Localizer:fast, accurate, open-source, and modular software package for superresolution microscopy

We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies

Time series prediction via aggregation : an oracle bound including numerical cost

We address the problem of forecasting a time series meeting the Causal Bernoulli Shift model, using a parametric set of predictors. The aggregation technique provides a predictor with well established and quite satisfying theoretical properties expressed by an oracle inequality for the prediction risk. The numerical computation of the aggregated predictor usually relies on a Markov chain Monte Carlo method whose convergence should be evaluated. In particular, it is crucial to bound the number of simulations needed to achieve a numerical precision of the same order as the prediction risk. In this direction we present a fairly general result which can be seen as an oracle inequality including the numerical cost of the predictor computation. The numerical cost appears by letting the oracle inequality depend on the number of simulations required in the Monte Carlo approximation. Some numerical experiments are then carried out to support our findings

A Study of Concurrency Bugs and Advanced Development Support for Actor-based Programs

The actor model is an attractive foundation for developing concurrent applications because actors are isolated concurrent entities that communicate through asynchronous messages and do not share state. Thereby, they avoid concurrency bugs such as data races, but are not immune to concurrency bugs in general. This study taxonomizes concurrency bugs in actor-based programs reported in literature. Furthermore, it analyzes the bugs to identify the patterns causing them as well as their observable behavior. Based on this taxonomy, we further analyze the literature and find that current approaches to static analysis and testing focus on communication deadlocks and message protocol violations. However, they do not provide solutions to identify livelocks and behavioral deadlocks. The insights obtained in this study can be used to improve debugging support for actor-based programs with new debugging techniques to identify the root cause of complex concurrency bugs.Comment: - Submitted for review - Removed section 6 "Research Roadmap for Debuggers", its content was summarized in the Future Work section - Added references for section 1, section 3, section 4.3 and section 5.1 - Updated citation

Optimal dietary energy and amino acids for gilt development: Growth, body composition, feed intake, and carcass composition traits

The objective of this study was to determine if body composition of developing gilts could be altered at the onset of estrus by ad libitum feeding diets differing in standard ileal digestible (SID) lysine and ME using levels that are within those used in practice by pig producers in the United States. Crossbred Large White × Landrace gilts (n = 1,221), housed in groups, were randomly allotted to 6 corn–soybean diets in a 2 × 3 factorial arrangement formulated to provide 2 SID lysine and 3 ME levels. Gilts received grower diets formulated to provide 0.86 (low) or 1.02% (high) SID lysine and 2.94 (low), 3.25 (medium), or 3.57 (high) Mcal of ME/kg from 100 d of age until approximately 90 kg BW. Then, gilts were fed finisher diets containing 0.73 (low) or 0.85% (high) SID lysine and 2.94 (low), 3.26 (medium) or 3.59 (high) Mcal of ME/kg until 260 d of age. The medium SID lysine and medium-ME diets were based on an informal survey from the U.S. commercial swine industry to obtain average levels that are currently being formulated for developing gilts. Gilts were weighed and backfat thickness and loin area were recorded at the beginning of the trial and then every 28 d. Feed intake (FI) was recorded as feed disappearance within the pen at 2-wk intervals. Lysine (g) and ME (Mcal) consumed were calculated based on diet formulations. At approximately 260 d of age, gilts were slaughtered and warm carcass weight and fat thickness were recorded. There were no differences between lysine or ME levels for growth and body composition, except for backfat, which was slightly greater for gilts fed a high-ME diet. Gilts fed high-ME diets had a lower FI but a greater ME intake compared with gilts fed low ME (P \u3c 0.05). Additionally, gilts fed the high-ME diet had lower FI and lysine intake per kilogram of BW gain when compared with gilts fed low- or medium-ME diets (P \u3c 0.05). However, there was no difference in the megacalories consumed per kilogram of BW gain among treatments (P \u3e 0.05). Carcasses from gilts fed the high-ME diet were 3.3 and 2.5 kg heavier than those from gilts fed the low- or medium-ME diets (P \u3c 0.05). Despite significant differences in the lysine:ME ratio in the diets, no changes in growth or body composition occurred, likely due to compensatory changes in FI in response to dietary ME content. Caloric efficiency (Mcal to deposit 1 kg of BW) was similar among treatments

Constraint algorithm for k-presymplectic Hamiltonian systems. Application to singular field theories

The k-symplectic formulation of field theories is especially simple, since only tangent and cotangent bundles are needed in its description. Its defining elements show a close relationship with those in the symplectic formulation of mechanics. It will be shown that this relationship also stands in the presymplectic case. In a natural way, one can mimick the presymplectic constraint algorithm to obtain a constraint algorithm that can be applied to $k$-presymplectic field theory, and more particularly to the Lagrangian and Hamiltonian formulations of field theories defined by a singular Lagrangian, as well as to the unified Lagrangian-Hamiltonian formalism (Skinner--Rusk formalism) for k-presymplectic field theory. Two examples of application of the algorithm are also analyzed.Comment: 22 p

Super-Resolution Imaging Strategies for Cell Biologists Using a Spinning Disk Microscope

In this study we use a spinning disk confocal microscope (SD) to generate super-resolution images of multiple cellular features from any plane in the cell. We obtain super-resolution images by using stochastic intensity fluctuations of biological probes, combining Photoactivation Light-Microscopy (PALM)/Stochastic Optical Reconstruction Microscopy (STORM) methodologies. We compared different image analysis algorithms for processing super-resolution data to identify the most suitable for analysis of particular cell structures. SOFI was chosen for X and Y and was able to achieve a resolution of ca. 80 nm; however higher resolution was possible >30 nm, dependant on the super-resolution image analysis algorithm used. Our method uses low laser power and fluorescent probes which are available either commercially or through the scientific community, and therefore it is gentle enough for biological imaging. Through comparative studies with structured illumination microscopy (SIM) and widefield epifluorescence imaging we identified that our methodology was advantageous for imaging cellular structures which are not immediately at the cell-substrate interface, which include the nuclear architecture and mitochondria. We have shown that it was possible to obtain two coloured images, which highlights the potential this technique has for high-content screening, imaging of multiple epitopes and live cell imaging

Black Holes as Effective Geometries

Gravitational entropy arises in string theory via coarse graining over an underlying space of microstates. In this review we would like to address the question of how the classical black hole geometry itself arises as an effective or approximate description of a pure state, in a closed string theory, which semiclassical observers are unable to distinguish from the "naive" geometry. In cases with enough supersymmetry it has been possible to explicitly construct these microstates in spacetime, and understand how coarse-graining of non-singular, horizon-free objects can lead to an effective description as an extremal black hole. We discuss how these results arise for examples in Type II string theory on AdS_5 x S^5 and on AdS_3 x S^3 x T^4 that preserve 16 and 8 supercharges respectively. For such a picture of black holes as effective geometries to extend to cases with finite horizon area the scale of quantum effects in gravity would have to extend well beyond the vicinity of the singularities in the effective theory. By studying examples in M-theory on AdS_3 x S^2 x CY that preserve 4 supersymmetries we show how this can happen.Comment: Review based on lectures of JdB at CERN RTN Winter School and of VB at PIMS Summer School. 68 pages. Added reference

On strong causal binomial approximation for stochastic processes

This paper considers binomial approximation of continuous time stochastic processes. It is shown that, under some mild integrability conditions, a process can be approximated in mean square sense and in other strong metrics by binomial processes, i.e., by processes with fixed size binary increments at sampling points. Moreover, this approximation can be causal, i.e., at every time it requires only past historical values of the underlying process. In addition, possibility of approximation of solutions of stochastic differential equations by solutions of ordinary equations with binary noise is established. Some consequences for the financial modelling and options pricing models are discussed

Group Space Allowance Has Little Effect on Sow Health, Productivity, or Welfare in a Free-Access Stall System

Free-access stalls allow sows to choose the protection of a stall or use of a shared group space. This study investigated the effect of group space width, 0.91 (SS), 2.13 (IS), and 3.05 (LS) m, on the health, production, behavior, and welfare of gestating sows. Nine replications of 21 (N = 189) gestating sows were used. At gestational d 35.4 ± 2.3, the pregnant sows were distributed into 3 pens of 7 sows, where they remained until 104.6 ± 3.5 d. Each treatment pen had 7 free-access stalls and a group space that together provided 1.93 (SS), 2.68 (IS), or 3.24 (LS) m2/sow. Baseline measurements were obtained before mixing. Back fat depth, BW, BCS, and lameness were measured monthly, and skin lesions were scored weekly. Blood was collected monthly for hematological, immunological, and cortisol analyses. Sow behavior was video recorded continuously during the initial 4 d of treatment and 24 h every other week thereafter. Behavior was analyzed for location, posture, pen investigation, social contact, and aggression. Skin response to the mitogen concanavalin A (Con A) was tested at mean gestational d 106. Litter characteristics including size and weight were collected at birth and weaning. The data were analyzed using a mixed model. Multiple comparisons were adjusted with the Tukey-Kramer and Bejamini-Hochberg methods. Group space allowance had no effect on any measure of sow health, physiology, or production (P ≥ 0.10). Sows in the SS, IS, and LS pens spent 77.88% ± 3.88%, 66.02% ± 3.87%, and 63.64% ± 3.91%, respectively, of their time in the free-access stalls (P = 0.12). However, SS sows used the group space less than IS and LS sows (P = 0.01). Overall, pen investigatory behavior was not affected by group space allowance (P = 0.91). Sows in the LS pens spent more time in a social group than SS sows (P = 0.02), whereas sows in IS pens were intermediate to, but not different from, the other treatments (P ≥ 0.10). The size of the social groups was also affected by the group space allowance (P = 0.03), with SS sows forming smaller groups than LS sows; again, IS sows were intermediate to, but not different from, the other treatments. Although the group space allowance had no measurable impact on the health, physiology, or productivity of the sows, the lower group space use and social contact of the SS sows reduced the behavioral diversity benefits of group housing and may indicate an avoidance of social stressors or a lack of physical comfort in the smallest pens