Structural Polymorphism of the Nucleosomal DNA and Implications for Protein Binding

A nucleosome forms a basic unit of the chromosome structure. A biologically relevant question is how much of the nucleosomal conformational space is accessible to protein-free DNA, and what proportion of the nucleosomal conformations are induced by bound histones. To investigate this, we have analysed high resolution xray crystal structure datasets of DNA in protein-free as well as protein-bound forms, and compared the dinucleotide step parameters for the two datasets with those for high resolution nucleosome structures. Our analysis shows that most of the dinucleotide step parameter values for the nucleosome structures lie within the range accessible to protein-free DNA, indirectly indicating that the histone core plays more of a stabilizing role. The nucleosome structures are observed to assume smooth and nearly planar curvature, implying that ‘normal’ B-DNA like parameters can give rise to a curved geometry at the gross structural level. Different nucleosome

Modeling chickpea growth and development: Nitrogen accumulation and use

Quantitative information regarding nitrogen (N) accumulation and its distribution to leaves, stems and grains under varying environmental and growth conditions are limited for chickpea (Cicer arietinum L.). The information is required for the development of crop growth models and also for assessment of the contribution of chickpea to N balances in cropping systems. Accordingly, these processes were quantified in chickpea under different environmental and growth conditions (still without water or N deficit) using four field experiments and 1325 N measurements. N concentration ([N]) in green leaves was 50 mg g-1 up to beginning of seed growth, and then it declined linearly to 30 mg g-1 at the end of seed growth phase. [N] in senesced leaves was 12 mg g-1. Stem [N] decreased from 30 mg g-1 early in the season to 8 mg g-1 in senesced stems at maturity. Pod [N] was constant (35 mg g-1), but grain [N] decreased from 60 mg g-1 early in seed growth to 43 mg g-1 at maturity. Total N accumulation ranged between 9 and 30 g m-2. N accumulation was closely linked to biomass accumulation until maturity. N accumulation efficiency (N accumulation relative to biomass accumulation) was 0.033 g g-1 where total biomass was -2 and during early growth period, but it decreased to 0.0176 g g-1 during the later growth period when total biomass was >218 g m-2. During vegetative growth (up to first-pod), 58% of N was partitioned to leaves and 42% to stems. Depending on growth conditions, 37-72% of leaf N and 12-56% of stem N was remobilized to the grains. The parameter estimates and functions obtained in this study can be used in chickpea simulation models to simulate N accumulation and distribution.

A computerized methodology for structural synthesis of kinematic chains: Part 1- Formulation

In an effort to develop a fully computerized approach for structural synthesis of kinematic chains the steps involved in the method of structural synthesis based on transformation of binary chains [38] have been recast in a format suitable for implementation on a digital computer. The methodology thus evolved has been combined with the algebraic procedures for structural analysis [44] to develop a unified computer program for structural synthesis and analysis of simple jointed kinematic chains with a degree of freedom 0. Applications of this program are presented in the succeeding parts of the paper.

A computerized methodology for structural synthesis of kinematic chains: Part 2 - Application to several fully or partially known cases

The reliability of the computer program for structural synthesis and analysis of simple-jointed kinematic chains developed in Part 1 has been established by applying it to several cases for whuch solutions are either fully or partially available in the literature, such as 7-link, zero-freedom chains; 8- and 10-link, single-freedom chains; 12-link, single-freedom binary chains; and 9-link, two-freedom chains. In the process some discrepancies in the results reported in previous literature have been brought to light.

A computerized methodology for structural synthesis of kinematic chains: Part 3 - application to the new case of 10-link, three- freedom chains

The unified computer program for structural synthesis and analysis developed in Part 1 has been employed to derive the new and complete collection of 97 10-link, three-freedom simple-jointed kinematic chains. The program shows that of these chains, 3 have total freedom, 70 have partial freedom and the remaining 24 have fractionated freedom and that the 97 chains yield a total of 676 distinct mechanisms.

Modeling growth of hydrogen bubbles in aluminum castings using the level-set method

A new approach is proposed to solve for the growth as well as the movement of hydrogen bubbles during solidification in aluminum castings. A level-set methodology has been adopted to handle this multiphase phenomenon. A microscale domain is considered and the growth and movement of hydrogen bubbles in this domain has been studied. The growth characteristics of hydrogen bubbles have been evaluated under free growth conditions in a melt having a hydrogen input caused b solidification occurring around the microdomain.

An investigation of structural, magnetic and dielectric properties of R2NiMnO6 (R = rare earth, Y)

We have investigated the structure, magnetic and dielectric properties of the double perovskite oxides, R2NiMnO6 (R = Pr, Nd, Sm, Gd, Tb, Dy, Ho and Y). We could refine powder X-ray diffraction patterns of all the phases on the basis of monoclinic (P2(1)/n) double perovskite structure where Ni and Mn atoms are ordered at 2c and 2d sites, respectively. All the phases are ferromagnetic insulators exhibiting relatively low dielectric loss and dielectric constants in the range 15-25. The ferromagnetic ordering temperature of the R2NiMnO6 series seems to correlate better with the radius of R3+ atoms than with the average Ni-O-Mn angle (phi) in the double perovskite structure. These results are consistent with all samples having Mn4+ and Ni2+ With minimal antisite disorder.

Constitutive modeling of shape memory alloy wire with non-local rate kinetics

A constitutive modeling approach for shape memory alloy (SMA) wire by taking into account the microstructural phase inhomogeneity and the associated solid-solid phase transformation kinetics is reported in this paper. The approach is applicable to general thermomechanical loading. Characterization of various scales in the non-local rate sensitive kinetics is the main focus of this paper. Design of SMA materials and actuators not only involve an optimal exploitation of the hysteresis loops during loading-unloading, but also accounts for fatigue and training cycle identifications. For a successful design of SMA integrated actuator systems, it is essential to include the microstructural inhomogeneity effects and the loading rate dependence of the martensitic evolution, since these factors play predominant role in fatigue. In the proposed formulation, the evolution of new phase is assumed according to Weibull distribution. Fourier transformation and finite difference methods are applied to arrive at the analytical form of two important scaling parameters. The ratio of these scaling parameters is of the order of 10(6) for stress-free temperature-induced transformation and 10(4) for stress-induced transformation. These scaling parameters are used in order to study the effect of microstructural variation on the thermo-mechanical force and interface driving force. It is observed that the interface driving force is significant during the evolution. Increase in the slopes of the transformation start and end regions in the stress-strain hysteresis loop is observed for mechanical loading with higher rates.

Effect of Structural Modification on the Quantum-Size Effect in II-VI Semiconducting Nanocrystals

The electronic structure of group II-VI semiconductors in the stable wurtzite form is analyzed using state-of-the-art ab initio approaches to extract a simple and chemically transparent tight-binding model. This model can be used to understand the variation in the bandgap with size, for nanoclusters of these compounds. Results complement similar information already available for same systems in the zinc blende structure. A comparison with all available experimental data on quantum size effects in group II-VI semiconductor nanoclusters establishes a remarkable agreement between theory and experiment in both structure types, thereby verifying the predictive ability of our approach. The significant dependence of the quantum size effect on the structure type suggests that the experimental bandgap change at a given size compared to the bulk bandgap, may be used to indicate the structural form of the nanoclusters, particularly in the small size limit, where broadening of diffraction features often make it difficult to unambiguously determine the structure.

Application of Maclaurin Series in Structural Analysis

In the simple theory of flexure of beams, the slope, bending moment, shearing force, load and other quantities are functions of a derivative of y with respect to x. It is shown that the elastic curve of a transversely loaded beam can be represented by the Maclaurin series. Substitution of the values of the derivatives gives a direct solution of beam problems. In this paper the method is applied to derive the Theorem or three moments and slope deflection equations. The method is extended to the solution of a rigid portal frame. Finally the method is applied to deduce results on which the moment distribution method of analyzing rigid frames is based.

DNA structural variability as a factor in gene expression and evolution

Redundant DNA can buffer sequence dependent structural deviations from an ideal double helix. Buffering serves a mechanistic function by reducing extraneous conformational effects which could interfere with readout or which would impose energetic constraints on evolution. It also serves an evolutionary function by allowing for gradual variations in conformation-dependent regulation of gene expression. Such gradualism is critical for the rate of evolution. The buffer structure concept provides a new interpretation for repetitive DNA and for exons and introns.

Factors related to seat belt use : A Turkish case

Seat belts are effective safety devices used to protect car occupants from severe injuries and fatalities during road vehicle accidents. Despite the proven effectiveness of seat belts, seat belt use rates are quite low, especially in developing countries, such as Turkey. The general aim of the present study was to investigate a large variety of factors related to seat belt use among Turkish car occupants using different perspectives and methods and therefore, to contribute to the design of effective seat belt use interventions for increasing seat belt use rates in Turkey. Five sub-studies were conducted within the present study. In the first sub-study, environmental (e.g., road type) and psycho-social factors (e.g., belt use by other car occupants) related to the seat belt use of front-seat occupants were investigated using observation techniques. Being male, of a young age, and traveling on city roads were the main factors negatively related to seat belt use. Furthermore, seat belt use by the drivers and front-seat passengers was highly correlated and a significant predictors of each other. In the second sub-study, the motivations of the car occupants for seat belt use and non-use were investigated using interview techniques. Situational conditions, such as traveling on city roads and for short distances, and not believing in the effectiveness and relevance of seat belt use for safety, were the most frequently reported reasons for not using a seat belt. Safety, habit and avoiding punishment were among the most frequently reported reasons for using a seat belt. In the third sub-study, the Theory of Planned Behavior (TPB) and the Health Belief Model (HBM) were applied to seat belt use using Structural Equation Modeling techniques. The TPB model showed a good fit to the data, whereas the HBM showed a poor fit to the data. Within the TPB model, attitude and subjective norm were significant predictors of intentions to use a seat belt on both urban and rural roads. In the fourth sub-study, seat belt use frequency and motivations for seat belt use among taxi drivers were investigated and compared between free-time and work-time driving using a survey. The results showed that taxi drivers used seat belts more when driving a private car in their free-times compared to when driving a taxi during their work-times. The lack of a legal obligation to use a seat belt in city traffic and fear of being attacked or robbed by the passengers were found as two specific reasons for not using a seat belt when driving a taxi. Lastly, in the fifth sub-study, the relationship of seat belt use to driver and health behaviors was investigated using a survey. Although seat belt use was related both to health and driver behaviors, factor analysis results showed that it grouped with driver behaviors. Based on the results of the sub-studies, a tentative empirical model showing different predictors of seat belt use was proposed. According to the model, safety and normative motivations and perceived physical barriers related to seat belt use are the three important predictors of seat belt use. Keywords: Seat belt use; environmental factors; psycho-social factors; safety and normative motivations; the Theory of Planned Behavior; the Health Belief Model; health behaviors; driver behaviors; front-seat occupants; taxi drivers; Turkey.

Structural and functional characterization of dendritic arbors and GABAergic synaptic inputs on interneurons and principal cells in the rat basolateral amygdala

The basolateral amygdala (BLA) is a complex brain region associated with processing emotional states, such as fear, anxiety, and stress. Some aspects of these emotional states are driven by the network activity of synaptic connections, derived from both local circuitry and projections to the BLA from other regions. Although the synaptic physiology and general morphological characteristics are known for many individual cell types within the BLA, the combination of morphological, electrophysiological, and distribution of neurochemical GABAergic synapses in a three-dimensional neuronal arbor has not been reported for single neurons from this region. The aim of this study was to assess differences in morphological characteristics of BLA principal cells and interneurons, quantify the distribution of GABAergic neurochemical synapses within the entire neuronal arbor of each cell type, and determine whether GABAergic synaptic density correlates with electrophysiological recordings of inhibitory postsynaptic currents. We show that BLA principal neurons form complex dendritic arborizations, with proximal dendrites having fewer spines but higher densities of neurochemical GABAergic synapses compared with distal dendrites. Furthermore, we found that BLA interneurons exhibited reduced dendritic arbor lengths and spine densities but had significantly higher densities of putative GABAergic synapses compared with principal cells, which was correlated with an increased frequency of spontaneous inhibitory postsynaptic currents. The quantification of GABAergic connectivity, in combination with morphological and electrophysiological measurements of the BLA cell types, is the first step toward a greater understanding of how fear and stress lead to changes in morphology, local connectivity, and/or synaptic reorganization of the BLA.

NMR Spectroscopic and X-Ray Structural Studies of Two Diazadiphosphetidines

The crystal structures of the two diazadiphosphetidines, [PhNP(OCH2CF3)]2 (1) and [MeNP(NMe2)(O2C6H4)]2 (2) have been determined. The trifluoroethoxy groups in (1) have a trans orientation. The phosphorus chemical shift for (1) is at 189.8 δ. On standing in solution, (1) transforms slowly (∼ 10 days) and almost completely into its 'high-field' (cis) isomer (142.2δ).

Structural Damage Detection Using Modal Curvature and Fuzzy Logic

A fuzzy logic system (FLS) with a new sliding window defuzzifier is proposed for structural damage detection using modal curvatures. Changes in the modal curvatures due to damage are fuzzified using Gaussian fuzzy sets and mapped to damage location and size using the FLS. The first four modal vectors obtained from finite element simulations of a cantilever beam are used for identifying the location and size of damage. Parametric studies show that modal curvatures can be used to accurately locate the damage; however, quantifying the size of damage is difficult. Tests with noisy simulated data show that the method detects damage very accurately at different noise levels and when some modal data are missing.