Function-based Intersubject Alignment of Human Cortical Anatomy

Making conclusions about the functional neuroanatomical organization of the human brain requires methods for relating the functional anatomy of an individual's brain to population variability. We have developed a method for aligning the functional neuroanatomy of individual brains based on the patterns of neural activity that are elicited by viewing a movie. Instead of basing alignment on functionally defined areas, whose location is defined as the center of mass or the local maximum response, the alignment is based on patterns of response as they are distributed spatially both within and across cortical areas. The method is implemented in the two-dimensional manifold of an inflated, spherical cortical surface. The method, although developed using movie data, generalizes successfully to data obtained with another cognitive activation paradigm—viewing static images of objects and faces—and improves group statistics in that experiment as measured by a standard general linear model (GLM) analysis

Fast Bootstrapping and Permutation Testing for Assessing Reproducibility and Interpretability of Multivariate fMRI Decoding Models

Multivariate decoding models are increasingly being applied to functional magnetic imaging (fMRI) data to interpret the distributed neural activity in the human brain. These models are typically formulated to optimize an objective function that maximizes decoding accuracy. For decoding models trained on full-brain data, this can result in multiple models that yield the same classification accuracy, though some may be more reproducible than others—i.e. small changes to the training set may result in very different voxels being selected. This issue of reproducibility can be partially controlled by regularizing the decoding model. Regularization, along with the cross-validation used to estimate decoding accuracy, typically requires retraining many (often on the order of thousands) of related decoding models. In this paper we describe an approach that uses a combination of bootstrapping and permutation testing to construct both a measure of cross-validated prediction accuracy and model reproducibility of the learned brain maps. This requires re-training our classification method on many re-sampled versions of the fMRI data. Given the size of fMRI datasets, this is normally a time-consuming process. Our approach leverages an algorithm called fast simultaneous training of generalized linear models (FaSTGLZ) to create a family of classifiers in the space of accuracy vs. reproducibility. The convex hull of this family of classifiers can be used to identify a subset of Pareto optimal classifiers, with a single-optimal classifier selectable based on the relative cost of accuracy vs. reproducibility. We demonstrate our approach using full-brain analysis of elastic-net classifiers trained to discriminate stimulus type in an auditory and visual oddball event-related fMRI design. Our approach and results argue for a computational approach to fMRI decoding models in which the value of the interpretation of the decoding model ultimately depends upon optimizing a joint space of accuracy and reproducibility

Counts-in-Cylinders in the Sloan Digital Sky Survey with Comparisons to N-body Simulations

Environmental statistics provide a necessary means of comparing the properties of galaxies in different environments and a vital test of models of galaxy formation within the prevailing, hierarchical cosmological model. We explore counts-in-cylinders, a common statistic defined as the number of companions of a particular galaxy found within a given projected radius and redshift interval. Galaxy distributions with the same two-point correlation functions do not necessarily have the same companion count distributions. We use this statistic to examine the environments of galaxies in the Sloan Digital Sky Survey, Data Release 4. We also make preliminary comparisons to four models for the spatial distributions of galaxies, based on N-body simulations, and data from SDSS DR4 to study the utility of the counts-in-cylinders statistic. There is a very large scatter between the number of companions a galaxy has and the mass of its parent dark matter halo and the halo occupation, limiting the utility of this statistic for certain kinds of environmental studies. We also show that prevalent, empirical models of galaxy clustering that match observed two- and three-point clustering statistics well fail to reproduce some aspects of the observed distribution of counts-in-cylinders on 1, 3 and 6-Mpc/h scales. All models that we explore underpredict the fraction of galaxies with few or no companions in 3 and 6-Mpc/h cylinders. Roughly 7% of galaxies in the real universe are significantly more isolated within a 6 Mpc/h cylinder than the galaxies in any of the models we use. Simple, phenomenological models that map galaxies to dark matter halos fail to reproduce high-order clustering statistics in low-density environments.Comment: 17 pages, 10 figures. Accepted, Ap

Disentangling galaxy environment and host halo mass

[Abridged] The properties of observed galaxies and dark matter haloes in simulations depend on their environment. The term environment has been used to describe a wide variety of measures that may or may not correlate with each other. Popular measures of environment include the distance to the N'th nearest neighbour, the number density of objects within some distance, or the mass of the host dark matter halo. We use results from the Millennium simulation and a semi-analytic model for galaxy formation to quantify the relations between environment and halo mass. We show that the environmental parameters used in the observational literature are in effect measures of halo mass, even if they are measured for a fixed stellar mass. The strongest correlation between environment and halo mass arises when the number of objects is counted out to a distance of 1.5-2 times the virial radius of the host halo and when the galaxies/haloes are required to be relatively bright/massive. For observational studies the virial radius is not easily determined, but the number of neighbours out to 1-2 Mpc/h gives a similarly strong correlation. For the distance to the N'th nearest neighbour the correlation with halo mass is nearly as strong provided N>2. We demonstrate that this environmental parameter becomes insensitive to halo mass if it is constructed from dimensionless quantities. This can be achieved by scaling the minimum luminosity/mass of neighbours to that of the object in question and by dividing the distance to a length scale associated with either the neighbour or the galaxy under consideration. We show how such a halo mass independent environmental parameter can be defined for observational and numerical studies. The results presented here will help future studies to disentangle the effects of halo mass and external environment on the properties of galaxies and dark matter haloes.Comment: 15 pages, 9 figures, 2 tables. Accepted by MNRA

Quenched Cold Accretion of a Large Scale Metal-Poor Filament due to Virial Shocking in the Halo of a Massive z=0.7 Galaxy

Using HST/COS/STIS and HIRES/Keck high-resolution spectra, we have studied a remarkable HI absorbing complex at z=0.672 toward the quasar Q1317+277. The HI absorption has a velocity spread of 1600 km/s, comprises 21 Voigt profile components, and resides at an impact parameter of D=58 kpc from a bright, high mass [log(M_vir/M_sun) ~ 13.7] elliptical galaxy that is deduced to have a 6 Gyr old, solar metallicity stellar population. Ionization models suggest the majority of the structure is cold gas surrounding a shock heated cloud that is kinematically adjacent to a multi-phase group of clouds with detected CIII, CIV and OVI absorption, suggestive of a conductive interface near the shock. The deduced metallicities are consistent with the moderate in situ enrichment relative to the levels observed in the z ~ 3 Ly-alpha forest. We interpret the HI complex as a metal-poor filamentary structure being shock heated as it accretes into the halo of the galaxy. The data support the scenario of an early formation period (z > 4) in which the galaxy was presumably fed by cold-mode gas accretion that was later quenched via virial shocking by the hot halo such that, by intermediate redshift, the cold filamentary accreting gas is continuing to be disrupted by shock heating. Thus, continued filamentary accretion is being mixed into the hot halo, indicating that the star formation of the galaxy will likely remain quenched. To date, the galaxy and the HI absorption complex provide some of the most compelling observational data supporting the theoretical picture in which accretion is virial shocked in the hot coronal halos of high mass galaxies.Comment: 20 pages, 9 figures, submitted to Ap

The Gaseous Environment of High-z Galaxies: Precision Measurements of Neutral Hydrogen in the Circumgalactic Medium of z ~ 2-3 Galaxies in the Keck Baryonic Structure Survey

We present results from the Keck Baryonic Structure Survey (KBSS), a unique spectroscopic survey designed to explore the connection between galaxies and intergalactic baryons. The KBSS is optimized for the redshift range z ~ 2-3, combining S/N ~ 100 Keck/HIRES spectra of 15 hyperluminous QSOs with densely sampled galaxy redshift surveys surrounding each QSO sightline. We perform Voigt profile decomposition of all 6000 HI absorbers within the full Lya forest in the QSO spectra. Here we present the distribution, column density, kinematics, and absorber line widths of HI surrounding 886 star-forming galaxies with 2.0 < z < 2.8 and within 3 Mpc of a QSO sightline. We find that N_HI and the multiplicity of HI components increase rapidly near galaxies. The strongest HI absorbers within ~ 100 physical kpc of galaxies have N_HI ~ 3 dex higher than those near random locations in the IGM. The circumgalactic zone of most enhanced HI absorption (CGM) is found within 300 kpc and 300 km/s of galaxies. Nearly half of absorbers with log(N_HI) > 15.5 are found within the CGM of galaxies meeting our photometric selection, while their CGM occupy only 1.5% of the cosmic volume. The spatial covering fraction, multiplicity of absorption components, and characteristic N_HI remain elevated to transverse distances of 2 physical Mpc. Absorbers with log(N_HI) > 14.5 are tightly correlated with the positions of galaxies, while absorbers with lower N_HI are correlated only on Mpc scales. Redshift anisotropies on Mpc scales indicate coherent infall toward galaxies, while on scales of ~100 physical kpc peculiar velocities of 260 km/s are indicated. The median Doppler widths of absorbers within 1-3 virial radii of galaxies are ~50% larger than randomly chosen absorbers of the same N_HI, suggesting higher gas temperatures and/or increased turbulence likely caused by accretion shocks and/or galactic winds.Comment: Accepted to Ap

Semi-empirical catalog of early-type galaxy-halo systems: dark matter density profiles, halo contraction and dark matter annihilation strength

With SDSS galaxy data and halo data from up-to-date N-body simulations we construct a semi-empirical catalog (SEC) of early-type systems by making a self-consistent bivariate statistical match of stellar mass (M_star) and velocity dispersion (sigma) with halo virial mass (M_vir). We then assign stellar mass profile and velocity dispersion profile parameters to each system in the SEC using their observed correlations with M_star and sigma. Simultaneously, we solve for dark matter density profile of each halo using the spherical Jeans equation. The resulting dark matter density profiles deviate in general from the dissipationless profile of NFW or Einasto and their mean inner density slope and concentration vary systematically with M_vir. Statistical tests of the distribution of profiles at fixed M_vir rule out the null hypothesis that it follows the distribution predicted by N-body simulations for M_vir ~< 10^{13.5-14.5} M_solar. These dark matter profiles imply that dark matter density is, on average, enhanced significantly in the inner region of halos with M_vir ~< 10^{13.5-14.5} M_solar supporting halo contraction. The main characteristics of halo contraction are: (1) the mean dark matter density within the effective radius has increased by a factor varying systematically up to ~ 3-4 at M_vir = 10^{12} M_solar, and (2) the inner density slope has a mean of ~ 1.3 with rho(r) ~ r^{-alpha} and a halo-to-halo rms scatter of rms(alpha) ~ 0.4-0.5 for 10^{12} M_solar ~< M_vir ~< 10^{13-14} M_solar steeper than the NFW profile (alpha=1). Based on our results we predict that halos of nearby elliptical and lenticular galaxies can, in principle, be promising targets for gamma-ray emission from dark matter annihilation.Comment: 43 pages, 20 figures, JCAP, revised and accepted versio

Dwarf galaxy formation with H2-regulated star formation

We describe cosmological galaxy formation simulations with the adaptive mesh refinement code Enzo that incorporate a star formation prescription regulated by the local abundance of molecular hydrogen. We show that this H2-regulated prescription leads to a suppression of star formation in low mass halos (M_h < ~10^10 M_sun) at z>4, alleviating some of the dwarf galaxy problems faced by theoretical galaxy formation models. H2 regulation modifies the efficiency of star formation of cold gas directly, rather than indirectly reducing the cold gas content with "supernova feedback". We determine the local H2 abundance in our most refined grid cells (76 proper parsec in size at z=4) by applying the model of Krumholz, McKee, & Tumlinson, which is based on idealized 1D radiative transfer calculations of H2 formation-dissociation balance in ~100 pc atomic--molecular complexes. Our H2-regulated simulations are able to reproduce the empirical (albeit lower z) Kennicutt-Schmidt relation, including the low Sigma_gas cutoff due to the transition from atomic to molecular phase and the metallicity dependence thereof, without the use of an explicit density threshold in our star formation prescription. We compare the evolution of the luminosity function, stellar mass density, and star formation rate density from our simulations to recent observational determinations of the same at z=4-8 and find reasonable agreement between the two.Comment: replaced with version published in Ap

Impact of baryon physics on dark matter structures: a detailed simulation study of halo density profiles

The back-reaction of baryons on the dark matter halo density profile is of great interest, not least because it is an important systematic uncertainty when attempting to detect the dark matter. Here, we draw on a large suite of high resolution cosmological hydrodynamical simulations, to systematically investigate this process and its dependence on the baryonic physics associated with galaxy formation. The inclusion of baryons results in significantly more concentrated density profiles if radiative cooling is efficient and feedback is weak. The dark matter halo concentration can in that case increase by as much as 30 (10) per cent on galaxy (cluster) scales. The most significant effects occur in galaxies at high redshift, where there is a strong anti-correlation between the baryon fraction in the halo centre and the inner slope of both the total and the dark matter density profiles. If feedback is weak, isothermal inner profiles form, in agreement with observations of massive, early-type galaxies. However, we find that AGN feedback, or extremely efficient feedback from massive stars, is necessary to match observed stellar fractions in groups and clusters, as well as to keep the maximum circular velocity similar to the virial velocity as observed for disk galaxies. These strong feedback models reduce the baryon fraction in galaxies by a factor of 3 relative to the case with no feedback. The AGN is even capable of reducing the baryon fraction by a factor of 2 in the inner region of group and cluster haloes. This in turn results in inner density profiles which are typically shallower than isothermal and the halo concentrations tend to be lower than in the absence of baryons.Comment: 20 pages, 14 figures, 1 table. MNRAS in press. Version 2: added a few references