Field test of multiple 1/10 scale tidal turbines in steady flows

Queen's University Belfast and Wave Barrier Ltd have developed a tidal testing platform to test hydrokinetic turbines at medium scale. Multiple turbines can be pushed through still water conditions, in steady-state pushing tests. Experiments were conducted to evaluate the interactions between two identical, mono-strut, horizontal axis tidal turbines (HATTs) of 1.5 m diameter (D) rotor. Their relative performance when located individually, in-plane and in-line are investigated. The data shows a high consistency in the power curves at different flow speeds, which indicates high repeatability in this Reynolds range. For an individual turbine, there is no performance difference when the rotor is mounted either upstream or downstream of the supporting structure. When placed in-plane, the turbines have no adverse effect on one another. When spaced in-line with 2D separation, there is a 63% reduction in the performance of the downstream turbine. At 6D downstream this performance reduction is still 59%, indicating some wake recovery between 2D and 6D, though the influence from the upstream rotor persists to at least 6D downstream of the first device. In contrast the performance of the downstream turbine when placed at 1.5D offset of the upstream device at 6D downstream is approximately recovered to the individual turbine performance.

Coastal upwelling drives intertidal assemblage structure and trophic ecology

ecosystems. Coastal oceanic upwelling, for example, has been associated with elevatedbiomass and abundance patterns of certain functional groups, e.g., corticated macroalgae.In the upwelling system of Northern Chile, we examined measures of intertidal macrobenthiccomposition, structure and trophic ecology across eighteen shores varying in theirproximity to two coastal upwelling centres, in a hierarchical sampling design (spatial scalesof >1 and >10 km). The influence of coastal upwelling on intertidal communities was confirmedby the stable isotope values (δ13C and δ15N) of consumers, including a dominantsuspension feeder, grazers, and their putative resources of POM, epilithic biofilm, andmacroalgae. We highlight the utility of muscle δ15N from the suspension feeding mussel,Perumytilus purpuratus, as a proxy for upwelling, supported by satellite data and previousstudies. Where possible, we used corrections for broader-scale trends, spatial autocorrelation,ontogenetic dietary shifts and spatial baseline isotopic variation prior to analysis. Ourresults showed macroalgal assemblage composition, and benthic consumer assemblagestructure, varied significantly with the intertidal influence of coastal upwelling, especiallycontrasting bays and coastal headlands. Coastal topography also separated differences inconsumer resource use. This suggested that coastal upwelling, itself driven by coastlinetopography, influences intertidal communities by advecting nearshore phytoplankton populationsoffshore and cooling coastal water temperatures. We recommend the isotopic valuesof benthic organisms, specifically long-lived suspension feeders, as in situ alternativesto offshore measurements of upwelling influence

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

BACKGROUND: Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis.

METHODS: In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer.

RESULTS: We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs.

CONCLUSION: To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors.

Impacts of invasive browsers on demographic rates and forest structure in New Zealand

Background/Question/Methods

Assessing the large scale impact of deer populations on forest structure and composition is important because of their increasing abundance in many temperate forests. Deer are invasive animals and sometimes thought to be responsible for immense damage to New Zealand’s forests. We report demographic changes taking place among 40 widespread indigenous tree species over 20 years, following a period of record deer numbers in the 1950s and a period of extensive hunting and depletion of deer populations during the 1960s and 1970s.

Results/Conclusions

Across a network of 578 plots there was an overall 13% reduction in sapling density of our study species with most remaining constant and a few declining dramatically. The effect of suppressed recruitment when deer populations were high was evident in the small tree size class (30 – 80 mm dbh). Stem density decreased by 15% and species with the greatest annual decreases in small tree density were those which have the highest rates of sapling recovery in exclosures indicating that deer were responsible. Densities of large canopy trees have remained relatively stable. There were imbalances between mortality and recruitment rates for 23 of the 40 species, 7 increasing and 16 in decline. These changes were again linked with sapling recovery in exclosures; species which recovered most rapidly following deer exclusion had the greatest net recruitment deficit across the wider landscape, indicating recruitment suppression by deer as opposed to mortality induced by disturbance and other herbivores. Species are not declining uniformly across all populations and no species are in decline across their entire range. Therefore we predict that with continued deer presence some forests will undergo compositional changes but that none of the species tested will become nationally extinct.

Impacts of invasive browsers on demographic rates and forest structure in New Zealand. Available from: http://www.researchgate.net/publication/267285500_Impacts_of_invasive_browsers_on_demographic_rates_and_forest_structure_in_New_Zealand [accessed Oct 9, 2015].

A large scale model experimental study of a tidal turbine in uniform steady flow

An experimental study measuring the performance and wake characteristics of a 1:10th scale horizontal axis turbine in steady uniform flow conditions is presented in this paper.
Large scale towing tests conducted in a lake were devised to model the performance of the tidal turbine and measure the wake produced. As a simplification of the marine environment, towing the turbine in a lake provides approximately steady, uniform inflow conditions. A 16m long x 6m wide catamaran was constructed for the test programme. This doubled as a towing rig and flow measurement platform, providing a fixed frame of reference for measurements in the wake of a horizontal axis tidal turbine. Velocity mapping was conducted using Acoustic Doppler Velocimeters.
The results indicate varying the inflow speed yielded little difference in the efficiency of the turbine or the wake velocity deficit characteristics provided the same tip speed ratio is used. Increasing the inflow velocity from 0.9 m/s to 1.2 m/s influenced the turbulent wake characteristics more markedly. The results also demonstrate that the flow field in the wake of a horizontal axis tidal turbine is strongly affected by the turbine support structure

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

Guided post-acceleration of laser-driven ions by a miniature modular structure

All-optical approaches to particle acceleration are currently attracting a significant research effort internationally. Although characterized by exceptional transverse and longitudinal emittance, laser-driven ion beams currently have limitations in terms of peak ion energy, bandwidth of the energy spectrum and beam divergence. Here we introduce the concept of a versatile, miniature linear accelerating module, which, by employing laser-excited electromagnetic pulses directed along a helical path surrounding the laser-accelerated ion beams, addresses these shortcomings simultaneously. In a proof-of-principle experiment on a university-scale system, we demonstrate post-acceleration of laser-driven protons from a flat foil at a rate of 0.5 GeVm^-1, already beyond what can be sustained by conventional accelerator technologies, with dynamic beam collimation and energy selection. These results open up new opportunities for the development of extremely compact and cost-effective ion accelerators for both established and innovative applications.

Fine-structure photoionization cross sections of Fe II

We present the first calculation of fine-structure photoionization cross sections for the ground state of singly ionized Fe. These large-scale ab initio calculations, limited to the near-threshold region, were performed in the close-coupling approximation using a Dirac–Coulomb R -matrix method implemented within a modified version of the DARC package. Our calculated cross sections reproduce in detail the resonance structures observed in previous experimental determinations.

Multivariate analysis of regional-scale geochemical data for environmental monitoring

A compositional multivariate approach is used to analyse regional scale soil geochemical data obtained as part of the Tellus Project generated by the Geological Survey Northern Ireland (GSNI). The multi-element total concentration data presented comprise XRF analyses of 6862 rural soil samples collected at 20cm depths on a non-aligned grid at one site per 2 km2. Censored data were imputed using published detection limits. Using these imputed values for 46 elements (including LOI), each soil sample site was assigned to the regional geology map provided by GSNI initially using the dominant lithology for the map polygon. Northern Ireland includes a diversity of geology representing a stratigraphic record from the Mesoproterozoic, up to and including the Palaeogene. However, the advance of ice sheets and their meltwaters over the last 100,000 years has left at least 80% of the bedrock covered by superficial deposits, including glacial till and post-glacial alluvium and peat. The question is to what extent the soil geochemistry reflects the underlying geology or superficial deposits. To address this, the geochemical data were transformed using centered log ratios (clr) to observe the requirements of compositional data analysis and avoid closure issues. Following this, compositional multivariate techniques including compositional Principal Component Analysis (PCA) and minimum/maximum autocorrelation factor (MAF) analysis method were used to determine the influence of underlying geology on the soil geochemistry signature. PCA showed that 72% of the variation was determined by the first four principal components (PC’s) implying “significant” structure in the data. Analysis of variance showed that only 10 PC’s were necessary to classify the soil geochemical data. To consider an improvement over PCA that uses the spatial relationships of the data, a classification based on MAF analysis was undertaken using the first 6 dominant factors. Understanding the relationship between soil geochemistry and superficial deposits is important for environmental monitoring of fragile ecosystems such as peat. To explore whether peat cover could be predicted from the classification, the lithology designation was adapted to include the presence of peat, based on GSNI superficial deposit polygons and linear discriminant analysis (LDA) undertaken. Prediction accuracy for LDA classification improved from 60.98% based on PCA using 10 principal components to 64.73% using MAF based on the 6 most dominant factors. The misclassification of peat may reflect degradation of peat covered areas since the creation of superficial deposit classification. Further work will examine the influence of underlying lithologies on elemental concentrations in peat composition and the effect of this in classification analysis.

A framework for experimental determination of localised vertical pedestrian forces on full-scale structures using wireless attitude and heading reference systems

A major weakness among loading models for pedestrians walking on flexible structures proposed in recent years is the various uncorroborated assumptions made in their development. This applies to spatio-temporal characteristics of pedestrian loading and the nature of multi-object interactions. To alleviate this problem, a framework for the determination of localised pedestrian forces on full-scale structures is presented using a wireless attitude and heading reference systems (AHRS). An AHRS comprises a triad of tri-axial accelerometers, gyroscopes and magnetometers managed by a dedicated data processing unit, allowing motion in three-dimensional space to be reconstructed. A pedestrian loading model based on a single point inertial measurement from an AHRS is derived and shown to perform well against benchmark data collected on an instrumented treadmill. Unlike other models, the current model does not take any predefined form nor does it require any extrapolations as to the timing and amplitude of pedestrian loading. In order to assess correctly the influence of the moving pedestrian on behaviour of a structure, an algorithm for tracking the point of application of pedestrian force is developed based on data from a single AHRS attached to a foot. A set of controlled walking tests with a single pedestrian is conducted on a real footbridge for validation purposes. A remarkably good match between the measured and simulated bridge response is found, indeed confirming applicability of the proposed framework.

Using UAV acquired photography and structure from motion techniques for studying glacier landforms: application to the glacial flutes at Isfallsglaciären

Glacier and ice sheet retreat exposes freshly deglaciated terrain which often contains small-scale fragile geomorphological features which could provide insight into subglacial or submarginal processes. Subaerial exposure results in potentially rapid landscape modification or even disappearance of the minor–relief landforms as wind, weather, water and vegetation impacts on the newly exposed surface. Ongoing retreat of many ice masses means there is a growing opportunity to obtain high resolution geospatial data from glacier forelands to aid in the understanding of recent subglacial and submarginal processes. Here we used an unmanned aerial vehicle to capture close-range aerial photography of the foreland of Isfallsglaciären, a small polythermal glacier situated in Swedish Lapland. An orthophoto and a digital elevation model with ~2 cm horizontal resolution were created from this photography using structure from motion software. These geospatial data was used to create a geomorphological map of the foreland, documenting moraines, fans, channels and flutes. The unprecedented resolution of the data enabled us to derive morphological metrics (length, width and relief) of the smallest flutes, which is not possible with other data products normally used for glacial landform metrics mapping. The map and flute metrics compare well with previous studies, highlighting the potential of this technique for rapidly documenting glacier foreland geomorphology at an unprecedented scale and resolution. The vast majority of flutes were found to have an associated stoss-side boulder, with the remainder having a likely explanation for boulder absence (burial or erosion). Furthermore, the size of this boulder was found to strongly correlate with the width and relief of the lee-side flute. This is consistent with the lee-side cavity infill model of flute formation. Whether this model is applicable to all flutes, or multiple mechanisms are required, awaits further study.