Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning

Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments. While deep learning approaches have proven useful for general cell segmentation tasks, existing segmentation tools for the yeast-microstructure setting rely on traditional machine learning approaches. Here we present convolutional neural networks trained for multiclass segmenting of individual yeast cells and discerning these from cell-similar microstructures. We give an overview of the datasets recorded for training, validating and testing the networks, as well as a typical use-case. We showcase the method's contribution to segmenting yeast in microstructured environments with a typical synthetic biology application in mind. The models achieve robust segmentation results, outperforming the previous state-of-the-art in both accuracy and speed. The combination of fast and accurate segmentation is not only beneficial for a posteriori data processing, it also makes online monitoring of thousands of trapped cells or closed-loop optimal experimental design feasible from an image processing perspective.Comment: IEEE CIBCB 2020 (accepted

Multiclass Yeast Segmentation in Microstructured Environments with Deep Learning

Cell segmentation is a major bottleneck in extracting quantitative single-cell information from microscopy data. The challenge is exasperated in the setting of microstructured environments. While deep learning approaches have proven useful for general cell segmentation tasks, existing segmentation tools for the yeast-microstructure setting rely on traditional machine learning approaches. Here we present convolutional neural networks trained for multiclass segmenting of individual yeast cells and discerning these from cell-similar microstructures. We give an overview of the datasets recorded for training, validating and testing the networks, as well as a typical use-case. We showcase the method's contribution to segmenting yeast in microstructured environments with a typical synthetic biology application in mind. The models achieve robust segmentation results, outperforming the previous state-of-the-art in both accuracy and speed. The combination of fast and accurate segmentation is not only beneficial for a posteriori data processing, it also makes online monitoring of thousands of trapped cells or closed-loop optimal experimental design feasible from an image processing perspective

Design Status of the CLIC 3-TeV Beam Delivery System and Damping Rings

We describe the present design status of beam delivery and damping rings for CLIC at 3 TeV cm energy, and outline our future plans. The beam delivery system comprises collimation, final focus and post-IP exit line. Critical design aspects include halo collimation, machine protection, beam removal, and thermal stability analysis. In order to attain the design spot size at the collision point, the damping rings must provide beams of extremely small emittances. In this paper, we focus on collimation and spent beam

θ13\theta_{13}, δ\delta and the neutrino mass hierarchy at a γ=350\gamma=350 double baseline Li/B β\beta-Beam

We consider a $\beta$-Beam facility where $^8$Li and $^8$B ions are accelerated at $\gamma = 350$, accumulated in a 10 Km storage ring and let decay, so as to produce intense $\bar \nu_e$ and $\nu_e$ beams. These beams illuminate two iron detectors located at $L \simeq 2000$ Km and $L \simeq 7000$ Km, respectively. The physics potential of this setup is analysed in full detail as a function of the flux. We find that, for the highest flux ($10 \times 10^{18}$ ion decays per year per baseline), the sensitivity to $\theta_{13}$ reaches $\sin^2 2 \theta_{13} \geq 2 \times10^{-4}$; the sign of the atmospheric mass difference can be identified, regardless of the true hierarchy, for $\sin^2 2 \theta_{13} \geq 4\times10^{-4}$; and, CP-violation can be discovered in 70% of the $\delta$-parameter space for $\sin^2 2 \theta_{13} \geq 10^{-3}$, having some sensitivity to CP-violation down to $\sin^2 2 \theta_{13} \geq 10^{-4}$ for $|\delta| \sim 90^\circ$.Comment: 35 pages, 20 figures. Minor changes, matches the published versio

Stability Considerations for Final Focus Systems of Future Linear Colliders

The final focus systems for the future linear colliders need to focus beams to nm-range spot sizes at the collision point. The design spot size varies from several nm for 500 GeV to the one nm range for 3 TeV. In order to keep the beams in collision and to maintain the luminosity stringent stability optimization must be applied. We discuss different sources of beam perturbations and estimate the expected beamline stability based on previous experimental observations. Possible measures for beam stabilization are discussed and plans of further collaborative efforts are outlined

A Very Intense Neutrino Super Beam Experiment for Leptonic CP Violation Discovery based on the European Spallation Source Linac: A Snowmass 2013 White Paper

Very intense neutrino beams and large neutrino detectors will be needed in order to enable the discovery of CP violation in the leptonic sector. We propose to use the proton linac of the European Spallation Source currently under construction in Lund, Sweden to deliver, in parallel with the spallation neutron production, a very intense, cost effective and high performance neutrino beam. The baseline program for the European Spallation Source linac is that it will be fully operational at 5 MW average power by 2022, producing 2 GeV 2.86 ms long proton pulses at a rate of 14 Hz. Our proposal is to upgrade the linac to 10 MW average power and 28 Hz, producing 14 pulses/s for neutron production and 14 pulses/s for neutrino production. Furthermore, because of the high current required in the pulsed neutrino horn, the length of the pulses used for neutrino production needs to be compressed to a few $\mu$s with the aid of an accumulator ring. A long baseline experiment using this Super Beam and a megaton underground Water Cherenkov detector located in existing mines 300-600 km from Lund will make it possible to discover leptonic CP violation at 5 $\sigma$ significance level in up to 50% of the leptonic Dirac CP-violating phase range. This experiment could also determine the neutrino mass hierarchy at a significance level of more than 3 $\sigma$ if this issue will not already have been settled by other experiments by then. The mass hierarchy performance could be increased by combining the neutrino beam results with those obtained from atmospheric neutrinos detected by the same large volume detector. This detector will also be used to measure the proton lifetime, detect cosmological neutrinos and neutrinos from supernova explosions. Results on the sensitivity to leptonic CP violation and the neutrino mass hierarchy are presented.Comment: 28 page

Hip fractures and area level socioeconomic conditions: a population-based study

Icks A, Haastert B, Wildner M, et al. Hip fractures and area level socioeconomic conditions: a population-based study. BMC Public Health. 2009;9(1):114.Background: Only a limited number of studies have analyzed the association between hip fracture incidence and socioeconomic conditions. Most, but not all found an association, and results are in part conflicting. The aim of our study was to evaluate the association between hip fractures and socioeconomic conditions in Germany, from 1995 to 2004, on a census tract area level. Methods: We used data from the national hospital discharge diagnosis register and data on socioeconomic and demographic characteristics of 131 census tracts from official statistics. Associations between the hip fracture incidence and socioeconomic conditions were analyzed by multiple Poisson regression models, taking overdispersion into account. Results: The risk of hip fracture decreased by 4% with a 7% increase (about one interquartile range) of non-German nationals. It decreased by 10% with a 6% increased rate of unemployment, increased by 7% with a 2% increase of the proportion of welfare recipients, and also increased by 3% with an increase of the proportion of single parent families of 1.9%. Conclusion: Our results showed weak associations between indicators of socioeconomic conditions at area level and hip fracture risk; the varied by type of indicator. We conclude that hip fracture incidence might be influenced by the socioeconomic context of a region, but further analysis using more specific markers for deprivation on a smaller scale and individual-level data are needed

Long Term Stability of the LHC Superconducting Cryodipoles after Outdoor Storage

The main superconducting dipoles for the LHC are being stored outdoors for periods from a few weeks to several years after conditioning with dry nitrogen gas. Such a storage before installation in the 27 km circumference tunnel may affect not only the mechanical and cryogenic functionality of the cryodipoles but also their quench and field performance. A dedicated task force was established to study all aspects of long term behaviour of the stored cryodipoles, with particular emphasis on electrical and vacuum integrity, quench training behaviour, magnetic field quality, performance of the thermal insulation, mechanical stability of magnet shape and of the interface between cold mass and cryostat, degradation ofmaterials and welds. In particular, one specifically selected cryodipole stored outdoors for more than one year, was retested at cold. In addition, various tests have been carried out on the cryodipole assembly and on the most critical subcomponents to study aspects such as the hygrothermal behaviour of the supporting system and the possible oxidation of the Multi Layer Insulation reflective films. This paper summarizes the main investigations carried out and their results

Comparison of hip fracture incidence and trends between Germany and Austria 1995-2004: An epidemiological study

Mann E, Meyer G, Haastert B, Icks A. Comparison of hip fracture incidence and trends between Germany and Austria 1995-2004: an epidemiological study. BMC Public Health. 2010;10(1): 46.Background Several studies evaluated variations in hip fracture incidences, as well as trends of the hip fracture incidences. Comparisons of trends are lacking so far. We compared the incidence rates and, in particular, its trends between Austria and Germany 1995 to 2004 analysing national hospital discharge diagnosis register data. Methods Annual frequencies of hip fractures and corresponding incidences per 100,000 person years were estimated, overall and stratified for sex and age, assuming Poisson distribution. Multiple Poisson regression models including country and calendar year, age and sex were used to analyse differences in incidence and trend. The difference of annual changes between the two countries was explored using an interaction term (calender year * country). Results Overall, the increase of hip fracture risk was 1.31 fold higher (95% CI 1.29-1.34) in Austria compared to Germany, adjusted for age, sex, and calendar year. The risk increase was comparable for both sexes (males: RR 1.35 (1.32-1.37), females: RR 1.31 (1.29-1.33)). Hip fracture trend from 1995 to 2004 indicates an increase in both countries without a statistically significant difference between Austria and Germany (interaction term: p = 0.67). Conclusion In this study comparing hip fracture incidences and its trend using pooled data, the incidence in Austria was 30% higher compared to its neighbouring country Germany. For both countries a similar increasing trend of hip fracture incidence over the 10-year study period was calculated. The results need confirmation by other studies