A Comparison of the Michigan and Fair Models: Further Results

This paper examines the equation-by-equation accuracy of the Michigan and Fair model using the method in Fair (1980). Emphasis is placed on examining the possible misspecification of the equations. In an earlier study, Fair and Alexander (1984), we used the method to examine the accuracy of the complete models. In the present study we are interested in the accuracy of the individual equations when considered in isolation from the rest of the model

Measuring the Size of Quasar Broad-Line Clouds Through Time Delay Light-Curve Anomalies of Gravitational Lenses

Intensive monitoring campaigns have recently attempted to measure the time delays between multiple images of gravitational lenses. Some of the resulting light-curves show puzzling low-level, rapid variability which is unique to individual images, superimposed on top of (and concurrent with) longer time-scale intrinsic quasar variations which repeat in all images. We demonstrate that both the amplitude and variability time-scale of the rapid light-curve anomalies, as well as the correlation observed between intrinsic and microlensed variability, are naturally explained by stellar microlensing of a smooth accretion disk which is occulted by optically-thick broad-line clouds. The rapid time-scale is caused by the high velocities of the clouds (~5x10^3 km/s), and the low amplitude results from the large number of clouds covering the magnified or demagnified parts of the disk. The observed amplitudes of variations in specific lenses implies that the number of broad-line clouds that cover ~10% of the quasar sky is ~10^5 per 4 pi steradian. This is comparable to the expected number of broad line clouds in models where the clouds originate from bloated stars.Comment: 19 pages, 9 figures. Submitted to Ap

Prevalence of the EH1 Groucho interaction motif in the metazoan Fox family of transcriptional regulators

<p>Abstract</p> <p>Background</p> <p>The Fox gene family comprises a large and functionally diverse group of <it>forkhead</it>-related transcriptional regulators, many of which are essential for metazoan embryogenesis and physiology. Defining conserved functional domains that mediate the transcriptional activity of Fox proteins will contribute to a comprehensive understanding of the biological function of Fox family genes.</p> <p>Results</p> <p>Systematic analysis of 458 protein sequences of the metazoan Fox family was performed to identify the presence of the engrailed homology-1 motif (eh1), a motif known to mediate physical interaction with transcriptional corepressors of the TLE/Groucho family. Greater than 50% of Fox proteins contain sequences with high similarity to the eh1 motif, including ten of the nineteen Fox subclasses (A, B, C, D, E, G, H, I, L, and Q) and Fox proteins of early divergent species such as marine sponge. The eh1 motif is not detected in Fox proteins of the F, J, K, M, N, O, P, R and S subclasses, or in yeast Fox proteins. The eh1-like motifs are positioned C-terminal to the winged helix DNA-binding domain in all subclasses except for FoxG proteins, which have an N-terminal motif. Two similar eh1-like motifs are found in the zebrafish FoxQ1 and in FoxG proteins of sea urchin and amphioxus. The identification of eh1-like motifs by manual sequence alignment was validated by statistical analyses of the Swiss protein database, confirming a high frequency of occurrence of eh1-like sequences in Fox family proteins. Structural predictions suggest that the majority of identified eh1-like motifs are short α-helices, and wheel modeling revealed an amphipathicity that supports this secondary structure prediction.</p> <p>Conclusion</p> <p>A search for eh1 Groucho interaction motifs in the Fox gene family has identified eh1-like sequences in greater than 50% of Fox proteins. The results predict a physical and functional interaction of TLE/Groucho corepressors with many members of the Fox family of transcriptional regulators. Given the functional importance of the eh1 motif in transcriptional regulation, our annotation of this motif in the Fox gene family will facilitate further study of the diverse transcriptional and regulatory roles of Fox family proteins.</p

Vibrational Sum-Frequency Spectroscopic Investigation of the Structure and Azimuthal Anisotropy of Propynyl-Terminated Si(111) Surfaces

Vibrational sum-frequency generation (VSFG) spectroscopy was used to investigate the orientation and azimuthal anisotropy of the C–H stretching modes for propynyl-terminated Si(111) surfaces, Si—C≡C—CH_3. VSFG spectra revealed symmetric and asymmetric C–H stretching modes in addition to a Fermi resonance mode resulting from the interaction of the asymmetric C–H bending overtone with the symmetric C–H stretching vibration. The polarization dependence of the C–H stretching modes was consistent with the propynyl groups oriented such that the Si—C≡C– bond is normal to the Si(111) surface. The azimuthal angle dependence of the resonant C–H stretching amplitude revealed no rotational anisotropy for the symmetric C–H stretching mode and a 3-fold rotational anisotropy for the asymmetric C–H stretching mode in registry with the 3-fold symmetric Si(111) substrate. The results are consistent with the expectation that the C–H stretching modes of a –CH_3 group are decoupled from the Si substrate due to a −C≡C– spacer. In contrast, the methyl-terminated Si(111) surface, Si–CH_3, was previously reported to have pronounced vibronic coupling of the methyl stretch modes to the electronic bath of bulk Si. Vacuum-annealing of propynyl-terminated Si(111) resulted in increased 3-fold azimuthal anisotropy for the symmetric stretch, suggesting that removal of propynyl groups from the surface upon annealing allowed the remaining propynyl groups to tilt away from the surface normal into one of three preferred directions toward the vacated neighbor sites