Identification of single stranded regions of DNA by enzymatic digestion with matrix-assisted laser desorption/ionization analysis

Elucidating structure function relationships of DNA in cellular processes requires fast, reliable methods that can be applied to picomole amounts of sample. Higher order structure can be inferred by distinguishing paired and unpaired regions. It is shown here that enzymatic digestion coupled with product analysis by matrix-assisted laser desorption ionization (MALDI) is able to identify unpaired bases within structured DNA regions. The method is demonstrated with DNA duplexes having a five nucleotide mismatch as a 5' overhang, a 3' overhang, and an internal loop. Exo- and endonuclease digestions are performed under solution conditions (temperature, annealing, and enzyme buffers) which promote base pairing and specific enzyme activity. For each type of mismatch, the length and sequence of the single stranded region can be inferred from MALDI spectra taken as a function of digestion time.     

Symmetry restoration in the asymmetric linear σ model at finite temperature

TheSU(2)xSU(2) asymmetric linear sigma model is studied in a mean field approximation. A first order transition persists up to a critical value of the symmetry breaking term where it terminates at a higher order point. For the physical value of the symmetry breaking we only see remmants of the phase transition.     

Filtrations, mixed complexes, and cyclic homology in mixed characteristic

We describe an approach to computing cyclic homology suited to ground rings of characteristicp or mixed characteristic. We illustrate the method by computing HC for coordinate rings of affine plane curves and for maximal orders of semisimple algebras.Partially supported by NSF Grant No. DMS-8807203 and NSA Grant No. MDA 904-92-H-3026.     

Optimizing neural network architectures using generalization error estimators

This paper addresses the optimization of neural network architectures. It is suggested to optimize the architecture by selecting the model with minimal estimated averaged generalization error. We consider a least-squares (LS) criterion for estimating neural network models, i.e., the associated model weights are estimated by minimizing the LS criterion. The quality of a particular estimated model is measured by the average generalization error. This is defined as the expected squared prediction error on a novel input-output sample averaged over all possible training sets. An essential part of the suggested architecture optimization scheme is to calculate an estimate of the average generalization error. We suggest using the GEN-estimator [9, 10] which allows for dealing with nonlinear, incomplete models, i.e., models which are not capable of modeling the underlying nonlinear relationship perfectly. In most neural network applications, it is impossible to suggest a perfect model, and consequently the ability to handle incomplete models is urgent. A concise derivation of the GEN-estimator is provided, and its qualities are demonstrated by comparative numerical studies.The Computational Neural Network Center, Electronics Institute, The Technical University of Denmark, Building 349. Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Radiofizika, Vol. 37, No. 9, pp. 1131–1147, September, 1994.     

A column switching technique for the determination of lidocaine and its metabolites in horse urine

Summary A rapid method is described for the determination of lidocaine and its metabolites in horse urine using a column switching technique and HPLC analysis. This procedure offers a sensitive assay without the need for time consuming extractions.     

Alternating-Sign Matrices and Domino Tilings (Part II)

We continue the study of the family of planar regions dubbed Aztec diamonds in our earlier article and study the ways in which these regions can be tiled by dominoes. Two more proofs of the main formula are given. The first uses the representation theory of GL(n). The second is more combinatorial and produces a generating function that gives not only the number of domino tilings of the Aztec diamond of order n but also information about the orientation of the dominoes (vertical versus horizontal) and the accessibility of one tiling from another by means of local modifications. Lastly, we explore a connection between the combinatorial objects studied in this paper and the square-ice model studied by Lieb.     

Breather trapping and breather transmission in a DNA model with an interface

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard-Bishop model is augmented with a term that includes the dipole-dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.