Gene-history correlation and population structure

Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.Comment: Revised and extended version: 26 pages, 5 figures, 1 tabl

Microsecond resolution of quasiparticle tunneling in the single-Cooper-pair-transistor

We present radio-frequency measurements on a single-Cooper-pair-transistor in which individual quasiparticle poisoning events were observed with microsecond temporal resolution. Thermal activation of the quasiparticle dynamics is investigated, and consequently, we are able to determine energetics of the poisoning and un-poisoning processes. In particular, we are able to assign an effective quasiparticle temperature to parameterize the poisoning rate.Comment: 4 pages, 4 fig

Inelastic collisions of ultra-cold heteronuclear molecules in an optical trap

Ultra-cold RbCs molecules in high-lying vibrational levels of the a$^3\Sigma^+$ ground electronic state are confined in an optical trap. Inelastic collision rates of these molecules with both Rb and Cs atoms are determined for individual vibrational levels, across an order of magnitude of binding energies. A simple model for the collision process is shown to accurately reproduce the observed scattering rates

Maximum-Likelihood Comparisons of Tully-Fisher and Redshift Data: Constraints on Omega and Biasing

We compare Tully-Fisher (TF) data for 838 galaxies within cz=3000 km/sec from the Mark III catalog to the peculiar velocity and density fields predicted from the 1.2 Jy IRAS redshift survey. Our goal is to test the relation between the galaxy density and velocity fields predicted by gravitational instability theory and linear biasing, and thereby to estimate $\beta_I = \Omega^{0.6}/b_I,$ where $b_I$ is the linear bias parameter for IRAS galaxies. Adopting the IRAS velocity and density fields as a prior model, we maximize the likelihood of the raw TF observables, taking into account the full range of selection effects and properly treating triple-valued zones in the redshift-distance relation. Extensive tests with realistic simulated galaxy catalogs demonstrate that the method produces unbiased estimates of $\beta_I$ and its error. When we apply the method to the real data, we model the presence of a small but significant velocity quadrupole residual (~3.3% of Hubble flow), which we argue is due to density fluctuations incompletely sampled by IRAS. The method then yields a maximum likelihood estimate $\beta_I=0.49\pm 0.07$ (1-sigma error). We discuss the constraints on $\Omega$ and biasing that follow if we assume a COBE-normalized CDM power spectrum. Our model also yields the 1-D noise noise in the velocity field, including IRAS prediction errors, which we find to be be 125 +/- 20 km/sec.Comment: 53 pages, 20 encapsulated figures, two tables. Submitted to the Astrophysical Journal. Also available at http://astro.stanford.edu/jeff

Galaxy Distances in the Nearby Universe: Corrections For Peculiar Motions

By correcting the redshift--dependent distances for peculiar motions through a number of peculiar velocity field models, we recover the true distances of a wide, all-sky sample of nearby galaxies (~ 6400 galaxies with velocities cz<5500 km/s), which is complete up to the blue magnitude B=14 mag. Relying on catalogs of galaxy groups, we treat ~2700 objects as members of galaxy groups and the remaining objects as field galaxies. We model the peculiar velocity field using: i) a cluster dipole reconstruction scheme; ii) a multi--attractor model fitted to the Mark II and Mark III catalogs of galaxy peculiar velocities. According to Mark III data the Great Attractor has a smaller influence on local dynamics than previously believed, whereas the Perseus-Pisces and Shapley superclusters acquire a specific dynamical role. Remarkably, the Shapley structure, which is found to account for nearly half the peculiar motion of the Local Group, is placed by Mark III data closer to the zone of avoidance with respect to its optical position. Our multi--attractor model based on Mark III data favors a cosmological density parameter Omega ~ 0.5 (irrespective of a biasing factor of order unity). Differences among distance estimates are less pronounced in the ~ 2000 - 4000 km/s distance range than at larger or smaller distances. In the last regions these differences have a serious impact on the 3D maps of the galaxy distribution and on the local galaxy density --- on small scales.Comment: 24 pages including (9 eps figures and 7 tables). Figures 1,2,3,4 are available only upon request. Accepted by Ap

Nearby Optical Galaxies: Selection of the Sample and Identification of Groups

In this paper we describe the Nearby Optical Galaxy (NOG) sample, which is a complete, distance-limited ($cz\leq$6000 km/s) and magnitude-limited (B$\leq$14) sample of $\sim$7000 optical galaxies. The sample covers 2/3 (8.27 sr) of the sky ($|b|>20^{\circ}$) and appears to have a good completeness in redshift (98%). We select the sample on the basis of homogenized corrected total blue magnitudes in order to minimize systematic effects in galaxy sampling. We identify the groups in this sample by means of both the hierarchical and the percolation {\it friends of friends} methods. The resulting catalogs of loose groups appear to be similar and are among the largest catalogs of groups presently available. Most of the NOG galaxies ($\sim$60%) are found to be members of galaxy pairs ($\sim$580 pairs for a total of $\sim$15% of objects) or groups with at least three members ($\sim$500 groups for a total of $\sim$45% of objects). About 40% of galaxies are left ungrouped (field galaxies). We illustrate the main features of the NOG galaxy distribution. Compared to previous optical and IRAS galaxy samples, the NOG provides a denser sampling of the galaxy distribution in the nearby universe. Given its large sky coverage, the identification of groups, and its high-density sampling, the NOG is suited for the analysis of the galaxy density field of the nearby universe, especially on small scales.Comment: 47 pages including 6 figures. Accepted for publication in Ap

MODISTools - downloading and processing MODIS remotely sensed data in R

Remotely sensed data – available at medium to high resolution across global spatial and temporal scales – are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R2 values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools)

Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans.

HERV-K113 and HERV-K115 have been considered to be among the youngest HERVs because they are the only known full-length proviruses that are insertionally polymorphic and maintain the open reading frames of their coding genes. However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older. A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking. Therefore, we sought to determine how recently HERVs were exogenous and infectious by examining sequence variation in the long terminal repeat (LTR) regions of all full-length HERV-K loci. We used the traditional method of inter-LTR comparison to analyze all full length HERV-Ks and determined that two insertions, HERV-K106 and HERV-K116 have no differences between their 5' and 3' LTR sequences, suggesting that these insertions were endogenized in the recent evolutionary past. Among these insertions with no sequence differences between their LTR regions, HERV-K106 had the most intact viral sequence structure. Coalescent analysis of HERV-K106 3' LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans

Economies of space and the school geography curriculum

This paper is about the images of economic space that are found in school curricula. It suggests the importance for educators of evaluating these representations in terms of the messages they contain about how social processes operate. The paper uses school geography texts in Britain since the 1970s to illustrate the different ways in which economic space has been represented to students, before exploring some alternative resources that could be used to provide a wider range of representations of economic space. The paper highlights the continued importance of understanding the politics of school knowledge