Now the wars are over: The past, present and future of Scottish battlefields

Battlefield archaeology has provided a new way of appreciating historic battlefields. This paper provides a summary of the long history of warfare and conflict in Scotland which has given rise to a large number of battlefield sites. Recent moves to highlight the archaeological importance of these sites, in the form of Historic Scotland’s Battlefields Inventory are discussed, along with some of the problems associated with the preservation and management of these important cultural sites

PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.

Microbial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification. Analysis of shotgun sequenced environmental DNA, known as metagenomics, avoids amplification bias but generates fragmentary, non-overlapping sequence reads that cannot be clustered by existing OTU-finding methods. To circumvent these limitations, we developed PhylOTU, a computational workflow that identifies OTUs from metagenomic SSU-rRNA sequence data through the use of phylogenetic principles and probabilistic sequence profiles. Using simulated metagenomic data, we quantified the accuracy with which PhylOTU clusters reads into OTUs. Comparisons of PCR and shotgun sequenced SSU-rRNA markers derived from the global open ocean revealed that while PCR libraries identify more OTUs per sequenced residue, metagenomic libraries recover a greater taxonomic diversity of OTUs. In addition, we discover novel species, genera and families in the metagenomic libraries, including OTUs from phyla missed by analysis of PCR sequences. Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity

Diffusive behavior for randomly kicked Newtonian particles in a spatially periodic medium

We prove a central limit theorem for the momentum distribution of a particle undergoing an unbiased spatially periodic random forcing at exponentially distributed times without friction. The start is a linear Boltzmann equation for the phase space density, where the average energy of the particle grows linearly in time. Rescaling time, the momentum converges to a Brownian motion, and the position is its time-integral showing superdiffusive scaling with time $t^{3/2}$. The analysis has two parts: (1) to show that the particle spends most of its time at high energy, where the spatial environment is practically invisible; (2) to treat the low energy incursions where the motion is dominated by the deterministic force, with potential drift but where symmetry arguments cancel the ballistic behavior.Comment: 55 pages. Some typos corrected from previous versio

Active contractility in actomyosin networks

Contractile forces are essential for many developmental processes involving cell shape change and tissue deformation. Recent experiments on reconstituted actomyosin networks, the major component of the contractile machinery, have shown that active contractility occurs above a threshold motor concentration and within a window of crosslink concentration. We present a microscopic dynamic model that incorporates two essential aspects of actomyosin self-organization: the asymmetric load response of individual actin filaments and the correlated motor-driven events mimicking myosin-induced filament sliding. Using computer simulations we examine how the concentration and susceptibility of motors contribute to their collective behavior and interplay with the network connectivity to regulate macroscopic contractility. Our model is shown to capture the formation and dynamics of contractile structures and agree with the observed dependence of active contractility on microscopic parameters including the contractility onset. Cooperative action of load-resisting motors in a force-percolating structure integrates local contraction/buckling events into a global contractile state via an active coarsening process, in contrast to the flow transition driven by uncorrelated kicks of susceptible motors.Comment: 15 pages, 4 main figures, 4 supplementary figure

Teaching introductory undergraduate Physics using commercial video games

Commercial video games are increasingly using sophisticated physics simulations to create a more immersive experience for players. This also makes them a powerful tool for engaging students in learning physics. We provide some examples to show how commercial off-the-shelf games can be used to teach specific topics in introductory undergraduate physics. The examples are selected from a course taught predominantly through the medium of commercial video games.Comment: Accepted to Physics Education, Fig1 does not render properly in this versio

Hard Instances of the Constrained Discrete Logarithm Problem

The discrete logarithm problem (DLP) generalizes to the constrained DLP, where the secret exponent $x$ belongs to a set known to the attacker. The complexity of generic algorithms for solving the constrained DLP depends on the choice of the set. Motivated by cryptographic applications, we study sets with succinct representation for which the constrained DLP is hard. We draw on earlier results due to Erd\"os et al. and Schnorr, develop geometric tools such as generalized Menelaus' theorem for proving lower bounds on the complexity of the constrained DLP, and construct sets with succinct representation with provable non-trivial lower bounds

Marked seasonal variation in the wild mouse gut microbiota

Recent studies have provided an unprecedented view of the microbial communities colonizing captive mice; yet the host and environmental factors that shape the rodent gut microbiota in their natural habitat remain largely unexplored. Here, we present results from a 2-year 16 S ribosomal RNA gene sequencing-based survey of wild wood mice (Apodemus sylvaticus) in two nearby woodlands. Similar to other mammals, wild mice were colonized by 10 bacterial phyla and dominated by the Firmicutes, Bacteroidetes and Proteobacteria. Within the Firmicutes, the Lactobacillus genus was most abundant. Putative bacterial pathogens were widespread and often abundant members of the wild mouse gut microbiota. Among a suite of extrinsic (environmental) and intrinsic (host-related) factors examined, seasonal changes dominated in driving qualitative and quantitative differences in the gut microbiota. In both years examined, we observed a strong seasonal shift in gut microbial community structure, potentially due to the transition from an insect- to a seed-based diet. This involved decreased levels of Lactobacillus, and increased levels of Alistipes (Bacteroidetes phylum) and Helicobacter. We also detected more subtle but statistically significant associations between the gut microbiota and biogeography, sex, reproductive status and co-colonization with enteric nematodes. These results suggest that environmental factors have a major role in shaping temporal variations in microbial community structure within natural populations

Dynamics of quantum dissipation systems interacting with Fermion and Boson grand canonical bath ensembles: Hierarchical equations of motion approach

A hierarchical equations of motion formalism for a quantum dissipation system in a grand canonical bath ensemble surrounding is constructed, on the basis of the calculus-on-path-integral algorithm, together with the parametrization of arbitrary non-Markovin bath that satisfies fluctuation-dissipation theorem. The influence functionals for both the Fermion or Boson bath interaction are found to be of the same path-integral expression as the canonical bath, assuming they all satisfy the Gaussian statistics. However, the equation of motion formalism are different, due to the fluctuation-dissipation theories that are distinct and used explicitly. The implications of the present work to quantum transport through molecular wires and electron transfer in complex molecular systems are discussed.Comment: 12page

Primary physical education, coaches and continuing professional development

This is an Author's Accepted Manuscript of an article published in Sport, Education and Society, 16(4), 485 - 505, 2011, copyright @ Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/13573322.2011.589645.Physical education (PE) in primary schools has traditionally been taught by qualified primary teachers. More recently, some teaching of PE in primary schools has been undertaken by coaches (mostly football coaches). These coaches hold national governing body awards but do not hold teaching qualifications. Thus, coaches may not be adequately prepared to teach PE in curriculum time. The purpose of this study was to evaluate the perceptions of a group of community-based football coaches working in primary schools for the impact of a Continuing Professional Development (CPD) programme on their ability to undertake ‘specified work’ to cover PE in primary schools. The programme focused on four areas identified as important to enable coaches to cover specified work: short- and medium-term planning, pedagogy, knowledge of the curriculum and reflection. Results showed that for the majority of coaches the CPD programme had made them more aware of the importance of these four areas and had helped to develop their knowledge and ability to put this into practice in covering planning, preparation and assessment time. However, further input is still required to develop coaches’ knowledge and understanding in all four areas, but especially their curriculum knowledge, as well as their ability to put these into practice consistently. These findings are discussed in relation to the implications of employing coaches to cover the teaching of PE in primary schools and, if employed, what CPD coaches need to develop the necessary knowledge, skill and understanding for covering specified work in schools