Two-phase analysis in consensus genetic mapping.

Numerous mapping projects conducted on different species have generated an abundance of mapping data. Consequently, many multilocus maps have been constructed using diverse mapping populations and marker sets for the same organism. The quality of maps varies broadly among populations, marker sets, and software used, necessitating efforts to integrate the mapping information and generate consensus maps. The problem of consensus genetic mapping (MCGM) is by far more challenging compared with genetic mapping based on a single dataset, which by itself is also cumbersome. The additional complications introduced by consensus analysis include inter-population differences in recombination rate and exchange distribution along chromosomes; variations in dominance of the employed markers; and use of different subsets of markers in different labs. Hence, it is necessary to handle arbitrary patterns of shared sets of markers and different level of mapping data quality. In this article, we introduce a two-phase approach for solving MCGM. In phase 1, for each dataset, multilocus ordering is performed combined with iterative jackknife resampling to evaluate the stability of marker orders. In this phase, the ordering problem is reduced to the well-known traveling salesperson problem (TSP). Namely, for each dataset, we look for order that gives minimum sum of recombination distances between adjacent markers. In phase 2, the optimal consensus order of shared markers is selected from the set of allowed orders and gives the minimal sum of total lengths of nonconflicting maps of the chromosome. This criterion may be used in different modifications to take into account the variation in quality of the original data (population size, marker quality, etc.). In the foregoing formulation, consensus mapping is considered as a specific version of TSP that can be referred to as "synchronized TSP." The conflicts detected after phase 1 are resolved using either a heuristic algorithm over the entire chromosome or an exact/heuristic algorithm applied subsequently to the revealed small non-overlapping regions with conflicts separated by non-conflicting regions. The proposed approach was tested on a wide range of simulated data and real datasets from maize.

Estimation of soft X-ray and EUV transition radiation power emitted from the MIRRORCLE-type tabletop synchrotron.

The tabletop synchrotron light sources MIRRORCLE-6X and MIRRORCLE-20SX, operating at electron energies E(el) = 6 MeV and E(el) = 20 MeV, respectively, can emit powerful transition radiation (TR) in the extreme ultraviolet (EUV) and the soft X-ray regions. To clarify the applicability of these soft X-ray and EUV sources, the total TR power has been determined. A TR experiment was performed using a 385 nm-thick Al foil target in MIRRORCLE-6X. The angular distribution of the emitted power was measured using a detector assembly based on an NE102 scintillator, an optical bundle and a photomultiplier. The maximal measured total TR power for MIRRORCLE-6X is P(max) approximately equal 2.95 mW at full power operation. Introduction of an analytical expression for the lifetime of the electron beam allows calculation of the emitted TR power by a tabletop synchrotron light source. Using the above measurement result, and the theoretically determined ratio between the TR power for MIRRORCLE-6X and MIRRORCLE-20SX, the total TR power for MIRRORCLE-20SX can be obtained. The one-foil TR target thickness is optimized for the 20 MeV electron energy. P(max) approximately equal 810 mW for MIRRORCLE-20SX is obtained with a single foil of 240 nm-thick Be target. The emitted bremsstrahlung is negligible with respect to the emitted TR for optimized TR targets. From a theoretically known TR spectrum it is concluded that MIRRORCLE-20SX can emit 150 mW of photons with E > 500 eV, which makes it applicable as a source for performing X-ray lithography. The average wavelength, \overline\lambda = 13.6 nm, of the TR emission of MIRRORCLE-20SX, with a 200 nm Al target, could provide of the order of 1 W EUV.

Theory and characteristics of transition radiation emitted by low-energy storage-ring synchrotrons for use in X-ray lithography.

Existing theory is developed further for description of transition radiation (TR) emitted by low-energy storage-ring synchrotrons. It takes into account the fact that the dielectric constant of the TR target material is a complex function, introduces an expression for the number of passes of an injected electron through the target, and accounts more precisely for the absorption of TR. It is shown that the consideration of the complexity of the dielectric constant results in notable changes of the TR spectrum for emitted photons with energies close to the ionization energies of the target material. Since such TR is used mostly for performing X-ray lithography (XRL), the sensitivity of the photoresist used in XRL is formulated. Maximization of this resist sensitivity can be used for designing optimum targets for XRL. Study of the transmission of TR through a commonly used XRL mask, and its partial absorption in a common photoresist, illustrates that TR emission with E = [490, 1860] eV is most useful for performing such XRL, while E approximately equal to 1 keV is best. It is shown that, for a particular target material, a target consisting of only one foil emits the most TR energy. Optimization of an Al target, based on maximization of the resist sensitivity, indicates that a target containing one Al foil with a thickness of about 200 nm would be best for performing XRL by our low-energy storage-ring synchrotron MIRRORCLE-20SX.

Constructing large-scale genetic maps using an evolutionary strategy algorithm.

This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with approximately 50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

Flow-graph approach for optical analysis of planar structures.

The flow-graph approach (FGA) is applied to optical analysis of isotropic stratified planar structures (ISPS's) at inclined light incidence. Conditions for the presence of coherent and noncoherent light interaction within ISPS's are determined. Examples of the use of FGA for calculation of the transmission and the reflection of two-layer ISPS's for different types of light interaction are given. The advantages of the use of FGA for optical analysis of ISPS's are discussed.