Variation in the intensity of selection on codon bias over time causes contrasting patterns of base composition evolution in Drosophila

Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism dataset from D. simulans. We analysed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism dataset from an African population of D. melanogaster. By using D. yakuba as an outgroup, we found clear evidence for selection on 4-fold sites along both lineages over a substantial period, with the intensity of selection increasing with GC content. Based on an explicit model of base composition evolution, we suggest that the observed AT-biased substitution pattern in both lineages is probably due to an ancestral reduction in selection intensity, and is unlikely to be the result of an increase in mutational bias towards AT alone. By using two polymorphism-based methods for estimating selection coefficients over different timescales, we show that the selection intensity on codon usage has been rather stable in D. simulans in the recent past, but the long-term estimates in D. melanogaster are much higher than the short-term ones, indicating a continuing decline in selection intensity, to such an extent that the short-term estimates suggest that selection is only active in the most GC-rich parts of the genome. Finally, we provide evidence for complex evolutionary patterns in the putatively neutral short introns, which cannot be explained by the standard GC-biased gene conversion model. These results reveal a dynamic picture of base composition evolution

Variational Monte Carlo Calculations of 3^3H and 4^4He with a relativistic Hamiltonian - II

In relativistic Hamiltonians the two-nucleon interaction is expressed as a sum of $\tilde{v}_{ij}$, the interaction in the ${\bf P}_{ij}=0$ rest frame, and the ``boost interaction'' $\delta v({\bf P}_{ij})$ which depends upon the total momentum ${\bf P}_{ij}$ and vanishes in the rest frame. The $\delta v$ can be regarded as a sum of four terms: $\delta v_{RE}$, $\delta v_{LC}$, $\delta v_{TP}$ and $\delta v_{QM}$; the first three originate from the relativistic energy-momentum relation, Lorentz contraction and Thomas precession, while the last is purely quantum. The contributions of $\delta v_{RE}$ and $\delta v_{LC}$ have been previously calculated with the variational Monte Carlo method for $^3$H and $^4$He. In this brief note we report the results of similar calculations for the contributions of $\delta v_{TP}$ and $\delta v_{QM}$. These are found to be rather small.Comment: 7 pages, P-94-09-07

Electromagnetic Dissociation of Nuclei in Heavy-Ion Collisions

Large discrepancies have been observed between measured Electromagnetic Dissociation(ED) cross sections and the predictions of the semiclassical Weiz\"acker-Williams-Fermi(WWF) method. In this paper, the validity of the semiclassical approximation is examined. The total cross section for electromagnetic excitation of a nuclear target by a spinless projectile is calculated in first Born approximation, neglecting recoil. The final result is expressed in terms of correlation functions and convoluted densities in configuration space. The result agrees with the WWF approximation to leading order(unretarded electric dipole approximation), but the method allows an analytic evaluation of the cutoff, which is determined by the details of the electric dipole transition charge density. Using the Goldhaber-Teller model of that density, and uniform charge densities for both projectile and target, the cutoff is determined for the total cross section in the nonrelativistic limit, and found to be smaller than values currently used for ED calculations. In addition, cross sections are calculated using a phenomenological momentum space cutoff designed to model final state interactions. For moderate projectile energies, the calculated ED cross section is found to be smaller than the semiclassical result, in qualitative agreement with experiment.Comment: 28 page

A deficit of ultraluminous X-ray sources in luminous infrared galaxies

We present results from a Chandra study of ultraluminous X-ray sources (ULXs) in a sample of 17 nearby (DL < 60 Mpc) luminous infrared galaxies (LIRGs), selected to have star formation rates (SFRs) in excess of 7 M⊙ yr−1 and low foreground Galactic column densities (NH ≲ 5 × 1020 cm−2). A total of 53 ULXs were detected and we confirm that this is a complete catalogue of ULXs for the LIRG sample. We examine the evolution of ULX spectra with luminosity in these galaxies by stacking the spectra of individual objects in three luminosity bins, finding a distinct change in spectral index at luminosity ∼2 × 1039 erg s−1. This may be a change in spectrum as 10 M⊙ black holes transit from an ∼ Eddington to a super-Eddington accretion regime, and is supported by a plausible detection of partially ionized absorption imprinted on the spectrum of the luminous ULX (LX ≈ 5 × 1039 erg s−1) CXOU J024238.9-000055 in NGC 1068, consistent with the highly ionized massive wind that we would expect to see driven by a super-Eddington accretion flow. This sample shows a large deficit in the number of ULXs detected per unit SFR (0.2 versus 2 ULXs, per M⊙ yr−1) compared to the detection rate in nearby (DL < 14.5 Mpc) normal star-forming galaxies. This deficit also manifests itself as a lower differential X-ray luminosity function normalization for the LIRG sample than for samples of other star-forming galaxies. We show that it is unlikely that this deficit is a purely observational effect. Part of this deficit might be attributable to the high metallicity of the LIRGs impeding the production efficiency of ULXs and/or a lag between the star formation starting and the production of ULXs; however, we argue that the evidence – including very low NULX/LFIR, and an even lower ULX incidence in the central regions of the LIRGs – shows that the main culprit for this deficit is likely to be the high column of gas and dust in these galaxies, that fuels the high SFR but also acts to obscure many ULXs from our view

Haloperidol and Ziprasidone for Treatment of Delirium in Critical Illness

BACKGROUND: There are conflicting data on the effects of antipsychotic medications on delirium in patients in the intensive care unit (ICU). METHODS: In a randomized, double-blind, placebo-controlled trial, we assigned patients with acute respiratory failure or shock and hypoactive or hyperactive delirium to receive intravenous boluses of haloperidol (maximum dose, 20 mg daily), ziprasidone (maximum dose, 40 mg daily), or placebo. The volume and dose of a trial drug or placebo was halved or doubled at 12-hour intervals on the basis of the presence or absence of delirium, as detected with the use of the Confusion Assessment Method for the ICU, and of side effects of the intervention. The primary end point was the number of days alive without delirium or coma during the 14-day intervention period. Secondary end points included 30-day and 90-day survival, time to freedom from mechanical ventilation, and time to ICU and hospital discharge. Safety end points included extrapyramidal symptoms and excessive sedation. RESULTS: Written informed consent was obtained from 1183 patients or their authorized representatives. Delirium developed in 566 patients (48%), of whom 89% had hypoactive delirium and 11% had hyperactive delirium. Of the 566 patients, 184 were randomly assigned to receive placebo, 192 to receive haloperidol, and 190 to receive ziprasidone. The median duration of exposure to a trial drug or placebo was 4 days (interquartile range, 3 to 7). The median number of days alive without delirium or coma was 8.5 (95% confidence interval [CI], 5.6 to 9.9) in the placebo group, 7.9 (95% CI, 4.4 to 9.6) in the haloperidol group, and 8.7 (95% CI, 5.9 to 10.0) in the ziprasidone group (P=0.26 for overall effect across trial groups). The use of haloperidol or ziprasidone, as compared with placebo, had no significant effect on the primary end point (odds ratios, 0.88 [95% CI, 0.64 to 1.21] and 1.04 [95% CI, 0.73 to 1.48], respectively). There were no significant between-group differences with respect to the secondary end points or the frequency of extrapyramidal symptoms. CONCLUSIONS: The use of haloperidol or ziprasidone, as compared with placebo, in patients with acute respiratory failure or shock and hypoactive or hyperactive delirium in the ICU did not significantly alter the duration of delirium. (Funded by the National Institutes of Health and the VA Geriatric Research Education and Clinical Center; MIND-USA ClinicalTrials.gov number, NCT01211522 .)

Ownership diversity and fragmentation: a barrier to urban centre resilience

Fragmentation of ownership has long been a recognised constraint to UK city centre development, a complexity that is growing in significance as centres try to manage the decline in physical retailing and transform obsolete retail units. Yet, our understanding of the structure of ownership and how that might be facilitating or inhibiting urban change remains weak. In this paper, the objective is to address this gap by examining the structure and diversity of land ownership in five retailing centres - Edinburgh, Glasgow, Hull, Liverpool, and Nottingham – between 2000–2017 using original databases created by linking administrative and commercial property data sets. Overall, the analysis finds property ownership to be spatially complex with ownership richness and diversity generally rising over the study period. The study also reveals that ownership structure has been shifting away from financial institutions towards overseas investors, private individuals and unlisted property companies, implying greater fragmentation of ownership. While the greater diversity in ownership should stimulate competition and innovation in property market practices, the shift in balance from equity-rich larger investors towards smaller and sometimes unknown investors makes urban centre management harder to manage. This suggests policymakers need to rethink the urban governance model to find a better way to galvanise the actions of this increasing disparate group of stakeholders if their visions of more resilient, mixed use city centres are to be realised

Simple multiplexing scheme for fibre optic grating sensor network

A new approach for the interrogation of a large number of fiber-optic grating sensors is proposed and demonstrated for a small number of sensors in which signal recovery is achieved by matching a receiving grating to its corresponding sensor. This technique is demonstrated for both quasi-static and periodic measurands, and the resolution achieved for a single sensor-receiving grating pair for quasi-static strain of 4.12µε

Dynamics of two colliding Bose-Einstein condensates in an elongated magneto-static trap

We study the dynamics of two interacting Bose-Einstein condensates, by numerically solving two coupled Gross-Pitaevskii equations at zero temperature. We consider the case of a sudden transfer of atoms between two trapped states with different magnetic moments: the two condensates are initially created with the same density profile, but are trapped into different magnetic potentials, whose minima are vertically displaced by a distance much larger than the initial size of both condensates. Then the two condensates begin to perform collective oscillations, undergoing a complex evolution, characterized by collisions between the two condensates. We investigate the effects of their mutual interaction on the center-of-mass oscillations and on the time evolution of the aspect ratios. Our theoretical analysis provides a useful insight into the recent experimental observations by Maddaloni et al., cond-mat/0003402.Comment: 8 pages, 7 figures, RevTe