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  • 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
  • Public defence: 2018-12-20 09:15 A1:111a, BMC, Uppsala
    Ahnfelt, Emelie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    In vitro evaluation of formulations used in the treatment of hepatocellular carcinoma2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Hepatocellular carcinoma (HCC) causes ~ 600,000 deaths annually, making it the second most deadly cancer form. HCC is classified into five stages and for the intermediate HCC treatment, the two most commonly used drug delivery systems (DDSs) are lipiodol-based emulsions and drug-eluting beads. The aims of this thesis were to develop in vitro methods suitable for studying these DDSs. It is important to investigate the release mechanisms and release rates with relevant in vitro methods, as this can improve the understanding of the in vivo performance. Miniaturized in vitro methods with sample reservoirs separated from the release medium by a diffusion barrier were developed and shown to be suitable for studying drug release from particle DDSs (Paper I). In Paper II these methods were further developed and used to study the release of doxorubicin (DOX) from the clinically used drug-eluting beads. DOX release rates were affected by the method set-up and the characteristics of the release medium. The choice of method and volume of release medium could improve the in vivo-likeness of the in vitro release profiles. Applied theoretical models suggested a film-controlled type of DOX release mechanism from the beads when self-aggregation, DOX-bead interaction, and DOX deprotonation were taken into account.

    A micropipette-assisted microscopy method was used to further improve the understanding of the release mechanism of amphiphilic molecules from the beads (Paper III). A detailed analysis suggested an internal depletion-layer model dependent on molecular self-aggregation for the release. It was further suggested that a simple ion-exchange mechanism is unrealistic in physiological conditions.

    The important pharmaceutical factors for the emulsion-based formulations were investigated in Paper IV. DOX solubility, lipid phase distribution, and emulsion stability increased when the contrast agent iohexol was added. Also, an increase in release half-life (h) was observed from emulsions with iohexol.

    The in vitro methods and theoretical models presented in this thesis can be used during development and optimization of future DDSs.

    List of papers
    1. A miniaturized in vitro release method for investigating drug-release mechanisms
    Open this publication in new window or tab >>A miniaturized in vitro release method for investigating drug-release mechanisms
    2015 (English)In: International Journal of Pharmaceutics, ISSN 0378-5173, E-ISSN 1873-3476, Vol. 486, no 1-2, p. 339-349Article in journal (Refereed) Published
    Abstract [en]

    We have evaluated a miniaturized in vitro method, based on the mDISS Profiler (TM) technique that enables on-line monitoring of drug release from a 21 mu l sample with 10 ml of release medium. Four model drugs in eight clinically used formulations, including both solid and non-solid drug delivery systems, were investigated. The acquired data were compared with historical in vitro release data from the same formulations. Use of the Weibull function to describe the in vitro drug-release profiles allowed discrimination between the selected formulations with respect to the drug-release mechanisms. Comparison of the release data from the same formulation in different in vitro set-ups showed that the methodology used can affect the mechanism of in vitro release. We also evaluated the ability of the in vitro methods to predict in vivo activity by comparing simulated plasma concentration-time profiles acquired from the application of the biopharmaceutical software GI-Sim to the in vitro observations. In summary, the simulations based on the miniaturized-method release data predicted the plasma profiles as well as or more accurately than simulations based on the historical release data in 71% of the cases and this miniaturized in vitro method appears to be applicable for both solid and non-solid formulations.

    Keywords
    In vitro release methods, Release mechanisms, Weibull function, GI-Sim, In vivo prediction
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-255064 (URN)10.1016/j.ijpharm.2015.03.076 (DOI)000353999100037 ()25843760 (PubMedID)
    Available from: 2015-06-22 Created: 2015-06-12 Last updated: 2018-10-30Bibliographically approved
    2. In Vitro Release Mechanisms of Doxorubicin From a Clinical Bead Drug-Delivery System
    Open this publication in new window or tab >>In Vitro Release Mechanisms of Doxorubicin From a Clinical Bead Drug-Delivery System
    2016 (English)In: Journal of Pharmaceutical Sciences, ISSN 0022-3549, E-ISSN 1520-6017, Vol. 105, no 11, p. 3387-3398Article in journal (Refereed) Published
    Abstract [en]

    The release rate of doxorubicin (DOX) from the drug-delivery system (DDS), DC Bead, was studied by 2 miniaturized in vitro methods: free-flowing and sample reservoir. The dependencies of the release mechanisms on in vitro system conditions were investigated experimentally and by theoretical modeling. An inverse relationship was found between release rates and bead size, most likely due to the greater total surface area. The release rates correlated positively with temperature, release medium volume, and buffer strength, although the release medium volume had larger effect than the buffer strength. The sample reservoir method generated slower release rates, which described the in vivo release profile more accurately than the free-flowing method. There was no difference between a pH of 6.3 or 7.4 on the release rate, implying that the slightly acidic tumor microenvironment is less importance for drug release. A positive correlation between stirring rate and release rate for all DDS sizes was observed, which suggests film controlled release. Theoretical modeling highlighted the influence of local equilibrium of protonation, self-aggregation, and bead material interactions of DOX. The theoretical release model might describe the observed larger sensitivity of the release rate to the volume of the release medium compared to buffer strength. A combination of miniaturized in vitro methods and theoretical modeling are useful to identify the important parameters and processes for DOX release from a micro gel-based DDS.

    Keywords
    controlled release, diffusion, dissolution, dissolution rate, drug-delivery systems, in vitro models, mathematical model, microspheres
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-311211 (URN)10.1016/j.xphs.2016.08.011 (DOI)000388268200018 ()27663384 (PubMedID)
    Funder
    Swedish Research Council, 521-2011-373
    Available from: 2016-12-22 Created: 2016-12-22 Last updated: 2018-10-30Bibliographically approved
    3. Single bead investigation of a clinical drug delivery system – a novel release mechanism
    Open this publication in new window or tab >>Single bead investigation of a clinical drug delivery system – a novel release mechanism
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    2018 (English)In: Journal of Controlled Release, ISSN 0168-3659, E-ISSN 1873-4995, Vol. 292, p. 235-247Article in journal (Other academic) Published
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-360988 (URN)10.1016/j.jconrel.2018.11.011 (DOI)
    Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-11-19
    4. In vitro evaluation of lipiodol-based emulsions in clinical use
    Open this publication in new window or tab >>In vitro evaluation of lipiodol-based emulsions in clinical use
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-360987 (URN)
    Available from: 2018-09-20 Created: 2018-09-20 Last updated: 2018-10-30
  • 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.
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    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
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    (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
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    (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
  • Public defence: 2018-12-21 13:15 Polhemsalen, Ångströmlaboratoriet, Uppsala
    Blomqvist, Björn Rune Helmer
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Gaussian process models of social change2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Social systems produce complex and nonlinear relationships in the indicator variables that describe them. Traditional statistical regression techniques are commonly used in the social sciences to study such systems. These techniques, such as standard linear regression, can prevent the discovery of the complex underlying mechanisms and rely too much on the expertise and prior beliefs of the data analyst. In this thesis, we present two methodologies that are designed to allow the data to inform us about these complex relations and provide us with interpretable models of the dynamics.

    The first methodology is a Bayesian approach to analysing the relationship between indicator variables by finding the parametric functions that best describe their interactions. The parametric functions with the highest model evidence are found by fitting a large number of potential models to the data using Bayesian linear regression and comparing their respective model evidence. The methodology is computationally fast due to the use of conjugate priors, and this allows for inference on large sets of models. The second methodology is based on a Gaussian processes framework and is designed to overcome the limitations of the first modelling approach. This approach balances the interpretability of more traditional parametric statistical methods with the predictability and flexibility of non-parametric Gaussian processes.

    This thesis contains four papers where we apply the methodologies to both real-life problems in the social sciences as well as on synthetic data sets. In paper I, the first methodology (Bayesian linear regression) is applied to the classic problem of how democracy and economic development interact. In paper II and IV, we apply the second methodology (Gaussian processes) to study changes in the political landscape and demographic shifts in Sweden in the last decades. In paper III, we apply the second methodology on a synthetic data set to perform parameter estimation on complex dynamical systems.

    List of papers
    1. Using Bayesian dynamical systems, model averaging and neural networks to determine interactions between socio-economic indicators
    Open this publication in new window or tab >>Using Bayesian dynamical systems, model averaging and neural networks to determine interactions between socio-economic indicators
    2018 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 5, article id e0196355Article in journal (Refereed) Published
    Abstract [en]

    Social and economic systems produce complex and nonlinear relationships in the indicator variables that describe them. We present a Bayesian methodology to analyze the dynamical relationships between indicator variables by identifying the nonlinear functions that best describe their interactions. We search for the 'best' explicit functions by fitting data using Bayesian linear regression on a vast number of models and then comparing their Bayes factors. The model with the highest Bayes factor, having the best trade-off between explanatory power and interpretability, is chosen as the 'best' model. To be able to compare a vast number of models, we use conjugate priors, resulting in fast computation times. We check the robustness of our approach by comparison with more prediction oriented approaches such as model averaging and neural networks. Our modelling approach is illustrated using the classical example of how democracy and economic growth relate to each other. We find that the best dynamical model for democracy suggests that long term democratic increase is only possible if the economic situation gets better. No robust model explaining economic development using these two variables was found.

    Place, publisher, year, edition, pages
    PUBLIC LIBRARY SCIENCE, 2018
    National Category
    Probability Theory and Statistics
    Identifiers
    urn:nbn:se:uu:diva-359665 (URN)10.1371/journal.pone.0196355 (DOI)000431757400027 ()29742126 (PubMedID)
    Available from: 2018-09-05 Created: 2018-09-05 Last updated: 2018-10-30Bibliographically approved
    2. Explaining and predicting the rise of a radical right-wing party using Gaussian processes
    Open this publication in new window or tab >>Explaining and predicting the rise of a radical right-wing party using Gaussian processes
    (English)In: Article in journal (Other academic) Submitted
    National Category
    Mathematics
    Identifiers
    urn:nbn:se:uu:diva-364653 (URN)
    Available from: 2018-10-30 Created: 2018-10-30 Last updated: 2018-10-30
    3. Model selection and parameter estimation of complex dynamical systems using semi-parametric Gaussian processes
    Open this publication in new window or tab >>Model selection and parameter estimation of complex dynamical systems using semi-parametric Gaussian processes
    (English)Manuscript (preprint) (Other academic)
    National Category
    Mathematics
    Research subject
    Mathematics with specialization in Applied Mathematics
    Identifiers
    urn:nbn:se:uu:diva-364652 (URN)
    Available from: 2018-10-30 Created: 2018-10-30 Last updated: 2018-10-30
    4. Last night in Sweden? Using Gaussian processes to study changing demographics at the level of municipalities
    Open this publication in new window or tab >>Last night in Sweden? Using Gaussian processes to study changing demographics at the level of municipalities
    (English)In: Article in journal (Other academic) Submitted
    National Category
    Mathematics
    Identifiers
    urn:nbn:se:uu:diva-364654 (URN)
    Available from: 2018-10-30 Created: 2018-10-30 Last updated: 2018-10-30
  • Public defence: 2018-12-21 13:15 Humanistiska teatern, Uppsala
    Schumann, Åsa
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Theology, Department of Theology.
    Vilken mening!?: En blandad metodstudie i religionspsykologi av meningsskapandets betydelse för skolungdomar2018Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The purpose of the study was to explore the role of religion in the development of a meaning system among Swedish adolescents by examining the interactions of their: sense of coherence (SOC), identity process (U-MICS), moral development (SRM-SF), and views on existential and religious questions.

    The study used a Mixed Methods Design, with a Sequential Explanatory Strategy consisting of quantitative and qualitative parts. In the quantitative part of the study, 90 students in 8th grade, 50 girls and 40 boys, participated. The qualitative part of the study consisted of 24 semi-structured interviews drawn from the original group.

    According to the results, there was a relation between SOC and the following variables in the identity process (U-MICS): commitment to school and reconsideration of commitment to friends, and commitment to school and perception of the importance of religion. The SOC value among girls was significantly lower than among boys. The results did not indicate a significant relationship between moral development, SOC values, and the religious variables.

    In the qualitative interview results, the participants in the commitment phase relating to school expressed more satisfaction with their school situations and relationships than those who were predominantly in the reconsideration of commitment phase. Those with a higher level of commitment to school were also more likely to express the view that religion was important in life. Interview material showed that those young people who expressed the belief that religion was important in life today or believed that religion constituted a potential future source of strength dominated the group with higher SOC. The results served to reinforce theoretical perspectives on the meaning-making function of religion. The study results suggest that safe and trustful relationships with peers and adults related closely to SOC values among these adolescents and were singled out as their most important sources of strength and support in life.

  • Public defence: 2019-01-11 13:00 B41, Uppsala
    Söderholm, Annika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology.
    The Importance of Being Promiscuous: Understanding enzyme function, specificity, and evolution through structure2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Enzymes are known to be amazingly specific and efficient catalysts. However, many enzymes also have so-called promiscuous functions, i.e., they are able to catalyze other reactions than their main one. The promiscuous activities are often low, serendipitous, and under neutral selection but if conditions arise that make them beneficial, they can play an important role in the evolution of new enzymes. In this thesis, I present three studies where we have characterized different enzyme families by structural and biochemical methods. The studies demonstrate the occurrence of enzyme promiscuity and its potential role in evolution and organismal adaptation.

    In the first study, I describe the characterization of wild type and mutant HisA enzymes from Salmonella enterica. In the first part of this study, we could clarify the mechanistic cycle of HisA by solving crystal structures that showed different conformations of wild type HisA in complex with its labile substrate ProFAR (N´-[(5´-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide). In the second part of this study, structures of mutant enzymes from a real-time evolution study provided us with an atomic-level description of how HisA had evolved a new function. The HisA mutants had acquired TrpF activity, either in addition to (bifunctional generalists) or instead of (TrpF specialists) their HisA activity. In the second study, I present the crystal structure and demonstrate promiscuous activity of the TrpC enzyme from Pseudomonas aeruginosa. The activity data demonstrates that the enzyme can turn over a substrate that lacks a substituent that was previously considered essential for catalysis. In the third study, I present the structural and functional characterization of SAM (S-Adenosyl methionine) hydrolases from bacteriophages. These enzymes were discovered because of their ability to rescue auxotrophic bacteria by inducing expression of a promiscuous bacterial enzyme.  

    List of papers
    1. Structure of a phage-encoded SAM hydrolase enzyme provides insights in substrate binding and catalysis
    Open this publication in new window or tab >>Structure of a phage-encoded SAM hydrolase enzyme provides insights in substrate binding and catalysis
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    SAM hydrolase, phage enzyme
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-366689 (URN)
    Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-22
    2. Two-step Ligand Binding in a (βα)8 Barrel Enzyme: Substrate-bound Structures Shed New Light on the Catalytic Cycle of HisA
    Open this publication in new window or tab >>Two-step Ligand Binding in a (βα)8 Barrel Enzyme: Substrate-bound Structures Shed New Light on the Catalytic Cycle of HisA
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    2015 (English)In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 290, no 41, p. 24657-24668Article in journal (Refereed) Published
    Abstract [en]

    HisA is a (βα)8 barrel enzyme that catalyzes the Amadori rearrangement of ProFAR to PRFAR in the histidine biosynthesis pathway and it is a paradigm for the study of enzyme evolution. Still, its exact catalytic mechanism has remained unclear. Here, we present crystal structures of wild type Salmonella enterica HisA (SeHisA) in its apo state and of mutants D7N and D7N/D176A in complex with two different conformations of the labile substrate ProFAR, which was structurally visualized for the first time. Site-directed mutagenesis and kinetics demonstrated that Asp7 acts as the catalytic base and Asp176 as the catalytic acid. The SeHisA structures with ProFAR display two different states of the long loops on the catalytic face of the structure, and demonstrate that initial binding of ProFAR to the active site is independent of loop interactions. When the long loops enclose the substrate, ProFAR adopts an extended conformation where its non-reacting half is in a product-like conformation. This change is associated with shifts in a hydrogen-bond network including His47, Asp129, Thr171 and Ser202, all shown to be functionally important. The closed-conformation structure is highly similar to the bi-functional HisA homologue PriA in complex with PRFAR, thus proving that structure and mechanism are conserved between HisA and PriA. This study clarifies the mechanistic cycle of HisA and provides a striking example of how an enzyme and its substrate can undergo coordinated conformational changes before catalysis.

    National Category
    Structural Biology
    Identifiers
    urn:nbn:se:uu:diva-260701 (URN)10.1074/jbc.M115.678086 (DOI)000362598300003 ()26294764 (PubMedID)
    Funder
    Swedish Research CouncilSwedish Foundation for Strategic Research EU, FP7, Seventh Framework Programme, 283570
    Available from: 2015-08-23 Created: 2015-08-23 Last updated: 2018-11-22
    3. Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes
    Open this publication in new window or tab >>Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes
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    2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 8, p. 4727-4732Article in journal (Refereed) Published
    Abstract [en]

    New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dynamics, kinetics, and mass spectrometry to explain the molecular innovations that arose during a previous real-time evolution experiment. In that experiment, the (βα)8 barrel enzyme HisA was under selection for two functions (HisA and TrpF), resulting in duplication and divergence of the hisA gene to encode TrpF specialists, HisA specialists, and bifunctional generalists. We found that selection affects enzyme structure and dynamics, and thus substrate preference, simultaneously and sequentially. Bifunctionality is associated with two distinct sets of loop conformations, each essential for one function. We observed two mechanisms for functional specialization: structural stabilization of each loop conformation and substrate-specific adaptation of the active site. Intracellular enzyme performance, calculated as the product of catalytic efficiency and relative expression level, was not linearly related to fitness. Instead, we observed thresholds for each activity above which further improvements in catalytic efficiency had little if any effect on growth rate. Overall, we have shown how beneficial substitutions selected during real-time evolution can lead to manifold changes in enzyme function and bacterial fitness. This work emphasizes the speed at which adaptive evolution can yield enzymes with sufficiently high activities such that they no longer limit the growth of their host organism, and confirms the (βα)8 barrel as an inherently evolvable protein scaffold.

    Keywords
    HisA, TrpF, adaptive evolution, enzyme performance threshold
    National Category
    Evolutionary Biology Structural Biology
    Research subject
    Biology with specialization in Structural Biology; Biochemistry; Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-320223 (URN)10.1073/pnas.1618552114 (DOI)000400358000052 ()
    Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2018-11-22Bibliographically approved
    4. A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function
    Open this publication in new window or tab >>A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function
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    2018 (English)In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, no 8, p. 1321-1330Article in journal (Refereed) Published
    Abstract [en]

    One key concept in the evolution of new functions is the ability of enzymes to perform promiscuous side-reactions that serve as a source of novelty that may become beneficial under certain conditions. Here, we identify a mechanism where a bacteriophage-encoded enzyme introduces novelty by inducing expression of a promiscuous bacterial enzyme. By screening for bacteriophage DNA that rescued an auxotrophic Escherichia coli mutant carrying a deletion of the ilvA gene, we show that bacteriophage-encoded S-adenosylmethionine (SAM) hydrolases reduce SAM levels. Through this perturbation of bacterial metabolism, expression of the promiscuous bacterial enzyme MetB is increased, which in turn complements the absence of IlvA. These results demonstrate how foreign DNA can increase the metabolic capacity of bacteria, not only by transfer of bona fide new genes, but also by bringing cryptic bacterial functions to light via perturbations of cellular physiology.

    Place, publisher, year, edition, pages
    Nature Publishing Group, 2018
    National Category
    Evolutionary Biology Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-355286 (URN)10.1038/s41559-018-0568-5 (DOI)000439505600024 ()
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg Foundation
    Available from: 2018-06-27 Created: 2018-06-27 Last updated: 2018-11-22Bibliographically approved
    5. Structure and substrate ambiguity of TrpC from Pseudomonas aeruginosa
    Open this publication in new window or tab >>Structure and substrate ambiguity of TrpC from Pseudomonas aeruginosa
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The enzyme TrpC catalyzes the formation of Indole-3-glycerol phosphate (IGP) from 1-(o-carboxyphenylamino) 1-deoxyribulose 5-phosphate as part of the tryptophan biosynthesis pathway. The reaction mechanism follows a series of condensation, decarboxylation, and dehydration. The decarboxylation has been assumed to constitute an essential step of the mechanism since no activity with decarboxylated substrate was observed in an early study on the TrpC:TrpF fusion protein from Escherichia coli (Smith 1962). Here, we refute this assumption by demonstrating IGP formation catalyzed by both TrpC from Pseudomonas aeruginosa and from E.coli. We show that P. aeruginosa TrpC is more active on decarboxylated substrate than E.coli TrpC and, by solving the crystal structure of P. aeruginosa TrpC, we provide structure-based hypotheses on their difference in promiscuous activity.

    Keywords
    TrpC, IGPS
    National Category
    Biochemistry and Molecular Biology
    Research subject
    Biochemistry
    Identifiers
    urn:nbn:se:uu:diva-366660 (URN)
    Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-30
  • Public defence: 2019-01-18 09:15 Room B21, Uppsala
    Jiang, Wangshu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology.
    Of spiders, bugs, and men: Structural and functional studies of proteins involved in assembly2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Protein assembly enables complex machineries while being economical with genetic information. However, protein assembly also constitutes a potential threat to the host, and needs to be carefully regulated.

    Sulfate is a common source of sulfur for cysteine synthesis in bacteria. A putative sulfate permease CysZ from Escherichia coli appears much larger than its apparent molecular mass when analyzed by chromatography and native gel. Clearly CysZ undergoes homo-oligomerization. Using isothermal titration calorimetry, we confirmed that CysZ binds to its putative substrate sulfate, and also sulfite with higher affinity. CysZ-mediated sulfate transport—in both E. coli whole cells and proteoliposomes—was inhibited in the presence of sulfite, indicating a feedback inhibition mechanism.

    Proteus mirabilis is a Gram-negative bacterium causing urinary tract infections. Its simultaneous expression of multiple fimbriae enables colonization and biofilm formation. Fimbriae are surface appendages assembled from protein subunits, with distal adhesins specifically recognizing host-cell receptors. We present the first three structures of P. mirabilis fimbrial adhesins. While UcaD and AtfE adopt the canonical immunoglobulin-like fold, MrpH has a previously unknown fold. The coordination of Zn or Cu ion by three conserved histidine residues in MrpH is required for MrpH-dependent biofilm formation.

    Spider silk is an assembly of large proteins called spidroins. The N-terminal domain (NT) of spidroins senses the pH decrease along the silk spinning gland, and transits from monomer to dimer. A locked NT dimer interlinks spidroin molecules into polymers. We identified a new asymmetric dimer form of NT by x-ray crystallography. With additional evidence from small angle x-ray scattering (SAXS), we propose the asymmetric dimer as a common intermediate of NT in silk formation.

    Alzheimer’s disease is a life-threatening dementia, where aggregation-prone Aβ peptides self-assemble into amyloid fibrils. Bri2 BRICHOS is a molecular chaperone that efficiently delays Aβ fibrillation, and protects the region of its pro-protein with high β-propensity from aggregation. Combining SAXS and microscale thermophoresis data, we confirmed binding between Bri2 BRICHOS and its native client peptide. Using site-directed mutagenesis, we showed that three conserved tyrosine residues in Bri2 BRICHOS are important for its anti-Aβ fibrillation activity.

    List of papers
    1. The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite
    Open this publication in new window or tab >>The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite
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    2014 (English)In: Biochimica et Biophysica Acta - Biomembranes, ISSN 0005-2736, E-ISSN 1879-2642, Vol. 1838, no 7, p. 1809-1816Article in journal (Refereed) Published
    Abstract [en]

    The Escherichia coli inner membrane protein CysZ mediates the sulfate uptake subsequently utilized for the synthesis of sulfur-containing compounds in cells. Here we report the purification and functional characterization of CysZ. Using Isothermal Titration Calorimetry, we have observed interactions between CysZ and its putative substrate sulfate. Additional sulfur-containing compounds from the cysteine synthesis pathway have also been analyzed for their abilities to interact with CysZ. Our results suggest that CysZ is dedicated to a specific pathway that assimilates sulfate for the synthesis of cysteine. Sulfate uptake via CysZ into E. coil whole cells and proteoliposome offers direct evidence of CysZ being able to mediate sulfate uptake. In addition, the cysteine synthesis pathway intermediate sulfite can interact directly with CysZ with higher affinity than sulfate. The sulfate transport activity is inhibited in the presence of sulfite, suggesting the existence of a feedback inhibition mechanism in which sulfite regulates sulfate uptake by CysZ. Sulfate uptake assays performed at different extracellular pH and in the presence of a proton uncoupler indicate that this uptake is driven by the proton gradient. (C) 2014 Elsevier B.V. All rights reserved.

    Keywords
    CysZ, Sulfate, Transport, Membrane protein, Inhibition
    National Category
    Biochemistry and Molecular Biology Biophysics
    Identifiers
    urn:nbn:se:uu:diva-227987 (URN)10.1016/j.bbamem.2014.03.003 (DOI)000336695300014 ()
    Available from: 2014-07-04 Created: 2014-07-02 Last updated: 2018-11-23Bibliographically approved
    2. Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis.
    Open this publication in new window or tab >>Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis.
    2018 (English)In: Acta crystallographica. Section D, Structural biology, ISSN 2059-7983, Vol. 74, no Pt 11, p. 1053-1062Article in journal (Refereed) Published
    Abstract [en]

    The important uropathogen Proteus mirabilis encodes a record number of chaperone/usher-pathway adhesive fimbriae. Such fimbriae, which are used for adhesion to cell surfaces/tissues and for biofilm formation, are typically important virulence factors in bacterial pathogenesis. Here, the structures of the receptor-binding domains of the tip-located two-domain adhesins UcaD (1.5 Å resolution) and AtfE (1.58 Å resolution) from two P. mirabilis fimbriae (UCA/NAF and ATF) are presented. The structures of UcaD and AtfE are both similar to the F17G type of tip-located fimbrial receptor-binding domains, and the structures are very similar despite having only limited sequence similarity. These structures represent an important step towards a molecular-level understanding of P. mirabilis fimbrial adhesins and their roles in the complex pathogenesis of urinary-tract infections.

    Keywords
    Proteus mirabilis, adhesins, fimbriae, urinary-tract infection
    National Category
    Structural Biology
    Identifiers
    urn:nbn:se:uu:diva-366693 (URN)10.1107/S2059798318012391 (DOI)30387764 (PubMedID)
    Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-23
    3. Structural basis for MrpH-dependent Proteus mirabilis biofilm formation
    Open this publication in new window or tab >>Structural basis for MrpH-dependent Proteus mirabilis biofilm formation
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Proteus mirabilis is a Gram-negative uropathogen and the major causative agent in catheter-associated  (CAUTI) and complicated UTIs. Mannose resistant Proteus-like fimbriae (MR/P) are crucially important for P. mirabilis infectivity and are required for biofilm formation and auto-aggregation, as well as for bladder and kidney colonisation. Here, the X-ray structure of the MR/P tip-located MrpH adhesin is reported. The structure has an unusual fold not previously observed, and contains a transition metal centre with Cu2+ or Zn2+ ligated by three conserved histidine residues and a ligand. Using metal complementation biofilm assays and site directed mutagenesis of the three histidines we show that an intact metal binding site occupied by zinc or copper is essential for MR/P-mediated biofilm formation. The studies presented here provide important clues as to the mechanism of MR/P-mediated biofilm formation and will serve as a starting point for identifying the physiological MR/P receptor(s).

    Keywords
    fimbriae; adhesins; biofilm; urinary tract infection; Proteus mirabilis
    National Category
    Structural Biology
    Identifiers
    urn:nbn:se:uu:diva-366696 (URN)
    Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-23
    4. Conversion of spidroin dope to spider silk involves an asymmetric dimer intermediate
    Open this publication in new window or tab >>Conversion of spidroin dope to spider silk involves an asymmetric dimer intermediate
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Structural Biology
    Identifiers
    urn:nbn:se:uu:diva-366699 (URN)
    Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-23
    5. Bri2 BRICHOS domain binds Bri23 and depends on conserved face A tyrosine residues for anti-amyloid activity
    Open this publication in new window or tab >>Bri2 BRICHOS domain binds Bri23 and depends on conserved face A tyrosine residues for anti-amyloid activity
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    (English)Manuscript (preprint) (Other academic)
    Keywords
    Bri2, BRICHOS, amyloid, Alzheimer's disease, molecular chaperone
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-366698 (URN)
    Available from: 2018-11-22 Created: 2018-11-22 Last updated: 2018-11-23
  • Public defence: 2019-01-18 13:15 B41, Uppsala
    Ibrahim, Moustafa M. A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Pharmacometric evaluation and improvement of models and study designs - applied in diabetes2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Pharmacometric models are increasingly used to improve the efficiency of the drug development process and increase our understanding of the studied underlying pathophysiological system. These models require assumptions for handling different types of data and the different model components, and the appropriateness of such assumptions must be carefully inspected for unbiased conclusions. The aim of this thesis was to develop new models, that by acknowledging the complexity of the data captures more information, and novel methodologies for model evaluation, as well as applying models to improve study designs, with practical illustrations in the therapeutic area of diabetes. Two new models were developed. An integrated minimal model was developed to enable clinical trial simulations in presence of endogenous insulin secretion while deriving the important physiological indices for clinical diagnosis. A multi-state model was developed for improved handling of survival data in presence of competing risks and interval-censored data. New methodologies for model evaluations were developed that include residual modeling and linearization for assessing possible improvements of the structural and statistical model components as well as using simulations to assess the captured information from the data between structurally different models. A mapping approach for parameters carrying similar information between different models was developed, allowing the derivation of physiological indices from the integrated glucose insulin model. Models were also successfully applied with the purpose of improving study designs, either based on anticipated drug effect or for assessment of physiological indices. In conclusion, new more informative models were developed by acknowledging the complexity of the data, novel methods were proposed and applied for model development/evaluation process, and models were used to improve study designs for clinical trials and clinical diagnosis. 

    List of papers
    1. Study Design Selection in Early Clinical Anti-Hyperglycemic Drug Development: A Simulation Study of Glucose Tolerance Tests
    Open this publication in new window or tab >>Study Design Selection in Early Clinical Anti-Hyperglycemic Drug Development: A Simulation Study of Glucose Tolerance Tests
    2018 (English)In: CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY, ISSN 2163-8306, Vol. 7, no 7, p. 432-441Article in journal (Refereed) Published
    Abstract [en]

    In antidiabetic drug development, phase I studies usually involve short-term glucose provocations. Multiple designs are available for these provocations (e.g., meal tolerance tests (MTTs) and graded glucose infusions (GGIs)). With a highly nonlinear, complex system as the glucose homeostasis, the various provocations will contribute with different information offering a rich choice. Here, we investigate the most appropriate study design in phase I for several hypothetical mechanisms of action of a study drug. Five drug effects in diabetes therapeutic areas were investigated using six study designs. Power to detect drug effect was assessed using the likelihood ratio test, whereas precision and accuracy of the quantification of drug effect was assessed using stochastic simulation and estimations. An overall summary was developed to aid designing the studies of antihyperglycemic drug development using model-based analysis. This guidance is to be used when the integrated glucose insulin model is used, involving the investigated drug mechanisms of action.

    Keywords
    Phase I clinical trials, study design, power, precision, pharmacometric simulations
    National Category
    Pharmaceutical Sciences
    Research subject
    Pharmaceutical Science
    Identifiers
    urn:nbn:se:uu:diva-316819 (URN)10.1002/psp4.12302 (DOI)000439996200002 ()29732710 (PubMedID)
    Available from: 2017-03-09 Created: 2017-03-09 Last updated: 2018-11-27Bibliographically approved
    2. Model-Based Residual Post-Processing for Residual Model Identification
    Open this publication in new window or tab >>Model-Based Residual Post-Processing for Residual Model Identification
    2018 (English)In: AAPS Journal, ISSN 1550-7416, E-ISSN 1550-7416, Vol. 20, no 5, article id 81Article in journal (Refereed) Published
    Abstract [en]

    The purpose of this study was to investigate if model-based post-processing of common diagnostics can be used as a diagnostic tool to quantitatively identify model misspecifications and rectifying actions. The main investigated diagnostic is conditional weighted residuals (CWRES). We have selected to showcase this principle with residual unexplained variability (RUV) models, where the new diagnostic tool is used to scan extended RUV models and assess in a fast and robust way whether, and what, extensions are expected to provide a superior description of data. The extended RUV models evaluated were autocorrelated errors, dynamic transform both sides, inter-individual variability on RUV, power error model, t-distributed errors, and time-varying error magnitude. The agreement in improvement in goodness-of-fit between implementing these extended RUV models on the original model and implementing these extended RUV models on CWRES was evaluated in real and simulated data examples. Real data exercise was applied to three other diagnostics: conditional weighted residuals with interaction (CWRESI), individual weighted residuals (IWRES), and normalized prediction distribution errors (NPDE). CWRES modeling typically predicted (i) the nature of model misspecifications, (ii) the magnitude of the expected improvement in fit in terms of difference in objective function value (Delta OFV), and (iii) the parameter estimates associated with the model extension. Alternative metrics (CWRESI, IWRES, and NPDE) also provided valuable information, but with a lower predictive performance of Delta OFV compared to CWRES. This method is a fast and easily automated diagnostic tool for RUV model development/evaluation process; it is already implemented in the software package PsN.

    Place, publisher, year, edition, pages
    SPRINGER, 2018
    Keywords
    conditional weighted residuals, diagnostics, model evaluation, nonlinear mixed effects models, residual error model
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-360174 (URN)10.1208/s12248-018-0240-7 (DOI)000437188800001 ()29968184 (PubMedID)
    Available from: 2018-09-13 Created: 2018-09-13 Last updated: 2018-11-27Bibliographically approved
    3. Optimal designs of intravenous glucose tolerance test for model-based assessments of insulin sensitivity and glucose effectiveness
    Open this publication in new window or tab >>Optimal designs of intravenous glucose tolerance test for model-based assessments of insulin sensitivity and glucose effectiveness
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-367058 (URN)
    Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2018-11-27
    4. Competing Risk Analysis of The Finnish Diabetes Prevention Study
    Open this publication in new window or tab >>Competing Risk Analysis of The Finnish Diabetes Prevention Study
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-367057 (URN)
    Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2018-11-27
    5. Variability Attribution for Automated Model Building
    Open this publication in new window or tab >>Variability Attribution for Automated Model Building
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-367056 (URN)
    Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2018-11-27
    6. The Integrated Glucose Insulin Minimal Model; An improved version
    Open this publication in new window or tab >>The Integrated Glucose Insulin Minimal Model; An improved version
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-367052 (URN)
    Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2018-11-27
    7. Translation between two models; Application with integrated glucose homeostasis models
    Open this publication in new window or tab >>Translation between two models; Application with integrated glucose homeostasis models
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-367050 (URN)
    Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2018-11-27
    8. Model-Based CWRES Analysis for Structural Model Assessment
    Open this publication in new window or tab >>Model-Based CWRES Analysis for Structural Model Assessment
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-367054 (URN)
    Available from: 2018-11-27 Created: 2018-11-27 Last updated: 2018-11-27
  • Public defence: 2019-01-21 13:15 2446, Uppsala
    Ngo, Tuan-Phong
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computer Systems.
    Model Checking of Software Systems under Weak Memory Models2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    When a program is compiled and run on a modern architecture, different optimizations may be applied to gain in efficiency. In particular, the access operations (e.g., read and write) to the shared memory may be performed in an out-of-order manner, i.e., in a different order than the order in which the operations have been issued by the program. The reordering of memory access operations leads to efficient use of instruction pipelines and thus an improvement in program execution times. However, the gain in this efficiency comes at a price. More precisely, programs running under modern architectures may exhibit unexpected behaviors by programmers. The out-of-order execution has led to the invention of new program semantics, called weak memory model (WMM). One crucial problem is to ensure the correctness of concurrent programs running under weak memory models.

    The thesis proposes three techniques for reasoning and analyzing concurrent programs running under WMMs. The first one is a sound and complete analysis technique for finite-state programs running under the TSO semantics (Paper II). This technique is based on a novel and equivalent semantics for TSO, called Dual TSO semantics, and on the use of well-structured transition framework. The second technique is an under-approximation technique that can be used to detect bugs under the POWER semantics (Paper III). This technique is based on bounding the number of contexts in an explored execution where, in each context, there is only one active process. The third technique is also an under-approximation technique based on systematic testing (a.k.a. stateless model checking). This approach has been used to develop an optimal and efficient systematic testing approach for concurrent programs running under the Release-Acquire semantics (Paper IV).

    The thesis also considers the problem of effectively finding a minimal set of fences that guarantees the correctness of a concurrent program running under WMMs (Paper I). A fence (a.k.a. barrier) is an operation that can be inserted in the program to prohibit certain reorderings between operations issued before and after the fence. Since fences are expensive, it is crucial to automatically find a minimal set of fences to ensure the program correctness. This thesis presents a method for automatic fence insertion in programs running under the TSO semantics that offers the best-known trade-off between the efficiency and optimality of the algorithm. The technique is based on a novel notion of correctness, called Persistence, that compares the behaviors of a program running under WMMs to that running under the SC semantics.

    List of papers
    1. The Best of Both Worlds: Trading efficiency and optimality in fence insertion for TSO
    Open this publication in new window or tab >>The Best of Both Worlds: Trading efficiency and optimality in fence insertion for TSO
    2015 (English)In: Programming Languages and Systems: ESOP 2015, Springer Berlin/Heidelberg, 2015, p. 308-332Conference paper, Published paper (Refereed)
    Abstract [en]

    We present a method for automatic fence insertion in concurrent programs running under weak memory models that provides the best known trade-off between efficiency and optimality. On the one hand, the method can efficiently handle complex aspects of program behaviors such as unbounded buffers and large numbers of processes. On the other hand, it is able to find small sets of fences needed for ensuring correctness of the program. To this end, we propose a novel notion of correctness, called persistence, that compares the behavior of the program under the weak memory semantics with that under the classical interleaving (SC) semantics. We instantiate our framework for the Total Store Ordering (TSO) memory model, and give an algorithm that reduces the fence insertion problem under TSO to the reachability problem for programs running under SC. Furthermore, we provide an abstraction scheme that substantially increases scalability to large numbers of processes. Based on our method, we have implemented a tool and run it successfully on a wide range benchmarks.

    Place, publisher, year, edition, pages
    Springer Berlin/Heidelberg, 2015
    Series
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 9032
    Keywords
    weak memory, correctness, verification, TSO, concurrent program
    National Category
    Computer Sciences
    Research subject
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-253645 (URN)10.1007/978-3-662-46669-8_13 (DOI)000361751400013 ()978-3-662-46668-1 (ISBN)
    Conference
    24th European Symposium on Programming, ESOP 2015, April 11–18, London, UK
    Projects
    UPMARC
    Available from: 2015-05-29 Created: 2015-05-29 Last updated: 2018-11-21
    2. A load-buffer semantics for total store ordering
    Open this publication in new window or tab >>A load-buffer semantics for total store ordering
    2018 (English)In: Logical Methods in Computer Science, ISSN 1860-5974, E-ISSN 1860-5974, Vol. 14, no 1, article id 9Article in journal (Refereed) Published
    Abstract [en]

    We address the problem of verifying safety properties of concurrent programs running over the Total Store Order (TSO) memory model. Known decision procedures for this model are based on complex encodings of store buffers as lossy channels. These procedures assume that the number of processes is fixed. However, it is important in general to prove the correctness of a system/algorithm in a parametric way with an arbitrarily large number of processes. 

    In this paper, we introduce an alternative (yet equivalent) semantics to the classical one for the TSO semantics that is more amenable to efficient algorithmic verification and for the extension to parametric verification. For that, we adopt a dual view where load buffers are used instead of store buffers. The flow of information is now from the memory to load buffers. We show that this new semantics allows (1) to simplify drastically the safety analysis under TSO, (2) to obtain a spectacular gain in efficiency and scalability compared to existing procedures, and (3) to extend easily the decision procedure to the parametric case, which allows obtaining a new decidability result, and more importantly, a verification algorithm that is more general and more efficient in practice than the one for bounded instances.

    Keywords
    Verification, TSO, concurrent program, safety property, well-structured transition system
    National Category
    Computer Sciences
    Research subject
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-337278 (URN)000426512000008 ()
    Projects
    UPMARC
    Available from: 2018-01-23 Created: 2017-12-21 Last updated: 2018-11-21
    3. Context-bounded analysis for POWER
    Open this publication in new window or tab >>Context-bounded analysis for POWER
    2017 (English)In: Tools and Algorithms for the Construction and Analysis of Systems: Part II, Springer, 2017, p. 56-74Conference paper, Published paper (Refereed)
    Abstract [en]

    We propose an under-approximate reachability analysis algorithm for programs running under the POWER memory model, in the spirit of the work on context-bounded analysis initiated by Qadeer et al. in 2005 for detecting bugs in concurrent programs (supposed to be running under the classical SC model). To that end, we first introduce a new notion of context-bounding that is suitable for reasoning about computations under POWER, which generalizes the one defined by Atig et al. in 2011 for the TSO memory model. Then, we provide a polynomial size reduction of the context-bounded state reachability problem under POWER to the same problem under SC: Given an input concurrent program P, our method produces a concurrent program P' such that, for a fixed number of context switches, running P' under SC yields the same set of reachable states as running P under POWER. The generated program P' contains the same number of processes as P and operates on the same data domain. By leveraging the standard model checker CBMC, we have implemented a prototype tool and applied it on a set of benchmarks, showing the feasibility of our approach.

    Place, publisher, year, edition, pages
    Springer, 2017
    Series
    Lecture Notes in Computer Science, ISSN 0302-9743, E-ISSN 1611-3349 ; 10206
    Keywords
    POWER, weak memory model, under approximation, translation, concurrent program, testing
    National Category
    Computer Systems
    Research subject
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-314901 (URN)10.1007/978-3-662-54580-5_4 (DOI)000440733400004 ()978-3-662-54579-9 (ISBN)
    Conference
    23rd International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS), 2017, April 22–29, Uppsala, Sweden
    Projects
    UPMARC
    Available from: 2017-03-31 Created: 2017-02-07 Last updated: 2018-11-21Bibliographically approved
    4. Optimal Stateless Model Checking under the Release-Acquire Semantics
    Open this publication in new window or tab >>Optimal Stateless Model Checking under the Release-Acquire Semantics
    2018 (English)In: SPLASH OOPSLA 2018, Boston, Nov 4-9, 2018, ACM Digital Library, 2018Conference paper, Published paper (Refereed)
    Abstract [en]

    We present a framework for efficient application of stateless model checking (SMC) to concurrent programs running under the Release-Acquire (RA) fragment of the C/C++11 memory model. Our approach is based on exploring the possible program orders, which define the order in which instructions of a thread are executed, and read-from relations, which define how reads obtain their values from writes. This is in contrast to previous approaches, which in addition explore the possible coherence orders, i.e., orderings between conflicting writes. Since unexpected test results such as program crashes or assertion violations depend only on the read-from relation, we avoid a potentially large source of redundancy. Our framework is based on a novel technique for determining whether a particular read-from relation is feasible under the RA semantics. We define an SMC algorithm which is provably optimal in the sense that it explores each program order and read-from relation exactly once. This optimality result is strictly stronger than previous analogous optimality results, which also take coherence order into account. We have implemented our framework in the tool Tracer. Experiments show that Tracer can be significantly faster than state-of-the-art tools that can handle the RA semantics.

    Place, publisher, year, edition, pages
    ACM Digital Library, 2018
    Keywords
    Software model checking, C/C++11, Release-Acquire, Concurrent program
    National Category
    Computer Systems
    Research subject
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-358241 (URN)
    Conference
    SPLASH OOPSLA 2018
    Projects
    UPMARC
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2018-11-21