905 results on '"Gardner, Jeffrey A."'
Search Results
2. Fixed drug eruption from atezolizumab
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Kearns, Donovan, Gardner, Jeffrey T, Kerstetter, Justin, and Furukawa, Betsy
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atezolizumab ,breast ,cancer ,fixed drug eruption - Abstract
Fixed drug eruption (FDE) is a cutaneous drug reaction that tends to recur in the same area (fixed location) upon re-exposure to the offending agent. We present a 48-year-old woman with FDE being treated for metastatic breast cancer with atezolizumab. We believe this is the first reported case of FDE secondary to atezolizumab. more...
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- 2022
Catalog
3. Embodying Inequality: Using Ethnographic Data to Teach Intersectionality
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Gardner, Jeffrey A. and McKinzie, Ashleigh E.
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This article analyzes the effectiveness of an activity we developed to help students better understand intersectionality. Intersectionality is an analytic concept that signifies ways that inequalities may overlap to create unique forms of privilege and subjugation. In the activity, students use assigned vignettes from the perspective of research participants in our own ethnographic data (including excerpts from interviews and field notes) to interact with peers assigned both similar and dissimilar perspectives and experiences. The vignettes draw attention to intersectionality in a way that helps students embody participants' experiences with privilege and subjugation. Our analysis of the activity's effectiveness demonstrates that when learning is interactive, is dialogical, and draws from real narratives, students and instructors can effectively explore nuanced interpretations of relatively tough concepts, such as intersectionality. We argue that the embodiment of ethnographic data is a useful mechanism for helping students connect abstract sociological concepts to uniquely experienced realities. more...
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- 2020
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4. Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems
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Gardner, Jeffrey G. and Schreier, Harold J.
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- 2021
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5. A Randomized Comparison of Positional Stability: The EZ-Blocker Versus Left-Sided Double-Lumen Endobronchial Tubes in Adult Patients Undergoing Thoracic Surgery
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Morris, Benjamin N., Fernando, Rohesh J., Garner, Chandrika R., Johnson, Sean D., Gardner, Jeffrey C., Marchant, Bryan E., Johnson, Kathleen N., Harris, Hannah M., Russell, Gregory B., Wudel, L. James, Jr, and Templeton, T. Wesley more...
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- 2021
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6. Excision and Transfer of Bacteroides Conjugative Integrated Elements
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Salyers, Abigail A., primary, Gardner, Jeffrey F., additional, and Shoemaker, Nadja B., additional
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- 2022
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7. Bacterial α-diglucoside metabolism: perspectives and potential for biotechnology and biomedicine
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Garcia, Cecelia A. and Gardner, Jeffrey G.
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- 2021
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8. Microbe Profile: Cellvibrio japonicus: living the sweet life via biomass break-down
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Gardner, Jeffrey G., primary
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- 2024
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9. Musashi 2 influences chronic lymphocytic leukemia cell survival and growth making it a potential therapeutic target
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Palacios, Florencia, Yan, Xiao-Jie, Ferrer, Gerardo, Chen, Shih-Shih, Vergani, Stefano, Yang, Xuejing, Gardner, Jeffrey, Barrientos, Jaqueline C., Rock, Philip, Burack, Richard, Kolitz, Jonathan E., Allen, Steven L., Kharas, Michael G., Abdel-Wahab, Omar, Rai, Kanti R., and Chiorazzi, Nicholas more...
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- 2021
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10. Final Technical Report: Functional characterization and regulatory modeling of lignocellulose deconstruction in the saprophytic bacterium Cellvibrio japonicus
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Gardner, Jeffrey, primary
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- 2022
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11. High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates
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Monge, Estela C., Levi, Marios, Forbin, Joseph N., Legesse, Mussie D., Udo, Basil A., deCarvalho, Tagide N., and Gardner, Jeffrey G.
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- 2020
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12. Indigenous Rights and Neoliberalism in Latin America
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Gardner, Jeffrey A., Richards, Patricia, Ratuva, Steven, Section editor, Airini, Section editor, and Ratuva, Steven, editor
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- 2019
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13. Dark matter halo occupation: environment and clustering
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Croft, Rupert, Di Matteo, Tiziana, Khandai, Nishikanta, Springel, Volker, Jana, Anirban, and Gardner, Jeffrey
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We use a large dark matter simulation of a LambdaCDM model to investigate the clustering and environmental dependence of the number of substructures in a halo. Focusing on redshift z=1, we find that the halo occupation distribution is sensitive at the tens of percent level to the surrounding density and to a lesser extent to asymmetry of the surrounding density distribution. We compute the autocorrelation function of halos as a function of occupation, building on the finding of Wechsler et al. (2006) and Gao and White (2007) that halos (at fixed mass) with more substructure are more clustered. We compute the relative bias as a function of occupation number at fixed mass, finding a strong relationship. At fixed mass, halos in the top 5% of occupation can have an autocorrelation function ~ 1.5-2 times higher than the mean. We also compute the bias as a function of halo mass, for fixed halo occupation. We find that for group and cluster sized halos, when the number of subhalos is held fixed, there is a strong anticorrelation between bias and halo mass. Such a relationship represents an additional challenge to the halo model., Comment: 13 pages, 10 figures, MNRAS submitted more...
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- 2011
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14. Terapixel imaging of cosmological simulations
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Feng, Yu, Croft, Rupert A. C., Di Matteo, Tiziana, Khandai, Nishikanta, Sargent, Randy, Nourbakhsh, Illah, Dille, Paul, Bartley, Chris, Springel, Volker, Jana, Anirban, and Gardner, Jeffrey
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
The increasing size of cosmological simulations has led to the need for new visualization techniques. We focus on Smoothed Particle Hydrodynamical (SPH) simulations run with the GADGET code and describe methods for visually accessing the entire simulation at full resolution. The simulation snapshots are rastered and processed on supercomputers into images that are ready to be accessed through a web interface (GigaPan). This allows any scientist with a web-browser to interactively explore simulation datasets in both in spatial and temporal dimensions, datasets which in their native format can be hundreds of terabytes in size or more. We present two examples, the first a static terapixel image of the MassiveBlack simulation, a P-GADGET SPH simulation with 65 billion particles, and the second an interactively zoomable animation of a different simulation with more than one thousand frames, each a gigapixel in size. Both are available for public access through the GigaPan web interface. We also make our imaging software publicly available., Comment: 9 pages, 6 figures, Link to the Gigapan image: http://gigapan.org/gigapans/76215/ Link to the TimeMachine animation: http://timemachine.gigapan.org/wiki/Evolution_of_the_Universe Link to Gaepsi: http://web.phys.cmu.edu/~yfeng1/gaepsi more...
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- 2011
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15. Three-Point Correlation Functions of SDSS Galaxies: Constraining Galaxy-Mass Bias
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McBride, Cameron K., Connolly, Andrew J., Gardner, Jeffrey P., Scranton, Ryan, Scoccimarro, Roman, Berlind, Andreas A., Marin, Felipe, and Schneider, Donald P.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We constrain the linear and quadratic bias parameters from the configuration dependence of the three-point correlation function (3PCF) in both redshift and projected space, utilizing measurements of spectroscopic galaxies in the Sloan Digital Sky Survey (SDSS) Main Galaxy Sample. We show that bright galaxies (M_r < -21.5) are biased tracers of mass, measured at a significance of 4.5 sigma in redshift space and 2.5 sigma in projected space by using a thorough error analysis in the quasi-linear regime (9-27 Mpc/h). Measurements on a fainter galaxy sample are consistent with an unbiased model. We demonstrate that a linear bias model appears sufficient to explain the galaxy-mass bias of our samples, although a model using both linear and quadratic terms results in a better fit. In contrast, the bias values obtained from the linear model appear in better agreement with the data by inspection of the relative bias, and yield implied values of sigma_8 that are more consistent with current constraints. We investigate the covariance of the 3PCF, which itself is a measurement of galaxy clustering. We assess the accuracy of our error estimates by comparing results from mock galaxy catalogs to jackknife re-sampling methods. We identify significant differences in the structure of the covariance. However, the impact of these discrepancies appears to be mitigated by an eigenmode analysis that can account for the noisy, unresolved modes. Our results demonstrate that using this technique is sufficient to remove potential systematics even when using less-than-ideal methods to estimate errors., Comment: 18 pages, 17 figures. Submitted to ApJ more...
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- 2010
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16. Detecting neutral hydrogen in emission at redshift z ~ 1
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Khandai, Nishikanta, Sethi, Shiv K., Di Matteo, Tiziana, Croft, Rupert A. C., Springel, Volker, Jana, Anirban, and Gardner, Jeffrey P.
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Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
We use a large N-body simulation to examine the detectability of HI in emission at redshift z ~ 1, and the constraints imposed by current observations on the neutral hydrogen mass function of galaxies at this epoch. We consider three different models for populating dark matter halos with HI, designed to encompass uncertainties at this redshift. These models are consistent with recent observations of the detection of HI in emission at z ~ 0.8. Whilst detection of 21 cm emission from individual halos requires extremely long integrations with existing radio interferometers, such as the Giant Meter Radio Telescope (GMRT), we show that the stacked 21 cm signal from a large number of halos can be easily detected. However, the stacking procedure requires accurate redshifts of galaxies. We show that radio observations of the field of the DEEP2 spectroscopic galaxy redshift survey should allow detection of the HI mass function at the 5-12 sigma level in the mass range 10^(11.4) M_sun/h < M_halo < 10^(12.5)M_sun/h, with a moderate amount of observation time. Assuming a larger noise level that corresponds to an upper bound for the expected noise for the GMRT, the detection significance for the HI mass function is still at the 1.7-3 sigma level. We find that optically undetected satellite galaxies enhance the HI emission profile of the parent halo, leading to broader wings as well as a higher peak signal in the stacked profile of a large number of halos. We show that it is in principle possible to discern the contribution of undetected satellites to the total HI signal, even though cosmic variance limitation make this challenging for some of our models., Comment: 14 pages, 9 figures, Submitted To MNRAS more...
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- 2010
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17. Three-Point Correlation Functions of SDSS Galaxies: Luminosity and Color Dependence in Redshift and Projected Space
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McBride, Cameron K., Connolly, Andrew J., Gardner, Jeffrey P., Scranton, Ryan, Newman, Jeffrey A., Scoccimarro, Roman, Zehavi, Idit, and Schneider, Donald P.
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Astrophysics - Cosmology and Extragalactic Astrophysics - Abstract
The three-point correlation function (3PCF) provides an important view into the clustering of galaxies that is not available to its lower order cousin, the two-point correlation function (2PCF). Higher order statistics, such as the 3PCF, are necessary to probe the non-Gaussian structure and shape information expected in these distributions. We measure the clustering of spectroscopic galaxies in the Main Galaxy Sample of the Sloan Digital Sky Survey (SDSS), focusing on the shape or configuration dependence of the reduced 3PCF in both redshift and projected space. This work constitutes the largest number of galaxies ever used to investigate the reduced 3PCF, using over 220,000 galaxies in three volume-limited samples. We find significant configuration dependence of the reduced 3PCF at 3-27 Mpc/h, in agreement with LCDM predictions and in disagreement with the hierarchical ansatz. Below 6 Mpc/h, the redshift space reduced 3PCF shows a smaller amplitude and weak configuration dependence in comparison with projected measurements suggesting that redshift distortions, and not galaxy bias, can make the reduced 3PCF appear consistent with the hierarchical ansatz. The reduced 3PCF shows a weaker dependence on luminosity than the 2PCF, with no significant dependence on scales above 9 Mpc/h. On scales less than 9 Mpc/h, the reduced 3PCF appears more affected by galaxy color than luminosty. We demonstrate the extreme sensitivity of the 3PCF to systematic effects such as sky completeness and binning scheme, along with the difficulty of resolving the errors. Some comparable analyses make assumptions that do not consistently account for these effects., Comment: 27 pages, 21 figures. Updated to match accepted version. Published in ApJ more...
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- 2010
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18. Genetic and enzymatic characterization of Amy13E from Cellvibrio japonicus reclassifies it as a cyclodextrinase also capable of α-diglucoside degradation
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Mascelli, Giulia M., primary, Garcia, Cecelia A., additional, and Gardner, Jeffrey G., additional
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- 2023
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19. A Pilot Survey of HI in Field Galaxies at Redshift z~0.2
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Catinella, Barbara, Haynes, Martha P., Giovanelli, Riccardo, Gardner, Jeffrey P., and Connolly, Andrew J.
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Astrophysics - Abstract
We present the first results of a targeted survey carried out with the 305 m Arecibo telescope to detect HI-line emission from galaxies at redshift z>0.16. The targets, selected from the Sloan Digital Sky Survey database, are non-interacting disk galaxies in relatively isolated fields. We present here the HI spectra and derived HI parameters for ten objects detected in this pilot program. All are massive disk galaxies in the redshift interval 0.17-0.25 (i.e. 2-3 Gyr look-back time), with HI masses M_HI=3-8 x 10^10 Msun and high gas mass fractions (HI - to - stellar mass ratios ~10-30%). Our results demonstrate the efficacy of exploiting Arecibo's large collecting area to measure the HI mass and rotational velocity of galaxies above redshift z=0.2. In particular, this sample includes the highest redshift detections of HI emission from individual galaxies made to date. Extension of this pilot program will allow us to study the HI properties of field galaxies at cosmological distances, thus complementing ongoing radio synthesis observations of cluster samples at z~0.2., Comment: Accepted for publication in ApJ Letters more...
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- 2008
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20. Enabling Rapid Development of Parallel Tree Search Applications
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Gardner, Jeffrey P., Connolly, Andrew, and McBride, Cameron
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Astrophysics - Abstract
Virtual observatories will give astronomers easy access to an unprecedented amount of data. Extracting scientific knowledge from these data will increasingly demand both efficient algorithms as well as the power of parallel computers. Nearly all efficient analyses of large astronomical datasets use trees as their fundamental data structure. Writing efficient tree-based techniques, a task that is time-consuming even on single-processor computers, is exceedingly cumbersome on massively parallel platforms (MPPs). Most applications that run on MPPs are simulation codes, since the expense of developing them is offset by the fact that they will be used for many years by many researchers. In contrast, data analysis codes change far more rapidly, are often unique to individual researchers, and therefore accommodate little reuse. Consequently, the economics of the current high-performance computing development paradigm for MPPs does not favor data analysis applications. We have therefore built a library, called Ntropy, that provides a flexible, extensible, and easy-to-use way of developing tree-based data analysis algorithms for both serial and parallel platforms. Our experience has shown that not only does our library save development time, it can also deliver excellent serial performance and parallel scalability. Furthermore, Ntropy makes it easy for an astronomer with little or no parallel programming experience to quickly scale their application to a distributed multiprocessor environment. By minimizing development time for efficient and scalable data analysis, we enable wide-scale knowledge discovery on massive datasets., Comment: Accepted to Challenges of Large Applications in Distributed Environments (CLADE) 2007, Monterey, CA. 9 pages and 3 figures more...
- Published
- 2007
21. Measuring the Halo Mass of z=3 Damped Ly-alpha Absorbers from the Absorber-Galaxy Cross-correlation
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Bouche, Nicolas, Gardner, Jeffrey P., Weinberg, David H., Katz, Neal, Dave, Romeel, and Lowenthal, James D.
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Astrophysics - Abstract
[Abridged] We test the reliability of a method to measure the mean halo mass of Damped Ly-alpha absorbers (DLAs). The method is based on measuring the ratio of the cross-correlation between DLAs and galaxies to the auto-correlation of the galaxies themselves ($w_{\rm dg}/w_{\rm gg}$), which is (in linear theory) the ratio of their bias factor. This is shown to be true irrespective of the galaxy redshift distribution, provided that one uses the same galaxies for the two correlation functions. The method is applicable to all redshifts. Here, we focus on z=3 DLAs and we demonstrate that the method robustly constrains the mean DLA halo mass using smoothed particle hydrodynamics (SPH) cosmological simulations. If we use the bias formalism of Mo & White with the DLA and galaxy mass distributions of these simulations, we predict a bias ratio of 0.771. Direct measurement from the simulations of $w_{\rm dg}/w_{\rm gg}$ st yields a ratio of 0.73+/-0.08, in excellent agreement with that prediction. Equivalently, inverting the measured correlation ratio to infer a mean DLA halo mass yields (log. averaging, in solar units)
=11.13+/-013, in excellent agreement with the true value in the simulations: 11.16. The cross- correlation method thus appears to yield a robust estimate of the average host halo mass even though the DLAs and the galaxies occupy a broad mass spectrum of halos, and massive halos contain multiple galaxies with DLAs. We show that the inferred mean DLA halo mass is independent of the galaxy sub-sample used, i.e. the cross-correlation technique is also reliable. Our results imply that the cross-correlation length between DLAs and LBGs is predicted to be, at most, 2.85 Mpc. Future observations will soon distinguish models in which DLAs are in low mass halos from those in which DLAs are in massive halos., Comment: 15 pages, 7 figures, to be published in ApJ 2005 July 20th (Full resolution of Fig.2 at http://www.mpe.mpg.de/~nbouche/papers/Xcorr/f2-orig.eps); minor changes to match the published text more...- Published
- 2005
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22. Systems analysis of the glycoside hydrolase family 18 enzymes from Cellvibrio japonicus characterizes essential chitin degradation functions
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Monge, Estela C., Tuveng, Tina R., Vaaje-Kolstad, Gustav, Eijsink, Vincent G.H., and Gardner, Jeffrey G.
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- 2018
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23. Dark Matter Subhaloes in Numerical Simulations
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Reed, Darren, Governato, Fabio, Quinn, Thomas, Gardner, Jeffrey, Stadel, Joachim, and Lake, George
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Astrophysics - Abstract
We use cosmological LCDM numerical simulations to model the evolution of the substructure population in sixteen dark matter haloes with resolutions of up to seven million particles within the virial radius. The combined substructure circular velocity distribution function (VDF) for hosts of 10^11 to 10^14 Msun at redshifts from zero to two or higher has a self-similar shape, is independent of host halo mass and redshift, and follows the relation: dn/dv=(1/8)(v_cmax/v_cmax,host)^-4. Halo to halo variance in the VDF is a factor of roughly two to four. At high redshifts, we find preliminary evidence for fewer large substructure haloes (subhaloes). Specific angular momenta are significantly lower for subhaloes nearer the host halo centre where tidal stripping is more effective. The radial distribution of subhaloes is marginally consistent with the mass profile for r >~ 0.3r_vir, where the possibility of artificial numerical disruption of subhaloes can be most reliably excluded by our convergence study, although a subhalo distribution that is shallower than the mass profile is favoured. Subhalo masses but not circular velocities decrease toward the host centre. Subhalo velocity dispersions hint at a positive velocity bias at small radii. There is a weak bias toward more circular orbits at lower redshift, especially at small radii. We additionally model a cluster in several power law cosmologies of P ~ k^n, and demonstrate that a steeper spectral index, n, results in significantly less substructure., Comment: minor revisions to match accepted version, MNRAS, 359, 1357 more...
- Published
- 2004
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24. Evolution of the Density Profiles of Dark Matter Haloes
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Reed, Darren, Governato, Fabio, Verde, Licia, Gardner, Jeffrey, Quinn, Thomas, Stadel, Joachim, Merritt, David, and Lake, George
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Astrophysics - Abstract
We use numerical simulations in a Lambda CDM cosmology to model density profiles in a set of 16 dark matter haloes with resolutions of up to 7 million particles within the virial radius. These simulations allow us to follow robustly the formation and evolution of the central cusp over a large mass range of 10^11 to 10^14 M_sun, down to approximately 0.5% of the virial radius, and from redshift 5 to the present. The cusp of the density profile is set at redshifts of 2 or greater and remains remarkably stable to the present time, when considered in non-comoving coordinates. We fit our haloes to a 2 parameter profile where the steepness of the asymptotic cusp is given by gamma, and its radial extent is described by the concentration, c_gamma. In our simulations, we find gamma = 1.4 - 0.08Log(M/M_*) for haloes of 0.01M_* to 1000M_*, with a large scatter of gamma ~ +/-0.3$; and c_gamma = 8*M/M_*^{-0.15}, with a large M/M_* dependent scatter roughly equal to +/- c_gamma. Our redshift zero haloes have inner slope parameters ranging approximately from r^{-1} to r^{-1.5}, with a median of roughly r^{-1.3}. This 2 parameter profile fit works well for all our halo types, whether or not they show evidence of a steep asymptotic cusp. We also model a cluster in power law cosmologies of P ~ k^n (n=0,-1,-2,-2.7). We find larger concentration radii and shallower cusps for steeper n. The minimum resolved radius is well described by the mean interparticle separation. The trend of steeper and more concentrated cusps for smaller $M/M_*$ haloes clearly shows that dwarf sized Lambda CDM haloes have, on average, significantly steeper density profiles within the inner few percent of the virial radius than inferred from recent observations. Code to reproduce this profile can be downloaded from http://www.icc.dur.ac.uk/~reed/profile.html, Comment: Code to reproduce this profile can be downloaded from http://www.icc.dur.ac.uk/~reed/profile.html Accepted version, minor changes, MNRAS, 357, 82 (abstract abridged) more...
- Published
- 2003
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25. Evolution of the Mass Function of Dark Matter Haloes
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Reed, Darren, Gardner, Jeffrey, Quinn, Thomas, Stadel, Joachim, Fardal, Mark, Lake, George, and Governato, Fabio
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Astrophysics - Abstract
We use a high resolution $\Lambda$CDM numerical simulation to calculate the mass function of dark matter haloes down to the scale of dwarf galaxies, back to a redshift of fifteen, in a 50 $h^{-1}$Mpc volume containing 80 million particles. Our low redshift results allow us to probe low $\sigma$ density fluctuations significantly beyond the range of previous cosmological simulations. The Sheth and Tormen mass function provides an excellent match to all of our data except for redshifts of ten and higher, where it overpredicts halo numbers increasingly with redshift, reaching roughly 50 percent for the $10^{10}-10^{11} \msun$ haloes sampled at redshift 15. Our results confirm previous findings that the simulated halo mass function can be described solely by the variance of the mass distribution, and thus has no explicit redshift dependence. We provide an empirical fit to our data that corrects for the overprediction of extremely rare objects by the Sheth and Tormen mass function. This overprediction has implications for studies that use the number densities of similarly rare objects as cosmological probes. For example, the number density of high redshift (z $\simeq$ 6) QSOs, which are thought to be hosted by haloes at 5$\sigma$ peaks in the fluctuation field, are likely to be overpredicted by at least a factor of 50%. We test the sensitivity of our results to force accuracy, starting redshift, and halo finding algorithm., Comment: v2: 9 pages, 11 figures, accepted by MNRAS with revisions. Includes additional numerical tests and error discussion, clarifications, and referee suggestions more...
- Published
- 2003
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26. The Infuence of Omega_baryon on High-Redshift Structure
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Gardner, Jeffrey P., Katz, Neal, Hernquist, Lars, and Weinberg, David H.
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Astrophysics - Abstract
We analyze high-redshift structure in three hydrodynamic simulations that have identical initial conditions and cosmological parameters and differ only in the value of the baryon density parameter, Omega_b=0.02, 0.05, 0.125. Increasing Omega_b does not change the fraction of baryons in the diffuse (unshocked) phase of the intergalactic medium, but it increases cooling rates and therefore transfers some baryons from the shocked intergalactic phase to the condensed phase associated with galaxies. Predictions of Lyman-alpha forest absorption are almost unaffected by changes of Omega_b provided that the UV background intensity is adjusted so that the mean opacity of the forest matches the observed value. The required UV background intensity scales as Omega_b^1.7, and the higher photoionization rate increases the gas temperature in low density regions. Damped Lyman-alpha absorption and Lyman limit absorption both increase with increasing Omega_b, though the impact is stronger for damped absorption and is weaker at z=4 than at z=2-3. The mass of cold gas and stars in high-redshift galaxies increases faster than Omega_b but slower than Omega_b^2, and the global star formation rate scales approximately as Omega_b^1.5. In the higher Omega_b models, the fraction of baryonic material within the virial radius of dark matter halos is usually higher than the universal fraction, indicating that gas dynamics and cooling can lead to over-representation of baryons in virialized systems. On the whole, our results imply a fairly intuitive picture of the influence of Omega_b on high-redshift structure, and we provide scalings that can be used to estimate the impact of Omega_b uncertainties on the predictions of hydrodynamic simulations., Comment: 22 pages, 9 figures, submitted to ApJ, high-resolution version availible at http://lahmu.phyast.pitt.edu/~gardner/publications/omegab.ps.gz more...
- Published
- 2001
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27. Metal Enrichment of the Intergalactic Medium in Cosmological Simulations
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Aguirre, Anthony, Hernquist, Lars, Schaye, Joop, Katz, Neal, Weinberg, David H., and Gardner, Jeffrey
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Astrophysics - Abstract
Observations have established that the diffuse intergalactic medium (IGM) at z ~ 3 is enriched to ~0.1-1% solar metallicity and that the hot gas in large clusters of galaxies (ICM) is enriched to 1/3-1/2 solar metallicity at z=0. Metals in the IGM may have been removed from galaxies (in which they presumably form) during dynamical encounters between galaxies, by ram-pressure stripping, by supernova-driven winds, or as radiation-pressure driven dust efflux. This study develops a method of investigating the chemical enrichment of the IGM and of galaxies, using already completed cosmological simulations. To these simulations, we add dust and (gaseous) metals, distributing the dust and metals in the gas according to three simple parameterized prescriptions, one for each enrichment mechanism. These prescriptions are formulated to capture the basic ejection physics, and calibrated when possible with empirical data. Our results indicate that dynamical removal of metals from >~ 3*10^8 solar mass galaxies cannot account for the observed metallicity of low-column density Ly-alpha absorbers, and that dynamical removal from >~ 3*10^10 solar mass galaxies cannot account for the ICM metallicities. Dynamical removal also fails to produce a strong enough mass-metallicity relation in galaxies. In contrast, either wind or radiation-pressure ejection of metals from relatively large galaxies can plausibly account for all three sets of observations (though it is unclear whether metals can be distributed uniformly enough in the low-density regions without overly disturbing the IGM, and whether clusters can be enriched quite as much as observed). We investigate in detail how our results change with variations in our assumed parameters, and how results for the different ejection processes compare. (Abridged), Comment: Minor revision, 1 figure added addressing diffusion of metals after their ejection. Accepted by ApJ. 31 EmulateApj Pages with 13 embedded postscript figures more...
- Published
- 2001
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28. Cooling Radiation and the Lyman-alpha Luminosity of Forming Galaxies
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Fardal, Mark A., Katz, Neal, Gardner, Jeffrey P., Hernquist, Lars, Weinberg, David H., and Davé, Romeel
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Astrophysics - Abstract
We examine the cooling radiation from forming galaxies in hydrodynamic simulations of the LCDM model (cold dark matter with a cosmological constant), focusing on the Ly-alpha line luminosities of high-redshift systems. Primordial composition gas condenses within dark matter potential wells, forming objects with masses and sizes comparable to the luminous regions of observed galaxies. As expected, the energy radiated in this process is comparable to the gravitational binding energy of the baryons, and the total cooling luminosity of the galaxy population peaks at z ~= 2. However, in contrast to the classical picture of gas cooling from the \sim 10^6 K virial temperature of a typical dark matter halo, we find that most of the cooling radiation is emitted by gas with T < 20,000 K. As a consequence, roughly 50% of this cooling radiation emerges in the Ly-alpha line. While a galaxy's cooling luminosity is usually smaller than the ionizing continuum luminosity of its young stars, the two are comparable in the most massive systems, and the cooling radiation is produced at larger radii, where the Ly-alpha photons are less likely to be extinguished by dust. We suggest, in particular, that cooling radiation could explain the two large (\sim 100 kpc), luminous (L_{Ly-alpha} \sim 10^{44} erg s^{-1}) ``blobs'' of Ly-alpha emission found in Steidel et al.'s (1999) narrow band survey of a z = 3 proto-cluster. Our simulations predict objects of the observed luminosity at about the right space density, and radiative transfer effects can account for the observed sizes and line widths. We discuss observable tests of this hypothesis for the nature of the Ly-alpha blobs, and we present predictions for the contribution of cooling radiation to the Ly-alpha luminosity function of galaxies as a function of redshift., Comment: Submitted to ApJ. 28 pages including 9 PS figures. Version with color figures available at http://donald.astro.umass.edu/~fardal/papers/cooling/cooling.html more...
- Published
- 2000
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29. Enrichment of the Intergalactic Medium by Radiation Pressure Driven Dust Efflux
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Aguirre, Anthony, Hernquist, Lars, Katz, Neal, Gardner, Jeffrey, and Weinberg, David
- Subjects
Astrophysics - Abstract
The presence of metals in hot cluster gas and in Ly-alpha absorbers, as well as the mass-metallicity relation of observed galaxies, suggest that galaxies lose a significant fraction of their metals to the intergalactic medium (IGM). Theoretical studies of this process have concentrated on metal removal by dynamical processes or supernova-driven winds. Here, we investigate the enrichment of the IGM by the expulsion of dust grains from galaxies by radiation pressure. We use already completed cosmological simulations, to which we add dust assuming that most dust can reach the equilibrium point between radiation pressure and gravitational forces. We find that the expulsion of dust and its subsequent (partial) destruction in the IGM can plausibly account for the observed level of C and Si enrichment of the z=3 IGM. At low-z, dust ejection and destruction could explain a substantial fraction of the metals in clusters, but it cannot account for all of the chemical species observed. Dust expelled by radiation pressure could give clusters a visual opacity of up to 0.2-0.5 mag in their central regions even after destruction by the hot intracluster medium; this value is interestingly close to limits and claimed observations of cluster extinction. We also comment on the implications of our results for the opacity of the general IGM. Finally, we suggest a possible `hybrid' scenario in which winds expel gas and dust into galaxy halos but radiation pressure distributes the dust uniformly through the IGM., Comment: 5 emulateapj pages including 3 figures. Accepted by ApJ Letters more...
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- 2000
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30. Dependence of Halo Properties on Interaction History, Environment and Cosmology
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Gardner, Jeffrey P.
- Subjects
Astrophysics - Abstract
I present results from numerical N-body simulations regarding the effect of merging events on the angular momentum distribution of galactic halos as well as a comparison of halo growth in Press-Schechter vs. N-body methods. A total of six simulations are used spanning 3 cosmologies: a standard flat Omega_0=1 model, an open Omega_0=0.3 model and a "tilted" flat Omega_0=1 model with spectral index n=0.8. In each model, one run was conducted using a spatially uniform grid of particles and one using a refined grid in a large void. In all three models and all environments tested, the mean angular momentum of merger remnants (halo interaction products with mass ratios 3:1 or less) is greater than non-merger remnants. Furthermore, the dispersion in the merger-remnant angular momentum distribution is smaller than the dispersion of the non-merger distribution. The interpretation most consistent with the data is that the orbital angular momentum of the interactors is important in establishing the final angular momentum of the merger product. I give the angular momentum distribution which describes the merger remnant population. I trace the most massive progenitor of L_* galactic-mass halos (uniform grid) and 10^{11} solar mass halos (refined void) from redshift z=0 back to z=5. Monte-Carlo mass histories match simulations reasonably well for the latter sample. I find that for halos of mass 10^{12} to 10^{14} solar masses, this method can underestimate the mass of progenitors by 20%, hence yielding improper formation redshifts of halos. With this caveat, however, the general shapes of halo mass histories and formation-time distributions are preserved., Comment: 17 pages, 7 postscript figures. Final version, accepted by ApJ more...
- Published
- 2000
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31. Metal Enrichment of the Intergalactic Medium at z=3 by Galactic Winds
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Aguirre, Anthony, Hernquist, Lars, Schaye, Joop, Weinberg, David, Katz, Neal, and Gardner, Jeffrey
- Subjects
Astrophysics - Abstract
Studies of quasar absorption lines reveal that the low density intergalactic medium at z ~ 3 is enriched to 0.001-0.01 solar metallicity. This enrichment may have occurred in an early generation of Population III stars at redshift z >~ 10, by protogalaxies at 6 <~ z <~ 10, or by larger galaxies at 3 <~ z <~ 6. This paper addresses the third possibility by calculating the enrichment of the IGM at z >~ 3 by galaxies of baryonic mass >~ 10^8.5 solar masses. We use already completed cosmological simulations to which we add a prescription for chemical evolution and metal ejection by winds, assuming that the winds have properties similar to those observed in local starbursts and Lyman-break galaxies. Results are given for a number of representative models, and we also examine the properties of the galaxies responsible for the enrichment as well as the physical effects responsible for wind escape and propagation. We find that winds of velocity >~ 200-300 km/s are capable of enriching the IGM to the mean level observed, though many low-density regions would remain metal free. Calibrated by observations of Lyman-break galaxies, our calculations suggest that most galaxies at z >~ 3 should drive winds that can escape and propagate to large radii. The primary effect limiting the enrichment of low-density IG gas in our scenario is then the travel time from high- to low-density regions, implying that the metallicity of low-density gas is a strong function of redshift., Comment: 8 emulateApJ figures, 5 postscript figures. Minor revisions since last posting to match version accepted to ApJ. Major Revision since original version more...
- Published
- 2000
- Full Text
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32. Simulations of Damped Lyman-Alpha and Lyman Limit Absorbers in Different Cosmologies: Implications for Structure Formation at High Redshift
- Author
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Gardner, Jeffrey P., Katz, Neal, Hernquist, Lars, and Weinberg, David H.
- Subjects
Astrophysics - Abstract
We use hydrodynamic cosmological simulations to study damped Lyman-alpha (DLA) and Lyman limit (LL) absorption at redshifts z=2-4 in five variants of the cold dark matter scenario. Our standard simulations resolve the formation of dense concentrations of neutral gas in halos with circular velocity v_c roughly 140 km/s for Omega_m=1 and 90 km/s for Omega_m=0.4, at z=2; an additional LCDM simulation resolves halos down to v_c approximately 50 km/s at z=3. We find a clear relation between HI column density and projected distance to the center of the nearest galaxy, with DLA absorption usually confined to galactocentric radii less than 10-15 kpc and LL absorption arising out to projected separations of 30 kpc or more. Detailed examination provides evidence of non-equilibrium effects on absorption cross-section. If we consider only absorption in the halos resolved by our standard simulations, then all five models fall short of reproducing the observed abundance of DLA and LL systems at these redshifts. If we extrapolate to lower halo masses, we find all four models are consistent with the observed abundance of DLA systems if the the extrapolated behavior extends to circular velocities roughly 50-80 km/s, and they may produce too much absorption if the relation continues to 40 km/s. Our results suggest that LL absorption is closely akin to DLA absorption, arising in less massive halos or at larger galactocentric radii but not caused by processes acting on a radically different mass scale., Comment: 33 pages with 10 embedded EPS figures. Substantially revised and updated from original version. Includes new high-resolution simulations. Accepted for publication in the ApJ more...
- Published
- 1999
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33. The Nature of Lyman Break Galaxies in Cosmological Hydrodynamic Simulations
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Davé, Romeel, Gardner, Jeffrey P., Hernquist, Lars, Katz, Neal, and Weinberg, David H.
- Subjects
Astrophysics - Abstract
What type of objects are being detected as $z\sim 3$ "Lyman break galaxies"? Are they predominantly the most massive galaxies at that epoch, or are many of them smaller galaxies undergoing a short-lived burst of merger-induced star formation? We attempt to address this question using high-resolution cosmological hydrodynamic simulations including star formation and feedback. Our $\Lambda$CDM simulation, together with Bruzual-Charlot population synthesis models, reproduces the observed number density and luminosity function of Lyman break galaxies when dust is incorporated. The inclusion of dust is crucial for this agreement. In our simulation, these galaxies are predominantly the most massive objects at this epoch, and have a significant population of older stars. Nevertheless, it is possible that our simulations lack the resolution and requisite physics to produce starbursts, despite having a physical resolution of $\la 700$ pc at z=3. Thus we cannot rule out merger-induced starburst galaxies also contributing to the observed population of high-redshift objects., Comment: 5 pages, contribution to the Proceedings of Rencontres Internationales de l'IGRAP, Clustering at High Redshift, Marseille 1999 more...
- Published
- 1999
34. Theoretical Modeling of the High Redshift Galaxy Population
- Author
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Weinberg, David H., Dave', Romeel, Gardner, Jeffrey P., Hernquist, Lars, and Katz, Neal
- Subjects
Astrophysics - Abstract
We review theoretical approaches to the study of galaxy formation, with emphasis on the role of hydrodynamic simulations in modeling the high redshift galaxy population. We present new predictions for the abundance of star-forming galaxies in the Lambda + cold dark matter model (Omega_m=0.4, Omega_L=0.6), combining results from several simulations to probe a wide range of redshift. At a threshold density of one object per arcmin^2 per unit z, these simulations predict galaxies with star formation rates of 2 msun/yr (z=10), 5 msun/yr (z=8), 20 msun/yr (z=6), 70-100 msun/yr (z=4-2), and 30 msun/yr (z=0.5). For galaxies selected at a fixed comoving space density n=0.003 h^3 Mpc^{-3], a (50 Mpc/h)^3 simulation predicts a galaxy correlation function (r/5 Mpc/h)^{-1.8} in comoving coordinates, essentially independent of redshift from z=4 to z=0.5. Different cosmological models predict global histories of star formation that reflect their overall histories of mass clustering, but robust numerical predictions of the comoving space density of star formation are difficult because the simulations miss the contribution from galaxies below their resolution limit. The LCDM model appears to predict a star formation history with roughly the shape inferred from observations, but it produces too many stars at low redshift, predicting Omega_* ~ 0.015 at z=0. We conclude with a brief discussion of this discrepancy and three others that suggest gaps in our current theory of galaxy formation: small disks, steep central halo profiles, and an excess of low mass dark halos. While these problems could fade as the simulations or observations improve, they could also guide us towards a new understanding of galactic scale star formation, the spectrum of primordial fluctuations, or the nature of dark matter., Comment: 12 pages, 3 figs. To be published in "Photometric Redshifts and High Redshift Galaxies", eds. R. Weymann, L. Storrie-Lombardi, M. Sawicki & R. Brunner, (San Francisco: ASP Conference Series) more...
- Published
- 1999
35. The Spatiality of Boundary Work : Political-Administrative Borders and Maya-Mam Collective Identification
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Gardner, Jeffrey A. and Richards, Patricia
- Published
- 2017
36. Indigenous borders: contesting the nation-state, belonging and racialization
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Gardner, Jeffrey A., primary and Warren, Sarah D., additional
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- 2023
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37. Tx’otx’ and la defensa del territorio : articulating Mam territory as an Indigenous cross-border nation
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Gardner, Jeffrey A., primary
- Published
- 2023
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38. RNAseq analysis of Cellvibrio japonicus during starch utilization differentiates between genes encoding carbohydrate active enzymes controlled by substrate detection or growth rate
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Garcia, Cecelia A., primary and Gardner, Jeffrey G., additional
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- 2023
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39. A case of nonuremic calciphylaxis of the penis responding to sodium thiosulfate therapy
- Author
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Lum, Kalisa, primary, Gardner, Jeffrey, additional, and Dao, Harry, additional
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- 2023
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40. On the origin of early type galaxies and the evolution of the interaction rate in the field
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Governato, F., Gardner, Jeffrey P., Stadel, J., Quinn, T., and Lake, G.
- Subjects
Astrophysics - Abstract
Using cosmological N-body simulations of critical (SCDM) and open (Omega_0=0.3, OCDM) cold dark matter models we have identified dark matter halos which are associated with the progenitors of present day bright early type galaxies. By following their merging history, we show how early type galaxies that formed within massive halos at redshift around 3 are now preferentially residing in clusters and groups. On the other hand, those that formed through major merging events between redshift 1 and the present have not yet been accreted into larger, virialized structures. This result is in agreement with analytical predictions in hierarchical clustering models. CDM models are able to explain both the ancient and uniform population of ellipticals that dominates in clusters together with the more recent and heterogeneous population of field ellipticals. Predictions for the comoving number density of bright early-type galaxies are given, and are shown to be consistent with the observed luminosity function. We predict that the number density of interacting bright binary galaxies, from which the field population of ellipticals may have originated, is proportional to (1+z)**4.2+-0.28 and (1+z)**2.5+-0.42 in SCDM and OCDM respectively. This result is consistent with previous analytical estimates and is discussed together with recent observational constraints., Comment: 9 pages, two ps figures (included), submitted to ApJ. Also available at http://star-www.dur.ac.uk/~fabio/index.html more...
- Published
- 1997
41. Testing Cosmological Models Against the Abundance of Damped Lyman-Alpha Absorbers
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Gardner, Jeffrey P., Katz, Neal, Weinberg, David H., and Hernquist, Lars
- Subjects
Astrophysics - Abstract
We calculate the number of damped Lyman-alpha absorbers expected in various popular cosmological models as a function of redshift and compare our predictions with observed abundances. The Press-Schechter formalism is used to obtain the distribution of halos with circular velocity in different cosmologies, and we calibrate the relation between circular velocity and absorption cross-section using detailed gas dynamical simulations of a ``standard'' cold dark matter (CDM) model. Because of this calibration, our approach makes more realistic assumptions about the absorption properties of collapsed objects than previous, analytic calculations of the damped Lyman-alpha abundance. CDM models with Omega_0=1, H_0=50, baryon density Omega_b=0.05, and scale-invariant primeval fluctuations reproduce the observed incidence and redshift evolution of damped Lyman-alpha absorption to within observational uncertainty, for both COBE normalization (sigma_8=1.2) and a lower normalization (sigma_8=0.7) that better matches the observed cluster abundance at z=0. A tilted (n=0.8, sigma_8=0.7) CDM model tends to underproduce absorption, especially at z=4. With COBE normalization, a CDM model with Omega_0=0.4, Omega_{Lambda}=0.6 gives an acceptable fit to the observed absorption; an open CDM model is marginally acceptable if Omega_0 is at least 0.4 and strongly inconsistent with the z=4 data if Omega_0=0.3. Mixed dark matter models tend not to produce sufficient absorption, being roughly comparable to tilted CDM models if Omega_{nu} = 0.2 and failing drastically if Omega_{nu} = 0.3., Comment: AASlatex, 13 pages w/ 2 embedded ps figures. To be published in ApJ, Sept. 1, 1997 more...
- Published
- 1997
- Full Text
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42. Tx'otx' and la defensa del territorio: articulating Mam territory as an Indigenous cross-border nation.
- Author
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Gardner, Jeffrey A.
- Abstract
This article examines the way the Maya-Mam, an Indigenous people divided by the Guatemala–Mexico border, define territory in relation to and across state borders. As state borders geographically, socially, culturally, and politically divide the pueblo Mam, state maps bolster these divisions and state subjugation by promoting a nation-state framework that circumscribes the Mam within its borders. However, the Mam are problematizing state depictions of spatiality: they denaturalize state borders by articulating alternative ontologies of territory. This study shows that in their everyday lives, Mam councils, activists, and individuals aim to promote broader cross-border Mam unification to better defend territory from potential harm. They use a dual-prong approach for articulating territory: through the development of narratives that draw upon a more holistic understanding of territory's 'nature' and by making counter-maps that incorporate Mam understanding of territory. I argue that these Indigenous efforts weave together a resistance to and refusal of state frames. [ABSTRACT FROM AUTHOR] more...
- Published
- 2024
- Full Text
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43. Indigenous borders: contesting the nation-state, belonging and racialization.
- Author
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Gardner, Jeffrey A. and Warren, Sarah D.
- Published
- 2024
- Full Text
- View/download PDF
44. The Population of Damped Lyman-alpha and Lyman Limit Systems in the Cold Dark Matter Model
- Author
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Gardner, Jeffrey P., Katz, Neal, Hernquist, Lars, and Weinberg, David H.
- Subjects
Astrophysics - Abstract
Lyman limit and damped Lyman-alpha absorption systems probe the distribution of collapsed, cold gas at high redshift. Numerical simulations that incorporate gravity and gas dynamics can predict the abundance of such absorbers in cosmological models. We develop a semi-analytical method to correct the numerical predictions for the contribution of unresolved low mass halos, and we apply this method to the Katz et al. (1996) simulation of the standard cold dark matter model ($\Omega=1$, $h=0.5$, $\Omega_b=0.05$, $\sigma_8=0.7$). Using this simulation and higher resolution simulations of individual low mass systems, we determine the relation between a halo's circular velocity $v_c$ and its cross section for producing Lyman limit or damped absorption. We combine this relation with the Press-Schechter formula for the abundance of halos to compute the number of absorbers per unit redshift. The resolution correction increases the predicted abundances by about a factor of two at z=2, 3, and 4, bringing the predicted number of damped absorbers into quite good agreement with observations. Roughly half of the systems reside in halos with circular velocities $v_c>100\kms$ and half in halos with $35\kms
150\kms$ typically harbor two or more systems capable of producing damped absorption. Even with the resolution correction, the predicted abundance of Lyman limit systems is a factor of three below observational estimates, signifying either a failure of standard CDM or a failure of these simulations to resolve the systems responsible for most Lyman limit absorption. By comparing simulations with and without star formation, we find that depletion of the gas supply by star formation affects absorption line statistics at $z>=2$ only for column densities exceeding $N_{HI}=10^{22} cm^{-2}$., Comment: AASlatex, 17 pages w/ 3 embedded ps figures. Submitted to ApJ more...- Published
- 1996
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45. The Challenge of Maintaining Research Collections in the 1990s
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Gardner, Jeffrey, primary
- Published
- 2019
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46. Custom fabrication of biomass containment devices using 3-D printing enables bacterial growth analyses with complex insoluble substrates
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Nelson, Cassandra E., Beri, Nina R., and Gardner, Jeffrey G.
- Published
- 2016
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47. The N-terminus of IntDOT forms hydrophobic interactions during Holliday Junction resolution
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Kolakowski, Adam J. and Gardner, Jeffrey F.
- Published
- 2016
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48. Structural and Functional Analysis of a Lytic Polysaccharide Monooxygenase Important for Efficient Utilization of Chitin in Cellvibrio japonicus
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Forsberg, Zarah, Nelson, Cassandra E., Dalhus, Bjørn, Mekasha, Sophanit, Loose, Jennifer S.M., Crouch, Lucy I., Røhr, Åsmund K., Gardner, Jeffrey G., Eijsink, Vincent G.H., and Vaaje-Kolstad, Gustav
- Published
- 2016
- Full Text
- View/download PDF
49. Data from Vitamin C Antagonizes the Cytotoxic Effects of Antineoplastic Drugs
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Heaney, Mark L., primary, Gardner, Jeffrey R., primary, Karasavvas, Nicos, primary, Golde, David W., primary, Scheinberg, David A., primary, Smith, Emily A., primary, and O'Connor, Owen A., primary
- Published
- 2023
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50. Supplementary Figure 1 from Vitamin C Antagonizes the Cytotoxic Effects of Antineoplastic Drugs
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Heaney, Mark L., primary, Gardner, Jeffrey R., primary, Karasavvas, Nicos, primary, Golde, David W., primary, Scheinberg, David A., primary, Smith, Emily A., primary, and O'Connor, Owen A., primary
- Published
- 2023
- Full Text
- View/download PDF
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