MACSIMS : multiple alignment of complete sequences information management system

BACKGROUND: In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. RESULTS: MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. CONCLUSION: MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications

Is there a difference between child self-ratings and parent proxy-ratings of the quality of life of children with a diagnosis of Attention Deficit Hyperactivity Disorder (ADHD)? A systematic review of the literature

There are contemporary indicators that parent proxy-ratings and child self-ratings of a child’s quality of life (QoL) are not interchangeable. This review examines dual informant studies to assess parent–child agreement on the QoL of children with attention-deficit/hyperactivity disorder. A systematic search of four major databases (PsycINFO, MEDLINE, EMBASE and Cochrane databases) was completed, and related peer-reviewed journals were hand-searched. Studies which reported quantitative QoL ratings for matched parent and child dyads were screened in accordance with relevant inclusion and exclusion criteria. Key findings were extracted from thirteen relevant studies, which were rated for conformity to the recommendations of an adapted version of the STROBE statement guidelines for observational studies. In the majority of studies reviewed, children rated their QoL more highly than their parents. There was some evidence for greater agreement on the physical health domain than psychosocial domains

Geographic Variation in Advertisement Calls in a Tree Frog Species: Gene Flow and Selection Hypotheses

In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD) or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation.We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR), note duration (ND), and dominant frequency (DF), along with snout-to-vent length.The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters.Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japonica. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with restricted gene flow

A Precision Measurement of the Lambda_c Baryon Mass

The $\Lambda_c^+$ baryon mass is measured using $\Lambda_c^+\to\Lambda K^0_S K^+$ and $\Lambda_c^+\to\Sigma^0 K^0_S K^+$ decays reconstructed in 232 fb$^{-1}$ of data collected with the BaBar detector at the PEP-II asymmetric-energy $e^+e^-$ storage ring. The $\Lambda_c^+$ mass is measured to be $2286.46\pm0.14\mathrm{MeV}/c^2$. The dominant systematic uncertainties arise from the amount of material in the tracking volume and from the magnetic field strength.Comment: 14 pages, 8 postscript figures, submitted to Phys. Rev.

Determinations of vertical bar V-ub vertical bar from inclusive semileptonic B decays with reduced model dependence

We report two novel determinations of vertical bar V-ub vertical bar with reduced model dependence, based on measurements of the mass distribution of the hadronic system in semileptonic B decays. Events are selected by fully reconstructing the decay of one B meson and identifying a charged lepton from the decay of the other B meson from Y(4S) -> B (B) over bar events. In one approach, we combine the inclusive (B) over bar -> X(u)l (v) over bar rate, integrated up to a maximum hadronic mass m(X) X-s gamma photon energy spectrum. We obtain vertical bar V-ub vertical bar = (4.43 +/- 0.38(stat) +/- 0.25(syst) +/- 0.29(theo)) x 10(-3). In another approach we measure the total (B) over bar -> X(u)l (v) over bar rate over the full phase space and find vertical bar V-ub vertical bar = 3.84 +/- 0.70(stat) +/- 0.30(syst) +/- 0.10(theo)) x 10(-3)

Observation of a Charmed Baryon Decaying to D0p at a Mass Near 2.94 GeV/c2

A search for charmed baryons decaying to D 0 p reveals two states: the Λ c ( 2880 ) + baryon and a previously unobserved state at a mass of [ 2939.8 ± 1.3 ( stat ) ± 1.0 ( syst ) ]     MeV / c 2 and with an intrinsic width of [ 17.5 ± 5.2 ( stat ) ± 5.9 ( syst ) ]     MeV . Consistent and significant signals are observed for the K − π + and K − π + π − π + decay modes of the D 0 in 287     fb − 1 annihilation data recorded by the BABAR detector at a center-of-mass energy of 10.58 GeV. There is no evidence in the D + p spectrum of doubly charged partners. The mass and intrinsic width of the Λ c ( 2880 ) + baryon and relative yield of the two baryons are also measured

Measurement of the CP asymmetry and branching fraction of B-0 ->rho K-0(0)

We present a measurement of the branching fraction and time-dependent CP asymmetry of B-0 -> POKO. The results are obtained from a data sample of 227 x 10(6) Y(4S) -> BB decays collected with the BABAR detector at the PEP-II asymmetric-energy B factory at Stanford Linear Accelerator Center. From a time-dependent maximum likelihood fit yielding 111 +/- 19 signal events, we find B(B-0 -> rho K-0(0)) = (4.9 +/- 0.8 +/- 0.9) x 10(-6), where the first error is statistical and the second systematic. We report the measurement of the CP parameters S-rho 0KS0 = 0.20 +/- 0.52 +/- 0.24 and C-rho 0KS0 = 0.64 +/- 0.41 +/- 0.20

Measurement of branching fractions and resonance contributions for B-0 ->(D)over-bar(0)K(+)pi(-) and search for B-0 ->(DK+)-K-0 pi(-) decays

Using 226x10(6) Upsilon(4S)-> B (B) over bar events collected with the BABAR detector at the PEP-II e(+)e(-) storage ring at the Stanford Linear Accelerator Center, we measure the branching fraction for B-0->(D) over bar (0)K(+)pi(-), excluding B-0-> D*-K+, to be B(B-0->(0)K(+)pi(-))=(88 +/- 15 +/- 9)x10(-6). We observe B-0->(D) over bar K-0(*)(892)(0) and B-0-> D-2(*)(2460)K--(+) contributions. The ratio of branching fractions B(B-0-> D*-K+)/B(B-0-> D(*-)pi(+))=(7.76 +/- 0.34 +/- 0.29)% is measured separately. The branching fraction for the suppressed mode B-0-> D(0)K(+)pi(-) is B(B-0-> D(0)K(+)pi(-))< 19x10(-6) at the 90% confidence level

Measurement of branching fractions and mass spectra of B -> K pi pi gamma

We present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B -> K pi pi gamma in the range m(K pi pi)pi(+)pi(-). Using 232x10(6) e(+)e(-)-> B (B) over bar events recorded by the BABAR experiment at the SLAC PEP-II asymmetric-energy storage ring, we measure the branching fractions B(B+-> K+pi(-)pi(+)gamma)=[2.95 +/- 0.13(stat)+/- 0.20(syst)]x10(-5), B(B-0 -> K+pi(-)pi(0)gamma)=[4.07 +/- 0.22(stat)+/- 0.31(syst)]x10(-5), B(B-0 -> K-0 pi(+)pi(-)gamma)=[1.85 +/- 0.21(stat)+/- 0.12(syst)]x10(-5), and B(B+-> K-0 pi(+)pi(0)gamma)=[4.56 +/- 0.42(stat)+/- 0.31(syst)]x10(-5)