An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7

Analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. Isolation of bacterial mRNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase PCR (qPCR), microarray, or RNA-seq. The goal of this work was to optimize the isolation of bacterial mRNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample. To improve the yield of bacterial RNA and reduce the number of plants required, an optimized method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of high-molecular-weight polyethylene glycol and hexadecyltrimethyl ammonium bromide. The new method increased the total yield of bacterial mRNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety.

New opportunities for secure communication networks using shaped femtosecond laser pulses inducing filamentation processes in the atmosphere

The current study discusses new opportunities for secure ground to satellite communications using shaped femtosecond pulses that induce spatial hole burning in the atmosphere for efficient communications with data encoded within super-continua generated by femtosecond pulses. Refractive index variation across the different layers in the atmosphere may be modelled using assumptions that the upper strata of the atmosphere and troposphere behaving as layered composite amorphous dielectric networks composed of resistors and capacitors with different time constants across each layer. Input-output expressions of the dynamics of the networks in the frequency domain provide the transmission characteristics of the propagation medium. Femtosecond pulse shaping may be used to optimize the pulse phase-front and spectral composition across the different layers in the atmosphere. A generic procedure based on evolutionary algorithms to perform the pulse shaping is proposed. In contrast to alternative procedures that would require ab initio modelling and calculations of the propagation constant for the pulse through the atmosphere, the proposed approach is adaptive, compensating for refractive index variations along the column of air between the transmitter and receiver.

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome.

Observing wind, aerosol particles, clouds and precipitation: Finland's new ground-based remote-sensing network

The Finnish Meteorological Institute, in collaboration with the University of Helsinki, has established a new ground-based remote-sensing network in Finland. The network consists of five topographically, ecologically and climatically different sites distributed from southern to northern Finland. The main goal of the network is to monitor air pollution and boundary layer properties in near real time, with a Doppler lidar and ceilometer at each site. In addition to these operational tasks, two sites are members of the Aerosols, Clouds and Trace gases Research InfraStructure Network (ACTRIS); a Ka band cloud radar at Sodankylä will provide cloud retrievals within CloudNet, and a multi-wavelength Raman lidar, PollyXT (POrtabLe Lidar sYstem eXTended), in Kuopio provides optical and microphysical aerosol properties through EARLINET (the European Aerosol Research Lidar Network). Three C-band weather radars are located in the Helsinki metropolitan area and are deployed for operational and research applications. We performed two inter-comparison campaigns to investigate the Doppler lidar performance, compare the backscatter signal and wind profiles, and to optimize the lidar sensitivity through adjusting the telescope focus length and data-integration time to ensure sufficient signal-to-noise ratio (SNR) in low-aerosol-content environments. In terms of statistical characterization, the wind-profile comparison showed good agreement between different lidars. Initially, there was a discrepancy in the SNR and attenuated backscatter coefficient profiles which arose from an incorrectly reported telescope focus setting from one instrument, together with the need to calibrate. After diagnosing the true telescope focus length, calculating a new attenuated backscatter coefficient profile with the new telescope function and taking into account calibration, the resulting attenuated backscatter profiles all showed good agreement with each other. It was thought that harsh Finnish winters could pose problems, but, due to the built-in heating systems, low ambient temperatures had no, or only a minor, impact on the lidar operation – including scanning-head motion. However, accumulation of snow and ice on the lens has been observed, which can lead to the formation of a water/ice layer thus attenuating the signal inconsistently. Thus, care must be taken to ensure continuous snow removal.

Nonlinear identification using orthogonal forward regression with nested optimal regularization

An efficient data based-modeling algorithm for nonlinear system identification is introduced for radial basis function (RBF) neural networks with the aim of maximizing generalization capability based on the concept of leave-one-out (LOO) cross validation. Each of the RBF kernels has its own kernel width parameter and the basic idea is to optimize the multiple pairs of regularization parameters and kernel widths, each of which is associated with a kernel, one at a time within the orthogonal forward regression (OFR) procedure. Thus, each OFR step consists of one model term selection based on the LOO mean square error (LOOMSE), followed by the optimization of the associated kernel width and regularization parameter, also based on the LOOMSE. Since like our previous state-of-the-art local regularization assisted orthogonal least squares (LROLS) algorithm, the same LOOMSE is adopted for model selection, our proposed new OFR algorithm is also capable of producing a very sparse RBF model with excellent generalization performance. Unlike our previous LROLS algorithm which requires an additional iterative loop to optimize the regularization parameters as well as an additional procedure to optimize the kernel width, the proposed new OFR algorithm optimizes both the kernel widths and regularization parameters within the single OFR procedure, and consequently the required computational complexity is dramatically reduced. Nonlinear system identification examples are included to demonstrate the effectiveness of this new approach in comparison to the well-known approaches of support vector machine and least absolute shrinkage and selection operator as well as the LROLS algorithm.

Distributed parallelization of greedy Mobile Network Optimization algorithms

The Mobile Network Optimization (MNO) technologies have advanced at a tremendous pace in recent years. And the Dynamic Network Optimization (DNO) concept emerged years ago, aimed to continuously optimize the network in response to variations in network traffic and conditions. Yet, DNO development is still at its infancy, mainly hindered by a significant bottleneck of the lengthy optimization runtime. This paper identifies parallelism in greedy MNO algorithms and presents an advanced distributed parallel solution. The solution is designed, implemented and applied to real-life projects whose results yield a significant, highly scalable and nearly linear speedup up to 6.9 and 14.5 on distributed 8-core and 16-core systems respectively. Meanwhile, optimization outputs exhibit self-consistency and high precision compared to their sequential counterpart. This is a milestone in realizing the DNO. Further, the techniques may be applied to similar greedy optimization algorithm based applications.

Optimizing mixing during the sponge cake manufacturing process

Sponge cakes have traditionally been manufactured using multistage mixing methods to enhance potential foam formation by the eggs. Today, use of all-in (single-stage) mixing methods is superseding multistage methods for large-scale batter preparation to reduce costs and production time. In this study, multistage and all-in mixing procedures and three final high-speed mixing times (3, 5, and 15 min) for sponge cake production were tested to optimize a mixing method for pilot-scale research. Mixing for 3 min produced batters with higher relative density values than did longer mixing times. These batters generated well-aerated cakes with high volume and low hardness. In contrast, after 5 and 15 min of high-speed mixing, batters with lower relative density and higher viscosity values were produced. Although higher bubble incorporation and retention were observed, longer mixing times produced better developed gluten networks, which stiffened the batters and inhibited bubble expansion during mixing. As a result, these batters did not expand properly and produced cakes with low volume, dense crumb, and high hardness values. Results for all-in mixing were similar to those for the multistage mixing procedure in terms of the physical properties of batters and cakes (i.e., relative density, elastic moduli, volume, total cell area, hardness, etc.). These results suggest the all-in mixing procedure with a final high-speed mixing time of 3 min is an appropriate mixing method for pilot-scale sponge cake production. The advantages of this method are reduced energy costs and production time.

The influence of shade and organic fertilizer treatments on the physiology and establishment of Theobroma cacao clones

Aims: This experiment aimed to determine whether the soil application of organic fertilizers can help the establishment of cacao and whether shade alters its response to fertilizers. Study Design: The 1.6 ha experiment was conducted over a period of one crop year (between April 2007 and March 2008) at the Cocoa Research Institute of Ghana. It involved four cacao genotypes (T 79/501, PA 150, P 30 [POS] and SCA 6), three shade levels (‘light’, ‘medium’ and ‘heavy’) and two fertilizer treatments (‘no fertilizer’, and ‘140 kg/ha of cacao pod husk ash (CPHA) plus poultry manure at 1,800 kg/ha). The experiment was designed as a split-plot with the cacao genotypes as the main plot factor and shade x fertilizer combinations as the sub-plots. Methodology: Gliricidia sepium and plantains (Musa sapientum) were planted in different arrangements to create the three temporary shade regimes for the cacao. Data were collected on temperature and relative humidity of the shade environments, initial soil nutrients, soil moisture, leaf N, P and K+ contents, survival, photo synthesis and growth of test plants. Results: The genotypes P 30 [POS] and SCA 6 showed lower stomatal conductance under non-limiting conditions. In the rainy seasons, plants under light shade had the highest CO2 assimilation rates. However, in the dry season, plants under increased shade recorded greater photosynthetic rates (P = .03). A significant shade x fertilizer interaction (P = .001) on photosynthesis in the dry season showed that heavier shade increases the benefits that young cacao gets from fertilizer application in that season. Conversely, shade should be reduced during the wet seasons to minimize light limitation to assimilation. Conclusion: Under ideal weather conditions young cacao exhibits genetic variability on stomatal conductance. Also, to optimize plant response to fertilizer application shade must be adjusted taking the prevailing weather condition into account.

Comparative analysis of performance and stability among composite cross populations, variety mixtures and pure lines of winter wheat in organic and conventional cropping systems

This study investigated the effects of increased genetic diversity in winter wheat (Triticum aestivum L.), either from hybridization across genotypes or from physical mixing of lines, on grain yield, grain quality, and yield stability in different cropping environments. Sets of pure lines (no diversity), chosen for high yielding ability or high quality, were compared with line mixtures (intermediate level of diversity), and lines crossed with each other in composite cross populations (CCPn, high diversity). Additional populations containing male sterility genes (CCPms) to increase outcrossing rates were also tested. Grain yield, grain protein content, and protein yield were measured at four sites (two organically-managed and two conventionally-managed) over three years, using seed harvested locally in each preceding year. CCPn and mixtures out-yielded the mean of the parents by 2.4% and 3.6%, respectively. These yield differences were consistent across genetic backgrounds but partly inconsistent across cropping environments and years. Yield stability measured by environmental variance was higher in CCPn and CCPms than the mean of the parents. An index of yield reliability tended to be higher in CCPn, CCPms and mixtures than the mean of the parents. Lin and Binns’ superiority values of yield and protein yield were consistently and significantly lower (i.e. better) in the CCPs than in the mean of the parents, but not different between CCPs and mixtures. However, CCPs showed greater early ground cover and plant height than mixtures. When compared with the (locally non-predictable) best-yielding pure line, CCPs and mixtures exhibited lower mean yield and somewhat lower yield reliability but comparable superiority values. Thus, establishing CCPs from smaller sets of high-performing parent lines might optimize their yielding ability. On the whole, the results demonstrate that using increased within-crop genetic diversity can produce wheat crops with improved yield stability and good yield reliability across variable and unpredictable cropping environments.

Enhancing prospective memory in mild cognitive impairment: the role of enactment

Prospective memory (PM) is a fundamental requirement for independent living which might be prematurely compromised in the neurodegenerative process, namely in mild cognitive impairment (MCI), a typical prodromal Alzheimer's disease (AD) phase. Most encoding manipulations that typically enhance learning in healthy adults are of minimal benefit to AD patients. However, there is some indication that these can display a recall advantage when encoding is accompanied by the physical enactment of the material. The aim of this study was to explore the potential benefits of enactment at encoding and cue-action relatedness on memory for intentions in MCI patients and healthy controls using a behavioral PM experimental paradigm. Method: We report findings examining the influence of enactment at encoding for PM performance in MCI patients and education-matched controls using a laboratory-based PM task with a factorial independent design. Results: PM performance was consistently superior when physical enactment was used at encoding and when target-action pairs were strongly associated. Importantly, these beneficial effects were cumulative and observable across both a healthy and a cognitively impaired lifespan as well as evident in the perceived subjective difficulty in performing the task. Conclusions: The identified beneficial effects of enacted encoding and semantic relatedness have unveiled the potential contribution of this encoding technique to optimize attentional demands through an adaptive allocation of resources strategies. We discuss our findings with respect to their potential impact on developing strategies to improve PM in AD sufferers.

Towards more precise sugar beet management based on geostatistical analysis of spatial variability within fields

Within-field variation in sugar beet yield and quality was investigated in three commercial sugar beet fields in the east of England to identify the main associated variables and to examine the possibility of predicting yield early in the season with a view to spatially variable management of sugar beet crops. Irregular grid sampling with some purposively-located nested samples was applied. It revealed the spatial variability in each sugar beet field efficiently. In geostatistical analyses, most variograms were isotropic with moderate to strong spatial dependency indicating a significant spatial variation in sugar beet yield and associated growth and environmental variables in all directions within each field. The Kriged maps showed spatial patterns of yield variability within each field and visual association with the maps of other variables. This was confirmed by redundancy analyses and Pearson correlation coefficients. The main variables associated with yield variability were soil type, organic matter, soil moisture, weed density and canopy temperature. Kriged maps of final yield variability were strongly related to that in crop canopy cover, LAI and intercepted solar radiation early in the growing season, and the yield maps of previous crops. Therefore, yield maps of previous crops together with early assessment of sugar beet growth may make an early prediction of within-field variability in sugar beet yield possible. The Broom’s Barn sugar beet model failed to account for the spatial variability in sugar yield, but the simulation was greatly improved when corrected for early canopy development cover and when the simulated yield was adjusted for weeds and plant population. Further research to optimize inputs to maximise sugar yield should target the irrigation and fertilizing of areas within fields with low canopy cover early in the season.

Exploring combinations of different color and facial expression stimuli for gaze-independent BCIs

Background: Some studies have proven that a conventional visual brain computer interface (BCI) based on overt attention cannot be used effectively when eye movement control is not possible. To solve this problem, a novel visual-based BCI system based on covert attention and feature attention has been proposed and was called the gaze-independent BCI. Color and shape difference between stimuli and backgrounds have generally been used in examples of gaze-independent BCIs. Recently, a new paradigm based on facial expression changes has been presented, and obtained high performance. However, some facial expressions were so similar that users couldn't tell them apart, especially when they were presented at the same position in a rapid serial visual presentation (RSVP) paradigm. Consequently, the performance of the BCI is reduced. New Method: In this paper, we combined facial expressions and colors to optimize the stimuli presentation in the gaze-independent BCI. This optimized paradigm was called the colored dummy face pattern. It is suggested that different colors and facial expressions could help users to locate the target and evoke larger event-related potentials (ERPs). In order to evaluate the performance of this new paradigm, two other paradigms were presented, called the gray dummy face pattern and the colored ball pattern. Comparison with Existing Method(s): The key point that determined the value of the colored dummy faces stimuli in BCI systems was whether the dummy face stimuli could obtain higher performance than gray faces or colored balls stimuli. Ten healthy participants (seven male, aged 21–26 years, mean 24.5 ± 1.25) participated in our experiment. Online and offline results of four different paradigms were obtained and comparatively analyzed. Results: The results showed that the colored dummy face pattern could evoke higher P300 and N400 ERP amplitudes, compared with the gray dummy face pattern and the colored ball pattern. Online results showed that the colored dummy face pattern had a significant advantage in terms of classification accuracy (p < 0.05) and information transfer rate (p < 0.05) compared to the other two patterns. Conclusions: The stimuli used in the colored dummy face paradigm combined color and facial expressions. This had a significant advantage in terms of the evoked P300 and N400 amplitudes and resulted in high classification accuracies and information transfer rates. It was compared with colored ball and gray dummy face stimuli.

Towards conceptualizing reverse service supply chains

Purpose – Recognizing the heterogeneity of services, this paper aims to clarify the characteristics of forward and the corresponding reverse supply chains of different services. Design/methodology/approach – The paper develops a two-dimensional typology matrix, representing four main clusters of services according to the degree of input standardization and the degree of output tangibility. Based on this matrix, this paper develops a typology and parsimonious conceptual models illustrating the characteristics of forward and the corresponding reverse supply chains of each cluster of services. Findings – The four main clusters of service supply chains have different characteristics. This provides the basis for the identification, presentation and explanation of the different characteristics of their corresponding reverse service supply chains. Research limitations/implications – The findings of this research can help future researchers to analyse, map and model forward and reverse service supply chains, and to identify potential research gaps in the area. Practical/implications – The findings of the research can help managers of service firms to gain better visibility of their forward and reverse supply chains, and refine their business models to help extend their reverse/closed-loop activities. Furthermore, the findings can help managers to better optimize their service operations to reduce service gaps and potentially secure new value-adding opportunities. Originality/value – This paper is the first, to the authors ' knowledge, to conceptualize the basic structure of the forward and reverse service supply chains while dealing with the high level of heterogeneity of services.

Mesenchymal Stem Cells and Bovine Bone Mineral in Sinus Lift Procedures-An Experimental Study in Sheep

Introduction: New reconstructive and less invasive methods have been searched to optimize bone formation and osseointegration of dental implants in maxillary sinus augmentation. Purpose: The aim of the presented ovine split-mouth study was to compare bovine bone mineral (BBM) alone and in combination with mesenchymal stem cells (MSCs) regarding their potential in sinus augmentation. Material and Methods: Bilateral sinus floor augmentations were performed in six adult sheep. BBM and MSCs were placed into the test side and only BBM in the contra-lateral control side of each sheep. Animals were sacrificed after 8 and 16 weeks. Augmentation sites were analyzed by computed tomography, histology, and histomorphometry. Results: The initial volumes of both sides were similar and did not change significantly with time. A tight connection between the particles of BBM and the new bone was observed histologically. Bone formation was significantly (p = 0.027) faster by 49% in the test sides. Conclusion: The combination of BBM and MSCs accelerated new bone formation in this model of maxillary sinus augmentation. This could allow early placement of implants.

Nitrogen Metabolism in leaves of a tank epiphytic bromeliad: Characterization of a spatial and functional division

The leaf is considered the most important vegetative organ of tank epiphytic bromeliads due to its ability to absorb and assimilate nutrients. However, little is known about the physiological characteristics of nutrient uptake and assimilation. In order to better understand the mechanisms utilized by some tank epiphytic bromeliads to optimize the nitrogen acquisition and assimilation, a study was proposed to verify the existence of a differential capacity to assimilate nitrogen in different leaf portions. The experiments were conducted using young plants of Vriesea gigantea. A nutrient solution containing NO(3)(-)/NH(4)(+) or urea as the sole nitrogen source was supplied to the tank of these plants and the activities of urease, nitrate reductase (NR), glutamine synthetase (GS) and glutamate dehydrogenase (NADH-GDH) were quantified in apical and basal leaf portions after 1, 3, 6, 9, 12, 24 and 48 h. The endogenous ammonium and urea contents were also analyzed. Independent of the nitrogen sources utilized, NR and urease activities were higher in the basal portions of leaves in all the period analyzed. On the contrary. GS and GDH activities were higher in apical part. It was also observed that the endogenous ammonium and urea had the highest contents detected in the basal region. These results suggest that the basal portion was preferentially involved in nitrate reduction and urea hydrolysis, while the apical region could be the main area responsible for ammonium assimilation through the action of GS and GDH activities. Moreover, it was possible to infer that ammonium may be transported from the base, to the apex of the leaves. In conclusion, it was suggested that a spatial and functional division in nitrogen absorption and NH(4)(+) assimilation between basal and apical leaf areas exists, ensuring that the majority of nitrogen available inside the tank is quickly used by bromeliad`s leaves. (C) 2011 Elsevier GmbH. All rights reserved.