Characterization of a highly biodiverse floodplain meadow using hyperspectral remote sensing within a plant functional trait framework

We assessed the potential for using optical functional types as effective markers to monitor changes in vegetation in floodplain meadows associated with changes in their local environment. Floodplain meadows are challenging ecosystems for monitoring and conservation because of their highly biodiverse nature. Our aim was to understand and explain spectral differences among key members of floodplain meadows and also characterize differences with respect to functional traits. The study was conducted on a typical floodplain meadow in UK (MG4-type, mesotrophic grassland type 4, according to British National Vegetation Classification). We compared two approaches to characterize floodplain communities using field spectroscopy. The first approach was sub-community based, in which we collected spectral signatures for species groupings indicating two distinct eco-hydrological conditions (dry and wet soil indicator species). The other approach was “species-specific”, in which we focused on the spectral reflectance of three key species found on the meadow. One herb species is a typical member of the MG4 floodplain meadow community, while the other two species, sedge and rush, represent wetland vegetation. We also monitored vegetation biophysical and functional properties as well as soil nutrients and ground water levels. We found that the vegetation classes representing meadow sub-communities could not be spectrally distinguished from each other, whereas the individual herb species was found to have a distinctly different spectral signature from the sedge and rush species. The spectral differences between these three species could be explained by their observed differences in plant biophysical parameters, as corroborated through radiative transfer model simulations. These parameters, such as leaf area index, leaf dry matter content, leaf water content, and specific leaf area, along with other functional parameters, such as maximum carboxylation capacity and leaf nitrogen content, also helped explain the species’ differences in functional dynamics. Groundwater level and soil nitrogen availability, which are important factors governing plant nutrient status, were also found to be significantly different for the herb/wetland species’ locations. The study concludes that spectrally distinguishable species, typical for a highly biodiverse site such as a floodplain meadow, could potentially be used as target species to monitor vegetation dynamics under changing environmental conditions.

Likelihood-free estimation of model evidence

Statistical methods of inference typically require the likelihood function to be computable in a reasonable amount of time. The class of “likelihood-free” methods termed Approximate Bayesian Computation (ABC) is able to eliminate this requirement, replacing the evaluation of the likelihood with simulation from it. Likelihood-free methods have gained in efficiency and popularity in the past few years, following their integration with Markov Chain Monte Carlo (MCMC) and Sequential Monte Carlo (SMC) in order to better explore the parameter space. They have been applied primarily to estimating the parameters of a given model, but can also be used to compare models. Here we present novel likelihood-free approaches to model comparison, based upon the independent estimation of the evidence of each model under study. Key advantages of these approaches over previous techniques are that they allow the exploitation of MCMC or SMC algorithms for exploring the parameter space, and that they do not require a sampler able to mix between models. We validate the proposed methods using a simple exponential family problem before providing a realistic problem from human population genetics: the comparison of different demographic models based upon genetic data from the Y chromosome.

Risk assessment of UK skylark populations using life-history and individual-based landscape models

Abstract: Following a workshop exercise, two models, an individual-based landscape model (IBLM) and a non-spatial life-history model were used to assess the impact of a fictitious insecticide on populations of skylarks in the UK. The chosen population endpoints were abundance, population growth rate, and the chances of population persistence. Both models used the same life-history descriptors and toxicity profiles as the basis for their parameter inputs. The models differed in that exposure was a pre-determined parameter in the life-history model, but an emergent property of the IBLM, and the IBLM required a landscape structure as an input. The model outputs were qualitatively similar between the two models. Under conditions dominated by winter wheat, both models predicted a population decline that was worsened by the use of the insecticide. Under broader habitat conditions, population declines were only predicted for the scenarios where the insecticide was added. Inputs to the models are very different, with the IBLM requiring a large volume of data in order to achieve the flexibility of being able to integrate a range of environmental and behavioural factors. The life-history model has very few explicit data inputs, but some of these relied on extensive prior modelling needing additional data as described in Roelofs et al.(2005, this volume). Both models have strengths and weaknesses; hence the ideal approach is that of combining the use of both simple and comprehensive modeling tools.

Effect of disease-selective predation on prey infected by contact and external sources

We propose and analyze a simple mathematical model for susceptible prey (S)–infected prey (I)–predator (P) interaction, where the susceptible prey population (S) is infected directly from external sources as well as through contact with infected class (I) and the predator completely avoids consuming the infected prey. The model is analyzed to obtain different thresholds of the key parameters under which the system exhibits stability around the biologically feasible equilibria. Through numerical simulations we display the effects of external infection and the infection through contact on the system dynamics in the absence as well as in the presence of the predator. We compare the system dynamics when infection occurs only through contact, with that when it occurs through contact and external sources. Our analysis demonstrates that under a disease-selective predation, stability and oscillations of the system is determined by two key parameters: the external infection rate and the force of infection through contact. Due to the introduction of external infection, the predator and the prey population show limit-cycle oscillations over a range parametric values. We suggest that while predicting the dynamics of such an eco-epidemiological system, the modes of infection and the infection rates might be carefully investigated.

The effect of (mis-specified) GARCH filters on the finite sample distribution of the BDS test

This paper considers the effect of using a GARCH filter on the properties of the BDS test statistic as well as a number of other issues relating to the application of the test. It is found that, for certain values of the user-adjustable parameters, the finite sample distribution of the test is far-removed from asymptotic normality. In particular, when data generated from some completely different model class are filtered through a GARCH model, the frequency of rejection of iid falls, often substantially. The implication of this result is that it might be inappropriate to use non-rejection of iid of the standardised residuals of a GARCH model as evidence that the GARCH model ‘fits’ the data.

Clouds and the atmospheric circulation response to warming

We study the effect of clouds on the atmospheric circulation response to CO2 quadrupling in an aquaplanet model with a slab-ocean lower boundary. The cloud effect is isolated by locking the clouds to either the control or 4xCO2 state in the shortwave (SW) or longwave (LW) radiation schemes. In our model, cloud-radiative changes explain more than half of the total poleward expansion of the Hadley cells, midlatitude jets, and storm tracks under CO2 quadrupling, even though they cause only one-fourth of the total global-mean surface warming. The effect of clouds on circulation results mainly from the SW cloud-radiative changes, which strongly enhance the Equator-to-pole temperature gradient at all levels in the troposphere, favoring stronger and poleward-shifted midlatitude eddies. By contrast, quadrupling CO2 while holding the clouds fixed causes strong polar amplification and weakened midlatitude baroclinicity at lower levels, yielding only a small poleward expansion of the circulation. Our results show that (a) the atmospheric circulation responds sensitively to cloud-driven changes in meridional and vertical temperature distribution, and (b) the spatial structure of cloud feedbacks likely plays a dominant role in the circulation response to greenhouse gas forcing. While the magnitude and spatial structure of the cloud feedback are expected to be highly model-dependent, an analysis of 4xCO2 simulations of CMIP5 models shows that the SW cloud feedback likely forces a poleward expansion of the tropospheric circulation in most climate models.

Climatology and variability of trace gases in extratropical double-tropopause regions from MLS, HIRDLS, and ACE-FTS measurements

Upper tropospheric and lower stratospheric measurements from the Aura Microwave Limb Sounder (MLS), the Aura High Resolution Dynamics Limb Sounder (HIRDLS), and the Atmospheric Chemistry Experiment-Fourier transform spectrometer (ACE-FTS) are used to present the first global climatological comparison of extratropical, nonpolar trace gas distributions in double-tropopause (DT) and single-tropopause (ST) regions. Stratospheric tracers, O3, HNO3, and HCl, have lower mixing ratios ∼2–8 km above the primary (lowermost) tropopause in DT than in ST regions in all seasons, with maximum Northern Hemisphere (NH) differences near 50% in winter and 30% in summer. Southern Hemisphere winter differences are somewhat smaller, but summer differences are similar in the two hemispheres. H2O in DT regions of both hemispheres shows strong negative anomalies in November through February and positive anomalies in July through October, reflecting the strong seasonal cycle in H2O near the tropical tropopause. CO and other tropospheric tracers examined have higher DT than ST values 2–7 km above the primary tropopause, with the largest differences in winter. Large DT-ST differences extend to high NH latitudes in fall and winter, with longitudinal maxima in regions associated with enhanced wave activity and subtropical jet variations. Results for O3 and HNO3 agree closely between MLS and HIRDLS, and differences from ACE-FTS are consistent with its sparse and irregular midlatitude sampling. Consistent signatures in climatological trace gas fields provide strong evidence that transport from the tropical upper troposphere into the layer between double tropopauses is an important pathway for stratosphere-troposphere exchange.

Advancements in decadal climate predictability: the role of nonoceanic drivers

We review recent progress in understanding the role of sea ice, land surface, stratosphere, and aerosols in decadal-scale predictability and discuss the perspectives for improving the predictive capabilities of current Earth system models (ESMs). These constituents have received relatively little attention because their contribution to the slow climatic manifold is controversial in comparison to that of the large heat capacity of the oceans. Furthermore, their initialization as well as their representation in state-of-the-art climate models remains a challenge. Numerous extraoceanic processes that could be active over the decadal range are proposed. Potential predictability associated with the aforementioned, poorly represented, and scarcely observed constituents of the climate system has been primarily inspected through numerical simulations performed under idealized experimental settings. The impact, however, on practical decadal predictions, conducted with realistically initialized full-fledged climate models, is still largely unexploited. Enhancing initial-value predictability through an improved model initialization appears to be a viable option for land surface, sea ice, and, marginally, the stratosphere. Similarly, capturing future aerosol emission storylines might lead to an improved representation of both global and regional short-term climatic changes. In addition to these factors, a key role on the overall predictive ability of ESMs is expected to be played by an accurate representation of processes associated with specific components of the climate system. These act as “signal carriers,” transferring across the climatic phase space the information associated with the initial state and boundary forcings, and dynamically bridging different (otherwise unconnected) subsystems. Through this mechanism, Earth system components trigger low-frequency variability modes, thus extending the predictability beyond the seasonal scale.

Morphological properties of superclusters of galaxies

We studied superclusters of galaxies in a volume-limited sample extracted from the Sloan Digital Sky Survey Data Release 7 and from mock catalogues based on a semi-analytical model of galaxy evolution in the Millennium Simulation. A density field method was applied to a sample of galaxies brighter than M(r) = -21+5 log h(100) to identify superclusters, taking into account selection and boundary effects. In order to evaluate the influence of the threshold density, we have chosen two thresholds: the first maximizes the number of objects (D1) and the second constrains the maximum supercluster size to similar to 120 h(-1) Mpc (D2). We have performed a morphological analysis, using Minkowski Functionals, based on a parameter, which increases monotonically from filaments to pancakes. An anticorrelation was found between supercluster richness (and total luminosity or size) and the morphological parameter, indicating that filamentary structures tend to be richer, larger and more luminous than pancakes in both observed and mock catalogues. We have also used the mock samples to compare supercluster morphologies identified in position and velocity spaces, concluding that our morphological classification is not biased by the peculiar velocities. Monte Carlo simulations designed to investigate the reliability of our results with respect to random fluctuations show that these results are robust. Our analysis indicates that filaments and pancakes present different luminosity and size distributions.

Identification of a novel ligand binding motif in the transthyretin channel

The design of therapeutic compounds targeting transthyretin (TTR) is challenging due to the low specificity of interaction in the hormone binding site. Such feature is highlighted by the interactions of TTR with diclofenac, a compound with high affinity for TTR, in two dissimilar modes, as evidenced by crystal structure of the complex. We report here structural analysis of the interactions of TTR with two small molecules, 1-amino-5-naphthalene sulfonate (1,5-AmNS) and 1-anilino-8-naphthalene sulfonate (1,8-ANS). Crystal structure of TTR: 1,8-ANS complex reveals a peculiar interaction, through the stacking of the naphthalene ring between the side-chain of Lys15 and Leu17. The sulfonate moiety provides additional interaction with Lys15` and a water-mediated hydrogen bond with Thr119`. The uniqueness of this mode of ligand recognition is corroborated by the crystal structure of TTR in complex with the weak analogue 1,5-AmNS, the binding of which is driven mainly by hydrophobic partition and one electrostatic interaction between the sulfonate group and the Lys15. The ligand binding motif unraveled by 1,8-ANS may open new possibilities to treat TTR amyloid diseases by the elucidation of novel candidates for a more specific pharmacophoric pattern. (C) 2009 Published by Elsevier Ltd.

Crystal structure and statistical coupling analysis of highly glycosylated peroxidase from royal palm tree (Roystonea regia)

Royal palm tree peroxidase (RPTP) is a very stable enzyme in regards to acidity, temperature, H(2)O(2), and organic solvents. Thus, RPTP is a promising candidate for developing H(2)O(2)-sensitive biosensors for diverse applications in industry and analytical chemistry. RPTP belongs to the family of class III secretory plant peroxidases, which include horseradish peroxidase isozyme C, soybean and peanut peroxidases. Here we report the X-ray structure of native RPTP isolated from royal palm tree (Roystonea regia) refined to a resolution of 1.85 angstrom. RPTP has the same overall folding pattern of the plant peroxidase superfamily, and it contains one heme group and two calcium-binding sites in similar locations. The three-dimensional structure of RPTP was solved for a hydroperoxide complex state, and it revealed a bound 2-(N-morpholino) ethanesulfonic acid molecule (MES) positioned at a putative substrate-binding secondary site. Nine N-glycosylation sites are clearly defined in the RPTP electron-density maps, revealing for the first time conformations of the glycan chains of this highly glycosylated enzyme. Furthermore, statistical coupling analysis (SCA) of the plant peroxidase superfamily was performed. This sequence-based method identified a set of evolutionarily conserved sites that mapped to regions surrounding the heme prosthetic group. The SCA matrix also predicted a set of energetically coupled residues that are involved in the maintenance of the structural folding of plant peroxidases. The combination of crystallographic data and SCA analysis provides information about the key structural elements that could contribute to explaining the unique stability of RPTP. (C) 2009 Elsevier Inc. All rights reserved.

Heteroscedastic controlled calibration model applied to analytical chemistry

In chemical analyses performed by laboratories, one faces the problem of determining the concentration of a chemical element in a sample. In practice, one deals with the problem using the so-called linear calibration model, which considers that the errors associated with the independent variables are negligible compared with the former variable. In this work, a new linear calibration model is proposed assuming that the independent variables are subject to heteroscedastic measurement errors. A simulation study is carried out in order to verify some properties of the estimators derived for the new model and it is also considered the usual calibration model to compare it with the new approach. Three applications are considered to verify the performance of the new approach. Copyright (C) 2010 John Wiley & Sons, Ltd.

Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT i.s stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.

Att lämna en värld : Om utgångsprocesser ur Jehovas vittnen

It is an everyday experience to realize that things do not turn out the as expected. But what if you realize that everything you have so far experienced as reality is illusion? This article is about former members of the Jehovah’s Witnesses who have had doubts about what they previously believed to be the Truth. The article also treats the exit process, from being a Jehovah’s Witness to becoming an ex-Jehovah’s Witness. The data consists of twenty qualitative interviews with ten Jehovah’s Witnesses and twenty qualitative interviews with ten former Jehovah’s Witnesses. The data also include a diary written during four years preceding an exit from the organization. The analysis was made through thematic concentration. Ontologically the analysis and the article are based on a constructionist view though it is mainly empirical with no further theoretical assessment. However, to be able to understand the results a contextual frame is sketched with two factors affecting members who make an exit. First there are tying factors that bind the person closer to the organization; these are closeness and friendship and confirmation. A secluding factor is something that secludes the member from the outside society; these factors are the work situation and »closed doors«. With high values on these factors the exit process will be more arduous. The results are presented through a process model in which different phases or steps in the exit process are described. The following steps in the process are: (1) different levels of doubts; (2) trying out doubts; (3) turning points; (4) different decisions; (5) different steps in execution; (6) floating; (7) relative neutrality. The process is defined as an altogether ambivalent and emotionally tough experience, but other parts of life may be affected as well, such as employment, social life, family life and career.

Parameterization Of Turbulence Models Using 3DVAR Data Assimilation

In this research the 3DVAR data assimilation scheme is implemented in the numerical model DIVAST in order to optimize the performance of the numerical model by selecting an appropriate turbulence scheme and tuning its parameters. Two turbulence closure schemes: the Prandtl mixing length model and the two-equation k-ε model were incorporated into DIVAST and examined with respect to their universality of application, complexity of solutions, computational efficiency and numerical stability. A square harbour with one symmetrical entrance subject to tide-induced flows was selected to investigate the structure of turbulent flows. The experimental part of the research was conducted in a tidal basin. A significant advantage of such laboratory experiment is a fully controlled environment where domain setup and forcing are user-defined. The research shows that the Prandtl mixing length model and the two-equation k-ε model, with default parameterization predefined according to literature recommendations, overestimate eddy viscosity which in turn results in a significant underestimation of velocity magnitudes in the harbour. The data assimilation of the model-predicted velocity and laboratory observations significantly improves model predictions for both turbulence models by adjusting modelled flows in the harbour to match de-errored observations. 3DVAR allows also to identify and quantify shortcomings of the numerical model. Such comprehensive analysis gives an optimal solution based on which numerical model parameters can be estimated. The process of turbulence model optimization by reparameterization and tuning towards optimal state led to new constants that may be potentially applied to complex turbulent flows, such as rapidly developing flows or recirculating flows.