A proposed increase in retinal field-of-view may lead to spatial shifts in images

Visual information determines majority of our spatial behavior. The eye projects a 2-D image of the world on the retina. We demonstrate that when a monocular-like imaging system operates entirely with optically dense fluids, an increase in field-of-view (FOV) is observed compared to an experimental condition, where the ocular medium is optically neutral. Resulting spatial shifts in the retinal image towards the fovea complement the photoreceptor distribution pattern, incidentally revealing a new role for ocular fluids in the image space. Possible effects on the perceived egocentric object location are discussed.Comment: 13 pages, 2 figures, 1 tabl

Identification of new reference genes for the normalisation of canine osteoarthritic joint tissue transcripts from microarray data

<p>Abstract</p> <p>Background</p> <p>Real-time reverse transcriptase quantitative polymerase chain reaction (real-time RT-qPCR) is the most accurate measure of gene expression in biological systems. The comparison of different samples requires the transformation of data through a process called normalisation. Reference or housekeeping genes are candidate genes which are selected on the basis of constitutive expression across samples, and allow the quantification of changes in gene expression. At present, no reference gene has been identified for any organism which is universally optimal for use across different tissue types or disease situations. We used microarray data to identify new reference genes generated from total RNA isolated from normal and osteoarthritic canine articular tissues (bone, ligament, cartilage, synovium and fat). RT-qPCR assays were designed and applied to each different articular tissue. Reference gene expression stability and ranking was compared using three different mathematical algorithms.</p> <p>Results</p> <p>Twelve new potential reference genes were identified from microarray data. One gene (mitochondrial ribosomal protein S7 [<it>MRPS7</it>]) was stably expressed in all five of the articular tissues evaluated. One gene HIRA interacting protein 5 isoform 2 [<it>HIRP5</it>]) was stably expressed in four of the tissues evaluated. A commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (<it>GAPDH</it>) was not stably expressed in any of the tissues evaluated. Most consistent agreement between rank ordering of reference genes was observed between <it>Bestkeeper©</it> and geNorm, although each method tended to agree on the identity of the most stably expressed genes and the least stably expressed genes for each tissue. New reference genes identified using microarray data normalised in a conventional manner were more stable than those identified by microarray data normalised by using a real-time RT-qPCR methodology.</p> <p>Conclusion</p> <p>Microarray data normalised by a conventional manner can be filtered using a simple stepwise procedure to identify new reference genes, some of which will demonstrate good measures of stability. Mitochondrial ribosomal protein S7 is a new reference gene worthy of investigation in other canine tissues and diseases. Different methods of reference gene stability assessment will generally agree on the most and least stably expressed genes, when co-regulation is not present.</p

Expression stability of commonly used reference genes in canine articular connective tissues

<p>Abstract</p> <p>Background</p> <p>The quantification of gene expression in tissue samples requires the use of reference genes to normalise transcript numbers between different samples. Reference gene stability may vary between different tissues, and between the same tissue in different disease states. We evaluated the stability of 9 reference genes commonly used in human gene expression studies. Real-time reverse transcription PCR and a mathematical algorithm were used to establish which reference genes were most stably expressed in normal and diseased canine articular tissues and two canine cell lines stimulated with lipolysaccaride (LPS).</p> <p>Results</p> <p>The optimal reference genes for comparing gene expression data between normal and diseased infrapatella fat pad were <it>RPL13A </it>and <it>YWHAZ </it>(M = 0.56). The ideal reference genes for comparing normal and osteoarthritic (OA) cartilage were <it>RPL13A </it>and <it>SDHA </it>(M = 0.57). The best reference genes for comparing normal and ruptured canine cranial cruciate ligament were <it>B2M </it>and <it>TBP </it>(M = 0.59). The best reference genes for normalising gene expression data from normal and LPS stimulated cell lines were <it>SDHA </it>and <it>YWHAZ </it>(K6) or <it>SDHA </it>and <it>HMBS </it>(DH82), which had expression stability (M) values of 0.05 (K6) and 0.07 (DH82) respectively. The number of reference genes required to reduce pairwise variation (V) to <0.20 was 4 for cell lines, 5 for cartilage, 7 for cranial cruciate ligament and 8 for fat tissue. Reference gene stability was not related to the level of gene expression.</p> <p>Conclusion</p> <p>The reference genes demonstrating the most stable expression within each different canine articular tissue were identified, but no single reference gene was identified as having stable expression in all different tissue types. This study underlines the necessity to select reference genes on the basis of tissue and disease specific expression profile evaluation and highlights the requirement for the identification of new reference genes with greater expression stability for use in canine articular tissue gene expression studies.</p

Attitudes towards the use and acceptance of eHealth technologies : a case study of older adults living with chronic pain and implications for rural healthcare

Acknowledgements The research described here is supported by the award made by the RCUK Digital Economy programme to the dot.rural Digital Economy Hub; award reference: EP/G066051/1. MC’s time writing the paper is funded by the Scottish Government’s Rural and Environmental Science and Analytical Services Division (RESAS) under Theme 8 ‘Vibrant Rural Communities’ of the Food, Land and People Programme (2011–2016). MC is also an Honorary Research Fellow at the Division of Applied Health Sciences, University of Aberdeen. The input of other members of the TOPS research team, Alastair Mort, Fiona Williams, Sophie Corbett, Phil Wilson and Paul MacNamee who contributed to be wider study and discussed preliminary findings reported here with the authors of the paper is acknowledged. We acknowledge the feedback on earlier versions of this paper provided by members of the Trans-Atlantic Rural Research Network, especially Stefanie Doebler and Carmen Hubbard. We also thank Deb Roberts for her comments.Peer reviewedPublisher PD

Kinetic Resolution in Asymmetric Epoxidation using Iminium Salt Catalysis

The first reported examples of kinetic resolution in epoxidation reactions using iminium salt catalysis are described, providing up to 99% ee in the epoxidation of racemic cis-chromenes

Atomic Spectral Features During Thermonuclear Flashes on Neutron Stars

The gravitational redshift measured by Cottam, Paerels and Mendez for the neutron star (NS) in the low-mass X-ray binary EXO 0748-676 depends on the identification of an absorption line during a type I burst as the H$\alpha$ line from hydrogenic Fe. We show that Fe is present above the photosphere as long as $\dot M>4\times 10^{-13}M_\odot {\rm yr^{-1}}$ during the burst. In this limit, the total Fe column is $N_{\rm Fe}\approx 3\times 10^{19}{\rm cm^{-2}}$ for incident material of solar abundances and only depends on the nuclear physics of the proton spallation. The Fe destruction creates many heavy elements with $Z<26$ which may imprint photo-ionization edges on the NS spectra during a radius expansion event or in a burst cooling tail. Detecting these features in concert with those from Fe would confirm a redshift measurement. We also begin to address the radiative transfer problem, and find that a concentrated Fe layer with $kT=1.2-1.4 {\rm keV}$ and column $N_{\rm Fe}= 7-20 \times 10^{20} {\rm cm}^{-2}$ (depending on the line depth) above the hotter continuum photosphere is required to create the H$\alpha$ line of the observed strength. This estimate must be refined by considerations of non-LTE effects as well as resonant line transport. Until these are carried out, we cannot say whether the Fe column from accretion and spallation is in conflict with the observations. We also show that hydrogenic Fe might remain in the photosphere due to radiative levitation from the high burst flux.Comment: Substantially revised version, to appear in Ap J Letter

Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

Mapping the landscape of possible macromolecular polymer sequences to their fitness in performing biological functions is a challenge across the biosciences. A paradigm is the case of aptamers, nucleic acids that can be selected to bind particular target molecules. We have characterized the sequence-fitness landscape for aptamers binding allophycocyanin (APC) protein via a novel Closed Loop Aptameric Directed Evolution (CLADE) approach. In contrast to the conventional SELEX methodology, selection and mutation of aptamer sequences was carried out in silico, with explicit fitness assays for 44 131 aptamers of known sequence using DNA microarrays in vitro. We capture the landscape using a predictive machine learning model linking sequence features and function and validate this model using 5500 entirely separate test sequences, which give a very high observed versus predicted correlation of 0.87. This approach reveals a complex sequence-fitness mapping, and hypotheses for the physical basis of aptameric binding; it also enables rapid design of novel aptamers with desired binding properties. We demonstrate an extension to the approach by incorporating prior knowledge into CLADE, resulting in some of the tightest binding sequences

Incorporating chemical signalling factors into cell-based models of growing epithelial tissues

In this paper we present a comprehensive computational framework within which the effects of chemical signalling factors on growing epithelial tissues can be studied. The method incorporates a vertex-based cell model, in conjunction with a solver for the governing chemical equations. The vertex model provides a natural mesh for the finite element method (FEM), with node movements determined by force laws. The arbitrary Lagrangian–Eulerian formulation is adopted to account for domain movement between iterations. The effects of cell proliferation and junctional rearrangements on the mesh are also examined. By implementing refinements of the mesh we show that the finite element (FE) approximation converges towards an accurate numerical solution. The potential utility of the system is demonstrated in the context of Decapentaplegic (Dpp), a morphogen which plays a crucial role in development of the Drosophila imaginal wing disc. Despite the presence of a Dpp gradient, growth is uniform across the wing disc. We make the growth rate of cells dependent on Dpp concentration and show that the number of proliferation events increases in regions of high concentration. This allows hypotheses regarding mechanisms of growth control to be rigorously tested. The method we describe may be adapted to a range of potential application areas, and to other cell-based models with designated node movements, to accurately probe the role of morphogens in epithelial tissues

Formation of Resonant Atomic Lines during Thermonuclear Flashes on Neutron Stars

Motivated by the measurement of redshifted Fe H$\alpha$ lines during type I X-ray bursts on EXO 0748-676 (Cottam, Paerels & Mendez), we study the formation of atomic Fe lines above the photosphere of a bursting neutron star ($k_BT_{\rm eff} \approx 1-2 {\rm keV}$). We discuss the effects of Stark broadening, resonant scattering and NLTE (level population) on the formation of hydrogenic Fe H$\alpha$, Ly$\alpha$ and P$\alpha$ lines. From the observed equivalent width of the Fe H$\alpha$ line, we find an implied Fe column of $1-3 \times 10^{20} {\rm cm}^{-2}$, which is 3-10 times larger than the Fe column calculated from the accretion/spallation model of Bildsten, Chang & Paerels. We also estimate that the implied Fe column is about a factor of 2-3 larger than a uniform solar metallicity atmosphere. We discuss the effects of rotational broadening and find that the rotation rate of \EXO must be slow, as confirmed by the recent measurement of a 45 Hz burst oscillation by Villarreal & Strohmayer. We also show that the Fe Ly$\alpha$ EW $\approx$ 15-20 eV (redshifted 11-15 eV) and the P$\alpha$ EW $\approx$ 4-7 eV (redshifted 3-5 eV) when the H$\alpha$ EW is 10 eV (redshifted 8 eV). The Ly$\alpha$ line is rotationally broadened to a depth of $\approx 10$, making it difficult to observe with {\it Chandra}. We also show that radiative levitation can likely support the Fe column needed to explain the line.Comment: 10 pages, 8 figures, to be published in Ap