Nearby Gas-Rich Low Surface Brightness Galaxies

We examine the Fisher-Tully cz<1000 km/s galaxy sample to determine whether it is a complete and representative sample of all galaxy types, including low surface brightness populations, as has been recently claimed. We find that the sample is progressively more incomplete for galaxies with (1) smaller physical diameters at a fixed isophote and (2) lower HI masses. This is likely to lead to a significant undercounting of nearby gas-rich low surface brightness galaxies. However, through comparisons to other samples we can understand how the nearby galaxy counts need to be corrected, and we see some indications of environmental effects that probably result from the local high density of galaxies.Comment: 12 page, 2 figures, to appear in Ap

Can Large-Scale Climatic Models Be Linked with Multiscale Ecological Studies? *

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72151/1/j.1523-1739.1993.07020256.x.pd

Can Large-Scale Climatic Models Be Linked with Multiscale Ecological Studies? *

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72151/1/j.1523-1739.1993.07020256.x.pd

X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor

The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe-ψ[CH(OH)CH_2N]-Pro-Ile-Val-OMe; the K_i is 0.24 nM. The hydroxyethylamine moiety, in place of the normal scissile bond of the substrate, is believed to mimic a tetrahedral reaction intermediate. The structure of the complex has been refined to an R factor of 0.146 at 2.4-Å resolution by using restrained least squares with rms deviations in bond lengths of 0.02 Å and bond angles of 4. The bound inhibitor diastereomer has the S configuration at the hydroxyethylamine chiral carbon, and the hydroxyl group is positioned between the active site aspartate carboxyl groups within hydrogen bonding distance. Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365

Circadian rhythmicity in murine blood:Electrical effects of malaria infection and anemia

Circadian rhythms are biological adaptations to the day-night cycle, whereby cells adapt to changes in the external environment or internal physiology according to the time of day. Whilst many cellular clock mechanisms involve gene expression feedback mechanisms, clocks operate even where gene expression is absent. For example, red blood cells (RBCs) do not have capacity for gene expression, and instead possess an electrophysiological oscillator where cytosolic potassium plays a key role in timekeeping. We examined murine blood under normal conditions as well as in two perturbed states, malaria infection and induced anemia, to assess changes in baseline cellular electrophysiology and its implications for the electrophysiological oscillator. Blood samples were analyzed at 4-h intervals over 2 days by dielectrophoresis, and microscopic determination of parasitemia. We found that cytoplasmic conductivity (indicating the concentration of free ions in the cytoplasm and related to the membrane potential) exhibited circadian rhythmic behavior in all three cases (control, malaria and anemia). Compared to control samples, cytoplasm conductivity was decreased in the anemia group, whilst malaria-infected samples were in antiphase to control. Furthermore, we identified rhythmic behavior in membrane capacitance of malaria infected cells that was not replicated in the other samples. Finally, we reveal the historically famous rhythmicity of malaria parasite replication is in phase with cytoplasm conductivity. Our findings suggest the electrophysiological oscillator can impact on malaria parasite replication and/or is vulnerable to perturbation by rhythmic parasite activities

The Lyman-alpha Forest Power Spectrum from the Sloan Digital Sky Survey

We measure the power spectrum, P_F(k,z), of the transmitted flux in the Ly-alpha forest using 3035 high redshift quasar spectra from the Sloan Digital Sky Survey. This sample is almost two orders of magnitude larger than any previously available data set, yielding statistical errors of ~0.6% and ~0.005 on, respectively, the overall amplitude and logarithmic slope of P_F(k,z). This unprecedented statistical power requires a correspondingly careful analysis of the data and of possible systematic contaminations in it. For this purpose we reanalyze the raw spectra to make use of information not preserved by the standard pipeline. We investigate the details of the noise in the data, resolution of the spectrograph, sky subtraction, quasar continuum, and metal absorption. We find that background sources such as metals contribute significantly to the total power and have to be subtracted properly. We also find clear evidence for SiIII correlations with the Ly-alpha forest and suggest a simple model to account for this contribution to the power. While it is likely that our newly developed analysis technique does not eliminate all systematic errors in the P_F(k,z) measurement below the level of the statistical errors, our tests indicate that any residual systematics in the analysis are unlikely to affect the inference of cosmological parameters from P_F(k,z). These results should provide an essential ingredient for all future attempts to constrain modeling of structure formation, cosmological parameters, and theories for the origin of primordial fluctuations.Comment: 92 pages, 45 of them figures, submitted to ApJ, data available at http://feynman.princeton.edu/~pmcdonal/LyaF/sdss.htm

The Linear Theory Power Spectrum from the Lyman-alpha Forest in the Sloan Digital Sky Survey

We analyze the SDSS Ly-alpha forest P_F(k,z) measurement to determine the linear theory power spectrum. Our analysis is based on fully hydrodynamic simulations, extended using hydro-PM simulations. We account for the effect of absorbers with damping wings, which leads to an increase in the slope of the linear power spectrum. We break the degeneracy between the mean level of absorption and the linear power spectrum without significant use of external constraints. We infer linear theory power spectrum amplitude Delta^2_L(k_p=0.009s/km,z_p=3.0)=0.452_{-0.057-0.116}^{+0.069+0.141} and slope n_eff=-2.321_{-0.047-0.102}^{+0.055+0.131} (possible systematic errors are included through nuisance parameters in the fit - a factor >~5 smaller errors would be obtained on both parameters if we ignored modeling uncertainties). The errors are correlated and not perfectly Gaussian, so we provide a chi^2 table to accurately describe the results. The result corresponds to sigma_8=0.85, n=0.94, for a LCDM model with Omega_m=0.3, Omega_b=0.04, and h=0.7, but is most useful in a combined fit with the CMB. The inferred curvature of the linear power spectrum and the evolution of its amplitude and slope with redshift are consistent with expectations for LCDM models, with the evolution of the slope, in particular, being tightly constrained. We use this information to constrain systematic contamination, e.g., fluctuations in the UV background. This paper should serve as a starting point for more work to refine the analysis, including technical improvements such as increasing the size and number of the hydrodynamic simulations, and improvements in the treatment of the various forms of feedback from galaxies and quasars.Comment: Improved presentation, including fit results for (z). Simple code to produce LyaF chi^2 given linear power spectrum available at: http://www.cita.utoronto.ca/~pmcdonal/code.htm

Is manganese-doped diamond a ferromagnetic semiconductor?

We use density-functional theoretical methods to examine the recent prediction, based on a mean-field solution of the Zener model, that diamond doped by Mn (with spin S=5/2) would be a dilute magnetic semiconductor that remains ferromagnetic well above room temperature. Our findings suggest this to be unlikely, for four reasons: (1) substitutional Mn in diamond has a low-spin S=1/2 ground state; (2) the substitutional site is energetically unfavorable relative to the much larger "divacancy" site; 3) Mn in the divacancy site is an acceptor, but with only hyperdeep levels, and hence the holes are likely to remain localized; (4) the calculated Heisenberg couplings between Mn in nearby divacancy sites are two orders of magnitude smaller than for substitutional Mn in germanium.Comment: 5 pages, 5 figure