FALCON: a software package for analysis of nestedness in bipartite networks

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Nestedness is a statistical measure used to interpret bipartite interaction data in several ecological and evolutionary contexts, e.g. biogeography (species-site relationships) and species interactions (plant-pollinator and host-parasite networks). Multiple methods have been used to evaluate nestedness, which differ in how the metrics for nestedness are determined. Furthermore, several different null models have been used to calculate statistical significance of nestedness scores. The profusion of measures and null models, many of which give conflicting results, is problematic for comparison of nestedness across different studies. We developed the FALCON software package to allow easy and efficient comparison of nestedness scores and statistical significances for a given input network, using a selection of the more popular measures and null models from the current literature. FALCON currently includes six measures and five null models for nestedness in binary networks, and two measures and four null models for nestedness in weighted networks. The FALCON software is designed to be efficient and easy to use. FALCON code is offered in three languages (R, MATLAB, Octave) and is designed to be modular and extensible, enabling users to easily expand its functionality by adding further measures and null models. FALCON provides a robust methodology for comparing the strength and significance of nestedness in a given bipartite network using multiple measures and null models. It includes an “adaptive ensemble” method to reduce undersampling of the null distribution when calculating statistical significance. It can work with binary or weighted input networks. FALCON is a response to the proliferation of different nestedness measures and associated null models in the literature. It allows easy and efficient calculation of nestedness scores and statistical significances using different methods, enabling comparison of results from different studies and thereby supporting theoretical study of the causes and implications of nestedness in different biological contexts

On Approximation of the Eigenvalues of Perturbed Periodic Schrodinger Operators

This paper addresses the problem of computing the eigenvalues lying in the gaps of the essential spectrum of a periodic Schrodinger operator perturbed by a fast decreasing potential. We use a recently developed technique, the so called quadratic projection method, in order to achieve convergence free from spectral pollution. We describe the theoretical foundations of the method in detail, and illustrate its effectiveness by several examples.Comment: 17 pages, 2 tables and 2 figure

The response of perennial and temporary headwater stream invertebrate communities to hydrological extremes

The headwaters of karst rivers experience considerable hydrological variability, including spates and streambed drying. Extreme summer flooding on the River Lathkill (Derbyshire, UK) provided the opportunity to examine the invertebrate community response to unseasonal spate flows, flow recession and, at temporary sites, streambed drying. Invertebrates were sampled at sites with differing flow permanence regimes during and after the spates. Following streambed drying at temporary sites, dewatered surface sediments were investigated as a refugium for aquatic invertebrates. Experimental rehydration of these dewatered sediments was conducted to promote development of desiccation-tolerant life stages. At perennial sites, spate flows reduced invertebrate abundance and diversity, whilst at temporary sites, flow reactivation facilitated rapid colonisation of the surface channel by a limited number of invertebrate taxa. Following streambed drying, 38 taxa were recorded from the dewatered and rehydrated sediments, with Oligochaeta being the most abundant taxon and Chironomidae (Diptera) the most diverse. Experimental rehydration of dewatered sediments revealed the presence of additional taxa, including Stenophylax sp. (Trichoptera: Limnephilidae) and Nemoura sp. (Plecoptera: Nemouridae). The influence of flow permanence on invertebrate community composition was apparent despite the aseasonal high-magnitude flood events

A new approach to the "apparent survival" problem: Estimating true survival rates from mark-recapture studies

Survival estimates generated from live capture-mark-recapture studies may be negatively biased due to the permanent emigration of marked individuals from the study area. In the absence of a robust analytical solution, researchers typically sidestep this problem by simply reporting estimates using the term "apparent survival." Here, we present a hierarchical Bayesian multistate model designed to estimate true survival by accounting for predicted rates of permanent emigration. Initially we use dispersal kernels to generate spatial projections of dispersal probability around each capture location. From these projections, we estimate emigration probability for each marked individual and use the resulting values to generate bias-adjusted survival estimates from individual capture histories. When tested using simulated data sets featuring variable detection probabilities, survival rates, and dispersal patterns, the model consistently eliminated negative biases shown by apparent survival estimates from standard models. When applied to a case study concerning juvenile survival in the endangered Cape Sable Seaside Sparrow (Ammodramus maritimus mirabilis), bias-adjusted survival estimates increased more than twofold above apparent survival estimates. Our approach is applicable to any capture-mark-recapture study design and should be particularly valuable for organisms with dispersive juvenile life stages.James J. Gilroy, Thomas Virzi, Rebecca L. Boulton, and Julie L. Lockwoo

Development of Stresses in Cohesionless Poured Sand

The pressure distribution beneath a conical sandpile, created by pouring sand from a point source onto a rough rigid support, shows a pronounced minimum below the apex (`the dip'). Recent work of the authors has attempted to explain this phenomenon by invoking local rules for stress propagation that depend on the local geometry, and hence on the construction history, of the medium. We discuss the fundamental difference between such approaches, which lead to hyperbolic differential equations, and elastoplastic models, for which the equations are elliptic within any elastic zones present .... This displacement field appears to be either ill-defined, or defined relative to a reference state whose physical existence is in doubt. Insofar as their predictions depend on physical factors unknown and outside experimental control, such elastoplastic models predict that the observations should be intrinsically irreproducible .... Our hyperbolic models are based instead on a physical picture of the material, in which (a) the load is supported by a skeletal network of force chains ("stress paths") whose geometry depends on construction history; (b) this network is `fragile' or marginally stable, in a sense that we define. .... We point out that our hyperbolic models can nonetheless be reconciled with elastoplastic ideas by taking the limit of an extremely anisotropic yield condition.Comment: 25 pages, latex RS.tex with rspublic.sty, 7 figures in Rsfig.ps. Philosophical Transactions A, Royal Society, submitted 02/9

Exploring the use of game making across the school curriculum

Computer games as part of education is a well-established topic for research, suggesting that creating games is linked to a range of cognitive and behavioural outcomes. Creating games in all subject disciplines is becoming increasingly possible due to the increasingly higher status of computing in schools across Europe and the prevalence of visual programming languages such as Scratch and Pocket Code. The use of games within education is not new; in a systematic review of 129 papers [1] found that playing games impacts across a range of areas including engagement, cognitive ability and, most commonly, knowledge acquisition and content understanding. However, while research has thus far examined game play and game based learning in education there is limited work focussing on the process of game creation as a method of classroom teaching. This is a prospect which is increasingly possible with the introduction of visual programming languages such as Scratch [2] and Pocket Code. It is suggested that playful learning through computer games could stimulate students’ intrinsic motivation ([3] and that knowledge creation can emerge through the construction of artefacts in a playful learning environment via the co-creation of games [4]. The research presented in this paper is from a pilot study examining the impact of game making in traditional primary and secondary school classrooms (5-18 years) in the United Kingdom (UK). The research, funded by Horizon 2020, is part of a wider European project; No-one Left Behind. In the UK the project has introduced game making into disciplines such as Religious Education, Science and History. Data indicates that although not all students found this a positive experience, computational thinking skills have increased, and students, disaffected with their learning, have re-engaged with learning, increasing their persistence and resulting in a deeper understanding of subject knowledge. In addition initial results suggest that game making has the potential to increase engagement with classroom learning and lead to increased learner satisfaction within lessons. Non-computing teachers have gained in confidence in developing game creation in their subject discipline, increasing their awareness of computational thinking. Barriers identified include teacher familiarity with programming as a means to teach non-STEM subject knowledge, a potential to decrease knowledge acquisition during the process of familiarisation with the teaching tool and a need for software developers to consider design for children with SEND. The project is changing the learning environment and emerging pedagogy has been identified which will be shared in this paper. As a result of the study lesson resources have been created for teachers to use across disciplines which are now available via the project URL; these will be shared in this paper

On Non Commutative G2 structure

Using an algebraic orbifold method, we present non-commutative aspects of $G_2$ structure of seven dimensional real manifolds. We first develop and solve the non commutativity parameter constraint equations defining $G_2$ manifold algebras. We show that there are eight possible solutions for this extended structure, one of which corresponds to the commutative case. Then we obtain a matrix representation solving such algebras using combinatorial arguments. An application to matrix model of M-theory is discussed.Comment: 16 pages, Latex. Typos corrected, minor changes. Version to appear in J. Phys.A: Math.Gen.(2005

The effects of climatic fluctuations and extreme events on running water ecosystems

Most research on the effects of environmental change in freshwaters has focused on incremental changes in average conditions, rather than fluctuations or extreme events such as heatwaves, cold snaps, droughts, floods or wildfires, which may have even more profound consequences. Such events are commonly predicted to increase in frequency, intensity and duration with global climate change, with many systems being exposed to conditions with no recent historical precedent. We propose a mechanistic framework for predicting potential impacts of environmental fluctuations on running water ecosystems by scaling up effects of fluctuations from individuals to entire ecosystems. This framework requires integration of four key components: effects of the environment on individual metabolism, metabolic and biomechanical constraints on fluctuating species interactions, assembly dynamics of local food webs and mapping the dynamics of the meta-community onto ecosystem function. We illustrate the framework by developing a mathematical model of environmental fluctuations on dynamically assembling food webs. We highlight (currently limited) empirical evidence for emerging insights and theoretical predictions. For example, widely supported predictions about the effects of environmental fluctuations are: high vulnerability of species with high per capita metabolic demands such as large-bodied ones at the top of food webs; simplification of food web network structure and impaired energetic transfer efficiency; reduced resilience and top-down relative to bottom-up regulation of food web and ecosystem processes. We conclude by identifying key questions and challenges that need to be addressed to develop more accurate and predictive bio-assessments of the effects of fluctuations, and implications of fluctuations for management practices in an increasingly uncertain world