Measure of synonymous codon usage diversity among genes in bacteria

<p>Abstract</p> <p>Background</p> <p>In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (<it>D</it>mean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome.</p> <p>Results</p> <p>The application of <it>D</it>mean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for <it>Helicobacter pylori</it>, but based on <it>D</it>mean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity.</p> <p>Conclusion</p> <p>We recommend that <it>D</it>mean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature.</p

Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from −0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species

Schatten p-norm inequalities related to an extended operator parallelogram law

Let $\mathcal{C}_p$ be the Schatten $p$-class for $p>0$. Generalizations of the parallelogram law for the Schatten 2-norms have been given in the following form: If $\mathbf{A}=\{A_1,A_2,...,A_n\}$ and $\mathbf{B}=\{B_1,B_2,...,B_n\}$ are two sets of operators in $\mathcal{C}_2$, then \sum_{i,j=1}^n\|A_i-A_j\|_2^2 + \sum_{i,j=1}^n\|B_i-B_j\|_2^2 = 2\sum_{i,j=1}^n\|A_i-B_j\|_2^2 - 2\Norm{\sum_{i=1}^n(A_i-B_i)}_2^2. In this paper, we give generalizations of this as pairs of inequalities for Schatten $p$-norms, which hold for certain values of $p$ and reduce to the equality above for $p=2$. Moreover, we present some related inequalities for three sets of operators.Comment: 8 page

Efficacy and duration of analgesia from a sustained-release lidocaine sheet in humans

BACKGROUNDWe have synthesized a sustained-releaselidocaine sheet (SRLS) and injectable sustained-release lidocaine particles(SRLP) using biodegradable polymers. In the present study, we performed anexploratory first clinical trial of the SRLS in healthy volunteers as a preludeto patient administration. This trial is meant as an initial intervention inultimately developing and refining the SRLP. METHODSWe evaluated the intensity and duration ofanalgesia of the SRLS compared with 8% lidocaine spray. In Protocol 1, weapplied the SRLS piece to the mucous membrane of the nasal vestibule. Weexamined the local pain threshold over 72 h after administration, and removedthe SRLS after 72 h. Individuals that finished Protocol 1 underwent Protocol 2,in which we applied 8% lidocaine spray. RESULTSTwelve volunteers were enrolled and seven ofthese volunteers finished Protocol 1. All seven individuals who completedProtocol 1 also completed Protocol 2. The mean pain thresholds were 32 g, 78 g,90 g, 90 g, 87 g, and 87 g at pre-administration and 4 h, 10 h, 24 h, 48 h, and72 h after administration, respectively, in Protocol 1, and 36 g, 85 g, 49 g,and 33 g at pre-administration and 15 min, 2 h, and 4 h, respectively, inProtocol 2. CONCLUSIONA sustained-release lidocaine usingbiodegradable polymers was applied as a sheet in humans for the first time inthe world. It maintained significant analgesia for 72 h without majortoxicities. Furthermore, degree of analgesia provided by the SRLS throughoutthe entire study was similar to that provided by the 8% lidocaine spray. It may suitable for management ofpostoperative pain especially in outpatients

Superconductivity protected by spin-valley locking in ion-gated MoS2

Symmetry-breaking has been known to play a key role in noncentrosymmetric superconductors with strong spin-orbit-interaction (SOI). The studies, however, have been so far mainly focused on a particular type of SOI, known as Rashba SOI, whereby the electron spin is locked to its momentum at a right-angle, thereby leading to an in-planar helical spin texture. Here we discuss electric-field-induced superconductivity in molybdenum disulphide (MoS2), which exhibits a fundamentally different type of intrinsic SOI manifested by an out-of-plane Zeeman-type spin polarization of energy valleys. We find an upper critical field of approximately 52 T at 1.5 K, which indicates an enhancement of the Pauli limit by a factor of four as compared to that in centrosymmetric conventional superconductors. Using realistic tight-binding calculations, we reveal that this unusual behaviour is due to an inter-valley pairing that is symmetrically protected by Zeeman-type spin-valley locking against external magnetic fields. Our study sheds a new light on the interplay of inversion asymmetry with SOI in confined geometries, and its unprecedented role in superconductivity.Comment: 37 pages, 11 figures, http://meetings.aps.org/Meeting/MAR15/Session/G11.1

New Short Term Prediction Method for Chemical Carcinogenicity by Hepatic Transcript Profiling Following 28-Day Toxicity Tests in Rats

We have previously shown the hepatic gene expression profiles of carcinogens in 28-day toxicity tests were clustered into three major groups (Group-1 to 3). Here, we developed a new prediction method for Group-1 carcinogens which consist mainly of genotoxic rat hepatocarcinogens. The prediction formula was generated by a support vector machine using 5 selected genes as the predictive genes and predictive score was introduced to judge carcinogenicity. It correctly predicted the carcinogenicity of all 17 Group-1 chemicals and 22 of 24 non-carcinogens regardless of genotoxicity. In the dose-response study, the prediction score was altered from negative to positive as the dose increased, indicating that the characteristic gene expression profile emerged over a range of carcinogen-specific doses. We conclude that the prediction formula can quantitatively predict the carcinogenicity of Group-1 carcinogens. The same method may be applied to other groups of carcinogens to build a total system for prediction of carcinogenicity