Enhancing Terminal Deoxynucleotidyl Transferase Activity on Substrates with 3' Terminal Structures for Enzymatic De Novo DNA Synthesis.

Enzymatic oligonucleotide synthesis methods based on the template-independent polymerase terminal deoxynucleotidyl transferase (TdT) promise to enable the de novo synthesis of long oligonucleotides under mild, aqueous conditions. Intermediates with a 3' terminal structure (hairpins) will inevitably arise during synthesis, but TdT has poor activity on these structured substrates, limiting its usefulness for oligonucleotide synthesis. Here, we described two parallel efforts to improve the activity of TdT on hairpins: (1) optimization of the concentrations of the divalent cation cofactors and (2) engineering TdT for enhanced thermostability, enabling reactions at elevated temperatures. By combining both of these improvements, we obtained a ~10-fold increase in the elongation rate of a guanine-cytosine hairpin

Housing, health, and happiness

Despite the importance of housing for people's well-being, there has been little work done to assess the causal impact of housing and housing improvement programs on health and welfare. In this paper the authors help fill this gap by investigating the impact of a large-scale effort by the Mexican government to replace dirt floors with cement floors on child health and adult happiness. They find that replacing dirt floors with cement floors significantly reduces parasitic infestations in young children, reduces diarrhea, reduces anemia, and improves cognitive development. Finally, they also find that this program leave adults substantially better off, as measured by satisfaction with their housing and quality of life and by their significantly lower rates of depression and perceived stress.Health Monitoring&Evaluation,Disease Control&Prevention,Housing&Human Habitats,Access to Finance,Construction Industry

Reduction of computer usage costs in predicting unsteady aerodynamic loadings caused by control surface motions: Analysis and results

Results of theoretical and numerical investigations conducted to develop economical computing procedures were applied to an existing computer program that predicts unsteady aerodynamic loadings caused by leading and trailing edge control surface motions in subsonic compressible flow. Large reductions in computing costs were achieved by removing the spanwise singularity of the downwash integrand and evaluating its effect separately in closed form. Additional reductions were obtained by modifying the incremental pressure term that account for downwash singularities at control surface edges. Accuracy of theoretical predictions of unsteady loading at high reduced frequencies was increased by applying new pressure expressions that exactly satisified the high frequency boundary conditions of an oscillating control surface. Comparative computer result indicated that the revised procedures provide more accurate predictions of unsteady loadings as well as providing reduction of 50 to 80 percent in computer usage costs

Nucleon spin structure at very high-x

Dyson-Schwinger equation treatments of the strong interaction show that the presence and importance of nonpointlike diquark correlations within the nucleon are a natural consequence of dynamical chiral symmetry breaking. Using this foundation, we deduce a collection of simple formulae, expressed in terms of diquark appearance and mixing probabilities, from which one may compute ratios of longitudinal-spin-dependent u- and d-quark parton distribution functions on the domain x =1. A comparison with predictions from other approaches plus a consideration of extant and planned experiments shows that the measurement of nucleon longitudinal spin asymmetries on x =1 can add considerably to our capacity for discriminating between contemporary pictures of nucleon structure.Comment: 6 pages, 1 table, 3 figures. To appear in Phys. Lett.

Semi-geostrophic particle motion and exponentially accurate normal forms

We give an exponentially-accurate normal form for a Lagrangian particle moving in a rotating shallow-water system in the semi-geostrophic limit, which describes the motion in the region of an exponentially-accurate slow manifold (a region of phase space for which dynamics on the fast scale are exponentially small in the Rossby number). The result extends to numerical solutions of this problem via backward error analysis, and extends to the Hamiltonian Particle-Mesh (HPM) method for the shallow-water equations where the result shows that HPM stays close to balance for exponentially-long times in the semi-geostrophic limit. We show how this result is related to the variational asymptotics approach of [Oliver, 2005]; the difference being that on the Hamiltonian side it is possible to obtain strong bounds on the growth of fast motion away from (but near to) the slow manifold

Coping with dating errors in causality estimation

We consider the problem of estimating causal influences between observed processes from time series possibly corrupted by errors in the time variable (dating errors) which are typical in palaeoclimatology, planetary science and astrophysics. "Causality ratio" based on the Wiener-Granger causality is proposed and studied for a paradigmatic class of model systems to reveal conditions under which it correctly indicates directionality of unidirectional coupling. It is argued that in the case of a priori known directionality, the causality ratio allows a characterization of dating errors and observational noise. Finally, we apply the developed approach to palaeoclimatic data and quantify the influence of solar activity on tropical Atlantic climate dynamics over the last two millennia. A stronger solar influence in the first millennium A.D. is inferred. The results also suggest a dating error of about 20 years in the solar proxy time series over the same period

The practical application of a finite difference method for analyzing transonic flow over oscillating airfoils and wings

Separating the velocity potential into steady and unsteady parts and linearizing the resulting unsteady equations for small disturbances was performed. The steady velocity potential was obtained first from the well known nonlinear equation for steady transonic flow. The unsteady velocity potential was then obtained from a linear differential equation in complex form with spatially varying coefficients. Since sinusoidal motion is assumed, the unsteady equation is independent of time. The results of an investigation into the relaxation-solution-instability problem was discussed. Concepts examined include variations in outer boundary conditions, a coordinate transformation so that the boundary condition at infinity may be applied to the outer boundaries of the finite difference region, and overlapping subregions. The general conclusion was that only a full direct solution in which all unknowns are obtained at the same time will avoid the solution instabilities of relaxation. An analysis of the one-dimensional form of the unsteady transonic equation was studied to evaluate errors between exact and finite difference solutions. Pressure distributions were presented for a low-aspect-ratio clipped delta wing at Mach number of 0.9 and for a moderate-aspect-ratio rectangular wing at a Mach number of 0.875

Resonance energy transfer from a fluorescent dye molecule to plasmon and electron-hole excitations of a metal nanoparticle

We study the distance dependence of the rate of electronic excitation energy transfer from a dye molecule to a metal nanoparticle. Using the spherical jellium model, we evaluate the rates corresponding to the excitation of l = 1, 2, and 3 modes of the nanoparticle. Our calculation takes into account both the electron-hole pair and the plasmon excitations of the nanoparticle. The rate follows conventional R^-6 dependence at large distances while small deviations from this behavior are observed at shorter distances. Within the framework of the jellium model, it is not possible to attribute the experimentally observed d^-4 dependence of the rate to energy transfer to plasmons or e-h pair excitations.Comment: 4 figure

A user's guide for V174, a program using a finite difference method to analyze transonic flow over oscillating wings

The design and usage of a pilot program using a finite difference method for calculating the pressure distributions over harmonically oscillating wings in transonic flow are discussed. The procedure used is based on separating the velocity potential into steady and unsteady parts and linearizing the resulting unsteady differential equation for small disturbances. The steady velocity potential which must be obtained from some other program, is required for input. The unsteady differential equation is linear, complex in form with spatially varying coefficients. Because sinusoidal motion is assumed, time is not a variable. The numerical solution is obtained through a finite difference formulation and a line relaxation solution method

Computation of the transonic perturbation flow fields around two- and three-dimensional oscillating wings

Analytical and empirical studies of a finite difference method for the solution of the transonic flow about an harmonically oscillating wing are presented along with a discussion of the development of a pilot program for three-dimensional flow. In addition, some two- and three-dimensional examples are presented