Spectrotemporal CT data acquisition and reconstruction at low dose.

PURPOSE: X-ray computed tomography (CT) is widely used, both clinically and preclinically, for fast, high-resolution anatomic imaging; however, compelling opportunities exist to expand its use in functional imaging applications. For instance, spectral information combined with nanoparticle contrast agents enables quantification of tissue perfusion levels, while temporal information details cardiac and respiratory dynamics. The authors propose and demonstrate a projection acquisition and reconstruction strategy for 5D CT (3D+dual energy+time) which recovers spectral and temporal information without substantially increasing radiation dose or sampling time relative to anatomic imaging protocols. METHODS: The authors approach the 5D reconstruction problem within the framework of low-rank and sparse matrix decomposition. Unlike previous work on rank-sparsity constrained CT reconstruction, the authors establish an explicit rank-sparse signal model to describe the spectral and temporal dimensions. The spectral dimension is represented as a well-sampled time and energy averaged image plus regularly undersampled principal components describing the spectral contrast. The temporal dimension is represented as the same time and energy averaged reconstruction plus contiguous, spatially sparse, and irregularly sampled temporal contrast images. Using a nonlinear, image domain filtration approach, the authors refer to as rank-sparse kernel regression, the authors transfer image structure from the well-sampled time and energy averaged reconstruction to the spectral and temporal contrast images. This regularization strategy strictly constrains the reconstruction problem while approximately separating the temporal and spectral dimensions. Separability results in a highly compressed representation for the 5D data in which projections are shared between the temporal and spectral reconstruction subproblems, enabling substantial undersampling. The authors solved the 5D reconstruction problem using the split Bregman method and GPU-based implementations of backprojection, reprojection, and kernel regression. Using a preclinical mouse model, the authors apply the proposed algorithm to study myocardial injury following radiation treatment of breast cancer. RESULTS: Quantitative 5D simulations are performed using the MOBY mouse phantom. Twenty data sets (ten cardiac phases, two energies) are reconstructed with 88 μm, isotropic voxels from 450 total projections acquired over a single 360° rotation. In vivo 5D myocardial injury data sets acquired in two mice injected with gold and iodine nanoparticles are also reconstructed with 20 data sets per mouse using the same acquisition parameters (dose: ∼60 mGy). For both the simulations and the in vivo data, the reconstruction quality is sufficient to perform material decomposition into gold and iodine maps to localize the extent of myocardial injury (gold accumulation) and to measure cardiac functional metrics (vascular iodine). Their 5D CT imaging protocol represents a 95% reduction in radiation dose per cardiac phase and energy and a 40-fold decrease in projection sampling time relative to their standard imaging protocol. CONCLUSIONS: Their 5D CT data acquisition and reconstruction protocol efficiently exploits the rank-sparse nature of spectral and temporal CT data to provide high-fidelity reconstruction results without increased radiation dose or sampling time.

A critical examination of node-similarity based graph matching algorithms

In this paper, we shall critically examine a special class of graph matching algorithms that follow the approach of node-similarity measurement. A high-level algorithm framework, namely node-similarity graph matching framework (NSGM framework), is proposed, from which, many existing graph matching algorithms can be subsumed, including the eigen-decomposition method of Umeyama, the polynomial-transformation method of Almohamad, the hubs and authorities method of Kleinberg, and the kronecker product successive projection methods of Wyk, etc. In addition, improved algorithms can be developed from the NSGM framework with respects to the corresponding results in graph theory. As the observation, it is pointed out that, in general, any algorithm which can be subsumed from NSGM framework fails to work well for graphs with non-trivial auto-isomorphism structure.

Multilevel refinement for combinatorial optimisation: boosting metaheuristic performance

The multilevel paradigm as applied to combinatorial optimisation problems is a simple one, which at its most basic involves recursive coarsening to create a hierarchy of approximations to the original problem. An initial solution is found, usually at the coarsest level, and then iteratively refined at each level, coarsest to finest, typically by using some kind of heuristic optimisation algorithm (either a problem-specific local search scheme or a metaheuristic). Solution extension (or projection) operators can transfer the solution from one level to another. As a general solution strategy, the multilevel paradigm has been in use for many years and has been applied to many problem areas (for example multigrid techniques can be viewed as a prime example of the paradigm). Overview papers such as [] attest to its efficacy. However, with the exception of the graph partitioning problem, multilevel techniques have not been widely applied to combinatorial problems and in this chapter we discuss recent developments. In this chapter we survey the use of multilevel combinatorial techniques and consider their ability to boost the performance of (meta)heuristic optimisation algorithms.

Three-dimensional simulation of the influence of convection on dendritic solidification

Bulk and interdendritic flow during solidification alters the microstructure development, potentially leading to the formation of defects. In this paper, a 3D numerical model is presented for the simulation of dendritic growth in the presence of fluid flow in both liquid and semi-solid zones during solidification. The dendritic growth was solved by the combination of a stochastic nucleation approach with a finite difference solution of the solute diffusion equation and. a projection method solution of the Navier-Stokes equations. The technique was applied first to simulate the growth of a single dendrite in 2D and 3D in an isothermal environment with forced fluid flow. Significant differences were found in the evolution of dendritic morphology when comparing the 2D and 3D results. In 3D the upstream arm has a faster growth velocity due to easier flow around the perpendicular arms. This also promotes secondary arm formation on the upstream arm. The effect of fluid flow on columnar dendritic growth and micro-segregation in constrained solidification conditions is then simulated. For constrained growth, 2D simulations lead to even greater inaccuracies as compared to 3D.

Decadal changes in climate and ecosystems in the North Atlantic Ocean and adjacent seas

Climate change is unambiguous and its effects are clearly detected in all functional units of the Earth system. This study presents new analyses of sea-surface temperature changes and show that climate change is affecting ecosystems of the North Atlantic. Changes are seen from phytoplankton to zooplankton to fish and are modifying the dominance of species and the structure, the diversity and the functioning of marine ecosystems. Changes also range from phenological to biogeographical shifts and have involved in some regions of the Atlantic abrupt ecosystem shifts. These alterations reflect a response of pelagic ecosystems to a warmer temperature regime. Mechanisms are complex because they are nonlinear exhibiting tipping points and varying in space and time. Sensitivity of organisms to temperature changes is high, implicating that a small temperature modification can have sustained ecosystem effects. Implications of these changes for biogeochemical cycles are discussed. Two observed changes detected in the North Sea that could have opposite effects on carbon cycle are discussed. Increase in phytoplankton, as inferred from the phytoplankton colour index derived from the Continuous Plankton Recorder (CPR) survey, has been detected in the North Sea. This pattern has been accompanied by a reduction in the abundance of the herbivorous species Calanus finmarchicus. This might have reduced the grazing pressure and increase diatomaceous ‘fluff’, therefore carbon export in the North Sea. Therefore, it could be argued that the biological carbon pump might increase in this region with sea warming. In the meantime, however, the mean size of organisms (calanoid copepods) has dropped. Such changes have implications for the turnover time of biogenic carbon in plankton organisms and the mean residence time of particulate carbon they produce. The system characterising the warmer period is more based on recycling and less on export. The increase in the minimum turnover time indicates an increase in the ecosystem metabolism, which can be considered as a response of the pelagic ecosystems to climate warming. This phenomenon could reduce carbon export. These two opposite patterns of change are examples of the diversity of mechanisms and pathways the ecosystems may exhibit with climate change. Oversimplification of current biogeochemical models, often due to lack of data and biological understanding, could lead to wrong projection on the direction ecosystems and therefore some biogeochemical cycles might take in a warmer world.

Modelling the Influence of Major Baltic Inflows on Near-Bottom Conditions at the Entrance of the Gulf of Finland

A coupled hydrodynamic-biogeochemical model was implemented in order to estimate the effects of Major Baltic Inflows on the near-bottom hydrophysical and biogeochemical conditions in the northern Baltic Proper and the western Gulf of Finland during the period 1991�2009. We compared results of a realistic reference run to the results of an experimental run where Major Baltic Inflows were suppressed. Further to the expected overall decrease in bottom salinity, this modelling experiment confirms that in the absence of strong saltwater inflows the deep areas of the Baltic Proper would become more anoxic, while in the shallower areas (western Gulf of Finland) near-bottom average conditions improve. Our experiment revealed that typical estuarine circulation results in the sporadic emergence of short-lasting events of near-bottom anoxia in the western Gulf of Finland due to transport of water masses from the Baltic Proper. Extrapolating our results beyond the modelled period, we speculate that the further deepening of the halocline in the Baltic Proper is likely to prevent inflows of anoxic water to the Gulf of Finland and in the longer term would lead to improvement in near-bottom conditions in the Baltic Proper. Our results reaffirm the importance of accurate representation of salinity dynamics in coupled Baltic Sea models serving as a basis for credible hindcast and future projection simulations of biogeochemical conditions.

Predicting future thermal habitat suitability of competing native and invasive fish species: from metabolic scope to oceanographic modelling

Global increase in sea temperatures has been suggested to facilitate the incoming and spread of tropical invaders. The increasing success of these species may be related to their higher physiological performance compared with indigenous ones. Here, we determined the effect of temperature on the aerobic metabolic scope (MS) of two herbivorous fish species that occupy a similar ecological niche in the Mediterranean Sea: the native salema (Sarpa salpa) and the invasive marbled spinefoot (Siganus rivulatus). Our results demonstrate a large difference in the optimal temperature for aerobic scope between the salema (21.8°C) and the marbled spinefoot (29.1°C), highlighting the importance of temperature in determining the energy availability and, potentially, the distribution patterns of the two species. A modelling approach based on a present-day projection and a future scenario for oceanographic conditions was used to make predictions about the thermal habitat suitability (THS, an index based on the relationship between MS and temperature) of the two species, both at the basin level (the whole Mediterranean Sea) and at the regional level (the Sicilian Channel, a key area for the inflow of invasive species from the Eastern to the Western Mediterranean Sea). For the present-day projection, our basin-scale model shows higher THS of the marbled spinefoot than the salema in the Eastern compared with the Western Mediterranean Sea. However, by 2050, the THS of the marbled spinefoot is predicted to increase throughout the whole Mediterranean Sea, causing its westward expansion. Nevertheless, the regional-scale model suggests that the future thermal conditions of Western Sicily will remain relatively unsuitable for the invasive species and could act as a barrier for its spread westward. We suggest that metabolic scope can be used as a tool to evaluate the potential invasiveness of alien species and the resilience to global warming of native species.

Global carbon budget 2014

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates, consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuel combustion and cement production (E-FF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (E-LUC), mainly deforestation, are based on combined evidence from land-cover-change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (G(ATM)) is computed from the annual changes in concentration. The mean ocean CO2 sink (S-OCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in S-OCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (S-LAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO2, and land-cover-change (some including nitrogen-carbon interactions). We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as +/- 1 sigma, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2004-2013), E-FF was 8.9 +/- 0.4 GtC yr(-1), E-LUC 0.9 +/- 0.5 GtC yr(-1), G(ATM) 4.3 +/- 0.1 GtC yr(-1), S-OCEAN 2.6 +/- 0.5 GtC yr(-1), and S-LAND 2.9 +/- 0.8 GtC yr(-1). For year 2013 alone, E-FF grew to 9.9 +/- 0.5 GtC yr(-1), 2.3% above 2012, continuing the growth trend in these emissions, E-LUC was 0.9 +/- 0.5 GtC yr(-1), G(ATM) was 5.4 +/- 0.2 GtC yr(-1), S-OCEAN was 2.9 +/- 0.5 GtC yr(-1), and S-LAND was 2.5 +/- 0.9 GtC yr(-1). G(ATM) was high in 2013, reflecting a steady increase in E-FF and smaller and opposite changes between S-OCEAN and S-LAND compared to the past decade (2004-2013). The global atmospheric CO2 concentration reached 395.31 +/- 0.10 ppm averaged over 2013. We estimate that E-FF will increase by 2.5% (1.3-3.5 %) to 10.1 +/- 0.6 GtC in 2014 (37.0 +/- 2.2 GtCO(2) yr(-1)), 65% above emissions in 1990, based on projections of world gross domestic product and recent changes in the carbon intensity of the global economy. From this projection of E-FF and assumed constant E-LUC for 2014, cumulative emissions of CO2 will reach about 545 +/- 55 GtC (2000 +/- 200 GtCO(2)) for 1870-2014, about 75% from E-FF and 25% from E-LUC. This paper documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this living data set (Le Quere et al., 2013, 2014). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP_2014).

Defining scenarios of future vectors of change in marine life and associated economic sectors

Addressing the multitude of challenges in marine policy requires an integrated approach that considers the multitude of drivers, pressures, and interests, from several disciplinary angles. Scenarios are needed to harmonise the analyses of different components of the marine system, and to deal with the uncertainty and complexity of the societal and biogeophysical dynamics in the system. This study considers a set of socio-economic scenarios to (1) explore possible futures in relation to marine invasive species, outbreak forming species, and gradual changes in species distribution and productivity; and (2) harmonise the projection modelling performed within associated studies. The exercise demonstrates that developing interdisciplinary scenarios as developed in this study is particularly complicated due to (1) the wide variety in endogeneity or exogeneity of variables in the different analyses involved; (2) the dual role of policy decisions as variables in a scenario or decisions to be evaluated and compared to other decisions; and (3) the substantial difference in time scale between societal and physical drivers.

Global Carbon Budget 2015

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and a methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates as well as consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover-change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models forced by observed climate, CO2, and land-cover change (some including nitrogen–carbon interactions). We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2005–2014), EFF was 9.0 ± 0.5 GtC yr−1, ELUC was 0.9 ± 0.5 GtC yr−1, GATM was 4.4 ± 0.1 GtC yr−1, SOCEAN was 2.6 ± 0.5 GtC yr−1, and SLAND was 3.0 ± 0.8 GtC yr−1. For the year 2014 alone, EFF grew to 9.8 ± 0.5 GtC yr−1, 0.6 % above 2013, continuing the growth trend in these emissions, albeit at a slower rate compared to the average growth of 2.2 % yr−1 that took place during 2005–2014. Also, for 2014, ELUC was 1.1 ± 0.5 GtC yr−1, GATM was 3.9 ± 0.2 GtC yr−1, SOCEAN was 2.9 ± 0.5 GtC yr−1, and SLAND was 4.1 ± 0.9 GtC yr−1. GATM was lower in 2014 compared to the past decade (2005–2014), reflecting a larger SLAND for that year. The global atmospheric CO2 concentration reached 397.15 ± 0.10 ppm averaged over 2014. For 2015, preliminary data indicate that the growth in EFF will be near or slightly below zero, with a projection of −0.6 [range of −1.6 to +0.5] %, based on national emissions projections for China and the USA, and projections of gross domestic product corrected for recent changes in the carbon intensity of the global economy for the rest of the world. From this projection of EFF and assumed constant ELUC for 2015, cumulative emissions of CO2 will reach about 555 ± 55 GtC (2035 ± 205 GtCO2) for 1870–2015, about 75 % from EFF and 25 % from ELUC. This living data update documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this data set (Le Quéré et al., 2015, 2014, 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center (doi:10.3334/CDIAC/GCP_2015).

Higher brain neurons succumb to acute stroke-like insult while lower brain neurons strongly resist

Pyramidal neurons (PyNs) in ‘higher’ brain are highly susceptible to acute stroke injury yet ‘lower’ brain regions better survive global ischemia, presumably because of better residual blood flow. Here we show that projection neurons in ‘lower’ brain regions of hypothalamus and brainstem intrinsically resist acute stroke-like injury independent of blood flow in the brain slice. In contrast `higher` projection neurons in neocortex, hippocampus, striatum and thalamus are highly susceptible. In live brain slices from rat deprived of oxygen and glucose (OGD), we imaged anoxic depolarization (AD) as it propagates through these regions. AD, the initial electrophysiological event of stroke, is a depolarizing front that drains residual energy in compromised gray matter. The extent of AD reliably determines ensuing damage in higher brain, but using whole-cell recordings we found that all CNS neurons do not generate a robust AD. Higher neurons generate strong AD and show no functional recovery in contrast to neurons in hypothalamus and brainstem that generate a weak and gradual AD. Most dramatically, lower neurons recover their membrane potential, input resistance and spike amplitude when oxygen and glucose is restored, while higher neurons do not. Following OGD, new recordings could be acquired in all lower (but not higher) brain regions, with some neurons even withstanding multiple OGD exposure. Two-photon laser scanning microscopy confirmed neuroprotection in lower, but not higher gray matter. Specifically pyramidal neurons swell and lose their dendritic spines post-OGD, whereas neurons in hypothalamus and brainstem display no such injury. Exposure to the Na+/K+ ATPase inhibitor ouabain (100 μM), induces depolarization similar to OGD in all cell types tested. Moreover, elevated [K+]o evokes spreading depression (SD), a milder version of AD, in higher brain but not hypothalamus or brainstem so weak AD correlates with the inability to generate SD. In summary, overriding the Na+/K+ pump using OGD, ouabain or elevated [K+]o evokes steep and robust depolarization of higher gray matter. We show that this important regional difference can be largely accounted for by the intrinsic properties of the resident neurons and that Na+/K+ ATPase pump efficiency is a major determining factor generating strong or weak spreading depolarizations.

On subspace lattices I. Closedness type properties and tensor products

We study properties of subspace lattices related to the continuity of the map Lat and the notion of reflexivity. We characterize various “closedness” properties in different ways and give the hierarchy between them. We investigate several properties related to tensor products of subspace lattices and show that the tensor product of the projection lattices of two von Neumann algebras, one of which is injective, is reflexive.

Self-consistent non-Markovian theory of a quantum-state evolution for quantum-information processing

We study non-Markovian decoherence phenomena by employing projection-operator formalism when a quantum system (a quantum bit or a register of quantum bits) is coupled to a reservoir. By projecting out the degree of freedom of the reservoir, we derive a non-Markovian master equation for the system, which is reduced to a Lindblad master equation in Markovian limit, and obtain the operator sum representation for the time evolution. It is found that the system is decohered slower in the non- Markovian reservoir than the Markovian because the quantum information of the system is memorized in the non-Markovian reservoir. We discuss the potential importance of non-Markovian reservoirs for quantum-information processing.

High harmonic generation by halogen anions and noble gas atoms in a laser field

A comparative study of high harmonic generation (HHG) by atoms and ions with active p-electrons is carried out in the theoretical framework of the rescattering mechanism. The substate with m(l) = 0, i.e. zero orbital momentum projection along the electric vector of a linearly polarized laser wave, is found to give the major contribution to the HHG rate. Our calculations for HHG by an H atom in an excited 2p-state demonstrate that the rate for recombination into a final state with a different value of m(l) (= +/- 1), is higher for lower harmonic orders N, while for higher N (beyond the plateau domain) the difference vanishes. For species with closed electron shells, the m(l)-changing transitions are forbidden by the Pauli exclusion principle. We report absolute HHG rates for halogen ions and noble gas atoms at various intensities. These results demonstrate that the Coulomb binding potential of the atoms considerably enhances both the ionization and recombination steps in the rescattering process. However, the weak binding energy of the anions allows lower orders of HHG to be efficiently produced at relatively low intensities, from which we conclude that observation of HHG by an anion is experimentally feasible.

Proton Radiography of a Laser-Driven Implosion

Protons accelerated by a picosecond laser pulse have been used to radiograph a 500 mu m diameter capsule, imploded with 300 J of laser light in 6 symmetrically incident beams of wavelength 1.054 mu m and pulse length 1 ns. Point projection proton backlighting was used to characterize the density gradients at discrete times through the implosion. Asymmetries were diagnosed both during the early and stagnation stages of the implosion. Comparison with analytic scattering theory and simple Monte Carlo simulations were consistent with a 3 +/- 1 g/cm(3) core with diameter 85 +/- 10 mu m. Scaling simulations show that protons > 50 MeV are required to diagnose asymmetry in ignition scale conditions.