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Now showing items 1 - 16 of 25

  • MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

    Niu, B.   Ye, K.   Zhang, Q.   Lu, C.   Xie, M.   McLellan, M. D.   Wendl, M. C.   Ding, L.  

    Motivation: Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR-electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.
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  • FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

    Niu, B.   Zhu, Z.   Fu, L.   Wu, S.   Li, W.  

    Fragment recruitment, a process of aligning sequencing reads to reference genomes, is a crucial step in metagenomic data analysis. The available sequence alignment programs are either slow or insufficient for recruiting metagenomic reads. We implemented an efficient algorithm, FR-HIT, for fragment recruitment. We applied FR-HIT and several other tools including BLASTN, MegaBLAST, BLAT, LAST, SSAHA2, SOAP2, BWA and BWA-SW to recruit four metagenomic datasets from different type of sequencers. On average, FR-HIT and BLASTN recruited significantly more reads than other programs, while FR-HIT is about two orders of magnitude faster than BLASTN. FR-HIT is slower than the fastest SOAP2, BWA and BWA-SW, but it recruited 1-5 times more reads.
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  • Coevolutionary Structure-Redesigned-Based Bacterial Foraging Optimization

    Niu, B.   Liu, J.   Wu, T.   Chu, X.H.   Wang, Z.X.   Liu, Y.M.  

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  • State-resolved dynamics of infrared photodesorption of CO from Ag(111)

    Fleck, L.   Niu, B.   Beuhler, R.J.   White, M.G.  

    We present state-resolved measurements for IR (1.17 eV, 1064 nm) photodesorption of CO physisorbed on a Ag(lll) surface. State-resolved detection of desorbed CO is performed via (1+1') resonant multiphoton ionization (REMPI) using coherent VUV radiation and time-of-flight mass spectrometry. The observed rotational and translational state distributions are well described by Maxwell-Boltzmann distributions with characteristic temperatures which indicate near equilibration of the rotational and translational degrees of freedom. These results are consistent with a photo-induced "thermal" desorption mechanism and are compared with the predictions of the classical heat-diffusion model
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  • Effect of solid solution formation on densification of spark plasma sintered ZrC ceramics with TiC as sintering aid

    Niu, B.   Zhang, F.   Ji, W.   Zhang, J. Y.   Fu, Z. Y.   Wang, W. M.  

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  • Minimal alveolar concentration of sevoflurane for induction of isoelectric electroencephalogram in middle-aged adults

    Niu, B.   Fang, Y.   Miao, J. M.   Yu, Y.   Cao, F.   Chen, H. X.   Zhang, Z. G.   Mei, W.   Tian, Y. K.  

    We determined the minimal alveolar concentration (MAC) of sevoflurane inducing an isoelectric EEG in 50 of adult subjects (MACie). We included 31 middle-aged subjects; 30 subjects finished the study protocol and received sevoflurane at preselected concentrations according to a modified Dixon up-and-down design starting at 1.7 vol with 0.2 vol steps size. General anaesthesia was induced and maintained with sevoflurane; tracheal intubation was facilitated with cisatracurium. After a period of 30 min before skin incision, the state of isoelectric EEG was considered as significant when a burst suppression ratio of 100 lasted for 1 min. The haemodynamic responses to skin incision and the vasopressor requirement to maintain stable haemodynamic status were also analysed according to the EEG state. MACie was 3.5 (95 confidence interval, 3.43.7) in middle-aged subjects. When compared with subjects not in isoelectric EEG state, subjects in isoelectric EEG state received more phenylephrine to maintain stable haemodynamics (10 of 10 compared with 7 of 20 subjects, P0.001) and experienced less sympathetic responses to skin incision (1 of 10 compared with 11 of 20 subjects, P0.024). MACie for sevoflurane was 2.1 times MAC for immobilization in phenobarbital premedicated middle-aged adults. Sevoflurane-induced isoelectric EEG state is associated with significant cardiovascular depression but reduced haemodynamic responses to skin incision.
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  • Sevoflurane-induced isoelectric EEG and burst suppression: differential and antagonistic effect of added nitrous oxide

    Niu, B.   Xiao, J. Y.   Fang, Y.   Zhou, B. Y.   Li, J.   Cao, F.   Tian, Y. K.   Mei, W.  

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  • PRMT5 enhances generation of induced pluripotent stem cells from dairy goat embryonic fibroblasts via down-regulation of p53

    Chu, Z.   Niu, B.   Zhu, H.   He, X.   Bai, C.   Li, G.   Hua, J.  

    ObjectivesProtein arginine methyltransferase 5 (PRMT5), is thought to play a role in epigenetic reprogramming of mouse germ cells. However, up to now there has been little information concerning its expression profile and effects on generation of induced pluripotent stem cells (iPSCs) from somatic cells, in livestock. Here, we have explored PRMT5 expression profiles in dairy goats and its consequences to derivation of iPSCs from dairy goat embryonic fibroblasts (GEFs). Materials and methodsWe investigated effects of PRMT5 on iPS-like cells production in vitro. alkaline phosphatase (AP) staining, QRT-PCR and western blotting analysis of expression of related markers were used to evaluate efficiency of generation of iPSCs derived from GEFs. ResultsThese showed PRMT5 to be a conservative gene widely expressed in various tissues and different-aged testes. PRMT5 overexpression in combination with OCT3/4, SOX2, KLF4 and C-MYC (POSKM) significantly increased number of AP positive iPS-like colony-derived GEFs compared to OSKM alone, in our dairy goats. Moreover, our results demonstrated that PRMT5 overexpression stimulated GEF proliferation and down-regulated p53, p21 (a target gene of p53) and the apoptotic marker caspase 3, to enhance somatic cell reprogramming. ConclusionThis study provides an efficient model for future studies on mechanisms underlying goat somatic cell reprogramming and differentiation.
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  • The Genome of the Plant Growth-Promoting Rhizobacterium Paenibacillus polymyxa M-1 Contains Nine Sites Dedicated to Nonribosomal Synthesis of Lipopeptides and Polyketides

    Niu, B.   Rueckert, C.   Blom, J.   Wang, Q.   Borriss, R.  

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  • Alloying and thermal behaviour of CoCrFeNiMn\r 0.5\r Ti\r 0.5\r high-entropy alloy synthesised by mechanical alloying

    Niu, B.   Ji, W.   Li, N.   Zhang, F.   Wu, Y.  

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  • [IEEE 2014 IEEE Congress on Evolutionary Computation (CEC) - Beijing, China (2014.7.6-2014.7.11)] 2014 IEEE Congress on Evolutionary Computation (CEC) - Particle swarm optimization for Integrated Yard Truck Scheduling and Storage Allocation Problem

    Niu, B.   Xie, T.   Duan, Q. Q   Tan, L. J.  

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  • [IEEE 2014 International Conference on Information Science, Electronics and Electrical Engineering (ISEEE) - Sapporo, Japan (2014.4.26-2014.4.28)] 2014 International Conference on Information Science, Electronics and Electrical Engineering - Particle swarm optimization for the truck scheduling in container terminals

    Niu, B.   Xie, T.   Chan, Felix T. S.   Tan, L. J.   Wang, Z. X  

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  • The optical properties of high quality ZnO/ZnMgO quantum wells on Si(111) substrates

    Su, S. C.   Ling, C. C.   Lu, Y. M.   Mei, T.   Zhao, L. Z.   Niu, B.  

    The ZnO/Zn0.85Mg0.15O multiple quantum wells (MQWs) were fabricated on Si(111) substrates by plasma-assisted molecular beam epitaxy (P-MBE) using ZnMgO as buffer layers. The RHEED images indicated that the MQWs were of high quality. The free exciton (FE) emission line originated from the well region and its phonon replicas (FE-1LO, FE-2LO and FE-3LO) were observed in the 86K photoluminescence (PL) spectrum. Blueshift of the FE line in the MQW sample as compared to that in the ZnO bulk was found at temperatures as high as room temperature. Time-resolved PL study on the FE line showed a fast lifetime of 140 ps. The high quality of the MQW structure was revealed by the observation of the quantum-confinement-induced blueshift and shortened lifetime of the FE emission. (C) 2011 Elsevier Ltd. All rights reserved.
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  • Backward Hopf bifurcation in a mathematical model for oncolytic virotherapy with the infection delay and innate immune effects (September,10.1080/17513758.2019.1667443,2019)

    Guo, Y.   Niu, B.   Tian, J. P.  

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  • Alloying and thermal behaviour of CoCrFeNiMn0.5Ti0.5 high-entropy alloy synthesised by mechanical alloying

    Niu, B.   Ji, W.   Li, N.   Zhang, F.   Wu, Y.  

    An inequi-atomic CoCrFeNiMn0.5Ti0.5 high-entropy alloy (HEA) was synthesised by mechanical alloying. The structural and morphological evolution of the alloy powder during the mechanical alloying process and the thermal behaviour of 60 h ball-milled HEA powder were investigated systematically. A simple body-centred cubic solid solution HEA structure was obtained when the blended powder was ball-milled longer than 36 h. A 60 h ball-milled powder had an average particle size of 3 mm and consisted of hard agglomerated crystalline particles with a crystal size of <20 nm. The body-centred cubic phase transformed into a face-centred cubic phase when the powder was annealed for 1 h at a temperature of 700 degrees C; the liquidus point of the face-centred cubic phases was 1402.8 degrees C.
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  • Phylogenetic Characterization Genome Segment 2 of Bluetongue Virus Strains Belonging to Serotypes 5,7 and 24 Isolated for the First Time in China During 2012 to 2014

    Yang, H.   Xiao, L.   Wang, J.   Meng, J.   Lv, M.   Liao, D.   Song, J.   Gao, L.   Xiong, H.   He, Y.   Niu, B.   Chuang, X.   Li, H.  

    Bluetongue is endemic in China, and Bluetongue virus (BTV) strains belonging to eight different serotypes (BTV-1, BTV-2, BTV-3, BTV-4, BTV-9, BTV-12, BTV-15 and BTV-16) had been isolated between 1996 and 1997. However, there has been a long pause in investigating the epidemiology of BTV infection since then. During 2012-2014, eight BTV strains belonging to serotypes 5, 7 and 24 were isolated for the first time in Yunnan and Guangdong provinces from the blood of sentinel animals. Phylogenetic analyses of genome segment 2 of these Chinese BTV strains grouped them into nucleotypes E, F and A, respectively, along with the reference strains of the same serotype. For each serotype, Chinese strains cluster together closely to form a China's sublineage. In addition, these strains were most closely related to strains from Africa, indicating that they may share a recent common ancestry with African strains. To our knowledge, this is the first time that BTV-5, BTV-7 and BTV-24 strains have been isolated in South-East Asia. These data will be beneficial for understanding the BTV epidemiology and improving diagnostic assays and control measures against bluetongue in China and its neighbouring countries in the Asia-Pacific region.
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