceptibility. The most significant main effect site that we identified is D10Mit170, and the most significant interactive sites are D6Mit389 and D16Mit131

Introducing PHAEDRA: a new spectral code for simulations of relativistic magnetospheres

We describe a new scheme for evolving the equations of force-free electrodynamics, the vanishing-inertia limit of magnetohydrodynamics. This pseudospectral code uses global orthogonal basis function expansions to take accurate spatial derivatives, allowing the use of an unstaggered mesh and the complete force-free current density. The method has low numerical dissipation and diffusion outside of singular current sheets. We present a range of one- and two-dimensional tests, and demonstrate convergence to both smooth and discontinuous analytic solutions. As a first application, we revisit the aligned rotator problem, obtaining a steady solution with resistivity localised in the equatorial current sheet outside the light cylinder.Comment: 23 pages, 18 figures, accepted for publication in MNRA

Foundations of Black Hole Accretion Disk Theory

This review covers the main aspects of black hole accretion disk theory. We begin with the view that one of the main goals of the theory is to better understand the nature of black holes themselves. In this light we discuss how accretion disks might reveal some of the unique signatures of strong gravity: the event horizon, the innermost stable circular orbit, and the ergosphere. We then review, from a first-principles perspective, the physical processes at play in accretion disks. This leads us to the four primary accretion disk models that we review: Polish doughnuts (thick disks), Shakura-Sunyaev (thin) disks, slim disks, and advection-dominated accretion flows (ADAFs). After presenting the models we discuss issues of stability, oscillations, and jets. Following our review of the analytic work, we take a parallel approach in reviewing numerical studies of black hole accretion disks. We finish with a few select applications that highlight particular astrophysical applications: measurements of black hole mass and spin, black hole vs. neutron star accretion disks, black hole accretion disk spectral states, and quasi-periodic oscillations (QPOs).Comment: 91 pages, 23 figures, final published version available at http://www.livingreviews.org/lrr-2013-

Garden and landscape-scale correlates of moths of differing conservation status: significant effects of urbanization and habitat diversity

Moths are abundant and ubiquitous in vegetated terrestrial environments and are pollinators, important herbivores of wild plants, and food for birds, bats and rodents. In recent years, many once abundant and widespread species have shown sharp declines that have been cited by some as indicative of a widespread insect biodiversity crisis. Likely causes of these declines include agricultural intensification, light pollution, climate change, and urbanization; however, the real underlying cause(s) is still open to conjecture. We used data collected from the citizen science Garden Moth Scheme (GMS) to explore the spatial association between the abundance of 195 widespread British species of moth, and garden habitat and landscape features, to see if spatial habitat and landscape associations varied for species of differing conservation status. We found that associations with habitat and landscape composition were species-specific, but that there were consistent trends in species richness and total moth abundance. Gardens with more diverse and extensive microhabitats were associated with higher species richness and moth abundance; gardens near to the coast were associated with higher richness and moth abundance; and gardens in more urbanized locations were associated with lower species richness and moth abundance. The same trends were also found for species classified as increasing, declining and vulnerable under IUCN (World Conservation Union) criteria

Cadmium hyperaccumulation protects Thlaspi caerulescens from leaf feeding damage by thrips (Frankliniella occidentalis)

Metal hyperaccumulation has been proposed as a plant defensive strategy. Here, we investigated whether cadmium (Cd) hyperaccumulation protected Thlaspi caerulescens from leaf feeding damage by thrips (Frankliniella occidentalis). Two ecotypes differing in Cd accumulation, Ganges (high) and Prayon (low), were grown in compost amended with 0-1000 mg Cd kg(-1) in two experiments under glasshouse conditions. F-2 and F-3 plants from the Prayon x Ganges crosses were grown with 5 mg Cd kg(-1). Plants were naturally colonized by thrips and the leaf feeding damage index (LFDI) was assessed. The LFDI decreased significantly with increasing Cd in both ecotypes, and correlated with shoot Cd concentration in a log-linear fashion. Prayon was more attractive to thrips than Ganges, but the ecotypic difference in the LFDI was largely accounted for by the shoot Cd concentration. In the F-2 and F-3 plants, the LFDI correlated significantly and negatively with shoot Cd, but not with shoot zinc (Zn) or sulphur (S) concentrations. We conclude that Cd hyperaccumulation deters thrips from feeding on T. caerulescens leaves, which may offer an adaptive benefit to the plant

Comb-Based Radio-Frequency Photonic Filters with Rapid Tunability and High Selectivity

Photonic technologies have received considerable attention for enhancement of radio-frequency (RF) electrical systems, including high-frequency analog signal transmission, control of phased arrays, analog-to-digital conversion, and signal processing. Although the potential of radio-frequency photonics for implementation of tunable electrical filters over broad RF bandwidths has been much discussed, realization of programmable filters with highly selective filter lineshapes and rapid reconfigurability has faced significant challenges. A new approach for RF photonic filters based on frequency combs offers a potential route to simultaneous high stopband attenuation, fast tunability, and bandwidth reconfiguration. In one configuration tuning of the RF passband frequency is demonstrated with unprecedented (~40 ns) speed by controlling the optical delay between combs. In a second, fixed filter configuration, cascaded four-wave mixing simultaneously broadens and smoothes comb spectra, resulting in Gaussian RF filter lineshapes exhibiting extremely high (>60 dB) main lobe to sidelobe suppression ratio and (>70 dB) stopband attenuation.Comment: Updated the submission with the most recent version of the pape

Infections in early life and childhood leukaemia risk: a UK case–control study of general practitioner records

We investigated infections in early life (diagnosed in general practice) and subsequent risk of childhood leukaemia in the UK General Practice Research Database (GPRD). All children born at GPRD practices and subsequently diagnosed with leukaemia were identified as cases and were individually matched (on year of birth, sex and practice) to up to 20 controls. The final analysis included 162 leukaemia cases and 2215 matched controls. Conditional logistic regression demonstrated no evidence that children with one or more recorded infection in the first year of life had a reduced risk of leukaemia (OR=1.05, 95%CI 0.69, 1.59; P=0.83) or acute lymphoblastic leukaemia (ALL; OR=1.05, 95%CI 0.64–1.74; P=0.84). Our study provides no support for the Greaves hypothesis, which proposes that reduced or delayed exposure to infections in early life increases the risk of childhood ALL

Biodiversity Loss and the Taxonomic Bottleneck: Emerging Biodiversity Science

Human domination of the Earth has resulted in dramatic changes to global and local patterns of biodiversity. Biodiversity is critical to human sustainability because it drives the ecosystem services that provide the core of our life-support system. As we, the human species, are the primary factor leading to the decline in biodiversity, we need detailed information about the biodiversity and species composition of specific locations in order to understand how different species contribute to ecosystem services and how humans can sustainably conserve and manage biodiversity. Taxonomy and ecology, two fundamental sciences that generate the knowledge about biodiversity, are associated with a number of limitations that prevent them from providing the information needed to fully understand the relevance of biodiversity in its entirety for human sustainability: (1) biodiversity conservation strategies that tend to be overly focused on research and policy on a global scale with little impact on local biodiversity; (2) the small knowledge base of extant global biodiversity; (3) a lack of much-needed site-specific data on the species composition of communities in human-dominated landscapes, which hinders ecosystem management and biodiversity conservation; (4) biodiversity studies with a lack of taxonomic precision; (5) a lack of taxonomic expertise and trained taxonomists; (6) a taxonomic bottleneck in biodiversity inventory and assessment; and (7) neglect of taxonomic resources and a lack of taxonomic service infrastructure for biodiversity science. These limitations are directly related to contemporary trends in research, conservation strategies, environmental stewardship, environmental education, sustainable development, and local site-specific conservation. Today’s biological knowledge is built on the known global biodiversity, which represents barely 20% of what is currently extant (commonly accepted estimate of 10 million species) on planet Earth. Much remains unexplored and unknown, particularly in hotspots regions of Africa, South Eastern Asia, and South and Central America, including many developing or underdeveloped countries, where localized biodiversity is scarcely studied or described. ‘‘Backyard biodiversity’’, defined as local biodiversity near human habitation, refers to the natural resources and capital for ecosystem services at the grassroots level, which urgently needs to be explored, documented, and conserved as it is the backbone of sustainable economic development in these countries. Beginning with early identification and documentation of local flora and fauna, taxonomy has documented global biodiversity and natural history based on the collection of ‘‘backyard biodiversity’’ specimens worldwide. However, this branch of science suffered a continuous decline in the latter half of the twentieth century, and has now reached a point of potential demise. At present there are very few professional taxonomists and trained local parataxonomists worldwide, while the need for, and demands on, taxonomic services by conservation and resource management communities are rapidly increasing. Systematic collections, the material basis of biodiversity information, have been neglected and abandoned, particularly at institutions of higher learning. Considering the rapid increase in the human population and urbanization, human sustainability requires new conceptual and practical approaches to refocusing and energizing the study of the biodiversity that is the core of natural resources for sustainable development and biotic capital for sustaining our life-support system. In this paper we aim to document and extrapolate the essence of biodiversity, discuss the state and nature of taxonomic demise, the trends of recent biodiversity studies, and suggest reasonable approaches to a biodiversity science to facilitate the expansion of global biodiversity knowledge and to create useful data on backyard biodiversity worldwide towards human sustainability

Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages

This study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments