AUTOMATED DETERMINATION OF [Fe/H] AND [C/Fe] FROM LOW-RESOLUTION SPECTROSCOPY

We develop an automated spectral synthesis technique for the estimation of metallicities ([Fe/H]) and carbon abundances ([C/Fe]) for metal-poor stars, including carbon-enhanced metal-poor stars, for which other methods may prove insufficient. This technique, autoMOOG, is designed to operate on relatively strong features visible in even low- to medium-resolution spectra, yielding results comparable to much more telescope-intensive high-resolution studies. We validate this method by comparison with 913 stars which have existing high-resolution and low- to medium-resolution to medium-resolution spectra, and that cover a wide range of stellar parameters. We find that at low metallicities ([Fe/H] less than or similar to -2.0), we successfully recover both the metallicity and carbon abundance, where possible, with an accuracy of similar to 0.20 dex. At higher metallicities, due to issues of continuum placement in spectral normalization done prior to the running of autoMOOG, a general underestimate of the overall metallicity of a star is seen, although the carbon abundance is still successfully recovered. As a result, this method is only recommended for use on samples of stars of known sufficiently low metallicity. For these low- metallicity stars, however, autoMOOG performs much more consistently and quickly than similar, existing techniques, which should allow for analyses of large samples of metal-poor stars in the near future. Steps to improve and correct the continuum placement difficulties are being pursued.

Diffraction theory of Fresnel lenses encoded in low-resolution devices

A mathematical model that describes the behavior of low-resolution Fresnel lenses encoded in any low-resolution device (e.g., a spatial light modulator) is developed. The effects of low-resolution codification, such the appearance of new secondary lenses, are studied for a general case. General expressions for the phase of these lenses are developed, showing that each lens behaves as if it were encoded through all pixels of the low-resolution device. Simple expressions for the light distribution in the focal plane and its dependence on the encoded focal length are developed and commented on in detail. For a given codification device an optimum focal length is found for best lens performance. An optimization method for codification of a single lens with a short focal length is proposed.

Diffraction theory of optimized low-resolution Fresnel encoded lenses

A mathematical model describing the behavior of low-resolution Fresnel encoded lenses (LRFEL's) encoded in any low-resolution device (e.g., a spatial light modulator) has recently been developed. From this model, an LRFEL with a short focal length was optimized by our imposing the maximum intensity of light onto the optical axis. With this model, analytical expressions for the light-amplitude distribution, the diffraction efficiency, and the frequency response of the optimized LRFEL's are derived.

A post-processing pipeline to reconstruct the developing fetal brain using low-resolution MRI

Introduction. Development of the fetal brain surfacewith concomitant gyrification is one of the majormaturational processes of the human brain. Firstdelineated by postmortem studies or by ultrasound, MRIhas recently become a powerful tool for studying in vivothe structural correlates of brain maturation. However,the quantitative measurement of fetal brain developmentis a major challenge because of the movement of the fetusinside the amniotic cavity, the poor spatial resolution,the partial volume effect and the changing appearance ofthe developing brain. Today extensive efforts are made todeal with the âeurooepost-acquisitionâeuro reconstruction ofhigh-resolution 3D fetal volumes based on severalacquisitions with lower resolution (Rousseau, F., 2006;Jiang, S., 2007). We here propose a framework devoted tothe segmentation of the basal ganglia, the gray-whitetissue segmentation, and in turn the 3D corticalreconstruction of the fetal brain. Method. Prenatal MRimaging was performed with a 1-T system (GE MedicalSystems, Milwaukee) using single shot fast spin echo(ssFSE) sequences in fetuses aged from 29 to 32gestational weeks (slice thickness 5.4mm, in planespatial resolution 1.09mm). For each fetus, 6 axialvolumes shifted by 1 mm were acquired (about 1 min pervolume). First, each volume is manually segmented toextract fetal brain from surrounding fetal and maternaltissues. Inhomogeneity intensity correction and linearintensity normalization are then performed. A highspatial resolution image of isotropic voxel size of 1.09mm is created for each fetus as previously published byothers (Rousseau, F., 2006). B-splines are used for thescattered data interpolation (Lee, 1997). Then, basalganglia segmentation is performed on this superreconstructed volume using active contour framework witha Level Set implementation (Bach Cuadra, M., 2010). Oncebasal ganglia are removed from the image, brain tissuesegmentation is performed (Bach Cuadra, M., 2009). Theresulting white matter image is then binarized andfurther given as an input in the Freesurfer software(http://surfer.nmr.mgh.harvard.edu/) to provide accuratethree-dimensional reconstructions of the fetal brain.Results. High-resolution images of the cerebral fetalbrain, as obtained from the low-resolution acquired MRI,are presented for 4 subjects of age ranging from 29 to 32GA. An example is depicted in Figure 1. Accuracy in theautomated basal ganglia segmentation is compared withmanual segmentation using measurement of Dice similarity(DSI), with values above 0.7 considering to be a verygood agreement. In our sample we observed DSI valuesbetween 0.785 and 0.856. We further show the results ofgray-white matter segmentation overlaid on thehigh-resolution gray-scale images. The results arevisually checked for accuracy using the same principlesas commonly accepted in adult neuroimaging. Preliminary3D cortical reconstructions of the fetal brain are shownin Figure 2. Conclusion. We hereby present a completepipeline for the automated extraction of accuratethree-dimensional cortical surface of the fetal brain.These results are preliminary but promising, with theultimate goal to provide âeurooemovieâeuro of the normal gyraldevelopment. In turn, a precise knowledge of the normalfetal brain development will allow the quantification ofsubtle and early but clinically relevant deviations.Moreover, a precise understanding of the gyraldevelopment process may help to build hypotheses tounderstand the pathogenesis of several neurodevelopmentalconditions in which gyrification have been shown to bealtered (e.g. schizophrenia, autismâeuro¦). References.Rousseau, F. (2006), 'Registration-Based Approach forReconstruction of High-Resolution In Utero Fetal MR Brainimages', IEEE Transactions on Medical Imaging, vol. 13,no. 9, pp. 1072-1081. Jiang, S. (2007), 'MRI of MovingSubjects Using Multislice Snapshot Images With VolumeReconstruction (SVR): Application to Fetal, Neonatal, andAdult Brain Studies', IEEE Transactions on MedicalImaging, vol. 26, no. 7, pp. 967-980. Lee, S. (1997),'Scattered data interpolation with multilevel B-splines',IEEE Transactions on Visualization and Computer Graphics,vol. 3, no. 3, pp. 228-244. Bach Cuadra, M. (2010),'Central and Cortical Gray Mater Segmentation of MagneticResonance Images of the Fetal Brain', ISMRM Conference.Bach Cuadra, M. (2009), 'Brain tissue segmentation offetal MR images', MICCAI.

Climate entropy budget of the HadCM3 atmosphere-ocean general circulation model and of FAMOUS, its low resolution version

The entropy budget is calculated of the coupled atmosphere–ocean general circulation model HadCM3. Estimates of the different entropy sources and sinks of the climate system are obtained directly from the diabatic heating terms, and an approximate estimate of the planetary entropy production is also provided. The rate of material entropy production of the climate system is found to be ∼50 mW m−2 K−1, a value intermediate in the range 30–70 mW m−2 K−1 previously reported from different models. The largest part of this is due to sensible and latent heat transport (∼38 mW m−2 K−1). Another 13 mW m−2 K−1 is due to dissipation of kinetic energy in the atmosphere by friction and Reynolds stresses. Numerical entropy production in the atmosphere dynamical core is found to be about 0.7 mW m−2 K−1. The material entropy production within the ocean due to turbulent mixing is ∼1 mW m−2 K−1, a very small contribution to the material entropy production of the climate system. The rate of change of entropy of the model climate system is about 1 mW m−2 K−1 or less, which is comparable with the typical size of the fluctuations of the entropy sources due to interannual variability, and a more accurate closure of the budget than achieved by previous analyses. Results are similar for FAMOUS, which has a lower spatial resolution but similar formulation to HadCM3, while more substantial differences are found with respect to other models, suggesting that the formulation of the model has an important influence on the climate entropy budget. Since this is the first diagnosis of the entropy budget in a climate model of the type and complexity used for projection of twenty-first century climate change, it would be valuable if similar analyses were carried out for other such models.

The advection of high-resolution tracers by low-resolution winds

The usefulness of any simulation of atmospheric tracers using low-resolution winds relies on both the dominance of large spatial scales in the strain and time dependence that results in a cascade in tracer scales. Here, a quantitative study on the accuracy of such tracer studies is made using the contour advection technique. It is shown that, although contour stretching rates are very insensitive to the spatial truncation of the wind field, the displacement errors in filament position are sensitive. A knowledge of displacement characteristics is essential if Lagrangian simulations are to be used for the inference of airmass origin. A quantitative lower estimate is obtained for the tracer scale factor (TSF): the ratio of the smallest resolved scale in the advecting wind field to the smallest “trustworthy” scale in the tracer field. For a baroclinic wave life cycle the TSF = 6.1 ± 0.3 while for the Northern Hemisphere wintertime lower stratosphere the TSF = 5.5 ± 0.5, when using the most stringent definition of the trustworthy scale. The similarity in the TSF for the two flows is striking and an explanation is discussed in terms of the activity of potential vorticity (PV) filaments. Uncertainty in contour initialization is investigated for the stratospheric case. The effect of smoothing initial contours is to introduce a spinup time, after which wind field truncation errors take over from initialization errors (2–3 days). It is also shown that false detail from the proliferation of finescale filaments limits the useful lifetime of such contour advection simulations to 3σ−1 days, where σ is the filament thinning rate, unless filaments narrower than the trustworthy scale are removed by contour surgery. In addition, PV analysis error and diabatic effects are so strong that only PV filaments wider than 50 km are at all believable, even for very high-resolution winds. The minimum wind field resolution required to accurately simulate filaments down to the erosion scale in the stratosphere (given an initial contour) is estimated and the implications for the modeling of atmospheric chemistry are briefly discussed.

Objective detection of sting jets in low-resolution datasets

Sting jets are transient coherent mesoscale strong wind features that can cause damaging surface wind gusts in extratropical cyclones. Currently, we have only limited knowledge of their climatological characteristics. Numerical weather prediction models require enough resolution to represent slantwise motions with horizontal scales of tens of kilometres and vertical scales of just a few hundred metres to represent sting jets. Hence, the climatological characteristics of sting jets and the associated extratropical cyclones can not be determined by searching for sting jets in low-resolution datasets such as reanalyses. A diagnostic is presented and evaluated for the detection in low-resolution datasets of atmospheric regions from which sting jets may originate. Previous studies have shown that conditional symmetric instability (CSI) is present in all storms studied with sting jets, while other, rapidly developing storms of a similar character but no CSI do not develop sting jets. Therefore, we assume that the release of CSI is needed for sting jets to develop. While this instability will not be released in a physically realistic way in low-resolution models (and hence sting jets are unlikely to occur), it is hypothesized that the signature of this instability (combined with other criteria that restrict analysis to moist mid-tropospheric regions in the neighbourhood of a secondary cold front) can be used to identify cyclones in which sting jets occurred in reality. The diagnostic is evaluated, and appropriate parameter thresholds defined, by applying it to three case studies simulated using two resolutions (with CSI-release resolved in only the higher-resolution simulation).

Predicting metal-binding site residues in low-resolution structural models

The accurate prediction of the biochemical function of a protein is becoming increasingly important, given the unprecedented growth of both structural and sequence databanks. Consequently, computational methods are required to analyse such data in an automated manner to ensure genomes are annotated accurately. Protein structure prediction methods, for example, are capable of generating approximate structural models on a genome-wide scale. However, the detection of functionally important regions in such crude models, as well as structural genomics targets, remains an extremely important problem. The method described in the current study, MetSite, represents a fully automatic approach for the detection of metal-binding residue clusters applicable to protein models of moderate quality. The method involves using sequence profile information in combination with approximate structural data. Several neural network classifiers are shown to be able to distinguish metal sites from non-sites with a mean accuracy of 94.5%. The method was demonstrated to identify metal-binding sites correctly in LiveBench targets where no obvious metal-binding sequence motifs were detectable using InterPro. Accurate detection of metal sites was shown to be feasible for low-resolution predicted structures generated using mGenTHREADER where no side-chain information was available. High-scoring predictions were observed for a recently solved hypothetical protein from Haemophilus influenzae, indicating a putative metal-binding site.

Automatic prediction of functional site regions in low-resolution protein structures

World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art structural prediction programs are now capable of generating at least low resolution structural models of target proteins. Accurate detection and classification of functional sites within both solved and modelled protein structures therefore represents an important challenge. We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. The method is designed primarily to require only backbone residue positions without the need for specific side-chain atoms to be present. In order to highlight effective site detection in low resolution structural models FuncSite was used to screen model proteins generated using mGenTHREADER on a set of newly released structures. We found effective metal site detection even for moderate quality protein models illustrating the robustness of the method.

A data assimilation method for using low-resolution Earth observation data in heterogeneous ecosystems

We present an approach for dealing with coarse-resolution Earth observations (EO) in terrestrial ecosystem data assimilation schemes. The use of coarse-scale observations in ecological data assimilation schemes is complicated by spatial heterogeneity and nonlinear processes in natural ecosystems. If these complications are not appropriately dealt with, then the data assimilation will produce biased results. The “disaggregation” approach that we describe in this paper combines frequent coarse-resolution observations with temporally sparse fine-resolution measurements. We demonstrate the approach using a demonstration data set based on measurements of an Arctic ecosystem. In this example, normalized difference vegetation index observations are assimilated into a “zero-order” model of leaf area index and carbon uptake. The disaggregation approach conserves key ecosystem characteristics regardless of the observation resolution and estimates the carbon uptake to within 1% of the demonstration data set “truth.” Assimilating the same data in the normal manner, but without the disaggregation approach, results in carbon uptake being underestimated by 58% at an observation resolution of 250 m. The disaggregation method allows the combination of multiresolution EO and improves in spatial resolution if observations are located on a grid that shifts from one observation time to the next. Additionally, the approach is not tied to a particular data assimilation scheme, model, or EO product and can cope with complex observation distributions, as it makes no implicit assumptions of normality.

Mode of operation and low-resolution structure of a multi-domain and hyperthermophilic endo-beta-1,3-glucanase from Thermotoga petrophila

1,3-beta-Glucan depolymerizing enzymes have considerable biotechnological applications including biofuel production, feedstock-chemicals and pharmaceuticals. Here we describe a comprehensive functional characterization and low-resolution structure of a hyperthermophilic laminarinase from Thermotoga petrophila (TpLam). We determine TpLam enzymatic mode of operation, which specifically cleaves internal beta-1,3-glucosidic bonds. The enzyme most frequently attacks the bond between the 3rd and 4th residue from the non-reducing end, producing glucose, laminaribiose and laminaritriose as major products. Far-UV circular dichroism demonstrates that TpLam is formed mainly by beta structural elements, and the secondary structure is maintained after incubation at 90 degrees C. The structure resolved by small angle X-ray scattering, reveals a multi-domain structural architecture of a V-shape envelope with a catalytic domain flanked by two carbohydrate-binding modules. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved.

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Including the sub-grid scale plume rise of vegetation fires in low resolution atmospheric transport models

We describe and begin to evaluate a parameterization to include the vertical transport of hot gases and particles emitted from biomass burning in low resolution atmospheric-chemistry transport models. This sub-grid transport mechanism is simulated by embedding a 1-D cloud-resolving model with appropriate lower boundary conditions in each column of the 3-D host model. Through assimilation of remote sensing fire products, we recognize which columns have fires. Using a land use dataset appropriate fire properties are selected. The host model provides the environmental conditions, allowing the plume rise to be simulated explicitly. The derived height of the plume is then used in the source emission field of the host model to determine the effective injection height, releasing the material emitted during the flaming phase at this height. Model results are compared with CO aircraft profiles from an Amazon basin field campaign and with satellite data, showing the huge impact that this mechanism has on model performance. We also show the relative role of each main vertical transport mechanisms, shallow and deep moist convection and the pyro-convection (dry or moist) induced by vegetation fires, on the distribution of biomass burning CO emissions in the troposphere.

Low resolution structural characterization of the Hsp70-interacting protein - Hip - from Leishmania braziliensis emphasizes its high asymmetry

The Hsp70 is an essential molecular chaperone in protein metabolism since it acts as a pivot with other molecular chaperone families. Several co-chaperones act as regulators of the Hsp70 action cycle, as for instance Hip (Hsp70-interacting protein). Hip is a tetratricopeptide repeat protein (TPR) that interacts with the ATPase domain in the Hsp70-ADP state, stabilizing it and preventing substrate dissociation. Molecular chaperones from protozoans, which can cause some neglected diseases, are poorly studied in terms of structure and function. Here, we investigated the structural features of Hip from the protozoa Leishmania braziliensis (LbHip), one of the causative agents of the leishmaniasis disease. LbHip was heterologously expressed and purified in the folded state, as attested by circular dichroism and intrinsic fluorescence emission techniques. LbHip forms an elongated dimer, as observed by analytical gel filtration chromatography, analytical ultracentrifugation and small angle X-ray scattering (SAXS). With the SAXS data a low resolution model was reconstructed, which shed light on the structure of this protein, emphasizing its elongated shape and suggesting its domain organization. We also investigated the chemical-induced unfolding behavior of LbHip and two transitions were observed. The first transition was related to the unfolding of the TPR domain of each protomer and the second transition of the dimer dissociation. Altogether. LbHip presents a similar structure to mammalian Hip, despite their low level of conservation, suggesting that this class of eukaryotic protein may use a similar mechanism of action. (C) 2012 Elsevier Inc. All rights reserved.

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

The peroxisome proliferator-activated receptors (PPARs) regulate genes involved in lipid and carbohydrate metabolism, and are targets of drugs approved for human use. Whereas the crystallographic structure of the complex of full length PPAR gamma and RXR alpha is known, structural alterations induced by heterodimer formation and DNA contacts are not well understood. Herein, we report a small-angle X-ray scattering analysis of the oligomeric state of hPPAR gamma alone and in the presence of retinoid X receptor (RXR). The results reveal that, in contrast with other studied nuclear receptors, which predominantly form dimers in solution, hPPAR gamma remains in the monomeric form by itself but forms heterodimers with hRXR alpha. The low-resolution models of hPPAR gamma/RXR alpha complexes predict significant changes in opening angle between heterodimerization partners (LBD) and extended and asymmetric shape of the dimer (LBD-DBD) as compared with X-ray structure of the full-length receptor bound to DNA. These differences between our SAXS models and the high-resolution crystallographic structure might suggest that there are different conformations of functional heterodimer complex in solution. Accordingly, hydrogen/deuterium exchange experiments reveal that the heterodimer binding to DNA promotes more compact and less solvent-accessible conformation of the receptor complex.