A Fast and Accurate Nonlinear Spectral Method for Image Recognition and Registration

This article addresses the problem of two- and higher dimensional pattern matching, i.e. the identification of instances of a template within a larger signal space, which is a form of registration. Unlike traditional correlation, we aim at obtaining more selective matchings by considering more strict comparisons of gray-level intensity. In order to achieve fast matching, a nonlinear thresholded version of the fast Fourier transform is applied to a gray-level decomposition of the original 2D image. The potential of the method is substantiated with respect to real data involving the selective identification of neuronal cell bodies in gray-level images.Comment: 4 pages, 3 figure

A design of experiments approach for the rapid formulation of a chemically defined medium for metabolic profiling of industrially important microbes

This is the final version. Available on open access from Public Library of Science via the DOI in this recordData Availability: All relevant data are within the manuscript and its Supporting Information files.Geobacillus thermoglucosidans DSM2542 is an industrially important microbe, however the complex nutritional requirements of Geobacilli confound metabolic engineering efforts. Previous studies have utilised semi-defined media recipes that contain complex, undefined, biologically derived nutrients which have unknown ingredients that cannot be quantified during metabolic profiling. This study used design of experiments to investigate how individual nutrients and interactions between these nutrients contribute to growth. A mathematically derived defined medium has been formulated that has been shown to robustly support growth of G. thermoglucosidans in two different environmental conditions (96-well plate and shake flask) and with a variety of lignocellulose-based carbohydrates. This enabled the catabolism of industrially relevant carbohydrates to be investigated.Shell Global Solutions BVUniversity of Exete

Spatial differences between stars and brown dwarfs: a dynamical origin?

We use $N$-body simulations to compare the evolution of spatial distributions of stars and brown dwarfs in young star-forming regions. We use three different diagnostics; the ratio of stars to brown dwarfs as a function of distance from the region's centre, $\mathcal{R}_{\rm SSR}$, the local surface density of stars compared to brown dwarfs, $\Sigma_{\rm LDR}$, and we compare the global spatial distributions using the $\Lambda_{\rm MSR}$ method. From a suite of twenty initially statistically identical simulations, 6/20 attain $\mathcal{R}_{\rm SSR} << 1$ $and$ $\Sigma_{\rm LDR} << 1$ $and$ $\Lambda_{\rm MSR} << 1$, indicating that dynamical interactions could be responsible for observed differences in the spatial distributions of stars and brown dwarfs in star-forming regions. However, many simulations also display apparently contradictory results - for example, in some cases the brown dwarfs have much lower local densities than stars ($\Sigma_{\rm LDR} << 1$), but their global spatial distributions are indistinguishable ($\Lambda_{\rm MSR} = 1$) and the relative proportion of stars and brown dwarfs remains constant across the region ($\mathcal{R}_{\rm SSR} = 1$). Our results suggest that extreme caution should be exercised when interpreting any observed difference in the spatial distribution of stars and brown dwarfs, and that a much larger observational sample of regions/clusters (with complete mass functions) is necessary to investigate whether or not brown dwarfs form through similar mechanisms to stars.Comment: 7 pages, 5 figures, accepted for publication in MNRA

Test beam Characterizations of 3D Silicon Pixel detectors

3D silicon detectors are characterized by cylindrical electrodes perpendicular to the surface and penetrating into the bulk material in contrast to standard Si detectors with planar electrodes on its top and bottom. This geometry renders them particularly interesting to be used in environments where standard silicon detectors have limitations, such as for example the radiation environment expected in an LHC upgrade. For the first time, several 3D sensors were assembled as hybrid pixel detectors using the ATLAS-pixel front-end chip and readout electronics. Devices with different electrode configurations have been characterized in a 100 GeV pion beam at the CERN SPS. Here we report results on unirradiated devices with three 3D electrodes per 50 x 400 um2 pixel area. Full charge collection is obtained already with comparatively low bias voltages around 10 V. Spatial resolution with binary readout is obtained as expected from the cell dimensions. Efficiencies of 95.9% +- 0.1 % for tracks parallel to the electrodes and of 99.9% +- 0.1 % at 15 degrees are measured. The homogeneity of the efficiency over the pixel area and charge sharing are characterized.Comment: 5 pages, 7 figure

Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications

This is the author accepted manusript. The final version is available from American Chemical Society via the DOI in this recordAccession Codes: The sequence data for the four Geobacillus spp. used in this study have been submitted to the NCBI Sequence Read Archive and are available under the accession number PRJNA521450.Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space

Design of Experiments Methodology to Build a Multifactorial Statistical Model Describing the Metabolic Interactions of Alcohol Dehydrogenase Isozymes in the Ethanol Biosynthetic Pathway of the Yeast Saccharomyces cerevisiae

This is the author accepted manuscript. The final version is available from the American Chemical Society via the DOI in this recordMultifactorial approaches can quickly and efficiently model complex, interacting natural or engineered biological systems in a way that traditional one-factor-at-a-time experimentation can fail to do. We applied a Design of Experiments (DOE) approach to model ethanol biosynthesis in yeast, which is well-understood and genetically tractable, yet complex. Six alcohol dehydrogenase (ADH) isozymes catalyze ethanol synthesis, differing in their transcriptional and post-translational regulation, subcellular localization, and enzyme kinetics. We generated a combinatorial library of all ADH gene deletions and measured the impact of gene deletion(s) and environmental context on ethanol production of a subset of this library. The data were used to build a statistical model that described known behaviors of ADH isozymes and identified novel interactions. Importantly, the model described features of ADH metabolic behavior without explicit a priori knowledge. The method is therefore highly suited to understanding and optimizing metabolic pathways in less well-understood systems.We wish to thank Dr. Alex Johns for helpful discussions. S.R.B. would also like to thank Shell Biodomain for funding for this PhD research project

Visualizing the Formation of the Kondo Lattice and the Hidden Order in URu2Si2

Heavy electronic states originating from the f atomic orbitals underlie a rich variety of quantum phases of matter. We use atomic scale imaging and spectroscopy with the scanning tunneling microscope (STM) to examine the novel electronic states that emerge from the uranium f states in URu2Si2. We find that as the temperature is lowered, partial screening of the f electrons' spins gives rise to a spatially modulated Kondo-Fano resonance that is maximal between the surface U atoms. At T=17.5 K, URu2Si2 is known to undergo a 2nd order phase transition from the Kondo lattice state into a phase with a hidden order parameter. From tunneling spectroscopy, we identify a spatially modulated, bias-asymmetric energy gap with a mean-field temperature dependence that develops in the hidden order state. Spectroscopic imaging further reveals a spatial correlation between the hidden order gap and the Kondo resonance, suggesting that the two phenomena involve the same electronic states

Simultaneous determination of wave speed and arrival time of reflected waves using the pressure-velocity loop

This is the post print version of the article. The official published version can be found at the link below.In a previous paper we demonstrated that the linear portion of the pressure–velocity loop (PU-loop) corresponding to early systole could be used to calculate the local wave speed. In this paper we extend this work to show that determination of the time at which the PU-loop first deviates from linearity provides a convenient way to determine the arrival time of reflected waves (Tr). We also present a new technique using the PU-loop that allows for the determination of wave speed and Tr simultaneously. We measured pressure and flow in elastic tubes of different diameters, where a strong reflection site existed at known distances away form the measurement site. We also measured pressure and flow in the ascending aorta of 11 anaesthetised dogs where a strong reflection site was produced through total arterial occlusion at four different sites. Wave speed was determined from the initial slope of the PU-loop and Tr was determined using a new algorithm that detects the sampling point at which the initial linear part of the PU-loop deviates from linearity. The results of the new technique for detecting Tr were comparable to those determined using the foot-to-foot and wave intensity analysis methods. In elastic tubes Tr detected using the new algorithm was almost identical to that detected using wave intensity analysis and foot-to-foot methods with a maximum difference of 2%. Tr detected using the PU-loop in vivo highly correlated with that detected using wave intensity analysis (r 2 = 0.83, P < 0.001). We conclude that the new technique described in this paper offers a convenient and objective method for detecting Tr, and allows for the dynamic determination of wave speed and Tr, simultaneously

Testing the universality of star formation - I. Multiplicity in nearby star-forming regions

We have collated multiplicity data for five clusters (Taurus, Chamaeleon I, Ophiuchus, IC348, and the Orion Nebula Cluster). We have applied the same mass ratio (flux ratios of delta K <= 2.5) and primary mass cuts (~0.1-3.0 Msun) to each cluster and therefore have directly comparable binary statistics for all five clusters in the separation range 62-620 au, and for Taurus, Chamaeleon I, and Ophiuchus in the range 18-830 au. We find that the trend of decreasing binary fraction with cluster density is solely due to the high binary fraction of Taurus, the other clusters show no obvious trend over a factor of nearly 20 in density. With N-body simulations we attempt to find a set of initial conditions that are able to reproduce the density, morphology and binary fractions of all five clusters. Only an initially clumpy (fractal) distribution with an initial total binary fraction of 73 per cent (17 per cent in the range 62-620 au) is able to reproduce all of the observations (albeit not very satisfactorily). Therefore, if star formation is universal the initial conditions must be clumpy and with a high (but not 100 per cent) binary fraction. This could suggest that most stars, including M-dwarfs, form in binaries.Comment: Accepted for publication in MNRAS, 19 pages, 22 figure

A Tale of Three Cities : OmegaCAM discovers multiple sequences in the color-magnitude diagram of the Orion Nebula Cluster

Reproduced with permission from Astronomy & Astrophysics, © 2017 ESO. Published by EDP Sciences.As part of the Accretion Discs in H$\alpha$ with OmegaCAM (ADHOC) survey, we imaged in r, i and H-alpha a region of 12x8 square degrees around the Orion Nebula Cluster. Thanks to the high-quality photometry obtained, we discovered three well-separated pre-main sequences in the color-magnitude diagram. The populations are all concentrated towards the cluster's center. Although several explanations can be invoked to explain these sequences we are left with two competitive, but intriguing, scenarios: a population of unresolved binaries with an exotic mass ratio distribution or three populations with different ages. Independent high-resolution spectroscopy supports the presence of discrete episodes of star formation, each separated by about a million years. The stars from the two putative youngest populations rotate faster than the older ones, in agreement with the evolution of stellar rotation observed in pre-main sequence stars younger than 4 Myr in several star forming regions. Whatever the final explanation, our results prompt for a revised look at the formation mode and early evolution of stars in clusters.Peer reviewedFinal Published versio