Genetic Improvement of Livestock for Organic Farming Systems

Organic farming which experienced a constant rise over the last two decades is a system based on sustainability and on a concept tending towards functional integrity. Legislation as well as the wish to produce separately from conventional farming raise the question whether organic farming should be conducted completely apart from conventional farming or not. This paper discusses the aspects that affect animal breeding under these circumstances, e.g., maintaining genetic diversity by using local breeds and possible G×E interactions which might occur when breeds adapted to conventional farming systems are used in organic farming. Ways of modelling G×E are presented, moreover examples of G×E in dairy cattle, swine, and poultry are given. Trends in selection index theory–designing multi-trait breeding goals including functional traits on one hand, and developing methods for using customised selection indices on the other hand–support breeding work for organic farming systems. It is concluded that before the technical issues can be addressed, all parties involved, farmers, consumers as well as legislators, have to agree on the socio-cultural conditions under which organic farming should be conducted

Partial-measurement back-action and non-classical weak values in a superconducting circuit

We realize indirect partial measurement of a transmon qubit in circuit quantum electrodynamics by interaction with an ancilla qubit and projective ancilla measurement with a dedicated readout resonator. Accurate control of the interaction and ancilla measurement basis allows tailoring the measurement strength and operator. The tradeoff between measurement strength and qubit back-action is characterized through the distortion of a qubit Rabi oscillation imposed by ancilla measurement in different bases. Combining partial and projective qubit measurements, we provide the solid-state demonstration of the correspondence between a non-classical weak value and the violation of a Leggett-Garg inequality.Comment: 5 pages, 4 figures, and Supplementary Information (8 figures

Probing dynamics of an electron-spin ensemble via a superconducting resonator

We study spin relaxation and diffusion in an electron-spin ensemble of nitrogen impurities in diamond at low temperature (0.25-1.2 K) and polarizing magnetic field (80-300 mT). Measurements exploit mode- and temperature-dependent coupling of hyperfine-split sub-ensembles to the resonator. Temperature-independent spin linewidth and relaxation time suggest that spin diffusion limits spin relaxation. Depolarization of one sub-ensemble by resonant pumping of another indicates fast cross-relaxation compared to spin diffusion, with implications on use of sub-ensembles as independent quantum memories.Comment: 5 pages, 5 figures, and Supplementary Information (2 figures

A platform independent communication library for distributed computing

We present MPWide, a platform independent communication library for performing message passing between supercomputers. Our library couples several local MPI applications through a long distance network using, for example, optical links. The implementation is deliberately kept light-weight, platform independent and the library can be installed and used without administrative privileges. The only requirements are a C++ compiler and at least one open port to a wide area network on each site. In this paper we present the library, describe the user interface, present performance tests and apply MPWide in a large scale cosmological N-body simulation on a network of two computers, one in Amsterdam and the other in Tokyo

FabSim3: An automation toolkit for verified simulations using high performance computing

A common feature of computational modelling and simulation research is the need to perform many tasks in complex sequences to achieve a usable result. This will typically involve tasks such as preparing input data, pre-processing, running simulations on a local or remote machine, post-processing, and performing coupling communications, validations and/or optimisations. Tasks like these can involve manual steps which are time and effort intensive, especially when it involves the management of large ensemble runs. Additionally, human errors become more likely and numerous as the research work becomes more complex, increasing the risk of damaging the credibility of simulation results. Automation tools can help ensure the credibility of simulation results by reducing the manual time and effort required to perform these research tasks, by making more rigorous procedures tractable, and by reducing the probability of human error due to a reduced number of manual actions. In addition, efficiency gained through automation can help researchers to perform more research within the budget and effort constraints imposed by their projects. This paper presents the main software release of FabSim3, and explains how our automation toolkit can improve and simplify a range of tasks for researchers and application developers. FabSim3 helps to prepare, submit, execute, retrieve, and analyze simulation workflows. By providing a suitable level of abstraction, FabSim3 reduces the complexity of setting up and managing a large-scale simulation scenario, while still providing transparent access to the underlying layers for effective debugging. The tool also facilitates job submission and management (including staging and curation of files and environments) for a range of different supercomputing environments. Although FabSim3 itself is application-agnostic, it supports a provably extensible plugin system where users automate simulation and analysis workflows for their own application domains. To highlight this, we briefly describe a selection of these plugins and we demonstrate the efficiency of the toolkit in handling large ensemble workflows.EPSRC under grant agreement EP/W007711/1, as well as by the VECMA and HiDALGO projects, which have received funding from the European Union Horizon 2020 research and innovation programme under grant agreement nos 800925 and 824115. In addition, FabFlee was supported by the ITFLOWS project and FabCovid19 by the STAMINA project, both of which have received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 882986 and No 883441 respectivel

Plasma oxyphytosterols most likely originate from hepatic oxidation and subsequent spill-over in the circulation

We evaluated oxyphytosterol (OPS) concentrations in plasma and various tissues of two genetically modified mouse models with either increased cholesterol (apoE KO mice) or increased cholesterol and plant sterol (PS) concentrations (apoExABCG8 dKO mice). Sixteen female apoE KO and 16 dKO mice followed the same standard, low OPS-chow diet. Animals were euthanized at 36 weeks to measure PS and OPS concentrations in plasma, brain, liver and aortic tissue. Cholesterol and oxysteml (OS) concentrations were analyzed as reference for sterol oxidation in general. Plasma campesterol (24.1 +/- 4.3 vs. 11.8 +/- 3.0 mg/dL) and sitosterol (67.4 +/- 12.7 vs. 4.9 +/- 1.1 mg/dL) concentrations were severely elevated in the dKO compared to the apoE KO mice (p < 0.001). Also, in aortic and brain tissue, PS levels were significantly elevated in dKO. However, plasma, aortic and brain OPS concentrations were comparable or even lower in the dKO mice. In contrast, in liver tissue, both PS and OPS concentrations were severely elevated in the dKO compared to apoE KO mice (sum OPS: 7.4 +/- 1.6 vs. 4.1 +/- 0.8 ng/mg, p < 0.001). OS concentrations followed cholesterol concentrations in plasma and all tissues suggesting ubiquitous oxidation. Despite severely elevated PS concentrations, OPS concentrations were only elevated in liver tissue, suggesting that OPS are primarily formed in the liver and plasma concentrations originate from hepatic spill-over into the circulation

Spinal Cord Ischemia Related to Disc Herniation:Case Report and a Review of the Literature

Symptoms of spinal cord ischemia can mimic myelopathy due to spinal cord compression in the acute phase. Thoracic disc herniation with limited spinal cord compression but rapid progression of neurological symptoms causes a clinical dilemma as to whether emergency decompression should be performed. We report a case of acute progressive myelopathy due to spinal cord ischemia related to thoracic disc herniation initially managed by Th8 laminectomy with reduction of the herniated disc. Repeat imaging showed T2-weighted hyperintensity in the posterior cord. The clinical and radiological course supports posterior spinal artery ischemia. This case illustrates and a review of the literature shows that thoracic disc herniation may be complicated by ischemic myelopathy even in the absence of cord compression

Mastering the scales: A survey on the benefits of multiscale computing software

Electronic supplementary material is available online at https://doi.org/10.6084/m9. figshare.c.4352660.© 2019 The Authors. In the last few decades, multiscale modeling has emerged as one of the dominant modeling paradigms in many areas of science and engineering. Its rise to dominance is primarily driven by advancements in computing power and the need to model systems of increasing complexity. The multiscale modeling paradigm is now accompanied by a vibrant ecosystem of multiscale computing software (MCS) which promise to address many challenges in the development of multiscale applications. In this paper, we define the common steps in the multiscale application development process and investigate to what degree a set of 22 representative MCS tools enhance each development step. We observe several gaps in the features provided by MCS tools, specially for application deployment and the preparation and management of production runs. In addition, we find that many MCS tools are tailored to a particular multiscale computing pattern, even though they are otherwise application agnostic. We conclude that the gaps we identify are characteristic of a field that is still maturing and features that enhance the deployment and production steps of multiscale application development are desirable for the long term success of MCS in its application fields.The European Union’s Horizon 2020 research, innovation programme under grant agreement and the project “Task-based load balancing and auto-tuning in particle simulations”European Union’s Horizon 2020 Research and Innovation Programme under grant agreement nos. 800925 and 671564; ‘Task-based load balancing and auto-tuning in particle simulations’ project (TaLPas), grant no. 01IH16008B