PPD v1.0—an integrated, web-accessible database of experimentally determined protein pK(a) values

The Protein pK(a) Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pK(a) values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pK(a) archive and as a source of data that allows for the development and improvement of pK(a) prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information. The database can be found at the following URL:

Assessment of maximum aerobic capacity and anaerobic threshold of elite ballet dancers

An athlete’s cardiorespiratory profile, maximal aerobic capacity and anaerobic threshold, is affected by their training regimen and competition demands. The purpose of the present study is to ascertain whether there are company rank differences in maximal aerobic capacity and anaerobic threshold in elite classical ballet dancers. Seventy-four volunteers (M=34, F=40) were recruited from two full-time professional classical ballet companies. All participants completed a continuous incremental treadmill protocol with a 1 km.h-1 speed increase at the end of each 1-minute stage until termination criteria had been achieved (e.g. voluntary cessation, RER <1.15, heart rate ±5b.min-1 of estimated HRmax). Peak VO2 (5-breathe smooth) was recorded and anaerobic threshold calculated using ventilatory curve and ventilatory equivalents methods. Statistical analysis reported between-subject effects for gender (F1,67=35.18; p<0.001) and rank (F1,67=8.67; p<0.001); post hoc tests reported soloists (39.5 ±5.15 ml.kg-1.min-1) as having significantly lower VO2 peak than artists (45.9 ±5.75 ml.kg-1.min-1, p<0.001) and principal dancers (48.07 ±3.24 ml.kg-1.min-1, p<0.001). Significant differences in anaerobic threshold were reported for age (F1,67=7.68; p=0.008), rank (F1,67=3.56; p=0.034); post hoc tests reported artists (75.8 ±5.45%) having significantly lower %AT than soloists (80.9 ±5.71, p<0.01) and principals (84.1 ±4.84%, p<0.001). The observed differences in VO2 peak and anaerobic threshold between the ranks in ballet companies is probably due to their different rehearsal and performance demands

The peculiar motions of early-type galaxies in two distant regions - VII. Peculiar velocities and bulk motions

We present peculiar velocities for 84 clusters of galaxies in two large volumes at distances between 6000 and 15000 km/s in the directions of Hercules-Corona Borealis and Perseus-Pisces-Cetus. These velocities are based on Fundamental Plane (FP) distance estimates for early-type galaxies in each cluster. We fit the FP using a maximum likelihood algorithm which accounts for both selection effects and measurement errors, and yields FP parameters with smaller bias and variance than other fitting procedures. We find a best-fit FP with coefficients consistent with the best existing determinations. We measure the bulk motions of the sample volumes using the 50 clusters with the best-determined peculiar velocities. We find the bulk motions in both regions are small, and consistent with zero at about the 5% level. The EFAR results are in agreement with the small bulk motions found by Dale et al. (1999) on similar scales, but are inconsistent with pure dipole motions having the large amplitudes found by Lauer & Postman (1994) and Hudson et al. (1999). The alignment of the EFAR sample with the Lauer & Postman dipole produces a strong rejection of a large-amplitude bulk motion in that direction, but the rejection of the Hudson et al. result is less certain because their dipole lies at a large angle to the main axis of the EFAR sample. We find the bulk motion of our sample is consistent with most cosmological models that approximately reproduce the shape and normalisation of the observed galaxy power spectrum. We conclude that existing measurements of large-scale bulk motions provide no significant evidence against standard models for the formation of structure.Comment: to appear in MNRAS, 27 pages, EFAR paper

The Phantom Bounce: A New Oscillating Cosmology

An oscillating universe cycles through a series of expansions and contractions. We propose a model in which ``phantom'' energy with $p < -\rho$ grows rapidly and dominates the late-time expanding phase. The universe's energy density is so large that the effects of quantum gravity are important at both the beginning and the end of each expansion (or contraction). The bounce can be caused by high energy modifications to the Friedmann equation, which make the cosmology nonsingular. The classic black hole overproduction of oscillating universes is resolved due to their destruction by the phantom energy.Comment: Four pages, one figure. V3: version to appear in JCA

The Peculiar Motions of Early-Type Galaxies in Two Distant Regions -- VII. Peculiar Velocities and Bulk Motions

We present peculiar velocities for 85 clusters of galaxies in two large volumes at distances between 6000 and 15 000 km s−1 in the directions of Hercules-Corona Borealis and Perseus-Pisces-Cetus (the EFAR sample). These velocities are based on Fundamental Plane (FP) distance estimates for early-type galaxies in each cluster. We fit the FP using a maximum likelihood algorithm which accounts for both selection effects and measurement errors, and yields FP parameters with smaller bias and variance than other fitting procedures. We obtain a best-fitting FP with coefficients consistent with the best existing determinations. We measure the bulk motions of the sample volumes using the 50 clusters with the best-determined peculiar velocities. We find that the bulk motions in both regions are small, and consistent with zero at about the 5 per cent level. The EFAR results are in agreement with the small bulk motions found by Dale et al. on similar scales, but are inconsistent with pure dipole motions having the large amplitudes found by Lauer & Postman and Hudson et al. The alignment of the EFAR sample with the Lauer & Postman dipole produces a strong rejection of a large-amplitude bulk motion in that direction, but the rejection of the Hudson et al. result is less certain because their dipole lies at a large angle to the main axis of the EFAR sample. We employ a window function covariance analysis to make a detailed comparison of the EFAR peculiar velocities with the predictions of standard cosmological models. We find that the bulk motion of our sample is consistent with most cosmological models that approximately reproduce the shape and normalization of the observed galaxy power spectrum. We conclude that existing measurements of large-scale bulk motions provide no significant evidence against standard models for the formation of structure

The B_s and D_s decay constants in 3 flavor lattice QCD

Capitalizing on recent advances in lattice QCD, we present a calculation of the leptonic decay constants f_{B_s} and f_{D_s} that includes effects of one strange sea quark and two light sea quarks. The discretization errors of improved staggered fermion actions are small enough to simulate with 3 dynamical flavors on lattices with spacings around 0.1 fm using present computer resources. By shedding the quenched approximation and the associated lattice scale ambiguity, lattice QCD greatly increases its predictive power. NRQCD is used to simulate heavy quarks with masses between 1.5 m_c and m_b. We arrive at the following results: f_{B_s} = 260 \pm 7 \pm 26 \pm 8 \pm 5 MeV and f_{D_s} = 290 \pm 20 \pm 29 \pm 29 \pm 6 MeV. The first quoted error is the statistical uncertainty, and the rest estimate the sizes of higher order terms neglected in this calculation. All of these uncertainties are systematically improvable by including another order in the weak coupling expansion, the nonrelativistic expansion, or the Symanzik improvement program.Comment: 4 page

The peculiar motions of early-type galaxies in two distant regions - II. The spectroscopic data

We present the spectroscopic data for the galaxies studied in the EFAR project, which is designed to measure the properties and peculiar motions of early-type galaxies in two distant regions. We have obtained 1319 spectra of 714 early-type galaxies over 33 observing runs on 10 different telescopes. We describe the observations and data reductions used to measure redshifts, velocity dispersions and the Mgb and Mg2 Lick linestrength indices. Detailed simulations and intercomparison of the large number of repeat observations lead to reliable error estimates for all quantities. The measurements from different observing runs are calibrated to a common zeropoint or scale before being combined, yielding a total of 706 redshifts, 676 velocity dispersions, 676 Mgb linestrengths and 582 Mg2 linestrengths. The median estimated errors in the combined measurements are dcz=20 km/s, dsigma/sigma=9.1%, dMgb/Mgb=7.2% and dMg2=0.015 mag. Comparison of our measurements with published datasets shows no systematic errors in the redshifts or velocity dispersions and only small zeropoint corrections to bring our linestrengths onto the standard Lick system. We have assigned galaxies to physical clusters by examining the line-of-sight velocity distributions based on EFAR and ZCAT redshifts, together with the projected distributions on the sky. We derive mean redshifts and velocity dispersions for these clusters, which will be used in estimating distances and peculiar velocities and to test for trends in the galaxy population with cluster mass. The spectroscopic parameters presented here for 706 galaxies combine high quality data, uniform reduction and measurement procedures, and detailed error analysis. They form the largest single set of velocity dispersions and linestrengths for early-type galaxies published to date.Comment: 27 pages, 18 figures, accepted by MNRA

The Peculiar Motions of Early‐Type Galaxies in Two Distant Regions. IV. The Photometric Fitting Procedure

The EFAR project is a study of 736 candidate early-type galaxies in 84 clusters lying in two regions toward Hercules-Corona Borealis and Perseus-Cetus at distances cz ≈ 6000-15,000 km s-1. In this paper we describe a new method of galaxy photometry adopted to derive the photometric parameters of the EFAR galaxies. The algorithm fits the circularized surface brightness profiles as the sum of two seeing-convolved components, an R1/4 and an exponential law. This approach allows us to fit the large variety of luminosity profiles displayed by the EFAR galaxies homogeneously and to derive (for at least a subset of these) bulge and disk parameters. Multiple exposures of the same objects are optimally combined and an optional sky-fitting procedure has been developed to correct for sky-subtraction errors. Extensive Monte Carlo simulations are analyzed to test the performance of the algorithm and estimate the size of random and systematic errors. Random errors are small, provided that the global signal-to-noise ratio of the fitted profiles is larger than ≈ 300. Systematic errors can result from (1) errors in the sky subtraction, (2) the limited radial extent of the fitted profiles, (3) the lack of resolution due to seeing convolution and pixel sampling, (4) the use of circularized profiles for very flattened objects seen edge-on, and (5) a poor match of the fitting functions to the object profiles. Large systematic errors are generated by the widely used simple R1/4 law to fit luminosity profiles when a disk component, as small as 20% of the total light, is present. The size of the systematic errors cannot be determined from the shape of the χ2 function near its minimum because extrapolation is involved. Rather, we must estimate them by a set of quality parameters, calibrated against our simulations, which take into account the amount of extrapolation involved to derive the total magnitudes, the size of the sky correction, the average surface brightness of the galaxy relative to the sky, the radial extent of the profile, its signal-to-noise ratio, the seeing value, and the reduced χ2 of the fit. We formulate a combined quality parameter Q, which indicates the expected precision of the fits. Errors in total magnitudes MTOT less than 0.05 mag and in half-luminosity radii Re less than 10% are expected if Q = 1, and less than 0.15 mag and 25% if Q = 2; 89% of the EFAR galaxies have fits with Q = 1 or Q = 2. The errors on the combined fundamental plane quantity FP = log Re-0.3SBe, where SBe is the average effective surface brightness, are smaller than 0.03 even if Q = 3. Thus, systematic errors on MTOT and Re only have a marginal effect on the distance estimates that involve FP. We show that the sequence of R1/n profiles, recently used to fit the luminosity profiles of elliptical galaxies, is equivalent (for n ≤ 8) to a subsample of R1/4 and exponential profiles, with appropriate scale lengths and disk-to-bulge ratios. This suggests that the variety of luminosity profiles shown by early-type galaxies may be due to the presence of a disk component

White-faced Darter distribution is associated with coniferous forests in Great Britain

Abstract 1) Understanding of dragonfly distributions is often geographically comprehensive but less so in ecological terms. 2) White-faced darter (Leucorhinnia dubia) is a lowland peatbog specialist dragonfly which has experienced population declines in Great Britain. White-faced darter are thought to rely on peat-rich pool complexes within woodland but this has not yet been empirically tested. 3) We used dragonfly recording data collected by volunteers of the British Dragonfly Society from 2005 to 2018 to model habitat preference for white-faced darter using species distribution models across Great Britain and, with a more detailed landcover dataset, specifically in the North of Scotland. 4) Across the whole of Great Britain our models used the proportion of coniferous forest within 1km as the most important predictor of habitat suitability but were not able to predict all current populations in England. 5) In the North of Scotland our models were more successful and suggest that habitats characterised by native coniferous forest and areas high potential evapotranspiration represent the most suitable habitat for white-faced darter. 6) We recommend that future white-faced darter monitoring should be expanded to include areas currently poorly surveyed but with high suitability in the North of Scotland. 7) Our results also suggest that white-faced darter management should concentrate on maintaining Sphagnum rich pool complexes and the maintenance and restoration of native forests in which these pool complexes occur