Retinal blood vessels extraction using probabilistic modelling

© 2014 Kaba et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.The analysis of retinal blood vessels plays an important role in detecting and treating retinal diseases. In this review, we present an automated method to segment blood vessels of fundus retinal image. The proposed method could be used to support a non-intrusive diagnosis in modern ophthalmology for early detection of retinal diseases, treatment evaluation or clinical study. This study combines the bias correction and an adaptive histogram equalisation to enhance the appearance of the blood vessels. Then the blood vessels are extracted using probabilistic modelling that is optimised by the expectation maximisation algorithm. The method is evaluated on fundus retinal images of STARE and DRIVE datasets. The experimental results are compared with some recently published methods of retinal blood vessels segmentation. The experimental results show that our method achieved the best overall performance and it is comparable to the performance of human experts.The Department of Information Systems, Computing and Mathematics, Brunel University

FOXA1 mutations alter pioneering activity, differentiation and prostate cancer phenotypes.

Mutations in the transcription factor FOXA1 define a unique subset of prostate cancers but the functional consequences of these mutations and whether they confer gain or loss of function is unknown1-9. Here, by annotating the landscape of FOXA1 mutations from 3,086 human prostate cancers, we define two hotspots in the forkhead domain: Wing2 (around 50% of all mutations) and the highly conserved DNA-contact residue R219 (around 5% of all mutations). Wing2 mutations are detected in adenocarcinomas at all stages, whereas R219 mutations are enriched in metastatic tumours with neuroendocrine histology. Interrogation of the biological properties of wild-type FOXA1 and fourteen FOXA1 mutants reveals gain of function in mouse prostate organoid proliferation assays. Twelve of these mutants, as well as wild-type FOXA1, promoted an exaggerated pro-luminal differentiation program, whereas two different R219 mutants blocked luminal differentiation and activated a mesenchymal and neuroendocrine transcriptional program. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) of wild-type FOXA1 and representative Wing2 and R219 mutants revealed marked, mutant-specific changes in open chromatin at thousands of genomic loci and exposed sites of FOXA1 binding and associated increases in gene expression. Of note, ATAC-seq peaks in cells expressing R219 mutants lacked the canonical core FOXA1-binding motifs (GTAAAC/T) but were enriched for a related, non-canonical motif (GTAAAG/A), which was preferentially activated by R219-mutant FOXA1 in reporter assays. Thus, FOXA1 mutations alter its pioneering function and perturb normal luminal epithelial differentiation programs, providing further support for the role of lineage plasticity in cancer progression

Viscosities of the Gay-Berne nematic liquid crystal

We present molecular dynamics simulation measurements of the viscosities of the Gay-Berne phenomenological model of liquid crystals in the nematic and isotropic phases. The temperature dependence of the rotational and shear viscosities, including the nonmonotonic behavior of one shear viscosity are in good agreement with experimental data. The bulk viscosities are significantly larger than the shear viscosities, again in agreement with experiment.Comment: 11 pages, 4 Postscript figures, Revte

A photometric redshift of z=1.8−0.3+0.4z=1.8^{+0.4}_{-0.3} for the \agile GRB 080514B

Aims: The AGILE gamma-ray burst GRB 080514B is the first burst with detected emission above 30 MeV and an optical afterglow. However, no spectroscopic redshift for this burst is known. Methods: We compiled ground-based photometric optical/NIR and millimeter data from several observatories, including the multi-channel imager GROND, as well as ultraviolet \swift UVOT and X-ray XRT observations. The spectral energy distribution of the optical/NIR afterglow shows a sharp drop in the \swift UVOT UV filters that can be utilized for the estimation of a redshift. Results: Fitting the SED from the \swift UVOT $uvw2$ band to the $H$ band, we estimate a photometric redshift of $z=1.8^{+0.4}_{-0.3}$, consistent with the pseudo redshift reported by Pelangeon & Atteia (2008) based on the gamma-ray data. Conclusions: The afterglow properties of GRB 080514B do not differ from those exhibited by the global sample of long bursts, supporting the view that afterglow properties are basically independent of prompt emission properties.Comment: submitted to A&A letter

Comprehensive vascular imaging using optical coherence tomography-based angiography and photoacoustic tomography

Studies have proven the relationship between cutaneous vasculature abnormalities and dermatological disorders, but to image vasculature noninvasively in vivo, advanced optical imaging techniques are required. In this study, we imaged a palm of a healthy volunteer and three subjects with cutaneous abnormalities with photoacoustic tomography (PAT) and optical coherence tomography with angiography extension (OCTA). Capillaries in the papillary dermis that are too small to be discerned with PAT are visualized with OCTA. From our results, we speculate that the PA signal from the palm is mostly from hemoglobin in capillaries rather than melanin, knowing that melanin concentration in volar skin is significantly smaller than that in other areas of the skin. We present for the first time OCTA images of capillaries along with the PAT images of the deeper vessels, demonstrating the complementary effective imaging depth range and the visualization capabilities of PAT and OCTA for imaging human skin in vivo. The proposed imaging system in this study could significantly improve treatment monitoring of dermatological diseases associated with cutaneous vasculature abnormalities

Ab Initio Molecular Dynamics Simulation of Liquid Ga_xAs_{1-x} Alloys

We report the results of ab initio molecular dynamics simulations of liquid Ga_xAs_{1-x} alloys at five different concentrations, at a temperature of 1600 K, just above the melting point of GaAs. The liquid is predicted to be metallic at all concentrations between x = 0.2 and x = 0.8, with a weak resistivity maximum near x = 0.5, consistent with the Faber-Ziman expression. The electronic density of states is finite at the Fermi energy for all concentrations; there is, however, a significant pseudogap especially in the As-rich samples. The Ga-rich density of states more closely resembles that of a free-electron metal. The partial structure factors show only a weak indication of chemical short-range order. There is also some residue of the covalent bonding found in the solid, which shows up in the bond-angle distribution functions of the liquid state. Finally, the atomic diffusion coefficients at 1600K are calculated to be 2.1 \times 10^{-4} cm^2/sec for Ga ions in Ga_{0.8}As_{0.2} and 1.7 \times 10^{-4} cm^2/sec for As ions in Ga_{0.2}As_{0.8}.Comment: 29 pages, 10 eps figures, accepted for publication in Phys. Rev.

Financial crises and the attainment of the SDGs: an adjusted multidimensional poverty approach

This paper analyses the impact of financial crises on the Sustainable Development Goal of eradicating poverty. To do so, we develop an adjusted Multidimensional Poverty Framework (MPF) that includes 15 indicators that span across key poverty aspects related to income, basic needs, health, education and the environment. We then use an econometric model that allows us to examine the impact of financial crises on these indicators in 150 countries over the period 1980–2015. Our analysis produces new estimates on the impact of financial crises on poverty’s multiple social, economic and environmental aspects and equally important captures dynamic linkages between these aspects. Thus, we offer a better understanding of the potential impact of current debt dynamics on Multidimensional Poverty and demonstrate the need to move beyond the boundaries of SDG1, if we are to meet the target of eradicating poverty. Our results indicate that the current financial distress experienced by many low-income countries may reverse the progress that has been made hitherto in reducing poverty. We find that financial crises are associated with an approximately 10% increase of extreme poor in low-income countries. The impact is even stronger in some other poverty aspects. For instance, crises are associated with an average decrease of government spending in education by 17.72% in low-income countries. The dynamic linkages between most of the Multidimensional Poverty indicators, warn of a negative domino effect on a number of SDGs related to poverty, if there is a financial crisis shock. To pre-empt such a domino effect, the specific SDG target 17.4 on attaining long-term debt sustainability through coordinated policies plays a key role and requires urgent attention by the international community

Melting of Partially Fluorinated Graphene: From Detachment of Fluorine Atoms to Large Defects and Random Coils

The melting of fluorographene is very unusual and depends strongly on the degree of fluorination. For temperatures below 1000 K, fully fluorinated graphene (FFG) is thermo-mechanically more stable than graphene but at T$_m\approx$2800 K FFG transits to random coils which is almost twice lower than the melting temperature of graphene, i.e. 5300 K. For fluorinated graphene (PFG) up to 30 % ripples causes detachment of individual F-atoms around 2000 K while for 40-60 % fluorination, large defects are formed beyond 1500 K and beyond 60% of fluorination F-atoms remain bonded to graphene until melting. The results agree with recent experiments on the dependence of the reversibility of the fluorination process on the percentage of fluorination.Comment: 16 pages, 6 figure

Mechanical properties of ceria nanorods and nanochains; The effect of dislocations, grain-boundaries and oriented attachment

We predict that the presence of extended defects can reduce the mechanical strength of a ceria nanorod by 70%. Conversely, the pristine material can deform near its theoretical strength limit. Specifically, atomistic models of ceria nanorods have been generated with full microstructure, including: growth direction, morphology, surface roughening (steps, edges, corners), point defects, dislocations and grain-boundaries. The models were then used to calculate the mechanical strength as a function of microstructure. Our simulations reveal that the compressive yield strengths of ceria nanorods, ca. 10 nm in diameter and without extended defects, are 46 and 36 GPa for rods oriented along [211] and [110] respectively, which represents almost 10% of the bulk elastic modulus and are associated with yield strains of about 0.09. Tensile yield strengths were calculated to be about 50% lower with associated yield strains of about 0.06. For both nanorods, plastic deformation was found to proceed via slip in the {001} plane with direction ã??110ã?? - a primary slip system for crystals with the fluorite structure. Dislocation evolution for the nanorod oriented along [110] was nucleated via a cerium vacancy present at the surface. A nanorod oriented along [321] and comprising twin-grain boundaries with {111} interfacial planes was calculated to have a yield strength of about 10 GPa (compression and tension) with the grain boundary providing the vehicle for plastic deformation, which slipped in the plane of the grain boundary, with an associated ã??110ã?? slip direction. We also predict, using a combination of atomistic simulation and DFT, that rutile-structured ceria is feasible when the crystal is placed under tension. The mechanical properties of nanochains, comprising individual ceria nanoparticles with oriented attachment and generated using simulated self-assembly, were found to be similar to those of the nanorod with grain-boundary. Images of the atom positions during tension and compression are shown, together with animations, revealing the mechanisms underpinning plastic deformation. For the nanochain, our simulations help further our understanding of how a crystallising ice front can be used to 'sculpt' ceria nanoparticles into nanorods via oriented attachment. © 2011 The Royal Society of Chemistry

Identification and characterization of a plastid-localized Arabidopsis glyoxylate reductase isoform: comparison with a cytosolic isoform and implications for cellular redox homeostasis and aldehyde detoxification

Enzymes that reduce the aldehyde chemical grouping (i.e. H-C=O) to its corresponding alcohol could be crucial in maintaining plant health. Recently, recombinant expression of a cytosolic enzyme from Arabidopsis thaliana (L.) Heynh (designated as glyoxylate reductase 1 or AtGR1) revealed that it effectively catalyses the in vitro reduction of both glyoxylate and succinic semialdehyde (SSA). In this paper, web-based bioinformatics tools revealed a second putative GR cDNA (GenBank Accession No. AAP42747; designated herein as AtGR2) that is 57% identical on an amino acid basis to GR1. Sequence encoding a putative targeting signal (N-terminal 43 amino acids) was deleted from the full-length GR2 cDNA and the resulting truncated gene was co-expressed with the molecular chaperones GroES/EL in Escherichia coli, enabling production and purification of soluble recombinant protein. Kinetic analysis revealed that recombinant GR2 catalysed the conversion of glyoxylate to glycolate (Km glyoxylate=34 μM), and SSA to γ-hydroxybutyrate (Km SSA=8.96 mM) via an essentially irreversible, NADPH-based mechanism. GR2 had a 350-fold higher preference for glyoxylate than SSA, based on the performance constants (kcat/Km). Fluorescence microscopic analysis of tobacco (Nicotiana tabacum L.) suspension cells transiently transformed with GR1 linked to the green fluorescent protein (GFP) revealed that GR1 was localized to the cytosol, whereas GR2-GFP was localized to plastids via targeting information contained within its N-terminal 45 amino acids. The identification and characterization of distinct plastidial and cytosolic glyoxylate reductase isoforms is discussed with respect to aldehyde detoxification and the plant stress response