High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas

Available online 4 May 2017The amygdala is composed of multiple nuclei with unique functions and connections in the limbic system and to the rest of the brain. However, standard in vivo neuroimaging tools to automatically delineate the amygdala into its multiple nuclei are still rare. By scanning postmortem specimens at high resolution (100–150 µm) at 7 T field strength (n = 10), we were able to visualize and label nine amygdala nuclei (anterior amygdaloid, cortico-amygdaloid transition area; basal, lateral, accessory basal, central, cortical medial, paralaminar nuclei). We created an atlas from these labels using a recently developed atlas building algorithm based on Bayesian inference. This atlas, which will be released as part of FreeSurfer, can be used to automatically segment nine amygdala nuclei from a standard resolution structural MR image. We applied this atlas to two publicly available datasets (ADNI and ABIDE) with standard resolution T1 data, used individual volumetric data of the amygdala nuclei as the measure and found that our atlas i) discriminates between Alzheimer's disease participants and age-matched control participants with 84% accuracy (AUC=0.915), and ii) discriminates between individuals with autism and age-, sex- and IQ-matched neurotypically developed control participants with 59.5% accuracy (AUC=0.59). For both datasets, the new ex vivo atlas significantly outperformed (all p < .05) estimations of the whole amygdala derived from the segmentation in FreeSurfer 5.1 (ADNI: 75%, ABIDE: 54% accuracy), as well as classification based on whole amygdala volume (using the sum of all amygdala nuclei volumes; ADNI: 81%, ABIDE: 55% accuracy). This new atlas and the segmentation tools that utilize it will provide neuroimaging researchers with the ability to explore the function and connectivity of the human amygdala nuclei with unprecedented detail in healthy adults as well as those with neurodevelopmental and neurodegenerative disorders.This work was supported by the PHS grant DA023427 and NICHD/ NIH grant F32HD079169 (Z.M.S); Feodor Lynen Postdoctoral Fellowship of the Alexander von Humboldt Foundation (D.K.); R21(MH106796), R21 (AG046657) and K01AG28521 (J.C.A.), the National Cancer Institute (1K25CA181632-01) as well as the Genentech Foundation (M.R.); the European Union's Horizon 2020 Marie Sklodowska-Curie grant agreement No 654911 (project ”THALAMODEL”) and ERC Starting Grant agreement No 677697 (project “BUNGEE-TOOLS”); and the Spanish Ministry of Economy and Competitiveness (MINECO) reference TEC2014-51882-P (J.E.I.); and the NVIDIA hardware award (M.R. and J.E.I.). Further support for this research was provided in part by the National Institute for Biomedical Imaging and Bioengineering (P41EB015896, R01EB006758, R21EB018907, R01EB019956, R01- EB013565), the National Institute on Aging (5R01AG008122, R01AG016495), the National Institute of Diabetes and Digestive and Kidney Diseases (1-R21-DK-108277-01), the National Institute for Neurological Disorders and Stroke (R01NS0525851, R21NS072652, R01NS070963, R01NS083534, 5U01NS086625), the Massachusetts ADRC (P50AG005134) and was made possible by the resources provided by Shared Instrumentation Grants 1S10RR023401, 1S10RR019307, and 1S10RR023043. Additional support was provided by the NIH Blueprint for Neuroscience Research (5U01-MH093765), part of the multi-institutional Human Connectome Project. In addition, BF has a financial interest in CorticoMetrics, a company whose medical pursuits focus on brain imaging and measurement technologies. BF's interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. The collection and sharing of the ADNI MRI data used in the evaluation was funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award number W81XWH-12-2- 0012). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Alzheimer's Association; Alzheimer's Drug Discovery Foundation; BioClinica, Inc.; Biogen Idec Inc.; Bristol-Myers Squibb Company; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; F. Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; GE Healthcare; Innogenetics, N.V.; IXICO Ltd.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Medpace, Inc.; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRx Research; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Piramal Imaging; Servier; Synarc Inc.; and Takeda Pharmaceutical Company. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www. fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California

Complementarity of information sent via different bases

We discuss quantitatively the complementarity of information transmitted by a quantum system prepared in a basis state in one out of several different mutually unbiased bases (MUBs). We obtain upper bounds on the information available to a receiver who has no knowledge of which MUB was chosen by the sender. These upper bounds imply a complementarity of information encoded via different MUBs and ultimately ensure the security in quantum key distribution protocols.Comment: 9 pages, references adde

Interstellar MHD Turbulence and Star Formation

This chapter reviews the nature of turbulence in the Galactic interstellar medium (ISM) and its connections to the star formation (SF) process. The ISM is turbulent, magnetized, self-gravitating, and is subject to heating and cooling processes that control its thermodynamic behavior. The turbulence in the warm and hot ionized components of the ISM appears to be trans- or subsonic, and thus to behave nearly incompressibly. However, the neutral warm and cold components are highly compressible, as a consequence of both thermal instability in the atomic gas and of moderately-to-strongly supersonic motions in the roughly isothermal cold atomic and molecular components. Within this context, we discuss: i) the production and statistical distribution of turbulent density fluctuations in both isothermal and polytropic media; ii) the nature of the clumps produced by thermal instability, noting that, contrary to classical ideas, they in general accrete mass from their environment; iii) the density-magnetic field correlation (or lack thereof) in turbulent density fluctuations, as a consequence of the superposition of the different wave modes in the turbulent flow; iv) the evolution of the mass-to-magnetic flux ratio (MFR) in density fluctuations as they are built up by dynamic compressions; v) the formation of cold, dense clouds aided by thermal instability; vi) the expectation that star-forming molecular clouds are likely to be undergoing global gravitational contraction, rather than being near equilibrium, and vii) the regulation of the star formation rate (SFR) in such gravitationally contracting clouds by stellar feedback which, rather than keeping the clouds from collapsing, evaporates and diperses them while they collapse.Comment: 43 pages. Invited chapter for the book "Magnetic Fields in Diffuse Media", edited by Elisabete de Gouveia dal Pino and Alex Lazarian. Revised as per referee's recommendation

The WHAM Northern Sky Survey and the Nature of the Warm Ionized Medium in the Galaxy

The Wisconsin H-Alpha Mapper (WHAM) has completed a velocity-resolved map of diffuse H-alpha emission of the entire northern sky, providing the first comprehensive picture of both the distribution and kinematics of diffuse ionized gas in the Galaxy. WHAM continues to advance our understanding of the physical conditions of the warm ionized medium through observations of other optical emission lines throughout the Galactic disk and halo. We discuss some highlights from the survey, including an optical window into the inner Galaxy and the relationship between HI and HII in the diffuse ISM.Comment: 9 pages, 3 figures. To be published in "How does the Galaxy work?", eds. E.J. Alfaro, E. Perez & J. Franco, Kluwer, held 23-27 June 2003 in Granada, Spain. Higher resolution version available at http://www.astro.wisc.edu/~madsen/prof/pubs.htm

Wind-Blown Bubbles around Evolved Stars

Most stars will experience episodes of substantial mass loss at some point in their lives. For very massive stars, mass loss dominates their evolution, although the mass loss rates are not known exactly, particularly once the star has left the main sequence. Direct observations of the stellar winds of massive stars can give information on the current mass-loss rates, while studies of the ring nebulae and HI shells that surround many Wolf-Rayet (WR) and luminous blue variable (LBV) stars provide information on the previous mass-loss history. The evolution of the most massive stars, (M > 25 solar masses), essentially follows the sequence O star to LBV or red supergiant (RSG) to WR star to supernova. For stars of mass less than 25 solar masses there is no final WR stage. During the main sequence and WR stages, the mass loss takes the form of highly supersonic stellar winds, which blow bubbles in the interstellar and circumstellar medium. In this way, the mechanical luminosity of the stellar wind is converted into kinetic energy of the swept-up ambient material, which is important for the dynamics of the interstellar medium. In this review article, analytic and numerical models are used to describe the hydrodynamics and energetics of wind-blown bubbles. A brief review of observations of bubbles is given, and the degree to which theory is supported by observations is discussed.Comment: To be published as a chapter in 'Diffuse Matter from Star Forming Regions to Active Galaxies' - A volume Honouring John Dyson. Eds. T. W. Harquist, J. M. Pittard and S. A. E. G. Falle. 22 pages, 12 figure

Massive Star Formation

This chapter reviews progress in the field of massive star formation. It focuses on evidence for accretion and current models that invoke high accretion rates. In particular it is noted that high accretion rates will cause the massive young stellar object to have a radius much larger than its eventual main sequence radius throughout much of the accretion phase. This results in low effective temperatures which may provide the explanation as to why luminous young stellar objects do not ionized their surroundings to form ultra-compact H II regions. The transition to the ultra-compact H II region phase would then be associated with the termination of the high accretion rate phase. Objects thought to be in a transition phase are discussed and diagnostic diagrams to distinguish between massive young stellar objects and ultra-compact H II regions in terms of line widths and radio luminosity are presented.Comment: 21 pages, 6 figures, chapter in Diffuse Matter from Star Forming Regions to Active Galaxies - A Volume Honouring John Dyson, Edited by T.W. Hartquist, J. M. Pittard, and S. A. E. G. Falle. Series: Astrophysics and Space Science Proceedings. Springer Dordrecht, 2007, p.6

Origin and Evolution of Saturn's Ring System

The origin and long-term evolution of Saturn's rings is still an unsolved problem in modern planetary science. In this chapter we review the current state of our knowledge on this long-standing question for the main rings (A, Cassini Division, B, C), the F Ring, and the diffuse rings (E and G). During the Voyager era, models of evolutionary processes affecting the rings on long time scales (erosion, viscous spreading, accretion, ballistic transport, etc.) had suggested that Saturn's rings are not older than 100 My. In addition, Saturn's large system of diffuse rings has been thought to be the result of material loss from one or more of Saturn's satellites. In the Cassini era, high spatial and spectral resolution data have allowed progress to be made on some of these questions. Discoveries such as the ''propellers'' in the A ring, the shape of ring-embedded moonlets, the clumps in the F Ring, and Enceladus' plume provide new constraints on evolutionary processes in Saturn's rings. At the same time, advances in numerical simulations over the last 20 years have opened the way to realistic models of the rings's fine scale structure, and progress in our understanding of the formation of the Solar System provides a better-defined historical context in which to understand ring formation. All these elements have important implications for the origin and long-term evolution of Saturn's rings. They strengthen the idea that Saturn's rings are very dynamical and rapidly evolving, while new arguments suggest that the rings could be older than previously believed, provided that they are regularly renewed. Key evolutionary processes, timescales and possible scenarios for the rings's origin are reviewed in the light of tComment: Chapter 17 of the book ''Saturn After Cassini-Huygens'' Saturn from Cassini-Huygens, Dougherty, M.K.; Esposito, L.W.; Krimigis, S.M. (Ed.) (2009) 537-57

What Physical Processes Drive the Interstellar Medium in the Local Bubble?

Recent 3D high-resolution simulations of the interstellar medium in a star form- ing galaxy like the Milky Way show that supernova explosions are the main driver of the structure and evolution of the gas. Its physical state is largely controlled by turbulence due to the high Reynolds numbers of the average flows. For a constant supernova rate a dynam- ical equilibrium is established within 200 Myr of simulation as a consequence of the setup of a galactic fountain. The resulting interstellar medium reveals a typical density/pressure pattern, i.e. distribution of so-called gas phases, on scales of 500–700 pc, with interstellar bubbles being a common phenomenon just like the Local Bubble and the Loop I superbub- ble, which are assumed to be interacting. However, modeling the Local Bubble is special, because it is driven by a moving group, passing through its volume, as it is inferred from the analysis of Hipparcos data. A detailed analysis reveals that between 14 and 19 super- novae have exploded during the last 15 Myr. The age of the Local Bubble is derived from comparison with HI and UV absorption line data to be 14.5±0.7 Myr. We further predict the 0.4merging of the two bubbles in about 3 Myr from now, when the interaction shell starts to fragment. The Local Cloud and its companion HI clouds are the consequence of a dynamical instability in the interaction shell between the Local and the Loop I bubble