SAR11 clade dominates ocean surface bacterioplankton communities

The most abundant class of bacterial ribosomal RNA genes detected in seawater DNA by gene cloning belongs to SAR11-an alpha-proteobacterial clade. Other than indications of their prevalence in seawater, little is known about these organisms. Here we report quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters. On average, the SAR11 clade accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions, members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the subeuphotic microbial community. By extrapolation, we estimate that globally there are 2.4 x 10(28) SAR11 cells in the oceans, half of which are located in the euphotic zone. Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth.     

A gene expression map of human chromosome 21 orthologues in the mouse

The DNA sequence of human chromosome 21 (HSA21) has opened the route for a systematic molecular characterization of all of its genes. Trisomy 21 is associated with Down's syndrome, the most common genetic cause of mental retardation in humans. The phenotype includes various organ dysmorphies, stereotypic craniofacial anomalies and brain malformations. Molecular analysis of congenital aneuploidies poses a particular challenge because the aneuploid region contains many protein-coding genes whose function is unknown. One essential step towards understanding their function is to analyse mRNA expression patterns at key stages of organism development. Seminal works in flies, frogs and mice showed that genes whose expression is restricted spatially and/or temporally are often linked with specific ontogenic processes. Here we describe expression profiles of mouse orthologues to HSA21 genes by a combination of large-scale mRNA in situ hybridization at critical stages of embryonic and brain development and in silico (computed) mining of expressed sequence tags. This chromosome-scale expression annotation associates many of the genes tested with a potential biological role and suggests candidates for the pathogenesis of Down's syndrome.     

Do seasonal unit roots matter for forecasting monthly industrial production?

We investigate the seasonal unit root properties of monthly industrial production series for 16 OECD countries within the context of a structural time series model. A basic version of this model assumes that there are 11 such seasonal unit roots. We propose to use model selection criteria (AIC and BIC) to examine if one or more of these are in fact stationary. We generally find that when these criteria indicate that a smaller number of seasonal unit roots can be assumed and hence that some seasonal roots are stationary, the corresponding model also gives more accurate one‐step‐ahead forecasts. Copyright © 2004 John Wiley & Sons, Ltd.     

Evolution and stability of holographic soliton pairs

Previous works concerning the generation of spatial optical solitons using interference pattern[1―5] can be divided into two categories: First, the interference of two beams was used to generate a periodic spatial pat-tern and then the pattern is injecte…     

Limited number of patrilines in horse domestication

Genetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome. In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site. These observations are consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the domestic horse.     

Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica

Tunicate embryos and larvae have small cell numbers and simple anatomical features in comparison with other chordates, including vertebrates. Although they branch near the base of chordate phylogenetic trees, their degree of divergence from the common chordate ancestor remains difficult to evaluate. Here we show that the tunicate Oikopleura dioica has a complement of nine Hox genes in which all central genes are lacking but a full vertebrate-like set of posterior genes is present. In contrast to all bilaterians studied so far, Hox genes are not clustered in the Oikopleura genome. Their expression occurs mostly in the tail, with some tissue preference, and a strong partition of expression domains in the nerve cord, in the notochord and in the muscle. In each tissue of the tail, the anteroposterior order of Hox gene expression evokes spatial collinearity, with several alterations. We propose a relationship between the Hox cluster breakdown, the separation of Hox expression domains, and a transition to a determinative mode of development.     

A Bayesian analysis of periodic integration

Recent empirical research into the seasonal and trend properties of macroeconomic time series using periodic models has resulted in strong evidence in favour of periodic integration (PI). PI implies that the differencing filter necessary to remove a stochastic trend varies across seasons and, hence, that seasonal fluctuations are related to the stochastic trend. Previous studies finding evidence of PI have used classical econometric techniques. In this paper, we investigate the possible sensitivity of this empirical result by using Bayesian techniques. An application of posterior odds analysis and highest posterior density interval tests to several quarterly UK macroeconomic series suggests strong evidence for PI, even when we allow for structural breaks in the deterministic seasonals. A predictive exercise indicates that PI usually outperforms other competing models in terms of out-of-sample forecasting. © 1997 John Wiley & Sons, Ltd.     

Forecasting stock market volatility using (non-linear) Garch models

In this paper we study the performance of the GARCH model and two of its non-linear modifications to forecast weekly stock market volatility. The models are the Quadratic GARCH (Engle and Ng, 1993) and the Glosten, Jagannathan and Runkle (1992) models which have been proposed to describe, for example, the often observed negative skewness in stock market indices. We find that the QGARCH model is best when the estimation sample does not contain extreme observations such as the 1987 stock market crash and that the GJR model cannot be recommended for forecasting.     

Model‐based forecast adjustment: With an illustration to inflation

This paper introduces the idea of adjusting forecasts from a linear time series model where the adjustment relies on the assumption that this linear model is an approximation of a nonlinear time series model. This way of creating forecasts could be convenient when inference for a nonlinear model is impossible, complicated or unreliable in small samples. The size of the forecast adjustment can be based on the estimation results for the linear model and on other data properties such as the first few moments or autocorrelations. An illustration is given for a first‐order diagonal bilinear time series model, which in certain properties can be approximated by a linear ARMA(1, 1) model. For this case, the forecast adjustment is easy to derive, which is convenient as the particular bilinear model is indeed cumbersome to analyze in practice. An application to a range of inflation series for low‐income countries shows that such adjustment can lead to some improved forecasts, although the gain is small for this particular bilinear time series model.