Conserving Approximations in Time-Dependent Density Functional Theory

In the present work we propose a theory for obtaining successively better approximations to the linear response functions of time-dependent density or current-density functional theory. The new technique is based on the variational approach to many-body perturbation theory (MBPT) as developed during the sixties and later expanded by us in the mid nineties. Due to this feature the resulting response functions obey a large number of conservation laws such as particle and momentum conservation and sum rules. The quality of the obtained results is governed by the physical processes built in through MBPT but also by the choice of variational expressions. We here present several conserving response functions of different sophistication to be used in the calculation of the optical response of solids and nano-scale systems.Comment: 11 pages, 4 figures, revised versio

Human impact on vegetation at the Alpine tree-line ecotone during the last millennium: lessons from high temporal and palynological resolution

Three mires and a small lake in the Swiss and Austrian Alps were studied palynologically at high resolution, covering the last 1,000, 400, 50 and 1,200years, respectively. Methodological lessons include: (1) Sub-decadal resolution in upper, little-decomposed peat layers reveals recurrent marked fluctuations in both percentages and influx of regional tree-pollen types, reflecting variations in pollen production rather than in plant-population sizes. (2) Intermittent, single-spectrum pollen maxima in samples of sub-decadal resolution indicate pollen transport in clumps. This type of pollen transport may remain unrecognized in sections with lower sampling resolution, which may then lead to inappropriate interpretation in terms of plant-population sizes. (3) The detection of short-lived phases of human impact in decomposed peat requires sampling intervals as close as 0.2cm. (4) PAR (pollen influx) may reflect vegetation dynamics more faithfully than percentages. Reliable PAR, however, is difficult to achieve in Alpine mires due to past human impact on peat growth, even when complex depth-age modelling techniques are used. Critical comparison of PAR with percentages is therefore essential. (5) Careful consideration of spatial scales in pollen signals (local-regional and subdivisions) is essential for a realistic palaeo-ecological interpretation. Results in terms of past human impact on vegetation are summarized as follows: (1) Trends in pollen types reflecting regional human action are in general agreement with earlier findings for the western Swiss Alps, allowing for regional differences. (2) All mires in the Alps investigated here and in an earlier study experienced human impact during the last millennium. The studied small lake, lying in sub-alpine pasture, records forest dynamics at a lower elevation since a.d. 80

Total energies from variational functionals of the Green function and the renormalized four-point vertex

We derive variational expressions for the grand potential or action in terms of the many-body Green function $G$ which describes the propagation of particles and the renormalized four-point vertex $\Gamma$ which describes the scattering of two particles in many-body systems. The main ingredient of the variational functionals is a term we denote as the $\Xi$-functional which plays a role analogously to the usual $\Phi$-functional studied by Baym (G.Baym, Phys.Rev. 127, 1391 (1962)) in connection with the conservation laws in many-body systems. We show that any $\Xi$-derivable theory is also $\Phi$-derivable and therefore respects the conservation laws. We further set up a computational scheme to obtain accurate total energies from our variational functionals without having to solve computationally expensive sets of self-consistent equations. The input of the functional is an approximate Green function $\tilde{G}$ and an approximate four-point vertex $\tilde{\Gamma}$ obtained at a relatively low computational cost. The variational property of the functional guarantees that the error in the total energy is only of second order in deviations of the input Green function and vertex from the self-consistent ones that make the functional stationary. The functionals that we will consider for practical applications correspond to infinite order summations of ladder and exchange diagrams and are therefore particularly suited for applications to highly correlated systems. Their practical evaluation is discussed in detail.Comment: 21 pages, 10 figures. Physical Review B (accepted

Genome-wide methylome analysis using MethylCap-seq uncovers 4 hypermethylated markers with high sensitivity for both adeno- and squamous-cell cervical carcinoma

Background: Cytology-based screening methods for cervical adenocarcinoma (ADC) and to a lesser extent squamous-cell carcinoma (SCC) suffer from low sensitivity. DNA hypermethylation analysis in cervical scrapings may improve detection of SCC, but few methylation markers have been described for ADC. We aimed to identify novel methylation markers for the early detection of both ADC and SCC. Results: Genome-wide methylation profiling for 20 normal cervices, 6 ADC and 6 SCC using MethylCap-seq yielded 53 candidate regions hypermethylated in both ADC and SCC. Verification and independent validation of the 15 most significant regions revealed 5 markers with differential methylation between 17 normals and 13 cancers. Quantitative methylation-specific PCR on cervical cancer scrapings resulted in detection rates ranging between 80% and 92% while between 94% and 99% of control scrapings tested negative. Four markers (SLC6A5, SOX1, SOX14 and TBX20) detected ADC and SCC with similar sensitivity. In scrapings from women referred with an abnormal smear (n = 229), CIN3+ sensitivity was between 36% and 71%, while between 71% and 93% of adenocarcinoma in situ (AdCIS) were detected; and CIN0/1 specificity was between 88% and 98%. Compared to hrHPV, the combination SOX1/SOX14 showed a similar CIN3+ sensitivity (80% vs. 75%, respectively, P>0.2), while specificity improved (42% vs. 84%, respectively, P < 10(-5)). Conclusion: SOX1 and SOX14 are methylation biomarkers applicable for screening of all cervical cancer types

The Leiden Ranking 2011/2012: Data collection, indicators, and interpretation

The Leiden Ranking 2011/2012 is a ranking of universities based on bibliometric indicators of publication output, citation impact, and scientific collaboration. The ranking includes 500 major universities from 41 different countries. This paper provides an extensive discussion of the Leiden Ranking 2011/2012. The ranking is compared with other global university rankings, in particular the Academic Ranking of World Universities (commonly known as the Shanghai Ranking) and the Times Higher Education World University Rankings. Also, a detailed description is offered of the data collection methodology of the Leiden Ranking 2011/2012 and of the indicators used in the ranking. Various innovations in the Leiden Ranking 2011/2012 are presented. These innovations include (1) an indicator based on counting a university's highly cited publications, (2) indicators based on fractional rather than full counting of collaborative publications, (3) the possibility of excluding non-English language publications, and (4) the use of stability intervals. Finally, some comments are made on the interpretation of the ranking, and a number of limitations of the ranking are pointed out

Levels of self-consistency in the GW approximation

We perform $GW$ calculations on atoms and diatomic molecules at different levels of self-consistency and investigate the effects of self-consistency on total energies, ionization potentials and on particle number conservation. We further propose a partially self-consistent $GW$ scheme in which we keep the correlation part of the self-energy fixed within the self-consistency cycle. This approximation is compared to the fully self-consistent $GW$ results and to the $G W_0$ and the $G_0W_0$ approximations. Total energies, ionization potentials and two-electron removal energies obtained with our partially self-consistent $GW$ approximation are in excellent agreement with fully self-consistent $GW$ results while requiring only a fraction of the computational effort. We also find that self-consistent and partially self-consistent schemes provide ionization energies of similar quality as the $G_0W_0$ values but yield better total energies and energy differences.Comment: 11 pages, 3 figures, 3 table

Refined stellar, orbital and planetary parameters of the eccentric HAT-P-2 planetary system

We present refined parameters for the extrasolar planetary system HAT-P-2 (also known as HD 147506), based on new radial velocity and photometric data. HAT-P-2b is a transiting extrasolar planet that exhibits an eccentric orbit. We present a detailed analysis of the planetary and stellar parameters, yielding consistent results for the mass and radius of the star, better constraints on the orbital eccentricity, and refined planetary parameters. The improved parameters for the host star are M_star = 1.36 +/- 0.04 M_sun and R_star = 1.64 +/- 0.08 R_sun, while the planet has a mass of M_p = 9.09 +/- 0.24 M_Jup and radius of R_p = 1.16 +/- 0.08 R_Jup. The refined transit epoch and period for the planet are E = 2,454,387.49375 +/- 0.00074 (BJD) and P = 5.6334729 +/- 0.0000061 (days), and the orbital eccentricity and argument of periastron are e = 0.5171 +/- 0.0033 and omega = 185.22 +/- 0.95 degrees. These orbital elements allow us to predict the timings of secondary eclipses with a reasonable accuracy of ~15 minutes. We also discuss the effects of this significant eccentricity including the characterization of the asymmetry in the transit light curve. Simple formulae are presented for the above, and these, in turn, can be used to constrain the orbital eccentricity using purely photometric data. These will be particularly useful for very high precision, space-borne observations of transiting planets.Comment: Revised version, accepted for publication in MNRAS, 11 pages, 6 figure

The Tip of the Red Giant Branch Distance to the Large Magellanic Cloud

We present the I-band luminosity function of the red giant branch stars in the Large Magellanic Cloud (LMC) using the data from the Magellanic Clouds Photometric Survey (Zaritsky, Harris & Thompson, 1997). Selecting stars in uncrowded, low-extinction regions, a discontinuity in the luminosity function is observed at I_0 = 14.54 mag. Identifying this feature with the tip of the red giant branch (TRGB), and adopting an absolute TRGB magnitude of -4.05 +- 0.04 mag based on the calibration of Lee, Freedman & Madore (1993), we obtain a distance modulus of 18.59 +- 0.09 (random) +- 0.16 (systematic) mag. If the theoretical TRGB calibration provided by Cassisi & Salaris (1997) is adopted instead, the derived distance would be 4% greater. The LMC distance modulus reported here, 18.59 +- 0.09, is larger by 0.09 mag (1-sigma) than the value that is most commonly used in the extragalactic distance scale calibrated by the period-luminosity relation of the Cepheid variable stars. Our TRGB distance modulus agrees with several RR Lyrae distances to the LMC based on HIPPARCOS parallaxes. Finally, we note that using the same MCPS data, we obtain a distance modulus of 18.29 +- 0.03 mag using the red clump method, which is shorter by 0.3 mag compared to the TRGB estimate.Comment: 19 pages, 5 figure

Near and Mid-IR Photometry of the Pleiades, and a New List of Substellar Candidate Members

We make use of new near and mid-IR photometry of the Pleiades cluster in order to help identify proposed cluster members. We also use the new photometry with previously published photometry to define the single-star main sequence locus at the age of the Pleiades in a variety of color-magnitude planes. The new near and mid-IR photometry extend effectively two magnitudes deeper than the 2MASS All-Sky Point Source catalog, and hence allow us to select a new set of candidate very low mass and sub-stellar mass members of the Pleiades in the central square degree of the cluster. We identify 42 new candidate members fainter than Ks =14 (corresponding to 0.1 Mo). These candidate members should eventually allow a better estimate of the cluster mass function to be made down to of order 0.04 solar masses. We also use new IRAC data, in particular the images obtained at 8 um, in order to comment briefly on interstellar dust in and near the Pleiades. We confirm, as expected, that -- with one exception -- a sample of low mass stars recently identified as having 24 um excesses due to debris disks do not have significant excesses at IRAC wavelengths. However, evidence is also presented that several of the Pleiades high mass stars are found to be impacting with local condensations of the molecular cloud that is passing through the Pleiades at the current epoch.Comment: Accepted to ApJS; data tables and embedded-figure version available at http://spider.ipac.caltech.edu/staff/stauffer/pleiades07

Tyrosine Kinase Inhibitors and Proton Pump Inhibitors:An Evaluation of Treatment Options

Tyrosine kinase inhibitors (TKIs) have rapidly become an established factor in oncology, and have been shown to be effective in a wide variety of solid and hematologic malignancies. Use of the oral administration route of TKIs offers flexibility and is convenient for the patient; however, despite these advantages, the oral route of administration also causes a highly relevant new problem. Acid-inhibitory drugs, such as proton pump inhibitors (PPIs), increase the intragastric pH, which may subsequently decrease TKI solubility, bioavailability, and treatment efficacy. Clear and practical advice on how to manage PPI use during TKI therapy is currently not available in the literature. Since PPIs are extensively used during TKI therapy, prescribers are presented with a big dilemma as to whether or not to continue the combined treatment, resulting in patients possibly being deprived of optimal therapy. When all pharmacological characteristics and data of either TKIs and PPIs are considered, practical and safe advice on how to manage this drug combination can be given