An increase in TcT_c under hydrostatic pressure in the superconducting doped topological insulator Nb0.25_{0.25}Bi2_2Se3_3

We report an unexpected positive hydrostatic pressure derivative of the superconducting transition temperature in the doped topological insulator \NBS via $dc$ SQUID magnetometry in pressures up to 0.6 GPa. This result is contrary to reports on the homologues \CBS and \SBS where smooth suppression of $T_c$ is observed. Our results are consistent with recent Ginzburg-Landau theory predictions of a pressure-induced enhancement of $T_c$ in the nematic multicomponent $E_u$ state proposed to explain observations of rotational symmetry breaking in doped Bi$_2$Se$_3$ superconductors.Comment: 5 pages, 5 figure

The English and Chinese language versions of the Short Form 12-item Health Survey are equivalent

Background: The Short Form 12-item Health Survey (SF-12v2) was originally developed in English, but it is also available in Hong Kong (HK) Chinese. While both language versions had their measurement properties well assessed in their respective populations, their measurement invariance in scores has not been examined. Therefore, we aimed to assess their measurement invariance. Methods: We conducted a cross-sectional study on individuals aged 18 years or older at a university campus. Those who were bilingual in English and Chinese were randomly assigned to self-complete either the standard English or the HK Chinese SF-12v2. Measurement invariance of the two components and eight scales of the SF-12v2 was concluded if the corresponding 90% confidence interval (CI) for the difference between the two language versions entirely fell within the minimal clinically important difference of ±3 units. Multiple-group confirmatory factor analysis (CFA) was also performed. Results: A total of 1013 participants completed the SF-12v2 (496 in English and 517 in HK Chinese), with a mean age of 22 years (Range 18–58), and 626 participants (62%) were female. There were no significant differences in demographics. Only the physical and mental components and the mental health (MH) scale had their 90% CIs (0.21 to 1.61, − 1.00 to 0.98, and − 0.86 to 2.84, respectively) completely fall within the ±3 units. The multiple-group CFA showed partial strict invariance. Conclusions: The English and HK Chinese versions of the SF-12v2 can be used in studies with their two components and MH scores pooled in the analysis

Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing

Establishing the pattern in peak heights within local sequence contexts improves the accuracy of base calling and the identification of DNA sequence variations in dye-terminator cycle sequencing. We have systematically examined pairs of sequence-tagged sites (STSs) that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by two recently commercialized dye-terminator chemistries, the dichloro-rhodamine (dRhodamine) and the energy transfer (BigDye) terminators. For sequencing traces generated with the dRhodamine terminators, the peak height of a particular base in 28 of 64 possible 3-base windows (44%) can be predicted by knowing just one or two bases 5\u27 to the base in question. For those generated with the BigDye terminators, the peak height of a particular base in 23 of 64 possible 3-base windows (36%) can be predicted by knowing the local sequence context. When the peak heights are binned slightly differently, 75% (48 out of 64 cases) of the base peaks generated by both dRhodamine and BigDye terminators fall in the middle half, confirming that the peak patterns of these two new dye terminator chemistries are much more even than those found in the original rhodamine dye terminator sequences

CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (http://covdb.microbiology.hku.hk), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis

Coronavirus Genomics and Bioinformatics Analysis

The drastic increase in the number of coronaviruses discovered and coronavirus genomes being sequenced have given us an unprecedented opportunity to perform genomics and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from 32% to 43%. Variable numbers of small ORFs are present between the various conserved genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera, Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999–2002, with estimated substitution rate of 4×10−4 to 2×10−2 substitutions per site per year. Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, between MHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses

Measurement of Cosmic-ray Muons and Muon-induced Neutrons in the Aberdeen Tunnel Underground Laboratory

We have measured the muon flux and production rate of muon-induced neutrons at a depth of 611 m water equivalent. Our apparatus comprises three layers of crossed plastic scintillator hodoscopes for tracking the incident cosmic-ray muons and 760 L of gadolinium-doped liquid scintillator for producing and detecting neutrons. The vertical muon intensity was measured to be $I_{\mu} = (5.7 \pm 0.6) \times 10^{-6}$ cm$^{-2}$s$^{-1}$sr$^{-1}$. The yield of muon-induced neutrons in the liquid scintillator was determined to be $Y_{n} = (1.19 \pm 0.08 (stat) \pm 0.21 (syst)) \times 10^{-4}$ neutrons/($\mu\cdot$g$\cdot$cm$^{-2}$). A fit to the recently measured neutron yields at different depths gave a mean muon energy dependence of $\left\langle E_{\mu} \right\rangle^{0.76 \pm 0.03}$ for liquid-scintillator targets.Comment: 14 pages, 17 figures, 3 table

AmpliTaq DNA polymerase, FS dye-terminator sequencing: Analysis of peak height patterns

Taq DNA polymerases in which the phenylalanine is substituted by a tyrosine at position 667 (Taq F667Y) are members of a new class of DNA polymerases that incorporate chain-terminating dideoxyribonucleoside triphosphates (ddNTPs) much more efficiently than the wild-type Taq DNA polymerase. Improved incorporation of ddNTPs into DNA during cycle sequencing using AmpliTaq DNA polymerase, FS (Taq-FS, a member of the Taq F667Y family), and dye-labeled primers results in nearly uniform peak heights in the sequencing trace. This is not the case when dye-labeled ddNTPs are used in Taq-FS cycle sequencing reactions. While the rate of dye-terminator incorporation is more efficient with Taq-FS, the peak pattern is still highly variable and different from that produced by the wild-type enzyme. We have systematically examined pairs of sequence-tagged sites that vary at only a single nucleotide to determine how base changes influence the peak heights of neighboring bases in sequencing traces generated by the Taq-FS dye-terminator chemistry. In 31 of 64 possible 3-base windows (48%), we find that the peak height of a particular base can be predicted by knowing just one or two bases 5\u27 to the base in question. We have also compared and contrasted the peak patterns produced by the Taq-FS enzyme with those previously identified for the wild-type enzyme. Establishing the patterns in peak heights within local sequence contexts can improve the accuracy of base-calling and the identification of polymorphisms/mutations when using the Taq-FS dye-terminator cycle-sequencing chemistry