Mining expressed sequences for single nucleotide polymorphisms in Pacific abalone Haliotis discus hannai

Although single nucleotide polymorphisms (SNPs) are important resources for population genetics, pedigree analysis and genomic mapping, such loci have not been reported in Pacific abalone so far. In this study, a bioinformatics strategy was adopted to discover SNPs within the expressed sequences (ESTs) of Pacific abalone, Haliotis discus hannai, and furthermore, polymerase chain reaction direct sequencing (PCR-DS) and allele-specific PCR (AS-PCR) were used for SNPs detection and genotype scoring respectively. A total of 5893 ESTs were assembled and 302 putative SNPs were identified. The average density of SNPs in ESTs was 1%. Fifty-two sets of sequencing primers were designed from SNPs flanking ESTs to amplify the genomic DNA, and 13 could generate products of expected size. Polymerase chain reaction direct sequencing of the amplification products from pooled DNA samples revealed 40 polymorphic SNP loci. Using a modified tetra-primer AS-PCR, seven mitochondrial and six nuclear SNPs were typed and characterized among 37 wild abalones. In conclusion, it is feasible to discover SNPs from number limited ESTs and the AS-PCR as a simple, robust and reliable assay could be a primary method for small- and medium-scale SNPs detection in abalones as well as other non-model organisms.

The Relationship between Decision Trees and the Scale of Train Data Set

Decision Trees need train samples in the train data set to get classification rules. If the number of train data was too small, the important information might be missed and thus the model could not explain the classification rules of data. While it is not affirmative that large scale of train data set can get well model. This Paper analysis the relationship between decision trees and the train data scale. We use nine decision tree algorithms to experiment the accuracy, complexity and robustness of decision tree algorithms. Some results are demonstrated.

Critical Sensitivity and Trans-Scale Fluctuations in Catastrophic Rupture

Rupture in the heterogeneous crust appears to be a catastrophe transition. Catastrophic rupture sensitively depends on the details of heterogeneity and stress transfer on multiple scales. These are difficult to identify and deal with. As a result, the threshold of earthquake-like rupture presents uncertainty. This may be the root of the difficulty of earthquake prediction. Based on a coupled pattern mapping model, we represent critical sensitivity and trans-scale fluctuations associated with catastrophic rupture. Critical sensitivity means that a system may become significantly sensitive near catastrophe transition. Trans-scale fluctuations mean that the level of stress fluctuations increases strongly and the spatial scale of stress and damage fluctuations evolves from the mesoscopic heterogeneity scale to the macroscopic scale as the catastrophe regime is approached. The underlying mechanism behind critical sensitivity and trans-scale fluctuations is the coupling effect between heterogeneity and dynamical nonlinearity. Such features may provide clues for prediction of catastrophic rupture, like material failure and great earthquakes. Critical sensitivity may be the physical mechanism underlying a promising earthquake forecasting method, the load-unload response ratio (LURR).

Toughness Of Ni/Al2O3 Interfaces As Dependent On Micron-Scale Plasticity And Atomistic-Scale Separation

Ceramic/metal interfaces were studied that fail by atomistic separation accompanied by plastic dissipation in the metal. The macroscopic toughness of the specific Ni alloy/Al2O3 interface considered is typically on the order of ten times the atomistic work of separation in mode I and even higher if combinations of mode I and mode II act on the interface. Inputs to the computational model of interface toughness are: (i) strain gradient plasticity applied to the Ni alloy with a length parameter determined by an indentation test, and (ii) a potential characterizing mixed mode separation of the interface fit to atomistic results. The roles of the several length parameters in the strain gradient plasticity are determined for indentation and crack growth. One of the parameters is shown to be of dominant importance, thus establishing that indentation can be used to measure the relevant length parameter. Recent results for separation of Ni/Al2O3 interfaces computed by atomistic methods are reviewed, including a set of results computed for mixed mode separation. An approximate potential fit to these results is characterized by the work of separation, the peak separation stress for normal separation and the traction-displacement relation in pure shearing of the interface. With these inputs, the model for steady-state crack growth is used to compute the toughness of the interface under mode I and under the full range of mode mix. The effect of interface strength and the work of separation on macroscopic toughness is computed. Fundamental implications for plasticity-enhanced toughness emerge.

Derivation Of A Nonlinear Reynolds Stress Model Using Renormalization Group Analysis And Two-Scale Expansion Technique

Adopting Yoshizawa's two-scale expansion technique, the fluctuating field is expanded around the isotropic field. The renormalization group method is applied for calculating the covariance of the fluctuating field at the lower order expansion. A nonlinear Reynolds stress model is derived and the turbulent constants inside are evaluated analytically. Compared with the two-scale direct interaction approximation analysis for turbulent shear flows proposed by Yoshizawa, the calculation is much more simple. The analytical model presented here is close to the Speziale model, which is widely applied in the numerical simulations for the complex turbulent flows.

Lithography-independent and large scale fabrication of a metal electrode nanogap

A lithography-independent and wafer scale method to fabricate a metal nanogap structure is demon-strated. Polysilicon was first dry etched using photoresist (PR) as the etch mask patterned by photolithography.Then, by depositing conformal SiO_2 on the polysilicon pattern, etching back SiO_2 anisotropically in the perpendic-ular direction and removing the polysilicon with KOH, a sacrificial SiO_2 spacer was obtained. Finally, after metal evaporation and lifting-off of the SiO_2 spacer, an 82 nm metal-gap structure was achieved. The size of the nanogap is not determined by the photolithography, but by the thickness of the SiO_2. The method reported in this paper is compatible with modern semiconductor technology and can be used in mass production.

Ten Years of the Relative Risk Model and Regional Scale Ecological Risk Assessment

It has been 10 years since the publication of the relative risk model (RRM) for regional scale ecological risk assessment. The approach has since been used successfully for a variety of freshwater, marine, and terrestrial environments in North America, South America, and Australia. During this period the types of stressors have been expanded to include more than contaminants. Invasive species, habitat loss, stream alteration and blockage, temperature, change in land use, and climate have been incorporated into the assessments. Major developments in the RRM have included the extensive use of geographical information systems, uncertainty analysis using Monte Carlo techniques, and its application to retrospective assessments to determine causation. The future uses of the RRM include assessments for forestry and conservation management, an increasing use in invasive species evaluation, and in sustainability. Developments in risk communication, the use of Bayesian approaches, and in uncertainty analyses are on the horizon.

Structural evolution of tensile deformed high-density polyethylene at elevated temperatures: Scanning synchrotron small- and wide-angle X-ray scattering studies

The structural evolution of an ice-quenched high-density polyethylene (HDPE) subjected to uniaxial tensile deformation at elevated temperatures was examined as a function of the imposed strains by means of combined synchrotron small-angle X-ray scattering (SAXS) and wide-angle X-ray scattering (WAXS) techniques. The data show that when stretching an isotropic sample with the spherulitic structure, intralamellar slipping of crystalline blocks was activated at small deformations, followed by a stress-induced fragmentation and recrystallization process yielding lamellar crystallites with their normal parallel to the stretching direction. Stretching of an isothermally crystallized HDPE sample at 120 degrees C exhibited changes of the SAXS diagram with strain similar to that observed for quenched HDPE elongated at room temperature, implying that the thermal stability of the crystal blocks composing the lamellae is only dependent on the crystallization temperature.