The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets

Modern microscope automation permits the collection of vast amounts of continuous anatomical imagery in both two and three dimensions. These large data sets present significant challenges for data storage, access, viewing, annotation and analysis. The cost and overhead of collecting and storing the data can be extremely high. Large data sets quickly exceed an individual's capability for timely analysis and present challenges in efficiently applying transforms, if needed. Finally annotated anatomical data sets can represent a significant investment of resources and should be easily accessible to the scientific community. The Viking application was our solution created to view and annotate a 16.5 TB ultrastructural retinal connectome volume and we demonstrate its utility in reconstructing neural networks for a distinctive retinal amacrine cell class. Viking has several key features. (1) It works over the internet using HTTP and supports many concurrent users limited only by hardware. (2) It supports a multi-user, collaborative annotation strategy. (3) It cleanly demarcates viewing and analysis from data collection and hosting. (4) It is capable of applying transformations in real-time. (5) It has an easily extensible user interface, allowing addition of specialized modules without rewriting the viewer

A perspective from extinct radionuclides on a Young Stellar Object: The Sun and its accretion disk

Meteorites, which are remnants of solar system formation, provide a direct glimpse into the dynamics and evolution of a young stellar object (YSO), namely our Sun. Much of our knowledge about the astrophysical context of the birth of the Sun, the chronology of planetary growth from micrometer-sized dust to terrestrial planets, and the activity of the young Sun comes from the study of extinct radionuclides such as 26Al (t1/2 = 0.717 Myr). Here we review how the signatures of extinct radionuclides (short-lived isotopes that were present when the solar system formed and that have now decayed below detection level) in planetary materials influence the current paradigm of solar system formation. Particular attention is given to tying meteorite measurements to remote astronomical observations of YSOs and modeling efforts. Some extinct radionuclides were inherited from the long-term chemical evolution of the Galaxy, others were injected into the solar system by a nearby supernova, and some were produced by particle irradiation from the T-Tauri Sun. The chronology inferred from extinct radionuclides reveals that dust agglomeration to form centimeter-sized particles in the inner part of the disk was very rapid (<50 kyr), planetesimal formation started early and spanned several million years, planetary embryos (possibly like Mars) were formed in a few million years, and terrestrial planets (like Earth) completed their growths several tens of million years after the birth of the Sun.Comment: 49 pages, 9 figures, 1 table. Uncorrected preprin

BPS black holes, the Hesse potential, and the topological string

The Hesse potential is constructed for a class of four-dimensional N=2 supersymmetric effective actions with S- and T-duality by performing the relevant Legendre transform by iteration. It is a function of fields that transform under duality according to an arithmetic subgroup of the classical dualities reflecting the monodromies of the underlying string compactification. These transformations are not subject to corrections, unlike the transformations of the fields that appear in the effective action which are affected by the presence of higher-derivative couplings. The class of actions that are considered includes those of the FHSV and the STU model. We also consider heterotic N=4 supersymmetric compactifications. The Hesse potential, which is equal to the free energy function for BPS black holes, is manifestly duality invariant. Generically it can be expanded in terms of powers of the modulus that represents the inverse topological string coupling constant, $g_s$, and its complex conjugate. The terms depending holomorphically on $g_s$ are expected to correspond to the topological string partition function and this expectation is explicitly verified in two cases. Terms proportional to mixed powers of $g_s$ and $\bar g_s$ are in principle present.Comment: 28 pages, LaTeX, added comment

Rapidly Rotating Atomic Gases

This article reviews developments in the theory of rapidly rotating degenerate atomic gases. The main focus is on the equilibrium properties of a single component atomic Bose gas, which (at least at rest) forms a Bose-Einstein condensate. Rotation leads to the formation of quantized vortices which order into a vortex array, in close analogy with the behaviour of superfluid helium. Under conditions of rapid rotation, when the vortex density becomes large, atomic Bose gases offer the possibility to explore the physics of quantized vortices in novel parameter regimes. First, there is an interesting regime in which the vortices become sufficiently dense that their cores -- as set by the healing length -- start to overlap. In this regime, the theoretical description simplifies, allowing a reduction to single particle states in the lowest Landau level. Second, one can envisage entering a regime of very high vortex density, when the number of vortices becomes comparable to the number of particles in the gas. In this regime, theory predicts the appearance of a series of strongly correlated phases, which can be viewed as {\it bosonic} versions of fractional quantum Hall states. This article describes the equilibrium properties of rapidly rotating atomic Bose gases in both the mean-field and the strongly correlated regimes, and related theoretical developments for Bose gases in lattices, for multi-component Bose gases, and for atomic Fermi gases. The current experimental situation and outlook for the future are discussed in the light of these theoretical developments.Comment: Published version + minor correction

Water induced sediment levitation enhances downslope transport on Mars

On Mars, locally warm surface temperatures (~293 K) occur, leading to the possibility of (transient) liquid water on the surface. However, water exposed to the martian atmosphere will boil, and the sediment transport capacity of such unstable water is not well understood. Here, we present laboratory studies of a newly recognized transport mechanism: “levitation” of saturated sediment bodies on a cushion of vapor released by boiling. Sediment transport where this mechanism is active is about nine times greater than without this effect, reducing the amount of water required to transport comparable sediment volumes by nearly an order of magnitude. Our calculations show that the effect of levitation could persist up to ~48 times longer under reduced martian gravity. Sediment levitation must therefore be considered when evaluating the formation of recent and present-day martian mass wasting features, as much less water may be required to form such features than previously thought

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus

Predatory Bdellovibrio bacteriovorus are natural antimicrobial organisms, killing other bacteria by whole-cell invasion. Self-protection against prey-metabolizing enzymes is important for the evolution of predation. Initial prey entry involves the predator’s peptidoglycan DD-endopeptidases, which decrosslink cell walls and prevent wasteful entry by a second predator. Here we identify and characterize a self-protection protein from B. bacteriovorus, Bd3460, which displays an ankyrin-based fold common to intracellular pathogens of eukaryotes. Co-crystal structures reveal Bd3460 complexation of dual targets, binding a conserved epitope of each of the Bd3459 and Bd0816 endopeptidases. Complexation inhibits endopeptidase activity and cell wall decrosslinking in vitro. Self-protection is vital — DBd3460 Bdellovibrio deleteriously decrosslink self-peptidoglycan upon invasion, adopt a round morpholog, and lose predatory capacity and cellular integrity. Our analysis provides the first mechanistic examination of self-protection in Bdellovibrio, documents protection-multiplicity for products of two different genomic loci, and reveals an important evolutionary adaptation to an invasive predatory bacterial lifestyle

Identification and characterization of a novel non-structural protein of bluetongue virus

Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77–79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell

Microbiology of the phyllosphere: a playground for testing ecological concepts

Many concepts and theories in ecology are highly debated, because it is often difficult to design decisive tests with sufficient replicates. Examples include biodiversity theories, succession concepts, invasion theories, coexistence theories, and concepts of life history strategies. Microbiological tests of ecological concepts are rapidly accumulating, but have yet to tap into their full potential to complement traditional macroecological theories. Taking the example of microbial communities on leaf surfaces (i.e. the phyllosphere), we show that most explorations of ecological concepts in this field of microbiology focus on autecology and population ecology, while community ecology remains understudied. Notable exceptions are first tests of the island biogeography theory and of biodiversity theories. Here, the phyllosphere provides the unique opportunity to set up replicated experiments, potentially moving fields such as biogeography, macroecology, and landscape ecology beyond theoretical and observational evidence. Future approaches should take advantage of the great range of spatial scales offered by the leaf surface by iteratively linking laboratory experiments with spatial simulation models

Induction of lymphokine-activated killer activity in rat splenocyte cultures: The importance of 2-mercaptoethanol and indomethacin

The role of 2-mercaptoethanol and indomethacin in the induction of lymphokine-activated killer (LAK) activity by interleukin-2 (IL-2) in rat splenocyte cultures was investigated. Spleens from 4-month-old male rats of five different strains were tested. Splenocytes were cultured for 3-5 days in the presence of IL-2 (1000 U/ml) and LAK activity was assessed by 4-h51Cr release assays with P815 and YAC-1 cells as targets. LAK activity could be induced by IL-2 in splenocytes from all rat strains, but only when 2-mercaptoethanol was present in the culture medium. Optimal LAK activity was induced when the 2-mercaptoethanol concentration in splenocyte cultures was at least 5 μM. Different rat strains showed differences in levels of in vitro induction of LAK activity. In the presence of 2-mercaptoethanol the level of LAK activity induced by IL-2 was high in BN and Lewis rats, intermediate in Wistar and Wag rats, and low in DZB rats. In the absence of 2-mercaptoethanol no or minimal LAK activity was induced. Furthermore we observed that addition of 50 μm indomethacin to the culture medium in the presence of 2-mercaptoethanol augmented the induction of LAK activity to some extent. In the absence of 2-mercaptoethanol, addition of indomethacin resulted only in low levels or no induction of LAK activity. We conclude that for optimal induction of LAK activity by IL-2 in rat splenocyte cultures 2-mercaptoethanol is essential, while indomethacin can only marginally further improve this induction

Compartments revealed in food-web structure

Compartments(1) in food webs are subgroups of taxa in which many strong interactions occur within the subgroups and few weak interactions occur between the subgroups(2). Theoretically, compartments increase the stability in networks(1-5), such as food webs. Compartments have been difficult to detect in empirical food webs because of incompatible approaches(6-9) or insufficient methodological rigour(8,10,11). Here we show that a method for detecting compartments from the social networking science(12-14) identified significant compartments in three of five complex, empirical food webs. Detection of compartments was influenced by food web resolution, such as interactions with weights. Because the method identifies compartmental boundaries in which interactions are concentrated, it is compatible with the definition of compartments. The method is rigorous because it maximizes an explicit function, identifies the number of non-overlapping compartments, assigns membership to compartments, and tests the statistical significance of the results(12-14). A graphical presentation(14) reveals systemic relationships and taxa-specific positions as structured by compartments. From this graphic, we explore two scenarios of disturbance to develop a hypothesis for testing how compartmentalized interactions increase stability in food webs(15-17).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62960/1/nature02115.pd