Automated parameterisation for multi-scale image segmentation on multiple layers

AbstractWe introduce a new automated approach to parameterising multi-scale image segmentation of multiple layers, and we implemented it as a generic tool for the eCognition® software. This approach relies on the potential of the local variance (LV) to detect scale transitions in geospatial data. The tool detects the number of layers added to a project and segments them iteratively with a multiresolution segmentation algorithm in a bottom-up approach, where the scale factor in the segmentation, namely, the scale parameter (SP), increases with a constant increment. The average LV value of the objects in all of the layers is computed and serves as a condition for stopping the iterations: when a scale level records an LV value that is equal to or lower than the previous value, the iteration ends, and the objects segmented in the previous level are retained. Three orders of magnitude of SP lags produce a corresponding number of scale levels. Tests on very high resolution imagery provided satisfactory results for generic applicability. The tool has a significant potential for enabling objectivity and automation of GEOBIA analysis

Measuring the Ellipticity of M 87* Images

The Event Horizon Telescope (EHT) images of the supermassive black hole at the center of the galaxy M 87 provided the first image of the accretion environment on horizon scales. General relativity predicts that the image of the shadow should be nearly circular, given the inclination angle of the black hole M 87*. A robust detection of ellipticity in the image reconstructions of M 87* could signal new gravitational physics on horizon scales. Here we analyze whether the imaging parameters used in EHT analyses are sensitive to ring ellipticity and measure the constraints on the ellipticity of M 87*. We find that the top set is unable to recover ellipticity. Even for simple geometric models, the true ellipticity is biased low, preferring circular rings. Therefore, to place a constraint on the ellipticity of M 87*, we measure the ellipticity of 550 simulated data sets of GRMHD simulations. We find that images with intrinsic axis ratios of 2:1 are consistent with the ellipticity seen from the EHT image reconstructions.Comment: accepted for publication to Ap

Antibody mimetic receptor proteins for label-free biosensors

The development of high sensitivity biosensors, for example for clinical diagnostics, requires the identification of suitable receptor molecules which offer high stability, specificity and affinity, even when embedded into solid-state biosensor transducers. Here, we present an electrochemical biosensor employing small synthetic receptor proteins (Mw < 15 kDa) which emulate antibodies but with improved stability, sensitivity and molecular recognition properties, in particular when immobilized on a solid sensor surface. The synthetic receptor protein is a non-antibody-based protein scaffold with variable peptide regions inserted to provide the specific binding, and was designed to bind anti-myc tag antibody (Mw � 150 kDa), as a proof-of-principle exemplar. Both the scaffold and the selected receptor protein were found to have high thermostability with melting temperatures of 101 �C and 85 �C, respectively. Furthermore, the secondary structures of the receptor protein were found to be very similar to that of the original native scaffold, despite the insertion of variable peptide loops that create the binding sites. A label-free electrochemical sensor was fabricated by functionalising a microfabricated gold electrode with the receptor protein. A change in the phase of the electrochemical impedance was observed when the biosensor was subjected to anti-myc tag antibodies at concentrations between 6.7 pM and 6.7 nM. These findings demonstrate that these non-antibody receptor proteins are excellent candidates for recognition molecules in label-free biosensors

Finding rare objects and building pure samples: Probabilistic quasar classification from low resolution Gaia spectra

We develop and demonstrate a probabilistic method for classifying rare objects in surveys with the particular goal of building very pure samples. It works by modifying the output probabilities from a classifier so as to accommodate our expectation (priors) concerning the relative frequencies of different classes of objects. We demonstrate our method using the Discrete Source Classifier, a supervised classifier currently based on Support Vector Machines, which we are developing in preparation for the Gaia data analysis. DSC classifies objects using their very low resolution optical spectra. We look in detail at the problem of quasar classification, because identification of a pure quasar sample is necessary to define the Gaia astrometric reference frame. By varying a posterior probability threshold in DSC we can trade off sample completeness and contamination. We show, using our simulated data, that it is possible to achieve a pure sample of quasars (upper limit on contamination of 1 in 40,000) with a completeness of 65% at magnitudes of G=18.5, and 50% at G=20.0, even when quasars have a frequency of only 1 in every 2000 objects. The star sample completeness is simultaneously 99% with a contamination of 0.7%. Including parallax and proper motion in the classifier barely changes the results. We further show that not accounting for class priors in the target population leads to serious misclassifications and poor predictions for sample completeness and contamination. (Truncated)Comment: MNRAS accepte

Spinodal decomposition in alkali feldspar studied by atom probe tomography

We used atom probe tomography to complement electron microscopy for the investigation of spinodal decomposition in alkali feldspar. To this end, gem-quality alkali feldspar of intermediate composition with a mole fraction of aK=0.43 of the K end-member was prepared from Madagascar orthoclase by ion-exchange with (NaK)Cl molten salt. During subsequent annealing at 550∘C and close to ambient pressure the ion-exchanged orthoclase unmixed producing a coherent lamellar intergrowth of Na-rich and K-rich lamellae. The chemical separation was completed, and equilibrium Na–K partitioning between the different lamellae was attained within four days, which was followed by microstructural coarsening. After annealing for 4 days, the wavelength of the lamellar microstructure was ≈17nm and it increased to ≈30nm after annealing for 16 days. The observed equilibrium compositions of the Na-rich and K-rich lamellae are in reasonable agreement with an earlier experimental determination of the coherent solvus. The excess energy associated with compositional gradients at the lamellar interfaces was quantified from the initial wavelength of the lamellar microstructure and the lamellar compositions as obtained from atom probe tomography using the Cahn–Hilliard theory. The capability of atom probe tomography to deliver quantitative chemical compositions at nm resolution opens new perspectives for studying the early stages of exsolution. In particular, it helps to shed light on the phase relations in nm scaled coherent intergrowth

A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.

Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A

Low-extinction windows in the inner Galactic Bulge

We built K band extinction maps in the area of two candidate low-extinction windows in the inner Bulge: W0.2-2.1 at (l,b) = (0.25o,-2.15o), and W359.4-3.1 at (l,b) = (359.40o,-3.10o). We employed JHKs photometry from the 2MASS Point Source Catalog. Extinction values were determined by fitting the upper giant branch found in the present 2MASS Ks x J-Ks diagrams to a de-reddened bulge stellar population reference giant branch. We tested the method on the well known Baade's and Sgr I windows: the 2MASS mean extinction values in these fields agreed well with those of previous studies. We confirm the existence of low-extinction windows in the regions studied, as local minima in the A_K maps reaching A_K values about 2 standard deviations below the mean values found in the neighbouring areas. Schlegel et al.'s (1998) FIR extinction maps, which integrate dust contributions throughout the Galaxy, are structurally similar to those derived with 2MASS photometry in the two studied windows. We thus conclude that the dust clouds affecting the 2MASS and FIR maps in these directions are basically the same and are located on foreground of the bulk of bulge stars. However, the A_K absolute values differ significantly. In particular, the FIR extinction values for W359.4-3.1 are a factor ~1.45 larger than those derived from the 2MASS photometry. Possible explanations of this effect are discussed. The lower Galactic latitudes of the low-extinction windows W359.4-3.1 and W0.2-2.1, as compared to Baade's Window, make them promising targets for detailed studies of more central bulge regions.Comment: 8 pages, 10 figures, LaTeX, aa.cls. To appear in Astron. & Astroph., in pres

Role of tyrosine M210 in the initial charge separation of reaction centers of Rhodobacter sphaeroides

Femtosecond spectroscopy was used in combination with site-directed mutagenesis to study the influence of tyrosine M210 (YM210) on the primary electron transfer in the reaction center of Rhodobacter sphaeroides. The exchange of YM210 to phenylalanine caused the time constant of primary electron transfer to increase from 3.5 f 0.4 ps to 16 f 6 ps while the exchange to leucine increased the time constant even more to 22 f 8 ps. The results suggest that tyrosine M210 is important for the fast rate of the primary electron transfer