A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series.

Understanding the regulatory mechanisms that are responsible for an organism's response to environmental change is an important issue in molecular biology. A first and important step towards this goal is to detect genes whose expression levels are affected by altered external conditions. A range of methods to test for differential gene expression, both in static as well as in time-course experiments, have been proposed. While these tests answer the question whether a gene is differentially expressed, they do not explicitly address the question when a gene is differentially expressed, although this information may provide insights into the course and causal structure of regulatory programs. In this article, we propose a two-sample test for identifying intervals of differential gene expression in microarray time series. Our approach is based on Gaussian process regression, can deal with arbitrary numbers of replicates, and is robust with respect to outliers. We apply our algorithm to study the response of Arabidopsis thaliana genes to an infection by a fungal pathogen using a microarray time series dataset covering 30,336 gene probes at 24 observed time points. In classification experiments, our test compares favorably with existing methods and provides additional insights into time-dependent differential expression.

Constraint-based Mining of Frequent Arrangements of Temporal Intervals

The problem of discovering frequent arrangements of temporal intervals is studied. It is assumed that the database consists of sequences of events, where an event occurs during a time-interval. The goal is to mine temporal arrangements of event intervals that appear frequently in the database. The motivation of this work is the observation that in practice most events are not instantaneous but occur over a period of time and different events may occur concurrently. Thus, there are many practical applications that require mining such temporal correlations between intervals including the linguistic analysis of annotated data from American Sign Language as well as network and biological data. Two efficient methods to find frequent arrangements of temporal intervals are described; the first one is tree-based and uses depth first search to mine the set of frequent arrangements, whereas the second one is prefix-based. The above methods apply efficient pruning techniques that include a set of constraints consisting of regular expressions and gap constraints that add user-controlled focus into the mining process. Moreover, based on the extracted patterns a standard method for mining association rules is employed that applies different interestingness measures to evaluate the significance of the discovered patterns and rules. The performance of the proposed algorithms is evaluated and compared with other approaches on real (American Sign Language annotations and network data) and large synthetic datasets.

Confidence intervals for half-life deviations from purchasing power parity

Existing point estimates of half-life deviations from purchasing power parity (PPP), around 3-5 years, suggest that the speed of convergence is extremely slow. This article assesses the degree of uncertainty around these point estimates by using local-to-unity asymptotic theory to construct confidence intervals that are robust to high persistence in small samples. The empirical evidence suggests that the lower bound of the confidence interval is between four and eight quarters for most currencies, which is not inconsistent with traditional price-stickiness explanations. However, the upper bounds are infinity for all currencies, so we cannot provide conclusive evidence in favor of PPP either. © 2005 American Statistical Association.

Addressing time intervals

One of the fundamental questions regarding the temporal ontology is what is time composed of. While the traditional time structure is based on a set of points, a notion that has been prevalently adopted in classical physics and mathematics, it has also been noticed that intervals have been widely adopted for expre~sion of common sense temporal knowledge, especially in the domain of artificial intelligence. However, there has been a longstanding debate on how intervals should be addressed, leading to two different approaches to the treatment of intervals. In the first, intervals are addressed as derived objects constructed from points, e.g., as sets of points, or as pairs of points. In the second, intervals are taken as primitive themselves. This article provides a critical examination of these two approaches. By means of proposing a definition of intervals in terms of points and types, we shall demonstrate that, while the two different approaches have been viewed as rivals in the literature, they are actually reducible to logically equivalent expressions under some requisite interpretations, and therefore they can also be viewed as allies.

A numerical approach to C-14 wiggle-match dating of organic deposits: best fits and confidence intervals

14C wiggle-match dating (WMD) of peat deposits uses the non-linear relationship between 14C age and calendar age to match the shape of a sequence of closely spaced peat 14C dates with the 14C calibration curve. A numerical approach to WMD enables the quantitative assessment of various possible wiggle-match solutions and of calendar year confidence intervals for sequences of 14C dates. We assess the assumptions, advantages, and limitations of the method. Several case-studies show that WMD results in more precise chronologies than when individual 14C dates are calibrated. WMD is most successful during periods with major excursions in the 14C calibration curve (e.g., in one case WMD could narrow down confidence intervals from 230 to 36 yr).

Tracking leatherback turtles (Dermochelys coriacea) during consecutive inter-nesting intervals: Further support for direct transmitter attachment

Over recent years there have been substantial efforts to record and interpret the post-nesting movements of leatherback turtles (Dermochelys coriacea) breeding in tropical regions. Less well documented are the movements undertaken by individual turtles during the breeding season itself, or more specifically between sequential nesting events. Such movements are of interest for two reasons: (1) gravid female leatherbacks may range extensively into the territorial waters and nesting beaches of neighbouring countries, raising questions for conservationists and population ecologists; and (2) the magnitude of movements themselves help elucidate underlying reproductive strategies (e.g. whether to rest near to the nesting or forage extensively). Here, satellite relay data loggers are used (SRDLs) to detail the movements and behaviour of two female leatherback turtles throughout three consecutive inter-nesting intervals in the Commonwealth of Dominica, West Indies. Both near-shore residence and extensive inter-nesting movements were recorded, contrasting previous studies, with movements away from the nesting beach increasing towards the end of the nesting season. Using this behavioural study as a backdrop, the suitability of attaching satellite transmitters directly to the carapace was additionally explored as an alternative approach to conventional harness deployments. Specifically, the principal aims were to (1) gather empirical data on speed of travel and (2) assess dive performance (aerobic dive limit) to enable comparisons with turtles previously fitted with harnesses elsewhere in the Caribbean (n = 6 turtles; Grenada, WI). This produced mixed results with animals bearing directly attached transmitters travelling significantly faster (55.21 km day(-1): SD 6.68) than harnessed individuals (39.80 km day(-1); SD 6.19); whilst no discernable difference in dive performance could be found between the two groups of study animals. (C) 2009 Elsevier B.V. All rights reserved.

Water temperature and internesting intervals for loggerhead (Caretta caretta) and green (Chelonia mydas) sea turtles

Temperature loggers were attached to the carapace of green turtles (Chelonia mydas) at Ascension Island and Cyprus and to loggerhead turtles (Caretta caretta) at Cyprus, in order to record the ambient temperature experienced by individuals during the internesting interval, i.e. the period between consecutive clutches being laid. Internesting intervals were relatively short (10-14 days) and mean ambient temperatures relatively warm (27-28degreesC), compared to previous observations for these species nesting in Japan, although a single internesting interval versus temperature relationship described all the data for these two species from the different areas. The implication is that water temperature has both a common and a profound effect on the length of the internesting interval for these two species: internesting intervals are shorter when the water is warmer. (C) 2002 Elsevier Science Ltd. All rights reserved.

Age-related reference intervals for lymphocyte subsets in whole blood of healthy individuals

Enumeration of various lymphocyte subsets is used widely in the diagnosis and monitoring of various disease states. With the development of flow cytometric technology and whole blood analysis, methodologies have become more sensitive. It is therefore important to establish reference intervals in normal, healthy individuals using these techniques to give a better indication of the border between health and disease. Since some lymphocyte subpopulations are known to change with age, we have enumerated common subsets in healthy individuals from all decades of adult life, including nonagenarian subjects. We report reference intervals for these subsets in each age group, which will be of use in diagnosis and disease monitoring, particularly in elderly subjects, the most rapidly expanding group within the population today.