CONTEST : a Controllable Test Matrix Toolbox for MATLAB

Large, sparse networks that describe complex interactions are a common feature across a number of disciplines, giving rise to many challenging matrix computational tasks. Several random graph models have been proposed that capture key properties of real-life networks. These models provide realistic, parametrized matrices for testing linear system and eigenvalue solvers. CONTEST (CONtrollable TEST matrices) is a random network toolbox for MATLAB that implements nine models. The models produce unweighted directed or undirected graphs; that is, symmetric or unsymmetric matrices with elements equal to zero or one. They have one or more parameters that affect features such as sparsity and characteristic pathlength and all can be of arbitrary dimension. Utility functions are supplied for rewiring, adding extra shortcuts and subsampling in order to create further classes of networks. Other utilities convert the adjacency matrices into real-valued coefficient matrices for naturally arising computational tasks that reduce to sparse linear system and eigenvalue problems

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with less changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: 1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation, and 2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.Comment: 14 pages, 8 figures, to be published in PLoS Computational Biolog

Subgraphs and network motifs in geometric networks

Many real-world networks describe systems in which interactions decay with the distance between nodes. Examples include systems constrained in real space such as transportation and communication networks, as well as systems constrained in abstract spaces such as multivariate biological or economic datasets and models of social networks. These networks often display network motifs: subgraphs that recur in the network much more often than in randomized networks. To understand the origin of the network motifs in these networks, it is important to study the subgraphs and network motifs that arise solely from geometric constraints. To address this, we analyze geometric network models, in which nodes are arranged on a lattice and edges are formed with a probability that decays with the distance between nodes. We present analytical solutions for the numbers of all 3 and 4-node subgraphs, in both directed and non-directed geometric networks. We also analyze geometric networks with arbitrary degree sequences, and models with a field that biases for directed edges in one direction. Scaling rules for scaling of subgraph numbers with system size, lattice dimension and interaction range are given. Several invariant measures are found, such as the ratio of feedback and feed-forward loops, which do not depend on system size, dimension or connectivity function. We find that network motifs in many real-world networks, including social networks and neuronal networks, are not captured solely by these geometric models. This is in line with recent evidence that biological network motifs were selected as basic circuit elements with defined information-processing functions.Comment: 9 pages, 6 figure

The holy blood and the holy grail: Myths of scientific racism and the pursuit of excellence in sport

Despite the continuing publication of research that suggests there is no scientific basis to 'race' as a biological category, theories of racial difference continue to be invoked within sport to explain the perceived dominance of black athletes. In the case of John Entine's controversial 'Taboo: why black athletes dominate sports and why we are afraid to talk about it' or undergraduate textbooks that suggest 'racial differences' in physique may significantly affect athletic performance, scientific racism is normalised in sport. In this article, the relationship between scientific racism and sport will be examined. Qualitative research with current sport scientists is used to investigate the socio-ethical tensions within the subject field of sport science between professionalism, scientism and the demand from external interests to produce results that help people in sport win medals. It will be shown that these tensions, combined with the history of race as a category in sport science, combine to create the discourse of scientific knowledge that reflects, rather than challenges, folk genetics of black athletic physicality

The British Influence in the Birth of Spanish Sport

Sports started to gain relevance in Spain around the end of the nineteenth century and the beginning of the twentieth century as a leisure and health option of the upper classes imported from Britain. Its early development was intertwined with the spread of other kinds of physical activities with much more tradition on the continent: gymnastics and physical education. First played by the ruling classes – aristocracy and high bourgeoisie – sports permeated towards petty bourgeoisie and middle classes in urban areas such as Madrid, Barcelona, San Sebastián and Santander. This pattern meant that the expansion of sports was unavoidably tied to the degree of industrialisation and cultural modernisation of the country. Since 1910, and mainly during the 1920s, sport grew in popularity as a spectacle and, toa much lesser degree, as a practice among the Spanish population

Tunable SNAP Microresonators via Internal Ohmic Heating

We demonstrate a thermally tunable Surface Nanoscale Axial Photonics (SNAP) platform. Stable tuning is achieved by heating a SNAP structure fabricated on the surface of a silica capillary with a metal wire positioned inside. Heating a SNAP microresonator with a uniform wire introduces uniform variation of its effective radius which results in constant shift of its resonance wavelengths. Heating with a nonuniform wire allows local nanoscale variation of the capillary effective radius, which enables differential tuning of the spectrum of SNAP structures as well as creation of temporary SNAP microresonators that exist only when current is applied. As an example, we fabricate two bottle microresonators coupled to each other and demonstrate differential tuning of their resonance wavelengths into and out of degeneracy with precision better than 0.2 pm. The developed approach is beneficial for ultraprecise fabrication of tunable ultralow loss parity-time symmetric, optomechanical, and cavity QED devices

Differential Gene Expression Regulated by Oscillatory Transcription Factors

Cells respond to changes in the internal and external environment by a complex regulatory system whose end-point is the activation of transcription factors controlling the expression of a pool of ad-hoc genes. Recent experiments have shown that certain stimuli may trigger oscillations in the concentration of transcription factors such as NF-B and p53 influencing the final outcome of the genetic response. In this study we investigate the role of oscillations in the case of three different well known gene regulatory mechanisms using mathematical models based on ordinary differential equations and numerical simulations. We considered the cases of direct regulation, two-step regulation and feed-forward loops, and characterized their response to oscillatory input signals both analytically and numerically. We show that in the case of indirect two-step regulation the expression of genes can be turned on or off in a frequency dependent manner, and that feed-forward loops are also able to selectively respond to the temporal profile of oscillating transcription factors

VirtuWind: Virtual and programmable industrial network prototype deployed in operational wind park.

With anticipated exponential growth of connected devices, future industrial networks require an open solutions architecture facilitated by standards and a strong ecosystem. Such solutions should also deal with range of quality of service requirements imposed by industrial networks. Preserving strict quality of service is particularly challenging when services pass across domains of multiple provides. VirtuWind aims to develop and demonstrate a Software Defined Networking and Network Function Virtualization ecosystem, based on an open, modular and secure framework to address stringent requirements of the industrial networks. A prototype of the framework for intra-domain and inter-domain scenarios will be showcased in real Wind Parks, as a representative use case of industrial networks. This paper details this vision and explains steps forward

How Ants Use Vision When Homing Backward

Ants can navigate over long distances between their nest and food sites using visual cues [1, 2]. Recent studies show that this capacity is undiminished when walking backward while dragging a heavy food item [3, 4, 5]. This challenges the idea that ants use egocentric visual memories of the scene for guidance [1, 2, 6]. Can ants use their visual memories of the terrestrial cues when going backward? Our results suggest that ants do not adjust their direction of travel based on the perceived scene while going backward. Instead, they maintain a straight direction using their celestial compass. This direction can be dictated by their path integrator [5] but can also be set using terrestrial visual cues after a forward peek. If the food item is too heavy to enable body rotations, ants moving backward drop their food on occasion, rotate and walk a few steps forward, return to the food, and drag it backward in a now-corrected direction defined by terrestrial cues. Furthermore, we show that ants can maintain their direction of travel independently of their body orientation. It thus appears that egocentric retinal alignment is required for visual scene recognition, but ants can translate this acquired directional information into a holonomic frame of reference, which enables them to decouple their travel direction from their body orientation and hence navigate backward. This reveals substantial flexibility and communication between different types of navigational information: from terrestrial to celestial cues and from egocentric to holonomic directional memories