Practical sensorless aberration estimation for 3D microscopy with deep learning

Estimation of optical aberrations from volumetric intensity images is a key step in sensorless adaptive optics for 3D microscopy. Recent approaches based on deep learning promise accurate results at fast processing speeds. However, collecting ground truth microscopy data for training the network is typically very difficult or even impossible thereby limiting this approach in practice. Here, we demonstrate that neural networks trained only on simulated data yield accurate predictions for real experimental images. We validate our approach on simulated and experimental datasets acquired with two different microscopy modalities, and also compare the results to non-learned methods. Additionally, we study the predictability of individual aberrations with respect to their data requirements and find that the symmetry of the wavefront plays a crucial role. Finally, we make our implementation freely available as open source software in Python

Using schedulers to test probabilistic distributed systems

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-012-0244-5. Copyright © 2012, British Computer Society.Formal methods are one of the most important approaches to increasing the confidence in the correctness of software systems. A formal specification can be used as an oracle in testing since one can determine whether an observed behaviour is allowed by the specification. This is an important feature of formal testing: behaviours of the system observed in testing are compared with the specification and ideally this comparison is automated. In this paper we study a formal testing framework to deal with systems that interact with their environment at physically distributed interfaces, called ports, and where choices between different possibilities are probabilistically quantified. Building on previous work, we introduce two families of schedulers to resolve nondeterministic choices among different actions of the system. The first type of schedulers, which we call global schedulers, resolves nondeterministic choices by representing the environment as a single global scheduler. The second type, which we call localised schedulers, models the environment as a set of schedulers with there being one scheduler for each port. We formally define the application of schedulers to systems and provide and study different implementation relations in this setting

Simulated impacts of relative climate change and river discharge regulation on sea ice and oceanographic conditions in the Hudson Bay Complex

In this analysis, we examine relative contributions from climate change and river discharge regulation to changes in marine conditions in the Hudson Bay Complex using a subset of five atmospheric forcing scenarios from the Coupled Model Intercomparison Project Phase 5 (CMIP5), river discharge data from the Hydrological Predictions for the Environment (HYPE) model, both naturalized (without anthropogenic intervention) and regulated (anthropogenically controlled through diversions, dams, reservoirs), and output from the Nucleus for European Modeling of the Ocean Ice-Ocean model for the 1981–2070 time frame. Investigated in particular are spatiotemporal changes in sea surface temperature, sea ice concentration and thickness, and zonal and meridional sea ice drift in response to (i) climate change through comparison of historical (1981–2010) and future (2021–2050 and 2041–2070) simulations, (ii) regulation through comparison of historical (1981–2010) naturalized and regulated simulations, and (iii) climate change and regulation combined through comparison of future (2021–2050 and 2041–2070) naturalized and regulated simulations. Also investigated is use of the diagnostic known as e-folding time spatial distribution to monitor changes in persistence in these variables in response to changing climate and regulation impacts in the Hudson Bay Complex. Results from this analysis highlight bay-wide and regional reductions in sea ice concentration and thickness in southwest and northeast Hudson Bay in response to a changing climate, and east-west asymmetry in sea ice drift response in support of past studies. Regulation is also shown to amplify or suppress the climate change signal. Specifically, regulation amplifies sea surface temperatures from April to August, suppresses sea ice loss by approximately 30% in March, contributes to enhanced sea ice drift speed by approximately 30%, and reduces meridional circulation by approximately 20% in January due to enhanced zonal drift. Results further suggest that the offshore impacts of regulation are amplified in a changing climate

AdS_7/CFT_6, Gauss-Bonnet Gravity, and Viscosity Bound

We study the relation between the causality and the positivity of energy bounds in Gauss-Bonnet gravity in AdS_7 background and find a precise agreement. Requiring the group velocity of metastable states to be bounded by the speed of light places a bound on the value of Gauss-Bonnet coupling. To find the positivity of energy constraints we compute the parameters which determine the angular distribution of the energy flux in terms of three independent coefficients specifying the three-point function of the stress-energy tensor. We then relate the latter to the Weyl anomaly of the six-dimensional CFT and compute the anomaly holographically. The resulting upper bound on the Gauss-Bonnet coupling coincides with that from causality and results in a new bound on viscosity/entropy ratio.Comment: 21 page, harvmac; v2: reference adde

Einstein-Gauss-Bonnet black strings

We construct uniform black-string solutions in Einstein-Gauss-Bonnet gravity for all dimensions $d$ between five and ten and discuss their basic properties. Closed form solutions are found by taking the Gauss-Bonnet term as a perturbation from pure Einstein gravity. Nonperturbative solutions are constructed by solving numerically the equations of the model. The Gregory-Laflamme instability of the black strings is explored via linearized perturbation theory. Our results indicate that new qualitative features occur for $d=6$, in which case stable configurations exist for large enough values of the Gauss-Bonnet coupling constant. For other dimensions, the black strings are dynamically unstable and have also a negative specific heat. We argue that this provides an explicit realization of the Gubser-Mitra conjecture, which links local dynamical and thermodynamic stability. Nonuniform black strings in Einstein-Gauss-Bonnet theory are also constructed in six spacetime dimensions.Comment: 33 pages, 11 figure

An anisotropic hybrid non-perturbative formulation for 4D N = 2 supersymmetric Yang-Mills theories

We provide a simple non-perturbative formulation for non-commutative four-dimensional N = 2 supersymmetric Yang-Mills theories. The formulation is constructed by a combination of deconstruction (orbifold projection), momentum cut-off and matrix model techniques. We also propose a moduli fixing term that preserves lattice supersymmetry on the deconstruction formulation. Although the analogous formulation for four-dimensional N = 2 supersymmetric Yang-Mills theories is proposed also in Nucl.Phys.B857(2012), our action is simpler and better suited for computer simulations. Moreover, not only for the non-commutative theories, our formulation has a potential to be a non-perturbative tool also for the commutative four-dimensional N = 2 supersymmetric Yang-Mills theories.Comment: 32 pages, final version accepted in JHE

F-Theorem without Supersymmetry

The conjectured F-theorem for three-dimensional field theories states that the finite part of the free energy on S^3 decreases along RG trajectories and is stationary at the fixed points. In previous work various successful tests of this proposal were carried out for theories with {\cal N}=2 supersymmetry. In this paper we perform more general tests that do not rely on supersymmetry. We study perturbatively the RG flows produced by weakly relevant operators and show that the free energy decreases monotonically. We also consider large N field theories perturbed by relevant double trace operators, free massive field theories, and some Chern-Simons gauge theories. In all cases the free energy in the IR is smaller than in the UV, consistent with the F-theorem. We discuss other odd-dimensional Euclidean theories on S^d and provide evidence that (-1)^{(d-1)/2} \log |Z| decreases along RG flow; in the particular case d=1 this is the well-known g-theorem.Comment: 34 pages, 2 figures; v2 refs added, minor improvements; v3 refs added, improved section 4.3; v4 minor improvement

Global Burden of Sickle Cell Anaemia in Children under Five, 2010-2050: Modelling Based on Demographics, Excess Mortality, and Interventions

The global burden of sickle cell anaemia (SCA) is set to rise as a consequence of improved survival in high-prevalence low- and middle-income countries and population migration to higher-income countries. The host of quantitative evidence documenting these changes has not been assembled at the global level. The purpose of this study is to estimate trends in the future number of newborns with SCA and the number of lives that could be saved in under-five children with SCA by the implementation of different levels of health interventions.First, we calculated projected numbers of newborns with SCA for each 5-y interval between 2010 and 2050 by combining estimates of national SCA frequencies with projected demographic data. We then accounted for under-five mortality (U5m) projections and tested different levels of excess mortality for children with SCA, reflecting the benefits of implementing specific health interventions for under-five patients in 2015, to assess the number of lives that could be saved with appropriate health care services. The estimated number of newborns with SCA globally will increase from 305,800 (confidence interval [CI]: 238,400-398,800) in 2010 to 404,200 (CI: 242,500-657,600) in 2050. It is likely that Nigeria (2010: 91,000 newborns with SCA [CI: 77,900-106,100]; 2050: 140,800 [CI: 95,500-200,600]) and the Democratic Republic of the Congo (2010: 39,700 [CI: 32,600-48,800]; 2050: 44,700 [CI: 27,100-70,500]) will remain the countries most in need of policies for the prevention and management of SCA. We predict a decrease in the annual number of newborns with SCA in India (2010: 44,400 [CI: 33,700-59,100]; 2050: 33,900 [CI: 15,900-64,700]). The implementation of basic health interventions (e.g., prenatal diagnosis, penicillin prophylaxis, and vaccination) for SCA in 2015, leading to significant reductions in excess mortality among under-five children with SCA, could, by 2050, prolong the lives of 5,302,900 [CI: 3,174,800-6,699,100] newborns with SCA. Similarly, large-scale universal screening could save the lives of up to 9,806,000 (CI: 6,745,800-14,232,700) newborns with SCA globally, 85% (CI: 81%-88%) of whom will be born in sub-Saharan Africa. The study findings are limited by the uncertainty in the estimates and the assumptions around mortality reductions associated with interventions.Our quantitative approach confirms that the global burden of SCA is increasing, and highlights the need to develop specific national policies for appropriate public health planning, particularly in low- and middle-income countries. Further empirical collaborative epidemiological studies are vital to assess current and future health care needs, especially in Nigeria, the Democratic Republic of the Congo, and India

The Early Stage of Bacterial Genome-Reductive Evolution in the Host

The equine-associated obligate pathogen Burkholderia mallei was developed by reductive evolution involving a substantial portion of the genome from Burkholderia pseudomallei, a free-living opportunistic pathogen. With its short history of divergence (∼3.5 myr), B. mallei provides an excellent resource to study the early steps in bacterial genome reductive evolution in the host. By examining 20 genomes of B. mallei and B. pseudomallei, we found that stepwise massive expansion of IS (insertion sequence) elements ISBma1, ISBma2, and IS407A occurred during the evolution of B. mallei. Each element proliferated through the sites where its target selection preference was met. Then, ISBma1 and ISBma2 contributed to the further spread of IS407A by providing secondary insertion sites. This spread increased genomic deletions and rearrangements, which were predominantly mediated by IS407A. There were also nucleotide-level disruptions in a large number of genes. However, no significant signs of erosion were yet noted in these genes. Intriguingly, all these genomic modifications did not seriously alter the gene expression patterns inherited from B. pseudomallei. This efficient and elaborate genomic transition was enabled largely through the formation of the highly flexible IS-blended genome and the guidance by selective forces in the host. The detailed IS intervention, unveiled for the first time in this study, may represent the key component of a general mechanism for early bacterial evolution in the host