PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification

The Berkeley Phylogenomics Group presents PhyloFacts, a structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts enables biologists to avoid the systematic errors associated with function prediction by homology through the integration of a variety of experimental data and bioinformatics methods in an evolutionary framework. Users can submit sequences for classification to families and functional subfamilies. PhyloFacts is available as a worldwide web resource from

Integrating TV/digital data spectrograph system

A 25-mm vidicon camera was previously modified to allow operation in an integration mode for low-light-level astronomical work. The camera was then mated to a low-dispersion spectrograph for obtaining spectral information in the 400 to 750 nm range. A high speed digital video image system was utilized to digitize the analog video signal, place the information directly into computer-type memory, and record data on digital magnetic tape for permanent storage and subsequent analysis

Automated Protein Subfamily Identification and Classification

Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own subfamily definitions can do so. Source code is available on the Web page. The Berkeley Phylogenomics Group PhyloFacts resource contains pre-calculated subfamily predictions and subfamily HMMs for more than 40,000 protein families and domains at http://phylogenomics.berkeley.edu/phylofacts/

A Measurement of the Semileptonic Branching Fraction of the B_s Meson

We report a measurement of the inclusive semileptonic branching fraction of the B_s meson using data collected with the BaBar detector in the center-of-mass (CM) energy region above the Upsilon(4S) resonance. We use the inclusive yield of phi mesons and the phi yield in association with a high-momentum lepton to perform a simultaneous measurement of the semileptonic branching fraction and the production rate of B_s mesons relative to all B mesons as a function of CM energy. The inclusive semileptonic branching fraction of the B_s meson is determined to be B(B_s to l nu X)=9.5 (+2.5/-2.0)(stat)(+1.1/-1.9)(syst)%, where l indicates the average of e and mu

Technology as Thirdspace:Teachers in Scottish schools engaging with and being challenged by digital technology in first COVID-19 lockdown

This paper looks at the impact of digital technology on teaching and learning in primary schools in Scotland during the first COVID-19 lockdown from March to June 2020. The pandemic has challenged our understanding of schooling as, for the first time in many years, schools as we know them were shut and the school building was removed as the site of teaching and learning. This paper uses the concept of Thirdspace as developed by Edward Soja (1996), where Thirdspace is understood as an in-between space between binaries that enables the possibility to think and act otherwise. Drawing from qualitative data from interviews with primary school teachers, this paper explores how the lockdown in general, and digital technology in particular, facilitated a Thirdspace in the first COVID-19 lockdown. Findings from the study indicate that engaging with digital technology offers the teacher more possibilities than they have come to expect in the physical space of traditional schooling.</p

Dependence of the Fundamental Plane Scatter on Galaxy Age

The fundamental plane (FP) has an intrinsic scatter that can not be explained purely by observational errors. Using recently available age estimates for nearby early type galaxies, we show that a galaxy's position relative to the FP depends on its age. In particular, the mean FP corresponds to ellipticals with an age of ~10 Gyr. Younger galaxies are systematically brighter with higher surface brightness relative to the mean relation. Old ellipticals form an `upper envelope' to the FP. For our sample of mostly non-cluster galaxies, age can account for almost half of the scatter in the B band FP. Distance determinations based on the FP may have a systematic bias, if the mean age of the sample varies with redshift. We also show that fundamental plane residuals, B-V colors and Mg_2 line strength are consistent with an ageing central burst superposed on an old stellar population. This reinforces the view that these age estimates are tracing the last major episode of star formation induced by a gaseous merger event. We briefly discuss the empirical `evolutionary tracks' of merger-remnants and young ellipticals in terms of their key observational parameters.Comment: 14 pages, Latex, 2 figures, accepted by ApJ Letter

Beating the Spin-Down Limit on Gravitational Wave Emission from the Vela Pulsar

We present direct upper limits on continuous gravitational wave emission from the Vela pulsar using data from the Virgo detector\u27s second science run. These upper limits have been obtained using three independent methods that assume the gravitational wave emission follows the radio timing. Two of the methods produce frequentist upper limits for an assumed known orientation of the star\u27s spin axis and value of the wave polarization angle of, respectively, 1.9\ee{-24} and 2.2\ee{-24}, with 95% confidence. The third method, under the same hypothesis, produces a Bayesian upper limit of 2.1\ee{-24}, with 95% degree of belief. These limits are below the indirect {\it spin-down limit} of 3.3\ee{-24} for the Vela pulsar, defined by the energy loss rate inferred from observed decrease in Vela\u27s spin frequency, and correspond to a limit on the star ellipticity of $\sim 10^{-3}$. Slightly less stringent results, but still well below the spin-down limit, are obtained assuming the star\u27s spin axis inclination and the wave polarization angles are unknown

An Oort cloud origin for the high-inclination, high-perihelion Centaurs

We analyse the origin of three Centaurs with perihelia in the range 15 AU to 30 AU, inclinations above 70 deg and semi-major axes shorter than 100 AU. Based on long-term numerical simulations we conclude that these objects most likely originate from the Oort cloud rather than the Kuiper Belt or Scattered Disc. We estimate that there are currently between 1 and 200 of these high-inclination, high-perihelion Centaurs with absolute magnitude H<8.Comment: Accepted for publication in MNRA

High-accuracy comparison of numerical relativity simulations with post-Newtonian expansions

Numerical simulations of 15 orbits of an equal-mass binary black hole system are presented. Gravitational waveforms from these simulations, covering more than 30 cycles and ending about 1.5 cycles before merger, are compared with those from quasi-circular zero-spin post-Newtonian (PN) formulae. The cumulative phase uncertainty of these comparisons is about 0.05 radians, dominated by effects arising from the small residual spins of the black holes and the small residual orbital eccentricity in the simulations. Matching numerical results to PN waveforms early in the run yields excellent agreement (within 0.05 radians) over the first $\sim 15$ cycles, thus validating the numerical simulation and establishing a regime where PN theory is accurate. In the last 15 cycles to merger, however, {\em generic} time-domain Taylor approximants build up phase differences of several radians. But, apparently by coincidence, one specific post-Newtonian approximant, TaylorT4 at 3.5PN order, agrees much better with the numerical simulations, with accumulated phase differences of less than 0.05 radians over the 30-cycle waveform. Gravitational-wave amplitude comparisons are also done between numerical simulations and post-Newtonian, and the agreement depends on the post-Newtonian order of the amplitude expansion: the amplitude difference is about 6--7% for zeroth order and becomes smaller for increasing order. A newly derived 3.0PN amplitude correction improves agreement significantly ($<1$ amplitude difference throughout most of the run, increasing to 4% near merger) over the previously known 2.5PN amplitude terms.Comment: Updated to agree with published version (various minor clarifications; added description of AH finder in Sec IIB; added discussion of tidal heating in Sec VC