<p>Applikationen Chemical Force Feedback (CFF) för haptisk och visuell molekylrendering som har utvecklats på Linköpings Universitet för att testa nyttan av haptik för undervisning av protein-ligand dockning för molekylär livsvetenskap behöver förbättras på ett antal punkter för att bättre kunna fungera som ett komplett</p><p>molekylvisualiserings-verktyg. Tidigare projekt som utvecklat applikationen har fokuserat mestadels på den haptiska delen av programmet, vilket gjort att den visuella aspekten kommit efter. Det här examensarbetet har implementerat diverse ny funktionalitet både för att förbättra direkt kännbara aspekter av programmet, samt att lägga grunden för framtida utökningar.</p><p>De huvudsakliga förbättringarna som det här exjobbet resulterat i inkluderar: För det första, integration av DSSP-algoritmen i programmet har gjort information om sekundärstrukturen hos protein tillgänglig för visualisering. För det andra, ett nytt renderings-system tillåter rendering av semitransparenta ytor på ett korrekt sätt samtidigt som det skapar en program-struktur som bättre lämpar sig för implementation av nya molekylrepresentationer. För det tredje, en filvals-komponent som fungerar i den haptiska scengrafen har designats för att göra programmets användargränssnitt mer tillgängligt.</p> / <p>The Chemical Force Feedback (CFF) visual and haptic molecule rendering application, being developed at Linköping University to evaluate the use of haptics as a teaching tool for protein-ligand docking in molecular life science requires several additional features to function as a mature protein visualization tool. Previous developments of the application have focused mostly on the haptic part of the program, leaving the visual representation somewhat under-developed.</p><p>This thesis project has implemented various features in order to both improve the immediate functionality of the application as well as lay down the foundation for future additions.</p><p>The main contributions of this thesis include: Firstly, integration of the DSSP algorithm has provided the application with secondary structure information for the protein visualization. Secondly, a new rendering system has provided support for rendering transparent surfaces in a correct way as well as simplifying future addition of new visual representations of molecules. Thirdly, a file-selection dialog have been implemented using the haptic scenegraph as a step toward the goal of making the user interface of the application more user-friendly.</p>

We consider three problems, motivated by questions in computational neuroscience, related to recovering continuous quantities from binary or discrete data or measurements in the context of sparse structure. First, we show that it is possible to recover the norms of sparse vectors given one-bit compressive measurements, and provide associated guarantees. Second, we present a novel algorithm for spike-sorting in neural data, which involves recovering continuous times and amplitudes of events using discrete bases. This method, Continuous Orthogonal Matching Pursuit, builds on algorithms used in compressive sensing. It exploits the sparsity of the signal and proceeds greedily, achieving gains in speed and accuracy over previous methods. Lastly, we present a Bayesian method making use of hierarchical priors for entropy rate estimation from binary sequences. / text

The objective of this research project was to develop a methodology to establish the potential of automated sorting for a minerals application. Such methodologies, have been developed for testwork in many established mineral processing disciplines. These techniques ensure that data is reproducible and that testing can be undertaken in a quick and efficient manner. Due to the relatively recent development of automated sorters as a mineral processing technique, such guidelines have yet to be established. The methodology developed was applied to two practical applications including the separation of a Ni/Cu sulphide ore. This experimentation also highlighted the advantages of multi-sensor sorting and illustrated a means by which sorters can be used as multi-output machines; generating a number of tailored concentrates for down-stream processing. This is in contrast to the traditional view of sorters as a simple binary, concentrate/waste pre-concentration technique. A further key result of the research was the emulation of expert-based training using unsupervised clustering techniques and neural networks for colour quantisation. These techniques add flexibility and value to sorters in the minerals industry as they do not require a trained expert and so allow machines to be optimised by mine operators as conditions vary. The techniques also have an advantage as they complete the task of colour quantisation in a fraction of the time taken for an expert and so lend themselves well to the quick and efficient determination of automated sorting for a minerals application. Future research should focus on the advancement and application of neural networks to colour quantisation in conjunction with tradition training methods Further to this research should concentrate on practical applications utilising a multi-sensor, multi-output approach to automated sorting.

published_or_final_version / Computer Science / Master / Master of Philosophy

The improvement of blood cell sorting techniques in recent years have attracted the attention of many researchers due to the possible benefits that these methods can lead in biology, regenerative medicine, materials science and therapeutic area. In this work a cell sorting technique based on filtration is described. The separation occurs by means of a microfluidic device, suitably designed, manufactured and tested, that is connected to an external experimental set-up. The fabrication process can be divided in two parts: at first it is described the manufacturing process of a filtering membrane, with holes of specific size that allow the passage of only certain cell types. Following the microfluidic device is fabricated through the mechanical micromilling. The membrane and the microdevice are suitably bonded and tested by means of an external connection with syringe pumps that inject blood samples at specific flow rates. The device is designed to separate blood cells and tumor cells only by using differences in size and shape. In particular during the first experiments red blood cells and platelets are sorted from white blood cells; in the other experiments red blood cells and platelets are separated from white blood cells and tumor cells. The microdevice has proven to be very efficient, in fact a capture efficiency of 99% is achieved. For this reason it could be used in identification and isolation of circulating tumor cells, a very rare cancer cell type whose presence in the bloodstream could be symptom of future solid tumor formation. The various experiments have also demonstrated that tumor cells survive even after the separation treatment, and then the suffered stress during the sorting process does not harm the biological sample.

Applikationen Chemical Force Feedback (CFF) för haptisk och visuell molekylrendering som har utvecklats på Linköpings Universitet för att testa nyttan av haptik för undervisning av protein-ligand dockning för molekylär livsvetenskap behöver förbättras på ett antal punkter för att bättre kunna fungera som ett komplett molekylvisualiserings-verktyg. Tidigare projekt som utvecklat applikationen har fokuserat mestadels på den haptiska delen av programmet, vilket gjort att den visuella aspekten kommit efter. Det här examensarbetet har implementerat diverse ny funktionalitet både för att förbättra direkt kännbara aspekter av programmet, samt att lägga grunden för framtida utökningar. De huvudsakliga förbättringarna som det här exjobbet resulterat i inkluderar: För det första, integration av DSSP-algoritmen i programmet har gjort information om sekundärstrukturen hos protein tillgänglig för visualisering. För det andra, ett nytt renderings-system tillåter rendering av semitransparenta ytor på ett korrekt sätt samtidigt som det skapar en program-struktur som bättre lämpar sig för implementation av nya molekylrepresentationer. För det tredje, en filvals-komponent som fungerar i den haptiska scengrafen har designats för att göra programmets användargränssnitt mer tillgängligt. / The Chemical Force Feedback (CFF) visual and haptic molecule rendering application, being developed at Linköping University to evaluate the use of haptics as a teaching tool for protein-ligand docking in molecular life science requires several additional features to function as a mature protein visualization tool. Previous developments of the application have focused mostly on the haptic part of the program, leaving the visual representation somewhat under-developed. This thesis project has implemented various features in order to both improve the immediate functionality of the application as well as lay down the foundation for future additions. The main contributions of this thesis include: Firstly, integration of the DSSP algorithm has provided the application with secondary structure information for the protein visualization. Secondly, a new rendering system has provided support for rendering transparent surfaces in a correct way as well as simplifying future addition of new visual representations of molecules. Thirdly, a file-selection dialog have been implemented using the haptic scenegraph as a step toward the goal of making the user interface of the application more user-friendly.

A cross sectional study of 22 commercial free stall farms was conducted to investigate associations between feeding and housing practices, ration variability, and measures of productivity of group-housed dairy cows. Farms were visited for 7 consecutive days in both summer and winter to collect measures related to management, milk production, environment, and ration characteristics. Feeding 2x/d compared to 1x/d was associated with greater group-average milk yield, DMI and less sorting against long particles. Provision of increased feed bunk space was associated with increased milk fat% and lower group-average SCC. Higher daily variability in energy content and % long particles in the ration was associated with lower group-average milk yield and efficiency of milk production. Overall, these results suggest that herd-level feeding and housing practices which increase access to consistent feed can improve group-level productivity and ultimately improve herd profitability. / Dairy Farmers of Ontario, Canadian Dairy Commission, Agriculture and Agri-food Canada, OMAFRA, Canadian Foundation for Innovation, Ontario Research Fund

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This thesis concerns waste management on construction sites and was conducted on behalf of ICA Fastigheter. Areas of concern: How can an environmentally-efficient waste management system on construction sites be defined?  What potential exists for exploiting the waste resources that are generated? How can the waste management be optimised by reducing the quantity of waste and by optimal sorting? How can the client of a project influence the waste management? The purpose of the work was to investigate sustainable waste management in the building and construction sector and to highlight waste as a resource from an environmental and economic perspective.The aim of the work was to define an environmentally-efficient waste management system, to analyse the potential that exists in waste management and to draw up guidelines for optimal waste management.The method consisted of a literature study, two visits to construction sites and four interviews.An environmentally-efficient waste management system means that the waste is managed in the following order of priority: Prevention      Reuse   Recycling      Energy recovery Landfill      The prevention of waste is an important area that has not been adequately explored by the building and construction industry. The quantities of waste could decrease with the implementation of measures such as ordering materials in the dimensions required, prefabricated components, logistics centres with Just-In-Time deliveries, less and improved packaging and less wrapping. The reuse of waste materials and temporary apparatus as well as the use of a return pallet system are examples of reuse that reduces the quantities of waste. In most cases the source sorting work is a matter of course and the proportion going to landfill is down at a low level. The source sorting can be optimised by sorting all materials that can be reused and recycled to use them as a resource. The client of a project has great opportunities to influence the waste management in a sustainable direction by placing demands on the contractor. Demands can be placed on measures to reduce the quantities of waste, on a specific level of source sorting and on the reporting and monitoring of statistics.