Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses.

Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one.

Unidirectional hybridization at a species' range boundary: implications for habitat tracking

Aim Introgressive hybridization between a locally rare species and a more abundant congener can drive population extinction via genetic assimilation, or the replacement of the rare species gene pool with that of the common species. To date, however, few studies have assessed the effects of such processes at the limits of species' distribution ranges. In this study, we have examined the potential for hybridization between range-edge populations of the wintergreen Pyrola minor and sympatric populations of Pyrola grandiflora. Location Qeqertarsuaq, Greenland and Churchill, Manitoba, Canada. Methods Genetic analysis of samples from Greenland and Canada was carried out using a combination of nuclear and chloroplast single nucleotide polymorphisms (SNPs). Results Analysis of nuclear SNPs confirmed hybridization in populations of morphologically intermediate individuals, as well as revealing the existence of cryptic hybrids in ostensibly morphologically pure P. minor populations. Analysis of chloroplast SNPs revealed that this hybridization is unidirectional and suggests that hybrids originate via pollen swamping of P. minor by the more common P. grandiflora. Main conclusions Extensive unidirectional hybridization may lead to the extinction of peripheral populations of P. minor where the two species grow sympatrically. Extinction could occur as a result of genetic assimilation where F1s are fertile, or via the removal of unidirectionally pollinated sterile F1s, or by a combination of these processes. This could compromise the ability of species to respond to climate change via habitat tracking, although the final outcome of these processes may ultimately depend on the rate of global climate change and its effect on the species' distributions. © 2009 Blackwell Publishing Ltd.

The finding of reduced estimated glomerular filtration rate is associated with increased mortality in a large UK population

BACKGROUND: CKD as defined by KDIGO/KDOQI has been shown to affect ~ 8.5% of the UK population. The prevalence of CKD in the UK is similar to that in the USA, yet incident dialysis rates are dramatically different. This retrospective cohort study investigates the association between reduced kidney function and mortality in a large UK population. METHODS: All serum creatinine results covering Northern Ireland's 1.7 million population were collected between 1 January 2001 and 31 December 2002. Estimated glomerular filtration rates (eGFR) were calculated for all serum creatinine measurements using four-variable MDRD equation (IDMS aligned). Patients were followed up for both all-cause and cardiovascular mortality data until the end of December 2006. Patients on renal replacement therapy were excluded. Subgroup analysis in the 75 345 subjects enrolled within a parallel primary care study permitted additional survival analysis with adjustment for traditional cardiovascular risk factors. RESULTS: A total of 1 967 827 serum creatinine results from 533 798 patients were collected. During the period of follow-up, 59 980 deaths occurred. In multivariate survival analysis, using eGFR as a time-varying covariate, a graded association between CKD (defined by eGFR) and all-cause mortality was identified. Compared with participants with an eGFR of > 60 mL/min/1.73 m(2), the adjusted hazard ratios (and 95% confidence intervals) for participants with an eGFR of 45-59 mL/min/1.73 m(2) was 1.02 (0.99-1.04), an eGFR of 30-44 mL/min/1.73 m(2) was 1.44 (1.40-1.47), an eGFR of 15-29 mL/min/1.73 m(2) was 2.12 (2.05-2.20) and an eGFR of

Globally synchronous climate change 2800 years ago: Proxy data from peat in South America

Initial findings from high-latitude ice-cores implied a relatively unvarying Holocene climate, in contrast to the major climate swings in the preceding late-Pleistocene. However, several climate archives from low latitudes imply a less than equable Holocene climate, as do recent studies on peat bogs in mainland north-west Europe, which indicate an abrupt climate cooling 2800 years ago, with parallels claimed in a range of climate archives elsewhere. A hypothesis that this claimed climate shift was global, and caused by reduced solar activity, has recently been disputed. Until now, no directly comparable data were available from the southern hemisphere to help resolve the dispute. Building on investigations of the vegetation history of an extensive mire in the Valle de Andorra, Tierra del Fuego, we took a further peat core from the bog to generate a high-resolution climate history through the use of determination of peat hurnification and quantitative leaf-count plant macrofossil analysis. Here, we present the new proxy-climate data from the bog in South America. The data are directly comparable with those in Europe, as they were produced using identical laboratory methods. They show that there was a major climate perturbation at the same time as in northwest European bogs. Its timinia, nature and apparent global synchronicity lend support to the notion of solar forcing of past climate change, amplified by oceanic circulation. This finding of a similar response simultaneously in both hemispheres may help validate and improve global climate models. That reduced solar activity might cause a global climatic change suggests that attention be paid also to consideration of any global climate response to increases in solar activity. This has implications for interpreting the relative contribution of climate drivers of recent 'global warming'. (c) 2006 Elsevier B.V. All rights reserved.

Construction of cDNA libraries from trifluoroacetic acid-solvated amphibian skin secretions: molecular cloning of multiple bombinin-like peptide precursor transcripts from a library of yellow-bellied toad (Bombina variegata) secretion

Amphibian skin secretions are renowned as complex mixtures of bioactive peptides many of which are analogues of endogenous regulatory peptides. While skin secretions can be obtained non-invasively for peptidome analysis, parallel studies on the granular gland transcriptome required specimen sacrifice. The aim of the present study was to analyse archived skin secretions to determine the robustness of bioactive peptide precursor-encoding polyadenylated mRNAs in an attempt to extract maximum molecular information from rare samples. A range of solvated skin secretion samples were examined after lyophilisation for their potential to generate viable and comprehensive cDNA libraries based upon polyadenylated mRNA capture and amplification/cloning using appropriate commercial kits. Here we present unequivocal data that the granular gland transcriptome persists in a PCR amenable format even after storage for as long as 12 years in 0.1%(v/v) aqueous trifluoroacetic acid (TFA). We used a pooled skin secretion sample (2 ml) from the yellow-bellied toad, Bombina variegata (n = 14), containing the equivalent of 5 mg/ml of lyophilised skin secretion, that had been used in part for peptide isolation purposes in 1998 and had been stored at - 20 °C since that time. In the first cloning experiment, 12 different bombinin-like peptide precursor cDNAs were cloned encoding 17 different bombinins, the majority of which were novel. Subsequently, bombesin and bradykinin-related peptide precursor transcripts have been cloned successfully. These data illustrate the unexpected stability/longevity of the transcriptome in these secretions — a finding with implications for both this field of research and for the wider field of molecular biology.

Doppler cooling of gallium atoms: 2. Simulation in complex multilevel systems

This paper derives a general procedure for the numerical solution of the Lindblad equations that govern the coherences arising from multicoloured light interacting with a multilevel system. A systematic approach to finding the conservative and dissipative terms is derived and applied to the laser cooling of p-block elements. An improved numerical method is developed to solve the time-dependent master equation and results are presented for transient cooling processes. The method is significantly more robust, efficient and accurate than the standard method and can be applied to a broad range of atomic and molecular systems. Radiation pressure forces and the formation of dynamic dark states are studied in the gallium isotope 66Ga.

A meta-analysis of latitudinal variations in life-history traits of roach, Rutilus rutilus, over its geographical range: linear or non-linear relationships?

1. We collated information from the literature on life history traits of the roach (a generalist freshwater fish), and analysed variation in absolute fecundity, von Bertalanffy parameters, and reproductive lifespan in relation to latitude, using both linear and non-linear regression models. We hypothesized that because most life history traits are dependent on growth rate, and growth rate is non-linearly related with temperature, it was likely that when analysed over the whole distribution range of roach, variation in key life history traits would show non-linear patterns with latitude.

Power Efficient Dynamic-Range Utilisation for DSP On FPGA

A power and resource efficient ‘dynamic-range utilisation’ technique to increase operational capacity of DSP IP cores by exploiting redundancy in the data epresentation of sampled analogue input data, is presented. By cleverly partitioning dynamic-range into separable processing threads, several data streams are computed concurrently on the same hardware. Unlike existing techniques which act solely to reduce power consumption due to sign extension, here the dynamic range is exploited to increase operational capacity while still achieving reduced power consumption. This extends an existing system-level, power efficient framework for the design of low power DSP IP cores, which when applied to the design of an FFT IP core in a digital receiver system gives an architecture requiring 50% fewer multipliers, 12% fewer slices and 51%-56% less power.

Neonatal control of sucking pressures

Human newborns appear to regulate sucking pressure when bottle feeding by employing, with similar precision, the same principle of control evidenced by adults in skilled behavior, such as reaching (Lee et al., 1998a). In particular, the present study of 12 full-term newborn infants indicated that the intraoral sucking pressures followed an internal dynamic prototype - an intrinsic tau-guide. The intrinsic tau-guide, a recent hypothesis of general tau theory is a time-varying quantity, tau(g), assumed to be generated within the nervous system. It corresponds to some quantity (e.g., electrical charge), chang ing with a constant second-order temporal derivative from a rest level to a goal level, in the sense that tau(g) equals tau of the gap between the quantity and its goal level at each time t. (tau of a gap is the rime-to-closure of the gap at the current closure-rate.) According to the hypoth esis, the infant senses tau(p), the tau of the gap between the current intraoral pressure and its goal level, and regulates intraoral pressure so that tau(p) and tau(g) remain coupled in a constant ratio, k; i.e., tau(p) = k tau(g). With k in the range 0-1, the tau-coupling would result in a bell-shaped rate of change pressure profile, as was, in fact, found. More specifically, the high mean r(2) values obtained when regressing tau(p) on tau(g), for both the increasing and decreasing suction periods of the infants' suck, supported a strong tau-coupling between tau(p) and tau(g). The mean k values were significantly higher In the Increasing suction period, indicating that the ending of the movement was more forceful, a finding which makes sense given the different functions of the two periods of the suck.