Combined use of two genetic fingerprinting methods, pulsed-field gel electrophoresis and ribotyping, for characterization of Escherichia coli O157 isolates from food animals, retail meats, and cases of human disease

Two genetic fingerprinting techniques, pulsed-field gel electrophoresis (PFGE) and ribotyping, were used to characterize 207 Escherichia coli O157 isolates from food animals, foods of animal origin, and cases of human disease (206 of the isolates were from the United Kingdom). In addition, 164 of these isolates were also phage typed. The isolates were divided into two general groups: (i) unrelated isolates not known to be epidemiologically linked (n = 154) and originating from food animals, foods and the environment, or humans and (ii) epidemiologically related isolates (n = 53) comprised of four related groups (RGs) originating either from one farm plus the abattoir where cattle from that farm were slaughtered or from one of three different English abattoirs. PFGE was conducted with the restriction endonuclease XbaI. while for ribotyping, two restriction endonucleases (PstI and SphI) were combined to digest genomic DNAs simultaneously. The 207 E. coli O157 isolates produced 97 PFGE profiles and 51 ribotypes. The two genetic fingerprinting methods had similar powers to discriminate the 154 epidemiologically unrelated E. coli O157 isolates in the study (Simpson's index of diversity [D] = 0.98 and 0.94 for PFGE typing and ribotyping, respectively). There was no correlation between the source of an isolate (healthy meat or milk animals, retail meats, or cases of human infection) and either particular PFGE or ribotype profiles or clusters. Combination of the results of both genetic fingerprinting methods produced 146 types, significantly more than when either of the two methods was used individually. Consequently, the superior discriminatory performance of the PFGE-ribotyping combination was proven in two ways: (i) by demonstrating that the majority of the E. coli O157 isolates with unrelated histories were indeed distinguishable types and (ii) by identifying some clonal groups among two of the four RGs of E. coli O157 isolates (comprising PFGE types different by just one or two bands), the relatedness of which would have remained unconfirmed otherwise.

Threats to an ecosystem service: pressures on pollinators

Insect pollinators of crops and wild plants are under threat globally and their decline or loss could have profound economic and environmental consequences. Here, we argue that multiple anthropogenic pressures – including land-use intensification, climate change, and the spread of alien species and diseases – are primarily responsible for insect-pollinator declines. We show that a complex interplay between pressures (eg lack of food sources, diseases, and pesticides) and biological processes (eg species dispersal and interactions) at a range of scales (from genes to ecosystems) underpins the general decline in insect-pollinator populations. Interdisciplinary research on the nature and impacts of these interactions will be needed if human food security and ecosystem function are to be preserved. We highlight key areas that require research focus and outline some practical steps to alleviate the pressures on pollinators and the pollination services they deliver to wild and crop plants.

Dynamics of the lower stratospheric circulation response to ENSO

A robust feature of the observed response to El Nin˜o–Southern Oscillation (ENSO) is an altered circulation in the lower stratosphere. When sea surface temperatures (SSTs) in the tropical Pacific are warmer there is enhanced upwelling and cooling in the tropical lower stratosphere and downwelling and warming in the midlatitudes, while the opposite is true of cooler SSTs. The midlatitude lower stratospheric response to ENSO is larger in the Southern Hemisphere (SH) than in the Northern Hemisphere (NH). In this study the dynamical version of the Canadian Middle Atmosphere Model (CMAM) is used to simulate 25 realizations of the atmospheric response to the 1982/83 El Nin˜o and the 1973/74 La Nin˜ a. This version ofCMAMis a comprehensive high-top general circulation model that does not include interactive chemistry. The observed lower stratospheric response to ENSO is well reproduced by the simulations, allowing them to be used to investigate the mechanisms involved. Both the observed and simulated responses maximize in December–March and so this study focuses on understanding the mechanisms involved in that season. The response in tropical upwelling is predominantly driven by anomalous transient synoptic-scale wave drag in the SH subtropical lower stratosphere, which is also responsible for the compensating SH midlatitude response. This altered wave drag stems from an altered upward flux of wave activity from the troposphere into the lower stratosphere between 208 and 408S. The altered flux of wave activity can be divided into two distinct components. In the Pacific, the acceleration of the zonal wind in the subtropics from the warmer tropical SSTs results in a region between the midlatitude and subtropical jets where there is an enhanced source of low phase speed eddies. At other longitudes, an equatorward shift of the midlatitude jet from the extratropical tropospheric response to El Nin˜o results in an enhanced source of waves of higher phase speeds in the subtropics. The altered resolved wave drag is only apparent in the SH and the difference between the two hemispheres can be related to the difference in the climatological jet structures in this season and the projection of the wind anomalies associated with ENSO onto those structures.

Stratospheric variability and tropospheric annular‐mode timescales

Climate models tend to exhibit much too persistent Southern Annular Mode (SAM) circulation anomalies in summer, compared to observations. Theoretical arguments suggest this bias may lead to an overly strong model response to anthropogenic forcing during this season, which is of interest since the largest observed changes in Southern Hemisphere high‐latitude climate over the last few decades have occurred in summer, and are congruent with the SAM. The origin of this model bias is examined here in the case of the Canadian Middle Atmosphere Model, using a novel technique to quantify the influence of stratospheric variability on tropospheric annular‐mode timescales. Part of the model bias is shown to be attributable to the too‐late breakdown of the stratospheric polar vortex, which allows the tropospheric influence of stratospheric variability to extend into early summer. However, the analysis also reveals an enhanced summertime persistence of the model’s SAM that is unrelated to either stratospheric variability or the bias in model stratospheric climatology, and is thus of tropospheric origin. No such feature is evident in the Northern Hemisphere. The effect of stratospheric variability in lengthening tropospheric annular‐mode timescales is evident in both hemispheres. While in the Southern Hemisphere the effect is restricted to late‐spring/early summer, in the Northern Hemisphere it can occur throughout the winter‐spring season, with the seasonality of peak timescales exhibiting considerable variability between different 50 year sections of the same simulation.

Beta event-related desynchronization as an index of individual differences in processing human facial expression: further investigations of autistic traits in typically developing adults

The human mirror neuron system (hMNS) has been associated with various forms of social cognition and affective processing including vicarious experience. It has also been proposed that a faulty hMNS may underlie some of the deficits seen in the autism spectrum disorders (ASDs). In the present study we set out to investigate whether emotional facial expressions could modulate a putative EEG index of hMNS activation (mu suppression) and if so, would this differ according to the individual level of autistic traits [high versus low Autism Spectrum Quotient (AQ) score]. Participants were presented with 3 s films of actors opening and closing their hands (classic hMNS mu-suppression protocol) while simultaneously wearing happy, angry, or neutral expressions. Mu-suppression was measured in the alpha and low beta bands. The low AQ group displayed greater low beta event-related desynchronization (ERD) to both angry and neutral expressions. The high AQ group displayed greater low beta ERD to angry than to happy expressions. There was also significantly more low beta ERD to happy faces for the low than for the high AQ group. In conclusion, an interesting interaction between AQ group and emotional expression revealed that hMNS activation can be modulated by emotional facial expressions and that this is differentiated according to individual differences in the level of autistic traits. The EEG index of hMNS activation (mu suppression) seems to be a sensitive measure of the variability in facial processing in typically developing individuals with high and low self-reported traits of autism.

Southern annular mode dynamics in observations and models, Part I: The influence of climatological zonal wind biases in a comprehensive GCM

A common bias among global climate models (GCMs) is that they exhibit tropospheric southern annular mode (SAM) variability that is much too persistent in the Southern Hemisphere (SH) summertime. This is of concern for the ability to accurately predict future SH circulation changes, so it is important that it be understood and alleviated. In this two-part study, specifically targeted experiments with the Canadian Middle Atmosphere Model (CMAM) are used to improve understanding of the enhanced summertime SAM persistence. Given the ubiquity of this bias among comprehensive GCMs, it is likely that the results will be relevant for other climate models. Here, in Part I, the influence of climatological circulation biases on SAM variability is assessed, with a particular focus on two common biases that could enhance summertime SAM persistence: the too-late breakdown of the Antarctic stratospheric vortex and the equatorward bias in the SH tropospheric midlatitude jet. Four simulations are used to investigate the role of each of these biases in CMAM. Nudging and bias correcting procedures are used to systematically remove zonal-mean stratospheric variability and/or remove climatological zonal wind biases. The SAM time-scale bias is not alleviated by improving either the timing of the stratospheric vortex breakdown or the climatological jet structure. Even in the absence of stratospheric variability and with an improved climatological circulation, the model time scales are biased long. This points toward a bias in internal tropospheric dynamics that is not caused by the tropospheric jet structure bias. The underlying cause of this is examined in more detail in Part II of this study.

Southern annular mode dynamics in observations and models, Part II: Eddy feedbacks

Many global climate models (GCMs) have trouble simulating Southern Annular Mode (SAM) variability correctly, particularly in the Southern Hemisphere summer season where it tends to be too persistent. In this two part study, a suite of experiments with the Canadian Middle Atmosphere Model (CMAM) is analyzed to improve our understanding of the dynamics of SAM variability and its deficiencies in GCMs. Here, an examination of the eddy-mean flow feedbacks is presented by quantification of the feedback strength as a function of zonal scale and season using a new methodology that accounts for intraseasonal forcing of the SAM. In the observed atmosphere, in the summer season, a strong negative feedback by planetary scale waves, in particular zonal wavenumber 3, is found in a localized region in the south west Pacific. It cancels a large proportion of the positive feedback by synoptic and smaller scale eddies in the zonal mean, resulting in a very weak overall eddy feedback on the SAM. CMAM is deficient in this negative feedback by planetary scale waves, making a substantial contribution to its bias in summertime SAM persistence. Furthermore, this bias is not alleviated by artificially improving the climatological circulation, suggesting that climatological circulation biases are not the cause of the planetary wave feedback deficiency in the model. Analysis of the summertime eddy feedbacks in the CMIP-5 models confirms that this is indeed a common problem among GCMs, suggesting that understanding this planetary wave feedback and the reason for its deficiency in GCMs is key to improving the fidelity of simulated SAM variability in the summer season.

Toward vicarious calibration of microwave remote-sensing satellites in arid environments

The Soil Moisture and Ocean Salinity (SMOS) satellite marks the commencement of dedicated global surface soil moisture missions, and the first mission to make passive microwave observations at L-band. On-orbit calibration is an essential part of the instrument calibration strategy, but on-board beam-filling targets are not practical for such large apertures. Therefore, areas to serve as vicarious calibration targets need to be identified. Such sites can only be identified through field experiments including both in situ and airborne measurements. For this purpose, two field experiments were performed in central Australia. Three areas are studied as follows: 1) Lake Eyre, a typically dry salt lake; 2) Wirrangula Hill, with sparse vegetation and a dense cover of surface rock; and 3) Simpson Desert, characterized by dry sand dunes. Of those sites, only Wirrangula Hill and the Simpson Desert are found to be potentially suitable targets, as they have a spatial variation in brightness temperatures of <4 K under normal conditions. However, some limitations are observed for the Simpson Desert, where a bias of 15 K in vertical and 20 K in horizontal polarization exists between model predictions and observations, suggesting a lack of understanding of the underlying physics in this environment. Subsequent comparison with model predictions indicates a SMOS bias of 5 K in vertical and 11 K in horizontal polarization, and an unbiased root mean square difference of 10 K in both polarizations for Wirrangula Hill. Most importantly, the SMOS observations show that the brightness temperature evolution is dominated by regular seasonal patterns and that precipitation events have only little impact.

Mobile-to-mobile MIMO transmit-receive diversity systems: analysis and performance in three-dimensional double-correlated channels

Mobile-to-mobile (M-to-M) communications are expected to play a crucial role in future wireless systems and networks. In this paper, we consider M-to-M multiple-input multiple-output (MIMO) maximal ratio combining system and assess its performance in spatially correlated channels. The analysis assumes double-correlated Rayleigh-and-Lognormal fading channels and is performed in terms of average symbol error probability, outage probability, and ergodic capacity. To obtain the receive and transmit spatial correlation functions needed for the performance analysis, we used a three-dimensional (3D) M-to-M MIMO channel model, which takes into account the effects of fast fading and shadowing. The expressions for the considered metrics are derived as a function of the average signal-to-noise ratio per receive antenna in closed-form and are further approximated using the recursive adaptive Simpson quadrature method. Numerical results are provided to show the effects of system parameters, such as distance between antenna elements, maximum elevation angle of scatterers, orientation angle of antenna array in the x–y plane, angle between the x–y plane and the antenna array orientation, and degree of scattering in the x–y plane, on the system performance. Copyright © 2011 John Wiley & Sons, Ltd.

A cross-calibration of GMS-5 thermal channels against ATSR-2

Motivated by the importance to weather and climate of the Indo-Pacific seas, we present a new calibration of the Visible Infrared Spin-Scan Radiometer (VISSR) on the geostationary meteorological satellite, GMS-5. VISSR imagery has significant potential for exploring the dynamics of the ocean and air–sea interactions in this poorly characterized region, by virtue of the VISSR's surface temperature retrieval capability and hourly sampling. However, the calibration of the thermal imagery supplied by the Japanese Meteorological Agency (JMA) is inconsistent with the spectral characteristics of the channels, and published details of the JMA calibration procedure are scant. We use the well-characterized Along-Track Scanning Radiometer 2 (ATSR-2) as a reference, and determine calibration corrections for GMS-5 VISSR. We obtain more credible VISSR brightness temperatures and demonstrate sea surface temperature (SST) retrieval that validates well against in situ measurements (bias ∼0.3 and scatter ∼0.4 K). Comparison with a widely used sea surface temperature analysis shows that the GMS-5 VISSR SST fields capture important spatial structure, absent in the analysis.

Infra-red laser ablative micromachining of parylene-C on SiO2substrates for rapid prototyping, high yield, human neuronal cell patterning

Cell patterning commonly employs photolithographic methods for the micro fabrication of structures on silicon chips. These require expensive photo-mask development and complex photolithographic processing. Laser based patterning of cells has been studied in vitro and laser ablation of polymers is an active area of research promising high aspect ratios. This paper disseminates how 800 nm femtosecond infrared (IR) laser radiation can be successfully used to perform laser ablative micromachining of parylene-C on SiO2 substrates for the patterning of human hNT astrocytes (derived from the human teratocarcinoma cell line (hNT)) whilst 248 nm nanosecond ultra-violet laser radiation produces photo-oxidization of the parylene-C and destroys cell patterning. In this work, we report the laser ablation methods used and the ablation characteristics of parylene-C for IR pulse fluences. Results follow that support the validity of using IR laser ablative micromachining for patterning human hNT astrocytes cells. We disseminate the variation in yield of patterned hNT astrocytes on parylene-C with laser pulse spacing, pulse number, pulse fluence and parylene-C strip width. The findings demonstrate how laser ablative micromachining of parylene-C on SiO2 substrates can offer an accessible alternative for rapid prototyping, high yield cell patterning with broad application to multi-electrode arrays, cellular micro-arrays and microfluidics.

Patterning and detailed study of human hNT astrocytes on parylene-C/silicon dioxide substrates to the single cell level

It is estimated that the adult human brain contains 100 billion neurons with 5–10 times as many astrocytes. Although it has been generally considered that the astrocyte is a simple supportive cell to the neuron, recent research has revealed new functionality of the astrocyte in the form of information transfer to neurons of the brain. In our previous work we developed a protocol to pattern the hNT neuron (derived from the human teratocarcinoma cell line (hNT)) on parylene-C/SiO2 substrates. In this work, we report how we have managed to pattern hNT astrocytes, on parylene-C/SiO2 substrates to single cell resolution. This article disseminates the nanofabrication and cell culturing steps necessary for the patterning of such cells. In addition, it reports the necessary strip lengths and strip width dimensions of parylene-C that encourage high degrees of cellular coverage and single cell isolation for this cell type. The significance in patterning the hNT astrocyte on silicon chip is that it will help enable single cell and network studies into the undiscovered functionality of this interesting cell, thus, contributing to closer pathological studies of the human brain.

Low cost, patterning of human hNT brain cells on parylene-C with UV & IR laser machining

This paper describes the use of 800nm femtosecond infrared (IR) and 248nm nanosecond ultraviolet (UV) laser radiation in performing ablative micromachining of parylene-C on SiO2 substrates for the patterning of human hNT astrocytes. Results are presented that support the validity of using IR laser ablative micromachining for patterning human hNT astrocytes cells while UV laser radiation produces photo-oxidation of the parylene-C and destroys cell patterning. The findings demonstrate how IR laser ablative micromachining of parylene-C on SiO2 substrates can offer a low cost, accessible alternative for rapid prototyping, high yield cell patterning.

Mapania sapuaniana (Cyperaceae), a new sedge species from Sarawak

Mapania sapuaniana, a spectacular new sedge species from Lanjak Entimau, Sarawak, is described and illustrated. It is closely related to M. richardsii and M. bomeensis but differs in having broad leaves with a distinct pseudopetiole, reddish purple or maroon coloration on the underside of the leaf and petiole and an inflorescence composed of several spikes.

Mapania multiflora, a distinctive new species of Cyperaceae (Mapanioideae) from Borneo

Mapania multiflora is described and illustrated. It is vegetatively similar to taxa with broad leaves and pseudopetioles, such as M. cuspidata. However, it is reproductively similar to sect. Thoractostachyum with a paniculate inflorescence and furrowed fruit. The DNA is similar to M. bancana in sect. Thoractostachyum, in the three sampled cpDNA regions: atpH-F, trnL-F and psbA-trnH. However, it is identical to none of these due to its unique combination of vegetative, reproductive and molecular characteristics.