Counter-rotating Accretion Disks

We consider accretion disks consisting of counter-rotating gaseous components with an intervening shear layer. Configurations of this type may arise from the accretion of newly supplied counter-rotating gas onto an existing co-rotating gas disk. For simplicity we consider the case where the gas well above the disk midplane is rotating with angular rate $+\Omega$ and that well below has the same properties but is rotating with rate $-\Omega$. Using the Shakura-Sunyaev alpha turbulence model, we find self-similar solutions where a thin (relative to the full disk thickness) equatorial layer accretes very rapidly, essentially at free-fall speed. As a result the accretion speed is much larger than it would be for an alpha disk rotating in one direction. Counter-rotating accretion disks may be a transient stage in the formation of counter-rotating galaxies and in the accretion of matter onto compact objects.Comment: 7 pages, 3 figures, aas2pp4.sty, submitted to Ap

High-accuracy numerical models of Brownian thermal noise in thin mirror coatings

Brownian coating thermal noise in detector test masses is limiting the sensitivity of current gravitational-wave detectors on Earth. Therefore, accurate numerical models can inform the ongoing effort to minimize Brownian coating thermal noise in current and future gravitational-wave detectors. Such numerical models typically require significant computational resources and time, and often involve closed-source commercial codes. In contrast, open-source codes give complete visibility and control of the simulated physics and enable direct assessment of the numerical accuracy. In this article, we use the open-source SpECTRE numerical-relativity code and adopt a novel discontinuous Galerkin numerical method to model Brownian coating thermal noise. We demonstrate that SpECTRE achieves significantly higher accuracy than a previous approach at a fraction of the computational cost. Furthermore, we numerically model Brownian coating thermal noise in multiple sub-wavelength crystalline coating layers for the first time. Our new numerical method has the potential to enable fast exploration of realistic mirror configurations, and hence to guide the search for optimal mirror geometries, beam shapes and coating materials for gravitational-wave detectors.Comment: 9 pages, 5 figures. Results are reproducible with the ancillary input file

A scalable elliptic solver with task-based parallelism for the SpECTRE numerical relativity code

Elliptic partial differential equations must be solved numerically for many problems in numerical relativity, such as initial data for every simulation of merging black holes and neutron stars. Existing elliptic solvers can take multiple days to solve these problems at high resolution and when matter is involved, because they are either hard to parallelize or require a large amount of computational resources. Here we present a new solver for linear and non-linear elliptic problems that is designed to scale with resolution and to parallelize on computing clusters. To achieve this we employ a discontinuous Galerkin discretization, an iterative multigrid-Schwarz preconditioned Newton-Krylov algorithm, and a task-based parallelism paradigm. To accelerate convergence of the elliptic solver we have developed novel subdomain-preconditioning techniques. We find that our multigrid-Schwarz preconditioned elliptic solves achieve iteration counts that are independent of resolution, and our task-based parallel programs scale over 200 million degrees of freedom to at least a few thousand cores. Our new code solves a classic black-hole binary initial-data problem faster than the spectral code SpEC when distributed to only eight cores, and in a fraction of the time on more cores. It is publicly accessible in the next-generation SpECTRE numerical relativity code. Our results pave the way for highly-parallel elliptic solves in numerical relativity and beyond.Comment: 24 pages, 18 figures. Results are reproducible with the ancillary input file

A Path Toward the Use of Trail Users’ Tweets to Assess Effectiveness of the Environmental Stewardship Scheme: An Exploratory Analysis of the Pennine Way National Trail

Large and unofficial data sets, for instance those gathered from social media, are increasingly being used in geographical research and explored as decision support tools for policy development. Social media data have the potential to provide new insight into phenomena about which there is little information from conventional sources. Within this context, this paper explores the potential of social media data to evaluate the aesthetic management of landscape. Specifically, this project utilises the perceptions of visitors to the Pennine Way National Trail, which passes through land managed under the Environmental Stewardship Scheme (ESS). The method analyses sentiment in trail users’ public Twitter messages (tweets) with the aim of assessing the extent to which the ESS maintains landscape character within the trail corridor. The method demonstrates the importance of filtering social media data to convert it into useful information. After filtering, the results are based on 161 messages directly related to the trail. Although small, this sample illustrates the potential for social media to be used as a cheap and increasingly abundant source of information. We suggest that social media data in this context should be seen as a resource that can complement, rather than replace, conventional data sources such as questionnaires and interviews. Furthermore, we provide guidance on how social media could be effectively used by conservation bodies, such as Natural England, which are charged with the management of areas of environmental value worldwide

An Adoption Framework for Mobile Augmented Reality Games: The Case of Pokémon Go

Pokémon Go was the first mobile augmented reality (AR) game to reach the top of the download charts of mobile applications. However, little is known about this new generation of mobile online AR games. Existing theories provide limited applicability for user understanding. Against this background, this research provides a comprehensive framework based on uses and gratification theory, technology risk research, and flow theory. The proposed framework aims to explain the drivers of attitudinal and intentional reactions, such as continuance in gaming or willingness to invest money in in-app purchases. A survey among 642 Pokémon Go players provides insights into the psychological drivers of mobile AR games. The results show that hedonic, emotional, and social benefits and social norms drive consumer reactions while physical risks (but not data privacy risks) hinder consumer reactions. However, the importance of these drivers differs depending on the form of user behavior

Open access transport models: A leverage point in sustainable transport planning

A large and growing body of evidence suggests fundamental changes are needed in transport systems, to tackle issues such as air pollution, physical inactivity and climate change. Transport models can play a major role in tackling these issues through the transport planning process, but they have historically been focussed on motorised modes (especially cars) and available only to professional transport planners working within the existing paradigm. Building on the principles of open access software, first developed in the context of geographic information systems, this paper develops and discusses the concept of open access transport models, which we define as models that are both developed using open source software and are available to be used by the public without the need for specialist training or the purchase of software licences. We explore the future potential of open access transport models to support the transition away from fossil fuels in the transport sector. We do this with reference to the literature on the use of tools in the planning process, and by exploring an example that is already in use: the ‘Propensity to Cycle Tool’. We conclude that open access transport models can be a leverage point in the planning process due to their ability to provide robust, transparent and actionable evidence that is available to a range of stakeholders, not just professional transport planners. Open access transport models represent a disruptive technology deserving further research and development, by planners, researchers and citizen scientists, including open source software developers and advocacy groups but, in order to fulfil their potential, they will require both financial and policy support from government bodies

Conformational changes during pore formation by the perforin-related protein pleurotolysin

Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ~70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function

On the assessment of landmark salience for human navigation

In this paper, we propose a conceptual framework for assessing the salience of landmarks for navigation. Landmark salience is derived as a result of the observer’s point of view, both physical and cognitive, the surrounding environment, and the objects contained therein. This is in contrast to the currently held view that salience is an inherent property of some spatial feature. Salience, in our approach, is expressed as a three-valued Saliency Vector. The components that determine this vector are Perceptual Salience, which defines the exogenous (or passive) potential of an object or region for acquisition of visual attention, Cognitive Salience, which is an endogenous (or active) mode of orienting attention, triggered by informative cues providing advance information about the target location, and Contextual Salience, which is tightly coupled to modality and task to be performed. This separation between voluntary and involuntary direction of visual attention in dependence of the context allows defining a framework that accounts for the interaction between observer, environment, and landmark. We identify the low-level factors that contribute to each type of salience and suggest a probabilistic approach for their integration. Finally, we discuss the implications, consider restrictions, and explore the scope of the framework

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies