Near-bed hydrodynamics and turbulence below a large-scale plunging breaking wave over a mobile barred bed profile

Funded by The research presented in this paper is part of the SINBAD project. Grant Number: STW (12058) and EPSRC (EP/J00507X/1, EP/J005541/1)

Parallel and Streaming Truth Discovery in Large-Scale Quantitative Crowdsourcing

ACKNOWLEDGEMENTS This research is based upon work supported in part by the U.S. ARL and U.K. Ministry of Defense under Agreement Number W911NF-06-3-0001, and by the NSF under award CNS-1213140. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views or represent the official policies of the NSF, the U.S. ARL, the U.S. Government, the U.K. Ministry of Defense or the U.K. Government. The U.S. and U.K. Governments are authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation hereon.

An investigation by AFM and TEM of the mechanism of anodic formation of nanoporosity in n-InP in KOH

The early stages of nanoporous layer formation, under anodic conditions in the absence of light, were investigated for n-type InP with a carrier concentration of ∼3× 1018 cm-3 in 5 mol dm-3 KOH and a mechanism for the process is proposed. At potentials less than ∼0.35 V, spectroscopic ellipsometry and transmission electron microscopy (TEM) showed a thin oxide film on the surface. Atomic force microscopy (AFM) of electrode surfaces showed no pitting below ∼0.35 V but clearly showed etch pit formation in the range 0.4-0.53 V. The density of surface pits increased with time in both linear potential sweep and constant potential reaching a constant value at a time corresponding approximately to the current peak in linear sweep voltammograms and current-time curves at constant potential. TEM clearly showed individual nanoporous domains separated from the surface by a dense ∼40 nm InP layer. It is concluded that each domain develops as a result of directionally preferential pore propagation from an individual surface pit which forms a channel through this near-surface layer. As they grow larger, domains meet, and the merging of multiple domains eventually leads to a continuous nanoporous sub-surface region.

A Measurement of the Proton Structure Function g2p at Low Q2

Experiments at Jefferson Lab have been conducted to extract the nucleon spin-dependent structure functions over a wide kinematic range. Higher moments of these quantities provide tests of QCD sum rules and predictions of chiral perturbation theory ($\chi$PT). While precise measurements of $g_{1}^n$, $g_{2}^n$, and $g_1^p$ have been extensively performed, the data of $g_2^p$ remain scarce. Discrepancies were found between existing data related to $g_2$ and theoretical predictions. Results on the proton at large $Q^2$ show a significant deviation from the Burkhardt-Cottingham sum rule, while results for the neutron generally follow this sum rule. The next-to-leading order $\chi$PT calculations exhibit discrepancy with data on the longitudinal-transverse polarizability $\delta_{LT}^n$. Further measurements of the proton spin structure function $g_2^p$ are desired to understand these discrepancies.

Experiment E08-027 (g2p) was conducted at Jefferson Lab in experimental Hall A in 2012. Inclusive measurements were performed with polarized electron beam and a polarized ammonia target to obtain the proton spin-dependent structure function $g_2^p$ at low Q$^2$ region (0.02$<$Q$^2$$<$0.2 GeV$^2$) for the first time. The results can be used to test the Burkhardt-Cottingham sum rule, and also allow us to extract the longitudinal-transverse spin polarizability of the proton, which will provide a benchmark test of $\chi$PT calculations. This thesis will present and discuss the very preliminary results of the transverse asymmetry and the spin-dependent structure functions $g_1^p$ and $g_2^p$ from the data analysis of the g2p experiment .

A first principles analysis of the effect of hydrogen concentration in hydrogenated amorphous silicon on the formation of strained Si-Si bonds and the optical and mobility gaps

In this paper, we use a model of hydrogenated amorphous silicon generated from molecular dynamics with density functional theory calculations to examine how the atomic geometry and the optical and mobility gaps are influenced by mild hydrogen oversaturation. The optical and mobility gaps show a volcano curve as the hydrogen content varies from undersaturation to mild oversaturation, with largest gaps obtained at the saturation hydrogen concentration. At the same time, mid-gap states associated with dangling bonds and strained Si-Si bonds disappear at saturation but reappear at mild oversaturation, which is consistent with the evolution of optical gap. The distribution of Si-Si bond distances provides the key to the change in electronic properties. In the undersaturation regime, the new electronic states in the gap arise from the presence of dangling bonds and strained Si-Si bonds, which are longer than the equilibrium Si-Si distance. Increasing hydrogen concentration up to saturation reduces the strained bonds and removes dangling bonds. In the case of mild oversaturation, the mid-gap states arise exclusively from an increase in the density of strained Si-Si bonds. Analysis of our structure shows that the extra hydrogen atoms form a bridge between neighbouring silicon atoms, thus increasing the Si-Si distance and increasing disorder in the sample.

Formation of sub-7 nm feature size PS-b-P4VP block copolymer structures by solvent vapour process

The nanometer range structure produced by thin films of diblock copolymers makes them a great of interest as templates for the microelectronics industry. We investigated the effect of annealing solvents and/or mixture of the solvents in case of symmetric Poly (styrene-block-4vinylpyridine) (PS-b-P4VP) diblock copolymer to get the desired line patterns. In this paper, we used different molecular weights PS-b-P4VP to demonstrate the scalability of such high χ BCP system which requires precise fine-tuning of interfacial energies achieved by surface treatment and that improves the wetting property, ordering, and minimizes defect densities. Bare Silicon Substrates were also modified with polystyrene brush and ethylene glycol self-assembled monolayer in a simple quick reproducible way. Also, a novel and simple in situ hard mask technique was used to generate sub-7nm Iron oxide nanowires with a high aspect ratio on Silicon substrate, which can be used to develop silicon nanowires post pattern transfer.

Global distributions of diazotrophs nitrogen fixation rates - Depth integrated values computed from a collection of source datasets - Contribution to the MAREDAT World Ocean Atlas of Plankton Functional Types

The MAREDAT atlas covers 11 types of plankton, ranging in size from bacteria to jellyfish. Together, these plankton groups determine the health and productivity of the global ocean and play a vital role in the global carbon cycle. Working within a uniform and consistent spatial and depth grid (map) of the global ocean, the researchers compiled thousands and tens of thousands of data points to identify regions of plankton abundance and scarcity as well as areas of data abundance and scarcity. At many of the grid points, the MAREDAT team accomplished the difficult conversion from abundance (numbers of organisms) to biomass (carbon mass of organisms). The MAREDAT atlas provides an unprecedented global data set for ecological and biochemical analysis and modeling as well as a clear mandate for compiling additional existing data and for focusing future data gathering efforts on key groups in key areas of the ocean. The present data set presents depth integrated values of diazotrophs nitrogen fixation rates, computed from a collection of source data sets.

Effects of pH on asexual reproduction and statolith formation of the scyphozoan, Aurelia labiata, 2010

Although anthropogenic infuences such as global warming, overfishing, and eutrophication may contribute to jellyfish blooms, little is known about the effects of ocean acidification on jellyfish. Most medusae form statoliths of calcium sulfate hemihydrate that are components of their balance organs (statocysts). This study was designed to test the effects of pH (7.9, within the average current range, 7.5, expected by 2100, and 7.2, expected by 2300) combined with two temperatures (9 and 15°C) on asexual reproduction and statolith formation of the moon jellyfish, Aurelia labiata. Polyp survival was 100% after 122 d in seawater in all six temperature and pH combinations. Because few polyps at 9°C strobilated, and temperature effects on budding were consistent with published results, we did not analyze data from those three treatments further. At 15°C, there were no significant effects of pH on the numbers of ephyrae or buds produced per polyp or on the numbers of statoliths per statocyst; however, statolith size was signi?cantly smaller in ephyrae released from polyps reared at low pH. Our results indicate that A. labiata polyps are quite tolerant of low pH, surviving and reproducing asexually even at the lowest tested pH; however, the effects of small statoliths on ephyra fitness are unknown. Future research on the behavior of ephyrae with small statoliths would further our understanding of how ocean acidi?cation may affect jellyfish survival in nature.

Gravity collapse structures in the Central Precordillera fold-andthrust belt, Argentina

Several landforms found in the fold-and-thrust belt area of Central Precordillera, Pre-Andes of Argentina, which were often associated with tectonic efforts, are in fact related to non-tectonic processes or gravitational superficial structures. These second-order structures, interpreted as gravitational collapse structures, have developed in the western flank of sierras de La Dehesa and Talacasto. These include rock-slides, rock falls, wrinkle folds, slip sheets and flaps, among others; which together constitute a monoclinal fold dipping between 30º and 60º to the west. Gravity collapse structures are parallel to the regional strike of the Sierra de la Dehesa and are placed in Ordovician limestones and dolomites. Their sloping towards the west, the presence of bed planes, fractures and joints; and the lithology (limestone interbedded with incompetent argillaceous banks) would have favored their occurrence. Movement of the detached structures has been controlled by lithology characteristics, as well as by bedding and joints. Detachment and initial transport of gravity collapse structures and rockslides in the western flank of the Sierra de la Dehesa were tightly controlled by three structural elements: 1) sliding surfaces developed on parallel bedded strata when dipping >30° in the slope direction; 2) Joint’s sets constitute lateral and transverse traction cracks which release extensional stresses and 3) Discontinuities fragmenting sliding surfaces.  Some other factors that could be characterized as local (lithology, structure and topography) and as regional (high seismic activity and possibly wetter conditions during the postglacial period) were determining in favoring the steady loss of the western mountain side in the easternmost foothills of Central Precordillera.

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.

Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis

Background: Esophageal adenocarcinoma (EA) is one of the fastest rising cancers in western countries. Barrett’s Esophagus (BE) is the premalignant precursor of EA. However, only a subset of BE patients develop EA, which complicates the clinical management in the absence of valid predictors. Genetic risk factors for BE and EA are incompletely understood. This study aimed to identify novel genetic risk factors for BE and EA.Methods: Within an international consortium of groups involved in the genetics of BE/EA, we performed the first meta-analysis of all genome-wide association studies (GWAS) available, involving 6,167 BE patients, 4,112 EA patients, and 17,159 representative controls, all of European ancestry, genotyped on Illumina high-density SNP-arrays, collected from four separate studies within North America, Europe, and Australia. Meta-analysis was conducted using the fixed-effects inverse variance-weighting approach. We used the standard genome-wide significant threshold of 5×10-8 for this study. We also conducted an association analysis following reweighting of loci using an approach that investigates annotation enrichment among the genome-wide significant loci. The entire GWAS-data set was also analyzed using bioinformatics approaches including functional annotation databases as well as gene-based and pathway-based methods in order to identify pathophysiologically relevant cellular pathways.Findings: We identified eight new associated risk loci for BE and EA, within or near the CFTR (rs17451754, P=4·8×10-10), MSRA (rs17749155, P=5·2×10-10), BLK (rs10108511, P=2·1×10-9), KHDRBS2 (rs62423175, P=3·0×10-9), TPPP/CEP72 (rs9918259, P=3·2×10-9), TMOD1 (rs7852462, P=1·5×10-8), SATB2 (rs139606545, P=2·0×10-8), and HTR3C/ABCC5 genes (rs9823696, P=1·6×10-8). A further novel risk locus at LPA (rs12207195, posteriori probability=0·925) was identified after re-weighting using significantly enriched annotations. This study thereby doubled the number of known risk loci. The strongest disease pathways identified (P<10-6) belong to muscle cell differentiation and to mesenchyme development/differentiation, which fit with current pathophysiological BE/EA concepts. To our knowledge, this study identified for the first time an EA-specific association (rs9823696, P=1·6×10-8) near HTR3C/ABCC5 which is independent of BE development (P=0·45).Interpretation: The identified disease loci and pathways reveal new insights into the etiology of BE and EA. Furthermore, the EA-specific association at HTR3C/ABCC5 may constitute a novel genetic marker for the prediction of transition from BE to EA. Mutations in CFTR, one of the new risk loci identified in this study, cause cystic fibrosis (CF), the most common recessive disorder in Europeans. Gastroesophageal reflux (GER) belongs to the phenotypic CF-spectrum and represents the main risk factor for BE/EA. Thus, the CFTR locus may trigger a common GER-mediated pathophysiology.

Formation of helical ion chains

We study the nonequilibrium dynamics of the linear to zigzag structural phase transition exhibited by an ion chain confined in a trap with periodic boundary conditions. The transition is driven by reducing the transverse confinement at a finite quench rate, which can be accurately controlled. This results in the formation of zigzag domains oriented along different transverse planes. The twists between different domains can be stabilized by the topology of the trap and under laser cooling the system has a chance to relax to a helical chain with nonzero winding number. Molecular dynamics simulations are used to obtain a large sample of possible trajectories for different quench rates. The scaling of the average winding number with different quench rates is compared to the prediction of the Kibble-Zurek theory, and a good quantitative agreement is found.

Implementing a structural continuity constraint and a halting method for the topology optimization of energy absorbers

This study investigates topology optimization of energy absorbing structures in which material damage is accounted for in the optimization process. The optimization objective is to design the lightest structures that are able to absorb the required mechanical energy. A structural continuity constraint check is introduced that is able to detect when no feasible load path remains in the finite element model, usually as a result of large scale fracture. This assures that designs do not fail when loaded under the conditions prescribed in the design requirements. This continuity constraint check is automated and requires no intervention from the analyst once the optimization process is initiated. Consequently, the optimization algorithm proceeds towards evolving an energy absorbing structure with the minimum structural mass that is not susceptible to global structural failure. A method is also introduced to determine when the optimization process should halt. The method identifies when the optimization method has plateaued and is no longer likely to provide improved designs if continued for further iterations. This provides the designer with a rational method to determine the necessary time to run the optimization and avoid wasting computational resources on unnecessary iterations. A case study is presented to demonstrate the use of this method.

A Scalable General Purpose System for Large-Scale Graph Processing

Graph analytics is an important and computationally demanding class of data analytics. It is essential to balance scalability, ease-of-use and high performance in large scale graph analytics. As such, it is necessary to hide the complexity of parallelism, data distribution and memory locality behind an abstract interface. The aim of this work is to build a scalable graph analytics framework that does not demand significant parallel programming experience based on NUMA-awareness.
The realization of such a system faces two key problems:
(i)~how to develop a scale-free parallel programming framework that scales efficiently across NUMA domains; (ii)~how to efficiently apply graph partitioning in order to create separate and largely independent work items that can be distributed among threads.

Energy efficiency optimization in hardware-constrained large-scale MIMO systems

Large-scale multiple-input multiple-output (MIMO) communication systems can bring substantial improvement in spectral efficiency and/or energy efficiency, due to the excessive degrees-of-freedom and huge array gain. However, large-scale MIMO is expected to deploy lower-cost radio frequency (RF) components, which are particularly prone to hardware impairments. Unfortunately, compensation schemes are not able to remove the impact of hardware impairments completely, such that a certain amount of residual impairments always exists. In this paper, we investigate the impact of residual transmit RF impairments (RTRI) on the spectral and energy efficiency of training-based point-to-point large-scale MIMO systems, and seek to determine the optimal training length and number of antennas which maximize the energy efficiency. We derive deterministic equivalents of the signal-to-noise-and-interference ratio (SINR) with zero-forcing (ZF) receivers, as well as the corresponding spectral and energy efficiency, which are shown to be accurate even for small number of antennas. Through an iterative sequential optimization, we find that the optimal training length of systems with RTRI can be smaller compared to ideal hardware systems in the moderate SNR regime, while larger in the high SNR regime. Moreover, it is observed that RTRI can significantly decrease the optimal number of transmit and receive antennas.