Spectral nonlocality, absolute equilibria and Kraichnan-Leith-Batchelor phenomenology in two-dimensional turbulent energy cascades

We study the degree to which Kraichnan–Leith–Batchelor (KLB) phenomenology describes two-dimensional energy cascades in α turbulence, governed by ∂θ/∂t+J(ψ,θ)=ν∇2θ+f, where θ=(−Δ)α/2ψ is generalized vorticity, and ψ^(k)=k−αθ^(k) in Fourier space. These models differ in spectral non-locality, and include surface quasigeostrophic flow (α=1), regular two-dimensional flow (α=2) and rotating shallow flow (α=3), which is the isotropic limit of a mantle convection model. We re-examine arguments for dual inverse energy and direct enstrophy cascades, including Fjørtoft analysis, which we extend to general α, and point out their limitations. Using an α-dependent eddy-damped quasinormal Markovian (EDQNM) closure, we seek self-similar inertial range solutions and study their characteristics. Our present focus is not on coherent structures, which the EDQNM filters out, but on any self-similar and approximately Gaussian turbulent component that may exist in the flow and be described by KLB phenomenology. For this, the EDQNM is an appropriate tool. Non-local triads contribute increasingly to the energy flux as α increases. More importantly, the energy cascade is downscale in the self-similar inertial range for 2.5<α<10. At α=2.5 and α=10, the KLB spectra correspond, respectively, to enstrophy and energy equipartition, and the triad energy transfers and flux vanish identically. Eddy turnover time and strain rate arguments suggest the inverse energy cascade should obey KLB phenomenology and be self-similar for α<4. However, downscale energy flux in the EDQNM self-similar inertial range for α>2.5 leads us to predict that any inverse cascade for α≥2.5 will not exhibit KLB phenomenology, and specifically the KLB energy spectrum. Numerical simulations confirm this: the inverse cascade energy spectrum for α≥2.5 is significantly steeper than the KLB prediction, while for α<2.5 we obtain the KLB spectrum.

Modeling ocean primary production: sensitivity to spectral resolution of attenuation and absorption of light

Modeling the vertical penetration of photosynthetically active radiation (PAR) through the ocean, and its utilization by phytoplankton, is fundamental to simulating marine primary production. The variation of attenuation and absorption of light with wavelength suggests that photosynthesis should be modeled at high spectral resolution, but this is computationally expensive. To model primary production in global 3d models, a balance between computer time and accuracy is necessary. We investigate the effects of varying the spectral resolution of the underwater light field and the photosynthetic efficiency of phytoplankton (α∗), on primary production using a 1d coupled ecosystem ocean turbulence model. The model is applied at three sites in the Atlantic Ocean (CIS (∼60°N), PAP (∼50°N) and ESTOC (∼30°N)) to include the effect of different meteorological forcing and parameter sets. We also investigate three different methods for modeling α∗ – as a fixed constant, varying with both wavelength and chlorophyll concentration [Bricaud, A., Morel, A., Babin, M., Allali, K., Claustre, H., 1998. Variations of light absorption by suspended particles with chlorophyll a concentration in oceanic (case 1) waters. Analysis and implications for bio-optical models. J. Geophys. Res. 103, 31033–31044], and using a non-spectral parameterization [Anderson, T.R., 1993. A spectrally averaged model of light penetration and photosynthesis. Limnol. Oceanogr. 38, 1403–1419]. After selecting the appropriate ecosystem parameters for each of the three sites we vary the spectral resolution of light and α∗ from 1 to 61 wavebands and study the results in conjunction with the three different α∗ estimation methods. The results show modeled estimates of ocean primary productivity are highly sensitive to the degree of spectral resolution and α∗. For accurate simulations of primary production and chlorophyll distribution we recommend a spectral resolution of at least six wavebands if α∗ is a function of wavelength and chlorophyll, and three wavebands if α∗ is a fixed value.

PPARGC1A sequence variation and cardiovascular risk-factor levels: a study of the main genetic effects and gene x environment interactions in children from the European Youth Heart Study.

AIMS/HYPOTHESIS: The PPARGC1A gene coactivates multiple nuclear transcription factors involved in cellular energy metabolism and vascular stasis. In the present study, we genotyped 35 tagging polymorphisms to capture all common PPARGC1A nucleotide sequence variations and tested for association with metabolic and cardiovascular traits in 2,101 Danish and Estonian boys and girls from the European Youth Heart Study, a multicentre school-based cross-sectional cohort study. METHODS: Fasting plasma glucose concentrations, anthropometric variables and blood pressure were measured. Habitual physical activity and aerobic fitness were objectively assessed using uniaxial accelerometry and a maximal aerobic exercise stress test on a bicycle ergometer, respectively. RESULTS: In adjusted models, nominally significant associations were observed for BMI (rs10018239, p = 0.039), waist circumference (rs7656250, p = 0.012; rs8192678 [Gly482Ser], p = 0.015; rs3755863, p = 0.02; rs10018239, beta = -0.01 cm per minor allele copy, p = 0.043), systolic blood pressure (rs2970869, p = 0.018) and fasting glucose concentrations (rs11724368, p = 0.045). Stronger associations were observed for aerobic fitness (rs7656250, p = 0.005; rs13117172, p = 0.008) and fasting glucose concentrations (rs7657071, p = 0.002). None remained significant after correcting for the number of statistical comparisons. We proceeded by testing for gene x physical activity interactions for the polymorphisms that showed nominal evidence of association in the main effect models. None of these tests was statistically significant. CONCLUSIONS/INTERPRETATION: Variants at PPARGC1A may influence several metabolic traits in this European paediatric cohort. However, variation at PPARGC1A is unlikely to have a major impact on cardiovascular or metabolic health in these children.

Spectral asymmetry of the massless Dirac operator on a 3-torus

Consider the massless Dirac operator on a 3-torus equipped with Euclidean metric and standard spin structure. It is known that the eigenvalues can be calculated explicitly: the spectrum is symmetric about zero and zero itself is a double eigenvalue. The aim of the paper is to develop a perturbation theory for the eigenvalue with smallest modulus with respect to perturbations of the metric. Here the application of perturbation techniques is hindered by the fact that eigenvalues of the massless Dirac operator have even multiplicity, which is a consequence of this operator commuting with the antilinear operator of charge conjugation (a peculiar feature of dimension 3). We derive an asymptotic formula for the eigenvalue with smallest modulus for arbitrary perturbations of the metric and present two particular families of Riemannian metrics for which the eigenvalue with smallest modulus can be evaluated explicitly. We also establish a relation between our asymptotic formula and the eta invariant.

Draft genome sequence of pseudomonas corrugata, a phytopathogenic bacterium with potential industrial applications

Pseudomonas corrugata was first described as the causal agent of a tomato disease called 'pith necrosis' yet it is considered as a biological resource in various fields such as biocontrol of plant diseases and production of industrially promising microbial biopolymers (mcl-PHA). Here we report the first draft genome sequence of this species.

Sequence analysis of a CTX-M-1 IncI1 plasmid found in Salmonella enterica 4,5,12,i:-, Escherichia coli and Klebsiella pneumoniae on a single UK pig farm

OBJECTIVES: In 2009, CTX-M Enterobacteriaceae and Salmonella isolates were recovered from a UK pig farm, prompting studies into the dissemination of the resistance and to establish any relationships between the isolates. METHODS: PFGE was used to elucidate clonal relationships between isolates whilst plasmid profiling, restriction analysis, sequencing and PCR were used to characterize the CTX-M-harbouring plasmids. RESULTS: Escherichia coli, Klebsiella pneumoniae and Salmonella 4,5,12:i:- and Bovismorbificans resistant to cefotaxime (n = 65) were recovered and 63 were shown by PCR to harbour a group 1 CTX-M gene. The harbouring hosts were diverse, but the group 1 CTX-M plasmids were common. Three sequenced CTX-M plasmids from E. coli, K. pneumoniae and Salmonella enterica serotype 4,5,12:i:- were identical except for seven mutations and highly similar to IncI1 plasmid ColIb-P9. Two antimicrobial resistance regions were identified: one inserted upstream of yacABC harbouring ISCR2 transposases, sul2 and floR; and the other inserted within shfB of the pilV shufflon harbouring the ISEcp1 transposase followed by blaCTX-M-1. CONCLUSIONS: These data suggest that an ST108 IncI1 plasmid encoding a blaCTX-M-1 gene had disseminated across multiple genera on this farm, an example of horizontal gene transfer of the blaCTX-M-1 gene.

On the spectra and pseudospectra of a class of non-self-adjoint random matrices and operators

In this paper we develop and apply methods for the spectral analysis of non-selfadjoint tridiagonal infinite and finite random matrices, and for the spectral analysis of analogous deterministic matrices which are pseudo-ergodic in the sense of E. B. Davies (Commun. Math. Phys. 216 (2001), 687–704). As a major application to illustrate our methods we focus on the “hopping sign model” introduced by J. Feinberg and A. Zee (Phys. Rev. E 59 (1999), 6433–6443), in which the main objects of study are random tridiagonal matrices which have zeros on the main diagonal and random ±1’s as the other entries. We explore the relationship between spectral sets in the finite and infinite matrix cases, and between the semi-infinite and bi-infinite matrix cases, for example showing that the numerical range and p-norm ε - pseudospectra (ε > 0, p ∈ [1,∞] ) of the random finite matrices converge almost surely to their infinite matrix counterparts, and that the finite matrix spectra are contained in the infinite matrix spectrum Σ. We also propose a sequence of inclusion sets for Σ which we show is convergent to Σ, with the nth element of the sequence computable by calculating smallest singular values of (large numbers of) n×n matrices. We propose similar convergent approximations for the 2-norm ε -pseudospectra of the infinite random matrices, these approximations sandwiching the infinite matrix pseudospectra from above and below.

Synergistic angular and spectral estimation of aerosol properties using CHRIS/PROBA-1 and simulated Sentinel-3~data

A method has been developed to estimate Aerosol Optical Depth (AOD), Fine Mode Fraction (FMF) and Single Scattering Albedo (SSA) over land surfaces using simulated Sentinel-3 data. The method uses inversion of a coupled surface/atmosphere radiative transfer model, and includes a general physical model of angular surface reflectance. An iterative process is used to determine the optimum value of the aerosol properties providing the best fit of the corrected reflectance values for a number of view angles and wavelengths with those provided by the physical model. A method of estimating AOD using only angular retrieval has previously been demonstrated on data from the ENVISAT and PROBA-1 satellite instruments, and is extended here to the synergistic spectral and angular sampling of Sentinel-3 and the additional aerosol properties. The method is tested using hyperspectral, multi-angle Compact High Resolution Imaging Spectrometer (CHRIS) images. The values obtained from these CHRIS observations are validated using ground based sun-photometer measurements. Results from 22 image sets using the synergistic retrieval and improved aerosol models show an RMSE of 0.06 in AOD, reduced to 0.03 over vegetated targets.

C. colchicum - variation measured by DNA sequence

Cyclamen colchicum has a mixed history in the hands of botanists. This paper examines the genetic identity of a group of wild Cyclamen populations from the Caucasus to discover whther they are Cyclamen colchicum, C. purpurascens or a mixture of the two. The collections supplemented by material collected at the type locality for C. colchicum, proved to be a single but variable genetic group of C. colchicum that was distinct from C. purpurascens.

Derivation of an urban materials spectral library through emittance and reflectance spectroscopy

Recent advances in thermal infrared remote sensing include the increased availability of airborne hyperspectral imagers (such as the Hyperspectral Thermal Emission Spectrometer, HyTES, or the Telops HyperCam and the Specim aisaOWL), and it is planned that an increased number spectral bands in the long-wave infrared (LWIR) region will soon be measured from space at reasonably high spatial resolution (by imagers such as HyspIRI). Detailed LWIR emissivity spectra are required to best interpret the observations from such systems. This includes the highly heterogeneous urban environment, whose construction materials are not yet particularly well represented in spectral libraries. Here, we present a new online spectral library of urban construction materials including LWIR emissivity spectra of 74 samples of impervious surfaces derived using measurements made by a portable Fourier Transform InfraRed (FTIR) spectrometer. FTIR emissivity measurements need to be carefully made, else they are prone to a series of errors relating to instrumental setup and radiometric calibration, which here relies on external blackbody sources. The performance of the laboratory-based emissivity measurement approach applied here, that in future can also be deployed in the field (e.g. to examine urban materials in situ), is evaluated herein. Our spectral library also contains matching short-wave (VIS–SWIR) reflectance spectra observed for each urban sample. This allows us to examine which characteristic (LWIR and) spectral signatures may in future best allow for the identification and discrimination of the various urban construction materials, that often overlap with respect to their chemical/mineralogical constituents. Hyperspectral or even strongly multi-spectral LWIR information appears especially useful, given that many urban materials are composed of minerals exhibiting notable reststrahlen/absorption effects in this spectral region. The final spectra and interpretations are included in the London Urban Micromet data Archive (LUMA; http://LondonClimate.info/LUMA/SLUM.html).

Self-assembly of a Model Peptide incorporating a Hexa-Histidine sequence attached to an Oligo-Alanine sequence, and binding to Gold NTA/Nickel nanoparticles

Amyloid fibrils are formed by a model surfactant-like peptide (Ala)10-(His)6 containing a hexahistidine tag. This peptide undergoes a remarkable two-step self-assembly process with two distinct critical aggregation concentrations (cac’s), probed by fluorescence techniques. A micromolar range cac is ascribed to the formation of prefibrillar structures, whereas a millimolar range cac is associated with the formation of well-defined but more compact fibrils. We examine the labeling of these model tagged amyloid fibrils using Ni-NTA functionalized gold nanoparticles (Nanogold). Successful labeling is demonstrated via electron microscopy imaging. The specificity of tagging does not disrupt the β-sheet structure of the peptide fibrils. Binding of fibrils and Nanogold is found to influence the circular dichroism associated with the gold nanoparticle plasmon absorption band. These results highlight a new approach to the fabrication of functionalized amyloid fibrils and the creation of peptide/nanoparticle hybrid materials.

Study of picosecond processes of an intercalated dipyridophenazine Cr(iii) complex bound to defined sequence DNAs using transient absorption and time-resolved infrared methods

Picosecond transient absorption (TA) and time-resolved infrared (TRIR) measurements of rac-[Cr(phen)2(dppz)]3+ (1) intercalated into double-stranded guanine-containing DNA reveal that the excited state is very rapidly quenched. As no evidence was found for the transient electron transfer products, it is proposed that the back electron transfer reaction must be even faster (<3 ps).

Nightside studies of coherent HF Radar spectral width behaviour

A previous case study found a relationship between high spectral width measured by the CUTLASS Finland HF radar and elevated electron temperatures observed by the EISCAT and ESR incoherent scatter radars in the postmidnight sector of magnetic local time. This paper expands that work by briefly re-examining that interval and looking in depth at two further case studies. In all three cases a region of high HF spectral width (>200 ms−1) exists poleward of a region of low HF spectral width (<200 ms^{−1}). Each case, however, occurs under quite different geomagnetic conditions. The original case study occurred during an interval with no observed electrojet activity, the second study during a transition from quiet to active conditions with a clear band of ion frictional heating indicating the location of the flow reversal boundary, and the third during an isolated substorm. These case studies indicate that the relationship between elevated electron temperature and high HF radar spectral width appears on closed field lines after 03:00 magnetic local time (MLT) on the nightside. It is not clear whether the same relationship would hold on open field lines, since our analysis of this relationship is restricted in latitude. We find two important properties of high spectral width data on the nightside. Firstly the high spectral width values occur on both open and closed field lines, and secondly that the power spectra which exhibit high widths are both single-peak and multiple-peak. In general the regions of high spectral width (>200 ms−1) have more multiple-peak spectra than the regions of low spectral widths whilst still maintaining a majority of single-peak spectra. We also find that the region of ion frictional heating is collocated with many multiplepeak HF spectra. Several mechanisms for the generation of high spectral width have been proposed which would produce multiple-peak spectra, these are discussed in relation to the data presented here. Since the regions of high spectral width are observed both on closed and open field lines the use of the boundary between low and high spectral width as an ionospheric proxy for the open/closed field line boundary is not a simple matter, if indeed it is possible at all.