Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data

Background: Disordered proteins need to be expressed to carry out specified functions; however, their accumulation in the cell can potentially cause major problems through protein misfolding and aggregation. Gene expression levels, mRNA decay rates, microRNA (miRNA) targeting and ubiquitination have critical roles in the degradation and disposal of human proteins and transcripts. Here, we describe a study examining these features to gain insights into the regulation of disordered proteins. Results: In comparison with ordered proteins, disordered proteins have a greater proportion of predicted ubiquitination sites. The transcripts encoding disordered proteins also have higher proportions of predicted miRNA target sites and higher mRNA decay rates, both of which are indicative of the observed lower gene expression levels. The results suggest that the disordered proteins and their transcripts are present in the cell at low levels and/or for a short time before being targeted for disposal. Surprisingly, we find that for a significant proportion of highly disordered proteins, all four of these trends are reversed. Predicted estimates for miRNA targets, ubiquitination and mRNA decay rate are low in the highly disordered proteins that are constitutively and/or highly expressed. Conclusions: Mechanisms are in place to protect the cell from these potentially dangerous proteins. The evidence suggests that the enrichment of signals for miRNA targeting and ubiquitination may help prevent the accumulation of disordered proteins in the cell. Our data also provide evidence for a mechanism by which a significant proportion of highly disordered proteins (with high expression levels) can escape rapid degradation to allow them to successfully carry out their function

The geology of the Falkland Islands

This report is complementary to the 1:250 000 scale geological map of the Falkland Islands compiled in 1998. The report and map are products of the Falkland Islands Geological Mapping Project (1996-1998). Geological observation and research in the Islands date from 1764. The Islands were visited during two pioneering scientific cruises in the 19th century. Subsequently, many scientists visited en route to the Antarctic or Patagonia. Geological affinities to other parts of the southern continents, especially South Africa, were noted early in the 20th century. There have been two previous attempts to create a geological map of the Islands, both motivated primarily by the search for economic mineral deposits onshore. In the last few decades much effort has been directed to understanding the Falklands’ place in Gondwana, the processes by which the Islands have moved to their present position by continental drift and the concomitant development of offshore sedimentary basins. Considerable progress in describing the superficial deposits was made in the 1970’s, and during the last ten years. The stratigraphic subdivisions of the geological sequence shown on the previous geological maps have been substantiated and defined more rigorously than before. In addition, several new stratigraphic units have been recognised. Each unit is described with an introductory summary of composition and distribution, followed by comments on nomenclature and stratigraphic relationships, associated landforms, distinguishing characters, and the criteria used to locate and survey the stratigraphic base. Detailed descriptions of composition, sedimentary structures and fossil content then lead to brief comments on the environment of deposition, age and correlation. The bedrock geological formations (‘solid geology’) can be divided into four age groups. The Proterozoic granites and amphibolite facies gneisses of the Cape Meredith Complex (about 1150 to 1000 million years old) are overlain in turn by sedimentary sequences of the ?Silurian to Devonian West Falkland Group and the Carboniferous to Permian Lafonia Group. Jurassic igneous rocks are widespread but only locally abundant. The West Falkland Group is dominated by sandstones, with some siltstones and mudstones. The oldest of four formations, the Port Stephens Formation, is divided into seven members, representing marine to fluvial environments. The basal member on East Falkland is probably the oldest part of the sedimentary sequence and might be latest Ordovician in age, but is more probably Silurian. The overlying Albemarle Member is notable for abundant trace fossils, mainly Skolithos, but also contains a new ichnospecies of Heimdallia. The succeeding marine Fox Bay Formation contains the Early to Middle Devonian Malvinokaffric invertebrate fossil fauna. One proximal facies member is recognised in the west. The Port Philomel Formation represents deltaic facies. It is notable for abundant fossil plant debris, most conspicuously lycophyte stems. The Late Devonian Port Stanley Formation, which includes the Stanley Quartzite, marks a return to marine conditions. The sandstones in the West Falkland Group are mostly quartz arenites and subarkoses, consistent with derivation from an area of stable continent crust. The West Falkland Group can be correlated with parts of the Cape Supergroup of South Africa

Scaling Flows and Dissipation in the Dilute Fermi Gas at Unitarity

We describe recent attempts to extract the shear viscosity of the dilute Fermi gas at unitarity from experiments involving scaling flows. A scaling flow is a solution of the hydrodynamic equations that preserves the shape of the density distribution. The scaling flows that have been explored in the laboratory are the transverse expansion from a deformed trap ("elliptic flow"), the expansion from a rotating trap, and collective oscillations. We discuss advantages and disadvantages of the different experiments, and point to improvements of the theoretical analysis that are needed in order to achieve definitive results. A conservative bound based on the current data is that the minimum of the shear viscosity to entropy density ration is that eta/s is less or equal to 0.5 hbar/k_B.Comment: 32 pages, prepared for "BCS-BEC crossoverand the Unitary Fermi Gas", Lecture Notes in Physics, W. Zwerger (editor), Fig. 5 corrected, note added; final version, corrected typo in equ. 9

Effect of early life antibiotic use on serologic responses to oral rotavirus vaccine in the MAL-ED birth cohort study

Background: Oral rotavirus vaccine efficacy is lower in low- and middle-income countries (LMICs) than in high-income countries. The degree to which antibiotic use impacts rotavirus vaccine immunogenicity in LMICs is unknown. Using data from a multisite prospective birth cohort study of malnutrition and enteric disease, MAL-ED, we examined the effect of early life antibiotic use on the immune response to rotavirus vaccine. Methods: We assessed whether antibiotic use from birth up to 7 days following rotavirus vaccine series completion was associated with rotavirus seropositivity at 7 months of age in Brazil, Peru, and South Africa using a modified Poisson regression. We then used parametric g-computation to estimate the impact of hypothetical interventions that treated all children and alternatively prevented inappropriate antibiotic treatments on seropositivity. Results: Of 537 children, 178 (33%) received at least one antibiotic course during the exposure window. Probability of seropositivity was 40% higher among children who had at least one course of antibiotics compared with those with no antibiotic exposure (PR: 1.40, 95% CI: 1.04, 1.89). There was no significant difference by the number of antibiotic courses received or total duration of antibiotics. Treating all children with antibiotics would be associated with a 19% (95% CI: 18%, 21%) absolute increase in seropositivity at 7 months. In contrast, removing inappropriate antibiotics would result in a 4% absolute reduction (95% CI: −5%, −2%) in seropositivity. Conclusions: Early life antibiotic use was associated with increased seropositivity. However, a hypothetical intervention to remove inappropriate antibiotics would have little effect on overall seropositivity. Further investigation into the underlying mechanisms of antibiotic use on the infant gut microbiome and immune response are needed

Transporting monovalent rotavirus vaccine efficacy estimates to an external target population: a secondary analysis of data from a randomised controlled trial in Malawi

Oral rotavirus vaccine efficacy estimates from randomised controlled trials are highly variable across settings. Although the randomised study design increases the likelihood of internal validity of findings, results from trials may not always apply outside the context of the study due to differences between trial participants and the target population. Here, we used a weight-based method to transport results from a monovalent rotavirus vaccine clinical trial conducted in Malawi between 2005 and 2008 to a target population of all trial-eligible children in Malawi, represented by data from the 2015-2016 Malawi Demographic and Health Survey (DHS). We reweighted trial participants to reflect the population characteristics described by the Malawi DHS. Vaccine efficacy was estimated for 1008 trial participants after applying these weights such that they represented trial-eligible children in Malawi. We also conducted subgroup analyses to examine the heterogeneous treatment effects by stunting and tuberculosis vaccination status at enrolment. In the original trial, the estimates of one-year vaccine efficacy against severe rotavirus gastroenteritis and any-severity rotavirus gastroenteritis in Malawi were 49.2% (95% CI 15.6%-70.3%) and 32.1% (95% CI 2.5%-53.1%), respectively. After weighting trial participants to represent all trial-eligible children in Malawi, vaccine efficacy increased to 62.2% (95% CI 35.5%-79.0%) against severe rotavirus gastroenteritis and 38.9% (95% CI 11.4%-58.5%) against any-severity rotavirus gastroenteritis. Rotavirus vaccine efficacy may differ between trial participants and target populations when these two populations differ. Differences in tuberculosis vaccination status between the trial sample and DHS population contributed to varying trial and target population vaccine efficacy estimates

Observation of a Narrow Resonance of Mass 2.46 GeV/c^2 Decaying to D_s^*+ pi^0 and Confirmation of the D_sJ^* (2317) State

Using 13.5 inverse fb of e+e- annihilation data collected with the CLEO II detector we have observed a narrow resonance in the Ds*+pi0 final state, with a mass near 2.46 GeV. The search for such a state was motivated by the recent discovery by the BaBar Collaboration of a narrow state at 2.32 GeV, the DsJ*(2317)+ that decays to Ds+pi0. Reconstructing the Ds+pi0 and Ds*+pi0 final states in CLEO data, we observe peaks in both of the corresponding reconstructed mass difference distributions, dM(Dspi0)=M(Dspi0)-M(Ds) and dM(Ds*pi0)=M(Ds*pi0)-M(Ds*), both of them at values near 350 MeV. We interpret these peaks as signatures of two distinct states, the DsJ*(2317)+ plus a new state, designated as the DsJ(2463)+. Because of the similar dM values, each of these states represents a source of background for the other if photons are lost, ignored or added. A quantitative accounting of these reflections confirms that both states exist. We have measured the mean mass differences = 350.0 +/- 1.2 [stat] +/- 1.0 [syst] MeV for the DsJ*(2317) state, and = 351.2 +/- 1.7 [stat] +/- 1.0 [syst] MeV for the new DsJ(2463)+ state. We have also searched, but find no evidence, for decays of the two states via the channels Ds*+gamma, Ds+gamma, and Ds+pi+pi-. The observations of the two states at 2.32 and 2.46 GeV, in the Ds+pi0 and Ds*+pi0 decay channels respectively, are consistent with their interpretations as (c anti-strange) mesons with orbital angular momentum L=1, and spin-parities of 0+ and 1+.Comment: 16 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, version to be published in Physical Review D; minor modifications and fixes to typographical errors, plus an added section on production properties. The main results are unchanged; they supersede those reported in hep-ex/030501

Measurement of the Charge Asymmetry in B→K∗(892)±π∓B\to K^* (892)^{\pm}\pi^{\mp}

We report on a search for a CP-violating asymmetry in the charmless hadronic decay B -> K*(892)+- pi-+, using 9.12 fb^-1 of integrated luminosity produced at \sqrt{s}=10.58 GeV and collected with the CLEO detector. We find A_{CP}(B -> K*(892)+- pi-+) = 0.26+0.33-0.34(stat.)+0.10-0.08(syst.), giving an allowed interval of [-0.31,0.78] at the 90% confidence level.Comment: 7 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, submitted to PR

Study of the q^2-Dependence of B --> pi ell nu and B --> rho(omega)ell nu Decay and Extraction of |V_ub|

We report on determinations of |Vub| resulting from studies of the branching fraction and q^2 distributions in exclusive semileptonic B decays that proceed via the b->u transition. Our data set consists of the 9.7x10^6 BBbar meson pairs collected at the Y(4S) resonance with the CLEO II detector. We measure B(B0 -> pi- l+ nu) = (1.33 +- 0.18 +- 0.11 +- 0.01 +- 0.07)x10^{-4} and B(B0 -> rho- l+ nu) = (2.17 +- 0.34 +0.47/-0.54 +- 0.41 +- 0.01)x10^{-4}, where the errors are statistical, experimental systematic, systematic due to residual form-factor uncertainties in the signal, and systematic due to residual form-factor uncertainties in the cross-feed modes, respectively. We also find B(B+ -> eta l+ nu) = (0.84 +- 0.31 +- 0.16 +- 0.09)x10^{-4}, consistent with what is expected from the B -> pi l nu mode and quark model symmetries. We extract |Vub| using Light-Cone Sum Rules (LCSR) for 0<= q^2<16 GeV^2 and Lattice QCD (LQCD) for 16 GeV^2 <= q^2 < q^2_max. Combining both intervals yields |Vub| = (3.24 +- 0.22 +- 0.13 +0.55/-0.39 +- 0.09)x10^{-3}$ for pi l nu, and |Vub| = (3.00 +- 0.21 +0.29/-0.35 +0.49/-0.38 +-0.28)x10^{-3} for rho l nu, where the errors are statistical, experimental systematic, theoretical, and signal form-factor shape, respectively. Our combined value from both decay modes is |Vub| = (3.17 +- 0.17 +0.16/-0.17 +0.53/-0.39 +-0.03)x10^{-3}.Comment: 45 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, submitted to PR

Search for CP Violation in D^0--> K_S^0 pi^+pi^-

We report on a search for CP violation in the decay of D0 and D0B to Kshort pi+pi-. The data come from an integrated luminosity of 9.0 1/fb of e+e- collisions at sqrt(s) ~ 10 GeV recorded with the CLEO II.V detector. The resonance substructure of this decay is well described by ten quasi-two-body decay channels (K*-pi+, K*0(1430)-pi+, K*2(1430)-pi+, K*(1680)-pi+, Kshort rho, Kshort omega, Kshort f0(980), Kshort f2(1270), Kshort f0(1370), and the ``wrong sign'' K*+ pi-) plus a small non-resonant component. We observe no evidence for CP violation in the amplitudes and phases that describe the decay D0 to K_S^0 pi+pi-.Comment: 10 pages, 3 figures, also available at http://w4.lns.cornell.edu/public/CLNS/, submitted to PR

Measurement of Lepton Momentum Moments in the Decay bar{B} \to X \ell \bar{\nu} and Determination of Heavy Quark Expansion Parameters and |V_cb|

We measure the primary lepton momentum spectrum in B-bar to X l nu decays, for p_l > 1.5 GeV/c in the B rest frame. From this, we calculate various moments of the spectrum. In particular, we find R_0 = [int(E_l>1.7) (dGam/dE_sl)*dE_l] / [int(E_l>1.5) (dGam/dE_sl)*dE_l] = 0.6187 +/- 0.0014_stat +/- 0.0016_sys and R_1 = [int(E_l>1.5) E_l(dGam/dE_sl)*dE_l] / [int(E_l>1.5) (dGam/dE_sl)*dE_l] = (1.7810 +/- 0.0007_stat +/- 0.0009_sys) GeV. We use these moments to determine non-perturbative parameters governing the semileptonic width. In particular, we extract the Heavy Quark Expansion parameters Lambda-bar = (0.39 +/- 0.03_stat +/- 0.06_sys +/- 0.12_th) GeV and lambda_1 = (-0.25 +/- 0.02_stat +/- 0.05_sys +/- 0.14_th) GeV^2. The theoretical constraints used are evaluated through order 1/M_B^3 in the non-perturbative expansion and beta_0*alpha__s^2 in the perturbative expansion. We use these parameters to extract |V_cb| from the world average of the semileptonic width and find |V_cb| = (40.8 +/- 0.5_Gam-sl +/- 0.4_(lambda_1,Lambda-bar)-exp +/- 0.9_th) x 10^-3. In addition, we extract the short range b-quark mass m_b^1S = (4.82 +/- 0.07_exp +/- 0.11_th) GeV/c^2. Finally, we discuss the implications of our measurements for the theoretical understanding of inclusive semileptonic processes.Comment: 21 pages postscript, also available through http://w4.lns.cornell.edu/public/CLNS, submitted to PR