Spin-3/2 baryons from an anisotropic lattice QCD action

The mass spectrum of baryons in the spin-3/2 sector is computed in quenched lattice QCD using a tadpole-improved anisotropic action. Both isospin 1/2 and 3/2 (the traditional decuplet) are considered, as well as members that contain strange quarks. States with positive and negative parities are isolated by parity projection, while states with spin-3/2 and spin-1/2 are separated by spin projection. The extent to which spin projection is needed is examined. The issue of optimal interpolating field is also investigated. The results are discussed in relation to previous calculations and experiment.Comment: modified version to appear in Phys Rev

Magnetic polarizability of hadrons from lattice QCD in the background field method

We present a calculation of hadron magnetic polarizability using the techniques of lattice QCD. This is carried out by introducing a uniform external magnetic field on the lattice and measuring the quadratic part of a hadron's mass shift. The calculation is performed on a $24^4$ lattice with standard Wilson actions at beta=6.0 (spacing $a=0.1$ fm) and pion mass down to about 500 MeV. Results are obtained for 30 particles covering the entire baryon octet ($n$, $p$, $\Sigma^0$, $\Sigma^-$, $\Sigma^+$, $\Xi^-$, $\Xi^0$, $\Lambda$) and decuplet ($\Delta^0$, $\Delta^-$, $\Delta^+$, $\Delta^{++}$, $\Sigma^{*0}$, $\Sigma^{*-}$, $\Sigma^{*+}$, $\Xi^{*0}$, $\Xi^{*-}$, $\Omega^-$), plus selected mesons ($\pi^0$, $\pi^+$, $\pi^-$, $K^0$, $K^+$, ${K}^-$, $\rho^0$, $\rho^+$, $\rho^-$, $K^{*0}$, $K^{*+}$, $K^{*-}$). The results are compared with available values from experiments and other theoretical calculations.Comment: 30 pages, 23 figures, 5 table

Electric Polarizability of Neutral Hadrons from Lattice QCD

By simulating a uniform electric field on a lattice and measuring the change in the rest mass, we calculate the electric polarizability of neutral mesons and baryons using the methods of quenched lattice QCD. Specifically, we measure the electric polarizability coefficient from the quadratic response to the electric field for 10 particles: the vector mesons $\rho^0$ and $K^{*0}$; the octet baryons n, $\Sigma^0$, $\Lambda_{o}^{0}$, $\Lambda_{s}^{0}$, and $\Xi^0$; and the decouplet baryons $\Delta^0$, $\Sigma^{*0}$, and $\Xi^{*0}$. Independent calculations using two fermion actions were done for consistency and comparison purposes. One calculation uses Wilson fermions with a lattice spacing of $a=0.10$fm. The other uses tadpole improved L\"usher-Weiss gauge fields and clover quark action with a lattice spacing $a=0.17$fm. Our results for neutron electric polarizability are compared to experiment.Comment: 25 pages, 20 figure

Electric Polarizability of Hadrons

The electric polarizability of a hadron allows an external electric field to shift the hadron mass. We try to calculate the electric polarizability for several hadrons from their quadratic response to the field at a=0.17fm using an improved gauge field and the clover quark action. Results are compared to experiment where available.Comment: 3 pgs, 5 figs, LATTICE2002(spectrum

User Preferences for Privacy Protection Methods in Mobile Health Apps: A Mixed-Methods Study

Background: Mobile health (mHealth) apps have the potential to facilitate convenient health care delivery and self-management of health. However, many users have concerns about their privacy when they use mHealth apps. Different apps provide different solutions for protecting users’ privacy. Objective: The purpose of this study was to determine user preferences among the several privacy protection methods used in current mHealth apps and the reasons behind their preferences. Methods: Five privacy protection methods currently used in mHealth apps were presented to a group of study participants who had mild or moderate depression and expressed concerns about privacy of information when they used mental health apps. After a demonstration of the methods, study participants were asked to fill out a questionnaire and indicate their perceived privacy protection level (PPPL) of each method, their preference rating for each method, and the privacy protection methods they had used in the past. A brief interview was then conducted to collect study participants’ comments on these methods and elicit the reasons for their preference ratings. Statistical analysis was performed to determine the statistical significance of differences in participants’ preference ratings and in the PPPLs obtained for the five methods. Study participants’ comments on the privacy protection methods and suggestions were noted and summarized. Results: Forty (40) study participants were selected from a large candidate pool using the IRB approved selection criteria. All study participants viewed the app demonstration and understood the five privacy protection methods properly, which was indicated by their correct sorting of the PPPL of the five methods in their answers to the questionnaire. All study participants specified their preferences with respect to these methods and provided the rationale behind their selections on the questionnaire and during the brief interview. The results indicate that the users preferred privacy protection methods with customizable modules in multi-purpose apps because of their convenience and strong privacy protection, where the customization can be done either in the app or via a Web portal. Conclusions: This study identified user preferred privacy protection methods. These identified privacy protection methods may be used in many types of apps that perform sensitive health information management to better protect users’ privacy and encourage more users to adopt these mHealth apps

Universal seeds for cDNA-to-genome comparison

<p>Abstract</p> <p>Background</p> <p>To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of a related species. So far, seed performance has been tested for comparisons between closely related species, such as human and mouse, or on simulated data. As the number and variety of genomes increases, it becomes desirable to identify a small set of <it>universal </it>seeds that perform optimally or near-optimally on a large range of comparisons.</p> <p>Results</p> <p>Using statistical regression methods, we investigate the sensitivity of seeds, in particular good seeds, between four cDNA-to-genome comparisons at different evolutionary distances (human-dog, human-mouse, human-chicken and human-zebrafish), and identify classes of comparisons that show similar seed behavior and therefore can employ the same seed. In addition, we find that with high confidence good seeds for more distant comparisons perform well on closer comparisons, within 98–99% of the optimal seeds, and thus represent universal good seeds.</p> <p>Conclusion</p> <p>We show for the first time that optimal and near-optimal seeds for distant species-to-species comparisons are more generally applicable to a wide range of comparisons. This finding will be instrumental in developing practical and user-friendly cDNA-to-genome alignment applications, to aid in the annotation of new model organisms.</p

Mechanisms of intron gain and loss in Drosophila

<p>Abstract</p> <p>Background</p> <p>It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect nearly every level of gene expression. Therefore, understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity.</p> <p>Results</p> <p>To investigate possible mechanisms of intron gain and loss, we identified 189 intron gain and 297 intron loss events among 11 Drosophila species. We then investigated these events for signatures of previously proposed mechanisms of intron gain and loss. This work constitutes the first comprehensive study into the specific mechanisms that may generate intron gains and losses in Drosophila. We report evidence of intron gain via transposon insertion; the first intron loss that may have occurred via non-homologous end joining; intron gains via the repair of a double strand break; evidence of intron sliding; and evidence that internal or 5' introns may not frequently be deleted via the self-priming of reverse transcription during mRNA-mediated intron loss. Our data also suggest that the transcription process may promote or result in intron gain.</p> <p>Conclusion</p> <p>Our findings support the occurrence of intron gain via transposon insertion, repair of double strand breaks, as well as intron loss via non-homologous end joining. Furthermore, our data suggest that intron gain may be enabled by or due to transcription, and we shed further light on the exact mechanism of mRNA-mediated intron loss.</p