| 1. |
- Nettelblad, Carl
(författare)
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Breakdown of methods for phasing and imputation in the presence of double genotype sharing
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- In genome-wide association studies, results have been improved through imputation of a denser marker set based on reference haplotypes and phasing of the genotype data. To better handle very large sets of reference haplotypes, pre-phasing with only study individuals has been suggested. We present a possible problem which is aggravated when pre-phasing strategies are used, and suggest a modification avoiding these issues with application to the MaCH tool.We evaluate the effectiveness of our remedy to a subset of Hapmap data, comparing the original version of MaCH and our modified approach. Improvements are demonstrated on the original data (phase switch error rate decresasing by 10%), but the differences are more pronounced in cases where the data is augmented to represent the presence of closely related individuals, especially when siblings are present (30% reduction in switch error rate in the presence of children, 47% reduction in the presence of siblings). When introducing siblings, the switch error rate in results from the unmodified version of MaCH increases significantly compared to the original data.The main conclusions of this investigation is that existing statistical methods for phasing and imputation of unrelated individuals might give subpar quality results if a subset of study individuals nonetheless are related. As the populations collected for general genome-wide association studies grow in size, including relatives might become more common. If a general GWAS framework for unrelated individuals would be employed on datasets where sub-populations originally collected as familial case-control sets are included, caution should also be taken regarding the quality of haplotypes.Our modification to MaCH is available on request and straightforward to implement. We hope that this mode, if found to be of use, could be integrated as an option in future standard distributions of MaCH.
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| 2. |
- Nettelblad, Carl
(författare)
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Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Background: In many contexts, pedigrees for individuals are known even though not all individuals have been fully genotyped. In one extreme case, the genotypes for a set of full siblings are known, with no knowledge of parental genotypes. We propose a method for inferring phased haplotypes and genotypes for all individuals, even those with missing data, in such pedigrees, allowing a multitude of classic and recent methods for linkage and genome analysis to be used more efficiently.Results: By artificially removing the founder generation genotype data from a well-studied simulated dataset, the quality of reconstructed genotypes in that generation can be verified. For the full structure of repeated matings with 15 offspring per mating, 10 dams per sire, 99.89% of all founder markers were phased correctly, given only the unphased genotypes for offspring. The accuracy was reduced only slightly, to 99.51%, when introducing a 2% error rate in offspring genotypes. When reduced to only 5 full-sib offspring in a single sire-dam mating, the corresponding percentage is 92.62%, which compares favorably with 89.28% from the leading Merlin package. Furthermore, Merlin is unable to handle more than approximately 10 sibs, as the number of states tracked rises exponentially with family size, while our approach has no such limit and handles 150 half-sibs with ease in our experiments.Conclusions: Our method is able to reconstruct genotypes for parents when genotype data is only available for offspring individuals, as well as haplotypes for all individuals. Compared to the Merlin package, we can handle larger pedigrees and produce superior results, mainly due to the fact that Merlin uses the Viterbi algorithm on the state space to infer the genotype sequence. Tracking of haplotype and allele origin can be used in any application where the marker set does not directly influence genotype variation influencing traits. Inference of genotypes can also reduce the effects of genotyping errors and missing data. The cnF2freq codebase implementing our approach is available under a BSD-style license.
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| 3. |
- Aldén, Liselotte, et al.
(författare)
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New and Ongoing Wind Power Research in Sweden 2018 : A compilation of Swedish research programs and new scientific publications on wind energy
- 2019
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Rapport (populärvet., debatt m.m.)abstract
- The Node for education and competence in the National network for wind utilization annually publishes a summary of new and ongoing wind power research in Sweden. The aim of this summary is to provide an easily accessible overview of what is happening annually in wind power research for interested parties. This compilation is divided into two sections. The first is a presentation of the research centres and research programmes active in wind power research in Sweden. Then a topic-based list of the wind power research published in 2018 follows where at least one of the authors is active at a Swedish university. Here one also can find doctoral and licentiate theses as well as theses at bachelor and master levels that have been published during the year.
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| 4. |
- Aldén, Liselotte, et al.
(författare)
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Utbildningsläget för vindkraftsutbildningar i Sverige läsåren 2017–18 och 2018–19
- 2019
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Rapport (populärvet., debatt m.m.)abstract
- Uppsala universitet Campus Gotland har nodansvar för utbildning och kompetensfrågor inom Nätverket för vindbruk. I noduppdraget ingår att sammanställa och publicera en analys av utbildningsläget en gång per år. Denna upplaga av Utbildningsläget för vindkraftsutbildningar i Sverige är mer omfattande än tidigare år genom att den innehåller utbildningsläget för två läsår, 2017–2018 och 2018–2019.
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| 5. |
- Manzetti, Sergio, et al.
(författare)
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Derivation of a Hamiltonian for formation of particles in a rotating system subjected to a homogeneous magnetic field
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Bose-einstein condensates have received wide attention in the last decades given their unique properties. In this study, we apply supersymmetry rules on an existing Hamiltonian and derive a new model which represents an inverse scattering problem with similarities to the circuit and the harmonic oscillator equations. The new Hamiltonian is analysed and its numerical solutions are presented. The results suggest that the SUSY Hamiltonian describes the formation of vortices in a homogeneous magnetic field in a rotating system.
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| 6. |
- Manzetti, Sergio, et al.
(författare)
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Formation of quantum vortices in a rotating sphere in an electromagnetic field
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Vortexes in three dimensional systems are an emerging topic of study in the realm of quantum physics, particle physics and magnetism. In this study we describe a new Hamiltonian, and solve it numerically for the description of vortices in a spherical model subjected to an electromagnetic field. The numerical analysis shows also that supersymmetric Hamiltonian describes quantized orbitals for atomic systems with vorticity included, which is to our knowledge novel and also describes electricity as composed of quasi-symmetric vortex bundles. Further work on analytical solutions is under development. The 3D solutions of the Hamiltonian are relevant for nuclear physics, in the physics of elementary particles, in geophysics, and in the physics of stellar bodies.
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| 7. |
- Manzetti, Sergio, et al.
(författare)
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Modelling the formation of atmospheric vortices on planet earth using a supersymmetric operator
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Macrophysical phenomena, such as turbulence, vorticity are normally modelled using fluid-mechanical differential equations and geodesics systems. Other methods may also be of importance to the meteorology community, such as quantum physical operators. In this study we use a novel Hamiltonian and study the vortex formation in the atmosphere of planet Earth under the effects of the gravity density stratification and the electromagnetic field of the planet. The results propose that vorticity in the atmosphere (high and low pressure systems) is driven in major part by the interplay between the earths magnetic field and gravity density. The results show that the quantized behaviour of atmospheric vortices lies in their dominant occurrence on the northern and southern hemispheres. The use of quantum mechanical operators in modelling planetary vorticity reveals also that these vortices arise from the core of the planet and manifest in a most pronounced manner on the surface of the earth where gravity density is experiencing an abrupt phase change. Further research is made on combining this model with earths atmospheric parameters, such as ocean temperatures and circulation, terrestrial oscillation and the sun's magnetic field. The results are important for future developments of climate and weather prediction models.
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| 8. |
- Manzetti, Sergio, et al.
(författare)
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Quantum vorticity in a rotating magnetic field
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Vortexes in superfluids are a critical part of quantum optics, quantum dynamics studies and quantum physics in general. The behavior of vortexes is modeled by models such as the Ginzburg-Landau formula, and other systems, where symmetry-breaking is an inevitable event upon vortex formation. In this paper, we present and study a supersymmetric Hamiltonian which allows formation of vortexes in a quantum hall system to occur from the boundaries, as in natural phenomena, without breaking the symmetry. We study the numerical solutions of the Hamiltonian under rotating magnetic field.
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| 9. |
- Manzetti, Sergio, 1975-, et al.
(författare)
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Simulating galactical vorticity using a supersymmetric operator
- 2020
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Rapport (populärvet., debatt m.m.)abstract
- Simulations of galactic vorticity require the development of complex systems of equations to generate models that account for the gravity, mass, kinetic, and electromagnetic effects which govern cluster behaviour. In this study, a relationship is outlined through a series of steps, between the Einstein equations, the Ricci equations and the gravitational model of comoslogical bodies. This series of steps are then followed by the generation of a group of equations, including a supersymmetric equation which describes vorticity under the presence of an electromagnetic field for quantized systems. The relationship between the Einstein equations and the equation for quantum vorticity is ultimately the described and we outline the model of galactic vorticity through a nonlinear cluster model, which has direct similarities to the Kosterlitz-Thouless model for vorticity in quasi-ordered systems. The resulting supersymmetric model for describing galactic vorticity we here show suggests that galactic vorticity broke symmetry already at T=0, and by the effect of the galactic halo around the periphery, generates nonlinear vorticity through the shear property of the wavefunction. Most interestingly, this property of the wavefunction, which generates autonomous vorticity by the mere presence of a halo-boundary of the galactic cluster is independent of temperature. We describe by this that the nonlinear relationship between vortices in the cluster leads to a cumulative effect which generates an exchange interaction at the macroscopic level between clusters which is the source of irregular moment of inertia of galaxies, that has been attributed to dark matter. Our theory is thus that galactic rotations are both fueled by the mass of the galaxy by classical physics means as well as the nonlinear vortex interaction between clusters.
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| 10. |
- Adams, Robin, et al.
(författare)
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What is the word for 'Engineering' in Swedish : Swedish students conceptions of their discipline
- 2007
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Engineering education in Sweden – as in the rest of the world – is experiencing a decline in student interest. There are concerns about the ways in which students think about engineering education, why they join an academic programme in engineering, and why they persist in their studies. In this context the aims of the Nationellt ämnesdidaktiskt Centrum för Teknikutbildning i Studenternas Sammanhang project (CeTUSS) is to investigate the student experience and to identify and support a continuing network of interested researchers, as well as in building capacity for disciplinary pedagogic investigation. The Stepping Stones project brings together these interests in a multi-researcher, multi-institutional study that investigates how tudents and academic staff perceive engineering in Sweden and in Swedish education. The first results of that project are reported here. As this study is situated uniquely in Swedish education, it allows for exploration of “a Swedish perspective” on conceptions of engineering. The Stepping Stones project was based on a model of research capacity-building previously instantiated in the USA and Australia (Fincher & Tenenberg, 2006).
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