Automatic landmarking for building biological shape models

We present a new method for automatic landmark extraction from the contours of biological specimens. Our ultimate goal is to enable automatic identification of biological specimens in photographs and drawings held in a database. We propose to use active appearance models for visual indexing of both photographs and drawings. Automatic landmark extraction will assist us in building the models. We describe the results of using our method on drawings and photographs of examples of diatoms, and present an active shape model built using automatically extracted data

Feature Neighbourhood Mutual Information for multi-modal image registration: An application to eye fundus imaging

© 2014 Elsevier Ltd. All rights reserved. Multi-modal image registration is becoming an increasingly powerful tool for medical diagnosis and treatment. The combination of different image modalities facilitates much greater understanding of the underlying condition, resulting in improved patient care. Mutual Information is a popular image similarity measure for performing multi-modal image registration. However, it is recognised that there are limitations with the technique that can compromise the accuracy of the registration, such as the lack of spatial information that is accounted for by the similarity measure. In this paper, we present a two-stage non-rigid registration process using a novel similarity measure, Feature Neighbourhood Mutual Information. The similarity measure efficiently incorporates both spatial and structural image properties that are not traditionally considered by MI. By incorporating such features, we find that this method is capable of achieving much greater registration accuracy when compared to existing methods, whilst also achieving efficient computational runtime. To demonstrate our method, we use a challenging medical image data set consisting of paired retinal fundus photographs and confocal scanning laser ophthalmoscope images. Accurate registration of these image pairs facilitates improved clinical diagnosis, and can be used for the early detection and prevention of glaucoma disease

Using Nonlinear Response to Estimate the Strength of an Elastic Network

Disordered networks of fragile elastic elements have been proposed as a model of inner porous regions of large bones [Gunaratne et.al., cond-mat/0009221, http://xyz.lanl.gov]. It is shown that the ratio $\Gamma$ of responses of such a network to static and periodic strain can be used to estimate its ultimate (or breaking) stress. Since bone fracture in older adults results from the weakening of porous bone, we discuss the possibility of using $\Gamma$ as a non-invasive diagnostic of osteoporotic bone.Comment: 4 pages, 4 figure

Cosmological distance indicators

We review three distance measurement techniques beyond the local universe: (1) gravitational lens time delays, (2) baryon acoustic oscillation (BAO), and (3) HI intensity mapping. We describe the principles and theory behind each method, the ingredients needed for measuring such distances, the current observational results, and future prospects. Time delays from strongly lensed quasars currently provide constraints on $H_0$ with < 4% uncertainty, and with 1% within reach from ongoing surveys and efforts. Recent exciting discoveries of strongly lensed supernovae hold great promise for time-delay cosmography. BAO features have been detected in redshift surveys up to z <~ 0.8 with galaxies and z ~ 2 with Ly-$\alpha$ forest, providing precise distance measurements and $H_0$ with < 2% uncertainty in flat $\Lambda$CDM. Future BAO surveys will probe the distance scale with percent-level precision. HI intensity mapping has great potential to map BAO distances at z ~ 0.8 and beyond with precisions of a few percent. The next years ahead will be exciting as various cosmological probes reach 1% uncertainty in determining $H_0$, to assess the current tension in $H_0$ measurements that could indicate new physics.Comment: Review article accepted for publication in Space Science Reviews (Springer), 45 pages, 10 figures. Chapter of a special collection resulting from the May 2016 ISSI-BJ workshop on Astronomical Distance Determination in the Space Ag

Cropland can support high bird diversity in heterogeneous rural tropical landscapes

Land-use change for crop production is one of the key drivers of habitat loss and fragmentation and consequently biodiversity loss and change in tropical regions. This may impact biodiversity-regulated ecosystem services; birds are important to crop health regulating services (e.g. seed dispersal, pest control) and disservices (e.g. seed predation, grain herbivory). However, knowledge is limited on how birds use heterogeneous agricultural landscapes and the consequences for spatial distribution and flow of services and disservices. We studied crop and non-crop–habitat associations of birds in forest–agricultural landscapes of the Kilombero Valley, Tanzania. We focused on dietary preference as a key trait impacting bird responses to land-use change, services, and disservices to crops. We surveyed birds across four main habitat types using repeated point counts, recording a total of 148 species. We found that crop habitats supported higher species richness and larger communities of potentially beneficial species to crop health, whereby 34.5% of invertebrate-feeding species were recorded in cropland. We found that habitat heterogeneity within the landscape supports bird functional diversity and that each habitat type supported unique communities of species. Furthermore, the number of species unique to forest habitats increased with increasing forest canopy closure. Our findings suggest that management strategies for maintaining trees and shrubs, and enhancing tree cover within the crop production landscape, can be effective approaches for maintaining bird diversity and services. However, in-depth studies on trade-offs with disservices need further exploration to mitigate negative impacts of birds on crop yields

Fitting the integrated Spectral Energy Distributions of Galaxies

Fitting the spectral energy distributions (SEDs) of galaxies is an almost universally used technique that has matured significantly in the last decade. Model predictions and fitting procedures have improved significantly over this time, attempting to keep up with the vastly increased volume and quality of available data. We review here the field of SED fitting, describing the modelling of ultraviolet to infrared galaxy SEDs, the creation of multiwavelength data sets, and the methods used to fit model SEDs to observed galaxy data sets. We touch upon the achievements and challenges in the major ingredients of SED fitting, with a special emphasis on describing the interplay between the quality of the available data, the quality of the available models, and the best fitting technique to use in order to obtain a realistic measurement as well as realistic uncertainties. We conclude that SED fitting can be used effectively to derive a range of physical properties of galaxies, such as redshift, stellar masses, star formation rates, dust masses, and metallicities, with care taken not to over-interpret the available data. Yet there still exist many issues such as estimating the age of the oldest stars in a galaxy, finer details ofdust properties and dust-star geometry, and the influences of poorly understood, luminous stellar types and phases. The challenge for the coming years will be to improve both the models and the observational data sets to resolve these uncertainties. The present review will be made available on an interactive, moderated web page (sedfitting.org), where the community can access and change the text. The intention is to expand the text and keep it up to date over the coming years.Comment: 54 pages, 26 figures, Accepted for publication in Astrophysics & Space Scienc

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02