BrainGlobe Atlas API: a common interface for neuroanatomical atlases

Summary: Neuroscientists routinely perform experiments aimed at recording or manipulating neural activity, uncovering physiological processes underlying brain function or elucidating aspects of brain anatomy. Understanding how the brain generates behaviour ultimately depends on merging the results of these experiments into a unified picture of brain anatomy and function. Brain atlases are crucial in this endeavour: by outlining the organization of brain regions they provide a reference upon which our understanding of brain function can be anchored. More recently, digital high-resolution 3d atlases have been produced for several model organisms providing an invaluable resource for the research community. Effective use of these atlases depends on the availability of an application programming interface (API) that enables researchers to develop software to access and query atlas data. However, while some atlases come with an API, these are generally specific for individual atlases, and this hinders the development and adoption of open-source neuroanatomy software. The BrainGlobe atlas API (BG-Atlas API) overcomes this problem by providing a common interface for programmers to download and process data across a variety of model organisms. By adopting the BG-Atlas API, software can then be developed agnostic to the atlas, increasing adoption and interoperability of packages in neuroscience and enabling direct integration of different experimental modalities and even comparisons across model organisms

Observation of Ferromagnetic Clusters in Bi0.125Ca0.875MnO3

The electron doped manganite system, Bi0.125Ca0.875MnO3, exhibits large bulk magnetization of unknown origin. To select amongst possible magnetic ordering models, we have conducted temperature and magnetic field dependent small-angle neutron scattering measurements. Nontrivial spin structure has been revealed. Ferromagnetic spin clusters form in the antiferromagnetic background when temperature is decreased to Tc~108K. With a further reduction in temperature or the application of external magnetic field, the clusters begin to form in larger numbers, which gives an overall enhancement of magnetization below Tc.Comment: 14 pages, 6 figue

Probing the Relation Between X-ray-Derived and Weak-Lensing-Derived Masses for Shear-Selected Galaxy Clusters: I. A781

We compare X-ray and weak-lensing masses for four galaxy clusters that comprise the top-ranked shear-selected cluster system in the Deep Lens Survey. The weak-lensing observations of this system, which is associated with A781, are from the Kitt Peak Mayall 4-m telescope, and the X-ray observations are from both Chandra and XMM-Newton. For a faithful comparison of masses, we adopt the same matter density profile for each method, which we choose to be an NFW profile. Since neither the X-ray nor weak-lensing data are deep enough to well constrain both the NFW scale radius and central density, we estimate the scale radius using a fitting function for the concentration derived from cosmological hydrodynamic simulations and an X-ray estimate of the mass assuming isothermality. We keep this scale radius in common for both X-ray and weak-lensing profiles, and fit for the central density, which scales linearly with mass. We find that for three of these clusters, there is agreement between X-ray and weak-lensing NFW central densities, and thus masses. For the other cluster, the X-ray central density is higher than that from weak-lensing by 2 sigma. X-ray images suggest that this cluster may be undergoing a merger with a smaller cluster. This work serves as an additional step towards understanding the possible biases in X-ray and weak-lensing cluster mass estimation methods. Such understanding is vital to efforts to constrain cosmology using X-ray or weak-lensing cluster surveys to trace the growth of structure over cosmic time.Comment: 14 pages, 7 figures, matches version in Ap

Visualizing anatomically registered data with Brainrender

Three-dimensional (3D) digital brain atlases and high-throughput brain wide imaging techniques generate large multidimensional datasets that can be registered to a common reference frame. Generating insights from such datasets depends critically on visualization and interactive data exploration, but this a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. Here, we present brainrender: an open-source Python package for interactive visualization of multidimensional datasets registered to brain atlases. Brainrender facilitates the creation of complex renderings with different data types in the same visualization and enables seamless use of different atlas sources. High-quality visualizations can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data

Response of selected plant and insect species to simulated solid rocket exhaust mixtures and to exhaust components from solid rocket fuels

The effects of solid rocket fuel (SRF) exhaust on selected plant and and insect species in the Merritt Island, Florida area was investigated in order to determine if the exhaust clouds generated by shuttle launches would adversely affect the native, plants of the Merritt Island Wildlife Refuge, the citrus production, or the beekeeping industry of the island. Conditions were simulated in greenhouse exposure chambers and field chambers constructed to model the ideal continuous stirred tank reactor. A plant exposure system was developed for dispensing and monitoring the two major chemicals in SRF exhaust, HCl and Al203, and for dispensing and monitoring SRF exhaust (controlled fuel burns). Plants native to Merritt Island, Florida were grown and used as test species. Dose-response relationships were determined for short term exposure of selected plant species to HCl, Al203, and mixtures of the two to SRF exhaust

Exploring Dark Energy with Next-Generation Photometric Redshift Surveys

The coming decade will be an exciting period for dark energy research, during which astronomers will address the question of what drives the accelerated cosmic expansion as first revealed by type Ia supernova (SN) distances, and confirmed by later observations. The mystery of dark energy poses a challenge of such magnitude that, as stated by the Dark Energy Task Force (DETF), nothing short of a revolution in our understanding of fundamental physics will be required to achieve a full understanding of the cosmic acceleration. The lack of multiple complementary precision observations is a major obstacle in developing lines of attack for dark energy theory. This lack is precisely what next-generation surveys will address via the powerful techniques of weak lensing (WL) and baryon acoustic oscillations (BAO) -- galaxy correlations more generally -- in addition to SNe, cluster counts, and other probes of geometry and growth of structure. Because of their unprecedented statistical power, these surveys demand an accurate understanding of the observables and tight control of systematics. This white paper highlights the opportunities, approaches, prospects, and challenges relevant to dark energy studies with wide-deep multiwavelength photometric redshift surveys. Quantitative predictions are presented for a 20000 sq. deg. ground-based 6-band (ugrizy) survey with 5-sigma depth of r~27.5, i.e., a Stage 4 survey as defined by the DETF

Size-selective nanoparticle growth on few-layer graphene films

We observe that gold atoms deposited by physical vapor deposition onto few layer graphenes condense upon annealing to form nanoparticles with an average diameter that is determined by the graphene film thickness. The data are well described by a theoretical model in which the electrostatic interactions arising from charge transfer between the graphene and the gold particle limit the size of the growing nanoparticles. The model predicts a nanoparticle size distribution characterized by a mean diameter D that follows a scaling law D proportional to m^(1/3), where m is the number of carbon layers in the few layer graphene film.Comment: 15 pages, 4 figure

Unavoidable Selection Effects in the Analysis of Faint Galaxies in the Hubble Deep Field: Probing the Cosmology and Merger History of Galaxies

(Abridged) We present a detailed analysis of the number count and photometric redshift distribution of faint galaxies in the Hubble Deep Field (HDF), paying a special attention to the selection effects including the cosmological dimming of surface brightness of galaxies. We find a considerably different result from previous studies ignoring the selection effects, and these effects should therefore be taken into account in the analysis. We find that the model of pure luminosity evolution (PLE) of galaxies in the Einstein-de Sitter (EdS) universe predicts much smaller counts than those observed at faint magnitude limits by a factor of more than 10, so that a very strong number evolution of galaxies with \eta > 3-4 must be invoked to reproduce the I_{814} counts, when parametrized as \phi^* \propto (1+z)^\eta. However we show that such a strong number evolution under realistic merging processes of galaxies can not explain the steep slope of the B_{450} and V_{606} counts, and it is seriously inconsistent with their photometric redshift distribution. We find that these difficulties still persist in an open universe with \Omega_0 > 0.2, but are resolved only when we invoke a $\Lambda$-dominated flat universe, after examining various systematic uncertainties in modeling the formation and evolution of galaxies. The present analysis revitalizes the practice of using faint number counts as an important cosmological test, giving one of the arguments against the EdS universe and suggests acceleration of the cosmic expansion by vacuum energy density. While a modest number evolution of galaxies with \eta ~ 1 is still necessary even in a Lambda-dominated universe, a stronger number evolution with \eta > 1 is rejected from the HDF data, giving a strong constraint on the merger history of galaxies.Comment: 24 pages, 15 figures, final version matching publication in ApJ. Some references added. The complete ps file of Table 3 is available at http://th.nao.ac.jp/~totani/images/paper/ty2000-table3.p

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

The anaerobic oxidation of methane by anaerobic methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for methane removal in ocean sediments. The mechanism of their syntrophy has been the subject of much research as traditional intermediate compounds, such as hydrogen and formate, failed to decouple the partners. Recent findings have indicated the potential for extracellular electron transfer from ANME archaea to SRB, though it is unclear how extracellular electrons are integrated into the metabolism of the SRB partner. We used metagenomics to reconstruct eight genomes from the globally distributed SEEP-SRB1 clade of ANME partner bacteria to determine what genomic features are required for syntrophy. The SEEP-SRB1 genomes contain large multiheme cytochromes that were not found in previously described free-living SRB and also lack periplasmic hydrogenases that may prevent an independent lifestyle without an extracellular source of electrons from ANME archaea. Metaproteomics revealed the expression of these cytochromes at in situ methane seep sediments from three sites along the Pacific coast of the United States. Phylogenetic analysis showed that these cytochromes appear to have been horizontally transferred from metal-respiring members of the Deltaproteobacteria such as Geobacter and may allow these syntrophic SRB to accept extracellular electrons in place of other chemical/organic electron donors