In-solution Y-chromosome capture-enrichment on ancient DNA libraries.

As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGC + YCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round

Magnetotunneling spectroscopy of mesoscopic correlations in two-dimensional electron systems

An approach to experimentally exploring electronic correlation functions in mesoscopic regimes is proposed. The idea is to monitor the mesoscopic fluctuations of a tunneling current flowing between the two layers of a semiconductor double-quantum-well structure. From the dependence of these fluctuations on external parameters, such as in-plane or perpendicular magnetic fields, external bias voltages, etc., the temporal and spatial dependence of various prominent correlation functions of mesoscopic physics can be determined. Due to the absence of spatially localized external probes, the method provides a way to explore the interplay of interaction and localization effects in two-dimensional systems within a relatively unperturbed environment. We describe the theoretical background of the approach and quantitatively discuss the behavior of the current fluctuations in diffusive and ergodic regimes. The influence of both various interaction mechanisms and localization effects on the current is discussed. Finally a proposal is made on how, at least in principle, the method may be used to experimentally determine the relevant critical exponents of localization-delocalization transitions.Comment: 15 pages, 3 figures include

Which Kubo formula gives the exact conductance of a mesoscopic disordered system?

In both research and textbook literature one often finds two ``different'' Kubo formulas for the zero-temperature conductance of a non-interacting Fermi system. They contain a trace of the product of velocity operators and single-particle (retarded and advanced) Green operators: $\text{Tr} (\hat{v}_x \hat{G}^r \hat{v}_x \hat{G}^a)$ or $\text{Tr} (\hat{v}_x \text{Im} \hat{G} \hat{v}_x \text{Im} \hat{G})$. The study investigates the relationship between these expressions, as well as the requirements of current conservation, through exact evaluation of such quantum-mechanical traces for a nanoscale (containing 1000 atoms) mesoscopic disordered conductor. The traces are computed in the semiclassical regime (where disorder is weak) and, more importantly, in the nonperturbative transport regime (including the region around localization-delocalization transition) where concept of mean free path ceases to exist. Since quantum interference effects for such strong disorder are not amenable to diagrammatic or nonlinear $\sigma$-model techniques, the evolution of different Green function terms with disorder strength provides novel insight into the development of an Anderson localized phase.Comment: 7 pages, 5 embedded EPS figures, final published version (note: PRB article has different title due to editorial censorship

Non Linear Current Response of a Many-Level Tunneling System: Higher Harmonics Generation

The fully nonlinear response of a many-level tunneling system to a strong alternating field of high frequency $\omega$ is studied in terms of the Schwinger-Keldysh nonequilibrium Green functions. The nonlinear time dependent tunneling current $I(t)$ is calculated exactly and its resonance structure is elucidated. In particular, it is shown that under certain reasonable conditions on the physical parameters, the Fourier component $I_{n}$ is sharply peaked at $n=\frac {\Delta E} {\hbar \omega}$, where $\Delta E$ is the spacing between two levels. This frequency multiplication results from the highly nonlinear process of $n$ photon absorption (or emission) by the tunneling system. It is also conjectured that this effect (which so far is studied mainly in the context of nonlinear optics) might be experimentally feasible.Comment: 28 pages, LaTex, 7 figures are available upon request from [email protected], submitted to Phys.Rev.

Heirloom rice in Ifugao: an ‘anti-commodity’ in the process of commodification

We analyse the marketing of ‘heirloom rices’ produced in the Cordillera mountains of northern Luzon, the Philippines, as the commodification of a historical ‘anti-commodity’. We contend that, historically, rice was produced for social, cultural and spiritual purposes but not primarily for sale or trade. The Ifugaos were able to sustain terraced wet-rice cultivation within a system of ‘escape agriculture’ because they were protected from Spanish interference by the friction of terrain and distance. ‘Heirloom rice’ is a boundary concept that enables social entrepreneurs to commodify traditional landraces. We analyse the implications for local rice production and conservation efforts.Templeton Foundatio

Measurements of Direct CP Violation, CPT Symmetry, and Other Parameters in the Neutral Kaon System

We present a series of measurements based on K -> pi+pi- and K -> pi0pi0 decays collected in 1996-1997 by the KTeV experiment (E832) at Fermilab. We compare these four K -> pipi decay rates to measure the direct CP violation parameter Re(e'/e) = (20.7 +- 2.8) x 10^-4. We also test CPT symmetry by measuring the relative phase between the CP violating and CP conserving decay amplitudes for K->pi+pi- (phi+-) and for K -> pi0pi0 (phi00). We find the difference between the relative phases to be Delta-phi = phi00 - phi+- = (+0.39 +- 0.50) degrees and the deviation of phi+- from the superweak phase to be phi+- - phi_SW =(+0.61 +- 1.19) degrees; both results are consistent with CPT symmetry. In addition, we present new measurements of the KL-KS mass difference and KS lifetime: Delta-m = (5261 +- 15) x 10^6 hbar/s and tauS = (89.65 +- 0.07) x 10^-12 s.Comment: Submitted to Phys. Rev. D, August 6, 2002; 37 pages, 32 figure

Observation of a Narrow Resonance of Mass 2.46 GeV/c^2 Decaying to D_s^*+ pi^0 and Confirmation of the D_sJ^* (2317) State

Using 13.5 inverse fb of e+e- annihilation data collected with the CLEO II detector we have observed a narrow resonance in the Ds*+pi0 final state, with a mass near 2.46 GeV. The search for such a state was motivated by the recent discovery by the BaBar Collaboration of a narrow state at 2.32 GeV, the DsJ*(2317)+ that decays to Ds+pi0. Reconstructing the Ds+pi0 and Ds*+pi0 final states in CLEO data, we observe peaks in both of the corresponding reconstructed mass difference distributions, dM(Dspi0)=M(Dspi0)-M(Ds) and dM(Ds*pi0)=M(Ds*pi0)-M(Ds*), both of them at values near 350 MeV. We interpret these peaks as signatures of two distinct states, the DsJ*(2317)+ plus a new state, designated as the DsJ(2463)+. Because of the similar dM values, each of these states represents a source of background for the other if photons are lost, ignored or added. A quantitative accounting of these reflections confirms that both states exist. We have measured the mean mass differences = 350.0 +/- 1.2 [stat] +/- 1.0 [syst] MeV for the DsJ*(2317) state, and = 351.2 +/- 1.7 [stat] +/- 1.0 [syst] MeV for the new DsJ(2463)+ state. We have also searched, but find no evidence, for decays of the two states via the channels Ds*+gamma, Ds+gamma, and Ds+pi+pi-. The observations of the two states at 2.32 and 2.46 GeV, in the Ds+pi0 and Ds*+pi0 decay channels respectively, are consistent with their interpretations as (c anti-strange) mesons with orbital angular momentum L=1, and spin-parities of 0+ and 1+.Comment: 16 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, version to be published in Physical Review D; minor modifications and fixes to typographical errors, plus an added section on production properties. The main results are unchanged; they supersede those reported in hep-ex/030501

Measurement of the Charge Asymmetry in B→K∗(892)±π∓B\to K^* (892)^{\pm}\pi^{\mp}

We report on a search for a CP-violating asymmetry in the charmless hadronic decay B -> K*(892)+- pi-+, using 9.12 fb^-1 of integrated luminosity produced at \sqrt{s}=10.58 GeV and collected with the CLEO detector. We find A_{CP}(B -> K*(892)+- pi-+) = 0.26+0.33-0.34(stat.)+0.10-0.08(syst.), giving an allowed interval of [-0.31,0.78] at the 90% confidence level.Comment: 7 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, submitted to PR

Study of the q^2-Dependence of B --> pi ell nu and B --> rho(omega)ell nu Decay and Extraction of |V_ub|

We report on determinations of |Vub| resulting from studies of the branching fraction and q^2 distributions in exclusive semileptonic B decays that proceed via the b->u transition. Our data set consists of the 9.7x10^6 BBbar meson pairs collected at the Y(4S) resonance with the CLEO II detector. We measure B(B0 -> pi- l+ nu) = (1.33 +- 0.18 +- 0.11 +- 0.01 +- 0.07)x10^{-4} and B(B0 -> rho- l+ nu) = (2.17 +- 0.34 +0.47/-0.54 +- 0.41 +- 0.01)x10^{-4}, where the errors are statistical, experimental systematic, systematic due to residual form-factor uncertainties in the signal, and systematic due to residual form-factor uncertainties in the cross-feed modes, respectively. We also find B(B+ -> eta l+ nu) = (0.84 +- 0.31 +- 0.16 +- 0.09)x10^{-4}, consistent with what is expected from the B -> pi l nu mode and quark model symmetries. We extract |Vub| using Light-Cone Sum Rules (LCSR) for 0<= q^2<16 GeV^2 and Lattice QCD (LQCD) for 16 GeV^2 <= q^2 < q^2_max. Combining both intervals yields |Vub| = (3.24 +- 0.22 +- 0.13 +0.55/-0.39 +- 0.09)x10^{-3}$ for pi l nu, and |Vub| = (3.00 +- 0.21 +0.29/-0.35 +0.49/-0.38 +-0.28)x10^{-3} for rho l nu, where the errors are statistical, experimental systematic, theoretical, and signal form-factor shape, respectively. Our combined value from both decay modes is |Vub| = (3.17 +- 0.17 +0.16/-0.17 +0.53/-0.39 +-0.03)x10^{-3}.Comment: 45 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, submitted to PR

Observation of the Ξc+\Xi_c^+ Charmed Baryon Decays to Σ+K−π+\Sigma^+ K^-\pi^+, Σ+Kˉ∗0\Sigma^+ \bar{K}^{*0}, and ΛK−π+π+\Lambda K^-\pi^+\pi^+

We have observed two new decay modes of the charmed baryon $\Xi_c^+$ into $\Sigma^+ K^-\pi^+$ and $\Sigma^+ \bar{K}^{*0}$ using data collected with the CLEO II detector. We also present the first measurement of the branching fraction for the previously observed decay mode $\Xi_c^+\to\Lambda K^-\pi^+\pi^+$. The branching fractions for these three modes relative to $\Xi_c^+\to\Xi^-\pi^+\pi^+$ are measured to be $1.18 \pm 0.26 \pm 0.17$, $0.92 \pm 0.27 \pm 0.14$, and $0.58 \pm 0.16 \pm 0.07$, respectively.Comment: 12 page uuencoded postscript file, postscript file also available through http://w4.lns.cornell.edu/public/CLN