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  • Engström, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Comparison of two HPLC columns: An attempt to improve analysis of carbohydrate-deficient transferrin2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    1ABSTRACTCarbohydrate-deficient transferrin (CDT) is a biomarker for excessive and long-running intake of alcohol. It is a form of transferrin called disialotransferrin that under normal circumstances is <2 % of total transferrin in human blood. An increase is seen when alcohol consumption exceeds450 g per week. CDT is analyzed in serum usinghigh performance liquid chromatography (HPLC) and UV/VIS detection. The purpose of this study was to investigate if an “in routine” method could be improved by switching columns.With ion exchange chromatography transferrin glycoforms are separated and quantified. The carbohydrate-deficient transferrin glycoforms have an isoelectric point between 5,7-5,9 that depends on the number of sialic acids on the molecule. With the use of a salt gradient and pH above the isoelectric point the glycoforms can beseparated depending on their affinity to the stationary phase. Batches with patient and control serum was first analyzed on the routine column Source 15Q PE and then on the alternative column Reprospher 200 SAX 5μm.Student’s t-test showed that the two methods’results correlated but were significantly different. A Bland-Altman plot illustrated differences between the two columns. High and low control serum values from Reprospher were lower than the accepted interval. In this study Reprospher’s stationary phase seemed to be affected to such an extent that stabile retention time, better resolution, and stabile values could not be achieved and because the information about the column was lacking an attempt to regeneratethe columnwas not conducted.

  • Lindblad, Linda
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Investigation of complement inhibition and blood coagulation by using Multiplate® and TEG® analyzer2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The complement system is a long and complicated event of reactions where activation leads to cleavage of different factors and ends with either inflammation or cell lysis.

        Recent studies have shown that the complement system and coagulation have some elements in common. Therefore in this study it was relevant to look at the inhibition of the complement system in two different whole blood analyses of coagulation activation, thromboelastography and impedance aggregometry. Thromboelastography, or TEG®, measures the clot forming properties of whole blood and the impedance aggregometry, or Multiplate®, measures platelets’ ability to adhere and aggregate to an electrode. Four different inhibitors where used: Eculizumab, C1 inhibitor, Compstatin and OMS721, which all inhibits different parts of the complement system.

        The curves from Multiplate® was presented in standard deviation and the number of reduction, while the results from TEG® was presented in before and after added inhibitor in graphs.

        In conclusion, impedance aggregometry show a more specific and secure results of the inhibitors effect, which was seen by that both C1 inihibitor and Compstatin had a major influence on the area under the curve (AUC). In TEG® there were no detectable difference, which could mean TEG® is not specific enough for platelets efficiency, which is affected by the complement inhibition.

  • Lindman, Elin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    A spectrophotometric method to analyze antibiotics in plasma: A validation study2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Antibiotic resistance is one of the most serious medical problems in the world. To counteract the increase in antibiotic resistance, new rapid and effective analytical methods are needed. To effectively treat infections in critically ill patients, optimal antibiotic dosages are required. DrugLog® is an instrument that uses a spectrophotometric method to analyze antibiotics in plasma in the wavelength range 200-800 nm. The aim of this study was to do a method validation of the instrument DrugLog®.

        The study material that was used was whole blood from healthy donor and routine citrate plasma samples from the laboratory. The precision of the method and stability of plasma, the best way to filtrate lipids from plasma and four antibiotics (meropenem, cefotaxime, vancomycin, piperacillin/tazobactam) were investigated.

        The precision of the method, measured as CV% was less than 0.62 and stability plasma showed a CV% of 135.74 after 24 h in room temperature. The stability for the different antibiotics after 24 h in room temperature showed a CV% of 8.11 for meropenem, 40.80 for vancomycin, 16.55 for cefotaxime and 2.92 for the combination antibiotic piperacillin/tazobactam. It was also determined that bacterial filter was the best way to remove lipids from plasma.

        In conclusion DrugLog® is a suitable instrument to analyze concentration of antibiotics in patients during antibiotic treatment, however further validations are needed. 

  • Öz, Diana
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Investigating distribution of DIO2 and MOT8 mRNA with quantitative reverse transcription-PCR and immunohistochemistry staining of endometrial and fallopian tube tissue2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Infertility is defined as not being able to conceive after 1 year of regular intercourse without use of contraception. Unexplained infertility is a diagnosis given to couples where the reason to infertility cannot be clarified even after the routine examination. Undefined infertility is a common and growing problem because most people are not aware of the fact that fertility decreases after the age of 35. Hyper- and hypothyroidism has been known to affect the menstrual cycle as well as increased risk of miscarriage. However, the specific effect of thyroid hormones on infertility has not yet been clarified. This study aims to compare the gene expression of two thyroid hormone receptors DIO2 and MOT8 in human endometrium and fallopian tube tissue from two phases of the menstruation cycle, follicular phase and lutheal phase. The methods used were RT-qPCR and immunohistochemistry, which showed a statistically significant difference in the expression of DIO2 and MOT8 between fallopian tube tissue and endometrium, but not between follicular and lutheal phase. However, MOT8 seemed to have a tendency to be down-regulated in the follicular phase but the results need to be validated with different endogenous controls and larger study groups.

  • Bouro Wallgren, Sofia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Tolerance to virus infections could explain increased winter colony survival observed in Varroa destructor-resistant honey bees2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Honey bee colonies all over Europe and North America have been declining dramatically for over three decades and is continuing to do so which is causing significant threats to economy, agriculture and ecosystems. The main reason behind the declining colonies is an ectoparasitic mite known as Varroa destructor and viruses vectored by the mite. In previous studies, it has been suggested that a unique mite-resistant subpopulation of honey bees (Apis mellifera) in Gotland, Sweden have developed adaptive tolerance to these viruses as they have managed to survive high mite infestation through natural selection without any mite control treatment. This indicates that there might be a correlation between resistance to Varroa destructor and virus tolerance. This project examined if a correlation between virus resistance and/or virus tolerance can be observed in Varroa-resistant honey bees from unique subpopulations in Europe covering Sweden, Norway, France and Netherlands. Results showed that no correlation could be established based on the findings in this project. However, significant differences in winter colony survival numbers between mite-resistant and mite-susceptible honey bees suggest that tolerance mechanisms could be present in these subpopulations. Further studies are required to verify this hypothesis.

  • Pilebro Lappalainen, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    A new quick method for screening of HPA-1 based on fluorescence conjugated antibodies2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Human platelet antigens (HPA) is located on the platelet surface and they are inherited both from the mother and the father. If a mother who is homozygous for HPA-1b carries a child who has inherited HPA-1a from the father, the mother is in danger to form antibodies against HPA-1a on the fetal platelet. This may cause the child to suffer from neonatal alloimmune thrombocytopenia (NAIT) that could lead to death. This can be prevented by platelet transfusion. EVA Biosensor Technology is a new method for detection of HPA-1 that is currently only approved for scientific research. The aim of this study was to evaluate EVAreader R6 and find HPA-1a negative platelet donors that can donate platelets to children born with NAIT. The test material consisted of blood samples from 513 male blood donors with blood group 0. The blood was lysed and tested in EVA-reader R6 from Davos Diagnostics. The result was shown on the screen after 10 min. The results that came out negative or intermediate was analyzed a second time. In total, nine HPA-1a negative donors and 503 HPA-1a positive donors were found. Approximately 2 % of the population is HPA-1a negative, which was reflected in the result. To make sure that the results are correct, a validation with an already existing method has to be made. The conclusion is that the EVA Biosensor Technology could be used for typing of HPA in the future, as long as the results from the validation is correct.

  • Johansson, Isabelle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    The Effect of Contrast Media on Several Common Laboratory Assays2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Contrast media are commonly used as an enhancement in several diagnostic imaging methods, which in today’s healthcare often are combined with blood works in diagnostics and surgical preparations, as well as to follow up on the patient’s recovery. To save time and money for both the hospital and the patients themselves, the ability to carry out both the radiological examination and the blood works within the same hospital visit would be preferred. However, there have been indications of a potential interference from the contrast media used, and therefore a waiting period is in place. The aim of this study was therefore to see if that waiting period was warranted by testing if contrast media does cause a significant interference in the most common analyses. This was investigated by infusing pooled samples with either iohexol or gadoteric acid, the active components of the most common contrast agents, at either a full dosage or a half dosage. These samples were then run by standard protocol and the results compared to control samples. The results showed that while some analyses proved affected, others proved unaffected or only insignificantly so. Some of the affected analyses were sodium, activated partial thrombin time and hemoglobin. While some analyses such as prostate specific antigen and prothrombin time were unaffected. Analysis of more samples is necessary to confirm the results, but the overall consensus is that while most analyses are unaffected the effects are too large and uncertain to comfortably disregard the waiting time.

  • Salih, Baraah
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    A comparative study of immunofluorescence, zinc sulphate centrifugal flotation and FASTest®GIARDIA strip for detection of Giardia in dogs and cats2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Giardia intestinalis is the most common parasite found in dogs and cats. It is traditionally diagnosed using a microscope. These methods include direct immunofluorescence, DIF, and zinc sulphate centrifugal flotation, ZnSO4 C-flotation. However, there are commercially available SNAP tests such as the FASTest® GIARDIA strip that is often used by dogs and cats owner to detect Giardia. The aim of this study was to compare the sensitivity, cost and labor intensity of these three methods for detection of Giardia. To investigate this, 150 samples from dogs and cats were examined at the National Veterinary Institute in Sweden. The samples were a mixture of diarrheic and non-diarrheic stool. Of the 150 stool samples 100 samples were examined with FASTest® GIARDIA strip while 150 samples were examined with DIF and ZnSO4 C-flotation. The results indicated that FASTest® GIARDIA strip had a sensitivity of 66.18 %, a cost of 100 Swedish crowns (SEK) per sample and was the easiest test to use. ZnSO4 C-flotation had a sensitivity of 89.90 %, cost 418.75 SEK and took about 15 minutes to perform. DIF had 100 % sensitivity and specificity and due to that it was used as a standard reference method. The cost for DIF was 300 SEK and took more than an hour to perform per sample. The conclusion from this study is that, FASTest® GIARDIA strip is not a recommended test for detection of Giardia despite their low cost and easiness to use. DIF and ZnSO4 C-flotation remain a better diagnostic option for detection of Giardia.

  • Svensson, Karolina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    Södergren, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    Andersson, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    Klintberg, Lena
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    Hjort, Klas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Microsystems Technology.
    High-pressure microfluidic electrochemical and image analysis dual detection for HPLC2018Conference paper (Other academic)
    Abstract [en]

    High-performance liquid chromatography (HPLC) is often set as the lab-based golden standard. For point-of-care and point-of-site applications, making HPLC portable, easy to use and low cost, is very desirable. To reach lower costs, one important task is the development of suitable detectors. Because of the potential for low cost and high performance, a dual-detection microfluidic chip with an electrochemical detector (ECD) and optical access for image analysis was evaluated at high pressure, downstream an HPLC column. For the image analysis, a camera and near-UV-light was used to extract absorption data. To validate the response, a spectrometer was coupled downstream the chip. The results of the three different detectors were comparable, with the camera providing similar absorbance-time chromatograms as the spectrometer. However, the ECD registered only peaks from one of two analytes. To conclude, this experimental setup has potential to provide better understanding of the capability for microfluidic HPLC systems.

  • Csonka, Enikö
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health).
    Method verification for aldosterone and renin assay - a reliable screening test for primary aldosteronism2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Primary aldosteronism (PA) is a common form of secondary hypertension with an international prevalence rates between 5 and 10 %. It is characterized by a high autonomous aldosterone production that causes cardiovascular damage, renin suppression, hypertension, sodium retention, potassium excretion and hypokalemia. The screening of PA is a simple test measuring aldosterone to renin ratio (ARR) with immunoassay method. This test is currently considered as the most reliable screening tool for PA.

        The main objective of the study was to evaluate an ELISA-method, for detection of aldosterone and renin in blood plasma, to be used for routine analysis in the laboratory. The second aim was to investigate the effect of refreezing samples, considering that cryoactivation of prorenin might occur.

        One hundred blood samples were analysed, in regard to aldosterone and renin, by using two commercial ELISA assays (DRG ELISA from DRG Diagnostics, Germany) on a Dynex DS2 instrument. In addition, the accuracy and precision of the methods were calculated. The effect of refreezing was investigated with a series of eight samples, which were analyzed twice on the same instrument.

        Both assays performed well. The resulting data showed good precision and accuracy. The correlation between the original and refreezed samples was good, r = 0.989 and r = 1.0 for aldosterone and renin respectively. Considering that the study only included eight samples, further investigation is recommended.

        Evaluation showed that both immunoassays are reliable in diagnostic use and the ELISA-method is suitable to implement in the laboratory for routine analysis.

  • Hammarbäck, Madelene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Development of a dynamic ex vivo culture system for human islets of langerhans2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Type 1 diabetes(T1D)is a disease that only gets more common. The etiology of the disease is not known but there are many existing theories about what the cause is. These different theories have been tested in vivoin rodents or invitro. The resultsfrom experiments done in those waysarenotall realistic because rodents differnotablyfrom humans,and when studies areperformed in vitrowith human isletsof Langerhans different hormones will accumulate. The aim of this studywas to establisha dynamic ex vivosystem in which stimulation of human islets of Langerhans can be performed in a more lifelike environment. To study islets in this system couldin the future lead to increased knowledge in the etiology of T1D.The perifusion system PERI-4.2 from Biorep Technologies together with an incubator with 37°Cand5% CO2were used to arrangethe ex vivosystem. An Insulin ELISA from Mercodia was performedto analyze the insulin secretion from the islets. Fourdifferent set ups for the system were tested and the last one showed the best results.In conclusion this study has shown that it is possible to preserve human islets of Langerhans in a dynamic ex vivosystem with a constant medium exchange if it is done under conditionswhere the islets are protected from shear forces from the supplying medium,together with a medium exchange rate which replaces the whole medium in at least one hour.

  • Stigers, Linnea
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Evaluation of Escherichia coli probiotic candidates for combating EHEC in the food chain using competition analysis in bovine feces2018Independent thesis Advanced level (professional degree), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Enterohemorrhagic E. coli, EHEC, is a verotoxin producing, zoonotic pathogen, which causes diseases in humans such as bloody or watery diarrhea. Microorganisms compete for limited living space, nutrients and other resources and therefore other microorganisms are EHECs biggest competitors. To avoid outbreaks and infections with EHEC, one possible approach is to use harmless but competitive bacteria as probiotics. Therefore, the aim of this study was to evaluate three probiotic E. coli strains and their ability to outcompete EHEC in bovine feces.

        Ten different cattle fecal samples from three different farms were used to mix with the three probiotic and EHEC strains. The mixture was diluted and cultivated at 0 h as a control and then incubated for 48 h at 20°C and 37°C before dilution and cultivation on CT-SMaC. Colonies was counted and ratios between EHEC and probiotic E. coli before and after incubation were calculated. Kruskal-Wallis test with Dunn’s test as post hoc test were used to see if observed reductions of EHEC were significant or not.

        In 37°C, strain 10 was the only strain producing a significant reduction of EHEC. In contrast, no significant reduction was observed at 20°C in any of the strains.

        Future research studying other factors and performed on live cattle models are necessary to confirm the usefulness of the studied probiotic candidates. However, these results indicate probiotics can be a useful tool to avoid infections and big outbreaks of EHEC in the future.

  • Wallert, John
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Gustafson, Emelie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Held, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, UCR-Uppsala Clinical Research Center. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Madison, Guy
    Department of Psychology, Umeå University, Umeå, Sweden.
    Norlund, Fredrika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    von Essen, Louise
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Olsson, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Clinical Psychology in Healthcare.
    Predicting Adherence to Internet-Delivered Psychotherapy for Symptoms of Depression and Anxiety After Myocardial Infarction: Machine Learning Insights From the U-CARE Heart Randomized Controlled Trial2018In: Journal of Medical Internet Research, ISSN 1438-8871, E-ISSN 1438-8871, Vol. 20, no 10, article id e10754Article in journal (Refereed)
    Abstract [en]

    Background: Low adherence to recommended treatments is a multifactorial problem for patients in rehabilitation after myocardial infarction (MI). In a nationwide trial of internet-delivered cognitive behavior therapy (iCBT) for the high-risk subgroup of patients with MI also reporting symptoms of anxiety, depression, or both (MI-ANXDEP), adherence was low. Since low adherence to psychotherapy leads to a waste of therapeutic resources and risky treatment abortion in MI-ANXDEP patients, identifying early predictors for adherence is potentially valuable for effective targeted care.

    Objectives: The goal of the research was to use supervised machine learning to investigate both established and novel predictors for iCBT adherence in MI-ANXDEP patients.

    Methods: Data were from 90 MI-ANXDEP patients recruited from 25 hospitals in Sweden and randomized to treatment in the iCBT trial Uppsala University Psychosocial Care Programme (U-CARE) Heart study. Time point of prediction was at completion of the first homework assignment. Adherence was defined as having completed more than 2 homework assignments within the 14-week treatment period. A supervised machine learning procedure was applied to identify the most potent predictors for adherence available at the first treatment session from a range of demographic, clinical, psychometric, and linguistic predictors. The internal binary classifier was a random forest model within a 3×10–fold cross-validated recursive feature elimination (RFE) resampling which selected the final predictor subset that best differentiated adherers versus nonadherers.

    Results: Patient mean age was 58.4 years (SD 9.4), 62% (56/90) were men, and 48% (43/90) were adherent. Out of the 34 potential predictors for adherence, RFE selected an optimal subset of 56% (19/34; Accuracy 0.64, 95% CI 0.61-0.68, P<.001). The strongest predictors for adherence were, in order of importance, (1) self-assessed cardiac-related fear, (2) sex, and (3) the number of words the patient used to answer the first homework assignment.

    Conclusions: For developing and testing effective iCBT interventions, investigating factors that predict adherence is important. Adherence to iCBT for MI-ANXDEP patients in the U-CARE Heart trial was best predicted by cardiac-related fear and sex, consistent with previous research, but also by novel linguistic predictors from written patient behavior which conceivably indicate verbal ability or therapeutic alliance. Future research should investigate potential causal mechanisms and seek to determine what underlying constructs the linguistic predictors tap into. Whether these findings replicate for other interventions outside of Sweden, in larger samples, and for patients with other conditions who are offered iCBT should also be investigated.

  • Drobin, Kimi
    et al.
    Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden.
    Assadi, Ghazaleh
    Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
    Hong, Mun-Gwan
    Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden.
    Andersson, Eni
    Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden.
    Fredolini, Claudia
    Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden.
    Forsström, Björn
    Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden.
    Reznichenko, Anna
    Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
    Akhter, Tahmina
    Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
    Ek, Weronica E
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
    Bonfiglio, Ferdinando
    Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden;Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, San Sebastián, Spain.
    Berner Hansen, Mark
    AstraZeneca R&D Mölndal, Innovative and Global Medicines, Mölndal, Sweden;Digestive Disease Center, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark.
    Sandberg, Kristian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
    Greco, Dario
    Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
    Repsilber, Dirk
    School of Medical Sciences, Örebro University, Örebro, Sweden.
    Schwenk, Jochen M.
    Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden.
    D’Amato, Mauro
    Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden;BioDonostia Health Research Institute, San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
    Halfvarson, Jonas
    Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci2018In: Inflammatory Bowel Diseases, ISSN 1078-0998, E-ISSN 1536-4844Article in journal (Refereed)
    Abstract [en]

    Background: Few studies have investigated the blood proteome of inflammatory bowel disease (IBD). We characterized the serum abundance of proteins encoded at 163 known IBD risk loci and tested these proteins for their biomarker discovery potential.

    Methods: Based on the Human Protein Atlas (HPA) antibody availability, 218 proteins from genes mapping at 163 IBD risk loci were selected. Targeted serum protein profiles from 49 Crohn’s disease (CD) patients, 51 ulcerative colitis (UC) patients, and 50 sex- and age-matched healthy individuals were obtained using multiplexed antibody suspension bead array assays. Differences in relative serum abundance levels between disease groups and controls were examined. Replication was attempted for CD-UC comparisons (including disease subtypes) by including 64 additional patients (33 CD and 31 UC). Antibodies targeting a potentially novel risk protein were validated by paired antibodies, Western blot, immuno-capture mass spectrometry, and epitope mapping.

    Results: By univariate analysis, 13 proteins mostly related to neutrophil, T-cell, and B-cell activation and function were differentially expressed in IBD patients vs healthy controls, 3 in CD patients vs healthy controls and 2 in UC patients vs healthy controls (q < 0.01). Multivariate analyses further differentiated disease groups from healthy controls and CD subtypes from UC (P < 0.05). Extended characterization of an antibody targeting a novel, discriminative serum marker, the laccase (multicopper oxidoreductase) domain containing 1 (LACC1) protein, provided evidence for antibody on-target specificity.

    Conclusions: Using affinity proteomics, we identified a set of IBD-associated serum proteins encoded at IBD risk loci. These candidate proteins hold the potential to be exploited as diagnostic biomarkers of IBD.

  • Gamstedt, E. Kristofer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Afshar, Reza
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Ahlgren, Anders
    Swedish National Maritime Museums, the Vasa Museum, Stockholm, Sweden.
    Preserving the Vasa ship: Research and development of a new support structure2018Conference paper (Other academic)
  • Kullberg, Christina
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Modern Languages, Romance Languages.
    Le Vernaculaire: A Brief Lexical History in French2018In: World Literatures: Exploring the Cosmopolitan-Vernacular Exchange / [ed] Stefan Helgesson, Yvonny Lindqvist, Annika Mörte-Alling, Helena Wulff, Stockholm: Stockholm University Press, 2018, p. 19-30Chapter in book (Refereed)
    Abstract [en]

    This article traces French early modern understandings of the word vernacular in order to see what kinds of conceptual possibilities lie in the very history of the word. The investigation takes its cue from what could be identified as a quest for the moment of emergence of literatures within recent theories of world literature, a search in which the notion of the vernacular has come to play a crucial role. By investigating the etymology of the word based on a corpus of major dictionaries and encyclopedias from the seventeenth up to the nineteenth centuries, and the ways in which the vernacular has been used since its first appearance in French in Rabelais’ Le Quart livre(1542) and how it has evolved in early modern times, this study will problematise the systemic understanding of vernacularisation in terms of localizable moments and constant power struggles and explore other possible interpretations of what the vernacular may mean.

  • Tavares da Costa, Marcus Vinicius
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Bolinsson, Jessica
    Tetra Pak AB, DSO Packaging Materials, Lund, Sweden.
    Fayet, Pierre
    Adhemon Sarl, Thin Technology, Lausanne, Switzerland.
    Gamstedt, E. Kristofer
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Experimental and numerical investigations to assess the interfacial strength of the ultrathin coatings on polymers substrates2018Conference paper (Refereed)
    Abstract [en]

    Metal coating with a nanometer scale thickness on flexible polymer substrates is an interesting combination for food packaging applications. This combination provides an enhancement of the barrier performance in the carton package [1, 2]. A concern is the cracking of the brittle coating when subjected to tension and bending in the manufacturing process. Such cracks can affect the permeability. In this study, the coatings were produced by atomic layer deposition of metal oxides, with thickness values between 4 and 20 nanometers on poly(ethylene terephthalate) substrate films.

    The interfacial strength between coating and substrate is known to affect the crack formation. We have used an experimental technique known as the Fragmentation test (see e.g. Ref. [3]) and an analytical model to quantify the interfacial strength. The fragmentation test was performed by in situ tensile loading in a scanning electron microscope stage to track the crack accumulation and subsequently to calculate interfacial shear strength. As the scanning electron and atomic force microscopy is becoming easier to use and more cost efficient, increased local information on crack geometry can be obtained. In this work, we explore a mixed numerical-experimental method to quantify the interfacial strength based on observed delamination emanating from coating cracks, as schematically outlined in the figure. The results from this alternative method are compared with those from the more established fragmentation test. The advantages and disadvantages of the two methods are discusses, as well as the accuracy of the assumptions in their underlying models.

  • Public defence: 2018-12-20 13:15 Rosénsalen, Uppsala
    Georgantzi, Kleopatra
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Neuropediatrics/Paediatric oncology.
    On the Diagnostics of Neuroblastoma: Clinical and Experimental Studies2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Neuroblastoma (NB) is one of the most common childhood cancers. Patients with low stage tumor have high survival rate, while those with advanced stage and/or unfavorable molecular biology have poor prognosis. A correct histopathological diagnosis, clinical stage, and identified genetic aberrations are crucial for treatment stratification according to current protocol. The tumor sample is obtained either by fine needle aspiration, cutting needle biopsy or open biopsy. NB exhibits neuroendocrine differentiation by showing immunoreactivity for chromogranin A (CgA), synaptophysin (syn), and neuron specific enolase (NSE) and 90% of the patients have increased levels of urine catecholamine metabolites.

    Experimental and clinical NB tumor samples were immunostained for somatostatin receptors (SSTRs) 1-5, somatostatin and CgA. Clinical tumor samples were also immunostained for syn, synaptic vesicle protein 2 (SV2), and vesicle monoamine transporter 1 (VMAT1) and 2 (VMAT 2). Blood samples from 92 patients were analyzed for level of CgA, NSE, and chromogranin B and compared with control groups. The urinary excretion of catecholamine metabolites was analyzed in samples collected at diagnosis. Clinical and laboratory data were extracted from patient records, including information on the diagnostic accuracy of ultrasound guided cutting needle biopsies (UCNB) and potential complications.

    We found that NB expressed the different SSTRs and that receptor 2 was the most frequently expressed before chemotherapy. Furthermore, NB tumors showed immunoreactivity for SV2, VMAT 1 and VMAT2 alongside CgA and syn. The immunoreactivity of SV2 was comparable to CgA and superior to syn. Patients with NB had higher blood concentrations of CgA and NSE compared with controls. Patients with advanced stage disease, MYCN amplification and 1 p deletion had higher concentrations of both CgA and NSE while only NSE was correlated to outcome with higher concentrations in the deceased patients.

    A high urinary excretion of homovanillic acid and dopamine were correlated to inferior outcome. UCNB were found to be safe and may provide all necessary diagnostic requirements for adequate therapy stratification according to current treatment protocols.

    List of papers
    1. Differentiated expression of somatostatin receptor subtypes in experimental models and clinical neuroblastoma
    Open this publication in new window or tab >>Differentiated expression of somatostatin receptor subtypes in experimental models and clinical neuroblastoma
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    2011 (English)In: Pediatric Blood & Cancer, ISSN 1545-5009, E-ISSN 1545-5017, Vol. 56, no 4, p. 584-589Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND:

    Neuroblastoma (NB) is a solid tumor of childhood originating from the adrenal medulla or sympathetic nervous system. Somatostatin (SS) is an important regulator of neural and neuroendocrine function, its actions being mediated through five specific membrane receptors. The aim of this study was to investigate the expression of the different somatostatin receptors (SSTRs) in NB tumor cells that may form targets for future therapeutic development.

    PROCEDURE:

    Tumor specimens from 11 children with stage II-IV disease were collected before and/or after chemotherapy. Experimental tumors derived from five human NB cell lines were grown subcutaneously in nude mice. Expression of SSRTs, the neuroendocrine marker chromogranin A (CgA) and SS was detected by immunohistochemistry using specific antibodies.

    RESULTS:

    SSTR2 was detected in 90%, SSTR5 in 79%, SSTR1 in 74%, SSTR3 in 68% whereas SSTR4 was expressed in 21% of the clinical tumors. The experimental tumors expressed SSTRs in a high but variable frequency. All clinical tumors showed immunoreactivity for CgA but not for SS.

    CONCLUSION:

    The frequent expression of SSTRs indicates that treatment with unlabeled or radiolabeled SS analogs should be further explored in NB.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-140509 (URN)10.1002/pbc.22913 (DOI)000287986700013 ()21120894 (PubMedID)
    Available from: 2011-01-05 Created: 2011-01-05 Last updated: 2018-10-31
    2. Chromogranin A and neuron-specific enolase in neuroblastoma: Correlation to stage and prognostic factors.
    Open this publication in new window or tab >>Chromogranin A and neuron-specific enolase in neuroblastoma: Correlation to stage and prognostic factors.
    Show others...
    2018 (English)In: Pediatric Hematology & Oncology, ISSN 0888-0018, E-ISSN 1521-0669, Vol. 35, no 2, p. 156-165Article in journal (Refereed) Published
    Abstract [en]

    Chromogranin A (CgA) and neuron specific enolase (NSE) are important markers in adult neuroendocrine tumors (NET). Neuroblastoma (NB) has certain neuroendocrine properties. The aim of this study was to correlate blood concentrations of CgA, chromogranin B (CgB), and NSE to prognostic factors and outcome in children with NB. Blood samples from 92 patients with NB, 12 patients with benign ganglioneuroma (GN), 21 patients with non-NB solid tumors, 10 patients with acute leukemias, and 69 healthy children, were analyzed. CgA concentrations were higher in neonates vs. children older than one month in the control group (p < 0.0001), and in neonates with NB vs. the control group (p < 0.01). CgA and NSE concentrations were higher in patients with stages 3 and 4 disease (p < 0.05 and p < 0.05), in patients having tumors with amplification of MYCN (p < 0.05 and p < 0.001), or chromosome 1 p deletion (p < 0.05 and p < 0.05). NSE correlated to the tumor size at diagnosis (p < 0.001) and to tumor related death (p < 0.01) in NB. CgA and NSE concentrations were elevated in patients with NB and especially in those with advanced disease. Both CgA and NSE correlated to genetic markers, while only NSE correlated to primary tumor size and outcome in NB. We found that CgA and NSE are clinically valuable tumor markers in NB and they merit prospective clinical evaluations as such.

    Keywords
    Chromogranin A, neuroblastoma, neuron-specific enolase, prognosis, tumor markers
    National Category
    Cancer and Oncology
    Identifiers
    urn:nbn:se:uu:diva-360970 (URN)10.1080/08880018.2018.1464087 (DOI)000446356300007 ()29737901 (PubMedID)
    Funder
    Swedish Childhood Cancer Foundation
    Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-12-07Bibliographically approved
    3. Synaptic Vesicle Protein 2 and Vesicular Monoamine Transporter 1 and 2 are expressed in Neuroblastoma
    Open this publication in new window or tab >>Synaptic Vesicle Protein 2 and Vesicular Monoamine Transporter 1 and 2 are expressed in Neuroblastoma
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    neuroblastoma, neuroendocrine, immunohistochemistry, urine-dopamine, urine-HVA, urine-VMA
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-364674 (URN)
    Available from: 2018-10-31 Created: 2018-10-31 Last updated: 2018-10-31
    4. Diagnostic Ultrasound-Guided Cutting Needle Biopsies in Neuroblastoma: a safe and efficient procedure
    Open this publication in new window or tab >>Diagnostic Ultrasound-Guided Cutting Needle Biopsies in Neuroblastoma: a safe and efficient procedure
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    ultrasound, biopsy, neuroblastoma, complications, child
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-364673 (URN)
    Available from: 2018-10-31 Created: 2018-10-31 Last updated: 2018-10-31
  • Mathieu, Emilie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Sipos, Agnes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Demeyere, Ellen
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Phipps, Dulcie
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Sakaveli, Dimitra
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Borbas, K. Eszter
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Lanthanide-based tools for the investigation of cellular environments2018In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, no 72, p. 10021-10035Article, review/survey (Refereed)
    Abstract [en]

    Biological probes constructed from lanthanides can provide a variety of readout signals, such as the luminescence of Eu(III), Tb(III), Yb(III), Sm(III) and Dy(III), and the proton relaxation enhancement of Gd(III) and Eu(II). For numerous applications the intracellular delivery of the lanthanide probe is essential. Here, we review the methods for the intracellular delivery of non-targeted complexes (i.e. where the overall complex structure enhances cellular uptake), as well as complexes attached to a targeting unit (i.e. to a peptide or a small molecule) that facilitates delivery. The cellular applications of lanthanide-based supramolecules (dendrimers, metal organic frameworks) are covered briefly. Throughout, we emphasize the techniques that can confirm the intracellular localization of the lanthanides and those that enable the determination of the fate of the probes once inside the cell. Finally, we highlight methods that have not yet been applied in the context of lanthanide-based probes, but have been successful in the intracellular delivery of other metal-based probes.

  • Yang, Yukai
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Statistics.
    Bauwens, Luc
    State-space models on the Stiefel manifold with a new approach to nonlinear filtering2018Report (Other academic)
    Abstract [en]

    We develop novel multivariate state-space models wherein the latent states evolve on the Stiefel manifold and follow a conditional matrix Langevin distribution.The latent states correspond to time-varying reduced rank parameter matrices, like the loadings in dynamic factor models and the parameters of cointegrating relations in vector error-correction models. The corresponding nonlinear filtering algorithms are developed and evaluated by means of simulation experiments.

  • Thomas, Mathew
    et al.
    Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Kleese-van Dam, Kerstin
    Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Marshall, Matthew J.
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Kuprat, Andrew
    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Carson, James
    Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas, USA.
    Lansing, Carina
    Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Guillen, Zoe
    Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Miller, Erin
    Radiation Detection and Nuclear Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Lanekoff, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Laskin, Julia
    Fundamental and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
    Towards Adaptive, Streaming Analysis of X-ray Tomography Data2015In: Synchrotron Radiation News, ISSN 0894-0886, E-ISSN 1931-7344, Vol. 28, no 2, p. 10-14Article in journal (Refereed)
    Abstract [en]

    Temporal and spatial resolution of chemical imaging methodologies such as X-ray tomography are rapidly increasing, leading to more complex experimental procedures and fast-growing data volumes. Automated analysis pipelines and big data analytics are becoming essential to effectively evaluate the results of such experiments. Offering those data techniques in an adaptive, streaming environment can further substantially improve the scientific discovery process by enabling experimental control and steering based on the evaluation of emerging phenomena as they are observed by the experiment. Pacific Northwest National Laboratory (PNNL)'s Chemical Imaging Initiative (CII, http://imaging.pnnl.gov/) has worked since 2011 towards developing a framework that allows users to rapidly compose and customize high-throughput experimental analysis pipelines for multiple instrument types. The framework, named “Rapid Experimental Analysis” (REXAN) Framework [1M. Thomas, 3D imaging of microbial biofilms: Integration of synchrotron imaging and an interactive visualization interface, Engineering in Medicine and Biology Society (EMBC), 2014 36th Annual International Conference of the IEEE, Chicago, IL, August 28 (2014). [Google Scholar]], is based on the idea of reusable component libraries and utilizes the PNNL-developed collaborative data management and analysis environment “Velo” to provide a user-friendly analysis and data management environment for experimental facilities. This article will discuss the capabilities established for X-ray tomography, review lessons learned, and provide an overview of our more recent work in the Analysis in Motion Initiative (AIM, http://aim.pnnl.gov/) at PNNL to provide REXAN capabilities in a streaming environment.

  • Lanekoff, Ingela
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Laskin, Julia
    Physical Sciences Division, Pacific Northwest National Laboratory, Richland, USA.
    Quantitative Mass Spectrometry Imaging of Molecules in Biological Systems2018In: Advances In Chromatography, Vol 54 / [ed] Grushka, E; Grinberg, N, Boca Raton: CRC Press, 2018, p. 43-72Chapter in book (Other academic)
  • Ravindran, Avinash
    et al.
    Karolinska Univ Hosp, Karolinska Inst, Dept Med Solna, Immunol & Allergy Unit, Stockholm, Sweden.
    Rönnberg, Elin
    Karolinska Univ Hosp, Karolinska Inst, Dept Med Solna, Immunol & Allergy Unit, Stockholm, Sweden.
    Dahlin, Joakim S.
    Karolinska Univ Hosp, Karolinska Inst, Dept Med Solna, Immunol & Allergy Unit, Stockholm, Sweden.
    Mazzurana, Luca
    Karolinska Univ Hosp, Karolinska Inst, Dept Med Huddinge, Ctr Infect Med, Stockholm, Sweden.
    Säfholm, Jesper
    Karolinska Inst, Inst Environm Med, Unit Expt Asthma & Allergy Res, Ctr Allergy Res, Stockholm, Sweden.
    Orre, Ann-Charlotte
    Karolinska Univ Hosp, Karolinska Inst, Dept Mol Med & Surg, Thorac Surg, Stockholm, Sweden.
    Al-Ameri, Mamdoh
    Karolinska Univ Hosp, Karolinska Inst, Dept Mol Med & Surg, Thorac Surg, Stockholm, Sweden.
    Peachell, Peter
    Univ Sheffield, Royal Hallamshire Hosp, Acad Unit Resp Med, Sheffield, S Yorkshire, England.
    Adner, Mikael
    Karolinska Inst, Inst Environm Med, Unit Expt Asthma & Allergy Res, Ctr Allergy Res, Stockholm, Sweden.
    Dahlen, Sven-Erik
    Karolinska Inst, Inst Environm Med, Unit Expt Asthma & Allergy Res, Ctr Allergy Res, Stockholm, Sweden.
    Mjösberg, Jenny
    Karolinska Univ Hosp, Karolinska Inst, Dept Med Huddinge, Ctr Infect Med, Stockholm, Sweden;Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden.
    Nilsson, Gunnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Haematology. Karolinska Univ Hosp, Karolinska Inst, Dept Med Solna, Immunol & Allergy Unit, Stockholm, Sweden.
    An Optimized Protocol for the Isolation and Functional Analysis of Human Lung Mast Cells2018In: Frontiers in Immunology, ISSN 1664-3224, E-ISSN 1664-3224, Vol. 9, article id 2193Article in journal (Refereed)
    Abstract [en]

    Background: Mast cells are tissue-resident inflammatory cells defined by their high granularity and surface expression of the high-affinity IgE receptor, Fc + RI, and CD117/KIT, the receptor for stem cell factor (SCF). There is a considerable heterogeneity among mast cells, both phenotypically and functionally. Human mast cells are generally divided into two main subtypes based on their protease content; the mucosa-associated MCT (tryptase positive and chymase negative mast cell) and the connective tissue associated-residing MCTC (tryptase and chymase positive mast cell). Human lung mast cells exhibit heterogeneity in terms of cellular size, expression of cell surface receptors, and secreted mediators. However, knowledge about human lung mast cell heterogeneity is restricted to studies using immunohistochemistry or purified mast cells. Whereas the former is limited by the number of cellular markers that can be analyzed simultaneously, the latter suffers from issues related to cell yield.

    Aim: To develop a protocol that enables isolation of human lung mast cells at high yields for analysis of functional properties and detailed analysis using single-cell based analyses of protein (flow cytometry) or RNA (RNA-sequencing) expression.

    Methods: Mast cells were isolated from human lung tissue by a sequential combination of washing, enzymatic digestion, mechanical disruption, and density centrifugation using Percoll (WEMP). As a comparison, we also isolated mast cells using a conventional enzyme-based protocol. The isolated cells were analyzed by flow cytometry.

    Results: We observed a significant increase in the yield of total human lung CD45(+) immune cells and an even more pronounced increase in the yield of CD117(+) mast cells with the WEMP protocol in comparison to the conventional protocols. In contrast, the frequency of the rare lymphocyte subset innate lymphoid cells group 2 (ILC2) did not differ between the two methods.

    Conclusion: The described WEMP protocol results in a significant increase in the yield of human lung mast cells compared to a conventional protocol. Additionally, the WEMP protocol enables simultaneous isolation of different immune cell populations such as lymphocytes, monocytes, and granulocytes while retaining their surface marker expression that can be used for advanced single-cell analyses including multi-color flow cytometry and RNA-sequencing.

  • Ersson, Nils Olov
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Förrådet av äldre instrument hos avdelningen för Oorganisk kemi, Uppsala Universitet: Beskrivning utgående från en dokumentation utförd 20082018Other (Other (popular science, discussion, etc.))
    Abstract [sv]

    Som del i masterexamen i museologi fick Hedda Gottberg och Rebecca Flodin 2008 i uppgift att dokumentera den samling av instrument som tillhörde avdelningen för Oorganisk kemi vid Uppsala Uni-versitet. Samlingen hade några år tidigare flyttats till en källarlokal i det nya Ångströmlaboratoriet i Uppsala. Denna dokumentation skedde under ledning av avdelningens prefekt Yvonne Brandt Anders-son och Nils Olov Ersson, pensionerad forskningsingenjör. Fotograferingen av alla föremålen, ofta från flera vinklar och alltid med angivande av föremålens angivna data, gav till resultat ett stort antal digitala filer. Ett urval av dessa fotografier med korta beskrivningar presenteras i denna skrift.

  • Ferdous, Md Ruknul
    et al.
    IHE Delft Inst Water Educ, Dept Integrated Water Syst & Governance, NL-2611 AX Delft, Netherlands;Univ Amsterdam, Fac Social & Behav Sci, NL-1012 WX Amsterdam, Netherlands.
    Wesselink, Anna
    IHE Delft Inst Water Educ, Dept Integrated Water Syst & Governance, NL-2611 AX Delft, Netherlands.
    Brandimarte, Luigia
    KTH, Dept Sustainable Dev Environm Sci & Engn, Stockholm, Sweden.
    Slager, Kymo
    Deltares, NL-2600 MH Delft, Netherlands.
    Zwarteveen, Margreet
    IHE Delft Inst Water Educ, Dept Integrated Water Syst & Governance, NL-2611 AX Delft, Netherlands;Univ Amsterdam, Fac Social & Behav Sci, NL-1012 WX Amsterdam, Netherlands.
    Di Baldassarre, Giuliano
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. IHE Delft Inst Water Educ, Dept Integrated Water Syst & Governance, NL-2611 AX Delft, Netherlands;CNDS, Ctr Nat Hazards & Disaster Sci, S-75236 Uppsala, Sweden.
    Socio-hydrological spaces in the Jamuna River floodplain in Bangladesh2018In: Hydrology and Earth System Sciences, ISSN 1027-5606, E-ISSN 1607-7938, Vol. 22, no 10, p. 5159-5173Article in journal (Refereed)
    Abstract [en]

    Socio-hydrology aims to understand the dynamics and co-evolution of coupled human-water systems, with research consisting of generic models as well as specific case studies. In this paper, we propose a concept to help bridge the gap between these two types of socio-hydrological studies: socio-hydrological spaces (SHSs). A socio-hydrological space is a geographical area in a landscape. Its particular combination of hydrological and social features gives rise to the emergence of distinct interactions and dynamics (patterns) between society and water. Socio-hydrological research on human-flood interactions has found two generic responses, "fight" or "adapt". Distilling the patterns resulting from these responses in case studies provides a promising way to relate contextual specificities to the generic patterns described by conceptual models. Through the use of SHSs, different cases can be compared globally without aspiring to capturing them in a formal model. We illustrate the use of SHS for the Jamuna floodplain, Bangladesh. We use narratives and experiences of local experts and inhabitants to empirically describe and delimit SHS. We corroborated the resulting classification through the statistical analysis of primary data collected for the purpose (household surveys and focus group discussions) and secondary data (statistics, maps etc.). Our example of the use of SHSs shows that the concept draws attention to how historical patterns in the co-evolution of social behaviour, natural processes and technological interventions give rise to different landscapes, different styles of living and different ways of organising livelihoods. This provides a texture to the more generic patterns generated by socio-hydrological models, promising to make the resulting analysis more directly useful for decision makers. We propose that the usefulness of this concept in other floodplains, and for other socio-hydrological systems than floodplains, should be explored.

  • Edfors, Fredrik
    et al.
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Hober, Andreas
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Linderbäck, Klas
    KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Maddalo, Gianluca
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Azimi, Alireza
    Karolinska Inst, Karolinska Univ Hosp, Dept Oncol Pathol, SE-17177 Stockholm, Sweden.
    Sivertsson, Åsa
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Tegel, Hanna
    KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Hober, Sophia
    KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Szigyarto, Cristina Al-Khalili
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Fagerberg, Linn
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    von Feilitzen, Kalle
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Oksvold, Per
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Lindskog, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Forsström, Björn
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden.
    Uhlen, Mathias
    KTH Royal Inst Technol, Sci Life Lab, SE-17121 Stockholm, Sweden;KTH Royal Inst Technol, Dept Prot Sci, SE-10691 Stockholm, Sweden;Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, DK-2970 Horsholm, Denmark.
    Enhanced validation of antibodies for research applications2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4130Article in journal (Refereed)
    Abstract [en]

    There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.

  • McMaster, Mary L.
    et al.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Berndt, Sonja, I
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Zhang, Jianqing
    Univ Alabama Birmingham, Sch Publ Hlth, Dept Epidemiol, Birmingham, AL 35233 USA;Univ Alabama Birmingham, Comprehens Canc Ctr, Birmingham, AL 35233 USA.
    Slager, Susan L.
    Mayo Clin, Dept Hlth Sci Res, Rochester, MN 55905 USA.
    Li, Shengchao Alfred
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Vajdic, Claire M.
    Univ New South Wales, Ctr Big Data Res Hlth, Sydney, NSW 2052, Australia.
    Smedby, Karin E.
    Solna Karolinska Inst, Dept Med, S-17176 Stockholm, Sweden;Karolinska Univ Hosp, Hematol Ctr, S-17176 Stockholm, Sweden.
    Yan, Huihuang
    Mayo Clin, Dept Hlth Sci Res, Rochester, MN 55905 USA.
    Birmann, Brenda M.
    Brigham & Womens Hosp, Dept Med, Channing Div Network Med, Boston, MA 02115 USA;Harvard Med Sch, Boston, MA 02115 USA.
    Brown, Elizabeth E.
    Univ Alabama Birmingham, Dept Pathol, Birmingham, AL 35233 USA.
    Smith, Alex
    Univ York, Dept Hlth Sci, York YO10 5DD, N Yorkshire, England.
    Kleinstern, Geffen
    Mayo Clin, Dept Hlth Sci Res, Rochester, MN 55905 USA.
    Fansler, Mervin M.
    Weill Cornell Grad Coll, Triinst Training Program Computat Biol & Med, New York, NY 10021 USA;Mem Sloan Kettering Canc Ctr, Canc Biol & Genet Program, New York, NY 10065 USA.
    Mayr, Christine
    Mem Sloan Kettering Canc Ctr, Canc Biol & Genet Program, New York, NY 10065 USA.
    Zhu, Bin
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Chung, Charles C.
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Park, Ju-Hyun
    Dongguk Univ, Dept Stat, Seoul 100715, South Korea.
    Burdette, Laurie
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Hicks, Belynda D.
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Hutchinson, Amy
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Teras, Lauren R.
    Amer Canc Soc, Epidemiol Res Program, Atlanta, GA 30303 USA.
    Adami, Hans-Olov
    Karolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden;Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA;Univ Oslo, Inst Hlth & Soc, Clin Effectiveness Res Grp, NO-0316 Oslo, Norway.
    Bracci, Paige M.
    Univ Calif San Francisco, Dept Epidemiol & Biostat, San Francisco, CA 94118 USA.
    McKay, James
    IARC, F-69372 Lyon, France.
    Monnereau, Alain
    INSERM, Ctr Res Epidemiol & Stat Sorbonne Paris Cit CRESS, Epidemiol Childhood & Adolescent Canc Grp, F-94807 Paris, France;Univ Paris 05, F-75006 Paris, France;Univ Bordeaux, Inst Bergonie, Registry Hematol Malignancies Gironde, Team EPICENE,Inserm,UMR 1219, F-33000 Bordeaux, France.
    Link, Brian K.
    Univ Iowa, Carver Coll Med, Dept Internal Med, Iowa City, IA 52242 USA.
    Vermeulen, Roel C. H.
    Univ Utrecht, Inst Risk Assessment Sci, NL-3508 TD Utrecht, Netherlands;Univ Med Ctr Utrecht, Julius Ctr Hlth Sci & Primary Care, NL-3584 CX Utrecht, Netherlands.
    Ansell, Stephen M.
    Mayo Clin, Dept Internal Med, Rochester, MN 55905 USA.
    Maria, Ann
    Mem Sloan Kettering Canc Ctr, Dept Med, New York, NY 10065 USA.
    Diver, W. Ryan
    Amer Canc Soc, Epidemiol Res Program, Atlanta, GA 30303 USA.
    Melbye, Mads
    Statens Serum Inst, Dept Epidemiol Res, Div Hlth Surveillance & Res, DK-2300 Copenhagen, Denmark;Stanford Univ, Dept Med, Sch Med, Stanford, CA 94305 USA.
    Ojesina, Akinyemi, I
    Univ Alabama Birmingham, Sch Publ Hlth, Dept Epidemiol, Birmingham, AL 35233 USA;Univ Alabama Birmingham, Comprehens Canc Ctr, Birmingham, AL 35233 USA.
    Kraft, Peter
    Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA;Harvard TH Chan Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA.
    Boffetta, Paolo
    Icahn Sch Med Mt Sinai, Tisch Canc Inst, New York, NY 10029 USA.
    Clavel, Jacqueline
    INSERM, Ctr Res Epidemiol & Stat Sorbonne Paris Cit CRESS, Epidemiol Childhood & Adolescent Canc Grp, F-94807 Paris, France;Univ Paris 05, F-75006 Paris, France.
    Giovannucci, Edward
    Brigham & Womens Hosp, Dept Med, Channing Div Network Med, Boston, MA 02115 USA;Harvard Med Sch, Boston, MA 02115 USA;Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA;Harvard TH Chan Sch Publ Hlth, Dept Nutr, Boston, MA 02115 USA.
    Besson, Caroline M.
    Inserm U1018, Ctr Rech Epidmiol St Populat CESP, Serv Hematol & Oncol, Ctr Hosp Versailles, F-78157 Villejuif, France.
    Canzia, Federico
    German Canc Res Ctr, Genom Epidemiol Grp, D-69120 Heidelberg, Germany.
    Travis, Ruth C.
    Univ Oxford, Canc Epidemiol Unit, Oxford OX3 7LF, England.
    Vineis, Paolo
    Imperial Coll London, MRC PHE Ctr Environm & Hlth, Sch Publ Hlth, London W2 1PG, England;Human Genet Fdn, I-10126 Turin, Italy.
    Weiderpass, Elisabete
    Karolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden;Univ Tromso, Arctic Univ Norway, Fac Hlth Sci, Dept Community Med, N-9019 Tromso, Norway;Canc Registry Norway, Dept Res, Inst Populat Based Canc Res, N-0379 Oslo, Norway;Folkhalsan Res Ctr, Genet Epidemiol Grp, Helsinki 00250, Finland;Univ Adelaide, Helsinki 00250, Finland.
    Montalvan, Rebecca
    Westat Corp, Rockville, MD 20850 USA.
    Wang, Zhaoming
    St Jude Childrens Res Hosp, Dept Computat Biol, Memphis, TN 38105 USA;NCI, Div Canc Epidemiol & Genet, Lab Translat Genom, Bethesda, MD 20877 USA.
    Yeager, Meredith
    Leidos Biomed Res Inc, Frederick Natl Lab Canc Res, Canc Genom Res Lab, Frederick, MD 20877 USA.
    Becker, Nikolaus
    German Canc Res Ctr, Div Canc Epidemiol, D-69120 Heidelberg, Baden Wurttembe, Germany.
    Benavente, Yolanda
    Hosp Llobregat, Catalan Inst Oncol IDIBELL, Canc Epidemiol Res Programme, Barcelona 08908, Spain;CIBER Epidemiol & Salud Publ CIBERESP, Madrid 28029, Spain.
    Brennan, Paul
    IARC, F-69372 Lyon, France.
    Foretova, Lenka
    Masaryk Mem Canc Inst, Dept Canc Epidemiol & Genet, Brno 65653, Czech Republic;MF MU, Brno 65653, Czech Republic.
    Maynadie, Marc
    Univ Burgundy, EA 4184, Registre Hemopathies Malignes Cote dOr, F-21070 Dijon, France.
    Nieters, Alexandra
    Univ Med Ctr Freiburg, Ctr Chron Immunodeficiency, D-79108 Freiburg, Baden Wurttembe, Germany.
    de Sanjose, Silvia
    Hosp Llobregat, Catalan Inst Oncol IDIBELL, Canc Epidemiol Res Programme, Barcelona 08908, Spain;CIBER Epidemiol & Salud Publ CIBERESP, Madrid 28029, Spain.
    Staines, Anthony
    Dublin City Univ, Sch Nursing & Human Sci, Dublin 9, Ireland.
    Conde, Lucia
    UCL, Bill Lyons Informat Ctr, UCL Canc Inst, London WC1E 6DD, England.
    Riby, Jacques
    Univ Alabama Birmingham, Sch Publ Hlth, Dept Epidemiol, Birmingham, AL 35233 USA;Univ Alabama Birmingham, Comprehens Canc Ctr, Birmingham, AL 35233 USA;Univ Calif Berkeley, Div Environm Hlth Sci, Sch Publ Hlth, Berkeley, CA 94720 USA.
    Glimelius, Bengt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Experimental and Clinical Oncology.
    Hjalgrim, Henrik
    Statens Serum Inst, Dept Epidemiol Res, Div Hlth Surveillance & Res, DK-2300 Copenhagen, Denmark;Rigshosp, Dept Hematol, DK-2100 Copenhagen, Denmark.
    Pradhan, Nisha
    Mem Sloan Kettering Canc Ctr, Dept Med, New York, NY 10065 USA.
    Feldman, Andrew L.
    Mayo Clin, Dept Lab Med & Pathol, Rochester, MN 55905 USA.
    Novak, Anne J.
    Mayo Clin, Dept Internal Med, Rochester, MN 55905 USA.
    Lawrence, Charles
    Westat Corp, Rockville, MD 20850 USA.
    Bassig, Bryan A.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Lan, Qing
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Zheng, Tongzhang
    Brown Univ, Dept Epidemiol, Providence, RI 02903 USA.
    North, Kari E.
    Univ N Carolina, Dept Epidemiol, Chapel Hill, NC 27599 USA;Univ N Carolina, Carolina Ctr Genome Sci, Chapel Hill, NC 27599 USA.
    Tinker, Lesley F.
    Fred Hutchinson Canc Res Ctr, Div Publ Hlth Sci, Seattle, WA 98117 USA.
    Cozen, Wendy
    Univ Southern Calif, USC Keck Sch Med, Dept Prevent Med, Los Angeles, CA 90033 USA;Univ Southern Calif, Norris Comprehens Canc Ctr, USC Keck Sch Med, Los Angeles, CA 90033 USA.
    Severson, Richard K.
    Wayne State Univ, Dept Family Med & Publ Hlth Sci, Detroit, MI 48201 USA.
    Hofmann, Jonathan N.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Zhang, Yawei
    Yale Sch Publ Hlth, Dept Environm Hlth Sci, New Haven, CT 06520 USA.
    Jackson, Rebecca D.
    Ohio State Univ, Div Endocrinol Diabet & Metab, Columbus, OH 43210 USA.
    Morton, Lindsay M.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Purdue, Mark P.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA;Ontario Hlth Study, Toronto, ON M5S 1C6, Canada.
    Chatterjee, Nilanjan
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA;Johns Hopkins Univ, Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21205 USA;Johns Hopkins Univ, Sch Med, Dept Oncol, Baltimore, MD 21205 USA.
    Offit, Kenneth
    Mem Sloan Kettering Canc Ctr, Dept Med, New York, NY 10065 USA.
    Cerhan, James R.
    Mayo Clin, Dept Hlth Sci Res, Rochester, MN 55905 USA.
    Chanock, Stephen J.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Rothman, Nathaniel
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA;Ontario Hlth Study, Toronto, ON M5S 1C6, Canada.
    Vijai, Joseph
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA;Johns Hopkins Univ, Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21205 USA;Johns Hopkins Univ, Sch Med, Dept Oncol, Baltimore, MD 21205 USA.
    Goldin, Lynn R.
    Mem Sloan Kettering Canc Ctr, Dept Med, New York, NY 10065 USA.
    Skibola, Christine F.
    Emory Univ, Dept Hematol & Med Oncol, Sch Med, Atlanta, GA 30322 USA.
    Caporaso, Neil E.
    NCI, Div Canc Epidemiol & Genet, Bethesda, MD 20892 USA.
    Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4182Article in journal (Refereed)
    Abstract [en]

    Waldenstrom macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40-31.03, P=1.36 x 10(-)(54)) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45-6.96, P = 8.75 x 10(-)(19)) . Both risk alleles are observed at a low frequency among controls (similar to 2-3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy.

  • Kahn, Suzana A.
    et al.
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Stem Cell Biol & Regenerat Med, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Canc Ctr, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Inst Canc Res, Sch Med, Stanford, CA 94305 USA.
    Wang, Xin
    Univ Toronto, Hosp Sick Children, Div Neurosurg, Arthur & Sonia Labatt Brain Tumor Res Ctr, Toronto, ON M5G 0A4, Canada.
    Nitta, Ryan T.
    Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Gholamin, Sharareh
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Stem Cell Biol & Regenerat Med, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Canc Ctr, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Theruvath, Johanna
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Hutter, Gregor
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Azad, Tej D.
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Wadi, Lina
    Ontario Inst Canc Res, Computat Biol Program, Toronto, ON M5G 0A3, Canada.
    Bolin, Sara
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology. Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Ramaswamy, Vijay
    Univ Toronto, Hosp Sick Children, Div Neurosurg, Arthur & Sonia Labatt Brain Tumor Res Ctr, Toronto, ON M5G 0A4, Canada.
    Esparza, Rogelio
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Liu, Kun-Wei
    Sanford Burnham Prebys Med Discovery Inst, Tumor Initiat & Maintenance Program, 2880 Torrey Pines Scen Dr, La Jolla, CA 92037 USA.
    Edwards, Michael
    Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Inst Canc Res, Sch Med, Stanford, CA 94305 USA.
    Johansson, Fredrik K.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sahoo, Debashis
    Univ Calif San Diego, Dept Pediat, San Diego, CA 92093 USA;Univ Calif San Diego, Dept Comp Sci & Engn, San Diego, CA 92093 USA.
    Li, Gordon
    Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA.
    Wechsler-Reya, Robert J.
    Sanford Burnham Prebys Med Discovery Inst, Tumor Initiat & Maintenance Program, 2880 Torrey Pines Scen Dr, La Jolla, CA 92037 USA.
    Reimand, Juri
    Ontario Inst Canc Res, Computat Biol Program, Toronto, ON M5G 0A3, Canada;Univ Toronto, Dept Med Biophys, Toronto, ON M5G 1L7, Canada.
    Cho, Yoon-Jae
    Stanford Univ, Ludwig Inst Canc Res, Sch Med, Stanford, CA 94305 USA.
    Taylor, Michael D.
    Univ Toronto, Hosp Sick Children, Div Neurosurg, Arthur & Sonia Labatt Brain Tumor Res Ctr, Toronto, ON M5G 0A4, Canada.
    Weissman, Irving L.
    Stanford Univ, Stem Cell Biol & Regenerat Med, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Canc Ctr, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Inst Canc Res, Sch Med, Stanford, CA 94305 USA.
    Mitra, Siddhartha S.
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Stem Cell Biol & Regenerat Med, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Canc Ctr, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Inst Canc Res, Sch Med, Stanford, CA 94305 USA;Univ Colorado, Sch Med, Childrens Hosp Colorado, Dept Pediat, Room P18-4114,Res Complex 1 North MS 8302, Aurora, CO 80045 USA.
    Cheshier, Samuel H.
    Stanford Univ, Lucile Packard Childrens Hosp, Div Pediat Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Stem Cell Biol & Regenerat Med, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Canc Ctr, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Dept Neurosurg, Sch Med, Stanford, CA 94305 USA;Stanford Univ, Ludwig Inst Canc Res, Sch Med, Stanford, CA 94305 USA;Univ Utah, Primary Childrens Hosp, Div Pediat Neurosurg, Dept Neurosurg, 100 North Mario Capecchi Dr Suite 3850, Salt Lake City, UT 84113 USA;Univ Utah, Huntsman Canc Inst, 100 North Mario Capecchi Dr Suite 3850, Salt Lake City, UT 84113 USA.
    Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4121Article in journal (Refereed)
    Abstract [en]

    Medulloblastoma is the most common malignant brain tumor of childhood. Group 3 medulloblastoma, the most aggressive molecular subtype, frequently disseminates through the leptomeningeal cerebral spinal fluid (CSF) spaces in the brain and spinal cord. The mechanism of dissemination through the CSF remains poorly understood, and the molecular pathways involved in medulloblastoma metastasis and self-renewal are largely unknown. Here we show that NOTCH1 signaling pathway regulates both the initiation of metastasis and the self-renewal of medulloblastoma. We identify a mechanism in which NOTCH1 activates BMI1 through the activation of TWIST1. NOTCH1 expression and activity are directly related to medulloblastoma metastasis and decreased survival rate of tumor-bearing mice. Finally, medulloblastoma-bearing mice intrathecally treated with anti-NRR1, a NOTCH1 blocking antibody, present lower frequency of spinal metastasis and higher survival rate. These findings identify NOTCH1 as a pivotal driver of Group 3 medulloblastoma metastasis and self-renewal, supporting the development of therapies targeting this pathway.

  • Vedung, Evert
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Institute for Housing and Urban Research. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Government.
    Lagen om kommunal energiplanering – tillkomst och politisk behandling1983Report (Other academic)
  • Lewandowska, Marta
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Clinical Neurophysiology.
    Bogatikov, Evgenii
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Clinical Neurophysiology.
    Hierlemann, Andreas R.
    Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.
    Rostedt Punga, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Clinical Neurophysiology.
    Long-Term High-Density Extracellular Recordings Enable Studies of Muscle Cell Physiology2018In: Frontiers in Physiology, ISSN 1664-042X, E-ISSN 1664-042X, Vol. 9, article id 1424Article in journal (Refereed)
    Abstract [en]

    Skeletal (voluntary) muscle is the most abundant tissue in the body, thus making it an important biomedical research subject. Studies of neuromuscular transmission, including disorders of ion channels or receptors in autoimmune or genetic neuromuscular disorders, require high-spatial-resolution measurement techniques and an ability to acquire repeated recordings over time in order to track pharmacological interventions. Preclinical techniques for studying diseases of neuromuscular transmission can be enhanced by physiologic ex vivo models of tissue-tissue and cell-cell interactions. Here, we present a method, which allows tracking the development of primary skeletal muscle cells from myoblasts into mature contracting myotubes over more than 2 months. In contrast to most previous studies, the myotubes did not detach from the surface but instead formed functional networks between the myotubes, whose electrical signals were observed over the entire culturing period. Primary cultures of mouse myoblasts differentiated into contracting myotubes on a chip that contained an array of 26,400 platinum electrodes at a density of 3,265 electrodes per mm(2). Our ability to track extracellular action potentials at subcellular resolution enabled study of skeletal muscle development and kinetics, modes of spiking and spatio-temporal relationships between muscles. The developed system in turn enables creation of a novel electrophysiological platform for establishing ex vivo disease models.

  • Henningsson, Anna J.
    et al.
    Div Lab Med, Clin Microbiol, Jonkoping, Region Jonkopin, Sweden;Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden.
    Lager, Malin
    Div Lab Med, Clin Microbiol, Jonkoping, Region Jonkopin, Sweden.
    Brannstrom, Rebecka
    Orebro Univ, Sch Med Sci, Orebro, Sweden.
    Tjernberg, Ivar
    Linkoping Univ, Dept Clin & Expt Med, Linkoping, Sweden;Linkoping Univ, Dept Clin Chem, Linkoping, Sweden;Linkoping Univ, Transfus Med Kalmar Cty Council, Linkoping, Sweden.
    Skogman, Barbro H.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Center for Clinical Research Dalarna. Falun Gen Hosp, Dept Pediat, Falun, Sweden.
    The chemokine CXCL13 in cerebrospinal fluid in children with Lyme neuroborreliosis2018In: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 37, no 10, p. 1983-1991Article in journal (Refereed)
    Abstract [en]

    Anti-Borrelia antibodies in the cerebrospinal fluid (CSF) are required for definite diagnosis of Lyme neuroborreliosis (LNB). However, children often present with early LNB, and antibody production in the CSF may not be demonstrated. Recent studies have suggested the chemokine CXCL13 to be an early marker for LNB. The aim of the study was to evaluate CXCL13 for laboratory diagnosis in pediatric LNB patients and to evaluate the association with pleocytosis in CSF, clinical features, and recovery. CSF samples were collected from LNB patients, classified as definite LNB (n = 44) or possible LNB (n = 22), and controls classified as non-LNB (n = 102) or other specific diagnoses (n = 23). CSF samples were analyzed with the recomBead CXCL13 assay (Mikrogen Diagnostik, Germany), cut-off 160 pg/mL. CXCL13 was significantly higher in LNB patients compared to controls (p < 0.001). Among LNB patients, 58/66 had elevated CXCL13, and among controls, 111/125 had CXCL13 levels under cut-off (sensitivity 88%, specificity 89%). In LNB patients with pleocytosis but no detectable anti-Borrelia antibodies in CSF (possible LNB), CXCL13 was elevated in 16/22 (73%). A weak correlation between CXCL13 and pleocytosis in CSF was found in LNB patients (Rho = 0.46, p < 0.01), but no differences in CXCL13 levels in relation to specific clinical features. In conclusion, CXCL13 is elevated in CSF in children with LNB, showing acceptable sensitivity and specificity. In patients with possible LNB, CXCL13 was elevated in a majority of cases (73%) and is suggested as a complementary diagnostic tool in pediatric LNB patients. CXCL13 was not associated with specific clinical features or recovery.

  • Svensson, Elin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Radboud Univ Nijmegen Med Ctr, Radboud Inst Hlth Sci, Dept Pharm, Nijmegen, Netherlands.
    du Bois, Jeannine
    TASK Appl Sci, Cape Town, South Africa.
    Kitshoff, Rene
    TASK Appl Sci, Cape Town, South Africa.
    de Jager, Veronique R.
    TASK Appl Sci, Cape Town, South Africa.
    Wiesner, Lubbe
    Univ Cape Town, Div Clin Pharmacol, Dept Med, Cape Town, South Africa.
    Norman, Jennifer
    Univ Cape Town, Div Clin Pharmacol, Dept Med, Cape Town, South Africa.
    Nachman, Sharon
    SUNY Stony Brook, Dept Pediat, Stony Brook, NY 11794 USA.
    Smith, Betsy
    NIAID, Div Aids, NIH, Bethesada, MA USA.
    Diacon, Andreas H.
    TASK Appl Sci, Cape Town, South Africa;Stellenbosch Univ, Div Med Physiol, Fac Med & Hlth Sci, Stellenbosch, South Africa.
    Hesseling, Anneke C.
    Stellenbosch Univ, Dept Paediat & Child Hlth, Desmond Tutu TB Ctr, Fac Med & Hlth Sci, Cape Town, South Africa.
    Garcia-Prats, Anthony J.
    Stellenbosch Univ, Dept Paediat & Child Hlth, Desmond Tutu TB Ctr, Fac Med & Hlth Sci, Cape Town, South Africa.
    Relative bioavailability of bedaquiline tablets suspended in water: Implications for dosing in children2018In: British Journal of Clinical Pharmacology, ISSN 0306-5251, E-ISSN 1365-2125, Vol. 84, no 10, p. 2384-2392Article in journal (Refereed)
    Abstract [en]

    Aims: Bedaquiline is an important novel drug for treatment of multidrug-resistant tuberculosis, but no paediatric formulation is yet available. This work aimed to explore the possibility of using the existing tablet formulation in children by evaluating the relative bioavailability, short-term safety, acceptability and palatability of suspended bedaquiline tablets compared to whole tablets.

    Methods: A randomized, open-label, two-period cross-over study was conducted in 24 healthy adult volunteers. Rich pharmacokinetic sampling over 48h was conducted at two occasions 14days apart in each participant after administration of 400mg bedaquiline (whole or suspended in water). The pharmacokinetic data were analysed with nonlinear mixed-effects modelling. A questionnaire was used to assess palatability and acceptability.

    Results: There was no statistically significant difference in the bioavailability of the suspended bedaquiline tables compared to whole. The nonparametric 95% confidence interval of the relative bioavailability of suspended bedaquiline tablets was 94-108% of that of whole bedaquiline tablets; hence, the predefined bioequivalence criteria were fulfilled. There were no Grade 3 or 4 or serious treatment emergent adverse events recorded in the study and no apparent differences between whole tablets and suspension regarding taste, texture or smell.

    Conclusions: The bioavailability of bedaquiline tablets suspended in water was the same as for tablets swallowed whole and the suspension was well tolerated. This suggests that the currently available bedaquiline formulation could be used to treat multidrug-resistant tuberculosis in children, to bridge the gap between when paediatric dosing regimens have been established and when a paediatric dispersible formulation is routinely available.

  • Hultin, Hella
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Endocrine Surgery.
    Stevens, Katharina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Upper Abdominal Surgery.
    Sundbom, Magnus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Upper Abdominal Surgery.
    Cholecalciferol Injections Are Effective in Hypovitaminosis D After Duodenal Switch: a Randomized Controlled Study2018In: Obesity Surgery, ISSN 0960-8923, E-ISSN 1708-0428, Vol. 28, no 10, p. 3007-3011Article in journal (Refereed)
    Abstract [en]

    Background: By treating obesity, one of the major epidemics of this past century, through bariatric surgery, we may cause complications due to malnourishment in a growing population. At present, vitamin D deficiency is of interest, especially in patients with inferior absorption of fat-soluble nutrients after biliopancreatic diversion with duodenal switch (BPD/DS).

    Methods: Twenty BPD/DS patients, approximately 4 years postoperatively, were randomized to either intramuscular supplementation of vitamin D with a single dose of 600,000 IU cholecalciferol, or a control group. Patients were instructed to limit their supplementation to 1400 IU of vitamin D and to avoid the influence of UV-B radiation; the study was conducted when sunlight is limited (December to May).

    Results: Despite oral supplementation, a pronounced deficiency in vitamin D was seen (injection 19.3; control 23.2 nmol/l) in both groups. The cholecalciferol injection resulted in elevated 25[OH]D levels at 1 month (65.4 nmol/l), which was maintained at 6 months (67.4 nmol/l). This resulted in normalization of intact parathyroid hormone (PTH) levels. No changes in vitamin D or PTH occurred in the control group.

    Conclusions: In BPD/DS patients, having hypovitaminosis D despite full oral supplementation, a single injection of 600,000 IU of cholecalciferol was effective in elevating vitamin D levels and normalizing levels of intact PTH. The treatment is simple and highly effective and thus recommended, especially in cases of reduced UV-B radiation.

  • Skogsdal, Yvonne Rosalie Elisabeth
    et al.
    Orebro Univ, Fac Med & Hlth, Maternal Hlth Care Unit, Orebro, Sweden.
    Karlsson, Jan Åke
    Orebro Univ, Univ Hlth Care Res Ctr, Fac Med & Hlth, Orebro, Sweden.
    Cao, Yang
    Orebro Univ, Sch Med Sci Clin Epidemiol & Biostat, Orebro, Sweden;Karolinska Inst, Inst Environm Med, Unit Biostat, Stockholm, Sweden.
    Fadl, Helena Elisabeth
    Orebro Univ, Dept Obstet & Gynecol, Fac Med & Hlth, Orebro, Sweden.
    Tydén, Tanja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Research group (Dept. of women´s and children´s health), Obstetrics and Reproductive Health Research.
    Contraceptive use and reproductive intentions among women requesting contraceptive counseling2018In: Acta Obstetricia et Gynecologica Scandinavica, ISSN 0001-6349, E-ISSN 1600-0412, Vol. 97, no 11, p. 1349-1357Article in journal (Refereed)
    Abstract [en]

    Introduction: Limited attention has been paid to the use of contraception in relation to women's family planning intentions. The aim of this study was to investigate the use of contraception during the most recent intercourse as well as the reproductive intentions of Swedish-speaking women requesting contraceptive counseling.

    Material and methods: Across-sectional baseline survey in a randomized controlled trial regarding reproductive life planning (before randomization). Women requesting contraceptive counseling answered questions about contraception and whether they wanted to have children/more children in the future.

    Results: In total, 1946 women participated: 33.7% (n = 656) parous and 65.7% (n = 1279) nulliparous. The majority, 87.1% (n = 1682), had used contraception during their latest intercourse; 64.6% (n = 1239) used short-acting reversible contraception, 22.8% (n = 443) used long-acting reversible contraception (LARC), and 12.9% (n = 251) had not used any contraception. A combined oral contraceptive was more common among nulliparous and LARC among parous. Among all women, 64.8% (n = 1253) intended to have children/more children in the future, among parous women 35.7% (n = 220) and among nulliparous 80.0% (n = 1033). Among women who did not intend to have children/more children, 22.6% (n = 60) of parous and 10% (n = 8) of nulliparous had not used contraceptives during their most recent intercourse.

    Conclusions: Women did not always use contraceptives that were suitable for their reproductive intentions. Questioning women who request contraceptive counseling about their pregnancy intention can give healthcare providers better opportunities for individualized counseling.

  • Carlsson, Jenny
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Fracture nucleation and continued crack growth on the cell scale in wood analysed by as high-resolution finite element model2016In: The Eccomas Congress 2016 Proceedings, 2016Conference paper (Refereed)
  • Carlsson, Jenny
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Joffre, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Dynamic crack propagation in wood fibre composites2017In: Svenska Mekanikdagar 2017, Uppsala 12 – 13 juni, 2017Conference paper (Refereed)
  • Carlsson, Jenny
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    High-velocity crack speed in wood fibre composites: an experimental and numerical study2017In: CFRAC 2017, International Conference on Computational Fracture and Failure of Materials and Structures, Book of abstracts, 2017, p. 155-Conference paper (Refereed)
  • Carlsson, Jenny
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Isaksson, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Dynamic crack propagation and crack tip shielding in porous materials analyzed by the phase field method for fracture2018Conference paper (Other academic)
  • Public defence: 2018-12-19 09:00 Polhemsalen, Uppsala
    Carstensen, Hauke
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Self-assembly of magnetic particles2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Self-assembly is the spontaneous formation of larger structures from small building blocks. This process is driven and determined by the interactions between the constituents. Examples of self assembly are found almost everywhere and, in particular, biological systems in general rely on a hierarchical formation of structures over a range of length scales. Technologically, self-assembly can be used to form mesoscopic structures and artificial crystals. In the case of particles with micrometer size suspended in a liquid phase, it is possible to use optical microscopy for the the investigation of self-assembly.

    In this thesis, the self-assembly of microbeads with tunable magnetic interactions is studied, based on the statistic analysis of microscope images and computer simulations. Magnetic and non-magnetic microbeads are suspended in a ferrofluid, which is a dispersion of magnetic nanoparticles in water. As a result, the magnetic properties of the microbeads in the ferrofluid are altered and can be described by effective magnetic susceptibilities and magnetic dipole moments, which can be tuned continuously. The liquid is confined between glass slides and effectively the microbeads are studied in a 2D geometry under a magnetic field, applied either in- or out-of-plane. The resulting structures are detected by image analysis algorithms, analyzed and correlated to the dipolar interaction between the beads, as well as to macroscopic quantities, like the particle density and ratio. For the in-plane field a phase transition from square to hexagonal lattice is observed. This phase transition is explained by the change in dipole interaction between the microbeads as the moments change from anti-parallel to parallel alignment.  For the out-of-plane field the situation becomes diverse and more phases appear. It turns out that the phase formation in this case is strongly dependent on the bead ratio, density and interactions.

    We identify regions in the phase diagram, where isolated beads, percolated structures, and crystals dominate. To cover a wide parameter range the experiments are complemented by computer simulations. The tools developed in this thesis enable us to construct phase diagrams extracted from direct imaging and dependence on the extracted relevant parameters.

    List of papers
    1. Phase formation in colloidal systems with tunable interaction
    Open this publication in new window or tab >>Phase formation in colloidal systems with tunable interaction
    2015 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 92, no 1, article id 012303Article in journal (Refereed) Published
    Abstract [en]

    Self-assembly is one of the most fascinating phenomena in nature and is one key component in the formation of hierarchical structures. The formation of structures depends critically on the interaction between the different constituents, and therefore the link between these interactions and the resulting structure is fundamental for the understanding of materials. We have realized a two-dimensional system of colloidal particles with tunable magnetic dipole forces. The phase formation is studied by transmission optical microscopy and a phase diagram is constructed. We report a phase transition from hexagonal to random and square arrangements when the magnetic interaction between the individual particles is tuned from antiferromagnetic to ferrimagnetic.

    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-259093 (URN)10.1103/PhysRevE.92.012303 (DOI)000357262700007 ()
    Funder
    Swedish Research Council, A0505501Carl Tryggers foundation , CT 13:513
    Available from: 2015-07-28 Created: 2015-07-27 Last updated: 2018-11-12Bibliographically approved
    2. Statistical analysis of phase formation in 2D colloidal systems
    Open this publication in new window or tab >>Statistical analysis of phase formation in 2D colloidal systems
    2018 (English)In: The European Physical Journal E Soft matter, ISSN 1292-8941, E-ISSN 1292-895X, Vol. 41, no 1, article id 9Article in journal (Refereed) Published
    Abstract [en]

    Colloidal systems offer unique opportunities for the study of phase formation and structure since their characteristic length scales are accessible to visible light. As a model system the two-dimensional assembly of colloidal magnetic and non-magnetic particles dispersed in a ferrofluid (FF) matrix is studied by transmission optical microscopy. We present a method to statistically evaluate images with thousands of particles and map phases by extraction of local variables. Different lattice structures and long-range connected branching chains are observed, when tuning the effective magnetic interaction and varying particle ratios.

    Place, publisher, year, edition, pages
    SPRINGER, 2018
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:uu:diva-346233 (URN)10.1140/epje/i2018-11615-x (DOI)000423452000001 ()29353322 (PubMedID)
    Funder
    The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), IG2011-2067Swedish Research Council, A0505501Carl Tryggers foundation , CT 13:513
    Available from: 2018-03-16 Created: 2018-03-16 Last updated: 2018-11-12Bibliographically approved
    3. Tunable self assembly of crystals and branching chain networks
    Open this publication in new window or tab >>Tunable self assembly of crystals and branching chain networks
    (English)Manuscript (preprint) (Other academic)
    National Category
    Condensed Matter Physics
    Research subject
    Physics
    Identifiers
    urn:nbn:se:uu:diva-365206 (URN)
    Available from: 2018-11-11 Created: 2018-11-11 Last updated: 2018-11-12
  • Flachskampf, Frank A.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Physiology.
    Nihoyannopoulos, Petros
    Imperial Coll London, NHLI, Hammersmith Hosp, London, England; Univ Athens, Cardiol, Athens, Greece.
    Our obsession with normal values2018In: ECHO RESEARCH AND PRACTICE, ISSN 2055-0464, Vol. 5, no 2, p. R17-R21Article, review/survey (Refereed)
    Abstract [en]

    Normal values provide the background for interpretation of quantitative imaging data and thus are essential information for daily routine. Nevertheless, the ways how normal values are obtained, presented and interpreted, often do not receive the attention they deserve. We review the concepts of normalcy, the implications of typical normal ranges including the types of distribution of normal data, the possibilities to index for confounding biological factors like body surface area and the limitations of the very concept of normal values, demonstrating that there are no easy statistical solutions for difficult clinical problems.

  • Chen, Zhe
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Hardware Accelerator of Matrix Multiplication on FPGAs: Hardware Accelerator of Matrix Multiplication on FPGAs2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    To solve the computational complexity and time-consuming problem of large matrix multiplication, this thesis design a hardware accelerator using parallel computation structure based on FPGA. After function simulation in ModelSim, matrix multiplication functional modules as a custom component used as a coprocessor in co-operation with Nios II CPU by Avalon bus interface. To analyze computation performance of the hardware accelerator, two software systems are designed for comparison. The results show that the hardware accelerator can improve the computational performance of matrix multiplication significantly.

  • Engström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Interacting Particle Inferencefor Probabilistic Programming in Haskell2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Probabilistic programming shows much promise as a declarative way to define statistical models, but inference is often expensive. A parallelisable particle Markovchain Monte Carlo sampler is implemented in Haskell and the domain-specific language Monad-Bayes. The method shows good performance compared to a single SMC sampler, but the full potential of the method could not be acheived.

  • Ringström, Adrián
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Literature.
    I själva verket: Herr Gustafsson själv: en vandring genom ett existentiellt inferno2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • Parsjö, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Gamification of Education in Starting a Business: A Surveyof Support for new Entrepreneurs2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This thesis project aims to survey current support for new entrepreneurs in Sweden,and users of a potential educational system in starting a business. The survey is intended to act as support for the design of a system that applies gamification to education in starting a business. By conducting interviews with experienced entrepreneurs and performing a thematic analysis of the interviews, strengths and weaknesses of knowledge possessed by entrepreneurs and support available to them is identified. Personas and scenarios are created based on the interviews, thematic analysis and background on entrepreneurship in Sweden, in order to provide a further understanding of the users of the system. Ultimately, recommendations for how gamification can be applied to the system are provided based on identified learningdomains, user requirements and user motivation. Notable in the results is that adaptability for different users is an essential design requirement for the system. The thesis project concludes that there is a need for improvement of support for startinga business and that gamification can be beneficial for the design of an educational system in starting a business.

  • Sandén, Oscar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Threat Management in Agile Organisations: Using the Results of a Threat Analysis in Agile Software Development2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A threat analysis of a computer system identifies and analyses threats to the systems and its assets. The process of handling the identified threats, verify the mitigations and to continuously discover new threats during agile development is difficult.

    By making use of the backlog to track threats and security-related tasks a transparent connection between the threats and their security controls is established.  In combination with other tools, a method of integrating the threat analysis into an agiledevelopment method is created.

    The method proposed in this thesis is a solution to the problem of integrating a threat analysis into a agile organisation and presents tools that can aid in a continuous threat-driven security work.

  • Kernen, Joakim
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Economics.
    Trends, cycles and institutions: -Job polarization and the business cycle in Europe2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This thesis studies the cyclical aspect of job polarization in Europe. Contributions include offering a comparison to the findings of previous research on the United States, and extending the analysis by introducing labor market institutions. The analysis is done in two parts, first showing that the observed link between job polarization and jobless recoveries in the US is observed in Europe, but not across all countries and business cycles. In Scandinavia, the process of job polarization appears smoother than the spurts observed in the US. The second part involves regression analyses of the relationship between labor market institutions, the business cycle and occupational employment. The results indicate that stricter labor market institutions are less robustly associated with Routine employment than other occupational groups and that Routine employment is more sensitive to the business cycle than other types of employment. Further, rigid labor market institutions may prevent some of the Routine decline associated with economic downturns, while not necessarily affecting the long run employment. Limitations of the analysis regards rough estimates of the key variables, number of observations and the lack of identification associated with cross-country analyses. 

  • Norén, Coco
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Modern Languages, Romance Languages.
    "C'est vrai puisque Kerstin l'a dit": Argumenter par autorité dans la conversation ordinaire2001In: Langage et référence: Mélanges offerts à Kerstin Jonasson à l'occasion de ses soixante ans / [ed] Hans Kronning, Coco Norén, Bengt Novén, Gunilla Ransbo, Lars-Göran Sundell, Brynja Svane, Uppsala: Acta Universitatis Upsaliensis, 2001, p. 439-447Chapter in book (Other academic)
  • Stattin, Pär
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Urology.
    Sandin, Fredrik
    Uppsala Univ Hosp, Reg Canc Ctr Uppsala Orebro, Uppsala, Sweden.
    Loeb, Stacy
    NYU, Dept Urol & Populat Hlth, New York, NY USA;Manhattan Vet Affairs, New York, NY USA.
    Robinson, David
    Ryhov Hosp, Dept Urol, Jonkoping, Sweden.
    Lissbrant, Ingela Franck
    Univ Goteborg, Dept Oncol, Inst Clin Sci, Sahlgrenska Acad, Gothenburg, Sweden.
    Lambe, Mats
    Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden.
    Public online reporting from a nationwide population-based clinical prostate cancer register2018In: BJU International, ISSN 1464-4096, E-ISSN 1464-410X, Vol. 122, no 1, p. 8-10Article in journal (Other academic)
  • Frassl, Marieke A
    et al.
    Hamilton, David P
    Denfeld, Blaize A
    de Eyto, Elvira
    Hampton, Stephanie E
    Keller, Philipp S
    Sharma, Sapna
    Lewis, Abigail S L
    Weyhenmeyer, Gesa A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    O'Reilly, Catherine M
    Lofton, Mary E
    Catalán, Núria
    Ten simple rules for collaboratively writing a multi-authored paper2018In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 14, no 11, article id e1006508Article in journal (Other academic)
    Abstract [en]

    Science is increasingly done in large teams, making it more likely that papers will be written by several authors from different institutes, disciplines, and cultural backgrounds. A small number of “Ten simple rules” papers have been written on collaboration and on writing but not on combining the two. Collaborative writing with multiple authors has additional challenges, including varied levels of engagement of coauthors, provision of fair credit through authorship or acknowledgements, acceptance of a diversity of work styles, and the need for clear communication. Miscommunication, a lack of leadership, and inappropriate tools or writing approaches can lead to frustration, delay of publication, or even the termination of a project.

    To provide insight into collaborative writing, we use our experience from the Global Lake Ecological Observatory Network (GLEON) to frame 10 simple rules for collaboratively writing a multi-authored paper. We consider a collaborative multi-authored paper to have three or more people from at least two different institutions. A multi-authored paper can be a result of a single discrete research project or the outcome of a larger research program that includes other papers based on common data or methods. The writing of a multi-authored paper is embedded within a broader context of planning and collaboration among team members. Our recommended rules include elements of both the planning and writing of a paper, and they can be iterative, although we have listed them in numerical order. It will help to revisit the rules frequently throughout the writing process. With the 10 rules outlined below, we aim to provide a foundation for writing multi-authored papers and conducting exciting and influential science.

  • Nowak-Sliwinska, Patrycja
    et al.
    Univ Lausanne, Univ Geneva, Fac Sci, Mol Pharmacol Grp,Sch Pharmaceut Sci,CMU, Rue Michel Servet 1, CH-1211 Geneva 4, Switzerland;Univ Geneva, Translat Res Ctr Oncohaematol, Geneva, Switzerland.
    Alitalo, Kari
    Univ Helsinki, Wihuri Res Inst & Translat Canc Biol Program, Helsinki, Finland.
    Allen, Elizabeth
    Katholieke Univ Leuven, Dept Oncol, Lab Tumor Microenvironm & Therapeut Resistance, VIB Ctr Canc Biol, Louvain, Belgium.
    Anisimov, Andrey
    Univ Helsinki, Wihuri Res Inst & Translat Canc Biol Program, Helsinki, Finland.
    Aplin, Alfred C.
    Univ Washington, Dept Pathol, Seattle, WA 98195 USA.
    Auerbach, Robert
    Univ Wisconsin, Madison, WI USA.
    Augustin, Hellmut G.
    Heidelberg Univ, Med Fac Mannheim, European Ctr Angiosci, Heidelberg, Germany;German Canc Res Ctr, Div Vasc Oncol & Metastasis Res, Heidelberg, Germany;German Canc Consortium, Heidelberg, Germany.
    Bates, David O.
    Univ Nottingham, Sch Med, Div Canc & Stem Cells, Nottingham, England.
    van Beijnum, Judy R.
    Vrije Univ Amsterdam, Dept Med Oncol, Canc Ctr Amsterdam, Angiogenesis Lab,Med Ctr, Boelelaan 1117, NL-1081 HV Amsterdam, Netherlands.
    Bender, R. Hugh F.
    Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92717 USA.
    Bergers, Gabriele
    Katholieke Univ Leuven, Dept Oncol, Lab Tumor Microenvironm & Therapeut Resistance, VIB Ctr Canc Biol, Louvain, Belgium;Univ Calif San Francisco, Dept Neurol Surg, Brain Tumor Res Ctr,Dept Neurol Surg, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA USA.
    Bikfalvi, Andreas
    Univ Bordeaux, Angiogenesis & Tumor Microenvironm Lab, INSERM, U1029, Pessac, France.
    Bischoff, Joyce
    Harvard Med Sch, Boston Childrens Hosp, Vasc Biol Program, Boston, MA USA;Harvard Med Sch, Boston Childrens Hosp, Dept Surg, Boston, MA USA.
    Boeck, Barbara C.
    Heidelberg Univ, Med Fac Mannheim, European Ctr Angiosci, Heidelberg, Germany;German Canc Res Ctr, Div Vasc Oncol & Metastasis Res, Heidelberg, Germany;German Canc Consortium, Heidelberg, Germany.
    Brooks, Peter C.
    Maine Med Ctr Res Inst, Ctr Mol Med, Scarborough, ME USA.
    Bussolino, Federico
    Univ Torino, Dept Oncol, Turin, Italy;Candiolo Canc Inst FPO IRCCS, I-10060 Candiolo, Italy.
    Cakir, Bertan
    Harvard Med Sch, Boston Childrens Hosp, Dept Ophthalmol, Boston, MA USA.
    Carmeliet, Peter
    Katholieke Univ Leuven, Dept Oncol, Lab Angiogenesis & Vasc Metab, Leuven, Belgium;Katholieke Univ Leuven, Leuven Canc Inst LKI, Leuven, Belgium;VIB, Ctr Canc Biol, Lab Angiogenesis & Vasc Metab, Leuven, Belgium.
    Castranova, Daniel
    Eunice Kennedy Shriver Natl Inst Child Hlth & Hum, Div Dev Biol, NIH, Bethesda, MD USA.
    Cimpean, Anca M.
    Victor Babes Univ Med & Pharm, Dept Microscop Morphol Histol, Angiogenesis Res Ctr, Timisoara, Romania.
    Cleaver, Ondine
    Univ Texas Southwestern Med Ctr Dallas, Dept Mol Biol, Ctr Regenerat Sci & Med, Dallas, TX 75390 USA.
    Coukos, George
    Univ Lausanne, Ludwig Inst Canc Res, Dept Oncol, Lausanne, Switzerland.
    Davis, George E.
    Univ Missouri, Sch Med, Dept Med Pharmacol & Physiol, Columbia, MO USA;Dalton Cardiovasc Ctr, Columbia, MO USA.
    De Palma, Michele
    Swiss Fed Inst Technol, Sch Life Sci, Lausanne, Switzerland.
    Dimberg, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology.
    Dings, Ruud P. M.
    Univ Arkansas Med Sci, Dept Radiat Oncol, Little Rock, AR 72205 USA.
    Djonov, Valentin
    Univ Bern, Inst Anat, Bern, Switzerland.
    Dudley, Andrew C.
    Univ Virginia, Dept Microbiol Immunol & Canc Biol, Charlottesville, VA USA;Univ Virginia, Emily Cour Canc Ctr, Charlottesville, VA USA.
    Dufton, Neil P.
    Imperial Coll London, Vasc Sci, Imperial Ctr Translat & Expt Med, Natl Heart & Lung Inst, London, England.
    Fendt, Sarah-Maria
    VIB Ctr Canc Biol, Lab Cellular Metab & Metab Regulat, Leuven, Belgium;Katholieke Univ Leuven, Lab Cellular Metab & Metab Regulat, Dept Oncol, Leuven, Belgium;Leuven Canc Inst, Leuven, Belgium.
    Ferrara, Napoleone
    Univ Calif San Diego, La Jolla, CA 92093 USA.
    Fruttiger, Marcus
    UCL, Inst Ophthalmol, London, England.
    Fukumura, Dai
    Massachusetts Gen Hosp, Dept Radiat Oncol, Edwin L Steele Labs, Boston, MA 02114 USA;Harvard Med Sch, Boston, MA 02114 USA.
    Ghesquiere, Bart
    VIB, VIB Ctr Canc Biol, Metabol Expertise Ctr, Leuven, Belgium;Katholieke Univ Leuven, Dept Oncol, Metabol Expertise Ctr, Leuven, Belgium.
    Gong, Yan
    Harvard Med Sch, Boston Childrens Hosp, Dept Ophthalmol, Boston, MA USA.
    Griffin, Robert J.
    Univ Arkansas Med Sci, Dept Radiat Oncol, Little Rock, AR 72205 USA.
    Harris, Adrian L.
    Univ Oxford, John Radcliffe Hosp, Mol Oncol Labs, Weatherall Inst Mol Med,Dept Oncol, Oxford, England.
    Hughes, Christopher C. W.
    Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92717 USA.
    Hultgren, Nan W.
    Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92717 USA.
    Iruela-Arispe, M. Luisa
    Univ Calif Los Angeles, MCDB, Los Angeles, CA USA.
    Irving, Melita
    Univ Lausanne, Ludwig Inst Canc Res, Dept Oncol, Lausanne, Switzerland.
    Jain, Rakesh K.
    Massachusetts Gen Hosp, Dept Radiat Oncol, Edwin L Steele Labs, Boston, MA 02114 USA;Harvard Med Sch, Boston, MA 02114 USA.
    Kalluri, Raghu
    Univ Texas MD Anderson Canc Ctr, Dept Canc Biol, Metastasis Res Ctr, Houston, TX 77030 USA.
    Kalucka, Joanna
    Katholieke Univ Leuven, Dept Oncol, Lab Angiogenesis & Vasc Metab, Leuven, Belgium;Katholieke Univ Leuven, Leuven Canc Inst LKI, Leuven, Belgium;VIB, Ctr Canc Biol, Lab Angiogenesis & Vasc Metab, Leuven, Belgium.
    Kerbel, Robert S.
    Univ Toronto, Dept Med Biophys, Sunnybrook Res Inst, Biol Sci Platform, Toronto, ON, Canada.
    Kitajewski, Jan
    Univ Illinois, Dept Physiol & Biophys, Chicago, IL 60680 USA.
    Klaassen, Ingeborg
    Univ Amsterdam, Ocular Angiogenesis Grp, Dept Ophthalmol, Acad Med Ctr, Amsterdam, Netherlands;Univ Amsterdam, Ocular Angiogenesis Grp, Dept Med Biol, Acad Med Ctr, Amsterdam, Netherlands.
    Kleinmann, Hynda K.
    George Washington Univ, Sch Med, Washington, DC USA.
    Koolwijk, Pieter
    Univ Lausanne, Dept Ophthalmol, Jules Gonin Eye Hosp, Fdn Asile Aveugles, Lausanne, Switzerland.
    Kuczynski, Elisabeth
    Univ Toronto, Dept Med Biophys, Sunnybrook Res Inst, Biol Sci Platform, Toronto, ON, Canada.
    Kwak, Brenda R.
    Univ Geneva, Dept Pathol & Immunol, Geneva, Switzerland.
    Marien, Koen
    HistoGeneX, Antwerp, Belgium.
    Melero-Martin, Juan M.
    Harvard Med Sch, Boston Childrens Hosp, Dept Cardiac Surg, Boston, MA USA.
    Munn, Lance L.
    Massachusetts Gen Hosp, Dept Radiat Oncol, Edwin L Steele Labs, Boston, MA 02114 USA;Harvard Med Sch, Boston, MA 02114 USA.
    Nicosia, Roberto F.
    Univ Washington, Dept Pathol, Seattle, WA 98195 USA;VA Puget Sound Hlth Care Syst, Pathol & Lab Med Serv, Seattle, WA USA.
    Noel, Agnes
    Univ Liege, Lab Tumor & Dev Biol, GIGA Canc, Liege, Belgium.
    Nurro, Jussi
    Univ Eastern Finland, Dept Biotechnol & Mol Med, Kuopio, Finland.
    Olsson, Anna-Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Petrova, Tatiana V.
    Ludwig Inst Canc Res Lausanne, Dept Oncol UNIL CHUV, Lausanne, Switzerland.
    Pietras, Kristian
    Dept Lab Med, Div Translat Canc Res, Lund, Sweden.
    Pili, Roberto
    Indiana Univ, Simon Canc Ctr, Genitourinary Program, Indianapolis, IN 46204 USA.
    Pollard, Jeffrey W.
    Univ Edinburgh, Med Res Council, Ctr Reprod Hlth, Coll Med & Vet Med, Edinburgh, Midlothian, Scotland.
    Post, Mark J.
    Maastricht Univ, Dept Physiol, Maastricht, Netherlands.
    Quax, Paul H. A.
    LUMC, Einthoven Lab Expt Vasc Med, Dept Surg, Leiden, Netherlands.
    Rabinovich, Gabriel A.
    Consejo Nacl Invest Cient & Tecn, Natl Council Sci & Tech Invest, Lab Immunopathol, Inst Biol & Expt Med, Buenos Aires, DF, Argentina.
    Raica, Marius
    Victor Babes Univ Med & Pharm, Dept Microscop Morphol Histol, Angiogenesis Res Ctr, Timisoara, Romania.
    Randi, Anna M.
    Imperial Coll London, Vasc Sci, Imperial Ctr Translat & Expt Med, Natl Heart & Lung Inst, London, England.
    Ribatti, Domenico
    Univ Bari, Med Sch, Dept Basic Med Sci Neurosci & Sensory Organs, Bari, Italy;Natl Canc Inst Giovanni Paolo II, Bari, Italy.
    Ruegg, Curzio
    Univ Fribourg, Dept Oncol Microbiol & Immunol, Fac Sci & Med, Fribourg, Switzerland.
    Schlingemann, Reinier O.
    Univ Amsterdam, Ocular Angiogenesis Grp, Dept Ophthalmol, Acad Med Ctr, Amsterdam, Netherlands;Univ Amsterdam, Ocular Angiogenesis Grp, Dept Med Biol, Acad Med Ctr, Amsterdam, Netherlands;Univ Lausanne, Dept Ophthalmol, Jules Gonin Eye Hosp, Fdn Asile Aveugles, Lausanne, Switzerland.
    Schulte-Merker, Stefan
    WWU, Inst Cardiovasc Organogenesis & Regenerat, Fac Med, Munster, Germany.
    Smith, Lois E. H.
    Harvard Med Sch, Boston Childrens Hosp, Dept Ophthalmol, Boston, MA USA.
    Song, Jonathan W.
    Ohio State Univ, Dept Mech & Aerosp Engn, Columbus, OH 43210 USA;Ohio State Univ, Ctr Comprehens Canc, Columbus, OH 43210 USA.
    Stacker, Steven A.
    Univ Melbourne, Tumour Angiogenesis & Microenvironm Program, Peter MacCallum Canc Ctr & Sir Peter MacCallum, Dept Oncol, Melbourne, Vic, Australia.
    Stalin, Jimmy
    WWU, Inst Cardiovasc Organogenesis & Regenerat, Fac Med, Munster, Germany.
    Stratman, Amber N.
    Eunice Kennedy Shriver Natl Inst Child Hlth & Hum, Div Dev Biol, NIH, Bethesda, MD USA.
    Van de Velde, Maureen
    Univ Liege, Lab Tumor & Dev Biol, GIGA Canc, Liege, Belgium.
    van Hinsbergh, Victor W. M.
    Univ Lausanne, Dept Ophthalmol, Jules Gonin Eye Hosp, Fdn Asile Aveugles, Lausanne, Switzerland.
    Vermeulen, Peter B.
    HistoGeneX, Antwerp, Belgium;Sint Augustinus & Univ Antwerp, Translat Canc Res Unit, GZA Hosp, Antwerp, Belgium.
    Waltenberger, Johannes
    Univ Munster, Med Fac, Albert Schweitzer Campus 1, Munster, Germany.
    Weinstein, Brant M.
    Eunice Kennedy Shriver Natl Inst Child Hlth & Hum, Div Dev Biol, NIH, Bethesda, MD USA.
    Xin, Hong
    Univ Calif San Diego, La Jolla, CA 92093 USA.
    Yetkin-Arik, Bahar
    Univ Amsterdam, Ocular Angiogenesis Grp, Dept Ophthalmol, Acad Med Ctr, Amsterdam, Netherlands;Univ Amsterdam, Ocular Angiogenesis Grp, Dept Med Biol, Acad Med Ctr, Amsterdam, Netherlands.
    Yla-Herttuala, Seppo
    Univ Eastern Finland, Dept Biotechnol & Mol Med, Kuopio, Finland.
    Yoder, Mervin C.
    Indiana Univ Sch Med, Dept Pediat, Indianapolis, IN 46202 USA.
    Griffioen, Arjan W.
    Vrije Univ Amsterdam, Dept Med Oncol, Canc Ctr Amsterdam, Angiogenesis Lab,Med Ctr, Boelelaan 1117, NL-1081 HV Amsterdam, Netherlands.
    Consensus guidelines for the use and interpretation of angiogenesis assays2018In: Angiogenesis, ISSN 0969-6970, E-ISSN 1573-7209, Vol. 21, no 3, p. 425-532Article, review/survey (Refereed)
    Abstract [en]

    The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference.