5,228 research outputs found
Descartes' rule of signs and the identifiability of population demographic models from genomic variation data
The sample frequency spectrum (SFS) is a widely-used summary statistic of
genomic variation in a sample of homologous DNA sequences. It provides a highly
efficient dimensional reduction of large-scale population genomic data and its
mathematical dependence on the underlying population demography is well
understood, thus enabling the development of efficient inference algorithms.
However, it has been recently shown that very different population demographies
can actually generate the same SFS for arbitrarily large sample sizes. Although
in principle this nonidentifiability issue poses a thorny challenge to
statistical inference, the population size functions involved in the
counterexamples are arguably not so biologically realistic. Here, we revisit
this problem and examine the identifiability of demographic models under the
restriction that the population sizes are piecewise-defined where each piece
belongs to some family of biologically-motivated functions. Under this
assumption, we prove that the expected SFS of a sample uniquely determines the
underlying demographic model, provided that the sample is sufficiently large.
We obtain a general bound on the sample size sufficient for identifiability;
the bound depends on the number of pieces in the demographic model and also on
the type of population size function in each piece. In the cases of
piecewise-constant, piecewise-exponential and piecewise-generalized-exponential
models, which are often assumed in population genomic inferences, we provide
explicit formulas for the bounds as simple functions of the number of pieces.
Lastly, we obtain analogous results for the "folded" SFS, which is often used
when there is ambiguity as to which allelic type is ancestral. Our results are
proved using a generalization of Descartes' rule of signs for polynomials to
the Laplace transform of piecewise continuous functions.Comment: Published in at http://dx.doi.org/10.1214/14-AOS1264 the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Understanding contextualised rational action - author's response
Understanding contextualised rational action - author's respons
A novel spectral method for inferring general diploid selection from time series genetic data
The increased availability of time series genetic variation data from
experimental evolution studies and ancient DNA samples has created new
opportunities to identify genomic regions under selective pressure and to
estimate their associated fitness parameters. However, it is a challenging
problem to compute the likelihood of nonneutral models for the population
allele frequency dynamics, given the observed temporal DNA data. Here, we
develop a novel spectral algorithm to analytically and efficiently integrate
over all possible frequency trajectories between consecutive time points. This
advance circumvents the limitations of existing methods which require
fine-tuning the discretization of the population allele frequency space when
numerically approximating requisite integrals. Furthermore, our method is
flexible enough to handle general diploid models of selection where the
heterozygote and homozygote fitness parameters can take any values, while
previous methods focused on only a few restricted models of selection. We
demonstrate the utility of our method on simulated data and also apply it to
analyze ancient DNA data from genetic loci associated with coat coloration in
horses. In contrast to previous studies, our exploration of the full fitness
parameter space reveals that a heterozygote advantage form of balancing
selection may have been acting on these loci.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS764 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Market regulation and firm performance: the case of smoking bans in the UK
This paper analyzes the effects of a ban on smoking in public places upon firms and
consumers. It presents a theoretical model and tests its predictions using unique data from
before and after the introduction of smoking bans in the UK. Cigarette smoke is a public bad,
and smokers and non-smokers differ in their valuation of smoke-free amenities. Consumer
heterogeneity implies that the market equilibrium may result in too much uniformity, whereas
social optimality requires a mix of smoking and non-smoking pubs (which can be
operationalized via licensing). If the market equilibrium has almost all pubs permitting
smoking (as is the case in the data) then a blanket ban reduces pub sales, profits, and
consumer welfare. We collect survey data from public houses and find that the Scottish
smoking ban (introduced in March 2006) reduced pub sales and harmed medium run
profitability. An event study analysis of the stock market performance of pub-holding
companies corroborates the negative effects of the smoking ban on firm performance
Holomorphic Bisectional Curvatures, Supersymmetry Breaking, and Affleck-Dine Baryogenesis
Working in supergravity, we utilize relations between holomorphic
sectional and bisectional curvatures of Kahler manifolds to constrain
Affleck-Dine baryogenesis. We show the following No-Go result: Affleck-Dine
baryogenesis cannot be performed if the holomorphic sectional curvature at the
origin is isotropic in tangent space; as a special case, this rules out spaces
of constant holomorphic sectional curvature (defined in the above sense) and in
particular maximally symmetric coset spaces. We also investigate scenarios
where inflationary supersymmetry breaking is identified with the supersymmetry
breaking responsible for mass splitting in the visible sector, using conditions
of sequestering to constrain manifolds where inflation can be performed.Comment: 9 page
Transverse Mass Distribution Characteristics of Production in Pb-induced Reactions and the Combinational Approach
The nature of invariant cross-sections and multiplicities in some
-induced reactions and some important ratio-behaviours of the
invariant multiplicities for various centralities of the collision will here be
dealt with in the light of a combinational approach which has been built up in
the recent past by the present authors. Next, the results would be compared
with the outcome of some of the simulation-based standard models for multiple
production in nuclear collisions at high energies. Finally, the implications of
all this would be discussed.Comment: 14 pages, 14 figures, a few changes have been made in the tex
Multiflow Transmission in Delay Constrained Cooperative Wireless Networks
This paper considers the problem of energy-efficient transmission in
multi-flow multihop cooperative wireless networks. Although the performance
gains of cooperative approaches are well known, the combinatorial nature of
these schemes makes it difficult to design efficient polynomial-time algorithms
for joint routing, scheduling and power control. This becomes more so when
there is more than one flow in the network. It has been conjectured by many
authors, in the literature, that the multiflow problem in cooperative networks
is an NP-hard problem. In this paper, we formulate the problem, as a
combinatorial optimization problem, for a general setting of -flows, and
formally prove that the problem is not only NP-hard but it is
inapproxmiable. To our knowledge*, these results provide
the first such inapproxmiablity proof in the context of multiflow cooperative
wireless networks. We further prove that for a special case of k = 1 the
solution is a simple path, and devise a polynomial time algorithm for jointly
optimizing routing, scheduling and power control. We then use this algorithm to
establish analytical upper and lower bounds for the optimal performance for the
general case of flows. Furthermore, we propose a polynomial time heuristic
for calculating the solution for the general case and evaluate the performance
of this heuristic under different channel conditions and against the analytical
upper and lower bounds.Comment: 9 pages, 5 figure
A Simple Testable Model of Baryon Number Violation: Baryogenesis, Dark Matter, Neutron-Antineutron Oscillation and Collider Signals
We study a simple TeV-scale model of baryon number violation which explains
the observed proximity of the dark matter and baryon abundances. The model has
constraints arising from both low and high-energy processes, and in particular,
predicts a sizable rate for the neutron-antineutron () oscillation
at low energy and the monojet signal at the LHC. We find an interesting
complementarity among the constraints arising from the observed baryon
asymmetry, ratio of dark matter and baryon abundances, oscillation
lifetime and the LHC monojet signal. There are regions in the parameter space
where the oscillation lifetime is found to be more constraining
than the LHC constraints, which illustrates the importance of the
next-generation oscillation experiments.Comment: 8 pages, 4 figures; minor changes, version to appear in Phys. Lett.
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