# Willamette University Faculty Publications

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Item St. Nicholas (Un)Preserve Us! Pickled Boys Resurrected in the Hatfield Library’s Praeces Piae(2003) Nicgorski, AnnShow more Item Dictyostelium Myosin Bipolar Thick Filament Formation: Importance of Charge and Specific Domains of the Myosin Rod(Public Library of Science, 2004-11) Altman, David; Hostetter, Daniel; Rice, Sarah; Dean, Sara; McMahon, Peggy M.; Sutton, Shirley; Tripathy, Ashutosh; Spudich, James A.Show more Myosin-II thick filament formation in Dictyostelium is an excellent system for investigating the phenomenon of self-assembly, as the myosin molecule itself contains all the information required to form a structure of defined size. Phosphorylation of only three threonine residues can dramatically change the assembly state of myosin-II. We show here that the C-terminal 68 kDa of the myosin-II tail (termed AD-Cterm) assembles in a regulated manner similar to full-length myosin-II and forms bipolar thick filament (BTF) structures when a green fluorescent protein (GFP) "head" is added to the N terminus. The localization of this GFP-AD-Cterm to the cleavage furrow of dividing Dictyostelium cells depends on assembly state, similar to full-length myosin-II. This tail fragment therefore represents a good model system for the regulated formation and localization of BTFs. By reducing regulated BTF assembly to a more manageable model system, we were able to explore determinants of myosin-II self-assembly. Our data support a model in which a globular head limits the size of a BTF, and the large-scale charge character of the AD-Cterm region is important for BTF formation. Truncation analysis of AD-Cterm tail fragments shows that assembly is delicately balanced, resulting in assembled myosin-II molecules that are poised to disassemble due to the phosphorylation of only three threonines.Show more Item Consistently large cosmic flows on scales of 100 h−1 Mpc: a challenge for the standard ΛCDM cosmology(Oxford Academic, 2009-12-23) Watkins, Richard; Feldman, Hume A.; Hudson, Michael J.Show more The bulk flow, i.e. the dipole moment of the peculiar velocity field, is a sensitive probe of matter density fluctuations on very large scales. However, the peculiar velocity surveys for which the bulk flow has been calculated have non-uniform spatial distributions of tracers, so that the bulk flow estimated does not correspond to that of a simple volume such as a sphere. Thus bulk flow estimates are generally not strictly comparable between surveys, even those whose effective depths are similar. In addition, the sparseness of typical surveys can lead to aliasing of small-scale power into what is meant to be a probe of the largest scales. Here we introduce a new method of calculating bulk flow moments where velocities are weighted to give an optimal estimate of the bulk flow of an idealized survey, with the variance of the difference between the estimate and the actual flow being minimized. These ‘minimum variance’ estimates can be designed to estimate the bulk flow on a particular scale with minimal sensitivity to small-scale power, and are comparable between surveys. We compile all major peculiar velocity surveys and apply this new method to them. We find that most surveys we studied are highly consistent with each other. Taken together the data suggest that the bulk flow within a Gaussian window of radius 50 h−1 Mpc is 407 ± 81 km s−1 toward l= 287°± 9°, b= 8°± 6°. The large-scale bulk motion is consistent with predictions from the local density field. This indicates that there are significant density fluctuations on very large scales. A flow of this amplitude on such a large scale is not expected in the WMAP5 (Wilkinson Microwave Anisotropy Probe) normalized Λ cold dark matter cosmology, for which the predicted one-dimensional rms velocity is ∼110 km s−1. The large amplitude of the observed bulk flow favours the upper values of the WMAP5 Ωmh2–σ8 error-ellipse, but even the point at the top of the WMAP595 per cent confidence ellipse predicts a bulk flow which is too low compared to that observed at >98 per cent confidence level.Show more Item Cosmic flows on 100 h−1 Mpc scales: standardized minimum variance bulk flow, shear and octupole moments(Oxford Academic, 2010-07-22) Feldman, Hume A.; Watkins, Richard; Hudson, Michael J.Show more The low-order moments, such as the bulk flow and shear, of the large-scale peculiar velocity field are sensitive probes of the matter density fluctuations on very large scales. In practice, however, peculiar velocity surveys are usually sparse and noisy, which can lead to the aliasing of small-scale power into what is meant to be a probe of the largest scales. Previously, we developed an optimal ‘minimum variance’ (MV) weighting scheme, designed to overcome this problem by minimizing the difference between the measured bulk flow (BF) and that which would be measured by an ideal survey. Here we extend this MV analysis to include the shear and octupole moments, which are designed to have almost no correlations between them so that they are virtually orthogonal. We apply this MV analysis to a compilation of all major peculiar velocity surveys, consisting of 4536 measurements. Our estimate of the BF on scales of ∼100 h−1 Mpc has a magnitude of |v| = 416 ± 78 km s −1 towards Galactic l= 282°± 11° and b= 6°± 6°. This result is in disagreement with Λ cold dark matter with Wilkinson Microwave Anisotropy Probe 5 (WMAP5) cosmological parameters at a high confidence level, but is in good agreement with our previous MV result without an orthogonality constraint, showing that the shear and octupole moments did not contaminate the previous BF measurement. The shear and octupole moments are consistent with WMAP5 power spectrum, although the measurement noise is larger for these moments than for the BF. The relatively low shear moments suggest that the sources responsible for the BF are at large distances.Show more Item A slight excess of large-scale power from moments of the peculiar velocity field(Oxford Academic, 2011-06-01) Macaulay, E.; Feldman, H.; Ferreira, P.G.; Hudson, M.J.; Watkins, R.Show more The peculiar motions of galaxies can be used to infer the distribution of matter in the Universe. It has recently been shown that measurements of the peculiar velocity field indicate an anomalously high bulk flow of galaxies in our local volume. In this paper, we find the implications of the high bulk flow for the power spectrum of density fluctuations. We find that analysing only the dipole moment of the velocity field yields an average power spectrum amplitude which is indeed much higher than the Λ cold dark matter (ΛCDM) value. However, by also including shear and octupole moments of the velocity field, and marginalizing over possible values for the growth rate, an average power spectrum amplitude which is consistent with the ΛCDM is recovered. We attempt to infer the shape of the matter power spectrum from moments of the velocity field, and find a slight excess of power on scales ∼1 h−1 Gpc.Show more Item Comparative Phylogeography of a Coevolved Community: Concerted Population Expansions in Joshua Trees and Four Yucca Moths(PLOS, 2011-10-18) Smith, Christopher Irwin; Tank, Shantel; Godsoe, William; Levenick, Jim; Strand, Eva; Esque, Todd; Pellmyr, OlleShow more Item Cosmic flows in the nearby universe from Type Ia supernovae(Oxford Academic, 2012-01-23) Turnbull, Stephen J.; Hudson, Michael J.; Feldman, Hume A.; Hicken, Malcolm; Kirshner, Robert P.; Watkins, RichardShow more Peculiar velocities are one of the only probes of very large scale mass density fluctuations in the nearby Universe. We present new ‘minimal variance’ bulk flow measurements based upon the ‘First Amendment’ compilation of 245 Type Ia supernovae (SNe) peculiar velocities and find a bulk flow of 249 ± 76 km s−1 in the direction l= 319°± 18°, b= 7°± 14°. The SNe bulk flow is consistent with the expectations of Λ cold dark matter (ΛCDM). However, it is also marginally consistent with the bulk flow of a larger compilation of non-SNe peculiar velocities. By comparing the SNe peculiar velocities to predictions of the IRAS Point Source Catalogue Redshift Survey (PSCz) galaxy density field, we find Ω0.55mσ8,lin= 0.40 ± 0.07, which is in agreement with ΛCDM. However, we also show that the PSCz density field fails to account for 150 ± 43 km s−1 of the SNe bulk motion.Show more Item Testing the minimum variance method for estimating large-scale velocity moments(Oxford Academic, 2012-09) Argarwal, Shankar; Feldman, Hume A.; Watkins, RichardShow more The estimation and analysis of large-scale bulk flow moments of peculiar velocity surveys is complicated by non-spherical survey geometry, the non-uniform sampling of the matter velocity field by the survey objects and the typically large measurement errors of the measured line-of-sight velocities. Previously, we have developed an optimal ‘;minimum variance’ (MV) weighting scheme for using peculiar velocity data to estimate bulk flow moments for idealized, dense and isotropic surveys with Gaussian radial distributions, that avoids many of these complications. These moments are designed to be easy to interpret and are comparable between surveys. In this paper, we test the robustness of our MV estimators using numerical simulations. Using MV weights, we estimate the bulk flow moments for various mock catalogues extracted from the LasDamas and the Horizon Run numerical simulations and compare these estimates to the moments calculated directly from the simulation boxes. We show that the MV estimators are unbiased and negligibly affected by non-linear flows.Show more Item Power Spectrum Estimation from Peculiar Velocity Catalogues(Oxford Academic, 2012-09-21) Macaulay, Edward; Watkins, Richard; Feldman, Hume A.; Ferreira, Pedro G.; Jaffe, Andrew H.; Agarwal, Shankar; Hudson, Michael J.Show more The peculiar velocities of galaxies are an inherently valuable cosmological probe, providing an unbiased estimate of the distribution of matter on scales much larger than the depth of the survey. Much research interest has been motivated by the high dipole moment of our local peculiar velocity field, which suggests a large-scale excess in the matter power spectrum and can appear to be in some tension with the Λ cold dark matter (ΛCDM) model. We use a composite catalogue of 4537 peculiar velocity measurements with a characteristic depth of 33 h−1 Mpc to estimate the matter power spectrum. We compare the constraints with this method, directly studying the full peculiar velocity catalogue, to results by Macaulay et al., studying minimum variance moments of the velocity field, as calculated by Feldman, Watkins & Hudson. We find good agreement with the ΛCDM model on scales of k > 0.01 h Mpc−1. We find an excess of power on scales of k < 0.01 h Mpc−1 with a 1σ uncertainty which includes the ΛCDM model. We find that the uncertainty in excess at these scales is larger than an alternative result studying only moments of the velocity field, which is due to the minimum variance weights used to calculate the moments. At small scales, we are able to clearly discriminate between linear and non-linear clustering in simulated peculiar velocity catalogues and find some evidence (although less clear) for linear clustering in the real peculiar velocity data.Show more Item Large-scale bulk flows from the Cosmicflows-2 catalogue(Oxford Academic, 2015-02-11) Watkins, Richard; Feldman, Hume A.Show more The Cosmicflows-2 catalogue is a compendium of peculiar velocity measurements. While it has many objects in common with the COMPOSITE catalogue, a previously analysed collection of peculiar velocity data found to give an unexpectedly large bulk flow on large scales, the data in Cosmicflows-2 have been reanalysed to ensure consistency between distances measured using different methods. In particular, a focus on accurate distances led the authors of the Cosmicflows-2 to not correct for homogeneous or inhomogeneous Malmquist bias, both or which are corrected for in the COMPOSITE compilation. We find remarkable agreement between the COMPOSITE and the Cosmicflows-2 if the small EFAR sample of clusters located in two dense superclusters is removed from both surveys, giving results that are inconsistent with the Λ cold dark matter standard model with Planck central parameters at the 98 per cent level. On smaller scales we find overall agreement between data sets and consistency with the standard model.Show more Item Thixotropy and Rheopexy of Muscle Fibers Probed Using Sinusoidal Oscillations(Public Library of Science, 2015-04-16) Altman, David; Minozzo, Fabio C.; Rassier, Dilson E.Show more Length changes of muscle fibers have previously been shown to result in a temporary reduction in fiber stiffness that is referred to as thixotropy. Understanding the mechanism of this thixotropy is important to our understanding of muscle function since there are many in stances in which muscle is subjected to repeated patterns of lengthening and shortening. By applying sinusoidal length changes to one end of single permeabilized muscle fibers and measuring the force response at the opposite end, we studied the history-dependent stiffness of both relaxed and activated muscle fibers. For length change oscillations greater than 1 Hz, we observed thixotropic behavior of activated fibers. Treatment of these fibers with EDTA and blebbistatin, which inhibits myosin-actin interactions, quashed this effect, suggesting that the mechanism of muscle fiber thixotropy is cross-bridge dependent. We modeled a half-sarcomere experiencing sinusoidal length changes, and our simulations suggest that thixotropy could arise from force-dependent cross-bridge kinetics. Surprisingly, we also observed that, for length change oscillations less than 1 Hz, the muscle fiber exhibited rheopexy. In other words, the stiffness of the fiber increased in response to the length changes. Blebbistatin and EDTA did not disrupt the rheopectic behavior, suggesting that a non-cross-bridge mechanism contributes to this phenomenon.Show more Item Sunscreen or Smokescreen?(2015-07-13) Silverstein, ToddShow more This letter to the Editor of the Chemical & Engineering News brings up the potential for sunscreen use in relation to increasing cancer rates. This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Chemical & Engineering News, copyright © American Chemical Society. To access the final edited and published work see http://cen.acs.org/articles/93/i28/Sunscreen-Smoke-Screen.html and http://pubs.acs.org/page/policy/articlesonrequest/index.html.Show more Item Easily Interpretable Bulk Flows: Continuing Tension with the Standard Cosmological Model(Oxford Academic, 2018-08-24) Watkins, Richard; Peery, Sarah; Feldman, Hume A.Show more We present an improved Minimal Variance (MV) method for using a radial peculiar velocity sample to estimate the average of the three-dimensional velocity field over a spherical volume, which leads to an easily interpretable bulk flow measurement. The only assumption required is that the velocity field is irrotational. The resulting bulk flow estimate is particularly insensitive to smaller scale flows. We also introduce a new constraint into the MV method that ensures that bulk flow estimates are independent of the value of the Hubble constant Ho; this is important given the tension between the locally measured Ho and that obtained from the cosmic background radiation observations. We apply our method to the \textit{CosmicFlows-3} catalogue and find that, while the bulk flows for shallower spheres are consistent with the standard cosmological model, there is some tension between the bulk flow in a spherical volume with radius 150\hmpc\ and its expectations; we find only a ∼2% chance of obtaining a bulk flow as large or larger in the standard cosmological model with \textit{Planck} parameters.Show more Item The Peculiar Velocity Correlation Function(Oxford Academic, 2018-08-24) Wang, Yuyu; Rooney, Christopher; Feldman, Hume A.; Watkins, RichardShow more We present an analysis of the two-point peculiar velocity correlation function using data from the CosmicFlows catalogues. The Millennium and MultiDark Planck 2 N-body simulations are used to estimate cosmic variance and uncertainties due to measurement errors. We compare the velocity correlation function to expectations from linear theory to constrain cosmological parameters. Using the maximum likelihood method, we find values of Ωm=0.315+0.205−0.135 and σ8=0.92+0.440−0.295, consistent with the Planck and Wilkinson Microwave Anisotropy Probe CMB derived estimates. However, we find that the cosmic variance of the correlation function is large and non-Gaussian distributed, making the peculiar velocity correlation function less than ideal as a probe of large-scale structure.Show more Item Solar-Powered Radio Tags Reveal Patterns of Post-Fledging Site Visitation in Adult and Juvenile Tree Swallows Tachycineta Bicolor(PLOS ONE, 2018-11-08) Pegan, Teresa M.; Craig, David P.; Gulson-Castillo, Eric R.; Gabrielson, Richard M.; Kerr, Wayne Bezner; MacCurdy, Robert; Powell, Steven P.; Winkler, David W.Show more The availability of small, lightweight tracking devices enhances our ability to study birds during mobile phases of their lives. Tree Swallows Tachycineta bicolor, a model species of wild songbird, are well-studied during their breeding season; but our understanding of their biology at other times of the year, when they are not tied to the fixed location of a nest, is more limited. We developed a lightweight radio tag with no battery (solar nanotag) to study the movements of small animals, and we deployed it to explore the behavior of Tree Swallows after the end of their summer breeding season. We tagged 32 breeding adult swallows and 36 juveniles and monitored their presence and absence at the breeding site during the post-fledging period. Although our observations are based on very small sample sizes, the tags revealed previously unknown patterns in Tree Swallow behavior during the post-breeding season. Some Tree Swallow fledglings continued to visit the site repeatedly in the months following the nesting season, with the latest detection occurring on September 30th; by contrast, all adults had permanently departed by the end of July. These results inform future hypotheses about post-breeding movements in Tree Swallows. But, more generally, the detection of tagged swallows on their distant wintering grounds, seven months after tagging, indicates the potential of studying small passerine movements throughout their entire lifetimes, and suggests a rich array of applications for these “Life Tags” to study the movements of small animals worldwide.Show more