Molecular cloning and comparative analysis of four beta-galactosidase genes from Bifidobacterium bifidum NCIMB41171

Bifidobacterium bifidum NCIMB41171 carries four genes encoding different beta-galactosidases. One of them, named bbgIII, consisted of an open reading frame of 1,935 amino acid (a.a.) residues encoding a protein with a multidomain structure, commonly identified on cell wall bound enzymes, having a signal peptide, a membrane anchor, FIVAR domains, immunoglobulin Ig-like and discoidin-like domains. The other three genes, termed bbgI, bbgII and bbgIV, encoded proteins of 1,291, 689 and 1,052 a.a. residues, respectively, which were most probably intracellularly located. Two cases of protein evolution between strains of the same species were identified when the a.a. sequences of the BbgI and BbgIII were compared with homologous proteins from B. bifidum DSM20215. The homologous proteins were found to be differentiated at the C-terminal a.a. part either due to a single nucleotide insertion or to a whole DNA sequence insertion, respectively. The bbgIV gene was located in a gene organisation surrounded by divergently transcribed genes putatively for sugar transport (galactoside-symporter) and gene regulation (LacI-transcriptional regulator), a structure that was found to be highly conserved in B. longum, B. adolescentis and B. infantis, suggesting optimal organisation shared amongst those species.

Detection of neural correlates of self-paced motor activity using empirical mode decomposition phase locking analysis

Transient episodes of synchronisation of neuronal activity in particular frequency ranges are thought to underlie cognition. Empirical mode decomposition phase locking (EMDPL) analysis is a method for determining the frequency and timing of phase synchrony that is adaptive to intrinsic oscillations within data, alleviating the need for arbitrary bandpass filter cut-off selection. It is extended here to address the choice of reference electrode and removal of spurious synchrony resulting from volume conduction. Spline Laplacian transformation and independent component analysis (ICA) are performed as pre-processing steps, and preservation of phase synchrony between synthetic signals. combined using a simple forward model, is demonstrated. The method is contrasted with use of bandpass filtering following the same preprocessing steps, and filter cut-offs are shown to influence synchrony detection markedly. Furthermore, an approach to the assessment of multiple EEG trials using the method is introduced, and the assessment of statistical significance of phase locking episodes is extended to render it adaptive to local phase synchrony levels. EMDPL is validated in the analysis of real EEG data, during finger tapping. The time course of event-related (de)synchronisation (ERD/ERS) is shown to differ from that of longer range phase locking episodes, implying different roles for these different types of synchronisation. It is suggested that the increase in phase locking which occurs just prior to movement, coinciding with a reduction in power (or ERD) may result from selection of the neural assembly relevant to the particular movement. (C) 2009 Elsevier B.V. All rights reserved.

Adaptive deadbeat control of stochastic systems

This paper considers the use of a discrete-time deadbeat control action on systems affected by noise. Variations on the standard controller form are discussed and comparisons are made with controllers in which noise rejection is a higher priority objective. Both load and random disturbances are considered in the system description, although the aim of the deadbeat design remains as a tailoring of reference input variations. Finally, the use of such a deadbeat action within a self-tuning control framework is shown to satisfy, under certain conditions, the self-tuning property, generally though only when an extended form of least-squares estimation is incorporated.

Detection of somaclonal variation during cocoa somatic embryogenesis characterised using cleaved amplified polymorphic sequence and the new freeware Artbio

The scarcity and stochastic nature of genetic mutations presents a significant challenge for scientists seeking to characterise de novo mutation frequency at specific loci. Such mutations can be particularly numerous during regeneration of plants from in vitro culture and can undermine the value of germplasm conservation efforts. We used cleaved amplified polymorphic sequence (CAPS) analysis to characterise new mutations amongst a clonal population of cocoa plants regenerated via a somatic embryogenesis protocol used previously for cocoa cryopreservation. Efficacy of the CAPS system for mutation detection was greatly improved after an ‘a priori’ in silico screen of reference target sequences for actual and potential restriction enzyme recognition sites using a new freely available software called Artbio. Artbio surveys known sequences for existing restriction enzyme recognition sites but also identifies all single nucleotide polymorphism (SNP) deviations from such motifs. Using this software, we performed an in silico screen of seven loci for restriction sites and their potential mutant SNP variants that were possible from 21 restriction enzymes. The four most informative locus-enzyme combinations were then used to survey the regenerant populations for de novo mutants. We characterised the pattern of point mutations and, using the outputs of Artbio, calculated the ratio of base substitution in 114 somatic embryo-derived cocoa regenerants originating from two explant genotypes. We found 49 polymorphisms, comprising 26.3% of the samples screened, with an inferred rate of 2.8 × 10−3 substitutions/screened base. This elevated rate is of a similar order of magnitude to previous reports of de novo microsatellite length mutations arising in the crop and suggests caution should be exercised when applying somatic embryogenesis for the conservation of plant germplasm.

The decomposition of some RDX and HMX based materials in the one dimensional time to explosion apparatus. Part 2. Estimating the violence of the cook-off event

Various methods of assessment have been applied to the One Dimensional Time to Explosion (ODTX) apparatus and experiments with the aim of allowing an estimate of the comparative violence of the explosion event to be made. Non-mechanical methods used were a simple visual inspection, measuring the increase in the void volume of the anvils following an explosion and measuring the velocity of the sound produced by the explosion over 1 metre. Mechanical methods used included monitoring piezo-electric devices inserted in the frame of the machine and measuring the rotational velocity of a rotating bar placed on the top of the anvils after it had been displaced by the shock wave. This last method, which resembles original Hopkinson Bar experiments, seemed the easiest to apply and analyse, giving relative rankings of violence and the possibility of the calculation of a “detonation” pressure.

Measuring societal awareness of the rural agrarian landscape: indicators and scale issues

The work presented in this report is part of the effort to define the landscape state and diversity indicator in the frame of COM (2006) 508 “Development of agri-environmental indicators for monitoring the integration of environmental concerns into the common agricultural policy”. The Communication classifies the indicators according to their level of development, which, for the landscape indicator is “in need of substantial improvements in order to become fully operational”. For this reason a full re-definition of the indicator has been carried out, following the initial proposal presented in the frame of the IRENA operation (“Indicator Reporting on the Integration of Environmental Concerns into Agricultural Policy”). The new proposal for the landscape state and diversity indicator is structured in three components: the first concerns the degree of naturalness, the second landscape structure, the third the societal appreciation of the rural landscape. While the first two components rely on a strong bulk of existing literature, the development of the methodology has made evident the need for further analysis of the third component, which is based on a newly proposed top-down approach. This report presents an in-depth analysis of such component of the indicator, and the effort to include a social dimension in large scale landscape assessment.

A global picture of the seasonal persistence of stratospheric ozone anomalies

Interannual anomalies in vertical profiles of stratospheric ozone, in both equatorial and extratropical regions, have been shown to exhibit a strong seasonal persistence, namely, extended temporal autocorrelations during certain times of the calendar year. Here we investigate the relationship between this seasonal persistence of equatorial and extratropical ozone anomalies using the SAGE‐corrected SBUV data set, which provides a long‐term ozone profile time series. For the regions of the stratosphere where ozone is under purely dynamical or purely photochemical control, the seasonal persistence of equatorial and extratropical ozone anomalies arises from distinct mechanisms but preserves an anticorrelation between tropical and extratropical anomalies established during the winter period. In the 16–10 hPa layer, where ozone is controlled by both dynamical and photochemical processes, equatorial ozone anomalies exhibit a completely different behavior compared to ozone anomalies above and below in terms of variability, seasonal persistence, and especially the relationship between equatorial and extratropical ozone. Cross‐latitude‐time correlations show that for the 16–10 hPa layer, Northern Hemisphere (NH) extratropical ozone anomalies show the same variability as equatorial ozone anomalies but lagged by 3–6 months. High correlation coefficients are observed during the time frame of seasonal persistence of ozone anomalies, which is June– December for equatorial ozone and shifts by approximately 3–6 months when going from the equatorial region to NH extratropics. Thus in the transition zone between dynamical and photochemical control, equatorial ozone anomalies established in boreal summer/autumn are mirrored by NH extratropical ozone anomalies with a time lag similar to transport time scales. Equatorial ozone anomalies established in boreal winter/spring are likewise correlated with ozone anomalies in the Southern Hemisphere extratropics with a time lag comparable to transport time scales, similar to what is seen in the NH. However, the correlations between equatorial and SH extratropical ozone in the 10–16 hPa layer are weak.

The structure of paranoia in the general population

Background: Psychotic phenomena appear to form a continuum with normal experience and beliefs, and may build on common emotional interpersonal concerns. Aims: We tested predictions that paranoid ideation is exponentially distributed and hierarchically arranged in the general population, and that persecutory ideas build on more common cognitions of mistrust, interpersonal sensitivity and ideas of reference. Method: Items were chosen from the Structured Clinical Interview for DSM-IV Axis II Disorders (SCID-II) questionnaire and the Psychosis Screening Questionnaire in the second British National Survey of Psychiatric Morbidity (n = 8580), to test a putative hierarchy of paranoid development using confirmatory factor analysis, latent class analysis and factor mixture modelling analysis. Results: Different types of paranoid ideation ranged in frequency from less than 2% to nearly 30%. Total scores on these items followed an almost perfect exponential distribution (r = 0.99). Our four a priori first-order factors were corroborated (interpersonal sensitivity; mistrust; ideas of reference; ideas of persecution). These mapped onto four classes of individual respondents: a rare, severe, persecutory class with high endorsement of all item factors, including persecutory ideation; a quasi-normal class with infrequent endorsement of interpersonal sensitivity, mistrust and ideas of reference, and no ideas of persecution; and two intermediate classes, characterised respectively by relatively high endorsement of items relating to mistrust and to ideas of reference. Conclusions: The paranoia continuum has implications for the aetiology, mechanisms and treatment of psychotic disorders, while confirming the lack of a clear distinction from normal experiences and processes.

A reprocessing for climate of sea surface temperature from the Along-Track Scanning Radiometers: a new retrieval scheme

We present a new coefficient-based retrieval scheme for estimation of sea surface temperature (SST) from the Along Track Scanning Radiometer (ATSR) instruments. The new coefficients are banded by total column water vapour (TCWV), obtained from numerical weather prediction analyses. TCWV banding reduces simulated regional retrieval biases to < 0.1 K compared to biases ~ 0.2 K for global coefficients. Further, detailed treatment of the instrumental viewing geometry reduces simulated view-angle related biases from ~ 0.1 K down to < 0.005 K for dual-view retrievals using channels at 11 and 12 μm. A novel analysis of trade-offs related to the assumed noise level when defining coefficients is undertaken, and we conclude that adding a small nominal level of noise (0.01 K) is optimal for our purposes. When applied to ATSR observations, some inter-algorithm biases appear as TCWV-related differences in SSTs estimated from different channel combinations. The final step in coefficient determination is to adjust the offset coefficient in each TCWV band to match results from a reference algorithm. This reference uses the dual-view observations of 3.7 and 11 μm. The adjustment is independent of in situ measurements, preserving independence of the retrievals. The choice of reference is partly motivated by uncertainty in the calibration of the 12 μm of Advanced ATSR. Lastly, we model the sensitivities of the new retrievals to changes to TCWV and changes in true SST, confirming that dual-view SSTs are most appropriate for climatological applications

Dissociation between the impact of evidence on eye movement target choice and confidence judgements

It has been suggested that the evidence used to support a decision to move our eyes and the confidence we have in that decision are derived from a common source. Alternatively, confidence may be based on further post-decisional processes. In three experiments we examined this. In Experiment 1, participants chose between two targets on the basis of varying levels of evidence (i.e., the direction of motion coherence in a Random-Dot-Kinematogram). They indicated this choice by making a saccade to one of two targets and then indicated their confidence. Saccade trajectory deviation was taken as a measure of the inhibition of the non-selected target. We found that as evidence increased so did confidence and deviations of saccade trajectory away from the non-selected target. However, a correlational analysis suggested they were not related. In Experiment 2 an option to opt-out of the choice was offered on some trials if choice proved too difficult. In this way we isolated trials on which confidence in target selection was high (i.e., when the option to opt-out was available but not taken). Again saccade trajectory deviations were found not to differ in relation to confidence. In Experiment 3 we directly manipulated confidence, such that participants had high or low task confidence. They showed no differences in saccade trajectory deviations. These results support post-decisional accounts of confidence: evidence supporting the decision to move the eyes is reflected in saccade control, but the confidence that we have in that choice is subject to further post-decisional processes.

A review of the cognitive effects observed in humans following acute supplementation with flavonoids, and their associated mechanisms of action

Flavonoids are polyphenolic compounds found in varying concentrations in many plant-based foods. Recent studies suggest that flavonoids can be beneficial to both cognitive and physiological health. Long term flavonoid supplementation over a period of weeks or months has been extensively investigated and reviewed, particularly with respect to cognitive ageing and neurodegenerative disease. Significantly less focus has been directed towards the short term effects of single doses of flavonoids on cognition. Here, we review 21 such studies with particular emphasis on the subclass and dose of flavonoids administered, the cognitive domains affected by flavonoid supplementation, and the effect size of the response. The emerging evidence suggests that flavonoids may be beneficial to attention, working memory, and psychomotor processing speed in a general population. Episodic memory effects are less well defined and may be restricted to child or older adult populations. The evidence also points towards a dose-dependent effect of flavonoids, but the physiological mechanisms of action remain unclear. Overall, there is encouraging evidence that flavonoid supplementation can benefit cognitive outcomes within an acute time frame of 0–6 h. But larger studies, combining cognitive and physiological measures, are needed to strengthen the evidence base.

Connecting climate model projections of global temperature change with the real world

Current state-of-the-art global climate models produce different values for Earth’s mean temperature. When comparing simulations with each other and with observations it is standard practice to compare temperature anomalies with respect to a reference period. It is not always appreciated that the choice of reference period can affect conclusions, both about the skill of simulations of past climate, and about the magnitude of expected future changes in climate. For example, observed global temperatures over the past decade are towards the lower end of the range of CMIP5 simulations irrespective of what reference period is used, but exactly where they lie in the model distribution varies with the choice of reference period. Additionally, we demonstrate that projections of when particular temperature levels are reached, for example 2K above ‘pre-industrial’, change by up to a decade depending on the choice of reference period. In this article we discuss some of the key issues that arise when using anomalies relative to a reference period to generate climate projections. We highlight that there is no perfect choice of reference period. When evaluating models against observations, a long reference period should generally be used, but how long depends on the quality of the observations available. The IPCC AR5 choice to use a 1986-2005 reference period for future global temperature projections was reasonable, but a case-by-case approach is needed for different purposes and when assessing projections of different climate variables. Finally, we recommend that any studies that involve the use of a reference period should explicitly examine the robustness of the conclusions to alternative choices.

Back to basics: how measures of lexical diversity can help discriminate between CEFR levels

This study contributes to ongoing discussions on how measures of lexical diversity (LD) can help discriminate between essays from second language learners of English, whose work has been assessed as belonging to levels B1 to C2 of the Common European Framework of Reference (CEFR). The focus is in particular on how different operationalisations of what constitutes a “different word” (type) impact on the LD measures themselves and on their ability to discriminate between CEFR levels. The results show that basic measures of LD, such as the number of different words, the TTR (Templin 1957) and the Index of Guiraud (Guiraud 1954) explain more variance in the CEFR levels than sophisticated measures, such as D (Malvern et al. 2004), HD-D (McCarthy and Jarvis 2007) and MTLD (McCarthy 2005) provided text length is kept constant across texts. A simple count of different words (defined as lemma’s and not as word families) was the best predictor of CEFR levels and explained 22 percent of the variance in overall scores on the Pearson Test of English Academic in essays written by 176 test takers.

Asymmetric oxidation of vinyl- and ethynyl terthiophene ligands in triruthenium complexes

A series of ruthenium(II) complexes [{RuCl(CO)(PMe3)3(–CHvCH–)}nX], 1a–1c (1a: n = 3, X = 3,3’’- dimethyl-2,2’:3’,2’’-terthiophene; 1b: n = 2, X = 2,2’-bithiophene; 1c: n = 2, X = 2,3-bis(3-methylthiophen- 2-yl)benzothiophene) and [{Cp*(dppe)2Ru(–CuC–)}3X], 1d (X = 3,3’’-dimethyl-2,2’:3’,2’’- terthiophene), were prepared and characterized by 1H, 13C and 31P NMR. Their redox, spectroscopic and bonding properties were studied with a range of spectro-electrochemical methods in combination with density functional theory calculations. The first two anodic steps observed for 1a and 1d are largely localized on the lateral frameworks of the molecular triangle, the direct conjugation between them being precluded due to the photostable open form of the dithienyl ethene moiety. The third anodic step is then mainly localized on the centerpiece of the triangular structure, affecting both bithiophene laterals. The experimental IR and UV-vis-NIR spectroelectrochemical data and, largely, also DFT calculations account for this explanation, being further supported by direct comparison with the anodic behavior of reference diruthenium complexes 1b and 1c.

LOFZY 2005 - Field experiment on Cyclones over the Norwegian Sea: meteorological measurements of the research aircraft Falcon, 23 autonomous water buoys and radiosoundings at the research vessel Celtic Explorer

The field campaign LOFZY 2005 (LOFoten ZYklonen, engl.: Cyclones) was carried out in the frame of Collaborative Research Centre 512, which deals with low-pressure systems (cyclones) and the climate system of the North Atlantic. Cyclones are of special interest due to their influence on the interaction between atmosphere and ocean. Cyclone activity in the northern part of the Atlantic Ocean is notably high and is of particular importance for the entire Atlantic Ocean. An area of maximum precipitation exists in front of the Norwegian Lofoten islands. One aim of the LOFZY field campaign was to clarify the role cyclones play in the interaction of ocean and atmosphere. In order to obtain a comprehensive dataset of cyclone activity and ocean-atmosphere interaction a field experiment was carried out in the Lofoten region during March and April 2005. Employed platforms were the Irish research vessel RV Celtic Explorer which conducted a meteorological (radiosondes, standard parameters, observations) and an oceanographic (CTD) program. The German research aircraft Falcon accomplished eight flight missions (between 4-21 March) to observe synoptic conditions with high spatial and temporal resolution. In addition 23 autonomous marine buoys were deployed in advance of the campaign in the observed area to measure drift, air-temperature and -pressure and water-temperature. In addition to the published datasets several other measurements were performed during the experiment. Corresonding datasets will be published in the near future and are available on request. Details about all used platforms and sensors and all performed measurements are listed in the fieldreport. The following datasets are available on request: ground data at RV Celtic Explorer