Spatio-temporal modeling of morphology and gene-expressions during C. elegans embryogenesis using a new imaging framework

Many aspects of ontogenesis, the process whereby an organism develops from the fertilized egg to a grown adult, are still poorly understood, despite having been studied since Aristotle's time. The advent of modern biology with the sequencing of entire genomes and mapping of all genes offers the promise that one day we will understand how genes function to regulate cell division and differentiation. These advances offer new possibilities to solve the question that humanity has been asking since the beginning of time, how is a new life created? The aim of this thesis is to establish methods to study when and where particular genes are expressed in the model organism Caenorhabditis elegans by means of microscopy. Ultimately, this will aid our understanding of embryology in more complex organisms and in human. The usefulness of the software is however not limited to embryology but is also useful for microscopy in general. In Paper I we present our open source software platform, Endrov (http://www.endrov.net), for image processing and microscopy. It is strongly modular and meant to allow tight integration with all kinds of infrastructure (microscopes, cameras, controllers, etc.) needed for modern biological and non-biological imaging. Endrov supports modern visualization, over 100 file formats, can connect to the OMERO image server and can control many modern light microscopes. We have also implemented 140 image processing algorithms and several types of annotations, e.g., for particle tracking, 3D surfaces, point-text annotation, neuron/vascular 4D annotation and more. A novel feature is the concept of laziness, which makes Endrov scale for large data sets and consequently makes it easier to prototype algorithms. The entire application is written in Java and consists of about 150 000 lines of code. In Paper II we have developed procedures to record wild-type C. elegans embryos in 3D over time (4D). Endrov was used to analyze the data and we generated a model of normal embryonic development complete up to the 150 cell-stage. The variance in cell positioning and division timing was calculated and the cell-cell contacts estimated. When compared to a previous model made from a squeezed embryo, our model has a higher time resolution and is more reproducible. In Paper III we have generated a revised list of all homeobox genes in C. elegans, showing that out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. A number of modules have been developed for analyzing and quantifying expression data. These are not only suitable for C. elegans but can also be used for other biological model systems. Special features include automatic adjustment of exposure time during recording resulting in an increased dynamic range beyond the limits of the microscope camera, and annotation of the cells in 3D rendered space. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of the patterns that we have recorded. In Paper IV we have extended the applicability of Endrov by using it to study the mitochondrial polymerase gamma (polg-1) in C. elegans. polg-1 deletion mutant alleles were analyzed for phenotypes using methods such as measuring lifespan and brood size, qPCR for mtDNA content and transcript levels, and light and TEM microscopy. The main findings were that homozygous polg-1 mutant animals develop normally, although later in the adult stage they exhibit compromised gonadal function, sterility, as well as reduced viability due to rupture at the vulva. 3D modeling of the gonad revealed structural abnormalities in the germline. Further, the few descendants that are generated are severely compromised and die during embryogenesis. We can deduce that while mtDNA copy number is a limiting factor for development, the maternally contributed mitochondria are enough to sustain development to adulthood. In summary, we have created the Endrov software framework that allows processing of large multidimensional microscopy image data sets and demonstrated that it can be applied to a wide range of problems

Vattnet stiger

Klimatförändringarna är en av vår tids stora utmaningar. Stigande havsnivåer, torrperioder och kraftiga skyfall, alla är de effekter av hur klimaten förändras. De här utmaningarna tillsammans med utmaningen om hur en hållbar stad byggs, en stad där vatten, natur och bebyggelse samspelar är bakgrunden till det här examensarbetet. Syftet med arbetet är dels att skapa en diskussion om ämnet och att uppnå en bättre förståelse och kunskap för hur det här samspelet kan se ut och vilka svårigheter och möjligheter som finns. Men även att utforska hur en gestaltning kan ses ut som både minimerar risker och som ger mervärden som biologiska värden. Föreliggande arbete har därför som mål att ta fram ett förslag för stadsdelen Tullkammarkajen i Halmstad som både kan hantera stigande vatten men som också ger biologiska mervärden. Arbetet har utgått från en designprocess. Till grund för designprocessen ligger en teoretisk bakgrundsstudie och en studie över ett antal exempelplatser. Det färdiga förslaget visar en gestaltning som tar fasta på arbetets huvudsakliga syfte och mål och visar på hur en alternativ utformning kan se ut som både kan hantera ökade vattenmängder i staden samt ger mervärde i form av biologiska värden. Förslaget har utvärderats gentemot två andra alternativ genom ett flertal aspekter, vilket visade på fördelar och nackdelar både med det egna förslaget samt alternativ förslagen. Efter utvärderingen kan ingen generell rekommendation göras för vilket alternativ som bör användas, men det här arbetet kan ses som inspiration och vägledande i den fortsatta utredningen om hur Tullkammarkajen i Halmstad ska utvecklas.Climate change is one of the great challenges of our time. Rising sea levels, dry periods and cloudburst, all are they effects of changing climate. These challenges, together with the challenge of how to build a sustainable city, a city where water, nature and buildings interact is the background to this master thesis. The purpose of this thesis is partly to create a discussion on the subject and to gain a better understanding and knowledge of what this interaction can look like and what difficulties and opportunities that exist. It is also to explore how a design can look like that both minimizing the risks and provide benefits as biological values. The present thesis therefore aims to produce a proposal for the district of Tullkammarkajen in Halmstad, which can both handle rising water and provide biological benefits. The thesis is based on a design process. The basis of the design process is a theoretical background study and a study of some example sites. The final proposal present a design that addresses the main purpose and goals of this thesis and shows how an alternative design can look like that can both handle increased water levels in the city as well as provide added value in the form of biological values. The proposal has been evaluated against two other alternatives through a number of aspects, which both shows the advantages and disadvantages of the own proposal and the alternative proposals. After the evaluation, no general recommendation can be made for which alternative should be used. But this work can be seen as inspiration and guidance in the continuing investigation of how the Tullkammarkajen in Halmstad should be developed

Analytic Bootstrap for Perturbative Conformal Field Theories

Conformal field theories play a central role in theoretical physics with many applications ranging from condensed matter to string theory. The conformal bootstrap studies conformal field theories using mathematical consistency conditions and has seen great progress over the last decade. In this thesis we present an implementation of analytic bootstrap methods for perturbative conformal field theories in dimensions greater than two, which we achieve by combining large spin perturbation theory with the Lorentzian inversion formula. In the presence of a small expansion parameter, not necessarily the coupling constant, we develop this into a systematic framework, applicable to a wide range of theories. The first two chapters provide the necessary background and a review of the analytic bootstrap. This is followed by a chapter which describes the method in detail, taking the form of a practical guide to large spin perturbation theory by means of a step-by-step implementation. The second part of the thesis presents several explicit implementations of the framework, taking examples from a number of well-studied conformal field theories. We show how many literature results can be reproduced from a purely bootstrap perspective and how a variety of new results can be derived.Comment: DPhil thesis. 221 pages, 11 figures. Sections 6.3 and 6.4 contain some previously unpublished results. v2: typos correcte

Flexible Implementation of Model Predictive Control Using Sub-Optimal Solutions

The on-line computational demands of model predictive control (MPC) often prevents its application to processes where fast sampling is necessary. This report presents a strategy for reducing the computational delay resulting from the on-line optimization inherent in many MPC formulations. Recent results have shown that feasibility, rather than optimality, is a prerequisite for stabilizing MPC algorithms, implying that premature termination of the optimization procedure may be valid, without compromising stability. The main result included in the report is a termination criterion for the on-line optimization algorithm giving rise to a sub-optimal, yet stabilizing, MPC algorithm. The termination criterion, based on an associated delay-dependent cost index, quantifies the trade-off between successively improved control profiles resulting form the optimization algorithm and the potential performance degradation due to increasing computational delay. It is also shown how the cost index may be used in a dynamic scheduling application, where the processor time is shared between two MPC tasks executing on the same CPU

Streamlined Installation Process for Ericsson Enterprise Core

Companies all over the world are now preparing the transition towards the next milestone of modern industrialization: Industry 4.0. One key factor in enabling this leap is the new fth-generation (5G) mobile networking technology. Ericsson Enterprise Core (EEC), is a private 5G mobile network solution; offering bigger industrial complexes a complete network infrastructural package { enabling them to utilize this the new technology. The number of installations of EEC solutions is expected to increase in the oncoming years, as the number of sold units goes up. This installation can be quite complicated however and has so far only been conducted by experienced members of staff. To enable more personnel at the company to be able to conduct the installation, the process has to be simplifed and shortened compared to today. This faster and simplifed installation process is referred to as the 'Streamlined Installation Process for Ericsson Enterprise Core', which also is the title and goal of this master's thesis { conducted at Ericsson Lindholmen, Gothenburg, during the spring of 2020. A series of interviews were held with EEC installation instruction creators and EEC installers at Ericsson to reveal hurdles in the current installation process and why these had arisen. The result indicated a necessity for installers to possess extensive telecommunication knowledge to be able to fully conduct the installation process. This included, for example, Packet Core structure, 3GPP standard, and orientation with server hardware. A discrepancy in the instruction creators' and the installers' opinion was noted, regarding whether the documentation structure was intuitive. Finally, the two groups agreed upon the diffculties an installer can have with installation completion verifcation, where the installed instance has to be connected to real-time traffic in order for its functionality to be fully verifed. The methodology Design Thinking was used to ideate, produce, and test new instructions that enabled a more elective installation of the EEC solution. Included in the thesis is the result { a conceptual prototype on how the EEC instructions could be further supported to reach the goal stated above

Classical Codes and Chiral CFTs at Higher Genus

Higher genus modular invariance of two-dimensional conformal field theories (CFTs) is a largely unexplored area. In this paper, we derive explicit expressions for the higher genus partition functions of a specific class of CFTs: code CFTs, which are constructed using classical error-correcting codes. In this setting, the $\mathrm{Sp}(2g,\mathbb Z)$ modular transformations of genus $g$ Riemann surfaces can be recast as a simple set of linear maps acting on $2^g$ polynomial variables, which comprise an object called the code enumerator polynomial. The CFT partition function is directly related to the enumerator polynomial, meaning that solutions of the linear constraints from modular invariance immediately give a set of seemingly consistent partition functions at a given genus. We then find that higher genus constraints, plus consistency under degeneration limits of the Riemann surface, greatly reduces the number of possible code CFTs. This work provides a step towards a full understanding of the constraints from higher genus modular invariance on 2d CFTs.Comment: 48p