Standards for plant synthetic biology: A common syntax for exchange of DNA parts

© 2015 New Phytologist Trust. Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering

Observation of γγ → ττ in proton-proton collisions and limits on the anomalous electromagnetic moments of the τ lepton

The production of a pair of τ leptons via photon–photon fusion, γγ → ττ, is observed for the f irst time in proton–proton collisions, with a significance of 5.3 standard deviations. This observation is based on a data set recorded with the CMS detector at the LHC at a center-of-mass energy of 13 TeV and corresponding to an integrated luminosity of 138 fb−1. Events with a pair of τ leptons produced via photon–photon fusion are selected by requiring them to be back-to-back in the azimuthal direction and to have a minimum number of charged hadrons associated with their production vertex. The τ leptons are reconstructed in their leptonic and hadronic decay modes. The measured fiducial cross section of γγ → ττ is σfid obs = 12.4+3.8 −3.1 fb. Constraints are set on the contributions to the anomalous magnetic moment (aτ) and electric dipole moments (dτ) of the τ lepton originating from potential effects of new physics on the γττ vertex: aτ = 0.0009+0.0032 −0.0031 and |dτ| < 2.9×10−17ecm (95% confidence level), consistent with the standard model

Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.Biotechnological and Biological Sciences Research Council (BBSRC). Grant Numbers: BB/K005952/1, BB/L02182X/1 Synthetic Biology Research Centre ‘OpenPlant’ award. Grant Number: BB/L014130/1 Spanish MINECO. Grant Number: BIO2013‐42193‐R Engineering Nitrogen Symbiosis for Africa (ENSA) The Bill & Melinda Gates Foundation US Department of Energy, Office of Biological and Environmental. Grant Number: DE‐AC02‐05CH1123 COST Action. Grant Number: FA100

Optimierung der Anzahl an Daten für das Trainieren von GANs (Generative Adversarial Networks) für die automatisierte Segmentation in der Strahlentherapie

Abweichender Titel nach Übersetzung der Verfasserin/des VerfassersPurpose : Radiation oncology relies on the accuracy of organ-at-risk (OAR) and target structure delineations for dose calculations and treatment planning. The effect of inaccurate structure localization is more pronounced in particle therapy due to higher dose gradients in comparison to photon therapy. Manual segmentation is the gold standard even though inter-observer-variability and temporal anatomical changes influence subsequent dose calculations. However, manual segmentation is a time-consuming task, which makes it unfeasible for adaptive radiotherapy (ART). The increased workload due to multiple replannings could, therefore, benefit from automated segmentation. In particular, deep learning methods have already been used with great success in segmentation tasks and are currently investigated for their use in medical applications. Discriminative classifiers are one such method that is typically used for image segmentation. However, they suffer from small data sets resulting in overfitting, and typical loss functions do not guarantee spatial consistency. Generative adversarial networks (GANs), on the other hand, have shown promise in tackling those issues. This thesis aimed to compare GANs with convolutional neural networks (CNNs) based on the popular U-net architecture, as a type of discriminative classifier, on different sized training data. This was done to determine a potential benefit of using GANs for segmentation in radiation oncology. Both network architectures were trained, validated, and tested on segmentations of a subset of OARs in prostate cancer patients. Methods and Materials: Data of 360 patients, who were treated for prostate cancer at the Department of Radiation Oncology at the Medical University of Vienna, was investigated. The OARs were bladder, rectum, and the femoral heads. The CNN, as well as the GAN architecture, were trained on different training data sets consisting of 1, 6, 11, 16, 21, 26, and 100 patients. An extensive hyperparameter search was performed to identify the best settings for all observed structures. The performance of the networks was evaluated using metrics such as Dice similarity coefficient (DSC), sensitivity, precision, Hausdorff distance (HD), mean squared error (MSE), and root mean squared error (RMSE).Results: No significant difference could be observed for small training data set sizes between GAN and CNN when measured with the DSC. For sensitivity and precision, the networks did perform differently for certain data set sizes and OARs. The precision score of the GAN was higher for 6, 16, and 21 patients. For 1 and 6 patients in the training data set, the CNN performed better according to sensitivity. However, the sensitivity score of the GAN was higher for 16 patients. As sensitivity and precision are associated with over- and underrepresentation, this could indicate a correcting influence of the discriminator; however, there is no discernible trend amongst all patient data set sizes. For 100 patients, no significant difference was observed between the different architectures resulting in near-identical mean DSCs of bladder, rectum, and femoral heads of 0.89 ± 0.08, 0.84 ± 0.08, and 0.93 ± 0.06, respectively.Conclusion: In this thesis, no significant difference in performance between GAN and CNN could be observed. When compared to other factors, such as network architecture and data preprocessing, it might not be worth training GANs for image segmentation.8

Kalman filter for muon reconstruction in the CMS Phase-2 endcap calorimeter

At the High Luminosity phase of the LHC (HL-LHC), experiments will be exposed to numerous (approx. 140) simultaneous proton-proton collisions. To cope with such harsh environments, the CMS Collaboration is designing a new endcap calorimeter, referred to as the High-Granularity Calorimeters (HGCAL). As part of the detector upgrade, a novel reconstruction framework (TICL The Iterative CLustering) is being developed. The framework uses a hierarchical approach to build physics objects out of energy deposits and employs a wide range of both classical and machine learning algorithms, for different tasks in the reconstruction chain. Even though TICL is under continuous development, it has already shown outstanding performance in particle shower reconstruction.In this contribution, the development of a dedicated muon reconstruction within TICL is discussed. Such dedicated reconstruction is crucial for HGCAL, especially for inter-cell calibration and for expanding the global muon reconstruction to regions with pseudorapity > 2.4. The Kalman Filter (KF) algorithm is particularly suited to tackle this challenge, and it has already been tested and used extensively in many particle physics experiments for track reconstruction, including CMS. The performance of the KF algorithm for muon reconstruction in HGCAL under various conditions will be presented for the first time, as well as its capabilities and limitations as a tool for inter-cell calibration

Hydrocarbons as recorders of cosmic environments

Hydrocarbons are ubiquitous in the Cosmos. Carbon stars jettison large amounts of hydrocarbons into interstellar space and these are incorporated into forming planetary systems alongside newly synthesized hydrocarbon material. The structure of a hydrocarbon reveals its origin with non-biological, biological, low temperature, high temperature, reduced, oxidised and aqueously altered hydrocarbons all having structural features that imply their provenance. These features are explored throughout this work, with a focus on the insoluble macromolecular organic carbon of meteorites and comparative terrestrial samples. Analytical pyrolysis of macromolecular material in meteorites is a well established technique. By subjecting samples to multiple heating steps, rather than the more usual single step, new insights into the structure and composition of the macromolecular material have been obtained. In addition, simple typing of chondrites and a reconstruction of the conditions experienced on their asteroid parent bodies is possible using the products of pyrolysis. It is the carbonaceous chondrites that have received the most attention for their organic content but some ordinary chondrites also contain appreciable quantities of organic materials. The organic inventory of both carbonaceous and ordinary chondrites has been explored in this study. Carbonaceous chondrites contain authentic abiotic organic material and are in great demand for scientific analysis and experimentation. Yet these objects are extremely rare and valuable and there is a need for analogue materials that are available in larger quantities and on which specific experiments can be carried out. Uses of effective meteorite organic analogues include the training of personnel, testing of analytical methods, contamination studies, and optimisation of space mission instruments. Most of the carbon in carbonaceous chondrites is a non-biological aromatic and intractable macromolecular material and previously unsatisfactory analogues have included coals and other so-called type III kerogens. Following a comparison of a number of candidate materials a new analogue has been identified in reworked fossil soils from the Jurassic of southern England. This type IV kerogen displays great similarities to the macromolecular material in meteorites and can be employed to lessen the burden on our curated collections of rare carbonaceous meteorites. The thermal and chemical stability of hydrocarbons ensures that they exhibit excellent preservation potential and can often be found when other molecular information carriers have long since perished. This feature is important when studying planetary environments for indicators of biogenicity. Yet there is a multitude of information to process and the organic signals can often be confusing owing to diagenesis, catagenesis, oxidation and weathering. In this study a wide range of terrestrial and extraterrestrial materials have been examined using statistical techniques to develop a method for the discrimination of abiotic from biotic macromolecular materials, based only upon the distributions of simple aromatic hydrocarbons and related compounds. This has important implications for life-detection missions destined for Mars, which are currently under development.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Kalman filter for muon reconstruction in the CMS Phase-2 endcap calorimeter

The High Luminosity phase of the LHC (HL-LHC) will offer a greatly increased number of events for more precise standard model measurements and BSM searches. To cope with the harsh environment created by numerous simultaneous proton-proton collisions, the CMS Collaboration has begun construction of a new endcap calorimeter, the High-Granularity Calorimeters (HGCAL). As part of this project, a new reconstruction framework, TICL, is being developed, aiming to exploit the possibilities of heterogeneous computing, and employing machine learning elements. While TICL has shown impressive results for particle shower reconstruction in HGCAL, the proposed calorimeters' high granularity can be used to track muons. Precise tracking of externally identified muons through the calorimeter allows them to be used for the crucial task of following the evolving inter-cell relative response, and calibrating it, in order to maintain good energy resolution. In this contribution, we propose to integrate a Kalman Filter into the TICL framework for dedicated muon reconstruction. We present a comprehensive performance evaluation of the algorithm under various conditions akin to those at the HL-LHC. Finally, we discuss the capabilities and limitations of the Kalman Filter as a tool for inter-cell calibration

Organic geochemistry of late Jurassic paleosols (Dirt Beds) of Dorset, UK

Paleosols from the lower part of the Purbeck Limestone Group, which crops out extensively in Dorset, southern England, are shown to contain type IV kerogens. Comparisons with Mesozoic organic materials suggest that some of the paleosol kerogen is composed of fossil charcoal. The charcoal would have been produced by wildfires in the undergrowth of Purbeck gymnosperm forests. Contrasting the paleosol charcoal with laboratory produced counterparts suggest that, originally, significant amounts of functionalised organic matter should have persisted. Secondary oxidation and decay processes, therefore, must have removed all but the most resistant aromatic units in the charcoal. The importance of post-fire processes implies a strong influence on preservation from oxygen supply, water washing and host sediment type. These factors may have been related to pedogenesis, relative sea level and local fault movement in the late Jurassic. (C) 2012 Elsevier Ltd. All rights reserved.</p