Deriving the sampling errors of correlograms for general white noise

We derive the second-order sampling properties of certain autocovariance and autocorrelation estimators for sequences of independent and identically distributed samples. Specifically, the estimators we consider are the classic lag windowed correlogram, the correlogram with subtracted sample mean, and the fixed-length summation correlogram. For each correlogram we derive explicit formulas for the bias, covariance, mean square error and consistency for generalised higher-order white noise sequences. In particular, this class of sequences may have non-zero means, be complexed valued and also includes non-analytical noise signals. We find that these commonly used correlograms exhibit lag dependent covariance despite the fact that these processes are white and hence by definition do not depend on lag.Comment: Submitted to Biometrik

Sampling errors of correlograms with and without sample mean removal for higher-order complex white noise with arbitrary mean

We derive the bias, variance, covariance, and mean square error of the standard lag windowed correlogram estimator both with and without sample mean removal for complex white noise with an arbitrary mean. We find that the arbitrary mean introduces lag dependent covariance between different lags of the correlogram estimates in spite of the lack of covariance in white noise for non-zeros lags. We provide a heuristic rule for when the sample mean should be, and when it should not be, removed if the true mean is not known. The sampling properties derived here are useful is assesing the general statistical performance of autocovariance and autocorrelation estimators in different parameter regimes. Alternatively, the sampling properties could be used as bounds on the detection of a weak signal in general white noise.Comment: 11 pages, 2 figures, To be published in Journal of Time Series Analysi

Case study : a patient-clinician collaboration that identified and prioritized evidence gaps and stimulated research development

Copyright © 2013 Elsevier Inc. All rights reserved.Peer reviewedPostprin

Brain Localisation of Memory Chunks in Chessplayers

Chess experts store domain-specific representations in their long-term memory; due to the activation of such representations, they perform with high accuracy in tasks that require the maintenance of previously seen information. Chunk-based theories of expertise (chunking theory: Chase & Simon, 1973; template theory: Gobet & Simon, 1996) state that expertise is acquired mainly by the acquisition and storage in long-term memory of familiar chunks that allow quick recognition. We tested some predictions of these theories by using fMRI while chessplayers performed a recognition memory task. These theories predict that chessplayers access long-term memory chunks of domain-specific information, which are presumably stored in the temporal lobes. We also predicted that the recognition memory tasks would activate working memory areas in the frontal and parietal lobes. These predictions were supported by the data

Effect of genotype on duodenal expression of nutrient transporter genes in dairy cows

peer-reviewedBackground Studies have shown clear differences between dairy breeds in their feed intake and production efficiencies. The duodenum is critical in the coordination of digestion and absorption of nutrients. This study examined gene transcript abundance of important classes of nutrient transporters in the duodenum of non lactating dairy cows of different feed efficiency potential, namely Holstein-Friesian (HF), Jersey (JE) and their F1 hybrid. Duodenal epithelial tissue was collected at slaughter and stored at -80°C. Total RNA was extracted from tissue and reverse transcribed to generate cDNA. Gene expression of the following transporters, namely nucleoside; amino acid; sugar; mineral; and lipid transporters was measured using quantitative real-time RT-PCR. Data were statistically analysed using mixed models ANOVA in SAS. Orthogonal contrasts were used to test for potential heterotic effects and spearman correlation coefficients calculated to determine potential associations amongst gene expression values and production efficiency variables. Results While there were no direct effects of genotype on expression values for any of the genes examined, there was evidence for a heterotic effect (P < 0.05) on ABCG8, in the form of increased expression in the F1 genotype compared to either of the two parent breeds. Additionally, a tendency for increased expression of the amino acid transporters, SLC3A1 (P = 0.072), SLC3A2 (P = 0.081) and SLC6A14 (P = 0.072) was also evident in the F1 genotype. A negative (P < 0.05) association was identified between the expression of the glucose transporter gene SLC5A1 and total lactational milk solids yield, corrected for body weight. Positive correlations (P < 0.05) were also observed between the expression values of genes involved in common transporter roles. Conclusion This study suggests that differences in the expression of sterol and amino acid transporters in the duodenum could contribute towards the documented differences in feed efficiency between HF, JE and their F1 hybrid. Furthermore, positive associations between the expression of genes involved in common transporter roles suggest that these may be co-regulated. The study identifies potential candidates for investigation of genetic variants regulating nutrient transport and absorption in the duodenum in dairy cows, which may be incorporated into future breeding programmes

The neurochemical basis of photic entrainment of the circadian pacemaker

Circadian rhythmicity in mammals is controlled by the action of a light-entrainable hypothalamus, in association with two cell clusters known as the supra chiasmatic nuclei (SCN). In the absence of temporal environmental clues, this pacemaker continues to measure time by an endogenous mechanism (clock), driving biochemical, physiological, and behavioral rhythms that reflect the natural period of the pacemaker oscillation. This endogenous period usually differs slightly from 24 hours (i.e., circadian). When mammals are maintained under a 24 hour light-dark (LD) cycle, the pacemaker becomes entrained such that the period of the pacemaker oscillation matches that of the LD cycle. Potentially entraining photic information is conveyed to the SCN via a direct retinal projection, the retinohypothalamic tract (RHT). RHT neurotransmission is thought to be mediated by the release of excitatory amino acids (EAA) in the SCN. In support of this hypothesis, recent experiments using nocturnal rodents have shown that EAA antagonists block the effects of light on pacemaker-driven behavioral rhythms, and attenuate light induced gene expression in SCN cells. An understanding of the neurochemical basis of the photic entrainment process would facilitate the development of pharmacological strategies for maintaining synchrony among shift workers in environments, such as the Space Station, which provide unreliable or conflicting temporal photic clues

Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus

We provide experimental evidence of a replication enhancer element (REE) within the capsid gene of tick-borne encephalitis virus (TBEV, genus Flavivirus). Thermodynamic and phylogenetic analyses predicted that the REE folds as a long stable stem–loop (designated SL6), conserved among all tick-borne flaviviruses (TBFV). Homologous sequences and potential base pairing were found in the corresponding regions of mosquito-borne flaviviruses, but not in more genetically distant flaviviruses. To investigate the role of SL6, nucleotide substitutions were introduced which changed a conserved hexanucleotide motif, the conformation of the terminal loop and the base-paired dsRNA stacking. Substitutions were made within a TBEV reverse genetic system and recovered mutants were compared for plaque morphology, single-step replication kinetics and cytopathic effect. The greatest phenotypic changes were observed in mutants with a destabilized stem. Point mutations in the conserved hexanucleotide motif of the terminal loop caused moderate virus attenuation. However, all mutants eventually reached the titre of wild-type virus late post-infection. Thus, although not essential for growth in tissue culture, the SL6 REE acts to up-regulate virus replication. We hypothesize that this modulatory role may be important for TBEV survival in nature, where the virus circulates by non-viraemic transmission between infected and non-infected ticks, during co-feeding on local rodents

Pfaffian representations of cubic surfaces

Let K be a field of characteristic zero. We describe an algorithm which requires a homogeneous polynomial F of degree three in K[x_0,x_1,x_2,x_3] and a zero A of F in P^3_K and ensures a linear pfaffian representation of V(F) with entries in K[x_0,x_1,x_2,x_3], under mild assumptions on F and A. We use this result to give an explicit construction of (and to prove the existence of) a linear pfaffian representation of V(F), with entries in K'[x_0,x_1,x_2,x_3], being K' an algebraic extension of K of degree at most six. An explicit example of such a construction is given.Comment: 17 pages. Expanded with some remarks. Published with minor corrections in Geom. Dedicat