953 resultados para Phenotypic Covariance Matrices


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Vertical divergence of CO2 fluxes is observed over two Midwestern AmeriFlux forest sites. The differences in ensemble averaged hourly CO2 fluxes measured at two heights above canopy are relatively small (0.2–0.5 μmol m−2 s−1), but they are the major contributors to differences (76–256 g C m−2 or 41.8–50.6%) in estimated annual net ecosystem exchange (NEE) in 2001. A friction velocity criterion is used in these estimates but mean flow advection is not accounted for. This study examines the effects of coordinate rotation, averaging time period, sampling frequency and co-spectral correction on CO2 fluxes measured at a single height, and on vertical flux differences measured between two heights. Both the offset in measured vertical velocity and the downflow/upflow caused by supporting tower structures in upwind directions lead to systematic over- or under-estimates of fluxes measured at a single height. An offset of 1 cm s−1 and an upflow/downflow of 1° lead to 1% and 5.6% differences in momentum fluxes and nighttime sensible heat and CO2 fluxes, respectively, but only 0.5% and 2.8% differences in daytime sensible heat and CO2 fluxes. The sign and magnitude of both offset and upflow/downflow angle vary between sonic anemometers at two measurement heights. This introduces a systematic and large bias in vertical flux differences if these effects are not corrected in the coordinate rotation. A 1 h averaging time period is shown to be appropriate for the two sites. In the daytime, the absolute magnitudes of co-spectra decrease with height in the natural frequencies of 0.02–0.1 Hz but increase in the lower frequencies (<0.01 Hz). Thus, air motions in these two frequency ranges counteract each other in determining vertical flux differences, whose magnitude and sign vary with averaging time period. At night, co-spectral densities of CO2 are more positive at the higher levels of both sites in the frequency range of 0.03–0.4 Hz and this vertical increase is also shown at most frequencies lower than 0.03 Hz. Differences in co-spectral corrections at the two heights lead to a positive shift in vertical CO2 flux differences throughout the day at both sites. At night, the vertical CO2 flux differences between two measurement heights are 20–30% and 40–60% of co-spectral corrected CO2 fluxes measured at the lower levels of the two sites, respectively. Vertical differences of CO2 flux are relatively small in the daytime. Vertical differences in estimated mean vertical advection of CO2 between the two measurement heights generally do not improve the closure of the 1D (vertical) CO2 budget in the air layer between the two measurement heights. This may imply the significance of horizontal advection. However, a reliable assessment of mean advection contributions in annual NEE estimate at these two AmeriFlux sites is currently an unsolved problem.

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We consider a new class of non-self-adjoint matrices that arise from an indefinite self- adjoint linear pencil of matrices, and obtain the spectral asymptotics of the spectra as the size of the matrices diverges to infinity. We prove that the spectrum is qualitatively different when a certain parameter c equals 0, and when it is non-zero, and that certain features of the spectrum depend on Diophantine properties of c.

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Sensible heat fluxes (QH) are determined using scintillometry and eddy covariance over a suburban area. Two large aperture scintillometers provide spatially integrated fluxes across path lengths of 2.8 km and 5.5 km over Swindon, UK. The shorter scintillometer path spans newly built residential areas and has an approximate source area of 2-4 km2, whilst the long path extends from the rural outskirts to the town centre and has a source area of around 5-10 km2. These large-scale heat fluxes are compared with local-scale eddy covariance measurements. Clear seasonal trends are revealed by the long duration of this dataset and variability in monthly QH is related to the meteorological conditions. At shorter time scales the response of QH to solar radiation often gives rise to close agreement between the measurements, but during times of rapidly changing cloud cover spatial differences in the net radiation (Q*) coincide with greater differences between heat fluxes. For clear days QH lags Q*, thus the ratio of QH to Q* increases throughout the day. In summer the observed energy partitioning is related to the vegetation fraction through use of a footprint model. The results demonstrate the value of scintillometry for integrating surface heterogeneity and offer improved understanding of the influence of anthropogenic materials on surface-atmosphere interactions.

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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.

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Airborne measurements within the urban mixing layer (360 m) over Greater London are used to quantify CO2 emissions at the meso-scale. Daytime CO2 fluxes, calculated by the Integrative Mass Boundary Layer (IMBL) method, ranged from 46 to 104 μmol CO2 m−2 s−1 for four days in October 2011. The day-to-day variability of IMBL fluxes is at the same order of magnitude as for surface eddy-covariance fluxes observed in central London. Compared to fluxes derived from emissions inventory, the IMBL method gives both lower (by −37%) and higher (by 19%) estimates. The sources of uncertainty of applying the IMBL method in urban areas are discussed and guidance for future studies is given.

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This study monitored the dynamics and diversity of the human faecal 'Atopobium cluster' over a 3-month period using a polyphasic approach. Fresh faecal samples were collected fortnightly from 13 healthy donors (6 males and 7 females) aged between 26 and 61 years. Fluorescence in situ hybridization was used to enumerate total (EUB338mix) and 'Atopobium cluster' (ATO291) bacteria, with counts ranging between 1.12 × 1011 and 9.95 × 1011, and 1.03 × 109 and 1.16 × 1011 cells (g dry weight faeces)-1, respectively. The 'Atopobium cluster' population represented 0.2-22 % of the total bacteria, with proportions donor-dependent. Denaturing gradient gel electrophoresis (DGGE) using 'Atopobium cluster'-specific primers demonstrated faecal populations of these bacteria were relatively stable, with bands identified as Collinsella aerofaciens, Collinsella intestinalis/Collinsella stercoris, Collinsella tanakaei, Coriobacteriaceae sp. PEAV3-3, Eggerthella lenta, Gordonibacter pamelaeae, Olsenella profusa, Olsenella uli and Paraeggerthella hongkongensis in the DGGE profiles of individuals. Colony PCR was used to identify 'Atopobium cluster' bacteria isolated from faeces (n = 224 isolates). 16S rRNA gene sequence analysis of isolates demonstrated Collinsella aerofaciens represented the predominant (88 % of isolates) member of the 'Atopobium cluster' found in human faeces, being found in nine individuals. Eggerthella lenta was identified in three individuals (3.6 % of isolates). Isolates of Collinsella tanakaei, an 'Enorma' sp. and representatives of novel species belonging to the 'Atopobium cluster' were also identified in the study. Phenotypic characterization of the isolates demonstrated their highly saccharolytic nature and heterogeneous phenotypic profiles, and 97 % of the isolates displayed lipase activity.

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Evidence is presented that the performance of the rationally designed MALDI matrix 4-chloro-α-cyanocinnamic acid (ClCCA) in comparison to its well-established predecessor α-cyano-4-hydroxycinnamic acid (CHCA) is significantly dependent on the sample preparation, such as the choice of the target plate. In this context, it becomes clear that any rational designs of MALDI matrices and their successful employment have to consider a larger set of physicochemical parameters, including sample crystallization and morphology/topology, in addition to parameters of basic (solution and/or gas-phase) chemistry.

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In order to achieve a safe swallowing in patients with dysphagia, liquids must be thickened. In this work, two commercial starch based thickeners dissolved in water, whole milk, apple juice and tomato juice were studied. The thickeners were Resource®, composed of modified maize starch and Nutilis®, composed of modified maize starch and gums. They were formulated at two different concentrations corresponding to nectar- and pudding-like consistencies. Influence of composition, concentration and food matrix on rheological properties and structure of the resulting pastes were analysed. Viscoelastic measurements and microscopic observations of the thickeners dissolved in water revealed structural differences due to the presence of gums. When the thickeners were dissolved in the other food matrices significant statistical interactions were found between the matrix and the thickener-type in both the viscoelastic and flow parameters. The most relevant differences were observed for the nectar-like consistency with Nutilis® thickener in milk and apple juice. These samples had lower zero viscosity values and higher loss tangent values, that corresponded to weaker structured systems. Light microscopy images showed that the matrix formed by swollen starch granules was interrupted by the presence of gums. The structure of the matrices in pudding-like formulations became more continuous irrespectively of the matrix employed, and also differences in viscoelasticity among samples diminished. Although differences were observed in zero shear viscosity values among samples, the viscosity of the beverages at 50 s−1 – commonly used as a reference for swallowing – was similar for all samples regardless of the matrix used.

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Barley can be classified into three major agronomic types, based on its seasonal growth habit (SGH): spring, winter and alternative. Winter varieties require exposure to vernalization to promote subsequent flowering and are autumn-sown. Spring varieties proceed to flowering in the absence of vernalization and are sown in the spring. The ‘alternative’ (also known as ‘facultative’) SGH is only loosely defined and can be sown in autumn or spring. Here, we investigate the molecular genetic basis of alternative barley. Analysis of the major barley vernalization (VRN-H1, VRN-H2) and photoperiod (PPD-H1, PPD-H2) response genes in a collection of 386 varieties found alternative SGH to be characterized by specific allelic combinations. Spring varieties possessed spring loci at one or both of the vernalization response loci, combined with long-day non-responsive ppd-H1 alleles and wild-type alleles at the short-day photoperiod response locus, PPD-H2. Winter varieties possessed winter alleles at both vernalization loci, in combination with the mutant ppd-H2 allele conferring delayed flowering under short-day photoperiods. In contrast, all alternative varieties investigated possessed a single spring allele (either at VRN-H1 or at VRN-H2) combined with mutant ppd-H2 alleles. This allelic combination is found only in alternative types and is diagnostic for alternative SGH in the collection studied. Analysis of flowering time under controlled environment found alternative varieties flowered later than spring control lines, with the difference most pronounced under short-day photoperiods. This work provides genetic characterization of the alternative SGH phenotype, allowing precise manipulation of SGH and flowering time within breeding programmes, and provides the molecular tools for classification of all three SGH categories within national variety registration processes.

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Sparse coding aims to find a more compact representation based on a set of dictionary atoms. A well-known technique looking at 2D sparsity is the low rank representation (LRR). However, in many computer vision applications, data often originate from a manifold, which is equipped with some Riemannian geometry. In this case, the existing LRR becomes inappropriate for modeling and incorporating the intrinsic geometry of the manifold that is potentially important and critical to applications. In this paper, we generalize the LRR over the Euclidean space to the LRR model over a specific Rimannian manifold—the manifold of symmetric positive matrices (SPD). Experiments on several computer vision datasets showcase its noise robustness and superior performance on classification and segmentation compared with state-of-the-art approaches.

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Although liquid matrix-assisted laser desorption/ionization (MALDI) has been used in mass spectrometry (MS) since the early introduction of MALDI, its substantial lack of sensitivity compared to solid (crystalline) MALDI was for a long time a major hurdle to its analytical competitiveness. In the last decade, this situation has changed with the development of new sensitive liquid matrices, which are often based on a binary matrix acid/base system. Some of these matrices were inspired by the recent progress in ionic liquid research, while others were developed from revisiting previous liquid MALDI work as well as from a combination of these two approaches. As a result, two high-performing liquid matrix classes have been developed, the ionic liquid matrices (ILMs) and the liquid support matrices (LSMs), now allowing MS measurements at a sensitivity level that is very close to the level of solid MALDI and in some cases even surpasses it. This chapter provides some basic information on a selection of highly successful representatives of these new liquid matrices and describes in detail how they are made and applied in MALDI MS analysis.

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In analysis of complex nuclear forensic samples containing lanthanides, actinides and matrix elements, rapid selective extraction of Am/Cm for quantification is challenging, in particular due the difficult separation of Am/Cm from lanthanides. Here we present a separation process for Am/Cm(III) which is achieved using a combination of AG1-X8 chromatography followed by Am/Cm extraction with a triazine ligand. The ligands tested in our process were CyMe4-BTPhen, CyMe4- BTBP, CA-BTP and CA-BTPhen. Our process allows for purification and quantification of Am and Cm (recoveries 80%–100%) and other major actinides in < 2d without the use of multiple columns or thiocyanate. The process is unaffected by high level Ca(II)/Fe(III)/Al(III) (10mg mL−1) and thus requires little pre-treatment of samples.

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Rates of phenotypic evolution vary widely in nature and these rates may often reflect the intensity of natural selection. Here we outline an approach for detecting exceptional shifts in the rate of phenotypic evolution across phylogenies. We introduce a simple new branch-specific metric ∆V/∆B that divides observed phenotypic change along a branch into two components: (1) that attributable to the background rate (∆B), and (2) that attributable to departures from the background rate (∆V). Where the amount of expected change derived from variation in the rate of morphological evolution doubles that explained by to the background rate (∆V/∆B > 2), we identify this as positive phenotypic selection. We apply our approach to six datasets, finding multiple instances of positive selection in each. Our results support the growing appreciation that the traditional gradual view of phenotypic evolution is rarely upheld, with a more episodic view taking its place. This moves focus away from viewing phenotypic evolution as a simple homogeneous process and facilitates reconciliation with macroevolutionary interpretations from a genetic perspective, paving the way to novel insights into the link between genotype and phenotype. The ability to detect positive selection when genetic data are unavailable or unobtainable represents an attractive prospect for extant species, but when applied to fossil data it can reveal patterns of natural selection in deep time that would otherwise be impossible.

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The hereditary spastic paraplegias are a heterogeneous group of degenerative disorders that are clinically classified as either pure with predominant lower limb spasticity, or complex where spastic paraplegia is complicated with additional neurological features, and are inherited in autosomal dominant, autosomal recessive or X-linked patterns. Genetic defects have been identified in over 40 different genes, with more than 70 loci in total. Complex recessive spastic paraplegias have in the past been frequently associated with mutations in SPG11 (spatacsin), ZFYVE26/SPG15, SPG7 (paraplegin) and a handful of other rare genes, but many cases remain genetically undefined. The overlap with other neurodegenerative disorders has been implied in a small number of reports, but not in larger disease series. This deficiency has been largely due to the lack of suitable high throughput techniques to investigate the genetic basis of disease, but the recent availability of next generation sequencing can facilitate the identification of disease- causing mutations even in extremely heterogeneous disorders. We investigated a series of 97 index cases with complex spastic paraplegia referred to a tertiary referral neurology centre in London for diagnosis or management. The mean age of onset was 16 years (range 3 to 39). The SPG11 gene was first analysed, revealing homozygous or compound heterozygous mutations in 30/97 (30.9%) of probands, the largest SPG11 series reported to date, and by far the most common cause of complex spastic paraplegia in the UK, with severe and progressive clinical features and other neurological manifestations, linked with magnetic resonance imaging defects. Given the high frequency of SPG11 mutations, we studied the autophagic response to starvation in eight affected SPG11 cases and control fibroblast cell lines, but in our restricted study we did not observe correlations between disease status and autophagic or lysosomal markers. In the remaining cases, next generation sequencing was carried out revealing variants in a number of other known complex spastic paraplegia genes, including five in SPG7 (5/97), four in FA2H (also known as SPG35) (4/97) and two in ZFYVE26/SPG15. Variants were identified in genes usually associated with pure spastic paraplegia and also in the Parkinson’s disease-associated gene ATP13A2, neuronal ceroid lipofuscinosis gene TPP1 and the hereditary motor and sensory neuropathy DNMT1 gene, highlighting the genetic heterogeneity of spastic paraplegia. No plausible genetic cause was identified in 51% of probands, likely indicating the existence of as yet unidentified genes.