Time walkers and spatial dynamics of ageing information

The distribution of information is essential for living system's ability to coordinate and adapt. Random walkers are often used to model this distribution process and, in doing so, one effectively assumes that information maintains its relevance over time. But the value of information in social and biological systems often decay and must continuously be updated. To capture the spatial dynamics of ageing information, we introduce time walkers. A time walker moves like a random walker, but interacts with traces left by other walkers, some representing older information, some newer. The traces forms a navigable information landscape. We quantify the dynamical properties of time walkers moving on a two-dimensional lattice and the quality of the information landscape generated by their movements. We visualise the self-similar landscape as a river network, and show that searching in this landscape is superior to random searching and scales as the length of loop-erased random walks

Weighted distances in scale-free preferential attachment models

We study three preferential attachment models where the parameters are such that the asymptotic degree distribution has infinite variance. Every edge is equipped with a non-negative i.i.d. weight. We study the weighted distance between two vertices chosen uniformly at random, the typical weighted distance, and the number of edges on this path, the typical hopcount. We prove that there are precisely two universality classes of weight distributions, called the explosive and conservative class. In the explosive class, we show that the typical weighted distance converges in distribution to the sum of two i.i.d. finite random variables. In the conservative class, we prove that the typical weighted distance tends to infinity, and we give an explicit expression for the main growth term, as well as for the hopcount. Under a mild assumption on the weight distribution the fluctuations around the main term are tight.Comment: Revised version, results are unchanged. 30 pages, 1 figure. To appear in Random Structures and Algorithm

Gene Expression Pattern Analysis of Anterior Hox Genes during Zebrafish (Danio rerio) Embryonic Development Reveals Divergent Expression Patterns from Other Teleosts

The regional identity of organs and organ systems along the anterior-posterior axis during embryonic development is patterned, in part, by Hox genes, which encode transcription factor proteins that activate or repress the expression of downstream target genes. Divergent nested Hox gene expression patterns may have had a role in facilitating morphological divergence of structures, such as the pharyngeal jaw apparatus, among evolutionarily divergent teleost fishes. Recent studies from several evolutionarily divergent teleosts, such as the Japanese Medaka (Oryzias latipes) and the Nile Tilapia (Oreochromis niloticus), have shown the presence of divergent expression patterns of several Hox genes within paralog groups 2–5 between these species. Specifically, these expression patterns were documented in the pharyngeal arches, which give rise to the pharyngeal jaw apparatus. While the expression patterns of several Zebrafish (Danio rerio) Hox genes that are orthologous to those of Medaka and Tilapia have been documented within the developing hindbrain and pharyngeal arches, many still have yet to be documented, especially within the pharyngeal arches during the postmigratory cranial neural crest cell stages. Here, we present the expression patterns of six Zebrafish Hox genes, hoxc3a, d3a, a4a, d4a, b5a, and c5a, within the pharyngeal arches during a postmigratory cranial neural crest cell stage and compare them to their orthologous genes of Medaka and Tilapia at similar stages. We show that while hoxc3a, d3a, and c5a of Zebrafish are absent from the pharyngeal arches, hoxa4a, d4a, and b5a show divergent expression patterns from their orthologs in Medaka and Tilapia. These observed divergences may be, in part, responsible for the divergent pharyngeal jaw apparatus structures exhibited by these fishes

Together, yet still not equal? Sex integration in equestrian sport

Sex segregation is a core organising principle of most modern sports and is a key element in the marginalisation and subordination of girls and women in sport and beyond. In this article I explore the only Olympic-level sport which is not organised around sex segregation – equestrian sport – in order to consider the implications of sex integration for female participants. I draw on a study conducted on elite riders that found that although sex integration in equestrian sport does not lead to female participants being excluded from high-level competition, men continue to perform disproportionately well. This suggests that although sex integration may be an important step towards breaking down gender hierarchies in sport, without accompanying wider changes in gender norms and expectations, sex integration alone will not be enough to achieve greater gender equality in equestrian sport

Hidden geometric correlations in real multiplex networks

Real networks often form interacting parts of larger and more complex systems. Examples can be found in different domains, ranging from the Internet to structural and functional brain networks. Here, we show that these multiplex systems are not random combinations of single network layers. Instead, they are organized in specific ways dictated by hidden geometric correlations between the individual layers. We find that these correlations are strong in different real multiplexes, and form a key framework for answering many important questions. Specifically, we show that these geometric correlations facilitate: (i) the definition and detection of multidimensional communities, which are sets of nodes that are simultaneously similar in multiple layers; (ii) accurate trans-layer link prediction, where connections in one layer can be predicted by observing the hidden geometric space of another layer; and (iii) efficient targeted navigation in the multilayer system using only local knowledge, which outperforms navigation in the single layers only if the geometric correlations are sufficiently strong. Our findings uncover fundamental organizing principles behind real multiplexes and can have important applications in diverse domains.Comment: Supplementary Materials available at http://www.nature.com/nphys/journal/v12/n11/extref/nphys3812-s1.pd

Force correlations and arches formation in granular assemblies

In the context of a simple microscopic schematic scalar model we study the effects of spatial correlations in force transmission in granular assemblies. We show that the parameters of the normalized weights distribution function, $P(v)\sim v^{\alpha}\exp(-v/\phi)$, strongly depend on the spatial extensions, $\xi_V$, of such correlations. We show, then, the connections between measurable macroscopic quantities and microscopic mechanisms enhancing correlations. In particular we evaluate how the exponential cut-off, $\phi(\xi_V)$, and the small forces power law exponent, $\alpha(\xi_V)$, depend on the correlation length, $\xi_V$. If correlations go to infinity, weights are power law distributed.Comment: 6 page

FixingTIM: Interactive exploration of sequence and structural data to identify functional mutations in protein families

Background: Knowledge of the 3D structure and functionality of proteins can lead to insight into the associated cellular processes, speed up the creation of pharmaceutical products, and develop drugs that are more effective in combating disease. Methods: We present the design and implementation of a visual mining and analysis tool to help identify protein mutations across a family of structural models and to help discover the effect of these mutations on protein function. We integrate 3D structure and sequence information in a common visual interface; multiple linked views and a computational backbone allow comparison at the molecular and atomic levels, while a novel trend-image visual abstraction allows for the sorting and mining of large collections of sequences and of their residues. Results: We evaluate our approach on the triosephosphate isomerase (TIM) family structural models and sequence data and show that our tool provides an effective, scalable way to navigate a family of proteins, as well as a means to inspect the structure and sequence of individual proteins. Conclusions: The TIM application shows that our tool can assist in the navigation of families of proteins, as well as in the exploration of individual protein structures. In conjunction with domain expert knowledge, this interactive tool can help provide biophysical insight into why specific mutations affect function and potentially suggest additional modifications to the protein that could be used to rescue functionality

A flexible and efficient template format for circular consensus sequencing and SNP detection

A novel template design for single-molecule sequencing is introduced, a structure we refer to as a SMRTbell™ template. This structure consists of a double-stranded portion, containing the insert of interest, and a single-stranded hairpin loop on either end, which provides a site for primer binding. Structurally, this format resembles a linear double-stranded molecule, and yet it is topologically circular. When placed into a single-molecule sequencing reaction, the SMRTbell template format enables a consensus sequence to be obtained from multiple passes on a single molecule. Furthermore, this consensus sequence is obtained from both the sense and antisense strands of the insert region. In this article, we present a universal method for constructing these templates, as well as an application of their use. We demonstrate the generation of high-quality consensus accuracy from single molecules, as well as the use of SMRTbell templates in the identification of rare sequence variants

On the making and taking of professionalism in the further education workplace

This paper examines the changing nature of professional practice in English further education. At a time when neo-liberal reform has significantly impacted on this under-researched and over-market-tested sector, little is known about who its practitioners are and how they construct meaning in their work. Sociological interest in the field has tended to focus on further education practitioners as either the subjects of market and managerial reform or as creative agents operating within the contradictions of audit and inspection cultures. In challenging such dualism, which is reflective of wider sociological thinking, the paper examines the ways in which agency and structure combine to produce a more transformative conception of the further education professional. The approach contrasts with a prevailing policy discourse that seeks to re-professionalise and modernise further education practice without interrogating either the terms of its professionalism or the neo-liberal practices in which it resides

NEON terrestrial field observations: designing continental-scale, standardized sampling.

Rapid changes in climate and land use and the resulting shifts in species distributions and ecosystem functions have motivated the development of the National Ecological Observatory Network (NEON). Integrating across spatial scales from ground sampling to remote sensing, NEON will provide data for users to address ecological responses to changes in climate, land use, and species invasion across the United States for at least 30 years. Although NEON remote sensing and tower sensor elements are relatively well known, the biological measurements are not. This manuscript describes NEON terrestrial sampling, which targets organisms across a range of generation and turnover times, and a hierarchy of measurable biological states. Measurements encompass species diversity, abundance, phenology, demography, infectious disease, ecohydrology, and biogeochemistry. The continental-scale sampling requires collection of comparable and calibrated data using transparent methods. Data will be publicly available in a variety of formats and suitable for integration with other long-term efforts. NEON will provide users with the data necessary to address large-scale questions, challenge current ecological paradigms, and forecast ecological change