CALCULATION OF THE MINIMUM NUMBER OF REPLICATE SPOTS REQUIRED FOR DETECTION OF SIGNIFICANT GENE EXPRESSION FOLD CHANGE IN MICROARRA Y EXPERIMENTS

Calculations for the number of per gene replicate spots in microarray experiments are presented for the purpose of obtaining estimates of the sampling variability present in microarray data, and for determining the minimum number of replicate spots required to achieve a high probability of detecting a significant fold change in gene expression. Our approach is based on data from control microarrays, and employs standard statistical estimation techniques. We have demonstrated the usefulness of our framework by analyzing two experimental data sets containing control array data. The minimum number of replicate spots required on a treatment array were calculated to achieve detection of a 3-fold increase in expression with 90%, 95% or 99% confidence. The inclusion of replicate spots on microarrays not only allows more accurate estimation of the variability present in an experiment, but more importantly increases the probability of detecting genes undergoing significant fold changes in expression, while substantially decreasing the probability of observing fold changes due to chance rather than true differential expression

Low- and high-frequency noise from coherent two-level systems

Recent experiments indicate a connection between the low- and high-frequency noise affecting superconducting quantum systems. We explore the possibilities that both noises can be produced by one ensemble of microscopic modes, made up, e.g., by sufficiently coherent two-level systems (TLS). This implies a relation between the noise power in different frequency domains, which depends on the distribution of the parameters of the TLSs. We show that a distribution, natural for tunneling TLSs, with a log-uniform distribution in the tunnel splitting and linear distribution in the bias, accounts for experimental observations.Comment: minor corrections, references adde

870 micron observations of nearby 3CRR radio galaxies

We present submillimeter continuum observations at 870 microns of the cores of low redshift 3CRR radio galaxies, observed at the Heinrich Hertz Submillimeter Telescope. The cores are nearly flat spectrum between the radio and submillimeter which implies that the submillimeter continuum is likely to be synchrotron emission and not thermal emission from dust. The emitted power from nuclei detected at optical wavelengths and in the X-rays is similar in the submillimeter, optical and X-rays. The submillimeter to optical and X-ray power ratios suggest that most of these sources resemble misdirected BL Lac type objects with synchrotron emission peaking at low energies. However we find three exceptions, the FR I galaxy 3C264 and the FR II galaxies 3C390.3 and 3C338 with high X-ray to submillimeter luminosity ratios. These three objects are candidate high or intermediate energy peaked BL Lac type objects. With additional infrared observations and from archival data, we compile spectral energy distributions (SEDs) for a subset of these objects. The steep dips observed near the optical wavelengths in many of these objects suggest that extinction inhibits the detection and reduces the flux of optical continuum core counterparts. High resolution near or mid-infrared imaging may provide better measurements of the underlying synchrotron emission peak.Comment: accepted for publication in A

Exact correlation functions of the BCS model in the canonical ensemble

We evaluate correlation functions of the BCS model for finite number of particles. The integrability of the Hamiltonian relates it with the Gaudin algebra ${\cal G}[sl(2)]$. Therefore, a theorem that Sklyanin proved for the Gaudin model, can be applied. Several diagonal and off-diagonal correlators are calculated. The finite size scaling behavior of the pairing correlation function is studied.Comment: 4 pages revtex; 2 figures .eps. Revised version to be published in Phys. Rev. Let

DESIGNING MICROARRAYS

Microarrays allow the simultaneous assessment of expression levels for thousands of genes across various treatment conditions and time. It has been shown that in these experiments expression levels can also be affected by factors in the printing of the slide, in the hybridization process, and in the post-hybridization process. Recently, variations of the incomplete block design were proposed as a way to avoid confounding the expression levels of interest with several of these nuisance factors. In this paper, we propose additional design procedures to remove factors that contribute to the spatial variability on a slide. This approach requires the use of replication, and involves designing how the replicates are to be positioned on the slide. We demonstrate these techniques using an experiment involving sixty-four genes, four replicates per slide, and five treatment conditions

Dynamic scaling approach to study time series fluctuations

We propose a new approach for properly analyzing stochastic time series by mapping the dynamics of time series fluctuations onto a suitable nonequilibrium surface-growth problem. In this framework, the fluctuation sampling time interval plays the role of time variable, whereas the physical time is treated as the analog of spatial variable. In this way we found that the fluctuations of many real-world time series satisfy the analog of the Family-Viscek dynamic scaling ansatz. This finding permits to use the powerful tools of kinetic roughening theory to classify, model, and forecast the fluctuations of real-world time series.Comment: 25 pages, 7 figures, 1 tabl

Nonlinear acoustic and microwave absorption in glasses

A theory of weakly-nonlinear low-temperature relaxational absorption of acoustic and electromagnetic waves in dielectric and metallic glasses is developed. Basing upon the model of two-level tunneling systems we show that the nonlinear contribution to the absorption can be anomalously large. This is the case at low enough frequencies, where freqeuency times the minimal relaxation time for the two-level system are much less than one. In dielectric glasses, the lowest-order nonlinear contribution is proportional to the wave's intensity. It is negative and exhibits anomalous frequency and temperature dependencies. In metallic glasses, the nonlinear contribution is also negative, and it is proportional to the square root of the wave's intensity and to the frequency. Numerical estimates show that the predicted nonlinear contribution can be measured experimentally

Thermodynamic properties of a small superconducting grain

The reduced BCS Hamiltonian for a metallic grain with a finite number of electrons is considered. The crossover between the ultrasmall regime, in which the level spacing, $d$, is larger than the bulk superconducting gap, $\Delta$, and the small regime, where $\Delta \gtrsim d$, is investigated analytically and numerically. The condensation energy, spin magnetization and tunneling peak spectrum are calculated analytically in the ultrasmall regime, using an approximation controlled by $1/\ln N$ as small parameter, where $N$ is the number of interacting electron pairs. The condensation energy in this regime is perturbative in the coupling constant $\lambda$, and is proportional to $d N \lambda^2 = \lambda^2 \omega_D$. We find that also in a large regime with $\Delta>d$, in which pairing correlations are already rather well developed, the perturbative part of the condensation energy is larger than the singular, BCS, part. The condition for the condensation energy to be well approximated by the BCS result is found to be roughly $\Delta > \sqrt{d \omega_D}$. We show how the condensation energy can, in principle, be extracted from a measurement of the spin magnetization curve, and find a re-entrant susceptibility at zero temperature as a function of magnetic field, which can serve as a sensitive probe for the existence of superconducting correlations in ultrasmall grains. Numerical results are presented which suggest that in the large $N$ limit the 1/N correction to the BCS result for the condensation energy is larger than $\Delta$.Comment: 17 pages, 7 figures, Submitted to Phys. Rev.

Novel methods for spatial prediction of soil functions within landscapes (SP0531)

Previous studies showed that soil patterns could be predicted in agriculturally managed landscapes by modelling and extrapolating from extensive existing but related integrated datasets. Based on these results we proposed to develop and apply predictive models of the relationships between environmental data and known soil patterns to predict capacity for key soil functions within diverse landscapes for which there is little detailed underpinning soil information available. Objectives were: To develop a high-level framework in which the non-specialist user-community could explore questions. To generate digital soil maps for three selected catchments at a target resolution of 1:50000 to provide the base information for soil function prediction. To use a modelling approach to predict the performance of key soil functions in catchments undergoing change but where only sparse or low resolution soil survey data are available. To use a modelling approach to assess the impact of different management scenarios and/or environmental conditions on the delivery of multiple soil functions within a catchment. To create a detailed outline of the requirements for ground-truthing to test the predicted model outputs at a catchment scale. To contribute to the development of a high-level framework for decision makers