Finding optimal threshold for correction error reads in DNA assembling

Background: DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DNA assembly algorithms. Existing algorithms, e.g. ECINDEL and SRCorr, correct the error reads by considering the number of times each length-k substring of the reads appear in the input. They treat those length-k substrings appear at least M times as correct substring and correct the error reads based on these substrings. However, since the threshold M is chosen without any solid theoretical analysis, these algorithms cannot guarantee their performances on error correction. Results: In this paper, we propose a method to calculate the probabilities of false positive and false negative when determining whether a length-k substring is correct using threshold M. Based on this optimal threshold M that minimizes the total errors (false positives and false negatives). Experimental results on both real data and simulated data showed that our calculation is correct and we can reduce the total error substrings by 77.6% and 65.1% when compared to ECINDEL and SRCorr respectively. Conclusion: We introduced a method to calculate the probability of false positives and false negatives of the length-k substring using different thresholds. Based on this calculation, we found the optimal threshold to minimize the total error of false positive plus false negative. © 2009 Chin et al; licensee BioMed Central Ltd.published_or_final_versio

Coralline Sr/Ca and Mg/Ca thermometer for the northern South China Sea: calibration and primary application high resolution on high-resolution SST reconstructing

利用全谱直读等离子体光谱(ICP2AES) 的分析方法精确分析了南海珊瑚的SrPCa 和MgPCa 比值,结合实测表层海水温度(SST),标定了海南岛南部三亚海域和西沙海域两个滨珊瑚的SrPCa 和MgPCa 温度计。在此基础上,尝试对两个南海北部全新世时期的珊瑚进行SST记录重建。结果显示约540aB.P. (小冰期) 西沙海域夏季月均SST 较现代低约1℃,而约6 500aB.P. (大暖期) 海南岛三亚海域夏季月均SST则高出现代1.0～1.5℃。The method for precisely and simultaneously measuring the coralline Sr/Ca and Mg/Ca ratios was established using inductively coupled plasma atomic emission spectrometry (ICP-AES). Using this method, the high-resolution Sr/Ca and Mg/Ca ratios of two Porites lutea from Sanya, South Hainan Island and Xisha Islands were measured. By comparing to the instrumentally measured sea surface temperatures in these two areas, the coralline Sr/Ca thermometer and the Mg/Ca thermometer were calibrated. These two thermometers can provide SST records with an error bar < 0.2℃, and they are suitable for high-resolution SST reconstructions in these areas. Based on these two thermometers, two short SST records were reconstructed from two Holocene Porites corals of the northern South China Sea. The results indicated that the monthly summer SSTs in Xisha Islands at about 540 years ago (the Little Ice Age) were 1℃ lower than that at present, and the monthly summer SSTs in Sanya, southern Hainan Island at 6 500 years ago (the Megathermal) were about 1℃ to 1 5℃ higher than that at present.published_or_final_versio

High incidence of thrombophilia detected in Chinese patients with venous thrombosis

Venous thromboembolism is rare in Chinese. To determine the incidence and disease profile of thrombophilia in Chinese patients with thrombosis, 52 unselected Chinese patients with documented venous thrombosis were studied for the presence of thrombophilia. Levels of antithrombin III (AT III), protein C (PC) and protein S (PS) as well as the presence of acquired lupus anticoagulant (LA) and anticardiolipin antibody (ACA) were investigated. Thirty patients were found to be abnormal. These consisted of 5 AT III deficiencies, 9 PC deficiencies, 10 PS deficiencies, 1 combined PC and PS deficiency (all in the heterozygous range), and 5 patients with LA and/or ACA. When the patients with LA and/or ACA are excluded, the incidence of hereditary thrombophilia is 25/47 i.e. 53.2% which is much higher than those reported in studies of Caucasian patients selected under strict criteria. Family studies performed in 16 cases of hereditary thrombophilia revealed involvement in 11 cases (68.7%); a total of 36 heterozygous family members were affected, most of which remain asymptomatic. Although 35 events predisposing to thrombosis (27 pregnancies, 1 oral contraceptive consumption and 7 surgical operations) were identified among these index patients, and the heterozygous family members, thrombosis was observed on only 6 occasions (17.1%). The data suggest that pregnancy and surgery do not carry the same degree of thrombotic risk in Chinese as in the Caucasian population with heterozygous AT III, PC and PS deficiency.published_or_final_versio

Isolation and Purification of Sesquiterpene Lactones from Ixeris sonchifolia (Bunge) Hance by High-Speed Counter- Current Chromatography and Semi-Preparative High Performance Liquid Chromatography

Purpose: To isolate and purify sesquiterpene lactones from Ixeris sonchifolia (Bunge) Hance by highspeed counter-current chromatography (HSCCC).Methods: I. sonchifolia was extracted with water and then loaded on a glass column (10 ~ 1500 cm containing 3000g D101 macroporous resin) where various concentrations of aqueous ethanol (0, 10, 30, 50, and 95 %) were used to elute the column successively. The 50 % ethanol fraction was  purified by HSCCC using a solvent system comprised of ethyl acetate: n-butanol: methanol: water (4: 6: 1: 20, v/v), and semi-preparative high performance liquid chromatography (HPLC). The chemical structures of thecomponents obtained were further confirmed by high-resolution mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMR).Results: Three compounds, including ixerin Z1 (0.7 mg), ixerin Z (11.4 mg), and 11, 13α-dihydroixerin Z (8.2 mg), with purity of 96.2, 98.2, and 98.4 %, respectively, were obtained from 200 mg each of the 50 % ethanol fraction.Conclusion: HSCCC is a rapid and effective method for isolating and purifying sesquiterpene lactones from I. sonchifolia.Keywords: Sesquiterpene lactones, High-speed counter-current chromatography, Ixeris sonchifolia, Ixerin, 13α-Dihydroixeri

Design and Testing of Cesium Atomic Concentration Detection System Based on TDLAS

In order to better build the Neutral Beam Injector with Negative Ion Source (NNBI), the pre-research on key technologies has been carried out for the Comprehensive Research Facility for Fusion Technology (CRAFT). Cesium seeding into negative-ion sources is a prerequisite to obtain the required negative hydrogen ion. The performance of ion source largely depends on the cesium conditions in the source. It is very necessary to quantitatively measure the amount of cesium in the source during the plasma on and off periods (vacuum stage). This article uses the absorption peak of cesium atoms near 852.1nm to build a cesium atom concentration detection system based on Tunable Diode Laser Absorption Spectroscopy (TDLAS) technology. The test experiment based on the cesium cell is carried out, obtained the variation curve of cesium concentration at different temperatures. The experimental results indicate that: the system detection range is within 5*10E6-2.5*10E7 pieces/cm3 and the system resolution better than 1*10E6 pieces/cm3.Comment: 8 pages,7 figures, the 20th International Symposium on Laser-Aided Plasma Diagnostic

Variation of structural vibration characteristics versus non-uniform temperature distribution

Author name used in this manuscript: You-Lin Xu2010-2011 > Academic research: refereed > Publication in refereed journalAccepted ManuscriptPublishe

Genome maps across 26 human populations reveal population-specific patterns of structural variation.

Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range genome analysis platforms, such as optical mapping, one can identify large SVs (&gt;2 kb) across the genome in one experiment. Analyzing optical genome maps of 154 individuals from the 26 populations sequenced in the 1000 Genomes Project, we find that phylogenetic population patterns of large SVs are similar to those of single nucleotide variations in 86% of the human genome, while ~2% of the genome has high structural complexity. We are able to characterize SVs in many intractable regions of the genome, including segmental duplications and subtelomeric, pericentromeric, and acrocentric areas. In addition, we discover ~60 Mb of non-redundant genome content missing in the reference genome sequence assembly. Our results highlight the need for a comprehensive set of alternate haplotypes from different populations to represent SV patterns in the genome

Mapping the unconventional orbital texture in topological crystalline insulators

The newly discovered topological crystalline insulators (TCIs) harbor a complex band structure involving multiple Dirac cones. These materials are potentially highly tunable by external electric field, temperature or strain and could find future applications in field-effect transistors, photodetectors, and nano-mechanical systems. Theoretically, it has been predicted that different Dirac cones, offset in energy and momentum-space, might harbor vastly different orbital character, a unique property which if experimentally realized, would present an ideal platform for accomplishing new spintronic devices. However, the orbital texture of the Dirac cones, which is of immense importance in determining a variety of materials properties, still remains elusive in TCIs. Here, we unveil the orbital texture in a prototypical TCI Pb$_{1-x}$Sn$_x$Se. By using Fourier-transform (FT) scanning tunneling spectroscopy (STS) we measure the interference patterns produced by the scattering of surface state electrons. We discover that the intensity and energy dependences of FTs show distinct characteristics, which can directly be attributed to orbital effects. Our experiments reveal the complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands in this new class of topological materials, which could provide a different pathway towards future quantum applications