Detecting chimeric 5''''l3''''UTRs with cross-chromosomal splicing by bioinformatics

The 5'/3' UTRs of mRNA are crucial in transla-tional regulation, and several serious diseases are believed tobe associated with abnormal splicing of these parts of themRNA sequence. In this work a novel method which usessequence alignment database searching for detecting chi-meric 5'3' UTRs with cross-chromosomal splicing is reported.Eight highly credible instances of cross-chromosomal splic-ing have been found using this method, representing addi-tional confirmation of the existence of cross-chromosomalsplicing events provided by bioinformatics tools. Since noconserved motif has been found in any of the eight instances,and at the same time current prediction algorithms produceonly trivial secondary structures at the "splicing sites", it isnot possible to identify any specific signal leading to thesplicing.     

A new method for splice site prediction based on the sequence patterns of splicing signals and regulatory elements

It is of significance for splice site prediction to develop novel algorithms that combine the sequence patterns of regulatory elements such as enhancers and silencers with the patterns of splicing signals. In this paper, a statistical model of splicing signals was built based on the entropy density profile （EDP） method, weight array method （WAM） and K test; moreover, the model of splicing regulatory elements was developed by an unsupervised self-learning method to detect motifs associated with regulatory elements. With two models incorporated, a multi-level support vector machine （SVM） system was devised to perform ab initio prediction for splice sites originating from DNA sequence in eukaryotic genome. Results of large scale tests on human genomic splice sites show that the new method achieves a comparative high performance in splice site prediction. The method is demonstrated to be with at least the same level of performance and usually better performance than the existing SpliceScan method based on modeling regulatory elements, and shown to have higher accuracies than the traditional methods with modeling splicing signals such as the GeneSplicer. In particular, the method has evident advantage over splice site prediction for the genes with lower GC content.     

Green chemistry: C-C coupling and asymmetric reduction by innovative catalysis

A catalytic method has been developed, which allows aryl halides to couple with various electron-rich olefins to give 1,1＇-substituted olefins. The palladium-catalysed coupling in ionic liquid solvent proceeds with high efficiency and remarkable regioselectivity without the need for any costly or toxic halide scavengers. Parallel to this, an environmentally-appealing method for the asymmetric reduction of ketones has been established, with which a variety of chiral alcohols can be accessed with high enantioselectivity in water with no need for any organic solvents. The same chemistry has been explored for the reduction of aldehydes, which is shown to be fast and highly chemoselective. These methods add new tools to the armoury of synthetic chemists.     

Green chemistry: C-C coupling and asymmetric reduction by innovative catalysis

A catalytic method has been developed, which allows aryl halides to couple with various electron-rich olefins to give 1,1’-substituted olefins. The palladium-catalysed coupling in ionic liquid solvent proceeds with high efficiency and remarkable regioselectivity without the need for any costly or toxic halide scavengers. Parallel to this, an environmentally-appealing method for the asymmetric reduction of ketones has been established, with which a variety of chiral alcohols can be accessed with high enantioselectivity in water with no need for any organic solvents. The same chemistry has been explored for the reduction of aldehydes, which is shown to be fast and highly chemoselective. These methods add new tools to the armoury of synthetic chemists.     

Magnetic fabrics in fault-related fold and its relation with finite strain: an example from Mingjiang thrust structures in Western Sichuan

The anisotropy of magnetic susceptibility (AMS) is a quick, effective and sensitive technique used to measure the weakly deformed sedimentary rocks, and also a reliable method to reveal the deforming mechanisms of fault-related folds. In Longmenshan front belt, a typical cross-section of fault-related folds is chosen to study the AMS. A total of 224 oriented specimens have been drilled at 23 different sampling sites which were distributed at the key structural positions of this structural section developed in the Xujiahe formation of the upper Triassic. Six elementary types of magnetic fabrics are recognized and established through this AMS study: Da sedimentary fabric; 2) an initial deformation fabric; 3) a pencil structure fabric; 4) a weak cleavage fabric; 5) a strong cleavage fabric; 6) a stretching lineation fabric. It has been found that most of magnetic fabrics are characterized by fabrics of weak deformation which belong to the pure-shear results of a pre-folding layer parallel shortening (LPS). In the fault-bend fold, almost all magnetic fabrics are the initial deformation fabrics of weak deformation, and denote that the deformation in the forelimb is stronger than that in the backlimb and no finite strain is shown in the footwall. While in the fault-propagation fold, finite strains are concentrated in the trishear zone where magnetic fabric results are approximately consistent with the estimated consequences of the kinematic model. The tectonic stress field indicated by the magnetic fabrics is basically the same along the whole structural section and shows a NW to SE compression and shortening which is accordant with the regional compressive stress field of the Longmenshan fold-thrust belt.     

Magnetic fabrics in fault-related fold and its relation with finite strain: an example from Mingjiang thrust structures in Western Sichuan

The anisotropy of magnetic susceptibility (AMS) is a quick, effective and sensitive technique used to measure the weakly deformed sedimentary rocks, and also a reliable method to reveal the deforming mechanisms of fault-related folds. In Longmenshan front belt, a typical cross-section of fault-related folds is chosen to study the AMS. A total of 224 oriented specimens have been drilled at 23 different sampling sites which were distributed at the key structural positions of this structural section developed in the Xujiahe formation of the upper Triassic. Six elementary types of magnetic fabrics are recognized and established through this AMS study: 1) a sedimentary fabric; 2) an initial deformation fabric; 3) a pencil structure fabric; 4) a weak cleavage fabric; 5) a strong cleavage fabric; 6) a stretching lineation fabric. It has been found that most of magnetic fabrics are characterized by fabrics of weak deformation which belong to the pure-shear results of a pre-folding layer parallel shortening (LPS). In the fault-bend fold, almost all magnetic fabrics are the initial deformation fabrics of weak deformation, and denote that the deformation in the forelimb is stronger than that in the backlimb and no finite strain is shown in the footwall. While in the fault-propagation fold， finite strains are concentrated in the trishear zone where magnetic fabric results are approximately consistent with the estimated consequences of the kinematic model. The tectonic stress field indicated by the magnetic fabrics is basically the same along the whole structural section and shows a NW to SE compression and shortening which is accordant with the regional compressive stress field of the Longmenshan fold-thrust belt.     

Delayed resistance to Cucumber mosaic virus mediated by 3′ UTR-derived hairpin RNA

RNA silencing has been shown to function in the plant antivirus defense response,leading to viral RNA degradation induced by vsiRNA-containing RISC cleavage activity.Cucumber mosaic virus(CMV) 3′UTR sequences share a high conservation of nucleotide sequence and secondary structures that are important for CMV replication.Here,in an attempt to simultaneously target the multiple genomic and subgenomic RNAs of CMV for degradation,CMV 3′UTR were used to design hairpin RNA(hpRNA) to transform tobacco(Xanthi.nc) so as to constitutively produce viral siRNAs.Most of the transgenic plants expressing CMV Q strain(Q-CMV,subgroup Ⅱ strain) RNA3 3′UTR-derived hpRNA showed de-layed resistance to Q-CMV infection and exhibited recovery phenotypes.Compared with Q-CMV-in-oculated leaves,the upper leaves showed weak or no disease symptoms and a reduced accumulation level of viral RNAs.Together with transient assays,our results indicate that the 3′UTR-derived siRNAs were biologically active in targeting viral RNA for degradation.Recovery resistance in transgenic plants was also observed against subgroup IB strain SD-CMV infection,indicating a broad-spectrum anti-CMV effect of the 3′UTR-based antiviral silencing.Northern blot assays indicated that there was no strong correlation between the degree of resistance and the accumulation level of 3′UTR-derived siRNAs,suggesting that to target a highly structured RNA,such as the CMV 3′UTR,the quantity of siRNAs may not be the only determinant of silencing efficiency.Target RNA secondary structures may also affect target accessibility,siRNA-containing RISC-target recognition and the consequent antiviral effect.     

Phase-field simulation on microstructure evolution of D0_(19) phase in γ/γ′structure of Co–Al–W superalloys

The morphological evolution and precipitation kinetics of γ′ and D0_(19)(Co_3 W) phase in Co–Al–W alloys at 900 °C have been studied by applying Phase-field method and experiment in order to understand the transformation process of γ′ phase and D0_(19) phase. The growth processes of D0_(19) phase and precipitation of γ′ phase under elastic fields were simulated through coupling with thermodynamics and dynamics databases. The simulation results indicate that the misfit δ≥ 0.53% has a greater impact on γ′ particle morphology in γ/γ′ structure.Co–Al–W alloy with low Al and high W is one of the factors to promote the precipitation of D0_(19) phase. Three stages during aging, namely the γ′ phase incubation stage, the γ′ phase fast nucleation and growth stage, and the transformation from γ′ phase to D0_(19) phase stage can be observed with the non-constant coarsening rate that varying with the decrease of γ′ phase. The particle size distribution(PSD) during the precipitation of D0_(19) phase is more in line with MLSW theory than LSW theory. This simulation results are in good agreement with the experiment results to help analyze microstructure evolution of Co–Al–W alloy.     

Manganese (Ⅲ) Acetate:A Versatile Reagent in Organic Chemistry

1 Results Free radical reactions have become increasingly important,as well as a very attractive tool,in organic synthesis within the last two decades,due to their powerful,selective,specific,and mild reaction abilities.Mn(OAc)3 mediated oxidative free radical reactions have been extensively developed in the last twenty years[1,6].Numerous regio-,chemo-,and stereoselective synthetic methods have been developed in both inter-and intramolecular reactions,and have detailed the progress of Mn(OAc)3 mediated oxidative free radical reactions. The selective oxidation of enones led to α′-acetoxy-enones by Mn(OAc)3 oxidation.In general,Mn(OAc)3 oxidations are characterized by higher α′-regioselectivity and chemical yields,and milder reaction conditions,in turn tolerating many sensitive functional groups.The use of Mn(OAc)3 in combination with other carboxylic acids or manganese(Ⅱ) carboxylates extends this methodology to the preparation of a variety of α′-acyloxyenones that are otherwise inaccessible in a one-step procedure.We developed a general method for the synthesis of biaryls starting from arylhydrazines and aromatic solvents in the presence of Mn(OAc)3.We showed for the first time that Mn(OAc)3 is a versatile reagent for the generation of aryl radicals from arylhydrazines.In a subsequent work,we extended this method for the synthesis of heterobiaryls,which was able to be achieved in thepresence of heteroaromatic compounds such as furan and thiophene. Another biaryl coupling reaction starting with arylboronic acids,mediated by Mn(OAc)3,was developed.The treatment of arylboronic acids with Mn(OAc)3 in benzene at reflux temperature afforded the corresponding biphenyl in high yields[7].     

Programmed cell death in Laminaria japonica (Phaeophyta) tissues infected with alginic acid decomposing bacterium

TdT-mediated dUTP-biotin nick end labeling (TUNEL) is a sensitive and valid method for detecting DNA cleavage in programmed cell death (PCD). Using this method, DNA cleavage was observed in Laminaria japonica sporophytic tissues, which were infected with alginic acid decomposing bacterium. It was found that DNA cleavage occurred 5 min after the infection, the fragments with 3′-OH groups of cleaved nuclear DNA increased with time of infection and spread from the infection site. Although no typical DNA ladder (200 bp/180 bp) was detected by routine agarose gel electrophoresis, the cleavage of nuclear DNA fragments of 97～48.5 kb could be detected by pulsed field gel electrophoresis (PFGE). By using CaspGLOWTM fluorescein active caspase-3 staining method, caspase-3 activity has been detected in response to the infection of alginic acid decomposing bacterium. Our results are similar to the observations in hypersensitive response (HR) of higher plant, suggesting that the rapid cell death of L. Japonica infected by alginic acid decomposing bacterium might be involved in PCD, and indicating that the occurrence of PCD is an active defense process against the pathogen's infection.     

Simulation of mode conversion at the magnetopause

Two-dimensional(2-D)and three-dimensional(3-D)hybrid simulations are carried out for mode conversion from fast mode compressional wave to kinetic Alfvn waves(KAWs)at the inhomogeneous magnetopause boundary.For cases in which the incident fast wave propagates in the xz plane,with the magnetopause normal along x and the background magnetic field pointing along z,the 2-D (xz)simulation shows that KAWs with large wave number kxρi～1 are generated near the Alfve′n resonance surface,whereρi is the ion Larmor radius.Several nonlinear wave properties are manifest in the mode conversion process.Harmonics of the driver frequency are generated.As a result of nonlinear wave interaction,the mode conversion region and its spectral width are broadened.In the 3-D simulation,after this first stage of the mode conversion to KAWs with large kx,a subsequent generation of KAW modes of finite ky is observed in the later stage,through a nonlinear parametric decay process.Since the nonlinear cascade to ky can lead to massive transport at the magnetopause,the simulation results provide an effective transport mechanism at the plasma boundaries in space as well as laboratory plasmas.     

SEM analysis of the changes of carbon layer structure of mesocarbon microbeads heat-treated at different temperatures

Mesocarbon microbeads (MCMB) with narrow size distribution, excellent sphericity and no obvious conglutination have been prepared with a coal tar pitch containing quinoline insolubles (QI) as the raw material. Optical microscopy and scanning electron microscopy (SEM) are used to examine the structure of the MCMB. It has been found that SEM technique shows the structural information of MCMB clearly in the form of micrographs even when the structure of MCMB is complex, while the optical technique is useful for analysis of the regular structure of the mesophase spheres but cannot be effectively used to analyze either the complex structure of the green MCMB or the structures of the further heat-treated ones at different temperatures. According to the characteristics of the carbon layers, the structures of the as-prepared MCMB in the present experiment could be classified as (I) Parallel Layer type structure and (2) Bent Layer type structure with the carbon layers gathering at one or two points in the MCMB. In the experiments, SEM is also utilized to investigate the structures of MCMB that are heat-treated at different temperatures. It has been found that the MCMB without any further heat-treatment show no layered-carbons, while the ones heat-treated at temperaturehigher than 1000℃ exhibit obvious layered carbons across their sections. When increasing the heat-treatment temperature, the carbon layers become thinner and flatter.     

COMPUTER SIMULATION OF TWO-DIMENSIONAL TEMPERATURE FIELD FOR CASTING SOLIDIFICATION

Based on the mathematical model of Fourier Heat Conductivity Equations, this paper firstchooses an alternating-direction-implicit (ADI) type of finite difference method as the numericalcalculation method which is absolutely convergent and stable for time steps of any size when usedto calculate the temperature field. Then, the generalized programs are designed with FORTRANlanguage which can be used to calculate two-dimensional temperature field of casting solidificationof cast steel or cast iron for any shape. The calculated results about their solidification tendencyobtained from the above programs are found in good agreement with the experimental ones. Inaddition, we have measured the thermal properties of the furane resin sand which is the mouldingmaterial to make steel ingot moulds.     

Splicing-site recognition of rice （Oryza sativa L. ） DNA sequences by support vector machines

Motivation: It was found that high accuracy splicing-site recognition of rice ( Oryza satlva L. ) DNA sequence is especially difficult. We described a new method for the splicing-site recognition of rice DNA sequences. Method: Based on the intron in eukaryotic organisms conforming to the principle of GT-AG, we used support vector machines (SVM) to predict the splicing sites. By machine learning, we built a model and used it to test the effect of the test data set of true and pseudo splicing sites. Results : The prediction accuracy we obtained was 87.53% at the true 5‘ end splicing site and 87.37% at the true 3‘ end splicing sites. The results suggested that the SVM approach could achieve higher accuracy than the previous approaches.     

Study of the interaction of DNA and histones by spin-stretching and droplet evaporation

Molecular combing is a powerful and simple method for aligning DNA molecules onto a surface. Using this technique combined with fluorescence microscopy, DNA-histone complexes are stretched on a hydrophobic polymethyl methacrylate (PMMA) surface and observed directly. We have developed a new method to stretch single DNA-histone complexes, termed spin-stretching. The results show that the histones markedly enhance DNA binding to the PMMA surface. DNA winds around the histones and therefore decreases in length. The number of histones that bind to each DNA molecule is found to correlate with the histone concentration. The combed DNA-histone complexes are found to depend on two factors: the binding force on the surface and the centrifugal force at its local position. Na+ ions should compete with histones for binding to DNA; however, the observed competitive binding effect of Na+ ions at low concentrations was negligible.     

MICkNN: Multi-Instance Covering kNN Algorithm

Mining from ambiguous data is very important in data mining. This paper discusses one of the tasks for mining from ambiguous data known as multi-instance problem. In multi-instance problem, each pattern is a labeled bag that consists of a number of unlabeled instances. A bag is negative if all instances in it are negative. A bag is positive if it has at least one positive instance. Because the instances in the positive bag are not labeled, each positive bag is an ambiguous. The mining aim is to classify unseen bags. The main idea of existing multi-instance algorithms is to find true positive instances in positive bags and convert the multi-instance problem to the supervised problem, and get the labels of test bags according to predict the labels of unknown instances. In this paper, we aim at mining the multi-instance data from another point of view, i.e., excluding the false positive instances in positive bags and predicting the label of an entire unknown bag. We propose an algorithm called Multi-Instance Covering kNN (MICkNN) for mining from multi-instance data. Briefly, constructive covering algorithm is utilized to restructure the structure of the original multi-instance data at first. Then, the kNN algorithm is applied to discriminate the false positive instances. In the test stage, we label the tested bag directly according to the similarity between the unseen bag and sphere neighbors obtained from last two steps. Experimental results demonstrate the proposed algorithm is competitive with most of the state-of-the-art multi-instance methods both in classification accuracy and running time.     

An Open Platform for Processing IFC Model Versions

The IFC initiative from the International Alliance of Interoperability has been developing since the mid-nineties through several versions. This paper addresses the problem of binding the growing number of IFC versions and their EXPRESS definitions to programming environments (Java and .NET). The solution developed in this paper automates the process of generating early binding classes, whenever a new version of the IFC model is released. Furthermore, a runtime instantiation of the generated early binding classes takes place by importing IFC-STEP ISO 10303-P21 models. The user can navigate the IFC STEP model with relevance to the defining EXPRESS-schema, modify, delete, and create new instances. These functionalities are considered to be a basis for any IFC based implementation. It enables researchers to experiment the IFC model independently from any software application.     

A Study on Modifying the Calculation Model of Valid Opening Size of Heat - bonded Nonwoven Fabrics

It has been found that there are marked errors in the value of valid opening size of heat-bonded nonwoven fabrics between theoretical calculations and engineering measurements. A new modified theoretical model is advanced in this paper. The equivalent diameter of the pore of a fibre web is used to calculate the valid opening size instead of the maximum diameter of inscribed circle used, because the fibres in practical fibre webs are flexible elastomers with definite diameters and the pore of fibre web may produce deformation in screening teat and engineering usage. The results show that the theoretical calculations coincide well with the engineering measurements. This method offers a theoretical basis for computer simulation to the performance of filters of heatbonded nonwoven fabrics.