A 3D Fully Convolutional Neural Network With Top-Down Attention-Guided Refinement for Accurate and Robust Automatic Segmentation of Amygdala and Its Subnuclei

Recent advances in deep learning have improved the segmentation accuracy of subcortical brain structures, which would be useful in neuroimaging studies of many neurological disorders. However, most existing deep learning based approaches in neuroimaging do not investigate the specific difficulties that exist in segmenting extremely small but important brain regions such as the subnuclei of the amygdala. To tackle this challenging task, we developed a dual-branch dilated residual 3D fully convolutional network with parallel convolutions to extract more global context and alleviate the class imbalance issue by maintaining a small receptive field that is just the size of the regions of interest (ROIs). We also conduct multi-scale feature fusion in both parallel and series to compensate the potential information loss during convolutions, which has been shown to be important for small objects. The serial feature fusion enabled by residual connections is further enhanced by a proposed top-down attention-guided refinement unit, where the high-resolution low-level spatial details are selectively integrated to complement the high-level but coarse semantic information, enriching the final feature representations. As a result, the segmentations resulting from our method are more accurate both volumetrically and morphologically, compared with other deep learning based approaches. To the best of our knowledge, this work is the first deep learning-based approach that targets the subregions of the amygdala. We also demonstrated the feasibility of using a cycle-consistent generative adversarial network (CycleGAN) to harmonize multi-site MRI data, and show that our method generalizes well to challenging traumatic brain injury (TBI) datasets collected from multiple centers. This appears to be a promising strategy for image segmentation for multiple site studies and increased morphological variability from significant brain pathology

Testing the blast wave model with Swift GRBs

The complex structure of the light curves of Swift GRBs has made the identification of breaks, and the interpretation of the blast wave caused by the burst, more difficult than in the pre-Swift era. We aim to identify breaks, which are possibly hidden, and to constrain the blast wave parameters; electron energy distribution, p, density profile of the circumburst medium, k, and the continued energy injection index, q. We do so by comparing the observed multi-wavelength light curves and X-ray spectra of our sample to the predictions of the blast wave model. We can successfully interpret all of the bursts in our sample of 10, except two, within this framework and we can estimate, with confidence, the electron energy distribution index for 6 of the sample. Furthermore we identify jet breaks in a number of the bursts. A statistical analysis of the distribution of p reveals that, even in the most conservative case of least scatter, the values are not consistent with a single, universal value. The values of k suggest that the circumburst density profiles are not drawn from only one of the constant density or wind-like media populations.Comment: 14 pages, accepted by MNRAS after minor changes, including extension of discussion (section 4.3

The position of graptolites within Lower Palaeozoic planktic ecosystems.

An integrated approach has been used to assess the palaeoecology of graptolites both as a discrete group and also as a part of the biota present within Ordovician and Silurian planktic realms. Study of the functional morphology of graptolites and comparisons with recent ecological analogues demonstrates that graptolites most probably filled a variety of niches as primary consumers, with modes of life related to the colony morphotype. Graptolite coloniality was extremely ordered, lacking any close morphological analogues in Recent faunas. To obtain maximum functional efficiency, graptolites would have needed varying degrees of coordinated automobility. A change in lifestyle related to ontogenetic changes was prevalent within many graptolite groups. Differing lifestyle was reflected by differing reproductive strategies, with synrhabdosomes most likely being a method for rapid asexual reproduction. Direct evidence in the form of graptolithophage 'coprolitic' bodies, as well as indirect evidence in the form of probable defensive adaptations, indicate that graptolites comprised a food item for a variety of predators. Graptolites were also hosts to a variety of parasitic organisms and provided an important nutrient source for scavenging organisms

Magnetic Reconnection in Extreme Astrophysical Environments

Magnetic reconnection is a basic plasma process of dramatic rearrangement of magnetic topology, often leading to a violent release of magnetic energy. It is important in magnetic fusion and in space and solar physics --- areas that have so far provided the context for most of reconnection research. Importantly, these environments consist just of electrons and ions and the dissipated energy always stays with the plasma. In contrast, in this paper I introduce a new direction of research, motivated by several important problems in high-energy astrophysics --- reconnection in high energy density (HED) radiative plasmas, where radiation pressure and radiative cooling become dominant factors in the pressure and energy balance. I identify the key processes distinguishing HED reconnection: special-relativistic effects; radiative effects (radiative cooling, radiation pressure, and Compton resistivity); and, at the most extreme end, QED effects, including pair creation. I then discuss the main astrophysical applications --- situations with magnetar-strength fields (exceeding the quantum critical field of about 4 x 10^13 G): giant SGR flares and magnetically-powered central engines and jets of GRBs. Here, magnetic energy density is so high that its dissipation heats the plasma to MeV temperatures. Electron-positron pairs are then copiously produced, making the reconnection layer highly collisional and dressing it in a thick pair coat that traps radiation. The pressure is dominated by radiation and pairs. Yet, radiation diffusion across the layer may be faster than the global Alfv\'en transit time; then, radiative cooling governs the thermodynamics and reconnection becomes a radiative transfer problem, greatly affected by the ultra-strong magnetic field. This overall picture is very different from our traditional picture of reconnection and thus represents a new frontier in reconnection research.Comment: Accepted to Space Science Reviews (special issue on magnetic reconnection). Article is based on an invited review talk at the Yosemite-2010 Workshop on Magnetic Reconnection (Yosemite NP, CA, USA; February 8-12, 2010). 30 pages, no figure

Solitary magnetic perturbations at the ELM onset

Edge localised modes (ELMs) allow maintaining sufficient purity of tokamak H-mode plasmas and thus enable stationary H-mode. On the other hand in a future device ELMs may cause divertor power flux densities far in excess of tolerable material limits. The size of the energy loss per ELM is determined by saturation effects in the non-linear phase of the ELM, which at present is hardly understood. Solitary magnetic perturbations (SMPs) are identified as dominant features in the radial magnetic fluctuations below 100kHz. They are typically observed close (+-0.1ms) to the onset of pedestal erosion. SMPs are field aligned structures rotating in the electron diamagnetic drift direction with perpendicular velocities of about 10km/s. A comparison of perpendicular velocities suggests that the perturbation evoking SMPs is located at or inside the separatrix. Analysis of very pronounced examples showed that the number of peaks per toroidal turn is 1 or 2, which is clearly lower than corresponding numbers in linear stability calculations. In combination with strong peaking of the magnetic signals this results in a solitary appearance resembling modes like palm tree modes, edge snakes or outer modes. This behavior has been quantified as solitariness and correlated to main plasma parameters. SMPs may be considered as a signature of the non-linear ELM-phase originating at the separatrix or further inside. Thus they provide a handle to investigate the transition from linear to non-linear ELM phase. By comparison with data from gas puff imaging processes in the non-linear phase at or inside the separatrix and in the scrape-off-layer (SOL) can be correlated. A connection between the passing of an SMP and the onset of radial filament propagation has been found. Eventually the findings related to SMPs may contribute to a future quantitative understanding of the non-linear ELM evolution.Comment: submitted to Nuclear Fusio

On the Quantum Invariant for the Spherical Seifert Manifold

We study the Witten--Reshetikhin--Turaev SU(2) invariant for the Seifert manifold $S^3/\Gamma$ where $\Gamma$ is a finite subgroup of SU(2). We show that the WRT invariants can be written in terms of the Eichler integral of the modular forms with half-integral weight, and we give an exact asymptotic expansion of the invariants by use of the nearly modular property of the Eichler integral. We further discuss that those modular forms have a direct connection with the polyhedral group by showing that the invariant polynomials of modular forms satisfy the polyhedral equations associated to $\Gamma$.Comment: 36 page

Aqueous dune-like bedforms in Athabasca Valles and neighbouring locations utilized in palaeoflood reconstruction

Putative fluvial dunes have been identified within the Athabasca Valles and associated network of channels on Mars. Previous published work identified and measured bedforms in Athabasca Valles using photoclinometry methods on 2–3 m/pixel resolution Mars Orbiter Camera Narrow Angle images, and argued that these were created by an aqueous megaflood that occurred between 2 and 8 million years ago. This event is likely to have occurred due to geological activity associated with the Cerberus Fossae fracture system at the source of Athabasca Vallis. The present study has used higher resolution, 25 cm/pixel images from the Mars Reconnaissance Orbiter HiRISE camera, as well as stereo-derived digital terrain models and GIS software, to re-measure and evaluate these bedforms together with data from newly discovered neighbouring fields of bedforms. The analysis indicates that the bedforms are aqueous dunes, in that they occur in channel locations where dunes would be expected to be preserved and moreover they have geometries very similar to megaflood dunes on Earth. Dune geometries are used to estimate megaflood discharge rates, including uncertainty, which results support previous flood estimates that indicate that a flood with a discharge of ∼2 × 106m3s−1 created these bedforms

Pulsar-wind nebulae and magnetar outflows: observations at radio, X-ray, and gamma-ray wavelengths

We review observations of several classes of neutron-star-powered outflows: pulsar-wind nebulae (PWNe) inside shell supernova remnants (SNRs), PWNe interacting directly with interstellar medium (ISM), and magnetar-powered outflows. We describe radio, X-ray, and gamma-ray observations of PWNe, focusing first on integrated spectral-energy distributions (SEDs) and global spectral properties. High-resolution X-ray imaging of PWNe shows a bewildering array of morphologies, with jets, trails, and other structures. Several of the 23 so far identified magnetars show evidence for continuous or sporadic emission of material, sometimes associated with giant flares, and a few possible "magnetar-wind nebulae" have been recently identified.Comment: 61 pages, 44 figures (reduced in quality for size reasons). Published in Space Science Reviews, "Jets and Winds in Pulsar Wind Nebulae, Gamma-ray Bursts and Blazars: Physics of Extreme Energy Release

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02