128 research outputs found
Algorithms and Methods for Robust Processing and Analysis of Mass Spectrometry Data
Liquid chromatography-mass spectrometry (LC-MS) and mass spectrometry imaging (MSI) are two techniques that are routinely used to study proteins, peptides, and metabolites at a large scale. Thousands of biological compounds can be identified and quantified in a single experiment with LC-MS, but many studies fail to convert this data to a better understanding of disease biology. One of the primary reasons for this is low reproducibility, which in turn is partially due to inaccurate and/or inconsistent data processing. Protein biomarkers and signatures for various types of cancer are frequently discovered with LC-MS, but their behavior in independent cohorts is often inconsistent to that in the discovery cohort. Biomarker candidates must be thoroughly validated in independent cohorts, which makes the ability to share data across different laboratories crucial to the future success of the MS-based research fields. The emergence and growth of public repositories for MSI data is a step in the rightdirection. Still, many of those data sets remain incompatible one another due to inaccurate or incompatible preprocessing strategies. Ensuring compatibility between data generated in different labs is therefore necessary to gain access to the full potential of MS-based research. In two of the studies that I present in this thesis, we used LC-MS to characterize lymph node metastases from individuals with melanoma. Furthermore, my thesis work has resulted in two novel preprocessing methods for MSI data sets. The first one is a peak detection method that achieves considerably higher sensitivity for faintly expressed compounds than existing methods, and the second one is a accurate, robust, and general approach to mass alignment. Both algorithms deliberately rely on centroid spectra, which makes them compatible with most shared data sets. I believe that the improvements demonstrated by these methods can lead to a higher reproducibility in the MS-based research fields, and, ultimately, to a better understanding of disease processes
Das Haus des Sallust in Pompeji. Eine dreidimensionale archÀologische Dokumentation aus dem 19. Jahrhundert
Syftet med uppsatsen Àr att öka förstÄelsen för vilken betydelse kommunikation har för frontpersonalens reaktion pÄ en fusion mellan tjÀnsteföretag. Fusioner Àr ett vanligt förekommande bland dagens företag, sÄ Àven för tjÀnsteföretag. Frontpersonal anses vara sÀrskilt viktig i tjÀnsteföretag dÄ de i interaktion med företagets kunder förmedlar kvalitet. Vid fusion Àr det dÀrför viktigt att skapa förutsÀttningar för att tvÄ mötande personalgrupper tillsammans kan verka för fortsatt god kvalitet. Ett verktyg för att skapa sÄdana förutsÀttningar Àr kommunikation. Formell kommunikation kan anvÀndas till att skapa acceptans för en fusion och införa förÀndringar vid denna. En förutsÀttning för att frontpersonalen skall uppnÄ en högre förstÄelse har visat sig starkt beroende av möjligheten att föra tvÄvÀgskommunikation. Informell kommunikation har visats fungera som ett starkt stöd för att skapa acceptans och en positiv förestÀllning av en fusion. SÀrskilt viktig Àr den informella kommunikationen för att underlÀtta social integration.The purpose of the study is to increase understanding of the value of communication for first line staffs reactions to a merger between service organisations. Mergers are in modern age common between organisations and so also for service organisations. The first line staff are considered particularly important for service organisations due to their mediating role between company and customers where quality is transferred. At a merger it is therefore important to create conditions where two meeting personal groups together can continue to supply sufficient quality. A tool to create such conditions is communication. Formal communication can be used to create acceptance for a merger and to introduce changes in it. A prerequisite for front staff to achieve a higher understanding has proven to be highly dependent of the opportunity to conduct two-way communication. Informal communication has proven to function as strongly supportive in creating acceptance and a positive conception of a merger. Especially important is informal communication to facilitate social integration
Identifying deviations in forest databases by using data from satellite images
This thesis has focused on the possibility to use a satellite image method developed by Metria Mijöanalys to identify stands that are wrongly registered in Holmen Skogs database. The method is only intended for identifying stand with poor descriptions in Holmen's database that needs to be updated and not for updating the stand information.
The study area is located several km west of Hudiksvall on the borderline between GÀvleborgs- och VÀsternorrlands lÀn. The area is covered by a SPOT image from 2005. By which Metria Miljöanalys has made estimates of forest parameters for all stands in the area, and compared them with corresponding estimates according to the stand database. The stands in which the estimated and registered values differed more than a certain "threshold" value was marked as deviant. The total number of stands in the studies area is 8941, of which 1473 were marked as deviant.
To evaluate Metrias method, a number of random chosen stands marked as deviant where measured in field. Prior to the field inventory, the populations were divided into two strata, in one the populations marked as deviant and in the other strata, the rest. In both strata, a number of random stands were chosen. Most of the chosen stands were marked as deviant.
In this thesis, the method of using satellite images to estimate variables, such as volume and distribution of tree species, has been evaluated. The results show that at the threshold value used by Metria Miljöanalys (2*Ssat), about 25 % off all included stands were marked as deviant, of which about 50 % were truly deviant which corresponding to about 25 % of the truly deviant stands. The results also show that the method estimates the volume better than other variables. About 65 % of the stands registered as deviant in volume, truly was deviant. The time needed to measure all the 1090 stands marked as deviant by Metria Miljöanalys in field is about 3300 h.
Depending on the intentions with the method, two ways of working with the method can be chosen. A low threshold value gives a high number of deviant stands. This also means that a high number of stands that isn't truly deviant will be marked as deviant. On the opposite, a high threshold value will generate a lower number of stands marked as deviant. Of the stands marked as deviant, a higher number will be truly deviant. But this also means that a higher number of truly deviant stands won't be found. This thesis also shows that the method should be used to find deviant population, regardless of which variable that differ.Detta examensarbete har fokuserat pÄ att undersöka möjligheten att anvÀnda den satellitbildsmetod som utvecklats av Metria Miljöanalys för att identifiera felaktigt beskrivna bestÄnd i Holmen Skogs bestÄndsregister. Metoden Àr inte tÀnkt att anvÀndas för att uppdatera registret utan endast för att vÀlja ut bestÄnd som behöver ajourhÄllas i fÀlt. De variabler som ingÄtt i studien Àr volym (m3sk/ha) och trÀdslagsfördelning StudieomrÄdet ligger nÄgra mil vÀster om Hudiksvall pÄ grÀnsen mellan GÀvleborgs- och VÀstrnorrlands lÀn. OmrÄdet tÀcks av en SPOT-bild frÄn 2005, och med hjÀlp av den har Metria Miljöanalys tagit fram skattningar av de aktuella variablerna för samtliga bestÄnd och jÀmfört dem med motsvarande uppgifter frÄn det befintliga registret. De bestÄnd som hade en avvikelse större Àn ett visst tröskelvÀrde har dÀrefter markerats som felaktigt beskrivna i registret. Totalt omfattar Metrias analyser 8941 bestÄnd, varav 1473 markerats som felaktigt beskrivna. För att undersöka hur bra Metrias metod Àr pÄ att peka ut felaktigt beskrivna bestÄnd kontrollinventerades ett stickprov av dessa i fÀlt. Inför fÀltinventeringen delades bestÄnden in i tvÄ strata: ett som representerar de bestÄnd Metria markerat som felaktigt beskrivna och ett som representerar resterande bestÄnd. DÀrefter lottades ett antal bestÄnd ut i respektive strata. De flesta bestÄnd som kontrollinventerades tillhörde stratumet med potentiella felaktigt beskrivna bestÄnd, ett mindre antal inventerades Àven frÄn det andra stratumet, dvs bestÄnd som Àr korrekt beskrivna enligt satellitbildsmetoden. Vid fÀltinventeringen mÀttes grundyta per trÀdslag med relaskop, höjd med laserhöjdmÀtare samt diameter med mÄttband. Tester har utförts som visar hur stor andel av de felaktigt beskrivna bestÄnden i Holmens register som hittats med satellitbildsmetoden, hur mÄnga korrekt beskrivna bestÄnd som felaktigt pekats ut samt hur mÄnga av de felaktigt beskrivna bestÄnden som ej hittats. I testerna ingick att undersöka om satellitbildsmetoden Àr bÀttre pÄ att hitta fel i nÄgon av parametrarna volym och trÀdslagsblandning. Resultaten frÄn studien visar att vid det tröskelvÀrde som Metria Miljöanalys bedömt som rimligt (2*Ssat) utpekades ca 25 % av alla bestÄnd som felaktigt beskrivna i registret. Av dessa var ca 50 % ocksÄ felaktigt beskrivna enligt fÀltinventeringen, vilket motsvarar ca 25 % av det totala antalet bestÄnd som Àr felaktigt beskrivna i registret enligt fÀltinventeringen. Resultaten visar Àven att metoden var bÀst pÄ att hitta fel i totalvolymen, dÀr nÀstan 65 procent av bestÄnden som markerats som felaktigt beskrivna ocksÄ hade en felaktig totalvolym enligt fÀltinventeringen. TidsÄtgÄngen för att inventera de 1090 bestÄnd som satellitbildsmetoden identifierat som felaktigt beskrivet i registret vid ovan nÀmnda tröskelvÀrde Àr ca 3300 timmar. Beroende av vilken mÄlsÀttning man har med att anvÀnda sig av den framtagna satellitbildsmetoden för att hitta avvikelser i bestÄndsregistret sÄ finns olika alternativ att vÀlja mellan. Om man exempelvis vill inventera mycket och hitta flertalet av de felaktigt beskrivna bestÄnden i registret ska ett lÄgt tröskelvÀrd anvÀnds i satellitbildsmetoden. Detta betyder dock att ett stort antal korrekt beskrivna bestÄnd kommer att besökas i fÀlt. För att inte lÀgga ner alltför mycket tid pÄ att inventera bestÄnd i onödan bör grÀnsen för vilka bestÄnd som skall besökas i fÀlt lÀggas relativt högt. Detta leder dock till att man hittar fÀrre avvikelser i registret, men en stor del av de bestÄnd som inventeras Àr ocksÄ felaktigt beskrivna i registret. En annan slutsats som dragits Àr att metoden inte ger tillförlitlig information om vilken variabel som Àr felaktigt beskriven i registret
Virtual factory layouts from 3D laser scanning â A novel framework to define solid model requirements
In a world with increasing customer demands, manufacturing companies must develop and produce products more rapidly and adapt their production systems offline, to not disturb the ongoing processes. This creates a demand of using digital production development so that development can be performed in parallel with production. Virtual factory layouts (VFLs) are essential for companies in order to plan their factory layout and evaluate production scenarios. However, requirements for a VFL depends heavily on its purpose. For example, the requirements on a model for offline programming of robots are different from those on a model used to determine buffer locations. There is currently a lack of clear guidelines for how developed a VFL should be to fulfil said requirements, which contributes to unnecessary modelling time and variation in delivery quality. This paper aims to put the actual demands and requirements of a VFL in focus. By adapting a Level of Development-framework for establishment of Building Information Models (BIMs) and connecting it to the purpose of VFLs, development of a framework for detail and functionality level of VFLs is enabled. Such a purpose-oriented framework will help to define delivery packages suited for different circumstances, which will provide the modeler with knowledge of how much detail and functionality a specific model should contain. The increased clarity provided by the developed framework results in a clearer connection between expected result and actual output from a custom VFL project. Also, by connecting model properties or development to the model-purpose, the framework brings clarity and structure to a currently vague field. This provides means for a more efficient and accurate use of VFLs, which will support the rapid development of production facilities
Diastolic preparation for left ventricular ejection - A marker of inefficiency of the failing heart
AMS Collection Efficiencies of dry smog chamber aerosols, dependence on (NH4)2SO4, NH4NO3 and SOA fractions
Impact of dobutamine stress on diastolic energetic efficiency of healthy left ventricle: an in vivo kinetic energy analysis
The total kinetic energy (KE) of blood can be decomposed into mean KE (MKE) and turbulent KE (TKE), which are associated with the phase-averaged fluid velocity field and the instantaneous velocity fluctuations, respectively. The aim of this study was to explore the effects of pharmacologically induced stress on MKE and TKE in the left ventricle (LV) in a cohort of healthy volunteers. 4D Flow MRI data were acquired in eleven subjects at rest and after dobutamine infusion, at a heart rate that was âŒ60% higher than the one in rest conditions. MKE and TKE were computed as volume integrals over the whole LV and as data mapped to functional LV flow components, i.e., direct flow, retained inflow, delayed ejection flow and residual volume. Diastolic MKE and TKE increased under stress, in particular at peak early filling and peak atrial contraction. Augmented LV inotropy and cardiac frequency also caused an increase in direct flow and retained inflow MKE and TKE. However, the TKE/KE ratio remained comparable between rest and stress conditions, suggesting that LV intracavitary fluid dynamics can adapt to stress conditions without altering the TKE to KE balance of the normal left ventricle at rest
Visualization and quantification of 4D blood flow distribution and energetics in the right ventricle
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