Modeling image motion in airborne Three-Line-Array (TLA) push-broom cameras

This paper presents an image motion model for airborne three-line-array (TLA) push-broom cameras. Both aircraft velocity and attitude instability are taken into account in modeling image motion. Effects of aircraft pitch, roll, and yaw on image motion are analyzed based on geometric relations in designated coordinate systems. The image motion is mathematically modeled by image motion velocity multiplied by exposure time. Quantitative analysis to image motion velocity is then conducted in simulation experiments. The results have shown that image motion caused by aircraft velocity is space invariant while image motion caused by aircraft attitude instability is more complicated. Pitch,roll and yaw all contribute to image motion to different extents. Pitch dominates the along-track image motion and both roll and yaw greatly contribute to the cross-track image motion. These results provide a valuable base for image motion compensation to ensure high accuracy imagery in aerial photogrammetry.

Classification of cortical microcircuits based on micro-electrode-array data from slices of rat barrel cortex

The bewildering complexity of cortical microcircuits at the single cell level gives rise to surprisingly robust emergent activity patterns at the level of laminar and columnar local field potentials (LFPs) in response to targeted local stimuli. Here we report the results of our multivariate data-analytic approach based on simultaneous multi-site recordings using micro-electrode-array chips for investigation of the microcircuitary of rat somatosensory (barrel) cortex. We find high repeatability of stimulus-induced responses, and typical spatial distributions of LFP responses to stimuli in supragranular, granular, and infragranular layers, where the last form a particularly distinct class. Population spikes appear to travel with about 33 cm/s from granular to infragranular layers. Responses within barrel related columns have different profiles than those in neighbouring columns to the left or interchangeably to the right. Variations between slices occur, but can be minimized by strictly obeying controlled experimental protocols. Cluster analysis on normalized recordings indicates specific spatial distributions of time series reflecting the location of sources and sinks independent of the stimulus layer. Although the precise correspondences between single cell activity and LFPs are still far from clear, a sophisticated neuroinformatics approach in combination with multi-site LFP recordings in the standardized slice preparation is suitable for comparing normal conditions to genetically or pharmacologically altered situations based on real cortical microcircuitry.

Fine-grained multi-phase array designs

Hybrid multiprocessor architectures which combine re-configurable computing and multiprocessors on a chip are being proposed to transcend the performance of standard multi-core parallel systems. Both fine-grained and coarse-grained parallel algorithm implementations are feasible in such hybrid frameworks. A compositional strategy for designing fine-grained multi-phase regular processor arrays to target hybrid architectures is presented in this paper. The method is based on deriving component designs using classical regular array techniques and composing the components into a unified global design. Effective designs with phase-changes and data routing at run-time are characteristics of these designs. In order to describe the data transfer between phases, the concept of communication domain is introduced so that the producer–consumer relationship arising from multi-phase computation can be treated in a unified way as a data routing phase. This technique is applied to derive new designs of multi-phase regular arrays with different dataflow between phases of computation.

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.

Genetic responses to phosphorus deficiency

Background: Phosphorus (P) is an essential macronutrient for plants. Plants take up P as phosphate (Pi) from the soil solution. Since little Pi is available in most soils, P fertilizers are applied to crops. However, the use of P fertilizers is unsustainable and may cause pollution. Consequently, there is a need to develop more P-use-efficient (PUE) crops and precise methods to monitor crop P-status. Scope: Manipulating the expression of genes to improve the PUE of crops could reduce their P fertilizer requirement. This has stimulated research towards the identification of genes and signalling cascades involved in plant responses to P deficiency. Genes that respond to P deficiency can be grouped into 'early' genes that respond rapidly and often non-specifically to P deficiency, or 'late' genes that impact on the morphology, physiology or metabolism of plants upon Prolonged P deficiency. Summary: The use of micro-array technology has allowed researchers to catalogue the genetic responses of plants to P deficiency. Genes whose expression is altered by P deficiency include various transcription factors, which are thought to coordinate plant responses to P deficiency, and other genes involved in P acquisition and tissue P economy. Several common cis-regulatory elements have been identified in the promoters of these genes, suggesting that their expression might be coordinated. It is suggested that knowledge of the genes whose expression changes in response to P deficiency might allow the development of crops with improved PUE, and could be used in diagnostic techniques to monitor P deficiency in crops either directly using 'smart' indicator plants or indirectly through transcript profiling. The development of crops with improved PUE and the adoption of diagnostic technology could reduce production costs, minimize the use of a non-renewable resource, reduce pollution and enhance biodiversity.

Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array

The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database (http://pgrc.ipk-gatersleben.de/poci).

A Brassica exon array for whole-transcript gene expression profiling

Affymetrix GeneChip (R) arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip (R) arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip (R) arrays whose probes are localised primarily in 39 exons. Plant whole-transcript (WT) GeneChip (R) arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip (R) Brassica Exon 1.0 ST Array is a 5 mu M feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5), with <= 98 sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

Distribution and availability of trace elements in municipal solid waste composts

Trace element contamination is one of the main problems linked to the quality of compost, especially when it is produced from urban wastes, which can lead to high levels of some potentially toxic elements such as Cu, Pb or Zn. In this work, the distribution and bioavailability of five elements (Cu, Zn, Pb, Cr and Ni) were studied in five Spanish composts obtained from different feedstocks (municipal solid waste, garden trimmings, sewage sludge and mixed manure). The five composts showed high total concentrations of these elements, which in some cases limited their commercialization due to legal imperatives. First, a physical fractionation of the composts was performed, and the five elements were determined in each size fraction. Their availability was assessed by several methods of extraction (water, CaCl2–DTPA, the PBET extract, the TCLP extract, and sodium pyrophosphate), and their chemical distribution was assessed using the BCR sequential extraction procedure. The results showed that the finer fractions were enriched with the elements studied, and that Cu, Pb and Zn were the most potentially problematic ones, due to both their high total concentrations and availability. The partition into the BCR fractions was different for each element, but the differences between composts were scarce. Pb was evenly distributed among the four fractions defined in the BCR (soluble, oxidizable, reducible and residual); Cu was mainly found in the oxidizable fraction, linked to organic matter, and Zn was mainly associated to the reducible fraction (iron oxides), while Ni and Cr were mainly present almost exclusively in the residual fraction. It was not possible to establish a univocal relation between trace elements availability and their BCR fractionation. Given the differences existing for the availability and distribution of these elements, which not always were related to their total concentrations, we think that legal limits should consider availability, in order to achieve a more realistic assessment of the risks linked to compost use.

Concurrent recordings of bladder afferents from multiple nerves using a microfabricated PDMS microchannel electrode array

In this paper we present a compliant neural interface designed to record bladder afferent activity. We developed the implant's microfabrication process using multiple layers of silicone rubber and thin metal so that a gold microelectrode array is embedded within four parallel polydimethylsiloxane (PDMS) microchannels (5 mm long, 100 μm wide, 100 μm deep). Electrode impedance at 1 kHz was optimized using a reactive ion etching (RIE) step, which increased the porosity of the electrode surface. The electrodes did not deteriorate after a 3 month immersion in phosphate buffered saline (PBS) at 37 °C. Due to the unique microscopic topography of the metal film on PDMS, the electrodes are extremely compliant and can withstand handling during implantation (twisting and bending) without electrical failure. The device was transplanted acutely to anaesthetized rats, and strands of the dorsal branch of roots L6 and S1 were surgically teased and inserted in three microchannels under saline immersion to allow for simultaneous in vivo recordings in an acute setting. We utilized a tripole electrode configuration to maintain background noise low and improve the signal to noise ratio. The device could distinguish two types of afferent nerve activity related to increasing bladder filling and contraction. To our knowledge, this is the first report of multichannel recordings of bladder afferent activity.

Evaluation of an elastomer based gold microelectrode array for neural recording applications

We are reporting on the fabrication and electrical characterization of a novel elastomer based micro-cuff neural interface. Electrodes are gold (Au) tracks of sub-100nm thickness and are thermally evaporated on a 0.5 mm thick polydimethylsiloxane (PDMS) substrate. We investigate how electrode area and immersion in phosphate buffered saline (PBS) at 37°C influence electrode impedance. A microfluidic channel is bonded to the electrode array to form the cuff. In an acute, in-vivo, proof-of-principle recording, the device is capable of detecting light stroking and pinch of a hind leg of an anaesthetized rat.

Compliant Multi-electrode Micro-channel Array for Recording Afferent Nerve Activity

We have fabricated a compliant neural interface to record afferent nerve activity. Stretchable gold electrodes were evaporated on a polydimethylsiloxane (PDMS) substrate and were encapsulated using photo-patternable PDMS. The built-in microstructure of the gold film on PDMS allows the electrodes to twist and flex repeatedly, without loss of electrical conductivity. PDMS microchannels (5mm long, 100μm wide, 100μm deep) were then plasma bonded irreversibly on top of the electrode array to define five parallel-conduit implants. The soft gold microelectrodes have a low impedance of ~200kΩ at the 1kHz frequency range. Teased nerves from the L6 dorsal root of an anaesthetized Sprague Dawley rat were threaded through the microchannels. Acute tripolar recordings of cutaneous activity are demonstrated, from multiple nerve rootlets simultaneously. Confinement of the axons within narrow microchannels allows for reliable recordings of low amplitude afferents. This electrode technology promises exciting applications in neuroprosthetic devices including bladder fullness monitors and peripheral nervous system implants.

The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria

The rulAB operon of Pseudomonas spp. confers fitness traits on the host and has been suggested to be a hotspot for insertion of mobile elements that carry avirulence genes. Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1–FH6). Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat. ILEs from FH1 and FH5 were 9403 bp in length and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length and contained 16 ORFs. In all three ILEs, the first 5.1 kb (containing ORFs 1–4) were structurally conserved and contained three predicted site-specific recombinases/integrases and a tetR homologue. Downstream of these resided ORFs of the ‘variable side’ with structural and sequence similarity to those encoding survival traits on the fitness enhancing plasmid pGRT1 (ILEFH1 and ILEFH5) and the NR-II virulence region of genomic island PAGI-5 (ILEFH4). Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.

Array based detection of antibiotic resistance genes in Gram negative bacteria isolated from retail poultry meat in the UK and Ireland

The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an attempt to reduce the spread of multi-resistant Gram negative bacteria. Given the inexorable spread of antibiotic resistance there is an increasing need for improved monitoring of our food. Using selective media, Gram negative bacteria were isolated from retail chicken of UK-Intensively reared (n = 27), Irish-Intensively reared (n = 19) and UK-Free range (n = 30) origin and subjected to an oligonucleotide based array system for the detection of 47 clinically relevant antibiotic resistance genes (ARGs) and two integrase genes. High incidences of β-lactamase genes were noted in all sample types, acc (67%), cmy (80%), fox (55%) and tem (40%) while chloramphenicol resistant determinants were detected in bacteria from the UK poultry portions and were absent in bacteria from the Irish samples. Denaturing Gradient Gel Electrophoresis (DGGE) was used to qualitatively analyse the Gram negative population in the samples and showed the expected diversity based on band stabbing and DNA sequencing. The array system proved to be a quick method for the detection of antibiotic resistance gene (ARG) burden within a mixed Gram negative bacterial population.

Cost function for sub-agent elements in multi-agent energy management system

Distributed generation plays a key role in reducing CO2 emissions and losses in transmission of power. However, due to the nature of renewable resources, distributed generation requires suitable control strategies to assure reliability and optimality for the grid. Multi-agent systems are perfect candidates for providing distributed control of distributed generation stations as well as providing reliability and flexibility for the grid integration. The proposed multi-agent energy management system consists of single-type agents who control one or more gird entities, which are represented as generic sub-agent elements. The agent applies one control algorithm across all elements and uses a cost function to evaluate the suitability of the element as a supplier. The behavior set by the agent's user defines which parameters of an element have greater weight in the cost function, which allows the user to specify the preference on suppliers dynamically. This study shows the ability of the multi-agent energy management system to select suppliers according to the selection behavior given by the user. The optimality of the supplier for the required demand is ensured by the cost function based on the parameters of the element.

The role of the harmonic vector average in motion integration

The local speeds of object contours vary systematically with the cosine of the angle between the normal component of the local velocity and the global object motion direction. An array of Gabor elements whose speed changes with local spatial orientation in accordance with this pattern can appear to move as a single surface. The apparent direction of motion of plaids and Gabor arrays has variously been proposed to result from feature tracking, vector addition and vector averaging in addition to the geometrically correct global velocity as indicated by the intersection of constraints (IOC) solution. Here a new combination rule, the harmonic vector average (HVA), is introduced, as well as a new algorithm for computing the IOC solution. The vector sum can be discounted as an integration strategy as it increases with the number of elements. The vector average over local vectors that vary in direction always provides an underestimate of the true global speed. The HVA, however, provides the correct global speed and direction for an unbiased sample of local velocities with respect to the global motion direction, as is the case for a simple closed contour. The HVA over biased samples provides an aggregate velocity estimate that can still be combined through an IOC computation to give an accurate estimate of the global velocity, which is not true of the vector average. Psychophysical results for type II Gabor arrays show perceived direction and speed falls close to the IOC direction for Gabor arrays having a wide range of orientations but the IOC prediction fails as the mean orientation shifts away from the global motion direction and the orientation range narrows. In this case perceived velocity generally defaults to the HVA.