On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence.

BACKGROUND: In eukaryotes, most DNA-binding proteins exert their action as members of large effector complexes. The presence of these complexes are revealed in high-throughput genome-wide assays by the co-occurrence of the binding sites of different complex components. Resampling tests are one route by which the statistical significance of apparent co-occurrence can be assessed. RESULTS: We have investigated two resampling approaches for evaluating the statistical significance of binding-site co-occurrence. The permutation test approach was found to yield overly favourable p-values while the independent resampling approach had the opposite effect and is of little use in practical terms. We have developed a new, pragmatically-devised hybrid approach that, when applied to the experimental results of an Polycomb/Trithorax study, yielded p-values consistent with the findings of that study. We extended our investigations to the FL method developed by Haiminen et al, which derives its null distribution from all binding sites within a dataset, and show that the p-value computed for a pair of factors by this method can depend on which other factors are included in that dataset. Both our hybrid method and the FL method appeared to yield plausible estimates of the statistical significance of co-occurrences although our hybrid method was more conservative when applied to the Polycomb/Trithorax dataset.A high-performance parallelized implementation of the hybrid method is available. CONCLUSIONS: We propose a new resampling-based co-occurrence significance test and demonstrate that it performs as well as or better than existing methods on a large experimentally-derived dataset. We believe it can be usefully applied to data from high-throughput genome-wide techniques such as ChIP-chip or DamID. The Cooccur package, which implements our approach, accompanies this paper.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Flat-top oscillons in an expanding universe

Oscillons are extremely long lived, oscillatory, spatially localized field configurations that arise from generic initial conditions in a large number of non-linear field theories. With an eye towards their cosmological implications, we investigate their properties in an expanding universe. We (1) provide an analytic solution for one dimensional oscillons (for the models under consideration) and discuss their generalization to 3 dimensions, (2) discuss their stability against long wavelength perturbations and (3) estimate the effects of expansion on their shapes and life-times. In particular, we discuss a new, extended class of oscillons with surprisingly flat tops. We show that these flat topped oscillons are more robust against collapse instabilities in (3+1) dimensions than their usual counterparts. Unlike the solutions found in the small amplitude analysis, the width of these configurations is a non-monotonic function of their amplitudes.Comment: v2-matches version published in Phys. Rev D. Updated references and minor modification to section 4.

InP homojunction solar cell performance on the LIPS 3 flight experiment

Performance data for the NASA Lewis Research Center indium phosphide n+p homojunction solar cell module on the LIPS 3 Flight Experiment is presented. The objective of the experiment is to measure the performance of InP cells in the natural radiation environment of the 1100 km altitude, 60+ deg inclination orbit. Analysis of flight data indicates that the performance of the four cells throughout the first year is near expected values. No degradation in short-circuit current was seen, as was expected from radiation tolerance studies of similar cells. Details of the cell structure and flight module design are discussed. The results of the temperature dependency and radiation tolerance studies necessary for normalization and analysis of the data are included

Factors Influencing Willingness-to-Pay for the Energy Star Label

In the United States, nearly 17 percent of greenhouse gas emissions come from residential energy use. Increases in energy efficiency for the residential sector can generate significant energy savings and emissions reductions. Consumer labels, such as USEPA’s Energy Star, promote conservation by providing consumers with information on energy usage for household appliances. This study examines how the Energy Star label affects consumer preferences for refrigerators. An online survey of a national sample of adults suggest that consumers are, on average, willing to pay an extra $249.82 to$349.30 for a refrigerator that has been awarded the Energy Star label. Furthermore, the results provide evidence that willingness to pay was motivated by both private (energy cost savings) and public (environmental) benefits.Energy Star, willingness-to-pay, eco-label, Consumer/Household Economics, Demand and Price Analysis, Environmental Economics and Policy,

Broadband-tunable LP01_{01} mode frequency shifting by Raman coherence waves in H2_2-filled hollow-core PCF

When a laser pump beam of sufficient intensity is incident on a Raman-active medium such as hydrogen gas, a strong Stokes signal, red-shifted by the Raman transition frequency {\Omega}$_R$, is generated. This is accompanied by the creation of a "coherence wave" of synchronized molecular oscillations with wavevector {\Delta}{\beta} determined by the optical dispersion. Within its lifetime, this coherence wave can be used to shift by {\Omega}$_R$ the frequency of a third "mixing" signal, provided phase-matching is satisfied, i.e., {\Delta}{\beta} is matched. Conventionally this can be arranged using non-collinear beams or higher-order waveguide modes. Here we report collinear phase-matched frequency shifting of an arbitrary mixing signal using only the fundamental LP$_{01}$ modes of a hydrogen-filled hollow-core PCF. This is made possible by the S-shaped dispersion curve that occurs around the pressure-tunable zero dispersion point. Phase-matched frequency shifting by 125 THz is possible from the UV to the near-IR. Long interaction lengths and tight modal confinement reduce the peak intensities required, allowing conversion efficiencies in excess of 70%. The system is of great interest in coherent anti-Stokes Raman spectroscopy and for wavelength-conversion of broadband laser sources.Comment: 4 pages, 7 figures, supplementary materia

EC91-102 C Nebraska Spring Wheat, Oats, Barley, Canola and Crambe Variety Tests 1991

Extension circular 91-102-C: This circular is a progress report of Nebraska spring wheat, oats, barley, canola and crambe variety trials conducted in 1991 by personnel of the agronomy department and the Northeast and Panhandle Centers and their associated agricultural laboratories

Consistency and Variation in Spatial Reference

Modeling the meaning and use of linguistic expressions describing spatial relationships holding between a target object and a landmark object requires an understanding of both the consistency and variation in human performance in this area. Previous research [Herskovits 1985] attempts to account for some of this variation in terms of the angular deviation holding among objects in thevisual display. This approach is shown to fail to account for the full range of human variation inperformance, and a specific alternative algorithm is offered which is grounded in task variability and the notions of corridor and centroid. The significance to this algorithm of task variation, of theseparation of semantic from pragmatic issues, and of the role of function and structure is discusse