An asymptotic sampling formula for the coalescent with Recombination

Ewens sampling formula (ESF) is a one-parameter family of probability distributions with a number of intriguing combinatorial connections. This elegant closed-form formula first arose in biology as the stationary probability distribution of a sample configuration at one locus under the infinite-alleles model of mutation. Since its discovery in the early 1970s, the ESF has been used in various biological applications, and has sparked several interesting mathematical generalizations. In the population genetics community, extending the underlying random-mating model to include recombination has received much attention in the past, but no general closed-form sampling formula is currently known even for the simplest extension, that is, a model with two loci. In this paper, we show that it is possible to obtain useful closed-form results in the case the population-scaled recombination rate $\rho$ is large but not necessarily infinite. Specifically, we consider an asymptotic expansion of the two-locus sampling formula in inverse powers of $\rho$ and obtain closed-form expressions for the first few terms in the expansion. Our asymptotic sampling formula applies to arbitrary sample sizes and configurations.Comment: Published in at http://dx.doi.org/10.1214/09-AAP646 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Past plant use in Jordan as revealed by archaeological and ethnoarchaeological phytolith signatures

Ninety-six phytolith samples were analysed from seven archaeological sites ranging from the Pre-Pottery Neolithic to the Classical period and from two ethnoarchaeological sites in Jordan. The aims were to test the possibility of detecting past irrigation with the methodology outlined by Madella et al. (2009) and Jenkins et al. (Chapter 21, this volume) and to study the contextual and temporal variation of plant use in Jordan. We utilised a water availability index using the proportion of phytolith types and ordination statistical methods to explore the similarities between the phytolith assemblages. The result of applying the irrigation methodology was promising, with contexts from water channels showing the greatest indication of water availability. Changes in plant use through time were also apparent with regard to phytolith densities and taxonomy. Date palm was identified in the Pottery Neolithic, providing one of the earliest records for this taxon in Jordan. This study shows the potential of both the water availability index and the value of inter-site comparison of phytolith assemblages

Dendritic cells activated with products released by schistosome larvae drive Th2-type immune responses, which can be inhibited by manipulation of CD40 costimulation

The early immune events in response to infective larvae of the parasitic helminth Schistosoma mansoni are poorly understood, but here for the first time we report on the potential of products released by schistosome larvae (material released in the first 3 It after transformation [0-3hRP]) to stimulate the maturation of dendritic cells (DC) and alter their T-cell-polarizing function. This was performed in comparison with lipopolysaccharide (LPS) and zymosan A, which classically activate DC to prime for Th1- and Th2-type responses, respectively. In our study, immature bone marrow-derived DC stimulated in vitro with 0-3hRP exhibited up-regulated expression of major histocompatibility complex class II, CD40, and CD86 and increased production of interleukin 12p40 (IL-12p40) and IL-6, albeit at lower levels than in response to LPS or zymosan A. Using an in vitro ovalbumin peptide-restricted priming assay, DC matured with 0-3hRP exhibited a potent capacity to drive Th2 polarization of CD4(+) cells from DO11.10 transgenic mice. This was characterized by increased IL-4 production (but not gamma interferon) of a magnitude similar to that primed by DC matured with zymosan A. Inoculation of DO11.10 mice with 0-3hRP-activated DC pulsed with ovalbumin peptide also led to the development of a Th2-type polarized response in the skin-draining lymph nodes and spleen. However, ligation of CD40 on DC by anti-CD40 antibody treatment reversed the ability of 0-3hRP-activated DC to prime for Th2-type responses and instead caused the induction of a more Th1-type response

Tractable diffusion and coalescent processes for weakly correlated loci

Widely used models in genetics include the Wright-Fisher diffusion and its moment dual, Kingman's coalescent. Each has a multilocus extension but under neither extension is the sampling distribution available in closed-form, and their computation is extremely difficult. In this paper we derive two new multilocus population genetic models, one a diffusion and the other a coalescent process, which are much simpler than the standard models, but which capture their key properties for large recombination rates. The diffusion model is based on a central limit theorem for density dependent population processes, and we show that the sampling distribution is a linear combination of moments of Gaussian distributions and hence available in closed-form. The coalescent process is based on a probabilistic coupling of the ancestral recombination graph to a simpler genealogical process which exposes the leading dynamics of the former. We further demonstrate that when we consider the sampling distribution as an asymptotic expansion in inverse powers of the recombination parameter, the sampling distributions of the new models agree with the standard ones up to the first two orders.Comment: 34 pages, 1 figur

Aspects of Nucleon Chiral Perturbation Theory

I review recent progress made in the calculation of nucleon properties in the framework of heavy baryon CHPT. Topics include: Compton scattering, $\pi N$ scattering, the anatomy of a low-energy constant and the induced pseudoscalar form factor.Comment: plain TeX (macro included), 12pp, lecture delivered at the workshop on "Chiral Dynamics: Theory and Experiments", MIT, July 25-29, 199

Multiplexed Memory-Insensitive Quantum Repeaters

Long-distance quantum communication via distant pairs of entangled quantum bits (qubits) is the first step towards more secure message transmission and distributed quantum computing. To date, the most promising proposals require quantum repeaters to mitigate the exponential decrease in communication rate due to optical fiber losses. However, these are exquisitely sensitive to the lifetimes of their memory elements. We propose a multiplexing of quantum nodes that should enable the construction of quantum networks that are largely insensitive to the coherence times of the quantum memory elements.Comment: 5 pages, 4 figures. Accepted for publication in PR

Hilbert Series for Flavor Invariants of the Standard Model

The Hilbert series is computed for the lepton flavor invariants of the Standard Model with three generations including the right-handed neutrino sector needed to generate light neutrino masses via the see-saw mechanism. We also compute the Hilbert series of the quark flavor invariants for the case of four generations.Comment: 6 page

Addressing Ethical Issues in Studying Men’s Traumatic Stress

Like many human experiences, traumatic stress is highly gendered. Over the past several decades, a sub-stantial number of empirical studies have explored ethical issues in traumatic stress research. However, these studies have typically reported female samples or failed to account for the influence of gender in their analyses of mixed-sex samples. By extension, ethical issues that are relevant to male participants in traumatic stress research are poorly understood. After briefly exploring why the vulnerabilities of male participants are under-explored in traumatic stress research, this article highlights many ethical issues that are important to address when men participate in traumatic stress research, concluding with some sugges-tions for how these might be taken up to advance the field

Microwave radiometric studies and ground truth measurements of the NASA/USGS Southern California test site

The field measurement program conducted at the NASA/USGS Southern California Test Site is discussed. Ground truth data and multifrequency microwave brightness data were acquired by a mobile field laboratory operating in conjunction with airborne instruments. The ground based investigations were performed at a number of locales representing a variety of terrains including open desert, cultivated fields, barren fields, portions of the San Andreas Fault Zone, and the Salton Sea. The measurements acquired ground truth data and microwave brightness data at wavelengths of 0.8 cm, 2.2 cm, and 21 cm