2,942 research outputs found
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
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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 for
the -state Potts antiferromagnet on families of cyclic and twisted cyclic
(M\"obius) strip graphs composed of -sided polygons. Our results suggest a
general rule concerning the maximal region in the complex plane to which
one can analytically continue from the physical interval where . The
chromatic zeros and their accumulation set exhibit the rather
unusual property of including support for 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, , 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, , of nonanalyticities in . 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 .Comment: 27 pages, Latex, 17 figs. J. Phys. A, in pres
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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 as the chromatic polynomial for coloring an -vertex
graph with colors, and considering the limiting function , a fundamental question in graph theory is the
following: is analytic or not at the origin
of the plane? (where the complex generalization of is assumed). This
question is also relevant in statistical mechanics because
, where is the ground state entropy of the
-state Potts antiferromagnet on the lattice graph , and the
analyticity of at is necessary for the large- series
expansions of . Although is analytic at for many
, there are some for which it is not; for these, has no
large- 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 is analytic at and explains the
nonanalyticity where it occurs. We also construct infinite families of graphs
with functions that are non-analytic at and investigate the
properties of these functions. Our results are consistent with the conjecture
that a sufficient condition for to be analytic at is
that is a regular lattice graph . (This is known not to be a
necessary condition).Comment: 22 pages, Revtex, 4 encapsulated postscript figures, to appear in
Phys. Rev.
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