HBVRegDB: annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

BACKGROUND

The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (approximately 3.2 kb) but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses.

RESULTS

These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx). It also contains analyses based on curated HBV alignments. Information about conserved regions - including primary conservation (e.g. CDS-Plotcon) and RNA secondary structure predictions (e.g. Alidot) - is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser) adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences.

CONCLUSION

HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

Inference of transcriptional regulation using gene expression data from the bovine and human genomes

Background

Gene expression is in part regulated by sequences in promoters that bind transcription factors. Thus, co-expressed genes may have shared sequence motifs representing putative transcription factor binding sites (TFBSs). However, for agriculturally important animals the genomic sequence is often incomplete. The more complete human genome may be able to be used for this prediction by taking advantage of the expected evolutionary conservation in TFBSs between the species.

Results

A method of de novo TFBS prediction based on MEME was implemented, tested, and validated on a muscle-specific dataset.

Muscle specific expression data from EST library analysis from cattle was used to predict sets of genes whose expression was enriched in muscle and cardiac tissues. The upstream 1500 bases from calculated orthologous genes were extracted from the human reference set. A set of common motifs were discovered in these promoters. Slightly over one third of these motifs were identified as known TFBSs including known muscle specific binding sites. This analysis also predicted several highly statistically significantly overrepresented sites that may be novel TFBS.

An independent analysis of the equivalent bovine genomic sequences was also done, this gave less detailed results than the human analysis due to both the quality of orthologue prediction and assembly in promoter regions. However, the most common motifs could be detected in both sets.

Conclusion

Using promoter sequences from human genes is a useful approach when studying gene expression in species with limited or non-existing genomic sequence. As the bovine genome becomes better annotated it can in turn serve as the reference genome for other agriculturally important ruminants, such as sheep, goat and deer.

Traditional birth attendant training for improving health behaviours and pregnancy outcomes

BACKGROUND

Between the 1970s and 1990s, the World Health Organization promoted traditional birth attendant (TBA) training as one strategy to reduce maternal and neonatal mortality. To date, evidence in support of TBA training remains limited and conflicting.

OBJECTIVES

To assess effects of TBA training on health behaviours and pregnancy outcomes.

SEARCH STRATEGY

We searched the Trials Registers of the Cochrane Pregnancy and Childbirth Group and Cochrane Effective Practice and Organisation of Care Group (EPOC) (June 2006); electronic databases representing fields of education, social, and health sciences (inception to June 2006); the internet; and contacted experts.

SELECTION CRITERIA

Published and unpublished randomized controlled trials (RCT), controlled before/after and interrupted time series studies comparing trained and untrained TBAs or women cared for/living in areas served by TBAs.

DATA COLLECTION AND ANALYSIS

Three authors independently assessed study quality and extracted data.

MAIN RESULTS

Four studies, involving over 2000 TBAs and nearly 27,000 women, are included. One cluster-randomized trial found significantly lower rates in the intervention group regarding stillbirths (adjusted OR 0.69, 95% confidence interval (CI) 0.57 to 0.83, P < 0.001), perinatal death rate (adjusted OR 0.70, 95% CI 0.59 to 0.83, P < 0.001) and neonatal death rate (adjusted OR 0.71, 95% CI 0.61 to 0.82, P < 0.001). Maternal death rate was lower but not significant (adjusted OR 0.74, 95% CI 0.45 to 1.22, P = 0.24) while referral rates were significantly higher (adjusted OR 1.50, 95% CI 1.18 to 1.90, P < 0.001). A controlled before/after study among women who were referred to a health service found perinatal deaths decreased in both intervention and control groups with no significant difference between groups (OR 1.02, 95% CI 0.59 to 1.76, P = 0.95). Similarly, the mean number of monthly referrals did not differ between groups (P = 0.321). One RCT found a significant difference in advice about introduction of complementary foods (OR 2.07, 95% CI 1.10 to 3.90, P = 0.02) but no significant difference for immediate feeding of colostrum (OR 1.37, 95% CI 0.62 to 3.03, P = 0.44). Another RCT found no significant differences in frequency of postpartum haemorrhage (OR 0.94, 95% CI 0.76 to 1.17, P = 0.60) among women cared for by trained versus TBAs.

AUTHORS' CONCLUSIONS

The potential of TBA training to reduce peri-neonatal mortality is promising when combined with improved health services. However, the number of studies meeting the inclusion criteria is insufficient to provide the evidence base needed to establish training effectiveness.

Evidence of a broad structure at an invariant mass of 4.32 GeV/c2 in the reaction e+e- --> pi+pi-psi(2S) measured at BABAR

We present a measurement of the cross section of the process e(+)e(-)-->pi(+)pi(-)psi(2S) from threshold up to 8 GeV center-of-mass energy using events containing initial-state radiation, produced at the SLAC PEP-II e(+)e(-) storage rings. The study is based on 298 fb(-1) of data recorded with the BABAR detector. A structure is observed in the cross section not far above threshold, near 4.32 GeV. We also investigate the compatibility of this structure with the Y(4260) previously reported by this experiment.

Measurement of branching fractions and mass spectra of B-->Kpipigamma

We present a measurement of the partial branching fractions and mass spectra of the exclusive radiative penguin processes B-->Kpipigamma in the range m(Kpipi)<1.8 GeV/c(2). We reconstruct four final states: K(+)pi(-)pi(+)gamma, K(+)pi(-)pi(0)gamma, K(S)(0)pi(-)pi(+)gamma, and K(S)(0)pi(+)pi(0)gamma, where K(S)(0)-->pi(+)pi(-). Using 232 x 10(6) e(+)e(-)-->BB 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)] x 10(-5), B(B(0)-->K(+)pi(-)pi(0)gamma)=[4.07+/-0.22(stat)+/-0.31(syst)] x 10(-5), B(B(0)-->K(0)pi(+)pi(-)gamma)=[1.85+/-0.21(stat)+/-0.12(syst)] x 10(-5), and B(B(+)-->K(0)pi(+)pi(0)gamma)=[4.56+/-0.42(stat)+/-0.31(syst)] x 10(-5).

Measurement of the pseudoscalar decay constant fDs using charm-tagged events in e+e- collisions at square root s=10.58 GeV

Using 230.2 fb-1 of e+e- annihilation data collected with the BABAR detector at and near the peak of the Upsilon(4S) resonance, 489+/-55 events containing the pure leptonic decay Ds+-->micro;+numicro have been isolated in charm-tagged events. The ratio of partial widths Gamma(D+-->micro+numicro)/Gamma(Ds+-->phipi+) is measured to be 0.143+/-0.018+/-0.006 allowing a determination of the pseudoscalar decay constant fDs=(283+/-17+/-7+/-14) MeV. The errors are statistical, systematic, and from the Ds+-->phipi+ branching ratio, respectively.

Observation of decays B0-->Ds(*)+ pi- and B0-->Ds(*)- K+

We report the observation of decays B{0}-->D{s}{(*)+}pi- and B{0}-->D{s}{(*)-}K+ in a sample of 230 x 10(6) Upsilon(4S)-->BB[over] events recorded with the BABAR detector at the SLAC PEP-II asymmetric-energy e+ e- storage ring. We measure the branching fractions B(B{0}-->D{s}{+}pi-)=(1.3+/-0.3(stat)+/-0.2(syst))x10(-5), B(B{0}-->D{s}{-} K+)=(2.5+/-0.4(stat)+/-0.4(syst))x10(-5), B(B{0}-->D{s}{*+}pi-)=(2.8+/-0.6(stat)+/-0.5(syst))x10(-5), and B(B{0}-->D{s}{*-}K+)=(2.0+/-0.5(stat)+/-0.4(syst))x10(-5). The significances of the measurements to differ from zero are 5, 9, 6, and 5 standard deviations, respectively. This is the first observation of B{0}-->D{s}{+}pi-, B{0}-->D{s}{*+}pi-, and B{0}-->D{s}{*-}K+ decays.

Search for lepton flavor violating decays tau(+/-) --> l(+/-)pi0, l(+/-)eta, l(+/-)eta'

A search for lepton flavor violating decays of the tau lepton to a lighter mass lepton and a pseudoscalar meson has been performed using 339 fb;{-1} of e;{+}e;{-} annihilation data collected at a center-of-mass energy near 10.58 GeV by the BABAR detector at the SLAC PEP-II storage ring. No evidence of a signal has been found, and upper limits on the branching fractions are set at the 10;{-7} level.

Vector-tensor and vector-vector decay amplitude analysis of B0-->phiK*0

We perform an amplitude analysis of the decays B(0)-->phiK*(2)(1430)(0), phiK*(892)(0), and phi(Kpi)(0)(S-wave) with a sample of about 384x10(6) BB[over ] pairs recorded with the BABAR detector. The fractions of longitudinal polarization f(L) of the vector-tensor and vector-vector decay modes are measured to be 0.853(-0.069+0.061)+/-0.036 and 0.506+/-0.040+/-0.015, respectively. Overall, twelve parameters are measured for the vector-vector decay and seven parameters for the vector-tensor decay, including the branching fractions and parameters sensitive to CP violation.

Measurement of the CP asymmetry and branching fraction of B0-->rho0K0

We present a measurement of the branching fraction and time-dependent CP asymmetry of B(0)-->rho0K0. The results are obtained from a data sample of 227x10(6) Upsilon(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)-->rho0K0)=(4.9+/-0.8+/-0.9)x10(-6), where the first error is statistical and the second systematic. We report the measurement of the CP parameters S(rho)(0)K(0)S=0.20+/-0.52+/-0.24 and C(rho)(0)K(0)S=0.64+/-0.41+/-0.20.

Observation of B-->eta'K* and evidence for B+-->eta'rho+

We present an observation of B-->eta'K*. The data sample corresponds to 232x10(6) BB[over ] pairs collected with the BABAR detector at the PEP-II asymmetric-energy B factory at the Stanford Linear Accelerator Center. We measure the branching fractions (in units of 10(-6)) B(B(0)-->eta'K*0)=3.8+/-1.1+/-0.5 and B(B+-->eta'K*+)=4.9(1.7)(+1.9)+/-0.8, where the first error is statistical and the second systematic. A simultaneous fit results in the observation of B-->eta'K* with B(B-->eta'K*)=4.1(-0.9)(+1.0)+/-0.5. We also search for B-->eta'rho and eta'f(0)(980)(f(0)-->pi+pi-) with results and 90% confidence level upper limits B(B+-->eta'rho+)=8.7(-2.8-1.3)(+3.1+2.3) (<14), B(B(0)-->eta'rho0)<3.7, and B(B(0)-->eta'f(0)(980)(f(0)-->pi+pi-))<1.5. Charge asymmetries in the channels with significant yields are consistent with zero.

Observation of CP violation in B --> eta'K0 decays

We present measurements of the time-dependent CP-violation parameters S and C in B(0) --> eta(')K(0) decays. The data sample corresponds to 384 x 10(6) BB pairs produced by e(+)e(-) annihilation at the Upsilon(4S). The results are S=0.58+/-0.10+/-0.03 and C=-0.16+/-0.07+/-0.03. We observe mixing-induced CP violation with a significance of 5.5 standard deviations in this b --> s penguin dominated mode.

Observation of a Charmed Baryon Decaying to D;{0}p at a Mass Near 2.94 GeV/c;{2}

A search for charmed baryons decaying to D(0)p reveals two states: the Lambdac(2880)+ baryon and a previously unobserved state at a mass of [2939.8+/-1.3(stat)+/-1.0(syst)] MeV/c2 and with an intrinsic width of [17.5+/-5.2(stat)+/-5.9(syst)] MeV. Consistent and significant signals are observed for the K(-)pi(+) and K(-)pi(+)pi(-)pi(+) decay modes of the D0 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 Lambdac(2880)+ baryon and relative yield of the two baryons are also measured.

Measurements of branching fraction, polarization, and charge asymmetry of B(+/-)-->rho(+/-)rho(0) and a search for B(+/-)-->rho(+/-)f(0)(980)

We measure the branching fraction (B), polarization (f(L)), and CP asymmetry (A(CP)) of B(+/-)-->rho(+/-)rho(0) decays and search for the decay B(+/-)-->rho(+/-)f(0)(980) based on a data sample of 231.8 x 10(6) Upsilon(4S)-->BB decays collected with the BABAR detector at the SLAC PEP-II asymmetric-energy B factory. In B(+/-)-->rho(+/-)rho(0) decays we measure B=(16.8+/-2.2+/-2.3) x 10(-), f(L)=0.905+/-0.042(-0.027)(+0.023), and A(CP)=-0.12+/-0.13+/-0.10, and find an upper limit on the branching fraction of B(+/-)-->rho(+/-)f(0)(980)(-->pi(+)pi(-)) decays of 1.9 x 10(-6) at 90% confidence level.

Observation of B(+)-->phiphiK(+) and evidence for B(0)-->phiphiK(0) below eta(c) threshold

We report measurements of the decays B(+)-->phiphiK(+) and B(0)-->phiphiK(0) using a sample of 231 x 10(6) BB pairs collected with the BABAR detector at the PEP-II asymmetric-energy B factory at the Stanford Linear Accelerator Center. The branching fractions are measured to be B(B(+)-->phiphiK(+))=(7.5+/-1.0(stat)+/-0.7(syst)) x 10(-6) and B(B(0)-->phiphiK(0))=(4.1(-1.4)(+1.7)(stat)+/-0.4(syst)) x 10(-6) for a phiphi invariant mass below 2.85 GeV/c(2).

Observation of an excited charm baryon Omega c* decaying to Omega c0gamma

We report the first observation of an excited singly charmed baryon Omega c* (css) in the radiative decay Omega c0gamma, where the Omega c0 baryon is reconstructed in the decays to the final states Omega(-)pi+, Omega(-)pi+pi0, Omega(-)pi+pi(-)pi+, and Xi(-)K(-)pi+pi+. This analysis is performed using a data set of 230.7 fb(-1) collected by the BABAR detector at the PEP-II asymmetric-energy B factory at the Stanford Linear Accelerator Center. The mass difference between the Omega c* and the Omega c0 baryons is measured to be 70.8+/-1.0(stat)+/-1.1(syst) MeV/c2. We also measure the ratio of inclusive production cross sections of Omega c* and Omega c0 in e+e(-) annihilation.

Search for D0-D0 mixing and branching-ratio measurement in the decay D0-->K+ pi- pi0

We analyze 230.4 fb;{-1} of data collected with the BABAR detector at the PEP-II e;{+}e;{-} collider at SLAC to search for evidence of D0-D[over ];{0} mixing using regions of phase space in the decay D;{0}-->K;{+}pi;{-}pi;{0}. We measure the time-integrated mixing rate R_{M}=(0.023_{-0.014};{+0.018}(stat.)+/-0.004(syst.))%, and R_{M}<0.054% at the 95% confidence level, assuming CP invariance. The data are consistent with no mixing at the 4.5% confidence level. We also measure the branching ratio for D;{0}-->K;{+}pi;{-}pi;{0} relative to D;{0}-->K;{-}pi;{+}pi;{0} to be (0.214+/-0.008(stat.)+/-0.008(syst.))%.

Observation of a new Ds meson decaying to DK at a mass of 2.86 GeV/c2

We observe a new D_{s} meson with mass (2856.6+/-1.5_{stat}+/-5.0_{syst}) MeV/c;{2} and width (48+/-7_{stat}+/-10_{syst}) MeV/c;{2} decaying into D0K+ and D;{+}K_{S};{0}. In the same mass distributions, we also observe a broad structure with mass (2688+/-4_{stat}+/-3_{syst}) MeV/c;{2} and width (112+/-7_{stat}+/-36_{syst}) MeV/c;{2}. To obtain this result, we use 240 fb;{-1} of data recorded by the BABAR detector at the PEP-II asymmetric-energy e;{+}e;{-} storage rings at the Stanford Linear Accelerator Center running at center-of-mass energies near 10.6 GeV.

Measurement of the B-->pi l nu branching fraction and determination of absolute value of V(ub) with tagged B mesons

We report a measurement of the B-->pi l nu branching fraction based on 211 fb(-1) of data collected with the BABAR detector. We use samples of B0 and B+ mesons tagged by a second B meson reconstructed in a semileptonic or hadronic decay and combine the results assuming isospin symmetry to obtain B(B(0)-->pi- l+ nu) = (1.33+/-0.17stat+/-0.11syst) x 10(-4). We determine the magnitude of the Cabibbo-Kobayashi-Maskawa matrix element absolute value V(ub) by combining the partial branching fractions measured in ranges of the momentum transfer squared and theoretical calculations of the form factor. Using a recent lattice QCD calculation, we find absolute value V(ub) = (4.5+/-0.5stat+/-0.3syst(+0.7) -0.5FF x 10(-3), where the last error is due to the normalization of the form factor.

Measurements of branching fractions, polarizations, and direct CP-violation asymmetries in B-->rhoK* and B-->f0(980)K* decays

We report searches for B-meson decays to the charmless final states rhoK* and f0(980)K* with a sample of 232x10(6) BB pairs collected with the BABAR detector at the PEP-II e+e- collider. We measure in units of 10(-6) the following branching fractions, where the first error quoted is statistical and the second systematic, or upper limits are given at the 90% confidence level: B(B+-->rho0K*+)<6.1, B(B+-->rho+K*0)=9.6+/-1.7+/-1.5, B(B0-->rho-K*+)<12.0, B(B0-->rho0K*0)=5.6+/-0.9+/-1.3, B(B+-->f0(980)K*+)=5.2+/-1.2+/-0.5, and B(B0-->f0(980)K*0)<4.3. For the significant modes, we also measure the fraction of longitudinal polarization and the charge asymmetry: fL(B+-->rho+K*0)=0.52+/-0.10+/-0.04, fL(B0-->rho0K*0)=0.57+/-0.09+/-0.08, ACP(B+-->rho+K*0)=-0.01+/-0.16+/-0.02, ACP(B0-->rho0K*0)=0.09+/-0.19+/-0.02, and ACP(B+-->f0(980)K*+)=-0.34+/-0.21+/-0.03.

Measurement of branching fractions and charge asymmetries in B decays to an eta meson and a K* meson

We present measurements of branching fractions and charge asymmetries for the decays B-->etaK*, where K* indicates a spin 0, 1, or 2 Kpi system. The data sample corresponds to 344x10(6) BB pairs collected with the BABAR detector at the PEP-II asymmetric-energy e+ e- collider at SLAC. We measure the branching fractions (in units of 10(-6): B(B0-->etaK*0(892))=16.5+/-1.1+/-0.8, B(B+-->etaK*+(892))=18.9+/-1.8+/-1.3, B(B0-->eta(Kpi)0*0)=11.0+/-1.6+/-1.5, B(B+-->eta(Kpi)0*+)=18.2+/-2.6+/-2.6, B(B0-->etaK2*0(1430))=9.6+/-1.8+/-1.1, and B(B+-->etaK2*+(1430))=9.1+/-2.7+/-1.4. We also determine the charge asymmetries for all decay modes.

Observation of B+ --> K0K+ and B0 --> K0K0

We report observations of the b --> d penguin-dominated decays B+ --> K0K+ and B0 --> K0K0 in 316 fb(-1) of e+ e- collision data collected with the BABAR detector. We measure the branching fractions B(B+ --> K0K+) = (1.61+/-0.44+/-0.09) x 10(-6) and B(B0 --> K0K0 = (1.08+/-0.28+/-0.11) x 10(-6) and the CP-violating charge asymmetry A(CP)(K0K+) = 0.10+/-0.26+/-0.03. Using a vertexing technique previously employed in several analyses of all-neutral final states containing kaons, we report the first measurement of time-dependent CP-violating asymmetries in B0 --> K(S)0K(S)0, obtaining S = -1.28(-0.73-0.16)(+0.80+0.11) and C = -0.40+/-0.41+/-0.06. We also report improved measurements of the branching fraction B(B+ --> K0 pi+) = (23.9+/-1.1+/-1.0) x 10(-6) and CP-violating charge asymmetry A(CP)(K0 pi+) = -0.029+/-0.039+/-0.010.

Measurement of the branching fraction and photon energy moments of B-->Xs gamma and A(CP)(B --> X(s+d gamma))

The photon spectrum in B-->Xs gamma decay, where Xs is any strange hadronic state, is studied using a data sample of 88.5 x 10(6) e+ e- --> Upsilon(4S) --> BB decays collected by the BABAR experiment at the Stanford Linear Accelerator Center. The partial branching fraction, DeltaB(B --> Xs gamma) = (3.67+/-0.29(stat)+/-0.34(syst)+/-0.29(model)) x 10(-4), the first moment <E gamma> = 2.288+/-0.025+/-0.017+/-0.015 GeV, and the second moment E2(gamma) = 0.0328+/-0.0040+/-0.0023+/-0.0036 GeV2 are measured for the photon energy range 1.9 GeV < E gamma < 2.7 GeV. They are also measured for narrower E gamma ranges. The moments are then fit to recent theoretical calculations to extract the heavy quark expansion parameters m(b) and mu2(pi) and to extrapolate the partial branching fraction to E gamma > 1.6 GeV. In addition, the direct CP asymmetry A(CP)(B-->X(s+d gamma) is measured to be -0.110+/-0.115(stat)+/-0.017(syst).

Altered cerebral regulation in type 2 diabetic patients with cardiac autonomic neuropathy

AIMS/HYPOTHESIS

Assessment of cerebral regulation in diabetic patients is often problematic because of the presence of cardiac autonomic neuropathy. We evaluated the technique of oscillatory neck suction at 0.1 Hz to quantify cerebral regulation in diabetic patients and healthy control subjects.

SUBJECTS AND METHODS

In nine type 2 diabetic patients with cardiac autonomic neuropathy and 11 age-matched controls, we measured blood pressure and cerebral blood flow velocity responses to application of 0.1 Hz neck suction. We determined spectral powers and calculated the transfer function gain and phase shift between 0.1 Hz blood pressure and cerebral blood flow velocity oscillations as parameters of cerebral regulation.

RESULTS

In the patients and control subjects, neck suction did not significantly influence mean values of the RR interval, blood pressure and cerebral blood flow velocity. The powers of 0.1 Hz blood pressure and cerebral blood flow velocity oscillations increased in the control subjects, but remained stable in the patients. Transfer function gain remained stable in both groups. Phase shift decreased in the patients, but remained stable in control subjects.

CONCLUSIONS/INTERPRETATION

The absence of an increase in the power of 0.1 Hz blood pressure and cerebral blood flow velocity oscillations confirmed autonomic neuropathy in the diabetic patients. Gain analysis did not show altered cerebral regulation. The decrease in phase shift in the patients indicates a more passive transmission of neck suction-induced blood pressure fluctuations onto the cerebrovascular circulation, i.e. altered cerebral regulation, in the patients, and is therefore suited to identifying subtle impairment of cerebral regulation in these patients.