Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray

We have performed microarray hybridization studies on 40 clinical isolates from 12 common serovars within Salmonella enterica subspecies I to identify the conserved chromosomal gene pool. We were able to separate the core invariant portion of the genome by a novel mathematical approach using a decision tree based on genes ranked by increasing variance. All genes within the core component were confirmed using available sequence and microarray information for S. enterica subspecies I strains. The majority of genes within the core component had conserved homologues in Escherichia coli K-12 strain MG1655. However, many genes present in the conserved set which were absent or highly divergent in K-12 had close homologues in pathogenic bacteria such as Shigella flexneri and Pseudomonas aeruginosa. Genes within previously established virulence determinants such as SPI1 to SPI5 were conserved. In addition several genes within SPI6, all of SPI9, and three fimbrial operons (fim, bcf, and stb) were conserved within all S. enterica strains included in this study. Although many phage and insertion sequence elements were missing from the core component, approximately half the pseudogenes present in S. enterica serovar Typhi were conserved. Furthermore, approximately half the genes conserved in the core set encoded hypothetical proteins. Separation of the core and variant gene sets within S. enterica subspecies I has offered fundamental biological insight into the genetic basis of phenotypic similarity and diversity across S. enterica subspecies I and shown how the core genome of these pathogens differs from the closely related E. coli K-12 laboratory strain.

Variable and strain dependent colonisation of chickens by Escherichia coli O157

The prevalence of enterohaemorrhagic Escherichia coli (EHEC) O157 in poultry is considered minimal compared with other species, especially ruminants. However, deliberate inoculation studies have shown that poultry are readily and persistently infected by this organism but that the mechanism of colonisation is independent of intimin, a recognised factor in host-EHEC interactions in mammalian species, and may be dependent upon flagella. Few strains of EHEC O157 have been tested in poultry and here 1-day-old and 6-week-old chicks were inoculated with seven non-toxigenic E. coli O157 strains in separate experiments. Persistence was measured semi-quantitatively by bacteriological assessment of E. coli O157 cultured from cloacal swabs (shedding score). In the 1-day-old chick model that was monitored for 43 days, all seven strains established well after inoculation. In the 6-week-old chicken model, one strain established and gave consistently high shedding for the duration of the experiment (156 days). Whereas of the remaining six strains, two persisted for 113 days, two persisted for 43 days, one persisted for 22 days and one strain was never detected.

Developing new components for variable flow distribution system modelling in TRNSYS

This study attempts to fill the existing gap in the simulation of variable flow distribution systems through developing new pressure governing components. These components are able to capture the actual ever-changing system performance curve in variable flow distribution systems together with the prediction of controversial issues such as starving, over-flow and the lack of controllability on the flow rate of different branches in a hydronic system. The performance of the proposed components is verified using a case study under design and off-design circumstances. Full integration of the new components within the TRNSYS simulation package is another advantage of this study, which makes it more applicable for designers in both the design and commissioning of hydronic systems.

Simulating the interannual variability of major dust storms on Mars using variable lifting thresholds

The redistribution of a finite amount of martian surface dust during global dust storms and in the intervening periods has been modelled in a dust lifting version of the UK Mars General Circulation Model. When using a constant, uniform threshold in the model’s wind stress lifting parameterisation and assuming an unlimited supply of surface dust, multiannual simulations displayed some variability in dust lifting activity from year to year, arising from internal variability manifested in surface wind stress, but dust storms were limited in size and formed within a relatively short seasonal window. Lifting thresholds were then allowed to vary at each model gridpoint, dependent on the rates of emission or deposition of dust. This enhanced interannual variability in dust storm magnitude and timing, such that model storms covered most of the observed ranges in size and initiation date within a single multiannual simulation. Peak storm magnitude in a given year was primarily determined by the availability of surface dust at a number of key sites in the southern hemisphere. The observed global dust storm (GDS) frequency of roughly one in every 3 years was approximately reproduced, but the model failed to generate these GDSs spontaneously in the southern hemisphere, where they have typically been observed to initiate. After several years of simulation, the surface threshold field—a proxy for net change in surface dust density—showed good qualitative agreement with the observed pattern of martian surface dust cover. The model produced a net northward cross-equatorial dust mass flux, which necessitated the addition of an artificial threshold decrease rate in order to allow the continued generation of dust storms over the course of a multiannual simulation. At standard model resolution, for the southward mass flux due to cross-equatorial flushing storms to offset the northward flux due to GDSs on a timescale of ∼3 years would require an increase in the former by a factor of 3–4. Results at higher model resolution and uncertainties in dust vertical profiles mean that quasi-periodic redistribution of dust on such a timescale nevertheless appears to be a plausible explanation for the observed GDS frequency.

The neural bases of the short-term storage of verbal information are anatomically variable across individuals

What are the precise brain regions supporting the short-term retention of verbal information? A previous functional magnetic resonance imaging (fMRI) study suggested that they may be topographically variable across individuals, occurring, in most, in regions posterior to prefrontal cortex (PFC), and that detection of these regions may be best suited to a single-subject (SS) approach to fMRI analysis (Feredoes and Postle, 2007). In contrast, other studies using spatially normalized group-averaged (SNGA) analyses have localized storage-related activity to PFC. To evaluate the necessity of the regions identified by these two methods, we applied repetitive transcranial magnetic stimulation (rTMS) to SS- and SNGA-identified regions throughout the retention period of a delayed letter-recognition task. Results indicated that rTMS targeting SS analysis-identified regions of left perisylvian and sensorimotor cortex impaired performance, whereas rTMS targeting the SNGA-identified region of left caudal PFC had no effect on performance. Our results support the view that the short-term retention of verbal information can be supported by regions associated with acoustic, lexical, phonological, and speech-based representation of information. They also suggest that the brain bases of some cognitive functions may be better detected by SS than by SNGA approaches to fMRI data analysis.

The variable link between PNA and NAO in observations and in multi-century CGCM simulations

The link between the Pacific/North American pattern (PNA) and the North Atlantic Oscillation (NAO) is investigated in reanalysis data (NCEP, ERA40) and multi-century CGCM runs for present day climate using three versions of the ECHAM model. PNA and NAO patterns and indices are determined via rotated principal component analysis on monthly mean 500 hPa geopotential height fields using the varimax criteria. On average, the multi-century CGCM simulations show a significant anti-correlation between PNA and NAO. Further, multi-decadal periods with significantly enhanced (high anti-correlation, active phase) or weakened (low correlations, inactive phase) coupling are found in all CGCMs. In the simulated active phases, the storm track activity near Newfoundland has a stronger link with the PNA variability than during the inactive phases. On average, the reanalysis datasets show no significant anti-correlation between PNA and NAO indices, but during the sub-period 1973–1994 a significant anti-correlation is detected, suggesting that the present climate could correspond to an inactive period as detected in the CGCMs. An analysis of possible physical mechanisms suggests that the link between the patterns is established by the baroclinic waves forming the North Atlantic storm track. The geopotential height anomalies associated with negative PNA phases induce an increased advection of warm and moist air from the Gulf of Mexico and cold air from Canada. Both types of advection contribute to increase baroclinicity over eastern North America and also to increase the low level latent heat content of the warm air masses. Thus, growth conditions for eddies at the entrance of the North Atlantic storm track are enhanced. Considering the average temporal development during winter for the CGCM, results show an enhanced Newfoundland storm track maximum in the early winter for negative PNA, followed by a downstream enhancement of the Atlantic storm track in the subsequent months. In active (passive) phases, this seasonal development is enhanced (suppressed). As the storm track over the central and eastern Atlantic is closely related to the NAO variability, this development can be explained by the shift of the NAO index to more positive values.

Evaluating relative impact of virtual reality system variables on architectural design comprehension and presence - A variable-centered approach using fractional factorial experiment

The relative contributions of five variables (Stereoscopy, screen size, field of view, level of realism and level of detail) of virtual reality systems on spatial comprehension and presence are evaluated here. Using a variable-centered approach instead of an object-centric view as its theoretical basis, the contributions of these five variables and their two-way interactions are estimated through a 25-1 fractional factorial experiment (screening design) of resolution V with 84 subjects. The experiment design, procedure, measures used, creation of scales and indices, results of statistical analysis, their meaning and agenda for future research are elaborated.

Further evidence for variable synchrotron emission in XTE J1118+480 in outburst

We present simultaneous multicolor infrared and optical photometry of the black hole X-ray transient XTE J1118+480 during its short 2005 January outburst, supported by simultaneous X-ray observations. The variability is dominated by short timescales, ~10 s, although a weak superhump also appears to be present in the optical. The optical rapid variations, at least, are well correlated with those in X-rays. Infrared JHKs photometry, as in the previous outburst, exhibits especially large-amplitude variability. The spectral energy distribution (SED) of the variable infrared component can be fitted with a power law of slope α=-0.78+/-0.07, where F_ν~ν^α. There is no compelling evidence for evolution in the slope over five nights, during which time the source brightness decayed along almost the same track as seen in variations within the nights. We conclude that both short-term variability and longer timescale fading are dominated by a single component of constant spectral shape. We cannot fit the SED of the IR variability with a credible thermal component, either optically thick or thin. This IR SED is, however, approximately consistent with optically thin synchrotron emission from a jet. These observations therefore provide indirect evidence to support jet-dominated models for XTE J1118+480 and also provide a direct measurement of the slope of the optically thin emission, which is impossible, based on the average spectral energy distribution alone.

The dependent variable problem in quantitative studies of Active Labour Market Programmes: uncovering hidden dynamics?

The question of what explains variation in expenditures on Active Labour Market Programs (ALMPs) has attracted significant scholarship in recent years. Significant insights have been gained with respect to the role of employers, unions and dual labour markets, openness, and partisanship. However, there remain significant disagreements with respects to key explanatory variables such the role of unions or the impact of partisanship. Qualitative studies have shown that there are both good conceptual reasons as well as historical evidence that different ALMPs are driven by different dynamics. There is little reason to believe that vastly different programs such as training and employment subsidies are driven by similar structural, interest group or indeed partisan dynamics. The question is therefore whether different ALMPs have the same correlation with different key explanatory variables identified in the literature? Using regression analysis, this paper shows that the explanatory variables identified by the literature have different relation to distinct ALMPs. This refinement adds significant analytical value and shows that disagreements are at least partly due to a dependent variable problem of ‘over-aggregation’.

A generalised Bayesian instrumental variable approach under student t-distributed errors with application

Bayesian analysis is given of an instrumental variable model that allows for heteroscedasticity in both the structural equation and the instrument equation. Specifically, the approach for dealing with heteroscedastic errors in Geweke (1993) is extended to the Bayesian instrumental variable estimator outlined in Rossi et al. (2005). Heteroscedasticity is treated by modelling the variance for each error using a hierarchical prior that is Gamma distributed. The computation is carried out by using a Markov chain Monte Carlo sampling algorithm with an augmented draw for the heteroscedastic case. An example using real data illustrates the approach and shows that ignoring heteroscedasticity in the instrument equation when it exists may lead to biased estimates.

Variable binding and coreference in sentence comprehension: evidence from eye movements

The hypothesis that pronouns can be resolved via either the syntax or the discourse representation has played an important role in linguistic accounts of pronoun interpretation (e.g. Grodzinsky & Reinhart, 1993). We report the results of an eye-movement monitoring study investigating the relative timing of syntactically-mediated variable binding and discourse-based coreference assignment during pronoun resolution. We examined whether ambiguous pronouns are preferentially resolved via either the variable binding or coreference route, and in particular tested the hypothesis that variable binding should always be computed before coreference assignment. Participants’ eye movements were monitored while they read sentences containing a pronoun and two potential antecedents, a c-commanding quantified noun phrase and a non c-commanding proper name. Gender congruence between the pronoun and either of the two potential antecedents was manipulated as an experimental diagnostic for dependency formation. In two experiments, we found that participants’ reading times were reliably longer when the linearly closest antecedent mismatched in gender with the pronoun. These findings fail to support the hypothesis that variable binding is computed before coreference assignment, and instead suggest that antecedent recency plays an important role in affecting the extent to which a variable binding antecedent is considered. We discuss these results in relation to models of memory retrieval during sentence comprehension, and interpret the antecedent recency preference as an example of forgetting over time.

Impact of variable atmospheric and oceanic form drag on simulations of Arctic sea ice

Over Arctic sea ice, pressure ridges and floe andmelt pond edges all introduce discrete obstructions to the flow of air or water past the ice and are a source of form drag. In current climate models form drag is only accounted for by tuning the air–ice and ice–ocean drag coefficients, that is, by effectively altering the roughness length in a surface drag parameterization. The existing approach of the skin drag parameter tuning is poorly constrained by observations and fails to describe correctly the physics associated with the air–ice and ocean–ice drag. Here, the authors combine recent theoretical developments to deduce the total neutral form drag coefficients from properties of the ice cover such as ice concentration, vertical extent and area of the ridges, freeboard and floe draft, and the size of floes and melt ponds. The drag coefficients are incorporated into the Los Alamos Sea Ice Model (CICE) and show the influence of the new drag parameterization on the motion and state of the ice cover, with the most noticeable being a depletion of sea ice over the west boundary of the Arctic Ocean and over the Beaufort Sea. The new parameterization allows the drag coefficients to be coupled to the sea ice state and therefore to evolve spatially and temporally. It is found that the range of values predicted for the drag coefficients agree with the range of values measured in several regions of the Arctic. Finally, the implications of the new form drag formulation for the spinup or spindown of the Arctic Ocean are discussed.

Gaussian anamorphosis in the analysis step of the EnKF: a joint state-variable/observation approach

The analysis step of the (ensemble) Kalman filter is optimal when (1) the distribution of the background is Gaussian, (2) state variables and observations are related via a linear operator, and (3) the observational error is of additive nature and has Gaussian distribution. When these conditions are largely violated, a pre-processing step known as Gaussian anamorphosis (GA) can be applied. The objective of this procedure is to obtain state variables and observations that better fulfil the Gaussianity conditions in some sense. In this work we analyse GA from a joint perspective, paying attention to the effects of transformations in the joint state variable/observation space. First, we study transformations for state variables and observations that are independent from each other. Then, we introduce a targeted joint transformation with the objective to obtain joint Gaussianity in the transformed space. We focus primarily in the univariate case, and briefly comment on the multivariate one. A key point of this paper is that, when (1)-(3) are violated, using the analysis step of the EnKF will not recover the exact posterior density in spite of any transformations one may perform. These transformations, however, provide approximations of different quality to the Bayesian solution of the problem. Using an example in which the Bayesian posterior can be analytically computed, we assess the quality of the analysis distributions generated after applying the EnKF analysis step in conjunction with different GA options. The value of the targeted joint transformation is particularly clear for the case when the prior is Gaussian, the marginal density for the observations is close to Gaussian, and the likelihood is a Gaussian mixture.