Bernoulli free-boundary problems in strip-like domains and a property of permanent waves on water of finite depth

We study weak solutions for a class of free-boundary problems which includes as a special case the classical problem of travelling gravity waves on water of finite depth. We show that such problems are equivalent to problems in fixed domains and study the regularity of their solutions. We also prove that in very general situations the free boundary is necessarily the graph of a function.

A universal primer for isolation of fragments of a gene encoding phytoene desaturase for use in virus-induced gene silencing (VIGS) studies

We have been using Virus-Induced Gene Silencing (VIGS) to test the function of genes that are candidates for involvement in floral senescence. Although VIGS is a powerful tool for assaying the effects of gene silencing in plants, relatively few taxa have been studied using this approach, and most that have are in the Solanaceae. We typically use silencing of phytoene desaturase (PDS) in preliminary tests of the feasibility of using VIGS. Silencing this gene, whose product is involved in carotene biosynthesis, results in a characteristic photobleaching phenotype in the leaves. We have found that efficient silencing requires the use of fragments that are more than 90% homologous to the target gene. To simplify testing the effectiveness of VIGS in a range of species, we designed a set of universal primers to a region of the PDS gene that is highly conserved among species, and that therefore allows an investigator to isolate a fragment of the homologous PDS gene from the species of interest. We report the sequences of these primers and the results of VIGS experiments in horticultural species from the Asteraceae, Leguminosae, Balsaminaceae and Solanaceae.

Operator performance evaluation of controlled depth of field in a stereographically displayed virtual environment

Retinal blurring resulting from the human eye's depth of focus has been shown to assist visual perception. Infinite focal depth within stereoscopically displayed virtual environments may cause undesirable effects, for instance, objects positioned at a distance in front of or behind the observer's fixation point will be perceived in sharp focus with large disparities thereby causing diplopia. Although published research on incorporation of synthetically generated Depth of Field (DoF) suggests that this might act as an enhancement to perceived image quality, no quantitative testimonies of perceptional performance gains exist. This may be due to the difficulty of dynamic generation of synthetic DoF where focal distance is actively linked to fixation distance. In this paper, such a system is described. A desktop stereographic display is used to project a virtual scene in which synthetically generated DoF is actively controlled from vergence-derived distance. A performance evaluation experiment on this system which involved subjects carrying out observations in a spatially complex virtual environment was undertaken. The virtual environment consisted of components interconnected by pipes on a distractive background. The subject was tasked with making an observation based on the connectivity of the components. The effects of focal depth variation in static and actively controlled focal distance conditions were investigated. The results and analysis are presented which show that performance gains may be achieved by addition of synthetic DoF. The merits of the application of synthetic DoF are discussed.

Judging size, distance and depth with an active telepresence system

A visual telepresence system has been developed at the University of Reading which utilizes eye tracing to adjust the horizontal orientation of the cameras and display system according to the convergence state of the operator's eyes. Slaving the cameras to the operator's direction of gaze enables the object of interest to be centered on the displays. The advantage of this is that the camera field of view may be decreased to maximize the achievable depth resolution. An active camera system requires an active display system if appropriate binocular cues are to be preserved. For some applications, which critically depend upon the veridical perception of the object's location and dimensions, it is imperative that the contribution of binocular cues to these judgements be ascertained because they are directly influenced by camera and display geometry. Using the active telepresence system, we investigated the contribution of ocular convergence information to judgements of size, distance and shape. Participants performed an open- loop reach and grasp of the virtual object under reduced cue conditions where the orientation of the cameras and the displays were either matched or unmatched. Inappropriate convergence information produced weak perceptual distortions and caused problems in fusing the images.

A simple relationship between volcanic sulfate aerosol optical depth and surface temperature change simulated in an atmosphere-ocean general circulation model.

In this study we quantify the relationship between the aerosol optical depth increase from a volcanic eruption and the severity of the subsequent surface temperature decrease. This investigation is made by simulating 10 different sizes of eruption in a global circulation model (GCM) by changing stratospheric sulfate aerosol optical depth at each time step. The sizes of the simulated eruptions range from Pinatubo‐sized up to the magnitude of supervolcanic eruptions around 100 times the size of Pinatubo. From these simulations we find that there is a smooth monotonic relationship between the global mean maximum aerosol optical depth anomaly and the global mean temperature anomaly and we derive a simple mathematical expression which fits this relationship well. We also construct similar relationships between global mean aerosol optical depth and the temperature anomaly at every individual model grid box to produce global maps of best‐fit coefficients and fit residuals. These maps are used with caution to find the eruption size at which a local temperature anomaly is clearly distinct from the local natural variability and to approximate the temperature anomalies which the model may simulate following a Tambora‐sized eruption. To our knowledge, this is the first study which quantifies the relationship between aerosol optical depth and resulting temperature anomalies in a simple way, using the wealth of data that is available from GCM simulations.

Quantifying the response of the ORAC aerosol optical depth retrieval for MSG SEVIRI to aerosol model assumptions

We test the response of the Oxford-RAL Aerosol and Cloud (ORAC) retrieval algorithm for MSG SEVIRI to changes in the aerosol properties used in the dust aerosol model, using data from the Dust Outflow and Deposition to the Ocean (DODO) flight campaign in August 2006. We find that using the observed DODO free tropospheric aerosol size distribution and refractive index increases simulated top of the atmosphere radiance at 0.55 µm assuming a fixed erosol optical depth of 0.5 by 10–15 %, reaching a maximum difference at low solar zenith angles. We test the sensitivity of the retrieval to the vertical distribution f the aerosol and find that this is unimportant in determining simulated radiance at 0.55 µm. We also test the ability of the ORAC retrieval when used to produce the GlobAerosol dataset to correctly identify continental aerosol outflow from the African continent and we find that it poorly constrains aerosol speciation. We develop spatially and temporally resolved prior distributions of aerosols to inform the retrieval which incorporates five aerosol models: desert dust, maritime, biomass burning, urban and continental. We use a Saharan Dust Index and the GEOS-Chem chemistry transport model to describe dust and biomass burning aerosol outflow, and compare AOD using our speciation against the GlobAerosol retrieval during January and July 2006. We find AOD discrepancies of 0.2–1 over regions of intense biomass burning outflow, where AOD from our aerosol speciation and GlobAerosol speciation can differ by as much as 50 - 70 %.

Transcriptional regulators of the GAD acid stress island are carried by effector protein-encoding prophages and indirectly control type III secretion in enterohemorrhagic Escherichia coli O157:H7

P>Type III secretion (T3S) plays a pivotal role in the colonization of ruminant hosts by Enterohemorrhagic Escherichia coli (EHEC). The T3S system translocates effector proteins into host cells to promote bacterial attachment and persistence. The repertoire and variation in prophage regions underpins differences in the pathogenesis and epidemiology of EHEC strains. In this study, we have used a collection of deletions in cryptic prophages and EHEC O157 O-islands to screen for novel regulators of T3S. Using this approach we have identified a family of homologous AraC-like regulators that indirectly repress T3S. These prophage-encoded secretion regulator genes (psr) are found exclusively on prophages and are associated with effector loci and the T3S activating Pch family of regulators. Transcriptional profiling, mutagenesis and DNA binding studies were used to show that these regulators usurp the conserved GAD acid stress resistance system to regulate T3S by increasing the expression of GadE (YhiE) and YhiF and that this regulation follows attachment to bovine epithelial cells. We further demonstrate that PsrA and effectors encoded within cryptic prophage CP933-N are required for persistence in a ruminant model of colonization.

Complete sequence and molecular epidemiology of IncK epidemic plasmid encoding bla(CTX-M-14)

Antimicrobial drug resistance is a global challenge for the 21st century with the emergence of resistant bacterial strains worldwide. Transferable resistance to beta-lactam antimicrobial drugs, mediated by production of extended-spectrum beta-lactamases (ESBLs), is of particular concern. In 2004, an ESBL-carrying IncK plasmid (pCT) was isolated from cattle in the United Kingdom. The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, bla(CTX-M-14). From this information, PCRs identifying novel features of pCT were designed and applied to isolates from several countries, showing that the plasmid has disseminated worldwide in bacteria from humans and animals. Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals.

Development and validation of a qPCR-based method for quantifying Shiga toxin-encoding and other lambdoid bacteriophages

P>To address whether seasonal variability exists among Shiga toxin-encoding bacteriophage (Stx phage) numbers on a cattle farm, conventional plaque assay was performed on water samples collected over a 17 month period. Distinct seasonal variation in bacteriophage numbers was evident, peaking between June and August. Removal of cattle from the pasture precipitated a reduction in bacteriophage numbers, and during the winter months, no bacteriophage infecting Escherichia coli were detected, a surprising occurrence considering that 1031 tailed-bacteriophages are estimated to populate the globe. To address this discrepancy a culture-independent method based on quantitative PCR was developed. Primers targeting the Q gene and stx genes were designed that accurately and discriminately quantified artificial mixed lambdoid bacteriophage populations. Application of these primer sets to water samples possessing no detectable phages by plaque assay, demonstrated that the number of lambdoid bacteriophage ranged from 4.7 x 104 to 6.5 x 106 ml-1, with one in 103 free lambdoid bacteriophages carrying a Shiga toxin operon (stx). Specific molecular biological tools and discriminatory gene targets have enabled virus populations in the natural environment to be enumerated and similar strategies could replace existing propagation-dependent techniques, which grossly underestimate the abundance of viral entities.

Is prospective memory enhanced by cue-action semantic relatedness and enactment at encoding?

Benefits and costs on prospective memory performance, of enactment at encoding and a semantic association between a cue-action word pair, were investigated in two experiments. Findings revealed superior performance for both younger and older adults following enactment, in contrast to verbal encoding, and when cue-action semantic relatedness was high. Although younger adults outperformed older adults, age did not moderate benefits of cue-action relatedness or enactment. Findings from a second experiment revealed that the inclusion of an instruction to perform a prospective memory task led to increments in response latency to items from the ongoing activity in which that task was embedded, relative to latencies when the ongoing task only was performed. However, this task interference ‘cost’ did not differ as a function of either cue-action relatedness or enactment. We argue that the high number of cue-action pairs employed here influenced meta-cognitive consciousness, hence determining attention allocation, in all experimental conditions.

Moderate drought alters biomass and depth distribution of fine roots in Norway spruce

A rain shelter experiment was conducted in a 90-year-old Norway spruce stand, in the Kysucké Beskydy Mts (Slovakia). Three rain shelters were constructed in the stand to prevent the rainfall from reaching the soil and to reduce water availability in the rhizosphere. Fine root biomass and necromass were repeatedly measured throughout a growing season by soil coring. We established the quantities of fine root biomass (live) and necromass (dead) at soil depths of 0-5, 5-15, 15-25, and 25-35 cm. Significant differences in soil moisture contents between control and drought plots were found in the top 15 cm of soil after 20 weeks of rainfall manipulation (lasting from early June to late October). Our observations show that even relatively light drought decreased total fine root biomass from 272.0 to 242.8 g m-2 and increased the amount of necromass from 79.2 to 101.2 g m-2 in the top 35 cm of soil. Very fine roots, i.e. those with diameter up to 1 mm, were more affected than total fine roots defined as 0-2 mm. The effect of reduced water availability was depth-specific, as a result we observed a modification of vertical distribution of fine roots. More roots in drought treatment were produced in the wetter soil horizons at 25-35 cm depth than at the surface. We conclude that fine and very fine root systems of Norway spruce have the capacity to re-allocate resources to roots at different depths in response to environmental signals, resulting in changes in necromass to biomass ratio.

Ground-based aerosol optical depth trends at three high-altitude sites in Switzerland and Southern Germany from 1995–2010

Ground-based aerosol optical depth (AOD) climatologies at three high-altitude sites in Switzerland (Jungfraujoch and Davos) and Southern Germany (Hohenpeissenberg) are updated and re-calibrated for the period 1995 – 2010. In addition, AOD time-series are augmented with previously unreported data, and are homogenized for the first time. Trend analysis revealed weak AOD trends (λ = 500 nm) at Jungfraujoch (JFJ; +0.007 decade-1), Davos (DAV; +0.002 decade-1) and Hohenpeissenberg (HPB; -0.011 decade-1) where the JFJ and HPB trends were statistically significant at the 95% and 90% confidence levels. However, a linear trend for the JFJ 1995 – 2005 period was found to be more appropriate than for 1995 – 2010 due to the influence of stratospheric AOD which gave a trend -0.003 decade-1 (significant at 95% level). When correcting for a recently available stratospheric AOD time-series, accounting for Pinatubo (1991) and more recent volcanic eruptions, the 1995 – 2010 AOD trends decreased slightly at DAV and HPB but remained weak at +0.000 decade-1 and -0.013 decade-1 (significant at 95% level). The JFJ 1995 – 2005 AOD time-series similarly decreased to -0.003 decade-1 (significant at 95% level). We conclude that despite a more detailed re40 analysis of these three time-series, which have been extended by five years to the end of 2010, a significant decrease in AOD at these three high-altitude sites has still not been observed.

Experimental and modeled UV erthemal irradiance under overcast conditions: the role of cloud optical depth

This paper evaluates the relationship between the cloud modification factor (CMF) in the ultraviolet erythe- mal range and the cloud optical depth (COD) retrieved from the Aerosol Robotic Network (AERONET) "cloud mode" algorithm under overcast cloudy conditions (confirmed with sky images) at Granada, Spain, mainly for non-precipitating, overcast and relatively homogenous water clouds. Empirical CMF showed a clear exponential dependence on experimental COD values, decreasing approximately from 0.7 for COD=10 to 0.25 for COD=50. In addition, these COD measurements were used as input in the LibRadtran radia tive transfer code allowing the simulation of CMF values for the selected overcast cases. The modeled CMF exhibited a dependence on COD similar to the empirical CMF, but modeled values present a strong underestimation with respect to the empirical factors (mean bias of 22 %). To explain this high bias, an exhaustive comparison between modeled and experimental UV erythemal irradiance (UVER) data was performed. The comparison revealed that the radiative transfer simulations were 8 % higher than the observations for clear-sky conditions. The rest of the bias (~14 %) may be attributed to the substantial underestimation of modeled UVER with respect to experimental UVER under overcast conditions, although the correlation between both dataset was high (R2 ~ 0.93). A sensitive test showed that the main reason responsible for that underestimation is the experimental AERONET COD used as input in the simulations, which has been retrieved from zenith radiances in the visible range. In this sense, effective COD in the erythemal interval were derived from an iteration procedure based on searching the best match between modeled and experimental UVER values for each selected overcast case. These effective COD values were smaller than AERONET COD data in about 80 % of the overcast cases with a mean relative difference of 22 %.