Mining whole sample mass spectrometry proteomics data for biomarkers: an overview

In this paper we aim to provide a concise overview of designing and conducting an MS proteomics experiment in such a way as to allow statistical analysis that may lead to the discovery of novel biomarkers. We provide a summary of the various stages that make up such an experiment, highlighting the need for experimental goals to be decided upon in advance. We discuss issues in experimental design at the sample collection stage, and good practise for standardising protocols within the proteomics laboratory. We then describe approaches to the data mining stage of the experiment, including the processing steps that transform a raw mass spectrum into a useable form. We propose a permutation-based procedure for determining the significance of reported error rates. Finally, because of its general advantages in speed and cost, we suggest that MS proteomics may be a good candidate for an early primary screening approach to disease diagnosis, identifying areas of risk and making referrals for more specific tests without necessarily making a diagnosis in its own right. Our discussion is illustrated with examples drawn from experiments on bovine blood serum conducted in the Centre for Proteomic Research (CPR) at Southampton University

A cycle-based evolutionary algorithm for the fixed-charge capacitated multi-commodity network design problem

This paper presents an evolutionary algorithm for the fixed-charge multicommodity network design problem (MCNDP), which concerns routing multiple commodities from origins to destinations by designing a network through selecting arcs, with an objective of minimizing the fixed costs of the selected arcs plus the variable costs of the flows on each arc. The proposed algorithm evolves a pool of solutions using principles of scatter search, interlinked with an iterated local search as an improvement method. New cycle-based neighborhood operators are presented which enable complete or partial re-routing of multiple commodities. An efficient perturbation strategy, inspired by ejection chains, is introduced to perform local compound cycle-based moves to explore different parts of the solution space. The algorithm also allows infeasible solutions violating arc capacities while performing the "ejection cycles", and subsequently restores feasibility by systematically applying correction moves. Computational experiments on benchmark MCNDP instances show that the proposed solution method consistently produces high-quality solutions in reasonable computational times

Potts-Percolation-Gauss Model of a Solid

We study a statistical mechanics model of a solid. Neighboring atoms are connected by Hookian springs. If the energy is larger than a threshold the "spring" is more likely to fail, while if the energy is lower than the threshold the spring is more likely to be alive. The phase diagram and thermodynamic quantities, such as free energy, numbers of bonds and clusters, and their fluctuations, are determined using renormalization-group and Monte-Carlo techniques.Comment: 10 pages, 12 figure

Ground State Entropy of the Potts Antiferromagnet on Cyclic Strip Graphs

We present exact calculations of the zero-temperature partition function (chromatic polynomial) and the (exponent of the) ground-state entropy $S_0$ for the $q$-state Potts antiferromagnet on families of cyclic and twisted cyclic (M\"obius) strip graphs composed of $p$-sided polygons. Our results suggest a general rule concerning the maximal region in the complex $q$ plane to which one can analytically continue from the physical interval where $S_0 > 0$. The chromatic zeros and their accumulation set ${\cal B}$ exhibit the rather unusual property of including support for $Re(q) < 0$ and provide further evidence for a relevant conjecture.Comment: 7 pages, Latex, 4 figs., J. Phys. A Lett., in pres

Mean Field Renormalization Group for the Boundary Magnetization of Strip Clusters

We analyze in some detail a recently proposed transfer matrix mean field approximation which yields the exact critical point for several two dimensional nearest neighbor Ising models. For the square lattice model we show explicitly that this approximation yields not only the exact critical point, but also the exact boundary magnetization of a semi--infinite Ising model, independent of the size of the strips used. Then we develop a new mean field renormalization group strategy based on this approximation and make connections with finite size scaling. Applying our strategy to the quadratic Ising and three--state Potts models we obtain results for the critical exponents which are in excellent agreement with the exact ones. In this way we also clarify some advantages and limitations of the mean field renormalization group approach.Comment: 16 pages (plain TeX) + 8 figures (PostScript, appended), POLFIS-TH.XX/9

Ground State Entropy of Potts Antiferromagnets on Cyclic Polygon Chain Graphs

We present exact calculations of chromatic polynomials for families of cyclic graphs consisting of linked polygons, where the polygons may be adjacent or separated by a given number of bonds. From these we calculate the (exponential of the) ground state entropy, $W$, for the q-state Potts model on these graphs in the limit of infinitely many vertices. A number of properties are proved concerning the continuous locus, ${\cal B}$, of nonanalyticities in $W$. Our results provide further evidence for a general rule concerning the maximal region in the complex q plane to which one can analytically continue from the physical interval where $S_0 > 0$.Comment: 27 pages, Latex, 17 figs. J. Phys. A, in pres

Avoiding a bad apple: insect pollination enhances fruit quality and economic value

Insect pollination is important for food production globally and apples are one of the major fruit crops which are reliant on this ecosystem service. It is fundamentally important that the full range of benefits of insect pollination to crop production are understood, if the costs of interventions aiming to enhance pollination are to be compared against the costs of the interventions themselves. Most previous studies have simply assessed the benefits of pollination to crop yield and ignored quality benefits and how these translate through to economic values. In the present study we examine the influence of insect pollination services on farmgate output of two important UK apple varieties; Gala and Cox. Using field experiments, we quantify the influence of insect pollination on yield and importantly quality and whether either may be limited by sub-optimal insect pollination. Using an expanded bioeconomic model we value insect pollination to UK apple production and establish the potential for improvement through pollination service management. We show that insects are essential in the production of both varieties of apple in the UK and contribute a total of £36.7 million per annum, over £6 million more than the value calculated using more conventional dependence ratio methods. Insect pollination not only affects the quantity of production but can also have marked impacts on the quality of apples, influencing size, shape and effecting their classification for market. These effects are variety specific however. Due to the influence of pollination on both yield and quality in Gala, there is potential for insect pollination services to improve UK output by up to £5.7 million per annum. Our research shows that continued pollinator decline could have serious financial implications for the apple industry but there is considerable scope through management of wild pollinators or using managed pollinator augmentation, to improve the quality of production. Furthermore, we show that it is critically important to consider all production parameters including quality, varietal differences and management costs when valuing the pollination service of any crop so investment in pollinator management can be proportional to its contribution

Exact sampling from non-attractive distributions using summary states

Propp and Wilson's method of coupling from the past allows one to efficiently generate exact samples from attractive statistical distributions (e.g., the ferromagnetic Ising model). This method may be generalized to non-attractive distributions by the use of summary states, as first described by Huber. Using this method, we present exact samples from a frustrated antiferromagnetic triangular Ising model and the antiferromagnetic q=3 Potts model. We discuss the advantages and limitations of the method of summary states for practical sampling, paying particular attention to the slowing down of the algorithm at low temperature. In particular, we show that such a slowing down can occur in the absence of a physical phase transition.Comment: 5 pages, 6 EPS figures, REVTeX; additional information at http://wol.ra.phy.cam.ac.uk/mackay/exac

Families of Graphs with W_r({G},q) Functions That Are Nonanalytic at 1/q=0

Denoting $P(G,q)$ as the chromatic polynomial for coloring an $n$-vertex graph $G$ with $q$ colors, and considering the limiting function $W(\{G\},q) = \lim_{n \to \infty}P(G,q)^{1/n}$, a fundamental question in graph theory is the following: is $W_r(\{G\},q) = q^{-1}W(\{G\},q)$ analytic or not at the origin of the $1/q$ plane? (where the complex generalization of $q$ is assumed). This question is also relevant in statistical mechanics because $W(\{G\},q)=\exp(S_0/k_B)$, where $S_0$ is the ground state entropy of the $q$-state Potts antiferromagnet on the lattice graph $\{G\}$, and the analyticity of $W_r(\{G\},q)$ at $1/q=0$ is necessary for the large-$q$ series expansions of $W_r(\{G\},q)$. Although $W_r$ is analytic at $1/q=0$ for many $\{G\}$, there are some $\{G\}$ for which it is not; for these, $W_r$ has no large-$q$ series expansion. It is important to understand the reason for this nonanalyticity. Here we give a general condition that determines whether or not a particular $W_r(\{G\},q)$ is analytic at $1/q=0$ and explains the nonanalyticity where it occurs. We also construct infinite families of graphs with $W_r$ functions that are non-analytic at $1/q=0$ and investigate the properties of these functions. Our results are consistent with the conjecture that a sufficient condition for $W_r(\{G\},q)$ to be analytic at $1/q=0$ is that $\{G\}$ is a regular lattice graph $\Lambda$. (This is known not to be a necessary condition).Comment: 22 pages, Revtex, 4 encapsulated postscript figures, to appear in Phys. Rev.