Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package

The concept of topographic mapping is central to the understanding of the visual system at many levels, from the developmental to the computational. It is important to be able to relate different coordinate systems, e.g. maps of the visual field and maps of the retina. Retinal maps are frequently based on flat-mount preparations. These use dissection and relaxing cuts to render the quasi-spherical retina into a 2D preparation. The variable nature of relaxing cuts and associated tears limits quantitative cross-animal comparisons. We present an algorithm, "Retistruct," that reconstructs retinal flat-mounts by mapping them into a standard, spherical retinal space. This is achieved by: stitching the marked-up cuts of the flat-mount outline; dividing the stitched outline into a mesh whose vertices then are mapped onto a curtailed sphere; and finally moving the vertices so as to minimise a physically-inspired deformation energy function. Our validation studies indicate that the algorithm can estimate the position of a point on the intact adult retina to within 8° of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates. Retistruct is used to investigate the organisation of the adult mouse visual system. We orient the retina relative to the nictitating membrane and compare this to eye muscle insertions. To align the retinotopic and visuotopic coordinate systems in the mouse, we utilised the geometry of binocular vision. In standard retinal space, the composite decussation line for the uncrossed retinal projection is located 64° away from the retinal pole. Projecting anatomically defined uncrossed retinal projections into visual space gives binocular congruence if the optical axis of the mouse eye is oriented at 64° azimuth and 22° elevation, in concordance with previous results. Moreover, using these coordinates, the dorsoventral boundary for S-opsin expressing cones closely matches the horizontal meridian

Methanol‐to‐Olefins in a Membrane Reactor with in situ Steam Removal – The Decisive Role of Coking

The reaction of methanol to light olefins and water (MTO) was studied in a fixed bed tubular membrane reactor using commercial SAPO-34 catalyst. In the fixed bed reactor without membrane support, the MTO reaction collapsed after 3 h time on stream. However, if the reaction by-product steam is in situ extracted from the reactor through a hydrophilic tubular LTA membrane, the reactor produces long-term stable about 60% ethene and 10% propene. It is shown that the reason for the superior performance of the membrane-assisted reactor is not the prevention of catalyst damage caused by steam but the influence of the water removal on the formation of different carbonaceous residues inside the SAPO-34 cages. Catalytically beneficial methylated 1 or 2 ring aromatics have been found in a higher percentage in the MTO reaction with a water removal membrane compared to the MTO reaction without membrane support

Symmetry of Magnetically Ordered Quasicrystals

The notion of magnetic symmetry is reexamined in light of the recent observation of long range magnetic order in icosahedral quasicrystals [Charrier et al., Phys. Rev. Lett. 78, 4637 (1997)]. The relation between the symmetry of a magnetically-ordered (periodic or quasiperiodic) crystal, given in terms of a ``spin space group,'' and its neutron diffraction diagram is established. In doing so, an outline of a symmetry classification scheme for magnetically ordered quasiperiodic crystals is provided. Predictions are given for the expected diffraction patterns of magnetically ordered icosahedral crystals, provided their symmetry is well described by icosahedral spin space groups.Comment: 5 pages. Accepted for publication in Phys. Rev. Letter

LiCaFeF6 A zero strain cathode material for use in Li ion batteries

A new zero strain LiCaFeF6 cathode material for reversible insertion and extraction of lithium ions is presented. LiCaFeF6 is synthesized by a solid state reaction and processed to a conductive electrode composite via high energy ball milling. In the first cycle, a discharge capacity of 112 mAh g amp; 8315; is achieved in the voltage range from 2.0 V to 4.5 V. The electrochemically active redox couple is Fe3 amp; 8314; Fe2 amp; 8314; as confirmed by Mössbauer spectroscopy and X ray absorption spectroscopy. The compound has a trigonal colquiriite type crystal structure space group . By means of in situ and ex situ XRD as well as X ray absorption fine structure spectroscopy a reversible response to Li uptake release is found. For an uptake of 0.8 mol Li per formula unit only minimal changes occur in the lattice parameters causing a total change in unit cell volume of less than 0.5 . The spatial distribution of cations in the crystal structure as well as the linkage between their corresponding fluorine octahedra is responsible for this very small structural response. With its zero strain behaviour this material is expected to exhibit only negligible mechanical degradation. It may be used as a cathode material in future lithium ion batteries with strongly improved safety and cycle lif

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches