High-resolution diffusion-weighted brain MRI under motion

Magnetic resonance imaging is one of the fastest developing medical imaging techniques. It provides excellent soft tissue contrast and has been a leading tool for neuroradiology and neuroscience research over the last decades. One of the possible MR imaging contrasts is the ability to visualize diffusion processes. The method, referred to as diffusion-weighted imaging, is one of the most common clinical contrasts but is prone to artifacts and is challenging to acquire at high resolutions. This thesis aimed to improve the resolution of diffusion weighted imaging, both in a clinical and in a research context. While diffusion-weighted imaging traditionally has been considered a 2D technique the manuscripts and methods presented here explore 3D diffusion acquisitions with isotropic resolution. Acquiring multiple small 3D volumes, or slabs, which are combined into one full volume has been the method of choice in this work. The first paper presented explores a parallel imaging driven multi-echo EPI readout to enable high resolution with reduced geometric distortions. The work performed on diffusion phase correction lead to an understanding that was used for the subsequent multi-slab papers. The second and third papers introduce the diffusion-weighted 3D multi-slab echo-planar imaging technique and explore its advantages and performance. As the method requires a slightly increased acquisition time the need for prospective motion correction became apparent. The forth paper suggests a new motion navigator using the subcutaneous fat surrounding the skull for rigid body head motion estimation, dubbed FatNav. The spatially sparse representation of the fat signal allowed for high parallel imaging acceleration factors, short acquisition times, and reduced geometric distortions of the navigator. The fifth manuscript presents a combination of the high-resolution 3D multi-slab technique and a modified FatNav module. Unlike our first FatNav implementation, using a single sagittal slab, this modified navigator acquired orthogonal projections of the head using the fat signal alone. The combined use of both presented methods provides a promising start for a fully motion corrected high-resolution diffusion acquisition in a clinical setting

Charging Phenomena at the Interface Between High-k Dielectrics and SiOx Interlayers, Journal of Telecommunications and Information Technology, 2010, nr 1

The transition regions of GdSiO/SiOx and HfO2/SiOx interfaces have been studied with the high-k layers deposited on silicon substrates. The existence of transition regions was verified by medium energy ion scattering (MEIS) data and transmission electron microscopy (TEM). From measurements of thermally stimulated current (TSC), electron states were found in the transition region of the HfO2/SiOx structures, exhibiting instability attributed to the flexible structural molecular network expected to surround the trap volumes. The investigations were focused especially on whether the trap states belong to an agglomeration consisting of a single charge polarity or of a dipole constellation. We found that flat-band voltage shifts of MOS structures, that reach constant values for increasing oxide thickness, cannot be taken as unique evidence for the existence of dipole layers

Live imaging of leukocyte recruitment in a zebrafish model of chemical liver injury

Studying early immune responses to organ damage in situ requires animal models amenable to intravital imaging. Here, we used transparent zebrafish larvae, a powerful animal model for innate immunity, to measure leukocyte recruitment to damaged livers. Bath application of metronidazole (Mtz) to fish expressing nitroreductase (NTR) under a liver-specific promoter damaged the organ within 24 hours causing oxidative stress, distorted liver morphology, accumulation of TUNEL-positive cells, and transcriptional upregulation of apoptotic and antioxidant genes. Inflammatory gene transcription in damaged hepatocytes was attenuated. In line with predominant apoptosis, macrophages were massively recruited into Mtz/NTR-damaged livers. By contrast, neutrophil infiltration was more variable and delayed, consistent with less abundant necrosis and an attenuated inflammatory capacity of damaged hepatocytes

Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals

Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors

Influence of Ocean Acidification on a Natural Winter-to-Summer Plankton Succession : First Insights from a Long-Term Mesocosm Study Draw Attention to Periods of Low Nutrient Concentrations

Every year, the oceans absorb about 30% of anthropogenic carbon dioxide (CO2) leading to a re-equilibration of the marine carbonate system and decreasing seawater pH. Today, there is increasing awareness that these changes-summarized by the term ocean acidification (OA)-could differentially affect the competitive ability of marine organisms, thereby provoking a restructuring of marine ecosystems and biogeochemical element cycles. In winter 2013, we deployed ten pelagic mesocosms in the Gullmar Fjord at the Swedish west coast in order to study the effect of OA on plankton ecology and biogeochemistry under close to natural conditions. Five of the ten mesocosms were left unperturbed and served as controls (similar to 380 mu atm pCO(2)), whereas the others were enriched with CO2-saturated water to simulate realistic end-of-the-century carbonate chemistry conditions (mu 760 mu atm pCO(2)). We ran the experiment for 113 days which allowed us to study the influence of high CO2 on an entire winter-to-summer plankton succession and to investigate the potential of some plankton organisms for evolutionary adaptation to OA in their natural environment. This paper is the first in a PLOS collection and provides a detailed overview on the experimental design, important events, and the key complexities of such a "long-term mesocosm" approach. Furthermore, we analyzed whether simulated end-of-the-century carbonate chemistry conditions could lead to a significant restructuring of the plankton community in the course of the succession. At the level of detail analyzed in this overview paper we found that CO2-induced differences in plankton community composition were non-detectable during most of the succession except for a period where a phytoplankton bloom was fueled by remineralized nutrients. These results indicate: (1) Long-term studies with pelagic ecosystems are necessary to uncover OA-sensitive stages of succession. (2) Plankton communities fueled by regenerated nutrients may be more responsive to changing carbonate chemistry than those having access to high inorganic nutrient concentrations and may deserve particular attention in future studies.Peer reviewe

Evaluating Response Images From Protein Quantification

Gyros Protein Technologies develops instruments for automated immunoassays. Fluorescent antibodies are added to samples and excited with a laser. This results in a 16-bit image where the intensity is correlated to concentration of bound antibody. Artefacts may appear on the images due to dust, fibers or other problems, which affect the quantification. This project seeks to automatically detect such artifacts by classifying the images as good or bad using Deep Convolutional Neural Networks (DCNNs). To augment the dataset a simulation approach is used and a simulation program is developed that generates images based on developed simulation models. Several classification models are tested as well as different techniques used for training. The highest performing classifier is a VGG16 DCNN, pre-trained on simulated images, which reaches 94.8% accuracy. There are many sub-classes in the bad class, and many of these are very underrepresented in both the training and test datasets. This means that not much can be said of the classification power of these sub-classes. The conclusion is therefore that until more of this rare data can be collected, focus should lie on classifying the other more common examples. Using the approaches from this project, we believe this could result in a high performing product

Evaluating Response Images From Protein Quantification

Gyros Protein Technologies develops instruments for automated immunoassays. Fluorescent antibodies are added to samples and excited with a laser. This results in a 16-bit image where the intensity is correlated to concentration of bound antibody. Artefacts may appear on the images due to dust, fibers or other problems, which affect the quantification. This project seeks to automatically detect such artifacts by classifying the images as good or bad using Deep Convolutional Neural Networks (DCNNs). To augment the dataset a simulation approach is used and a simulation program is developed that generates images based on developed simulation models. Several classification models are tested as well as different techniques used for training. The highest performing classifier is a VGG16 DCNN, pre-trained on simulated images, which reaches 94.8% accuracy. There are many sub-classes in the bad class, and many of these are very underrepresented in both the training and test datasets. This means that not much can be said of the classification power of these sub-classes. The conclusion is therefore that until more of this rare data can be collected, focus should lie on classifying the other more common examples. Using the approaches from this project, we believe this could result in a high performing product

Logistik i byggbranschen : För förbättrad arbetsmiljö och effektivitet

Logistics and supply chain management in the construction sector is an area with great potential for improvements. Today, a lot of the workers time is spent on non-value adding activities. Research has shown that waste is a large proportion of the total production cost in building projects today. The purpose of this report is to analyze problems concerning logistics in the construction sector. Two of Skanska’s construction projects in Uppsala have been analyzed to identify problems. The goal of the thesis is to suggest solutions regarding logistics that will improve the work environment and efficiency. The result shows that companies would benefit from using smart logistic services like just in time deliveries and third party logistics. Services like this should be used even if the circumstances of the project don’t require it, as they are conducive to a better working environment and heightened effectivity. Recommendations include having well defined routines and selecting a person responsible for receiving deliveries. Communication and cooperation with other parties in the supply chain is also important. Planning and any subsequent follow-ups have to be carried out effectively and efficiently. Logistik inom byggbranschen är ett område där det finns stora möjlig- heter för förbättringar och effektiviseringar. En stor andel av yrkesarbe- tarnas arbetstid går idag åt till icke värdeskapande aktiviteter. Under- sökningar har visat att endast 50 % av arbetstiden används till effektivt arbete. (Byggchefen, 2006) Det tillsammans med andra former av slöseri leder till stora kostnader. Slöseriet i byggprojekt uppskattas vara så stort som 30-35 % av projektetens produktionskostnad. (Josephson & Saukkoriipi, 2005) Syftet med examensarbetet är att genom intervjuer, enkäter och obser- vationer undersöka logistikproblem inom byggbranschen. Två av Skanskas byggprojekt i Uppsala undersöks i denna rapport för att iden- tifiera problem. Målet med examensarbetet är att ta fram lösningsför- slag som förbättrar arbetsmiljö och effektivitet genom förbättrade lös- ningar kring logistik. Rapporten visar att företag inom byggbranschen bör satsa på utomstå- ende tjänster med smarta logistiklösningar för att förbättra arbetsmiljö och effektivitet. Lösningar som kan användas är behovsstyrda leveran- ser och tredjepartslogistik med tjänster som sampackning, mellanlag- ring och inbärningstjänster. Tjänsterna kan vara bra att använda även då omständigheterna runt projektet ej kräver det eftersom det ger bättre arbetsmiljö och effektivitet. Rekommendationer ges till att ha tydliga rutiner och utse en ansvarig person för mottagning av material. Samarbete och kommunikation med övriga aktörer i försörjningskedjan är viktig. Även planering och upp- följning av denna är nödvändig för att logistiken ska kunna fungera på ett effektivt sätt.

Image-space navigators

This chapter explores existing solutions from the literature that utilize MR-based navigators operating in the image domain to provide estimates of motion. Some general considerations are discussed, along with the pros and cons of an image-based approach

Logistik i byggbranschen : För förbättrad arbetsmiljö och effektivitet

Logistics and supply chain management in the construction sector is an area with great potential for improvements. Today, a lot of the workers time is spent on non-value adding activities. Research has shown that waste is a large proportion of the total production cost in building projects today. The purpose of this report is to analyze problems concerning logistics in the construction sector. Two of Skanska’s construction projects in Uppsala have been analyzed to identify problems. The goal of the thesis is to suggest solutions regarding logistics that will improve the work environment and efficiency. The result shows that companies would benefit from using smart logistic services like just in time deliveries and third party logistics. Services like this should be used even if the circumstances of the project don’t require it, as they are conducive to a better working environment and heightened effectivity. Recommendations include having well defined routines and selecting a person responsible for receiving deliveries. Communication and cooperation with other parties in the supply chain is also important. Planning and any subsequent follow-ups have to be carried out effectively and efficiently. Logistik inom byggbranschen är ett område där det finns stora möjlig- heter för förbättringar och effektiviseringar. En stor andel av yrkesarbe- tarnas arbetstid går idag åt till icke värdeskapande aktiviteter. Under- sökningar har visat att endast 50 % av arbetstiden används till effektivt arbete. (Byggchefen, 2006) Det tillsammans med andra former av slöseri leder till stora kostnader. Slöseriet i byggprojekt uppskattas vara så stort som 30-35 % av projektetens produktionskostnad. (Josephson & Saukkoriipi, 2005) Syftet med examensarbetet är att genom intervjuer, enkäter och obser- vationer undersöka logistikproblem inom byggbranschen. Två av Skanskas byggprojekt i Uppsala undersöks i denna rapport för att iden- tifiera problem. Målet med examensarbetet är att ta fram lösningsför- slag som förbättrar arbetsmiljö och effektivitet genom förbättrade lös- ningar kring logistik. Rapporten visar att företag inom byggbranschen bör satsa på utomstå- ende tjänster med smarta logistiklösningar för att förbättra arbetsmiljö och effektivitet. Lösningar som kan användas är behovsstyrda leveran- ser och tredjepartslogistik med tjänster som sampackning, mellanlag- ring och inbärningstjänster. Tjänsterna kan vara bra att använda även då omständigheterna runt projektet ej kräver det eftersom det ger bättre arbetsmiljö och effektivitet. Rekommendationer ges till att ha tydliga rutiner och utse en ansvarig person för mottagning av material. Samarbete och kommunikation med övriga aktörer i försörjningskedjan är viktig. Även planering och upp- följning av denna är nödvändig för att logistiken ska kunna fungera på ett effektivt sätt.