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Linear Form (linear + form)
Selected AbstractsBent and Linear Forms of the (,-Oxo)bis[trichloroferrate(III)] Dianion: An Intermolecular Effect , Structural, Electronic and Magnetic PropertiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 23 2003Agustí Lledós Abstract We have analyzed the great diversity of Fe,O,Fe angles, 140,180°, found in the X-ray structures of the (,-oxo)bis[trichloroferrate(III)] dianion [Cl3FeOFeCl3]2, from both experimental and theoretical points of view. Theoretical calculations show that only the linear isomer is found as a minimum on the potential energy surface. Detailed analysis of the crystal packing indicates that the angular form is due to attractive intermolecular interactions. Analysis of a selected reduced set of the 45 crystal structures retrieved from the Cambridge Structural Database allowed us to classify the bending of the [Cl3FeOFeCl3]2, dianion in three categories, depending on the balance and strength of the intermolecular O···H,X contacts. A crystal diffraction study on the bis(benzyltrimethylammonium) salt has shown both bent (144.6°) and linear (180°) forms of the (,-oxo)bis[trichloroferrate(III)] dianion. The magnetic susceptibility of this compound has been fitted by assuming two equally weighted contributions (Jang and Jlin) of the two forms, considering Jang , Jlin estimated by theoretical calculations. The obtained Jang and Jlin of ,117 and ,133 cm,1 respectively, agree well with B3LYP results. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Determination of haplotypes from single DNA molecules: a method for single-molecule barcoding,,HUMAN MUTATION, Issue 9 2007Ming Xiao Abstract Determining the haplotypes in a diploid individual is a major technical challenge in genetic studies of human complex traits. Here we report a method of molecular haplotyping by directly imaging multiple polymorphic sites on individual DNA molecules simultaneously. DNA fragments amplified by long-range PCR were labeled with fluorescent dyes at each polymorphic site using a modified gap-filled padlock probe ligation approach. The labeled DNA molecules were then stretched into linear form on a functionalized glass surface and imaged with multicolor total internal reflection fluorescence (TIRF) microscopy. By determining the colors and positions of the fluorescent labels with respect to the backbone at polymorphic sites, the haplotype can be inferred accurately, in a manner similar to reading a barcode, even when the DNA fragments are not fully labeled. The feasibility of this technology is demonstrated by the determination of the haplotype of a 9.3-kbp DNA fragment containing four SNPs. Hum Mutat 28(9), 913,921, 2007. Published 2007 Wiley-Liss, Inc. [source] Influences of grass and moss on runoff and sediment yield on sloped loess surfaces under simulated rainfallHYDROLOGICAL PROCESSES, Issue 18 2006Chengzhong Pan Abstract It is important to evaluate the impacts of grasses on soil erosion process so as to use them effectively to control soil and water losses on the Loess Plateau. Laboratory-simulated rainfall experiments were conducted to investigate the runoff and sediment processes on sloped loess surfaces with and without the aboveground parts of grasses and moss (GAM: grass and moss; NGAM: no grass and moss) under slope gradients of 5°, 10°, 15°, 20°, 25° and 30°. The results show that runoff from GAM and NGAM plots increased up to a slope gradient of 10° and decreased thereafter, whereas the runoff coefficients increased with gradient. The average runoff rates and runoff coefficients of NGAM plots were less than those of GAM plots except for the 5° slope. This behaviour may be due to the reduction in water infiltration under moss. The difference between GAM and NGAM plots in average runoff rates varied from 1·4 to 8%. At the same gradients, NGAM plots yielded significantly (, = 0·05) more sediment than GAM plots. Average sediment deliveries for different slopes varied from 0·119 to 3·794 g m,2 min,1 from GAM plots, and from 0·765 to 16·128 g m,2 min,1 from NGAM plots. Sediment yields from GAM plots were reduced by 45 to 85%, compared with those from the NGAM plots. Plots at 30° yielded significantly higher sediments than at the other gradients. Total sediments S increased with slope gradients G in a linear form, i.e. S = 9·25G , 39·6 with R2 = 0·77*, for the GAM plots, and in an exponential model, i.e. S = 40·4 exp(0·1042G) with R2 = 0·93**, for the NGAM plots. In all cases, sediment deliveries decreased with time, and reached a relative steady state at a rainfall duration of 14 min. Compared with NGAM plots, the final percentage reductions in sediment delivery from GAM plots were higher than those at the initial time of rainfall at all slopes. Copyright © 2006 John Wiley & Sons, Ltd. [source] Having your water and drinking it too: resource limitation modifies density regulationJOURNAL OF ANIMAL ECOLOGY, Issue 1 2008COREY J. A. BRADSHAW Determining the interaction between extrinsic and intrinsic drivers of variation in population abundance through time continues to challenge ecologists. Chamaillé-Jammes and colleagues (this issue) examined African elephant time series to explore how water availability alters the density feedback mechanisms restricting population growth. The relationship between population growth rate and density shifted from an upward convex to a more linear form after controlling for rainfall. Spatial variation in water availability also attenuated density dependence as elephants adjusted their distribution relative to current environmental conditions. This work has important climate change implications for the conservation management of African herbivores. [source] Robust H, glucose control in diabetes using a physiological modelAICHE JOURNAL, Issue 12 2000Robert S. Parker A robust H, controller was developed to deliver insulin via a mechanical pump in Type I diabetic patients. A fundamental nonlinear diabetic patient model was linearized and then reduced to a third-order linear form for controller synthesis. Uncertainty in the nonlinear model was characterized by up to ±40% variation in eight physiological parameters. A sensitivity analysis identified the three-parameter set having the most significant effect on glucose and insulin dynamics over the frequency range of interest , = [0.002, 0.2] (rad/min). This uncertainty was represented in the frequency domain and incorporated in the controller design. Controller performance was assessed in terms of its ability to track a normoglycemic set point (81.1 mg/dL) in response to a 50 g meal disturbance. In the nominal continuous-time case, the controller maintained glucose concentrations within ±3.3 mg/dL of set point. A controller tuned to accommodate uncertainty yielded a maximum deviation of 17.6 mg/dL for the worst-case parameter variation. [source] THE ANALYSIS OF STRESS RELAXATION DATA OF SOME VISCOELASTIC FOODS USING A TEXTURE ANALYZER,JOURNAL OF TEXTURE STUDIES, Issue 4 2006H. SINGH ABSTRACT Uniaxial compression test for dough and several commercial products like jello, mozzarella cheese, cheddar cheese, tofu and sausage (cooked and uncooked) was performed using a texture analyzer (TA). Percent stress relaxation (%SR ), k1 (initial rate of relaxation), k2 (extent of relaxation) and relaxation time (RT) were calculated and compared for different products. The TA software was used to convert the raw SR data into a linear form. Constants k1 and k2 were determined from the intercept and slope of the linear data. Higher values of %SR and k2 (90 and 9, respectively) indicated higher elasticity for jello, whereas wheat flour dough samples showed the lowest values (20,30) for %SR and 1 to 2 for k2. The RT and k1 values were not good indicators for differentiating different products based on their viscoelastic behavior. Measurement of RT was limited by the maximum time for which the data were collected, whereas k1, because of its mathematical form, needed careful interpretation. In this study, %SR was found to be a good measure to interpret viscoelasticity of different food samples. [source] Linear least-squares method for unbiased estimation of T1 from SPGR signalsMAGNETIC RESONANCE IN MEDICINE, Issue 2 2008Lin-Ching Chang Abstract The longitudinal relaxation time, T1, can be estimated from two or more spoiled gradient recalled echo images (SPGR) acquired with different flip angles and/or repetition times (TRs). The function relating signal intensity to flip angle and TR is nonlinear; however, a linear form proposed 30 years ago is currently widely used. Here we show that this linear method provides T1 estimates that have similar precision but lower accuracy than those obtained with a nonlinear method. We also show that T1 estimated by the linear method is biased due to improper accounting for noise in the fitting. This bias can be significant for clinical SPGR images; for example, T1 estimated in brain tissue (800 ms < T1 < 1600 ms) can be overestimated by 10% to 20%. We propose a weighting scheme that correctly accounts for the noise contribution in the fitting procedure. Monte Carlo simulations of SPGR experiments are used to evaluate the accuracy of the estimated T1 from the widely-used linear, the proposed weighted-uncertainty linear, and the nonlinear methods. We show that the linear method with weighted uncertainties reduces the bias of the linear method, providing T1 estimates comparable in precision and accuracy to those of the nonlinear method while reducing computation time significantly. Magn Reson Med 60:496,501, 2008. © 2008 Wiley-Liss, Inc. [source] Association Models for Clustered Data with Binary and Continuous ResponsesBIOMETRICS, Issue 1 2010Lanjia Lin Summary We consider analysis of clustered data with mixed bivariate responses, i.e., where each member of the cluster has a binary and a continuous outcome. We propose a new bivariate random effects model that induces associations among the binary outcomes within a cluster, among the continuous outcomes within a cluster, between a binary outcome and a continuous outcome from different subjects within a cluster, as well as the direct association between the binary and continuous outcomes within the same subject. For the ease of interpretations of the regression effects, the marginal model of the binary response probability integrated over the random effects preserves the logistic form and the marginal expectation of the continuous response preserves the linear form. We implement maximum likelihood estimation of our model parameters using standard software such as PROC NLMIXED of SAS. Our simulation study demonstrates the robustness of our method with respect to the misspecification of the regression model as well as the random effects model. We illustrate our methodology by analyzing a developmental toxicity study of ethylene glycol in mice. [source] The Chemistry of Escapin: Identification and Quantification of the Components in the Complex Mixture Generated by an L -Amino Acid Oxidase in the Defensive Secretion of the Sea Snail Aplysia californicaCHEMISTRY - A EUROPEAN JOURNAL, Issue 7 2009Michiya Kamio Dr. Abstract A complex mixture of products in an enzymatic reaction: Aplysia californica releases amino acid oxidase and its substrate lysine in defensive secretions to produce a mixture of multiple compounds (see figure). Escapin is an L -amino acid oxidase in the ink of a marine snail, the sea hare Aplysia californica, which oxidizes L -lysine (1) to produce a mixture of chemicals which is antipredatory and antimicrobial. The goal of our study was to determine the identity and relative abundance of the constituents of this mixture, using molecules generated enzymatically with escapin and also using products of organic syntheses. We examined this mixture under the natural range of pH values for ink,from ,5 at full strength to ,8 when fully diluted in sea water. The enzymatic reaction likely forms an equilibrium mixture containing the linear form ,-keto-,-aminocaproic acid (2), the cyclic imine ,1 -piperidine-2-carboxylic acid (3), the cyclic enamine ,2 -piperidine-2-carboxylic acid (4), possibly the linear enol 6-amino-2-hydroxy-hex-2-enoic acid (7), the ,-dihydroxy acid 6-amino-2,2-dihydroxy-hexanoic acid (8), and the cyclic aminol 2-hydroxy-piperidine-2-carboxylic acid (9). Using NMR and mass spectroscopy, we show that 3 is the major component of this enzymatic product at any pH, but at more basic conditions, the equilibrium shifts to produce relatively more 4, and at acidic conditions, the equilibrium shifts to produce relatively more 2, 7, and/or 9. Studies of escapin's enzyme kinetics demonstrate that because of the high concentrations of escapin and L -lysine in the ink secretion, millimolar concentrations of 3, H2O2, and ammonia are produced, and also lower concentrations of 2, 4, 7, and 9 as a result. We also show that reactions of this mixture with H2O2 produce ,-aminovaleric acid (5) and ,-valerolactam (6), with 6 being the dominant component under the naturally acidic conditions of ink. Thus, the product of escapin's action on L -lysine contains an equilibrium mixture that is more complex than previously known for any L -amino acid oxidase. [source] Mechanism of DNA damage by cadmium and interplay of antioxidant enzymes and agentsENVIRONMENTAL TOXICOLOGY, Issue 2 2007Veera L. D. Badisa Abstract Cadmium is an environmental toxicant, which causes cancer in different organs. It was found that it damages DNA in the various tissues and cultured cell lines. To investigate the mechanism of DNA damage, we have studied the effect of cadmium-induced DNA damage in plasmid pBR322 DNA, and the possible ameliorative effects of antioxidative agents under in vitro conditions. It was observed that cadmium alone did not cause DNA damage. However, it caused DNA damage in the presence of hydrogen peroxide, in a dose dependent manner, because of production of hydroxyl radicals. Findings from this study show the conversion of covalently closed circular double-stranded pBR 322 DNA to the open circular and linear forms of DNA when treated with 10 ,M cadmium and various concentrations of H2O2. The conversion was due to nicking in DNA strands. The observed rate of DNA strand breakage was dependent on H2O2 concentration, temperature, and time. Metallothionein I failed to prevent cadmium-induced DNA nicking in the presence of H2O2. Of the two antioxidant enzymes (catalase and superoxide dismutase) studied, only catalase conferred significant (50,60%) protection. EDTA and DMSO exhibited protection similar to catalase, while mannitol showed only about 20% protection against DNA damage. Ethyl alcohol failed to ameliorate cadmium-induced DNA strands break. From this study, it is plausible to infer that cadmium in the presence of hydrogen peroxide causes DNA damage probably by the formation of hydroxyl ions. These results may indicate that cadmium in vivo could play a major role in the DNA damage induced by oxidative stress. © 2007 Wiley Periodicals, Inc. Environ Toxicol 22: 144,151, 2007. [source] Numerical error patterns for a scheme with hermite interpolation for 1 + 1 linear wave equationsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 5 2004Zuojin Zhu Abstract Numerical error patterns were presented when the fourth-order scheme based on Hermite interpolation was used to solve the 1 + 1 linear wave equation. Since most non-linear equations for real systems can be converted into linear forms by using proper transformations, this study certainly pertains its practical significance. The analytical solution was obtained under inhomogeneous initial and boundary conditions. It was found that not only the Hurst index of an error train at a given position but also its spatial distribution is dependent on the ratio of temporal to spatial intervals. The solution process with the fourth-order scheme based on Hermite interpolation diverges as the ratio is greater than unity. The results show that regular error pattern and smaller maxima of absolute values of numerical errors can be obtained when the ratio is set as unity; while chaotic phenomena for the numerical error propagation process can appear when the ratio is less than unity. It was found that it is better to choose the ratio as unity for the numerical solution of 1 + 1 linear wave equation with the scheme; while other selections for the ratio in the scheme can bring about chaotic patterns for the numerical errors. Copyright © 2004 John Wiley & Sons, Ltd. [source] Characterization of point mutations in the cdtA gene of the cytolethal distending toxin of Actinobacillus actinomycetemcomitansMOLECULAR MICROBIOLOGY, Issue 5 2005Linsen Cao Summary The Cdt is a family of gram-negative bacterial toxins that typically arrest eukaryotic cells in the G0/G1 or G2/M phase of the cell cycle. The toxin is a heterotrimer composed of the cdtA, cdtB and cdtC gene products. Although it has been shown that the CdtA protein subunit binds to cells in culture and in an enzyme-linked immunosorbent assay (CELISA) the precise mechanisms by which CdtA interacts with CdtB and CdtC has not yet been clarified. In this study we employed a random mutagenesis strategy to construct a library of point mutations in cdtA to assess the contribution of individual amino acids to binding activity and to the ability of the subunit to form biologically active holotoxin. Single unique amino acid substitutions in seven CdtA mutants resulted in reduced binding of the purified recombinant protein to Chinese hamster ovary cells and loss of binding to the fucose-containing glycoprotein, thyroglobulin. These mutations clustered at the 5,- and 3,-ends of the cdtA gene resulting in amino acid substitutions that resided outside of the aromatic patch region and a conserved region in CdtA homologues. Three of the amino acid substitutions, at positions S165N (mutA81), T41A (mutA121) and C178W (mutA221) resulted in gene products that formed holotoxin complexes that exhibited a 60% reduction (mutA81) or loss (mutA121, mutA221) of proliferation inhibition. A similar pattern was observed when these mutant holotoxins were tested for their ability to induce cell cycle arrest and to convert supercoiled DNA to relaxed and linear forms in vitro. The mutations in mutA81 and mutA221 disrupted holotoxin formation. The positions of the amino acid substitutions were mapped in the Haemophilus ducreyi Cdt crystal structure providing some insight into structure and function. [source] Homo- and heteropolynuclear copper(II) complexes containing a new diimine,dioxime ligand and 1,10-phenanthroline: synthesis, characterization, solvent-extraction studies, catalase-like functions and DNA cleavage abilitiesAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 12 2009Bülent Dede Abstract A series of homo-, heterodinuclear and homotrinuclear copper(II) complexes containing a new Schiff base ligand and 1,10-phenanthroline were synthesized. Based on results of elemental analyses, FTIR, 1H- and 13C-NMR spectra, conductivity measurements and magnetic susceptibility measurements, the complexes had general compositions {[Cu(L)(H2O)M(phen)2](ClO4)2 [M = Cu(II), Mn(II), Co(II)]} and {[Cu3(L)2(H2O)2](ClO4)2}. The metal:L:phen ratio is 2:1:2 for the dinuclear copper(II) complexes and the metal:L ratio was 3:2 for the trinuclear copper(II) complex. The liquid,liquid extraction of various transition metal cations [Mn(II), Co(II), Ni(II), Cu(II), Zn(II), Pb(II), Cd(II), Hg(II)] from the aqueous phase to the organic phase was carried out using the diimine,dioxime ligand. It was concluded that the ligand can effectively be used in solvent extraction of copper(II) from the aqueous phase to the organic phase. Furthermore, catalytic activitiy of the complexes for the disproportionation of hydrogen peroxide was also investigated in the presence of imidazole. Dinuclear copper(II),manganese(II) complex has some similarity to manganese catalase in structure and activity. The interaction between these complexes and DNA has also been investigated by agarose gel electrophoresis; we found that the homo- and heterodinuclear copper complexes can cleave supercoiled pBR322 DNA to nicked and linear forms in the presence of H2O2. Copyright © 2009 John Wiley & Sons, Ltd. [source] | ||||||||||||||||