SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

RNA-Seq, a method using next generation sequencing technologies to sequence the transcriptome, facilitates genome-wide analysis of splice junction sites. In this paper, we introduce SOAPsplice, a robust tool to detect splice junctions using RNA-Seq data without using any information of known splice junctions. SOAPsplice uses a novel two-step approach consisting of first identifying as many reasonable splice junction candidates as possible, and then, filtering the false positives with two effective filtering strategies. In both simulated and real datasets, SOAPsplice is able to detect many reliable splice junctions with low false positive rate. The improvement gained by SOAPsplice, when compared to other existing tools, becomes more obvious when the depth of sequencing is low. SOAPsplice is freely available at http://soap.genomics.org.cn/soapsplice.html

A Comprehensive Expression Profile of MicroRNAs in Porcine Pituitary

MicroRNAs (miRNAs) are an abundant class of small RNAs that regulate expressions of most genes. miRNAs play important roles in the pituitary, the “master” endocrine organ.However, we still don't know which role miRNAs play in the development of pituitary tissue or how much they contribute to the pituitary function. By applying a combination of microarray analysis and Solexa sequencing, we detected a total of 450 miRNAs in the porcine pituitary. Verification with RT-PCR showed a high degree of confidence for the obtained data. According to the current miRBase release17.0, the detected miRNAs included 169 known porcine miRNAs, 163 conserved miRNAs not yet identified in the pig, and 12 potentially new miRNAs not yet identified in any species, three of which were revealed using Northern blot. The pituitary might contain about 80.17% miRNA types belonging to the animal. Analysis of 10 highly expressed miRNAs with the Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the enriched miRNAs were involved not only in the development of the organ but also in a variety of inter-cell and inner cell processes or pathways that are involved in the function of the organ

A chromosome conformation capture ordered sequence of the barley genome

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Detection of splice junctions and gene fusions via short read alignment

published_or_final_versionComputer ScienceMasterMaster of Philosoph

Study on the matching rules and control mechanisms between flocculants and slurry settlement characteristics

In order to realise efficient, economic, low carbon and environmentally friendly slurry disposal, floc sedimentation velocity ( S _f ), supernatant volume ( V _s ), water content of bottom mud ( W _b ), supernatant turbidity ( N _s ) and pH value were determined by slurry sedimentation tests, specific resistance tests, and water quality analysis. Orthogonal tests were performed to analyze the matching rule and control mechanism between flocculants and the slurry settlement characteristics. The results show that polyaluminum chloride (PAC) and polyferric chloride (PFC) had a low dose and a fast sedimentation rate. The sedimentation effect of 20 ionic degree cationic polyacrylamide (CPAM-20) in organic flocculant is the best. Although flocculants can shorten the sedimentation time, excessive flocculants can also weaken the slurry separation effect. The sedimentation efficiency of organic flocculants is higher than that of inorganic flocculants, but it is easy to form foam on the supernatant surface. For the composite flocculants, the sensitivity sequence of S _f , V _s and W _b is PAC>CPAM-20>PFC. PAC plays a controlling role in the sedimentation effect of the slurry

Researches on grounding modes of the AC/DC hybrid system with various distributed renewable energy

With the considerable demand for distributed renewable energy and the significant increase of generalised DC loads, such as IT equipment, DC air-conditioner, electric vehicle, the traditional AC distribution network is no longer efficient. Driven by the rapid development of power electronics technology, the AC/ DC hybrid system is an effective way for large capacity AC/DC sources and loads efficient integrated. To ensure the stable operation of AC/DC hybrid system, the grounding mode analysis is necessary, which is the precondition for overvoltage analysis, lightning arrester configuration, and protection design. To select grounding mode of AC/DC hybrid system, the detailed system structure scheme is first determined considering the factors such as integrated object, reliability requirement, capacity of sources and loads, and converter type. Then the main connection scheme is selected considering the principle of line insulation, economy, and reliability. Based on the system structure and main connection scheme, a suitable grounding mode is selected for the AC/DC hybrid system with various distributed renewable energy, by weighing various factors such as power supply reliability, protection sensitivity, insulation level, and personal safety

Fabricating the Superhydrophobic Nickel and Improving Its Antifriction Performance by the Laser Surface Texturing

The superhydrophobic surface can change the friction property of the material, reduce the adhesion of the friction interface, and produce a certain slip, thereby reducing the friction coefficient. The laser has high energy, high density, and is especially suitable for the surface treatment of materials. The laser surface texturing is a good way to construct superhydrophobic surfaces. The experiment uses a nanosecond pulse laser to construct the groove texture on the nickel surface. The contact area between the air and the droplets retained on the rough surface is increased, effectively preventing the water droplets from entering the gully of the surface microstructure, reducing the water droplets and the solid surface. The contact area ultimately makes the surface exhibit excellent superhydrophobicity. A superhydrophobic nickel surface having an apparent contact angle of water (ACAW) of 160° and a sliding angle (SA) of less than 10° was prepared. The MM-W1B vertical universal friction and wear tester was used to test the groove texture samples with different depths. The surface texture can capture the wear debris generated by the wear and store the lubricant, which is beneficial to the formation of fluid dynamic pressure lubrication and improve the load. The friction coefficient is reduced from 0.65 of the unprocessed surfaces to 0.25 after the texturing, and the friction performance is greatly improved

Large-complex-surface defect detection by hybrid gradient threshold segmentation and image registration

Machine vision-based object detection techniques have been widely used in product inspection, defect detection, and dimension measurement. These techniques have largely improved the efficiency of industrial production and increased the level of production autonomy. However, demands on advance hardware design and image processing algorithms are needed for the quality inspection of a large-complex-surface. In order to solve this problem, a hybrid surface defect detection method is developed. An image of the product surface is first divided into two areas: background with similar features and special pattern area, such as product trademarks. For the background area, defects have significant differences in gray intensity from the normal area. Fault detection is conducted using a gradient threshold segmentation method that can limit segmentation errors arising from uneven illuminations. For the special pattern area, image registration and image difference are adopted to detect defects, which are adaptive to irregular image contents with discontinuous shapes and appearances. Experimental results indicate that the proposed method achieves about 1.21 times and 2.94 times higher accuracy, in F-measure, for large-complex-surface defect detection than the traditional methods of gradient threshold segmentation and template matching, respectively. The proposed image processing technique can be applied in product quality inspections

Monitoring Roadbed Stability in Permafrost Area of Qinghai–Tibet Railway by MT-InSAR Technology

Permafrost areas pose a threat to the safe operation of linear projects such as the Qinghai–Tibet railway due to the repeated alternating effects of frost heaving and thawing settlement of frozen soil in permafrost area. Time series InSAR technology can effectively obtain ground deformation information with an accuracy of up to millimeters. Therefore, it is of great significance to use time series InSAR technology to monitor the deformation of the permafrost section of the Qinghai–Tibet railway. This study uses multi-time InSAR (MT-InSAR) technology to monitor the deformation of the whole section of the Qinghai–Tibet railway, detect the uneven settlement of the railway roadbed in space, and detect the seasonal changes in the roadbed in the time domain. At the same time, the local deformation sections over the years are compared and discussed. The time series deformation monitoring results of the permafrost section Sentinel-1 data in 2020 show that the length of the railway roadbed from Tanggula station to Za’gya Zangbo station (TZ) section is approximately 620 m, the deformation of the east and west sides is uneven, and the average annual deformation difference is 60.68 mm/a. The impact of frozen soil in WangKun station to Budongquan station (WB) section on railway roadbed shows the distribution characteristics of high in the middle and low at both ends, and the maximum annual average settlement can reach −158.46 mm/a. This study shows that the deformation of permafrost varies with different ground layers. The impact of human activities on frozen soil deformation is less than that of topography and hydrothermal conditions. At the same time, the study determined that compared with other sections, the roadbed deformation of TZ and WB sections is more obvious