Dynamic causal modeling applied to fMRI data shows high reliability

Sensitivity, specificity, and reproducibility are vital to interpret neuroscientific results from functional magnetic resonance imaging (fMRI) experiments. Here we examine the scan–rescan reliability of the percent signal change (PSC) and parameters estimated using Dynamic Causal Modeling (DCM) in scans taken in the same scan session, less than 5 min apart. We find fair to good reliability of PSC in regions that are involved with the task, and fair to excellent reliability with DCM. Also, the DCM analysis uncovers group differences that were not present in the analysis of PSC, which implies that DCM may be more sensitive to the nuances of signal changes in fMRI data.

Antifungal activity of Bacillus subtilis filtrate to control Fusarium oxysporum f.sp. lentis, the causal organism of lentil vascular wilt

In dual cultures, the supernatant filtrate of the biological control agent Bacillus subtilis was evaluated against (Fusarium oxysporum f.sp. lentis) the causal organism of lentil vascular wilt. The antagonistic activity was evaluated as percent reduction of fungal growth (certainly due, in part, to the antifungal metabolites produced by the antagonistic bacterium). The in-vitro experiments showed that B. subtilis filtrate, whether solid or liquid media, had a strong inhibiting activity on the spore germination and mycelial growth of F. oxysporum f. sp. lentis. In a glasshouse experiment, soil was drenched with B. subtilis filtrate at 30 ml/kg (vol/wt) around seedlings of a susceptible lentil line (ILL 4605). In this treatment there was only 31% mortality compared with 100% kill of plants in the control treatment (P≤0.05).

Risk of foot and mouth disease associated with proximity in space and time to infected premises and the implications for control policy during the 2001 epidemic in Cumbria

An analysis was made that calculated the risk of disease for premises in the most heavily affected parts of the county of Cumbria during the foot-and-mouth disease epidemic in the UK in 2001. In over half the cases the occurrence of the disease was not directly attributable to a recently infected premises being located within 1.5 km. Premises more than 1.5 km from recently infected premises faced sufficiently high infection risks that culling within a 1.5 km radius of the infected premises alone could not have prevented the progress of the epidemic. A comparison of the final outcome in two areas of the county, south Penrith and north Cumbria, indicated that focusing on controlling the potential spread of the disease over short distances by culling premises contiguous to infected premises, while the disease continued to spread over longer distances, may have resulted in excessive numbers of premises being culled. Even though the contiguous cull in south Penrith appeared to have resulted in a smaller proportion of premises becoming infected, the overall proportion of premises culled was considerably greater than in north Cumbria, where, because of staff and resource limitations, a smaller proportion of premises contiguous to infected premises was culled

DNA variation in a 13-Mb region including the F9 gene: inferring the genealogical history and causal role of a hemophilia B mutation (IVS 5+13 A -> G)

About 5.5% of all UK hemophilia B patients have the base substitution IVS 5+13 A-->G as the only change in their factor (F)IX gene (F9). This generates a novel donor splice site which fits the consensus better than the normal intron 5 donor splice. Use of the novel splice site should result in a missense mutation followed by the abnormal addition of four amino acids to the patients' FIX. In order to explain the prevalence of this mutation, its genealogical history is examined. Analysis of restriction fragment length polymorphism in the 21 reference UK individuals (from different families) with the above mutation showed identical haplotypes in 19 while two differed from the rest and from each other. In order to investigate the history of the mutation and to verify that it had occurred independently more than once, the sequence variation in 1.5-kb segments scattered over a 13-Mb region including F9 was examined in 18 patients and 15 controls. This variation was then analyzed with a recently developed Bayesian approach that reconstructs the genealogy of the gene investigated while providing evidence of independent mutations that contribute disconnected branches to the genealogical tree. The method also provides minimum estimates of the age of the mutation inherited by the members of coherent trees. This revealed that 17 or 18 mutant genes descend from a founder who probably lived 450 years ago, while one patient carries an independent mutation. The independent recurrence of the IVS5+13 A-->G mutation strongly supports the conclusion that it is the cause of these patients' mild hemophilia.

A longitudinal study of perceptual grouping by proximity, luminance and shape in infants at two, four and six months

Grouping by luminance and shape similarity has previously been demonstrated in neonates and at 4 months, respectively. By contrast, grouping by proximity has hitherto not been investigated in infancy. This is also the first study to chart the developmental emergence of perceptual grouping longitudinally. Sixty-one infants were presented with a matrix of local stimuli grouped horizontally or vertically by luminance, shape or proximity at 2, 4, and 6 months. Infants were exposed to each set of stimuli for three presentation durations. Grouping was demonstrated for luminance similarity at the earliest testing age, 2 months, by shape similarity at 4 months, but was not observed for grouping by proximity. Grouping by shape similarity showed a distinctive pattern of grouping ability across exposure durations, which reflected familiarity preferences followed by novelty preferences. This remained stable across age. No link was found between the emergence of perceptual grouping ability and the exposure duration required to elicit grouping. We conclude by stressing the importance of longitudinal studies of infant development in furthering our understanding of human cognition, rather than relying on assumptions from the adult endstate.

Forecast impact of targeted observations: sensitivity to observation error and proximity to steep orography

For a targeted observations case, the dependence of the size of the forecast impact on the targeted dropsonde observation error in the data assimilation is assessed. The targeted observations were made in the lee of Greenland; the dependence of the impact on the proximity of the observations to the Greenland coast is also investigated. Experiments were conducted using the Met Office Unified Model (MetUM), over a limited-area domain at 24-km grid spacing, with a four-dimensional variational data assimilation (4D-Var) scheme. Reducing the operational dropsonde observation errors by one-half increases the maximum forecast improvement from 5% to 7%–10%, measured in terms of total energy. However, the largest impact is seen by replacing two dropsondes on the Greenland coast with two farther from the steep orography; this increases the maximum forecast improvement from 5% to 18% for an 18-h forecast (using operational observation errors). Forecast degradation caused by two dropsonde observations on the Greenland coast is shown to arise from spreading of data by the background errors up the steep slope of Greenland. Removing boundary layer data from these dropsondes reduces the forecast degradation, but it is only a partial solution to this problem. Although only from one case study, these results suggest that observations positioned within a correlation length scale of steep orography may degrade the forecast through the anomalous upslope spreading of analysis increments along terrain-following model levels.

Pseudomonas syringae pv. coryli, the causal agent of bacterial twig dieback of Corylus avellana

Thirty-eight bacterial strains isolated from hazelnut (Corylus avellana) cv. Tonda Gentile delle Langhe showing a twig dieback in Piedmont and Sardinia, Italy, were studied by a polyphasic approach. All strains were assessed by fatty acids analysis and repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using BOX and ERIC primer sets. Representative strains also were assessed by sequencing the 16S rDNA and hrpL genes, determining the presence of the syrB gene, testing their biochemical and nutritional characteristics, and determining their pathogenicity to hazelnut and other plants species or plant organs. Moreover, they were compared with reference strains of other phytopathogenic pseudomonads. The strains from hazelnut belong to Pseudomonas syringae (sensu latu), LOPAT group Ia. Both fatty acids and repetitive-sequence-based PCR clearly discriminate such strains from other Pseudomonas spp., including P. avellanae and other P. syringae pathovars as well as P. syringae pv. syringae strains from hazelnut. Also, the sequencing of 16S rDNA and hrpL genes differentiated them from P. avellanae and from P. syringae pv. syringae. They did not possess the syrB gene. Some nutritional tests also differentiated them from related P. syringae pathovars. Upon artificial inoculation, these strains incited severe twig diebacks only on hazelnut. Our results justify the creation of a new pathovar because the strains from hazelnut constitute a homogeneous group and a discrete phenon. The name of P. syringae pv. coryli is proposed and criteria for routine identification are presented.

The causal surface and its effect on distribution transparency in a distributed virtual environment

One goal in the development of distributed virtual environments (DVEs) is to create a system such that users are unaware of the distribution-the distribution should be transparent. The paper begins by discussing the general issues in DVEs that might make this possible, and a system that allows some level of distribution transparency is described. The system described suffers from effects of inconsistency, which in turn cause undesirable visual effects. The causal surface is introduced as a solution that removes these visual effects. The paper then introduces two determining factors of distribution transparency relating to user perception and performance. With regard to these factors, two hypotheses are stated relating to the causal surface. A user-trial on forty-five subjects is used to validate the hypotheses. A discussion of the results of the trial concludes that the causal surface solution does significantly improve the distribution transparency in a DVE.

Causal volumes in distributed virtual reality

Research to date has tended to concentrate on bandwidth considerations to increase scalability in distributed interactive simulation and virtual reality systems. This paper proposes that the major concern for latency in user interaction is that of the fundamental limit of communication rate due to the speed of light. Causal volumes and surfaces are introduced as a model of the limitations of causality caused by this fundamental delay. The concept of virtual world critical speed is introduced, which can be determined from the causal surface. The implications of the critical speed are discussed, and relativistic dynamics are used to constrain the object speed, in the same way speeds are bounded in the real world.

Maximising concurrency and scalability in a consistent, causal, distributed virtual reality system, whilst minimising the effect of network delays

The development of large scale virtual reality and simulation systems have been mostly driven by the DIS and HLA standards community. A number of issues are coming to light about the applicability of these standards, in their present state, to the support of general multi-user VR systems. This paper pinpoints four issues that must be readdressed before large scale virtual reality systems become accessible to a larger commercial and public domain: a reduction in the effects of network delays; scalable causal event delivery; update control; and scalable reliable communication. Each of these issues is tackled through a common theme of combining wall clock and causal time-related entity behaviour, knowledge of network delays and prediction of entity behaviour, that together overcome many of the effects of network delay.

Maximising concurrency and scalability in a consistent, causal, distributed virtual reality system, whilst minimising the effect of network delays

The development of large scale virtual reality and simulation systems have been mostly driven by the DIS and HLA standards community. A number of issues are coming to light about the applicability of these standards, in their present state, to the support of general multi-user VR systems. This paper pinpoints four issues that must be readdressed before large scale virtual reality systems become accessible to a larger commercial and public domain: a reduction in the effects of network delays; scalable causal event delivery; update control; and scalable reliable communication. Each of these issues is tackled through a common theme of combining wall clock and causal time-related entity behaviour, knowledge of network delays and prediction of entity behaviour, that together overcome many of the effects of network delays.

Extended Kalman filtering for robotic proximity sensing

The authors address the problems in using a fiber-optic proximity sensor to detect robot end-effector positioning errors in performing a contact task when uncertainties about target position exist. An extended Kalman filter approach is employed to solve the nonlinear filtering problem. Some experimental results are given.

Causal evidence for frontal involvement in memory target maintenance by posterior brain areas during distracter interference of visual working memory

Dorsolateral prefrontal cortex (DLPFC) is recruited during visual working memory (WM) when relevant information must be maintained in the presence of distracting information. The mechanism by which DLPFC might ensure successful maintenance of the contents of WM is, however, unclear; it might enhance neural maintenance of memory targets or suppress processing of distracters. To adjudicate between these possibilities, we applied time-locked transcranial magnetic stimulation (TMS) during functional MRI, an approach that permits causal assessment of a stimulated brain region's influence on connected brain regions, and evaluated how this influence may change under different task conditions. Participants performed a visual WM task requiring retention of visual stimuli (faces or houses) across a delay during which visual distracters could be present or absent. When distracters were present, they were always from the opposite stimulus category, so that targets and distracters were represented in distinct posterior cortical areas. We then measured whether DLPFC-TMS, administered in the delay at the time point when distracters could appear, would modulate posterior regions representing memory targets or distracters. We found that DLPFC-TMS influenced posterior areas only when distracters were present and, critically, that this influence consisted of increased activity in regions representing the current memory targets. DLPFC-TMS did not affect regions representing current distracters. These results provide a new line of causal evidence for a top-down DLPFC-based control mechanism that promotes successful maintenance of relevant information in WM in the presence of distraction.