Monte Carlo evidence on cointegration and causation

The small sample performance of Granger causality tests under different model dimensions, degree of cointegration, direction of causality, and system stability are presented. Two tests based on maximum likelihood estimation of error-correction models (LR and WALD) are compared to a Wald test based on multivariate least squares estimation of a modified VAR (MWALD). In large samples all test statistics perform well in terms of size and power. For smaller samples, the LR and WALD tests perform better than the MWALD test. Overall, the LR test outperforms the other two in terms of size and power in small samples.

The provenance and technology of Near Eastern glass: Oxygen isotopes by laser fluorination as a complement to strontium

The ability to make rapid measurements on small samples using laser fluorination enhances the potential of oxygen isotopes in the investigation of early inorganic materials and technologies. delta O-18 and Sr-87/Sr-86 values are presented for glass from two primary production sites, four secondary production sites and a consumer site in the Near East, dating from Late Antiquity to the medieval period. delta O-18 is in general slightly less effective than Sr-87/Sr-86 in discriminating between sources, as the spread of measured values from a single source is somewhat broader relative to the available range. However, while Sr-87/Sr-86 is derived predominantly from either the lime-bearing fraction of the glass-making sand or the plant ash used as a source of alkali, delta O-18 derives mainly from the silica. Thus the two measurements can provide complementary information. A comparison of delta O-18 for late Roman - Islamic glasses made on the coast of Syria-Palestine with those of previously analysed glasses from Roman Europe suggests that the European glasses are relatively enriched in O-18. This appears to contradict the view that most Roman glass was made using Levantine sand and possible interpretations are discussed.

Increased ovulation rate in Merino ewes immunized against small synthetic peptide fragments of the inhibin alpha subunit

Four experiments were carried out in Merino ewes during a period of 4 years to determine the long-term effects of immunization against different synthetic peptides mimicking the amine terminal of the or subunit of porcine inhibin. Peptides were conjugated to human serum albumin and 100-200 mu g emulsified in Freund's complete adjuvant for the primary immunization. Usually two booster injections were given at monthly intervals with 50-100 mu g conjugated peptide using either incomplete Freund's adjuvant or Montanide : Marcel. In some experiments a further immunization was carried in the next year. Blood samples were taken 10 days after each immunization, during the luteal phase, for estimation of gonadotrophin concentrations and determination of inhibin antibody titres. One day after blood sampling cloprostenol was used to induce luteolysis and laparoscopy was performed in the subsequent oestrous cycle. Immunization of ewes with synthetic peptides 1-32, 1-26, 7-26 and 8-30 resulted in large increases in the ovulation rate (OR). An approximately two-fold increase in OR was observed following the first booster immunization with these peptides and a three- to five-fold increase after the second booster immunization. Immunization with these large peptides resulted in a sustained increase in OR for a period of at least 1 year after the second booster immunization. Of the shorter peptides, peptides 10-26 and 13-26 gave a reasonable ovulatory response, although it was more difficult to obtain a response with peptides 1-16, 8-22, 13-25, 8-19 and 10-19; peptides 7-13 and 1-6 gave no response (but were examined for one breeding season only). The smaller peptides led to lower inhibin antibody titres that were not necessarily associated with increased follicle-stimulating hormone (FSH) or OR. More intensive blood sampling in one experiment showed that following primary immunization against peptide 1-32 there was a transient increase in plasma FSH which did not lead to an increased OR. Moreover, a prolonged period of raised FSH after the first booster was significantly correlated with increased OR. In these animals antibody titres were only slightly increased after primary immunization, but after the first booster immunization higher titres were observed that were significantly correlated with trough FSH values and the subsequent OR. These results are interpreted as showing that (1) to obtain an increase in OR peptides 1-32, 1-26 and 7-26 are suitable as immunogens; (2) smaller peptides are less reliable, often require multiple injections, and the response may be delayed; and (3) an extended period of raised plasma FSH is needed to give a large ovulatory response.

A technique to assess small-scale heterogeneity of chemical properties in soil aggregates

A new method is presented which allows the separation of the soil aggregate exterior from the aggregate core. The method employs a combination of aggregate freezing with rapid separation of aggregate exteriors using ultrasonic energy. The factors influencing the thickness of the removed aggregate surface layer include water content of the aggregate prior to freezing, temperature difference between that of the frozen aggregate and that of the liquid it is submerged in during sonification, sonification time and energy, and the type of the immersion liquid. The success of the method and the thickness of the removed aggregate surface were examined using barium ( Ba2+) as a tracer. Barium ( as BaCl2) is rapidly absorbed by soil and is present at only very low levels in natural soils. Surface layers of 0.2 - 0.4 cm thickness were successfully removed from aggregates of 1 - 4 cm diameter. Two examples are given from soils in northern NSW to demonstrate the occurrence of small- scale heterogeneity in soil chemical properties. Compared with the surface fraction, a 4 - 7% higher calcium concentration was found in the core fraction of a clay loam soil ( Dermosol). Conversely, on a cracking clay soil ( Vertosol), atrazine concentration was around 15 times greater in the aggregate surface fractions compared with core fractions. Compared with the traditional estimation of soil chemical properties on homogenised bulk soil samples, it is suggested that separate analysis of aggregate surface and core fractions could provide useful additional information on the relationships between soil properties and environmental responses.

Gene-expression profiling reveals distinct expression patterns for classic versus variant Merkel cell phenotypes and new classifier genes to distinguish Merkel cell from small-cell lung carcinoma

Merkel cell carcinoma (MCC) is a rare aggressive skin tumor which shares histopathological and genetic features with small-cell lung carcinoma (SCLC), both are of neuroendocrine origin. Comparable to SCLC, MCC cell lines are classified into two different biochemical subgroups designated as 'Classic' and 'Variant'. With the aim to identify typical gene-expression signatures associated with these phenotypically different MCC cell lines subgroups and to search for differentially expressed genes between MCC and SCLC, we used cDNA arrays to pro. le 10 MCC cell lines and four SCLC cell lines. Using significance analysis of microarrays, we defined a set of 76 differentially expressed genes that allowed unequivocal identification of Classic and Variant MCC subgroups. We assume that the differential expression levels of some of these genes reflect, analogous to SCLC, the different biological and clinical properties of Classic and Variant MCC phenotypes. Therefore, they may serve as useful prognostic markers and potential targets for the development of new therapeutic interventions specific for each subgroup. Moreover, our analysis identified 17 powerful classifier genes capable of discriminating MCC from SCLC. Real-time quantitative RT-PCR analysis of these genes on 26 additional MCC and SCLC samples confirmed their diagnostic classification potential, opening opportunities for new investigations into these aggressive cancers.

Genetic variability of Tomato spotted wilt virus in Australia and validation of real time RT-PCR for its detection in single and bulked leaf samples

The potential for large-scale use of a sensitive real time reverse transcription polymerase chain reaction (RT-PCR) assay was evaluated for the detection of Tomato spotted wilt virus (TSWV) in single and bulked leaf samples by comparing its sensitivity with that of DAS-ELISA. Using total RNA extracted with RNeasy (R) or leaf soak methods, real time RT-PCR detected TSWV in all infected samples collected from 16 horticultural crop species (including flowers, herbs and vegetables), two arable crop species, and four weed species by both assays. In samples in which DAS-ELISA had previously detected TSWV, real time RT-PCR was effective at detecting it in leaf tissues of all 22 plant species tested at a wide range of concentrations. Bulk samples required more robust and extensive extraction methods with real time RT-PCR, but it generally detected one infected sample in 1000 uninfected ones. By contrast, ELISA was less sensitive when used to test bulked samples, once detecting up to I infected in 800 samples with pepper but never detecting more than I infected in 200 samples in tomato and lettuce. It was also less reliable than real time RT-PCR when used to test samples from parts of the leaf where the virus concentration was low. The genetic variability among Australian isolates of TSWV was small. Direct sequencing of a 587 bp region of the nucleoprotein gene (S RNA) of 29 isolates from diverse crops and geographical locations yielded a maximum of only 4.3% nucleotide sequence difference. Phylogenetic analysis revealed no obvious groupings of isolates according to geographic origin or host species. TSWV isolates, that break TSWV resistance genes in tomato or pepper did not differ significantly in the N gene region studied, indicating that a different region of the virus genome is responsible for this trait.

Provenance of long-travelled dust determined with ultra-trace-element composition: A pilot study with samples from New Zealand glaciers

We report high-precision inductively coupled plasma mass spectrometric (ICP-MS) compositional data for 39 trace elements in a variety of dust deposits, trapped sediments and surface samples from New Zealand and Australia. Dusts collected from the surface of alpine glaciers in the Southern Alps, New Zealand, believed to have undergone long-distance atmospheric transport from Australia, are recognizable on account of their overabundances of Pb and Cu with respect to typical upper crustal values. Long-travelled dust from Australia therefore scavenges these and other metals (e.g. Zn, Sb and Cd) from the atmosphere during transport and deposition. Hence, due to anthropogenic pollution, long-travelled Australian dusts can be recognized by elevated metal contents. The relative abundance of 25 other elements that are not affected by atmospheric pollution, mineral sorting (Zr and Hf) and weathering/solubility (alkali and earth alkali elements) reflects the geochemistry of the dust source sediment. As a result, we are able to establish the provenance of dust using ultra-trace-element chemistry at regional scale. Comparison of long-travelled dust chemistry with potential Australian sources shows that fits of variable quality are obtained. We propose that the best fitting potential source chemistry most likely represents the major dust source area. A binary mixing model is used to demonstrate that admixture of small quantities of local dust provides an even better fitting dust chemistry for the long-travelled dusts. Copyright (c) 2005 John Wiley & Sons, Ltd.

Small-scale randomized controlled trials need more powerful methods of mediational analysis than the Baron-Kenny method

Objective: To devise more-effective physical activity interventions, the mediating mechanisms yielding behavioral change need to be identified. The Baron-Kenny method is most commonly used. but has low statistical power and May not identify mechanisms of behavioral change in small-to-medium size Studies. More powerful statistical tests are available, Study Design and Setting: Inactive adults (N = 52) were randomized to either a print or a print-plus-telephone intervention. Walking and exercise-related social support Were assessed at baseline, after file intervention, and 4 weeks later. The Baron-Kenny and three alternative methods of mediational analysis (Freedman-Schatzkin; MacKinnon et al.: bootstrap method) were used to examine the effects of social support on initial behavior change and maintenance. Results: A significant mediational effect of social support on initial behavior change was indicated by the MacKinnon et al., bootstrap. and. marginally. Freedman-Schatzkin methods, but not by the Baron-Kenny method. No significant mediational effecl of social support on maintenance of walking was found. Conclusions: Methodologically rigorous intervention studies to identify mediators of change in physical activity are costly and labor intensive, and may not be feasible with large samples. The Use of statistically powerful tests of mediational effects in small-scale studies can inform the development of more effective interventions. (C) 2006 Elsevier Inc. All rights reserved.

Handedness in twins: Joint analysis of data from 35 samples

Simultaneous analysis of handedness data from 35 samples of twins (with a combined sample size of 21,127 twin pairs) found a small but significant additive genetic effect accounting for 25.47% of the variance (95% confidence interval [CI] 15.69-29.51%). No common environmental influences were detected (C = 0.00; 95% Cl 0.00-7.67%), with the majority of the variance, 74.53%, explained by factors unique to the individual (95% Cl 70.49-78.67%). No significant heterogeneity was observed within studies that used similar methods to assess handedness, or across studies that used different methods. At an individual level the majority of studies had insufficient power to reject a purely unique environmental model due to insufficient power to detect familial aggregation. This lack of power is seldom mentioned within studies, and has contributed to the misconception that twin studies of handedness are not informative.

On the absolute calibration of bench-top small-angle X-ray scattering instruments: a comparison of different standard methods

Absolute calibration relates the measured (arbitrary) intensity to the differential scattering cross section of the sample, which contains all of the quantitative information specific to the material. The importance of absolute calibration in small-angle scattering experiments has long been recognized. This work details the absolute calibration procedure of a small-angle X-ray scattering instrument from Bruker AXS. The absolute calibration presented here was achieved by using a number of different types of primary and secondary standards. The samples were: a glassy carbon specimen, which had been independently calibrated from neutron radiation; a range of pure liquids, which can be used as primary standards as their differential scattering cross section is directly related to their isothermal compressibility; and a suspension of monodisperse silica particles for which the differential scattering cross section is obtained from Porod's law. Good agreement was obtained between the different standard samples, provided that care was taken to obtain significant signal averaging and all sources of background scattering were accounted for. The specimen best suited for routine calibration was the glassy carbon sample, due to its relatively intense scattering and stability over time; however, initial calibration from a primary source is necessary. Pure liquids can be used as primary calibration standards, but the measurements take significantly longer and are, therefore, less suited for frequent use.

Radiative Relaxation Quantum Yields for Synthetic Eumelanin

We report absolute values for the radiative relaxation quantum yield of synthetic eumelanin as a function of excitation energy. These values were determined by correcting for pump beam attenuation and emission reabsorption in both eumelanin samples and fluorescein standards over a large range of concentrations. Our results confirm that eumelanins are capable of dissipating >99.9% of absorbed UV and visible radiation through nonradiative means. Furthermore, we have found that the radiative quantum yield of synthetic eumelanin is excitation energy dependent. This observation is supported by corrected emission spectra, which also show a clear dependence of both peak position and peak width on excitation energy. Our findings indicate that photoluminescence emission in eumelanins is derived from ensembles of small chemically distinct oligomeric units that can be selectively pumped. This hypothesis lends support to the theory that the basic structural unit of eumelanin is oligomeric rather than heteropolymeric.

Turbulence in Small Sub-Tropical Estuary with Semi-Diurnal Tides

In natural estuaries, contaminant transport is driven by the turbulent momentum mixing. The predictions of scalar dispersion can rarely be predicted accurately because of a lack of fundamental understanding of the turbulence structure in estuaries. Herein detailed turbulence field measurements were conducted at high frequency and continuously for up to 50 hours per investigation in a small subtropical estuary with semi-diurnal tides. Acoustic Doppler velocimetry was deemed the most appropriate measurement technique for such small estuarine systems with shallow water depths (less than 0.5 m at low tides), and a thorough post-processing technique was applied. The estuarine flow is always a fluctuating process. The bulk flow parameters fluctuated with periods comparable to tidal cycles and other large-scale processes. But turbulence properties depended upon the instantaneous local flow properties. They were little affected by the flow history, but their structure and temporal variability were influenced by a variety of mechanisms. This resulted in behaviour which deviated from that for equilibrium turbulent boundary layer induced by velocity shear only. A striking feature of the data sets is the large fluctuations in all turbulence characteristics during the tidal cycle. This feature was rarely documented, but an important difference between the data sets used in this study from earlier reported measurements is that the present data were collected continuously at high frequency during relatively long periods. The findings bring new lights in the fluctuating nature of momentum exchange coefficients and integral time and length scales. These turbulent properties should not be assumed constant.

Selection bias in gene extraction on the basis of microarray gene-expression data

In the context of cancer diagnosis and treatment, we consider the problem of constructing an accurate prediction rule on the basis of a relatively small number of tumor tissue samples of known type containing the expression data on very many (possibly thousands) genes. Recently, results have been presented in the literature suggesting that it is possible to construct a prediction rule from only a few genes such that it has a negligible prediction error rate. However, in these results the test error or the leave-one-out cross-validated error is calculated without allowance for the selection bias. There is no allowance because the rule is either tested on tissue samples that were used in the first instance to select the genes being used in the rule or because the cross-validation of the rule is not external to the selection process; that is, gene selection is not performed in training the rule at each stage of the cross-validation process. We describe how in practice the selection bias can be assessed and corrected for by either performing a cross-validation or applying the bootstrap external to the selection process. We recommend using 10-fold rather than leave-one-out cross-validation, and concerning the bootstrap, we suggest using the so-called. 632+ bootstrap error estimate designed to handle overfitted prediction rules. Using two published data sets, we demonstrate that when correction is made for the selection bias, the cross-validated error is no longer zero for a subset of only a few genes.

Detailed Measurements during a Transient Front in a Small Subtropical Estuary

High-resolution measurements of velocity and physio-chemistry were conducted before, during and after the passage of a transient front in a small subtropical system about 2.1 km upstream of the river mouth. Detailed acoustic Doppler velocimetry measurements, conducted continuously at 25 Hz, showed the existence of transverse turbulent shear between 300 s prior to the front passage and 1300 s after. This was associated with an increased level of suspended sediment concentration fluctuations, some transverse shear next to the bed and some surface temperature anomaly.

Comparison of BR and QR Eigenvalue Algorithms for Power System Small Signal Stability Analysis

The BR algorithm is a novel and efficient method to find all eigenvalues of upper Hessenberg matrices and has never been applied to eigenanalysis for power system small signal stability. This paper analyzes differences between the BR and the QR algorithms with performance comparison in terms of CPU time based on stopping criteria and storage requirement. The BR algorithm utilizes accelerating strategies to improve its performance when computing eigenvalues of narrowly banded, nearly tridiagonal upper Hessenberg matrices. These strategies significantly reduce the computation time at a reasonable level of precision. Compared with the QR algorithm, the BR algorithm requires fewer iteration steps and less storage space without depriving of appropriate precision in solving eigenvalue problems of large-scale power systems. Numerical examples demonstrate the efficiency of the BR algorithm in pursuing eigenanalysis tasks of 39-, 68-, 115-, 300-, and 600-bus systems. Experiment results suggest that the BR algorithm is a more efficient algorithm for large-scale power system small signal stability eigenanalysis.