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Structure Data (structure + data)
Selected AbstractsNon-Covalent Interactions of Organic Halogen Compounds with Aromatic Systems , Analyses of Crystal Structure DataEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 6 2005Dariusz Swierczynski Abstract The Cambridge Structural Database showed in mid 2002 about 20.000 structures containing halogen atoms and aryl rests with distances d between the aryl center and the halogen atom, which would allow both hydrogen bonds with the aromatic hydrogens and/or van der Waalsinteractions with the ,-cloud. The latter are characterized by short distances d and by small angles , between the vector along the aryl centroid,halogen line and the perpendicular vector originating in the aryl center (the plane normal). The cases with d < 3.0 Å for F; and d < 3.5 Å for Cl, Br or I (outliers neglected), and , , 10 ± 5°, indicating predominating van der Waals forces, amount to several hundreds. The majority of fragments exhibit larger d and , values, in line with avoidance of electrostatic repulsion between the negative partial charges of the halogens and the ,-cloud center, and with an increasing electrostatic attraction with the aromatic hydrogen atoms. The corresponding hydrogen bonds are characterized by longer distances d and by angle values of , > 60° (about 40 % of the fragments), with only very few cases close to linear hydrogen bonds (then with , = 90°). Compounds containing metal,halogen bonds were omitted in view of possible strong orientational interferences. The structures were screened with four different halogen binding modes, all of them containing the halogen attached to a carbon atom, but with different hybrizations at the connecting carbon centers. The results show only small differences in the distance distributions, with a slight preference for smaller , values for sp2 frameworks. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Contemporary and historical impacts of megaherbivores on the population structure of tree euphorbias in South African subtropical thicketAFRICAN JOURNAL OF ECOLOGY, Issue 1 2010Richard M. Cowling Abstract African elephant and black rhinoceros , both megaherbivores , impact negatively on the abundance of succulent plants, including tree succulents, in South Africa's subtropical thicket. We sampled 35 sites in subtropical thicket to assess historical and contemporary impacts of African elephant and black rhinoceros on the population structure of three species of succulent tree euphorbia. Population age structures were highly variable and showed no species-specific effects. Almost half the sites had growing populations dominated by young individuals. Sites having contemporary impacts had significantly fewer individuals in the 30,75 years age range, but this effect declined with increasing terrain slope. Eighty-one percent of sites assumed to have been impacted by megaherbivores historically had individuals that predated rhino and elephant extirpation in the region. This and other population age structure data indicate that megaherbivores and tree euphorbias coexisted historically on terrain of low relief. However, in areas not subject to contemporary impacts, euphorbia populations are likely to be much higher now than historically, owing to population relaxation after the extirpation of megaherbivores in the mid 1800s. Given the sensitivity of tree euphorbias to megaherbivore impacts, managers should consider monitoring the population structure of these species in order to identify thresholds of potential concern regarding megaherbivore impacts. Résumé L'éléphant et le rhinocéros africains , deux méga-herbivores , ont un impact négatif sur l'abondance de plantes succulentes, y compris des arbres succulents, dans les fourrés subtropicaux d'Afrique du Sud. Nous avons prélevé des échantillons dans 35 fourrés subtropicaux afin d'évaluer les impacts anciens et actuels des éléphants et des rhinos noirs africains sur la structure de la population de trois espèces d'euphorbes arborescentes succulentes. Les structures d'âges des populations étaient très variables et ne présentaient aucun effet spécifique des espèces. Près de la moitié des sites contenaient des populations en croissance dominées par de jeunes individus. Les sites qui présentaient des impacts actuels comptaient significativement moins d'individus de la classe d'âge comprise entre 30 et 75 ans, mais cet effet diminuait lorsque la pente du terrain s'accentuait. Quatre-vingt-un pour cent des sites supposés avoir subi jadis l'impact des méga-herbivores contenaient des individus qui dataient d'avant l'élimination des rhinos et des éléphants. Ceci, tout comme d'autres données sur la structure d'âge des populations, indique que les méga-herbivores et les euphorbes arborescentes ont longtemps coexisté sur les terrains de faible relief. Cependant, dans les zones qui ne subissent aucun impact actuel, les populations d'euphorbes sont susceptibles d'être beaucoup plus hautes aujourd'hui que jadis, en raison de la libération induite par l'élimination des méga-herbivores au milieu des années 1800. Etant donné la sensibilité des euphorbes arborescentes face aux impacts des méga-herbivores, les gestionnaires devraient envisager le suivi continu de la structure de la population de ces espèces afin de déterminer les seuils d'alerte potentiels en ce qui concerne les impacts des méga-herbivores. [source] New approaches for predicting protein retention time in hydrophobic interaction chromatography,JOURNAL OF MOLECULAR RECOGNITION, Issue 4 2006M. E. Lienqueo Abstract Hydrophobic interaction chromatography (HIC) is an important technique for the purification of proteins. In this paper, we review three different approaches for predicting protein retention time in HIC, based either on a protein's structure or on its amino-acidic composition, and we have extended one of these approaches. The first approach correlates the protein retention time in HIC with the protein average surface hydrophobicity. This methodology is based on the protein three-dimensional structure data and considers the hydrophobic contribution of the exposed amino acid residues as a weighted average. The second approach, which we have extended, is based on the high correlation level between the average surface hydrophobicity of a protein's hydrophobic interacting zone and its retention time in HIC. Finally, a third approach carries out a prediction of the average surface hydrophobicity of a protein, using only its amino-acidic composition, without knowing its three-dimensional structure. These models would make it possible to test different operating conditions for the purification of a target protein by computer simulations, and thus make it easier to select the optimal conditions, contributing to the rational design and optimization of the process. Copyright © 2006 John Wiley & Sons, Ltd. [source] New Keynesian Macroeconomics and the Term StructureJOURNAL OF MONEY, CREDIT AND BANKING, Issue 1 2010GEERT BEKAERT monetary policy; inflation target; term structure of interest rates; Phillips curve This article complements the structural New Keynesian macro framework with a no-arbitrage affine term structure model. Whereas our methodology is general, we focus on an extended macro model with unobservable processes for the inflation target and the natural rate of output that are filtered from macro and term structure data. We find that term structure information helps generate large and significant parameters governing the monetary policy transmission mechanism. Our model also delivers strong contemporaneous responses of the entire term structure to various macroeconomic shocks. The inflation target shock dominates the variation in the "level factor" whereas monetary policy shocks dominate the variation in the "slope and curvature factors." [source] Vibrational spectra of bis(L -ornithinium) chloride nitrate sulfateJOURNAL OF RAMAN SPECTROSCOPY, Issue 1 2005S. Ramaswamy Abstract The Raman and infrared absorption spectra of 2(C5H14N2O22+)·Cl,·NO3,·SO42, crystal containing three anions were recorded at room temperature and were interpreted in the light of crystal structure data. The presence of a carbonyl group was identified. The carboxylic group was found to exist as COOH. The formation of OH···O, NH···O and NH···Cl asymmetric hydrogen bonds contributes considerably to the crystal cohesion and is responsible for the changes in the position and intensity of several bands. The vibrational spectra show that the anions were found to coordinate through hydrogen bonding interactions to other ligands in the crystal. The lattice wavenumbers of the halide radical (chlorine anion) were also assigned in terms of hydrogen bond vibrations. Copyright © 2004 John Wiley & Sons, Ltd. [source] Error analysis in cross-correlation of sky maps: application to the Integrated Sachs,Wolfe detectionMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2007Anna Cabré ABSTRACT Constraining cosmological parameters from measurements of the Integrated Sachs,Wolfe effect requires developing robust and accurate methods for computing statistical errors in the cross-correlation between maps. This paper presents a detailed comparison of such error estimation applied to the case of cross-correlation of cosmic microwave background (CMB) and large-scale structure data. We compare theoretical models for error estimation with Monte Carlo simulations where both the galaxy and the CMB maps vary around a fiducial autocorrelation and cross-correlation model which agrees well with the current concordance , cold dark matter cosmology. Our analysis compares estimators both in harmonic and configuration (or real) space, quantifies the accuracy of the error analysis and discusses the impact of partial sky survey area and the choice of input fiducial model on dark energy constraints. We show that purely analytic approaches yield accurate errors even in surveys that cover only 10 per cent of the sky and that parameter constraints strongly depend on the fiducial model employed. Alternatively, we discuss the advantages and limitations of error estimators that can be directly applied to data. In particular, we show that errors and covariances from the jackknife method agree well with the theoretical approaches and simulations. We also introduce a novel method in real space that is computationally efficient and can be applied to real data and realistic survey geometries. Finally, we present a number of new findings and prescriptions that can be useful for analysis of real data and forecasts, and present a critical summary of the analyses done to date. [source] A very extended reionization epoch?MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 3 2005A. Melchiorri ABSTRACT The recent observations of cross temperature,polarization power spectra of the cosmic microwave background (CMB) made by the Wilkinson Microwave Anisotropy Probe (WMAP) satellite are in better agreement with a high value of the Thomson scattering optical depth ,, 0.17. This value is close to ,= 0.3, which is taken as the upper limit in the parameter extraction analysis made by the WMAP team. However, models with ,, 0.3 provide a good fit to current CMB data and are not significantly excluded when combined with large-scale structure data. By making use of a self-consistent reionization model, we verify the astrophysical feasibility of models with ,, 0.3. It turns out that current data on various observations related to the thermal and ionization history of the intergalactic medium are not able to rule out ,, 0.3. The possibility of a very extended reionization epoch can significantly undermine the WMAP constraints on crucial cosmological parameters such as the Hubble constant, the spectral index of primordial fluctuations and the amplitude of dark matter clustering. [source] The lepton asymmetry: the last chance for a critical-density cosmology?MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2001Julien Lesgourgues We use a wide range of observations to constrain cosmological models possessing a significant asymmetry in the lepton sector, which offer perhaps the best chance of reconciling a critical-density Universe with current observations. The simplest case, with massless neutrinos, fails to fit many experimental data and does not lead to an acceptable model. If the neutrinos have mass of order 1 eV (which is favoured by some neutrino observations), then models can be implemented which prove a good fit to the microwave anisotropies and large-scale structure data. However, taking into account the latest microwave anisotropy results, especially those from BOOMERANG, we show that the model can no longer accommodate the observed baryon fraction in clusters. Together with the observed acceleration of the present Universe, this puts considerable pressure on such critical-density models. [source] Collectin structure: A reviewPROTEIN SCIENCE, Issue 9 2000Kjell Håkansson Abstract Colleetins are animal calcium dependent lectins that target the carbohydrate structures on invading pathogens, resulting in the agglutination and enhanced clearance of the microorganism. These proteins form trimers that may assemble into larger oligomers. Each polypeptide chain consists of four regions: a relatively short N-terminal region, a collagen like region, an ,-helical coiled-coil, and the lectin domain. Only primary structure data are available for the N-terminal region, while the most important features of the collagen-like region can be derived from its homology with collagen. The structures of the ,-helical coiled-coil and the lectin domain are known from crystallographic studies of mannan binding protein (MBP) and lung surfactant protein D (SP-D). Carbohydrate binding has been structurally characterized in several complexes between MBP and carbohydrate; all indicate that the major interaction between carbohydrate and collectin is the binding of two adjacent carbohydrate hydroxyl group to a collectin calcium ion. In addition, these hydroxyl groups hydrogen bond to some of the calcium amino acid ligands. While each collectin trimer contains three such carbohydrate binding sites, deviation from the overall threefold symmetry has been demonstrated for SP-D, which may influence its binding properties. The protein surface between the three binding sites is positively charged in both MBP and SP-D. [source] Short-term dynamics and long-term recolonization of protozoa in soilTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2005SINA M. ADL Most studies of Protozoa in the soil are based on the "most probable number" (MPN) estimates from cultured sub-samples. This approach has been criticized in recent years by protistologists. In order to work around these criticisms, we have tried to develop a set of procedures that rely on direct counts, without culturing. We show that the method is more sensitive and requires less effort than the MPN approach. Our species extractions focus on "active species at the time of sampling", and we tried to estimate the variation between days, as species adjust to soil moisture and temperature changes over several days. These variations are compared to species composition and abundance fluctuations observed between seasons, in decomposing leaf litter bags. We also obtained abundance and community structure data based on samples from a 25-year agro-ecosystem chronosequence under no-tillage management. We found that direct count methods, without prior culturing of samples, were more sensitive in detecting changes over several days, over several months, and in decadal succession from field samples. This provides a great advantage over culture-based methods that generally fail to distinguish between encysted and re-activated species. [source] Generation and Evaluation of a Homology Model of PfGSK-3ARCHIV DER PHARMAZIE, Issue 6 2009Sebastian Kruggel Abstract Plasmodial GSK-3 is a potential new target for malaria therapy. For a structure-based design project, the three-dimensional information of the designated target is needed. Unfortunately, experimental structure data for plasmodial GSK-3 is not yet available. Homology building can be used to generate such three-dimensional structure data using structure information of a homologous protein. GSK-3 possesses a very flexible ATP-binding site, a fact reflected in the variety of X-ray structures of the human GSK-3, which are deposited in the protein data base and are crystallized with different ligands. We used ten different HsGSK-3, templates for the model building of plasmodial GSK-3 and generated 200 models for each template with different modeling protocols. The quality of the models was evaluated with different tools. The results of these evaluations were used to calculate a rank-by-rank consensus score. The top models of this were used to compile an ensemble of PfGSK-3 models that reflect the flexibility of the ATP-binding site and that will be used for the structure-based design of potential ATP-binding site inhibitors of PfGSK-3. [source] Mesoscale Patterns in the Floristic Composition of Forests in the Central Western Ghats of Karnataka, IndiaBIOTROPICA, Issue 4 2010B. R. Ramesh ABSTRACT We describe the mesoscale floristic patterns in the central Western Ghats of Karnataka, India, through combined analysis of woody species abundance and stand structure data from a network of ninety-six 1-ha sampling plots spread across 22,000 km2. A total of 61,906 individuals (,10 cm gbh) comprising 400 plant species from 254 genera and 75 families were recorded. Euphorbiaceae, Rubiaceae, Lauraceae and Moraceae families constituted 23.5 percent of the total number of species encountered. The relative dominance of species was skewed with Poecilonueron indicum, Xylia xylocarpa, Terminalia tomentosa and Anogeissus latifolia being dominant in some plots. Correspondence analysis (CA) and a nonmetric multidimensional scaling (NMDS) of plots by species abundances data showed similar arching patterns, with significant correlation between the first axis of CA and NMDS (r=0.77). Hierarchical clustering of plot scores along the three first CA axes resulted in splitting the plots into five different categories that broadly reflect the major bioclimatic features of the region. A multiscale bootstrapping test indicated that categorization of the wettest (wet evergreen group 1 and 2) and driest (dry deciduous) groups were robust (P<0.05 with 1000 bootstraps), while the remaining two transitional groups were uncertain (P=0.12 and 0.26 for moist deciduous and semi-evergreen group, respectively). Principal component analysis revealed that plots with similar floristic composition can encompass contrastingly different physiognomic structures (canopy cover, canopy height and mean tree diameter) probably in relation to their levels of disturbance. Observed patterns in the floristic composition have been discussed in the light of the complex interaction between the bioclimatic and disturbance regimes that characterize the region. [source] | |||||||||||||