Deep level transient spectroscopic study of oxygen implanted melt grown ZnO single crystal

Deep level traps in melt grown ZnO single crystal created by oxygen implantation and subsequent annealing in air were studied by deep level transient spectroscopy measurement between 80 and 300 K. The E C-0.29 eV trap (E3) was the dominant peak in the as-grown sample and no new defects were created in the as-O-implanted sample. The single peak feature of the deep level transient spectroscopy (DLTS) spectra did not change with the annealing temperature up to 750 °C, but the activation energy decreased to 0.22 eV. This was explained in terms of a thermally induced defect having a peak close to but inseparable from the original 0.29 eV peak. A systematic study on a wide range of the rate window for the DLTS measurement successfully separated the Arrhenius plot data originated from different traps. It was inferred that the E3 concentration in the samples did not change after the O-implantation. The traps at E C-0.11, E C-0.16 and E C-0.58 eV were created after annealing. The E C-0.16 eV trap was assigned to an intrinsic defect. No DLTS signal was found after the sample was annealed to 1200 °C. © 2011 IOP Publishing Ltd.postprin

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

PublishedEvaluation StudiesJournal ArticleResearch Support, Non-U.S. Gov'tRecently, several experimental techniques have emerged for probing RNA structures based on high-throughput sequencing. However, most secondary structure prediction tools that incorporate probing data are designed and optimized for particular types of experiments. For example, RNAstructure-Fold is optimized for SHAPE data, while SeqFold is optimized for PARS data. Here, we report a new RNA secondary structure prediction method, restrained MaxExpect (RME), which can incorporate multiple types of experimental probing data and is based on a free energy model and an MEA (maximizing expected accuracy) algorithm. We first demonstrated that RME substantially improved secondary structure prediction with perfect restraints (base pair information of known structures). Next, we collected structure-probing data from diverse experiments (e.g. SHAPE, PARS and DMS-seq) and transformed them into a unified set of pairing probabilities with a posterior probabilistic model. By using the probability scores as restraints in RME, we compared its secondary structure prediction performance with two other well-known tools, RNAstructure-Fold (based on a free energy minimization algorithm) and SeqFold (based on a sampling algorithm). For SHAPE data, RME and RNAstructure-Fold performed better than SeqFold, because they markedly altered the energy model with the experimental restraints. For high-throughput data (e.g. PARS and DMS-seq) with lower probing efficiency, the secondary structure prediction performances of the tested tools were comparable, with performance improvements for only a portion of the tested RNAs. However, when the effects of tertiary structure and protein interactions were removed, RME showed the highest prediction accuracy in the DMS-accessible regions by incorporating in vivo DMS-seq data.National Key Basic Research Program of China [2012CB316503]; National High-Tech Research and Development Program of China [2014AA021103]; National Natural Science Foundation of China [31271402]; Tsinghua University Initiative Scientific Research Program [2014z21045]; Hong Kong Research Grants Council Early Career Scheme [419612 to K.Y.]; National Science Foundation [1339282 to D.H.M.]; Computing Platform of the National Protein Facilities (Tsinghua University). Funding for open access charge: National Natural Science Foundation of China [31271402]

Erratum to : Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen

BACKGROUND The haemoflagellate Trypanosoma lewisi is a kinetoplastid parasite which, as it has been recently reported to cause human disease, deserves increased attention. Characteristic features of all kinetoplastid flagellates are a uniquely structured mitochondrial DNA or kinetoplast, comprised of a network of catenated DNA circles, and RNA editing of mitochondrial transcripts. The aim of this study was to describe the kinetoplast DNA of T. lewisi. METHODS/RESULTS In this study, purified kinetoplast DNA from T. lewisi was sequenced using high-throughput sequencing in combination with sequencing of PCR amplicons. This allowed the assembly of the T. lewisi kinetoplast maxicircle DNA, which is a homologue of the mitochondrial genome in other eukaryotes. The assembly of 23,745 bp comprises the non-coding and coding regions. Comparative analysis of the maxicircle sequence of T. lewisi with Trypanosoma cruzi, Trypanosoma rangeli, Trypanosoma brucei and Leishmania tarentolae revealed that it shares 78 %, 77 %, 74 % and 66 % sequence identity with these parasites, respectively. The high GC content in at least 9 maxicircle genes of T. lewisi (ATPase6; NADH dehydrogenase subunits ND3, ND7, ND8 and ND9; G-rich regions GR3 and GR4; cytochrome oxidase subunit COIII and ribosomal protein RPS12) implies that their products may be extensively edited. A detailed analysis of the non-coding region revealed that it contains numerous repeat motifs and palindromes. CONCLUSIONS We have sequenced and comprehensively annotated the kinetoplast maxicircle of T. lewisi. Our analysis reveals that T. lewisi is closely related to T. cruzi and T. brucei, and may share similar RNA editing patterns with them rather than with L. tarentolae. These findings provide novel insight into the biological features of this emerging human pathogen

Chromium removal from aqueous solution by a PEI-silica nanocomposite

It is essential and important to determine the adsorption mechanism as well as removal efficiency when using an adsorption technique to remove toxic heavy metals from wastewater. In this research, the removal efficiency and mechanism of chromium removal by a silica-based nanoparticle were investigated. A PEI-silica nanoparticle was synthesized by a one-pot technique and exhibited uniformly well-dispersed PEI polymers in silica particles. The adsorption capacity of chromium ions was determined by a batch adsorption test, with the PEI-silica nanoparticle having a value of 183.7 mg/g and monolayer sorption. Adsorption of chromium ions was affected by the solution pH and altered the nanoparticle surface chemically. First principles calculations of the adsorption energies for the relevant adsorption configurations and XPS peaks of Cr and N showed that Cr(VI), [HCrO4](-) is reduced to two species, Cr(III), CrOH2+ and Cr3+, by an amine group and that Cr(III) and Cr(VI) ions are adsorbed on different functional groups, oxidized N and NH3+

Determination of the number of J/ψ events with J/ψ → inclusive decays

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Measurement of the matrix element for the decay η′→ηπ +π -

The Dalitz plot of η⊃′→ηπ⊃+π⊃- decay is studied using (225.2±2.8)×106 J/ψ events collected with the BESIII detector at the BEPCII e⊃+e⊃- collider. With the largest sample of η⊃′ decays to date, the parameters of the Dalitz plot are determined in a generalized and a linear representation. Also, the branching fraction of J/ψ→γη⊃′ is determined to be (4.84±0.03±0.24)×10⊃-3, where the first error is statistical and the second systematic. © 2011 American Physical Society.published_or_final_versio

Higher-order multipole amplitude measurement in ψ ′→γχ c2

Using 106×106 ψ ′ events collected with the BESIII detector at the BEPCII storage ring, the higher-order multipole amplitudes in the radiative transition ψ ′→γχ c2→γπ +π -/γK +K - are measured. A fit to the χ c2 production and decay angular distributions yields M2=0.046±0. 010±0.013 and E3=0.015±0.008±0.018, where the first errors are statistical and the second systematic. Here M2 denotes the normalized magnetic quadrupole amplitude and E3 the normalized electric octupole amplitude. This measurement shows evidence for the existence of the M2 signal with 4.4σ statistical significance and is consistent with the charm quark having no anomalous magnetic moment. © 2011 American Physical Society.published_or_final_versio

First observation of the decays χcJ→π0π0π0π0

We present a study of the P-wave spin-triplet charmonium χ cJ decays (J=0, 1, 2) into π0π0π0π0. The analysis is based on 106×106 ψ⊃′ decays recorded with the BESIII detector at the BEPCII electron positron collider. The decay into the π0π0π0π0 hadronic final state is observed for the first time. We measure the branching fractions B(χ c0→π0π0π0π0)=(3.34±0. 06±0.44)×10⊃-3, B(χ c1→π0π0π0π0) =(0.57±0.03±0.08)×10⊃-3, and B(χ c2→π0π0π0π0)=(1.21±0.05±0.16) ×10⊃-3, where the uncertainties are statistical and systematical, respectively. © 2011 American Physical Society.published_or_final_versio

Study of a00(980)-f0(980) mixing

Using samples of 2.25×108 J/ψ events and 1.06×108 ψ ′ events collected with the BES III detector, we study the f 0(980)→a00(980) and a00(980)→f 0(980) transitions in the processes J/ψ→φf 0(980) →φa00(980) and χ c1→π0a00(980)→π0f 0(980), respectively. Evidence for f 0(980)→a00(980) is found with a significance of 3.4σ, while in the case of a00(980)→f 0(980) transition, the significance is 1.9σ. Measurements and upper limits of both branching ratios and mixing intensities are determined. © 2011 American Physical Society.published_or_final_versio