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  • Cronander, Joel
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Återskapande av naturliga trösklar i mindre vattendrag och våtmarker: Modellutveckling för simulering av förändradeflödesregimer2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In the late 20th century a decrease in coastal predatory fish in the Baltic Sea has been observed. It has been suggested that exploitation of the fish’s spawning habitats, mainly through draining of coastal wetlands, was one reason for the fish decline. To recreate spawn and growth areas, natural thresholds can be installed in trenches draining coastal wetlands. To quantify the effects of a natural threshold on water discharge in the drainage area under various water flow regimes modeling is needed.In this study, a hydraulic model was developed to estimate the effect of changing water discharges of three wetlands when natural thresholds are implemented, i.e. Maren, Hyllekärr and Brokhål, located on northern Öland. The model was run under different water flow regimes. Through an observed strong relation between catchment area and discharge, extreme discharge situations could be simulated. A method for investigating the effects of natural thresholds on upstream flow regimes has been developed with hydraulic modeling in HEC-RAS. To validate the model results, a comparison with empirical data during the spring flood 2017 was made.Model simulations showed that only water discharges in Brokhål behaved as expected, Maren behaved as expected for large flows and results for Hyllekärr were considered not being reliable. Validation showed that the elevation model for topography and bathymetry deviated from reality in all three wetlands. The elevation model has been identified as the single largest source of error in the water discharge model.From the model results, it is concluded that natural thresholds have none, or very minor effects on the upstream water flow regimes. It should however be emphasized that the model has major limitations, in particular the elevation model’s resolution. It is highly recommended to further develop the elevation model before further simulations on water discharges are made. The results from this study should only be considered as a first approximation where more detailed studies are needed to confirm that natural thresholds won’t result in major changes in upstream water flows.

  • Public defence: 2017-12-15 13:15 Auditorium minus, Uppsala
    Ander, Malin
    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.
    Cancer during adolescence: Psychological consequences and development of psychological treatment2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The overall aim of the present thesis was to examine long-term psychological distress following cancer during adolescence and to develop a tailored psychological intervention to reduce cancer-related distress experienced by young survivors of adolescent cancer that was feasible and acceptable.

    Study I adopted a longitudinal design, assessing health-related quality of life (HRQOL) and symptoms of anxiety and depression among adolescents diagnosed with cancer from shortly after diagnosis (n=61) up to 10 years after diagnosis (n=28). Findings suggest that development of HRQOL and anxiety and depression is not linear and whilst the majority adjust well, a subgroup report long-term elevated distress. In Study II, experiences of cancer-related psychological distress were explored using unstructured interviews. Participants described cancer treatment as a mental challenge, felt marked and hindered by the cancer experience, and struggled with feelings of inadequacy and insecurity, existential issues, and difficulties handling emotions. Study III was a preliminary investigation of individualised cognitive behavioural therapy (CBT), alongside the identification and conceptualisation of cancer-related concerns using cognitive-behavioural theory. Significant difficulties with recruitment were encountered. Participants reported cancer-related concerns conceptualised as social avoidance, fear and avoidance of emotions and bodily symptoms, imbalance in activity, and worry and rumination. In Study IV, the acceptability and feasibility of an internet-administered CBT based self-help intervention (ICBT) for young persons diagnosed with cancer during adolescence was examined using an uncontrolled design and embedded process evaluation. The study protocol for Study IV was included in this thesis along with preliminary findings demonstrating significant difficulties with recruitment.

    Overall, findings suggest that whilst the majority of survivors of adolescent cancer adjust well over time a subgroup report elevated levels of distress and a range of distressing cancer-related experiences. A number of cancer-related difficulties were identified in Study II and III, which may be used to inform the development of future psychological treatments for the population. Preliminary investigation of the psychological interventions examined within this thesis further highlights the need for future development work to enhance the feasibility and acceptability of psychological support for the population. 

    List of papers
    1. Development of health-related quality of life and symptoms of anxiety and depression among persons diagnosed with cancer during adolescence: a 10-year follow-up study
    Open this publication in new window or tab >>Development of health-related quality of life and symptoms of anxiety and depression among persons diagnosed with cancer during adolescence: a 10-year follow-up study
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    2016 (English)In: Psycho-Oncology, ISSN 1057-9249, E-ISSN 1099-1611, Vol. 25, no 5, 582-589 p.Article in journal (Refereed) Published
    Abstract [en]

    Objective: The main aim was to investigate the development of health-related quality of life (HRQOL) and symptoms of anxiety and depression in a cohort diagnosed with cancer during adolescence from shortly after up to 10 years after diagnosis.

    Methods: Participants (n = 61) completed the SF-36 and the HADS shortly; six, 12, and 18 months; and two, three, four, and 10 years (n = 28) after diagnosis. Polynomial change trajectories were used to model development.

    Results: Polynomial change trajectories showed an initial increase which abated over time into a decrease which abated over time for the SF-36 subscales Mental Health and Vitality; an initial decline which abated over time into an increase for HADS anxiety; and an initial decline which abated over time into an increase which abated over time for HADS depression. The SF-36 mental component summary showed no change from two to 10 years after diagnosis whereas the SF-36 physical component summary showed an increase from two years after diagnosis which declined over time. Ten years after diagnosis 29% reported possible anxiety.

    Conclusions: Development of HRQOL and symptoms of anxiety and depression appears to be nonlinear among persons diagnosed with cancer during adolescence. Well into permanent survivorship an increase in symptoms of anxiety is shown and approximately a third of the participants report possible anxiety. The findings indicate the need for: studies designed to pinpoint the times of highest psychological risk, clinical follow-up focusing on psychological problems, and development of effective psychological interventions for survivors of adolescent cancer

    National Category
    Cancer and Oncology Psychology (excluding Applied Psychology)
    Identifiers
    urn:nbn:se:uu:diva-262514 (URN)10.1002/pon.3965 (DOI)000374494700014 ()26361085 (PubMedID)
    External cooperation:
    Funder
    Swedish Cancer Society, 99 0347 01 0235 02 0690 03 0227 05 0189 10 0649 11 0649 12 0649Swedish Childhood Cancer Foundation, 1999/021 02/002 04/011 07/044 10/086
    Available from: 2015-09-16 Created: 2015-09-16 Last updated: 2017-10-31Bibliographically approved
    2. Exploration of Psychological Distress Experienced by Survivors of Adolescent Cancer
    Open this publication in new window or tab >>Exploration of Psychological Distress Experienced by Survivors of Adolescent Cancer
    (English)Manuscript (preprint) (Other academic)
    Keyword
    adolescence, cancer, psychological distress, psychological treatment, survivorship, qualitative methods
    National Category
    Medical and Health Sciences Psychology
    Research subject
    Medical Science; Psychology
    Identifiers
    urn:nbn:se:uu:diva-330127 (URN)
    Funder
    U‐Care: Better Psychosocial Care at Lower Cost? Evidence-based assessment and Psychosocial Care via Internet, a Swedish ExampleSwedish Childhood Cancer Foundation, 2013-0039; 2016-0004
    Available from: 2017-10-31 Created: 2017-10-31 Last updated: 2017-11-21
    3. A preliminary open trial of individualised cognitive behavioural therapy for young survivors of cancer during adolescence: initial findings and conceptualisation of distress
    Open this publication in new window or tab >>A preliminary open trial of individualised cognitive behavioural therapy for young survivors of cancer during adolescence: initial findings and conceptualisation of distress
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Objective: A subgroup of adolescent and young adult (AYA) survivors of cancer in adolescence report high levels of psychological distress. Empirically-supported treatments tailored to the concerns experienced by this population are lacking. The aims of this study were to (1) conduct a preliminary evaluation of an individualised cognitive behavioural therapy (CBT) intervention for adolescent and young adult (AYA) survivors of cancer during adolescence and (2) identify and conceptualise cancer-related psychological concerns using cognitive-behavioural theory.

    Methods: A single-arm trial in which ten AYA (17-25 years) survivors of cancer during adolescence were offered up to 15 sessions of individualised CBT guided by behavioural case formulations was undertaken. Clinical outcomes were assessed at baseline, post-treatment, and three months follow-up. Before commencing treatment, two individual qualitative interviews were conducted with each participant. Analysis of cancer-related concerns was guided by qualitative framework analysis and theoretical thematic analysis, and cognitive-behavioural theory was used to inform identification of themes.

    Results: Ten of 201 potential participants invited to participate were included resulting in an overall participation rate of 5%. Nine participants completed treatment and eight completed the follow-up assessment. The majority of concerns reported were cancer-related and conceptualised as social avoidance, fear and avoidance of emotions and bodily symptoms, low mood and unbalance in activity, and worry and rumination.

    Conclusions: Given significant difficulties with recruitment, further research is needed to examine barriers and the impact of mental health literacy and stigma on help seeking in the AYA cancer survivor population. Internet-administered CBT self-help tailored towards the main presenting concerns of AYA cancer survivors may be a promising solution.

    Keyword
    Adolescence, Cancer, Cognitive behaviour therapy, Psychological treatment, Tonår, Cancer, Kognitiv beteendeterapi, Psykologisk behandling
    National Category
    Psychology
    Research subject
    Medical Science
    Identifiers
    urn:nbn:se:uu:diva-330126 (URN)
    Funder
    U‐Care: Better Psychosocial Care at Lower Cost? Evidence-based assessment and Psychosocial Care via Internet, a Swedish ExampleSwedish Childhood Cancer Foundation, 2016-0004, 2013-0039
    Available from: 2017-10-31 Created: 2017-10-31 Last updated: 2017-10-31
    4. Guided Internet-Administered Self-Help to Reduce Symptoms Of Anxiety and Depression Among Adolescents and Young Adults Diagnosed With Cancer During Adolescence (U-CARE: YoungCan): study protocol for a feasibility trial
    Open this publication in new window or tab >>Guided Internet-Administered Self-Help to Reduce Symptoms Of Anxiety and Depression Among Adolescents and Young Adults Diagnosed With Cancer During Adolescence (U-CARE: YoungCan): study protocol for a feasibility trial
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    2017 (English)In: BMJ Open, ISSN 2044-6055, E-ISSN 2044-6055, Vol. 7, no 1, e013906Article in journal (Refereed) Published
    Abstract [en]

    Introduction A subgroup of adolescents and young adults diagnosed with cancer during adolescence reports elevated levels of anxiety and depressive symptoms and unmet needs for psychological support. Evidence-based psychological treatments tailored for this population are lacking. This protocol describes a feasibility study of a guided-internet-administered self-help programme (YoungCan) primarily targeting symptoms of anxiety and depression among young persons diagnosed with cancer during adolescence and of the planned study procedures for a future controlled trial. Methods/analysis The study is an uncontrolled feasibility trial with a pre-post and 3-month follow-up design. Potential participants aged 15-25years, diagnosed with cancer during adolescence, will be identified via the Swedish Childhood Cancer Registry. 30 participants will be included. Participants will receive YoungCan, a 12-week therapist-guided, internet-administered self-help programme consisting primarily of cognitive-behavioural therapy organised into individually assigned modules targeting depressive symptoms, worry and anxiety, body dissatisfaction and post-traumatic stress. Interactive peer support and psychoeducative functions are also available. Feasibility outcomes include: recruitment and eligibility criteria; data collection; attrition; resources needed to complete the study and programme; safety procedures; participants' and therapists' adherence to the programme; and participants' acceptability of the programme and study methodology. Additionally, mechanisms of impact will be explored and data regarding symptoms of anxiety, depression, post-traumatic stress, body dissatisfaction, reactions to social interactions, quality of life, axis I diagnoses according to the Mini International Neuropsychiatric Interview and healthcare service use will be collected. Exploratory analyses of changes in targeted outcomes will be conducted. Ethics/dissemination This feasibility protocol was approved by the Regional Ethical Review Board in Uppsala, Sweden (ref: 2016/210). Findings will be disseminated to relevant research, clinical, health service and patient communities through publications in peer-reviewed and popular science journals and presentations at scientific and clinical conferences.

    Keyword
    adolescence, cognitive behavioural therapy, feasibility study, neoplasms, psychological treatment
    National Category
    Psychology Cancer and Oncology
    Identifiers
    urn:nbn:se:uu:diva-313898 (URN)10.1136/bmjopen-2016-013906 (DOI)000395590300138 ()
    Funder
    Swedish Childhood Cancer Foundation, PR2013-0039
    Available from: 2017-01-25 Created: 2017-01-25 Last updated: 2017-10-31Bibliographically approved
  • Public defence: 2017-12-15 09:00 4101, Ångströmlaboratoriet, Uppsala
    Belova, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Computational dynamics – real and complex2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The PhD thesis considers four topics in dynamical systems and is based on one paper and three manuscripts.

    In Paper I we apply methods of interval analysis in order to compute the rigorous enclosure of rotation number. The described algorithm is supplemented with a method of proving the existence of periodic points which is used to check rationality of the rotation number.

    In Manuscript II we provide a numerical algorithm for computing critical points of the multiplier map for the quadratic family (i.e., points where the derivative of the multiplier with respect to the complex parameter vanishes).

    Manuscript III concerns continued fractions of quadratic irrationals. We show that the generating function corresponding to the sequence of denominators of the best rational approximants of a quadratic irrational is a rational function with integer coefficients. As a corollary we can compute the Lévy constant of any quadratic irrational explicitly in terms of its partial quotients.

    Finally, in Manuscript IV we develop a method for finding rigorous enclosures of all odd periodic solutions of the stationary Kuramoto-Sivashinsky equation. The problem is reduced to a bounded, finite-dimensional constraint satisfaction problem whose solution gives the desired information about the original problem. Developed approach allows us to exclude the regions in L2, where no solution can exist.

    List of papers
    1. Rigorous enclosures of rotation numbers by interval methods.
    Open this publication in new window or tab >>Rigorous enclosures of rotation numbers by interval methods.
    2016 (English)In: Journal of Computational Dynamics, ISSN 2158-2491, Vol. 3, no 1, 81-91 p.Article in journal (Refereed) Published
    Abstract [en]

    We apply set-valued numerical methods to compute an accurate enclosure of the rotation number. The described algorithm is supplemented with a method of proving the existence of periodic points, which is used to check the rationality of the rotation number. A few numerical experiments are presented to show that the implementation of interval methods produces a good enclosure of the rotation number of a circle map.

    Keyword
    rotation number, circle map, rigorous computation, interval arithmetic, set-valued mathematics
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-332153 (URN)10.3934/jcd.2016004 (DOI)
    Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-10-26
    2. Critical points of the multiplier map for the quadratic family.
    Open this publication in new window or tab >>Critical points of the multiplier map for the quadratic family.
    (English)Manuscript (preprint) (Other academic)
    Keyword
    multipliers, quadratic family
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-332157 (URN)
    Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-10-26
    3. Quadratic irrationals, generating functions and Lévy constants.
    Open this publication in new window or tab >>Quadratic irrationals, generating functions and Lévy constants.
    (English)Manuscript (preprint) (Other academic)
    Keyword
    continued fractions, generating functions
    National Category
    Mathematical Analysis
    Identifiers
    urn:nbn:se:uu:diva-332158 (URN)
    Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-10-26
    4. Finding all solutions of stationary Kuramoto-Sivashinsky equations.
    Open this publication in new window or tab >>Finding all solutions of stationary Kuramoto-Sivashinsky equations.
    (English)Manuscript (preprint) (Other academic)
    National Category
    Mathematics
    Identifiers
    urn:nbn:se:uu:diva-332279 (URN)
    Available from: 2017-10-26 Created: 2017-10-26 Last updated: 2017-10-26
  • Public defence: 2017-12-15 09:15 Polhemssalen, Uppsala
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins.                   

    We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography.

    The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution.

    Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal.

    The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.

    List of papers
    1. Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
    Open this publication in new window or tab >>Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
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    2015 (English)In: Optics Express, ISSN 1094-4087, Vol. 23, no 2, 1213-1231 p.Article in journal (Refereed) Published
    Abstract [en]

    In structural determination of crystalline proteins using intense femtosecond X-ray lasers, damage processes lead to loss of structural coherence during the exposure. We use a nonthermal description for the damage dynamics to calculate the ultrafast ionization and the subsequent atomic displacement. These effects degrade the Bragg diffraction on femtosecond time scales and gate the ultrafast imaging. This process is intensity and resolution dependent. At high intensities the signal is gated by the ionization affecting low resolution information first. At lower intensities, atomic displacement dominates the loss of coherence affecting high-resolution information. We find that pulse length is not a limiting factor as long as there is a high enough X-ray flux to measure a diffracted signal.

    Keyword
    Ultrafast lasers, UV, EUV, and X-ray lasers, X-ray imaging, Diffraction theory, Ultrafast phenomena
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-242136 (URN)10.1364/OE.23.001213 (DOI)000349166100061 ()
    Note

    De två första författarna delar förstaförfattarskapet.

    Available from: 2015-01-21 Created: 2015-01-21 Last updated: 2017-10-25Bibliographically approved
    2. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
    Open this publication in new window or tab >>Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
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    2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, 256-266 p.Article in journal (Refereed) Published
    Abstract [en]

    Serial femtosecond X-ray crystallography of protein nanocrystals using ultrashort and intense pulses from an X-ray free-electron laser has proved to be a successful method for structural determination. However, due to significant variations in diffraction pattern quality from pulse to pulse only a fraction of the collected frames can be used. Experimentally, the X-ray temporal pulse profile is not known and can vary with every shot. This simulation study describes how the pulse shape affects the damage dynamics, which ultimately affects the biological interpretation of electron density. The instantaneously detected signal varies during the pulse exposure due to the pulse properties, as well as the structural and electronic changes in the sample. Here ionization and atomic motion are simulated using a radiation transfer plasma code. Pulses with parameters typical for X-ray free-electron lasers are considered: pulse energies ranging from 10$\sp 4$ to 10$\sp 7$Jcm$\sp $-$2$ with photon energies from 2 to 12keV, up to 100fs long. Radiation damage in the form of sample heating that will lead to a loss of crystalline periodicity and changes in scattering factor due to electronic reconfigurations of ionized atoms are considered here. The simulations show differences in the dynamics of the radiation damage processes for different temporal pulse profiles and intensities, where ionization or atomic motion could be predominant. The different dynamics influence the recorded diffracted signal in any given resolution and will affect the subsequent structure determination.

    Keyword
    X-ray free-electron laser, serial femtosecond crystallography, radiation damage, plasma simulations
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-245210 (URN)10.1107/S1600577515002878 (DOI)000350641100007 ()
    Available from: 2015-02-25 Created: 2015-02-25 Last updated: 2017-10-25Bibliographically approved
    3. FreeDam 1.0 – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
    Open this publication in new window or tab >>FreeDam 1.0 – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    X-ray free-electron laser sources have the last decade been available to the scientific community. One of the most successful uses of these new machines has been crys- tallography. When samples are exposed to the intense short X-ray pulses provided by the X-ray free-electron laser, the sample becomes very fast highly ionized and the atomic structure is affected. Here we present a webtool for estimations of the ionization and temperatures in these types of experiments. 

    Keyword
    FreeDam, non-local thermodynamic equilibrium, x-ray free-electron laser, radiation damage, serial femtosecond x-ray crystallography, Cretin, simulation, database
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-329499 (URN)
    Available from: 2017-09-17 Created: 2017-09-17 Last updated: 2017-10-25
    4. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
    Open this publication in new window or tab >>Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
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    2015 (English)In: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, no 2, 225-238 p.Article in journal (Refereed) Published
    Abstract [en]

    Proteins that contain metal cofactors are expected to be highly radiation sensitive since the degree of X-ray absorption correlates with the presence of high-atomic-number elements and X-ray energy. To explore the effects of local damage in serial femtosecond crystallography (SFX), Clostridium ferredoxin was used as a model system. The protein contains two [4Fe–4S] clusters that serve as sensitive probes for radiation-induced electronic and structural changes. High-dose room-temperature SFX datasets were collected at the Linac Coherent Light Source of ferredoxin microcrystals. Difference electron density maps calculated from high-dose SFX and synchrotron data show peaks at the iron positions of the clusters, indicative of decrease of atomic scattering factors due to ionization. The electron density of the two [4Fe–4S] clusters differs in the FEL data, but not in the synchrotron data. Since the clusters differ in their detailed architecture, this observation is suggestive of an influence of the molecular bonding and geometry on the atomic displacement dynamics following initial photoionization. The experiments are complemented by plasma code calculations.

    Keyword
    free-electron laser, SFX, serial femtosecond crystallography, radiation damage, protein crystallography, metalloprotein
    National Category
    Structural Biology
    Identifiers
    urn:nbn:se:uu:diva-245011 (URN)10.1107/S1600577515002349 (DOI)000350641100004 ()
    Available from: 2015-02-23 Created: 2015-02-23 Last updated: 2017-10-25Bibliographically approved
    5. Ultrafast non-thermal heating of water initiated by an X-ray laser
    Open this publication in new window or tab >>Ultrafast non-thermal heating of water initiated by an X-ray laser
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-294554 (URN)
    Note

    De två första författarna delar förstaförfattarskapet

    Available from: 2016-05-24 Created: 2016-05-24 Last updated: 2017-11-06
    6. Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    Open this publication in new window or tab >>Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    2017 (English)In: IUCrJ, Vol. 4, no 6Article in journal (Refereed) Published
    Abstract [en]

    Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

    Keyword
    hit detection, plasma emission spectra, serial femtosecond crystallography, protein structure
    National Category
    Biophysics
    Research subject
    Physics with specialization in Biophysics
    Identifiers
    urn:nbn:se:uu:diva-331934 (URN)10.1107/S2052252517014154 (DOI)
    Available from: 2017-10-25 Created: 2017-10-25 Last updated: 2017-10-25
  • Lin, Yingbo
    et al.
    Karolinska Inst, Dept Pathol & Oncol, CCK R8 04, Stockholm, Sweden..
    Liu, Hongyu
    Karolinska Inst, Dept Pathol & Oncol, CCK R8 04, Stockholm, Sweden.;Guangdong Ocean Univ, Fisheries Coll, Lab Aquat Anim Nutr Feed, Zhanjiang, Peoples R China..
    Waraky, Ahmed
    Karolinska Inst, Dept Pathol & Oncol, CCK R8 04, Stockholm, Sweden..
    Haglund, Felix
    Karolinska Inst, Dept Pathol & Oncol, CCK R8 04, Stockholm, Sweden..
    Agarwal, Prasoon
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Experimental and Clinical Oncology. Karolinska Univ Hosp, Div Clin Immunol, Dept Lab Med LABMED H5, Stockholm, Sweden.
    Jernberg Wiklund, Helena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Experimental and Clinical Oncology.
    Warsito, Dudi
    Karolinska Inst, Dept Pathol & Oncol, CCK R8 04, Stockholm, Sweden..
    Larsson, Olle
    Karolinska Inst, Dept Pathol & Oncol, CCK R8 04, Stockholm, Sweden..
    SUMO-modified insulin-like growth factor 1 receptor (IGF-1R) increases cell cycle progression and cell proliferation2017In: Journal of Cellular Physiology, ISSN 0021-9541, E-ISSN 1097-4652, Vol. 232, no 10, 2722-2730 p.Article in journal (Refereed)
    Abstract [en]

    Increasing number of studies have shown nuclear localization of the insulin-like growth factor 1 receptor (nIGF-1R) in tumor cells and its links to adverse clinical outcome in various cancers. Any obvious cell physiological roles of nIGF-1R have, however, still not been disclosed. Previously, we reported that IGF-1R translocates to cell nucleus and modulates gene expression by binding to enhancers, provided that the receptor is SUMOylated. In this study, we constructed stable transfectants of wild type IGF1R (WT) and triple-SUMO-site-mutated IGF1R (TSM) using igf1r knockout mouse fibroblasts (R-). Cell clones (R-WT and R-TSM) expressing equal amounts of IGF1R were selected for experiments. Phosphorylation of IGF-1R, Akt, and Erk upon IGF-1 stimulation was equal in R-WT and R-TSM. WT was confirmed to enter nuclei. TSM did also undergo nuclear translocation, although to a lesser extent. This may be explained by that TSM heterodimerizes with insulin receptor, which is known to translocate to cell nuclei. R-WT proliferated substantially faster than R-TSM, which did not differ significantly from the empty vector control. Upon IGF-1 stimulationG1-S-phase progression of R-WT increased from 12 to 38%, compared to 13 to 20% of R-TSM. The G1-S progression of R-WT correlated with increased expression of cyclin D1, A, and CDK2, as well as downregulation of p27. This suggests that SUMO-IGF-1R affects upstream mechanisms that control and coordinate expression of cell cycle regulators. Further studies to identify such SUMO-IGF-1R dependent mechanisms seem important.

  • Dubiec, Anna
    et al.
    Polish Acad Sci, Museum & Inst Zool, Warsaw, Poland..
    Podmokla, Edyta
    Jagiellonian Univ, Inst Environm Sci, Krakow, Poland..
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Intra-individual changes in haemosporidian infections over the nesting period in great tit females2017In: Parasitology Research, ISSN 0932-0113, E-ISSN 1432-1955, Vol. 116, no 9, 2385-2392 p.Article in journal (Refereed)
    Abstract [en]

    Prevalence of haemosporidian parasites in bird populations varies temporally both between years and within a year. In contrast to variation at the population level, relatively little is known about variation in infection attributes at the individual level, especially in non-migratory species. We examined intra-individual changes in the presence and identity of haemosporidian parasites (genera Plasmodium and Haemoproteus) over the course of the nesting period in females of great tits (Parus major)-a species considered to be resident over much of its distribution range. Birds were sampled during two stages of the nesting period: nest building and nestling rearing. The mean time interval between sampling occasions was 43 days. Between the first and second samplings, 30.6% of females gained at least one parasite lineage and 18.5% lost the lineage. Haemoproteus gains were over three times more common than Plasmodium gains. The probability of the lineage gain decreased with the date of the first sampling, was higher in individuals in better body condition and differed between years, but was not associated with the host age. The probability of the lineage loss was not explained by any of the considered parameters except for year. These results indicate that in a large proportion of a population, infection attributes (presence/absence and/or parasite identity) may change over the nesting period and the occurrence of such changes may be associated with the individual quality. Consequently, this phenomenon should be taken into account to correctly interpret parasite-mediated effects.

  • Public defence: 2017-12-15 10:00 Lindhalsalen, Uppsala
    Martinossi-Allibert, Ivain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sexual Selection and Adaptation to Novel Environments2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The work included in this thesis aims at exploring the environmental sensitivity of benefits and costs of sexual selection through a combined empirical and theoretical effort, to increase our understanding of the impact of environmental change on sexually reproducing populations.Can sexual selection promote adaptation to novel environments? Sexual selection for good genes should accelerate adaptation by granting higher reproductive success to individuals of high genetic quality. However, sexual conflict is a frequent outcome of sexual reproduction and may often be detrimental to population fitness. Experimental evolution has shown that the role of sexual selection in adaptation is variable, because of a complex balance between the detrimental and beneficial effects described above.The present thesis is investigating the role of sexual selection in adaptation by focusing on the sex-specific strength of selection and the intensity of intralocus sexual conflict (IaSC) in ancestral and novel environments. The sex-specific strength of selection is a valuable proxy for the benefits of sexual reproduction, since a male-bias in selection caused by sexual selection should allow efficient purging of deleterious alleles with little impact on female fecundity and cost to population fitness.This thesis investigates both sex-specific selection and IaSC across benign and novel environments in two species of seed beetles, Callosobruchus maculatus and Acanthoscelides obtectus, and includes a theoretical model of the effect of environmental change on of sexual selection. The empirical part of my results indicates that, generally, selection at the adult stage is male biased but that this male bias may be reduced under stress, pointing towards reduced benefits of sexual selection under rapid environmental change. Additional simulations suggest that the frequency dependent nature of sexual selection alone could explain this trend. No empirical support was found for the reduction of IaSC under stress.It is becoming crucial today to understand the impact of environmental change on natural populations. This thesis brings new material adding to our understanding of the role of sexual selection within that particular issue. The outcome of sexual selection is dependent on a variety of mechanisms, such as good genes processes and sexual conflict, which are very likely to be dependent on ecological factors and specificity of the system studied. For that reason, carefully controlled experiments on laboratory systems and mathematical modelling are necessary steps that should ultimately lead to the study of similar questions in natural systems.

    List of papers
    1. Sex-specific selection under environmental stress in seed beetles
    Open this publication in new window or tab >>Sex-specific selection under environmental stress in seed beetles
    2017 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, no 1, 161-173 p.Article in journal (Refereed) Published
    Abstract [en]

    Sexual selection can increase rates of adaptation by imposing strong selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male-biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex-specific strengths of selection, environmental sensitivities and genotype-by-environment interactions and tested them in seed beetles by manipulating either larval host plant or rearing temperature. Using fourteen isofemale lines, we measured sex-specific reductions in fitness components, genotype-by-environment interactions and the strength of selection (variance in fitness) in the juvenile and adult stage. As predicted, variance in fitness increased with stress, was consistently greater in males than females for adult reproductive success (implying strong sexual selection), but was similar in the sexes in terms of juvenile survival across all levels of stress. Although genetic variance in fitness increased in magnitude under severe stress, heritability decreased and particularly so in males. Moreover, genotype-by-environment interactions for fitness were common but specific to the type of stress, sex and life stage, suggesting that new environments may change the relative alignment and strength of selection in males and females. Our study thus exemplifies how environmental stress can influence the relative forces of natural and sexual selection, as well as concomitant changes in genetic variance in fitness, which are predicted to have consequences for rates of adaptation in sexual populations.

    Place, publisher, year, edition, pages
    WILEY-BLACKWELL, 2017
    Keyword
    adaptation, Callosobruchus maculatus, environmental change, host plant, natural selection, population viability, sexual reproduction, sexual selection, stress, temperature
    National Category
    Zoology Ecology
    Identifiers
    urn:nbn:se:uu:diva-331971 (URN)10.1111/jeb.12996 (DOI)
    Funder
    EU, European Research Council, GENCON AdG-294333Swedish Research Council, 621-2010-5266 261-2014-4523
    Available from: 2017-10-20 Created: 2017-10-20 Last updated: 2017-10-24Bibliographically approved
    2. Intralocus Sexual Conflict and the Tragedy of the Commons in Seed Beetles
    Open this publication in new window or tab >>Intralocus Sexual Conflict and the Tragedy of the Commons in Seed Beetles
    Show others...
    2016 (English)In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 188, no 4, E98-E112 p.Article in journal (Refereed) Published
    Abstract [en]

    The evolution of male traits that inflict direct harm on females during mating interactions can result in a so-called tragedy of the commons, where selfish male strategies depress population viability. This tragedy of the commons can be magnified by intralocus sexual conflict (IaSC) whenever alleles that reduce fecundity when expressed in females spread in the population because of their benefits in males. We evaluated this prediction by detailed phenotyping of 73 isofemale lines of the seed beetle Callosobruchus maculatus. We quantified genetic variation in life history andmorphology, as well as associated covariance in male and female adult reproductive success. In parallel, we created replicated artificial populations of each line and measured their productivity. Genetic constraints limited independent trait expression in the sexes, and we identified several instances of sexually antagonistic covariance between traits and fitness, signifying IaSC. Population productivity was strongly positively correlated to female adult reproductive success but uncorrelated with male reproductive success. Moreover, male (female) phenotypic optima for several traits under sexually antagonistic selection were exhibited by the genotypes with the lowest (highest) population productivity. Our study forms a direct link between individuallevel sex-specific selection and population demography and places lifehistory traits at the epicenter of these dynamics.

    Keyword
    sexual selection, adaptation, sexual antagonism, sexual dimorphism, genetic architecture, population demography
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-305304 (URN)10.1086/687963 (DOI)000383774400001 ()27622882 (PubMedID)
    Funder
    Swedish Research CouncilEU, European Research Council, AdG-294333; AGINGSEXDIFF
    Available from: 2016-10-18 Created: 2016-10-14 Last updated: 2017-10-24Bibliographically approved
    3. The consequences of sexual selection in well-adapted and amaladapted populations of bean beetles: Sexual selection in maladapted populations
    Open this publication in new window or tab >>The consequences of sexual selection in well-adapted and amaladapted populations of bean beetles: Sexual selection in maladapted populations
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Whether sexual selection generally promotes or impedes population persistence remains an open question. Intralocus sexual conflict (IaSC) can render sexual selection in males detrimental to the population by increasing the frequency of alleles with positive effects on male reproductive success but negative effects on female fecundity. Recent modelling based on fitness landscape theory, however, indicates that the relative impact of IaSC may be reduced in maladapted populations and that sexual selection therefore might promote adaptation when it is most needed. Here, we test this prediction using bean beetles that had undergone 80 generations of experimental evolution on two alternative host plants. We isolated and assessed the effect of maladaptation on sex-specific strengths of selection and IaSC by cross-rearing the two experimental evolution regimes on the alternative hosts and estimating within-population genetic (co)variance for fitness in males and females. Two key predictions were upheld: males generally experienced stronger selection compared to females and maladaptation increased selection in females. However, maladaptation consistently decreased male-bias in the strength of selection and IaSC was not reduced in maladapted populations. These findings imply that sexual selection can be disrupted in stressful environmental conditions, thus reducing one of the potential benefits of sexual reproduction in maladapted populations.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-331970 (URN)
    Available from: 2017-10-20 Created: 2017-10-20 Last updated: 2017-10-24Bibliographically approved
    4. The efficiency of purifying sexual selection under environmental change
    Open this publication in new window or tab >>The efficiency of purifying sexual selection under environmental change
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Sexual selection can promote adaptation if sexually selected traits are reliable indicators of the bearer’s condition and overall genetic quality. Moreover, stronger sexual selection in males, as often reported in empirical studies, may efficiently purge deleterious alleles at a low cost to population productivity. However, such benefits of sexual selection have been suggested to be compromised during adaptation in a changing environment due to a disruption of the mate choice process. Indeed, substantial insight has been gained from previous theoretical and empirical studies focusing on exploring female choice and the reliability of male sexual signals across environments. In this study, we show that even if sexually selected traits are honest signals and accurately reflect condition in new environments, the efficacy of sexual selection is likely to be reduced under stress. We model the strength of sex-specific selection in a population with males competing among each other for fertilization success and females experiencing fecundity selection. We observe that, for most of the biologically relevant parameter space describing mating system variation, the strength of sexual selection is reduced relatively to fecundity selection as the population becomes increasingly maladapted under environmental change. This result, which is modulated by the characteristics of the mating system, is a direct consequence of the prominent role of social context (frequency-dependence) in sexual selection.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-332106 (URN)
    Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-10-27Bibliographically approved
  • Lagermalm, Fredrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Lundin, Alice
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Medarbetardriven affärsutveckling: En fallstudie på ett IT-konsultbolag2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Purpose

    To contribute to existing knowledge about how to motivate coworkers at consultancy firms to develop business ideas within the company, and how the management can structure and support the process.

    Research questions

    What incentives can improve the coworker-driven business development at a consultancy company? How should the consultant be supported through a process of business development, and by who? What are the qualifications and challenges at a consultancy company that affects the coworker-driven business development?

    Methodology

    This master thesis of 30 ECTS is based on an inductive case study at the IT consultancy firm IT-Con. Primary data was collected through 11 semi-structured interviews, 12 structured interviews, a digital poll with 71 respondents and 2 focus groups. The study was supported by secondary data through literature from the fields of organizational theory, leadership and communication all with focus on business development.

    Findings

    The need of a consequent but adaptable reward model, well communicated goals and transparency regarding resource allocation. The need of active and supportive leadership throughout the process and a long- term commitment from both the consultant and the leader. To avoid an extra burden on the involved employees and to maximize potential, this process should be integrated in the daily routine.

    Keywords

    Business development process, IT-Consultancy, Motivational theory, Active leadership, Communication 

  • Xing, Shan
    et al.
    Chinese Acad Sci, State Key Lab Loess & Quaternary Geol, Shaanxi Key Lab Accelerator Mass Spectrometry Tec, Xian AMS Ctr,Inst Earth Environm, Xian 710061, Shaanxi, Peoples R China..
    Hou, Xiaolin
    Chinese Acad Sci, State Key Lab Loess & Quaternary Geol, Shaanxi Key Lab Accelerator Mass Spectrometry Tec, Xian AMS Ctr,Inst Earth Environm, Xian 710061, Shaanxi, Peoples R China.;Techn Univ Denmark, Ctr Nucl Technol, DK-4000 Roskilde, Denmark..
    Aldahan, Ala
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. United Arab Emirates Univ, Dept Geol, Al Ain 17511, U Arab Emirates..
    Possnert, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, För teknisk-naturvetenskapliga fakulteten gemensamma enheter, Tandem Laboratory.
    Shi, Keliang
    Techn Univ Denmark, Ctr Nucl Technol, DK-4000 Roskilde, Denmark.;Lanzhou Univ, Sch Nucl Sci & Technol, Lanzhou 73000, Gansu, Peoples R China..
    Yi, Peng
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Hohai Univ, Coll Hydrol & Water Resources, Nanjing 210098, Jiangsu, Peoples R China..
    Zhou, Weijian
    Chinese Acad Sci, State Key Lab Loess & Quaternary Geol, Shaanxi Key Lab Accelerator Mass Spectrometry Tec, Xian AMS Ctr,Inst Earth Environm, Xian 710061, Shaanxi, Peoples R China..
    Water Circulation and Marine Environment in the Antarctic Traced by Speciation of I-129 and I-1272017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 7726Article in journal (Refereed)
    Abstract [en]

    Emissions of anthropogenic I-129 from human nuclear activities are now detected in the surface water of the Antarctic seas. Surface seawater samples from the Drake Passage, Bellingshausen, Amundsen, and Ross Seas were analyzed for total I-129 and I-127, as well as for iodide and iodate of these two isotopes. The variability of I-127 and I-129 concentrations and their species (I-127(-)/(IO3-)-I-127, I-129(-)/(IO3-)-I-129) suggest limited environmental impact where ((1.15-3.15) x 10(6) atoms/L for I-129 concentration and (0.61-1.98) x 10(-11) for I-129/I-127 atomic ratios are the lowest ones compared to the other oceans. The iodine distribution patterns provide useful information on surface water transport and mixing that are vital for better understanding of the Southern Oceans effects on the global climate change. The results indicate multiple spatial interactions between the Antarctic Circumpolar Current (ACC) and Antarctic Peninsula Coastal Current (APCC). These interactions happen in restricted circulation pathways that may partly relate to glacial melting and icebergs transport. Biological activity during the warm season should be one of the key factors controlling the reduction of iodate in the coastal water in the Antarctic.

  • Asan, Noor Badariah
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Noreland, Daniel
    Umea Univ, Dept Comp Sci, SE-90187 Umea, Sweden..
    Hassan, Emadeldeen
    Umea Univ, Dept Comp Sci, SE-90187 Umea, Sweden.;Menoufia Univ, Dept Elect & Elect Commun, Menoufia 32952, Egypt..
    Redzwan, Syaiful
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Rydberg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Blokhuis, Taco J.
    Maastricht Univ, Dept Surg, Med Ctr, P Debyelaan 25, NL-6229 HX Maastricht, Netherlands..
    Carlsson, Per-Ola
    Univ Hosp, Dept Med Sci Transplantat & Regenerat Med, SE-75185 Uppsala, Sweden..
    Voigt, Thiemo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Augustine, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Intra-body microwave communication through adipose tissue2017In: HEALTHCARE TECHNOLOGY LETTERS, ISSN 2053-3713, Vol. 4, no 4, 115-121 p.Article in journal (Refereed)
    Abstract [en]

    The human body can act as a medium for the transmission of electromagnetic waves in the wireless body sensor networks context. However, there are transmission losses in biological tissues due to the presence of water and salts. This Letter focuses on lateral intra-body microwave communication through different biological tissue layers and demonstrates the effect of the tissue thicknesses by comparing signal coupling in the channel. For this work, the authors utilise the R-band frequencies since it overlaps the industrial, scientific and medical radio (ISM) band. The channel model in human tissues is proposed based on electromagnetic simulations, validated using equivalent phantom and ex-vivo measurements. The phantom and ex-vivo measurements are compared with simulation modelling. The results show that electromagnetic communication is feasible in the adipose tissue layer with a low attenuation of approximate to 2 dB per 20 mm for phantom measurements and 4 dB per 20 mm for ex-vivo measurements at 2 GHz. Since the dielectric losses of human adipose tissues are almost half of ex-vivo tissue, an attenuation of around 3 dB per 20 mm is expected. The results show that human adipose tissue can be used as an intra-body communication channel.

  • Public defence: 2017-12-13 13:00 Auditorium Minus, Uppsala
    Jha, Paridhi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    ‘Two Sides of a Coin’: Quality of Childbirth Services in Indian Public Health Facilities, from the Perspectives of Women and their Care Providers2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background: Skilled birth attendance, usually available by promoting childbirth at health care institutions in low-resource settings, is known to prevent maternal and neonatal morbidity and mortality. While institutional childbirths in India have increased at an exponential rate, the infrastructure, material and manpower resources to support this practice are lagging, raising concerns about the quality of childbirth services.

    Methodology: A mixed-method approach was used in this project: in-depth interviews with women (n= 13); and focus-group-discussions with the care providers (n=27) were conducted and analysed using Grounded Theory. A cross-sectional survey (n= 1004) assessed prevalence of Fear of Birth (FoB) and postnatal depressive symptoms (PND), along with satisfaction with childbirth services among women in the immediate postpartum period.

    Results: The system of cashless childbirth provided at the public health facilities, in the women’s experiences, came at the hidden cost of them having to make themselves subordinate to the offered services. The prevalence of FoB and PND was 13.1% and 17.1%, respectively, and these were significantly associated (p < 0.001). Among women with vaginal births (VB), 41.2% had experienced a perineal wound and 59% of them underwent repair without local anaesthesia. While the majority of the women were satisfied (VB 68.7%; Caesarean births 79.2%) with the services; women having VBs at Community Health Centres (nearly 81%) were more commonly satisfied compared to those at the District Hospitals (nearly 60%) (p < 0.001). From the care providers’ perspective, maintaining quality of childbirth services was like a balancing act between the realities of low-resource settings with stakeholders’ expectations. While the providers remained proud and committed; the challenges often left them fatigued, disillusioned, irritable and sceptical.

    Conclusion: There is a need to improve the sensitivity with which childbirth services are being delivered to women coming to public health facilities; as well as towards improving the care providers’ work conditions. Suboptimal birth experiences are associated with the women’s perinatal mental health and satisfaction, while perpetual work challenges may make the care providers frustrated and/or apathetic. Improving manpower resources could reduce work-stress in care providers and thereby improve childbirth processes.

    List of papers
    1. Cashless childbirth, but at a cost: A grounded theory study on quality of intrapartum care in public health facilities in India
    Open this publication in new window or tab >>Cashless childbirth, but at a cost: A grounded theory study on quality of intrapartum care in public health facilities in India
    Show others...
    2016 (English)In: Midwifery, ISSN 0266-6138, E-ISSN 1532-3099, Vol. 39, 78-86 p.Article in journal (Refereed) Published
    Abstract [en]

    Aim: this study aimed to explore and understand the perceptions and experiences of women regarding quality of care received during childbirth in public health facilities. Design: qualitative in-depth interviews were conducted and analysed using the Grounded Theory approach. Participants: thirteen women who had given vaginal birth to a healthy newborn infant. Setting: participants were interviewed in their homes in one district of Chhattisgarh, India. Data collection: the interview followed a pre-tested guide comprising one key question: How did the women experience and perceive the care provided during labour and childbirth? Findings: 'cashless childbirth but at a cost: subordination during childbirth' was identified as the core category. Women chose a public health facility due to their socio-economic limitations, and to have a cashless and safe childbirth. Participants expressed a sense of trust in public health facilities, and verbalised that free food and ambulance services provided by the government were appreciated. Care during normal birth was medicalised, and women lacked control over the process of their labour. Often, the women experienced verbal and physical abuse, which led to passive acceptance of all the services provided to avoid confrontation with the providers. Conclusions: increasingly higher numbers of women give birth in public health facilities in Chhattisgarh, India, and women who have no alternative place to have a safe and normal birth are the main beneficiaries. The labour rooms are functional, but there is a need for improvement of interpersonal processes, information-sharing, and sensitive treatment of women seeking childbirth services in public health facilities.

    Keyword
    Birth experience, Institutional delivery, Abuse, Communication, Care providers, Grounded theory
    National Category
    Obstetrics, Gynecology and Reproductive Medicine
    Identifiers
    urn:nbn:se:uu:diva-299546 (URN)10.1016/j.midw.2016.04.012 (DOI)000377935800011 ()27321724 (PubMedID)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2016-07-25 Created: 2016-07-22 Last updated: 2017-10-16Bibliographically approved
    2. Fear of Childbirth and Depressive Symptoms among Postnatal Women: A Cross-sectional Survey from Chhattisgarh, India
    Open this publication in new window or tab >>Fear of Childbirth and Depressive Symptoms among Postnatal Women: A Cross-sectional Survey from Chhattisgarh, India
    2017 (English)In: Women and Birth, ISSN 1871-5192, E-ISSN 1878-1799Article in journal (Refereed) Epub ahead of print
    Keyword
    Depression/depressiveve symptoms; EPDS; Fear of Birth (phobic disorders); Institutional births; WDEQ Version B
    National Category
    Medical and Health Sciences
    Research subject
    Health Care Research
    Identifiers
    urn:nbn:se:uu:diva-331599 (URN)10.1016/j.wombi.2017.07.003 (DOI)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2017-10-16 Created: 2017-10-16 Last updated: 2017-10-18Bibliographically approved
    3. Satisfaction with childbirth services provided in public health facilities: results from a cross-sectional survey among postnatal women in Chhattisgarh, India
    Open this publication in new window or tab >>Satisfaction with childbirth services provided in public health facilities: results from a cross-sectional survey among postnatal women in Chhattisgarh, India
    2017 (English)In: Global Health Action, ISSN 1654-9716, E-ISSN 1654-9880Article in journal (Refereed) Accepted
    Place, publisher, year, edition, pages
    Taylor & Francis Group, 2017
    Keyword
    Hindi-translated Scale for 30 Measuring Maternal Satisfaction; intrapartum care; institutional births; Caesarean section; quality of care
    National Category
    Medical and Health Sciences
    Research subject
    Health Care Research
    Identifiers
    urn:nbn:se:uu:diva-331601 (URN)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2017-10-16 Created: 2017-10-16 Last updated: 2017-10-18Bibliographically approved
    4. “The balancing act”: Maintaining the quality of childbirth services in low-resource settings- a Grounded Theory study exploring nurse-midwives’ perceptions and experiences of providing services in public health facilities of Chhattisgarh, India
    Open this publication in new window or tab >>“The balancing act”: Maintaining the quality of childbirth services in low-resource settings- a Grounded Theory study exploring nurse-midwives’ perceptions and experiences of providing services in public health facilities of Chhattisgarh, India
    Show others...
    2017 (English)Article in journal (Refereed) Submitted
    National Category
    Medical and Health Sciences
    Research subject
    Health Care Research
    Identifiers
    urn:nbn:se:uu:diva-331602 (URN)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2017-10-16 Created: 2017-10-16 Last updated: 2017-10-26Bibliographically approved
  • Public defence: 2017-12-15 13:00 Humanistiska Teatern, Uppsala
    Börjesson, Lisa
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of ALM.
    Resources for scholarly documentation in professional service organizations: A study of Swedish development-led archaeology report writing2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This information studies dissertation deals with the problem that results from research outside academia risk to receive little or no attention if communicated through reports, instead of in mainstream academic genres like research journal articles. The case in focus is Swedish development-led (DL) archaeology, i.e. state regulated archaeology preceding land development. Swedish DL archaeology is organized as a semi-regulated market. The organizations competing on the market are professional service organizations selling research services to land developers. Regional government departments, county administrative boards, function as intermediaries setting up procurement-like processes.

    In previous research on archaeological documentation, the problem with non-use of reports has been described as depending on cultural issues of access, possible to solve if individuals make efforts to communicate and use extra-academic results. This dissertation offers an alternative definition of the problem, highlighting a different set of solutions. The aim is to further the understanding of how the distribution of research duties to professional service organizations affects the scholarly documentation in Swedish archaeology. The aim is met through identification, operationalization and analysis of resources available to report writing DL archaeology practitioners, and an analysis of how practitioners draw on these resources. The results further the understanding of how reports are shaped within the DL archaeology institution. In view of these results, efforts to solve issues of access should target the organization of research in the archaeology discipline, and specifically how scholarly documentation is governed on the archaeology market.

    The dissertation draws on science and technology studies, practice theory, and document theory for the design of the study of documentation resources and contexts in extra-academic research. A mixed methods approach is applied to capture regulative, institutional, and infrastructural resources, and practitioners’ use thereof. Dissertation papers I-III contain analyses of concrete instantiations of the resources: information policy, documentation ideals, and information source use. The fourth paper presents an analysis of how practitioners draw on these resources in their everyday report writing. The dissertation concerns archaeology specifically, but serves as grounds to inquire into the premises for scholarly documentation in other areas of extra-academic research and knowledge-making as well.

    List of papers
    1. Information Policy for (Digital) Information in Archaeology: current state and suggestions for development
    Open this publication in new window or tab >>Information Policy for (Digital) Information in Archaeology: current state and suggestions for development
    2015 (English)In: Internet Archaeology, ISSN 1363-5387, E-ISSN 1363-5387, no 40Article in journal (Refereed) Published
    Abstract [en]

    The introduction of digital data capturing and management technologies has transformed information practices in archaeology. Digital documentation and digital infrastructures are integrated in archaeologists' daily work now more than ever. International and national institutions and projects have contributed to the development of digital archiving and curation practices. Because knowledge production in archaeology depends heavily on documentation and information dissemination, and on retrieval of past documentation, the question of how information is managed is profoundly intertwined with the possibilities for knowledge production. Regulations at different levels articulate demands and expectations from the emerging digital information practices, but how are these different regulations coordinated, and do they support archaeological knowledge production?

    In this article we look into the state of information policy - the sum of principles guiding decisions about information - in archaeology and related areas. The aim of the article is to shed light on how information policy directs practice in archaeology, and to show that analysis of such policies is therefore vital. Information policy in legislation and guidelines in Swedish archaeology serves as a case study, and examples from development-led archaeology and the museum sector illustrate how information policies have varied roles across different heritage sectors. There are historical and local trajectories in the policy documents specific to Sweden, but the discussion shows that the emergence of Swedish policies have many parallels with processes in other countries. The article provides recommendations for information policy development for archaeology and related areas.

    Keyword
    Digital humanities; cultural heritage sector; digital heritage; digital archaeology; digital museums; information policy; digital agendas; digitization
    National Category
    Information Studies Archaeology
    Research subject
    Library and Information Science
    Identifiers
    urn:nbn:se:uu:diva-275630 (URN)10.11141/ia.40.4 (DOI)
    Projects
    ARKDIS
    Funder
    Swedish Research Council, 340-2012-5751
    Available from: 2016-02-04 Created: 2016-02-04 Last updated: 2017-10-20Bibliographically approved
    2. Beyond information policy: Conflicting documentation ideals in extra-academic knowledge making practices
    Open this publication in new window or tab >>Beyond information policy: Conflicting documentation ideals in extra-academic knowledge making practices
    2016 (English)In: Journal of Documentation, ISSN 0022-0418, E-ISSN 1758-7379, Vol. 72, no 4, 674-695 p.Article in journal (Refereed) Published
    Abstract [en]

    Purpose – The purpose of this paper is to explore and explicate documentation ideals parallel to information policy, and by means of this analysis demonstrate how the concept “documentation ideals” is an analytical tool for engaging with political and institutional contexts of information practices.

    Design/methodology/approach – The paper is based on a case study of documentation ideals in a debate about quality in archaeological documentation. The methodology draws on idea analysis, and on the science and technology studies’ controversy studies approach.

    Findings – The paper explicates three documentation ideals, how these ideals allocate responsibility for documentation to different actors, how the ideals assign roles to practitioners, and how the ideals point to different beneficiaries of the documentation. Furthermore, the analysis highlights ideas about two different means to reach the documentation ideals.

    Research limitations/implications – The case’s debate reflects opinions of Northern European professionals.

    Social implications – The paper illuminates how documentation ideals tweak and even contest formal information policy in claims on the documentation and on the practitioners doing documentation.

    Originality/value – Documentation ideal analysis is crucial as a complement to formal information policy analysis and to analysis guided by practice theory in attempts to understand the contexts of information practices and documentation, insights central for developing information literacies.

    Keyword
    Archaeology, Information practices, Information policy, Controversy studies, Documentation ideals, Idea analysis, Knowledge making practices
    National Category
    Information Studies
    Research subject
    Library and Information Science
    Identifiers
    urn:nbn:se:uu:diva-277190 (URN)10.1108/JDOC-10-2015-0134 (DOI)000379787000004 ()
    Projects
    ARKDIS
    Funder
    Swedish Research Council, 340-2012-5751
    Available from: 2016-02-17 Created: 2016-02-17 Last updated: 2017-10-20Bibliographically approved
    3. Grey literature – grey sources?: Nuancing the view on professional documentation: the case of Swedish archaeology
    Open this publication in new window or tab >>Grey literature – grey sources?: Nuancing the view on professional documentation: the case of Swedish archaeology
    2015 (Swedish)In: Journal of Documentation, ISSN 0022-0418, E-ISSN 1758-7379, Vol. 71, no 6, 1158-1182 p.Article in journal (Refereed) Published
    Abstract [en]

    Purpose

    This study aims at nuancing the perception about professional documentation (a.k.a. ‘grey literature’), assuming perception of documentation being a cultural aspect of accessibility.

    Design/methodology/approach

    The study explores variations within the archaeological report genre through a bibliometric analysis of source use. Source characteristics are explored as well as correlations between report authors and source originators. Statistical frequency distribution is complemented by a correspondence analysis and a k-Means cluster analysis to explore patterns. The patterns are interpreted as ‘frames of references’ and related to circumstances for archaeological work. The study also discusses source representations.

    Findings

    The source use patterns reveal a latent variation, not visible in the general analysis: a professional/academic frame of reference (mainly among authors affiliated with incorporated businesses and sole proprietorships) and an administrative frame of reference (mainly among authors affiliated with government agencies, foundations and member associations) emerge.

    Research limitations/implications

    The study focuses on Swedish field evaluation reports. Future research could 1) test the results in relation to other types of reports, and 2) go beyond the document perspective to explore source use in documentation practices.

    Social implications

    The results on variations in frames of references among report writers have implication for report readers and user. The results should also be considered in archaeology management and policy-making. On the level of source representation the results call for clarifications of vague representations and possibly omitted sources.

    Originality/value

    This study contextualises archaeological information use and focuses on variations in professional archaeology which has received little previous research attention. The bibliometric approach complements previous qualitative studies of archaeological information.

    Keyword
    Documentation; Reports; Grey literature; Information sources; Information use: Referencing; Bibliometrics; Sociology of professions; Archaeology
    National Category
    Information Studies
    Identifiers
    urn:nbn:se:uu:diva-246514 (URN)10.1108/JD-09-2014-0137 (DOI)000369171600003 ()
    Funder
    Swedish Research Council, 340-2012-5751
    Available from: 2015-03-08 Created: 2015-03-08 Last updated: 2017-10-20Bibliographically approved
    4. Research outside academia?: An analysis of resources in extra-academic report writing
    Open this publication in new window or tab >>Research outside academia?: An analysis of resources in extra-academic report writing
    2016 (English)In: Proceedings of the Association for Information Science and Technology, 2016Conference paper, Published paper (Refereed)
    Abstract [en]

    A significant part of all research takes place in extra-academic organizations. Practitioner researchers often present their results in publications different from those in academia, e.g. in reports, sometimes (and here) referred to as “gray literature”. Gray literature is increasingly available online. However, availability does not mean that reports are exploited to their full potential in research. Disciplines like archaeology have substantial problems with the scholarly communication and knowledge sharing between extra-academic and academic research. This paper approaches this problem from a report-user perspective. For the benefit of potential report users’ gray literature literacies, report-writing practices are analyzed by means of practice theory. Qualitative interviews with six practitioner researchers in Swedish archaeology firms make up the material. The analysis focuses on how report writers draw on regulative, institutional, and infrastructural resources in their practices. Based on the findings about the practices in which reports are written and become informative, the paper presents seven suggestions supporting report users’ potential to critically analyze and use report content. The results contribute to the information science field with insights into extra-academic information practices, and as input in a wider critical discussion of the information-related conditions for research outside academia.

    Keyword
    Scholarly communication; Practitioner researchers; Grey literature; Archaeology; Practice theory
    National Category
    Information Studies
    Research subject
    Library and Information Science
    Identifiers
    urn:nbn:se:uu:diva-303766 (URN)
    Conference
    Annual Meeting of the Association for Information Science and Technology, Copenhagen, Denmark Oct. 14-18, 2016
    Projects
    ARKDIS
    Funder
    Swedish Research Council, 340-2012-5751
    Available from: 2016-09-23 Created: 2016-09-23 Last updated: 2017-10-20
  • Public defence: 2017-12-15 13:15 ITC 2446, Uppsala
    Francisco Rodríguez, María Andreína
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computing Science. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Analysis, synthesis and application of automaton-based constraint descriptions2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Constraint programming (CP) is a technology in which a combinatorial problem is modelled as a conjunction of constraints on variables ranging over given initial domains, and optionally an objective function on the variables. Such a model is given to a general-purpose solver performing systematic search to find constraint-satisfying domain values for the variables, giving an optimal value to the objective function. A constraint predicate (also known as a global constraint) does two things: from the modelling perspective, it allows a modeller to express a commonly occurring combinatorial substructure, for example that a set of variables must take distinct values; from the solving perspective, it comes with a propagation algorithm, called a propagator, which removes some but not necessarily all impossible values from the current domains of its variables when invoked during search.

    Although modern CP solvers have many constraint predicates, often a predicate one would like to use is not available. In the past, the choices were either to reformulate the model or to write one's own propagator. In this dissertation, we contribute to the automatic design of propagators for new predicates.

    Integer time series are often subject to constraints on the aggregation of the features of all maximal occurrences of some pattern. For example, the minimum width of the peaks may be constrained. Automata allow many constraint predicates for variable sequences, and in particular many time-series predicates, to be described in a high-level way. Our first contribution is an algorithm for generating an automaton-based predicate description from a pattern, a feature, and an aggregator.

    It has previously been shown how to decompose an automaton-described constraint on a variable sequence into a conjunction of constraints whose predicates have existing propagators. This conjunction provides the propagation, but it is unknown how to propagate it efficiently. Our second contribution is a tool for deriving, in an off-line process, implied constraints for automaton-induced constraint decompositions to improve propagation. Further, when a constraint predicate functionally determines a result variable that is unchanged under reversal of a variable sequence, we provide as our third contribution an algorithm for deriving an implied constraint between the result variables for a variable sequence, a prefix thereof, and the corresponding suffix.

    List of papers
    1. Automatic generation of descriptions of time-series constraints
    Open this publication in new window or tab >>Automatic generation of descriptions of time-series constraints
    2017 (English)In: Proc. 29th International Conference on Tools with Artificial Intelligence, IEEE Computer Society, 2017Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    IEEE Computer Society, 2017
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-332145 (URN)
    Conference
    ICTAI 2017, November 6–8, Boston, MA
    Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-11-09Bibliographically approved
    2. Generation of implied constraints for automaton-induced decompositions
    Open this publication in new window or tab >>Generation of implied constraints for automaton-induced decompositions
    2013 (English)In: Proc. 25th International Conference on Tools with Artificial Intelligence, IEEE Computer Society, 2013, 1076-1083 p.Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    IEEE Computer Society, 2013
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-218040 (URN)10.1109/ICTAI.2013.160 (DOI)978-1-4799-2971-9 (ISBN)
    Conference
    ICTAI 2013, November 4-6, Herndon, VA
    Available from: 2014-02-06 Created: 2014-02-06 Last updated: 2017-10-24Bibliographically approved
    3. Implied constraints for AUTOMATON constraints
    Open this publication in new window or tab >>Implied constraints for AUTOMATON constraints
    2015 (English)In: Global Conference on Artificial Intelligence: GCAI 2015, Manchester, UK: Cool Press , 2015, 113-126 p.Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Manchester, UK: Cool Press, 2015
    Series
    EasyChair Proceedings in Computing, ISSN 2040-557X ; 36
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-268653 (URN)
    Conference
    GCAI 2015, October 16–18, Tbilisi, Georgia
    Funder
    Swedish Research Council
    Available from: 2015-12-18 Created: 2015-12-09 Last updated: 2017-10-24Bibliographically approved
    4. Time-series constraints: Improvements and application in CP and MIP contexts
    Open this publication in new window or tab >>Time-series constraints: Improvements and application in CP and MIP contexts
    Show others...
    2016 (English)In: Integration of AI and OR Techniques in Constraint Programming, Springer, 2016, 18-34 p.Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2016
    Series
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 9676
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-298447 (URN)10.1007/978-3-319-33954-2_2 (DOI)000378993700002 ()978-3-319-33953-5 (ISBN)
    Conference
    CPAIOR 2016, May 29 – June 1, Banff, Canada
    Available from: 2016-05-12 Created: 2016-07-04 Last updated: 2017-10-24Bibliographically approved
    5. Linking prefixes and suffixes for constraints encoded using automata with accumulators
    Open this publication in new window or tab >>Linking prefixes and suffixes for constraints encoded using automata with accumulators
    Show others...
    2014 (English)In: Principles and Practice of Constraint Programming: CP 2014, Springer, 2014, 142-157 p.Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2014
    Series
    Lecture Notes in Computer Science, 8656
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-238534 (URN)10.1007/978-3-319-10428-7_13 (DOI)978-3-319-10427-0 (ISBN)
    Conference
    CP 2014, September 8–12, Lyon, France
    Funder
    Swedish Research Council
    Available from: 2014-09-12 Created: 2014-12-13 Last updated: 2017-10-24Bibliographically approved
    6. Systematic derivation of bounds and glue constraints for time-series constraints
    Open this publication in new window or tab >>Systematic derivation of bounds and glue constraints for time-series constraints
    Show others...
    2016 (English)In: Principles and Practice of Constraint Programming: CP 2016, Springer, 2016, 13-29 p.Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2016
    Series
    Lecture Notes in Computer Science, 9892
    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-302048 (URN)10.1007/978-3-319-44953-1_2 (DOI)000389019700003 ()978-3-319-44952-4 (ISBN)
    Conference
    CP 2016, September 5–9, Toulouse, France
    Funder
    Swedish Research Council, 2011-6133Swedish Research Council, 2012-4908
    Available from: 2016-08-23 Created: 2016-08-29 Last updated: 2017-10-24Bibliographically approved
  • Aaboud, M.
    et al.
    Bergeås Kuutmann, Elin
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Bokan, Petar
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Brenner, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Ekelöf, Tord
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Ellert, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Ferrari, Arnaud
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Gradin, P. O. Joakim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Isacson, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Mårtensson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Öhman, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Rangel Smith, Camila
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    De Bruin, Pedro Sales
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Zwalinski, L.
    Search for direct top squark pair production in events with a Higgs or Z boson, and missing transverse momentum in root s=13 TeV pp collisions with the ATLAS detector2017In: Journal of High Energy Physics (JHEP), ISSN 1126-6708, E-ISSN 1029-8479, no 8, 006Article in journal (Refereed)
    Abstract [en]

    A search for direct top squark pair production resulting in events with either a same-flavour opposite-sign dilepton pair with invariant mass compatible with a Z boson or a pair of jets compatible with a Standard Model (SM) Higgs boson (h) is presented. Requirements on the missing transverse momentum, together with additional selections on leptons, jets, jets identified as originating from b-quarks are imposed to target the other decay products of the top squark pair. The analysis is performed using proton-proton collision data at root s = 13 TeV collected with the ATLAS detector at the LHC in 20152016, corresponding to an integrated luminosity of 36.1 fb(-1). No excess is observed in the data with respect to the SM predictions. The results are interpreted in two sets of models. In the first set, direct production of pairs of lighter top squarks ((t) over tilde (1)) with long decay chains involving Z or Higgs bosons is considered. The second set includes direct pair production of the heavier top squark pairs ((t) over tilde (2)) decaying via (t) over tilde (2) -> Z (t) over tilde (1) or (t) over tilde (2) -> h (t) over tilde (1). The results exclude at 95% confidence level (t) over tilde (2) and (t) over tilde (1) masses up to about 800 GeV, extending the exclusion region of supersymmetric parameter space covered by previous LHC searches.

  • Jalil, Ali
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    MedicReminder: Ett system för att öka patientens följsamhettill läkemedelsbehandling2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    This thesis has aimed to develop an application that helps people remember to taketheir medicine on time. The applications main function is to notify the user when it's time to take their medicine. The target users for this app is people that consumes several dos of medicine each day which in this case is older people and people that have troubles remembering to take their medicine on time.The challenge was to design a useful interface that even people with limited technical knowledge can use it. However, the acceptance of the application was to have satisfied users that can use all the functionalities that the application has to offer.The required experience was gathered from user interviews and usability-testsessions. Design principals of user-driven development was applied to insure the maximum usability and minimum complexity for using the functions. The Evaluation of all these sessions resulted to a mobile application that has beentested by target users. Results from users shows us improvements in the daily dosetaking making it much easier for the users remembering to take their medicine ontime. All together resulted to a great usability experience making it easy to use thetechnology to simplify people's daily tasks

  • Ahlbom, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Quadratic Programming Modelsin Strategic Sourcing Optimization2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Strategic sourcing allows for optimizing purchases on a large scale.Depending on the requirements of the client and the offers provided forthem, finding an optimal or even a near-optimal solution can become computationally hard. Mixed integer programming (MIP), where theproblem is modeled as a set of linear expressions with an objectivefunction for which an optimal solution results in a minimum objectivevalue, is particularly suitable for finding competitive results. However, given the research and improvements continually being made for quadratic programming (QP), which allows for objective functions with quadratic expressions as well, comparing runtimes and objective values for finding optimal and approximate solutions is advised: for hard problems, applying the correct methods may decrease runtimes by severalorders of magnitude. In this report, comparisons between MIP and QPmodels used in four different problems with three different solverswere made, measuring both optimization and approximation performance interms of runtimes and objective values. Experiments showed that while QP holds an advantage over MIP in some cases, it is not consistentlyefficient enough to provide a significant improvement in comparison with, for example, using a different solver.

  • Garousi, Javad
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Andersson, Ken G.
    KTH Royal Inst Technol, Dept Prot Technol.
    Dam, Johan H.
    Odense Univ Hosp, Dept Nucl Med.
    Olsen, Birgitte B.
    Odense Univ Hosp, Dept Nucl Med..
    Mitran, Bogdan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Molecular Imaging.
    Orlova, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Molecular Imaging.
    Buijs, Jos
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medical Radiation Science.
    Ståhl, Stefan
    KTH Royal Inst Technol, Dept Prot Technol.
    Löfblom, John
    KTH Royal Inst Technol, Dept Prot Technol.
    Thisgaard, Helge
    Odense Univ Hosp, Dept Nucl Med.
    Tolmachev, Vladimir
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    The use of radiocobalt as a label improves imaging of EGFR using DOTA-conjugated Affibody molecule2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, 5961Article in journal (Refereed)
    Abstract [en]

    Several anti-cancer therapies target the epidermal growth factor receptor (EGFR). Radionuclide imaging of EGFR expression in tumours may aid in selection of optimal cancer therapy. The In-111-labelled DOTA-conjugated Z(EGFR:2377) Affibody molecule was successfully used for imaging of EGFR-expressing xenografts in mice. An optimal combination of radionuclide, chelator and targeting protein may further improve the contrast of radionuclide imaging. The aim of this study was to evaluate the targeting properties of radiocobalt-labelled DOTA-Z(EGFR:2377). DOTA-Z(EGFR:2377) was labelled with Co-57 (T-1/2 = 271.8 d), Co-55 (T-1/2 = 17.5 h), and, for comparison, with the positron-emitting radionuclide Ga-68 (T-1/2 = 67.6 min) with preserved specificity of binding to EGFR-expressing A431 cells. The long-lived cobalt radioisotope Co-57 was used in animal studies. Both Co-57-DOTA-Z(EGFR:2377) and Ga-68-DOTA-Z(EGFR:2377) demonstrated EGFR-specific accumulation in A431 xenografts and EGFR-expressing tissues in mice. Tumour-to-organ ratios for the radiocobalt-labelled DOTA-Z(EGFR:2377) were significantly higher than for the gallium-labelled counterpart already at 3 h after injection. Importantly, Co-57-DOTA-Z(EGFR:2377) demonstrated a tumour-to-liver ratio of 3, which is 7-fold higher than the tumour-to-liver ratio for (68)GaDOTA-Z(EGFR:2377). The results of this study suggest that the positron-emitting cobalt isotope 55Co would be an optimal label for DOTA-Z(EGFR:2377) and further development should concentrate on this radionuclide as a label.

  • Sepulveda, Jorge I. Ramirez
    et al.
    Karolinska Univ Hosp, Karolinska Inst, Dept Med, Unit Expt Rheumatol, SE-17176 Stockholm, Sweden..
    Kvarnstrom, Marika
    Karolinska Univ Hosp, Karolinska Inst, Dept Med, Unit Expt Rheumatol, SE-17176 Stockholm, Sweden..
    Eriksson, Per
    Linkoping Univ, Div Rheumatol, Dept Clin Expt Med, Linkoping, Sweden..
    Mandl, Thomas
    Skane Univ Hosp, Dept Rheumatol, Malmo, Sweden..
    Norheim, Katrine Braekke
    Stavanger Univ Hosp, Dept Internal Med, Clin Immunol Unit, Stavanger, Norway..
    Johnsen, Svein Joar
    Stavanger Univ Hosp, Dept Internal Med, Clin Immunol Unit, Stavanger, Norway..
    Hammenfors, Daniel
    Univ Bergen, Dept Clin Sci, Broegelmann Res Lab, Bergen, Norway.;Haukeland Hosp, Dept Rheumatol, Bergen, Norway..
    Jonsson, Malin V.
    Univ Bergen, Dept Clin Sci, Broegelmann Res Lab, Bergen, Norway.;Univ Bergen, Sect Oral & Maxillofacial Radiol, Dept Clin Dent, Bergen, Norway..
    Skarstein, Kathrine
    Univ Bergen, Dept Clin Med, Gade Lab Pathol, Bergen, Norway.;Haukeland Hosp, Dept Pathol, Bergen, Norway..
    Brun, Johan G.
    Univ Bergen, Dept Clin Sci, Broegelmann Res Lab, Bergen, Norway.;Haukeland Hosp, Dept Rheumatol, Bergen, Norway..
    Rönnblom, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Forsblad-d'Elia, Helena
    Umea Univ, Dept Publ Hlth & Clin Med, Rheumatol, Umea, Sweden..
    Bucher, Sara Magnusson
    Orebro Univ, Fac Med & Hlth, Dept Rheumatol, Orebro, Sweden..
    Baecklund, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Theander, Elke
    Skane Univ Hosp, Dept Rheumatol, Malmo, Sweden..
    Omdal, Roald
    Stavanger Univ Hosp, Dept Internal Med, Clin Immunol Unit, Stavanger, Norway..
    Jonsson, Roland
    Univ Bergen, Dept Clin Sci, Broegelmann Res Lab, Bergen, Norway.;Haukeland Hosp, Dept Rheumatol, Bergen, Norway..
    Nordmark, Gunnel
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wahren-Herlenius, Marie
    Karolinska Univ Hosp, Karolinska Inst, Dept Med, Unit Expt Rheumatol, SE-17176 Stockholm, Sweden..
    Long-term follow-up in primary Sjogren's syndrome reveals differences in clinical presentation between female and male patients2017In: Biology of Sex Differences, ISSN 2042-6410, Vol. 8, 25Article in journal (Refereed)
    Abstract [en]

    Background: Despite men being less prone to develop autoimmune diseases, male sex has been associated with a more severe disease course in several systemic autoimmune diseases. In the present study, we aimed to investigate differences in the clinical presentation of primary Sjogren's syndrome (pSS) between the sexes and establish whether male sex is associated with a more severe form of long-term pSS. Methods: Our study population included 967 patients with pSS (899 females and 68 males) from Scandinavian clinical centers. The mean follow-up time (years) was 8.8 +/- 7.6 for women and 8.5 +/- 6.2 for men (ns). Clinical data including serological and hematological parameters and glandular and extraglandular manifestations were compared between men and women. Results: Male patient serology was characterized by more frequent positivity for anti-Ro/SSA and anti-La/SSB (p = 0. 02), and ANA (p = 0.02). Further, men with pSS were more frequently diagnosed with interstitial lung disease (p = 0. 008), lymphadenopathy (p = 0.04) and lymphoma (p = 0.007). Conversely, concomitant hypothyroidism was more common among female patients (p = 0.009). Conclusions: We observe enhanced serological responses and higher frequencies of lymphoma-related extraglandular manifestations in men with pSS. Notably, lymphoma itself was also significantly more common in men. These observations may reflect an aggravated immune activation and a more severe pathophysiological state in male patients with pSS and indicate a personalized managing of the disease due to the influence of the sex of patients with pSS.

  • Warensjö Lemming, Eva
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Byberg, Liisa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Melhus, Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical pharmacogenomics and osteoporosis.
    Wolk, Alicja
    Karolinska Inst, Inst Environm Med, Div Nutr Epidemiol.
    Michaëlsson, Karl
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Long-term a posteriori dietary patterns and risk of hip fractures in a cohort of women2017In: European Journal of Epidemiology, ISSN 0393-2990, E-ISSN 1573-7284, Vol. 32, no 7, 605-616 p.Article in journal (Refereed)
    Abstract [en]

    Dietary pattern analysis is a useful tool to study the importance of food components in the context of a diet and how they relate to health and disease. The association between dietary patterns and fractures is at present uncertain. We aimed to study associations between dietary patterns and risk of hip fracture in the Swedish Mammography Cohort, including 56,736 women (median baseline age 52 years). Diet data was collected in food frequency questionnaires at two investigations and dietary patterns were defined by principal component analysis using 31 food groups. Information on hip fractures was collected from the Swedish National Patient Register. Multivariable adjusted hazard ratios (HR) with 95% confidence intervals (CI) were estimated in Cox proportional hazards regression analysis. The two patterns identified-the healthy and Western/convenience dietary patterns-were time-updated and analysed. During a median follow-up time of 25.5 years, 4997 women experienced a hip fracture. Hip fracture rate was 31% lower in the highest compared to the lowest quartile of the healthy dietary pattern [HR (95% CI) 0.69 (0.64; 0.75)]. In contrast, women in the highest compared to the lowest quartile of the Western/convenience dietary pattern had a 50% higher [HR (95% CI) 1.50 (1.38; 1.62)] hip fracture rate. Further, in each stratum of a Western/convenience dietary pattern a higher adherence to a healthy dietary pattern was associated with less hip fractures. The present results suggest that a varied healthy diet may be beneficial for the prevention of fragility fractures in women.

  • Petersen, Julian
    et al.
    Karolinska Inst, Sect Receptor Biol & Signaling, Dept Physiol & Pharmacol, S-17177 Stockholm, Sweden..
    Wright, Shane C.
    Karolinska Inst, Sect Receptor Biol & Signaling, Dept Physiol & Pharmacol, S-17177 Stockholm, Sweden..
    Rodriguez, David
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden..
    Matricon, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lahav, Noa
    Hebrew Univ Jerusalem, Inst Chem, IL-91904 Jerusalem, Israel..
    Vromen, Aviv
    Hebrew Univ Jerusalem, Inst Chem, IL-91904 Jerusalem, Israel..
    Friedler, Assaf
    Hebrew Univ Jerusalem, Inst Chem, IL-91904 Jerusalem, Israel..
    Stromqvist, Johan
    Single Technol AB, SE-11428 Stockholm, Sweden..
    Wennmalm, Stefan
    Royal Inst Technol, Dept Appl Phys, Expt Biomol Phys Grp, Sci Life Lab, SE-17165 Solna, Sweden..
    Carlsson, Jens
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Schulte, Gunnar
    Karolinska Inst, Sect Receptor Biol & Signaling, Dept Physiol & Pharmacol, S-17177 Stockholm, Sweden.;Masaryk Univ, Dept Expt Biol, Fac Sci, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, 226Article in journal (Refereed)
    Abstract [en]

    G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors. They can exist and act as dimers, but the requirement of dimers for agonist-induced signal initiation and structural dynamics remains largely unknown. Frizzled 6 (FZD6) is a member of Class F GPCRs, which bind WNT proteins to initiate signaling. Here, we show that FZD6 dimerizes and that the dimer interface of FZD6 is formed by the transmembrane a-helices four and five. Most importantly, we present the agonist-induced dissociation/re-association of a GPCR dimer through the use of live cell imaging techniques. Further analysis of a dimerization-impaired FZD6 mutant indicates that dimer dissociation is an integral part of FZD6 signaling to extracellular signal-regulated kinases1/2. The discovery of agonistdependent dynamics of dimers as an intrinsic process of receptor activation extends our understanding of Class F and other dimerizing GPCRs, offering novel targets for dimerinterfering small molecules.

  • Gerasimova, Julia V.
    et al.
    Russian Acad Sci, Komarov Bot Inst, Prof Popova St 2, St Petersburg 197376, Russia..
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Taxonomy and nomenclature of seven names in Bacidia (Ramalinaceae, Lecanorales) described from Russia2017In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 316, no 3, 292-296 p.Article in journal (Refereed)
    Abstract [en]

    We aim to increase understanding and improve taxonomy of seven names currently treated in Bacidia that were described from Russian territory based on material collected during 19th-century expeditions: Bacidia alborussula, B. freshfieldii, B. graminum, B. indigens, B. primigenia, B. subabbrevians, and B. xylophila. B. alborussula, B. graminum, and B. indigens are transferred here to Haematomma, Lecania, and Bacidina, respectively. Bacidia freshfieldii and B. subabbrevians belong in the Ramalinaceae and are provisionally kept in Bacidia even though none of them is congeneric with the type of that genus. B. primigenia belongs in Arthrorhaphis, but we refrain from making any new combination owing to its questionable status as a species distinct from A. grisea. B. xylophila is a younger synonym of Lecania subfuscula. We designate lectotypes for names previously not typified and for which syntypes exist: Lecidea alborussula, L. graminum, L. indigens, and L. subabbrevians.

  • Gustavsson, Martin
    et al.
    Stockholms centrum för forskning om offentlig sektor (Score), Stockholms universitet och Handelshögskolan i Stockholm.
    Melldahl, Andreas
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Educational Sciences, Department of Education.
    Länsteatrarnas ekonomiska handlingsutrymme: Intäkter, utgifter och personal 1980–20152017Report (Other academic)
    Abstract [sv]

    Rapporten redovisar hur länsteatrarnas inkomster, utgifter och personalstyrka har förändrats mellan 1980 och 2015, en period som präglats av tre olika kulturpolitiska reformer (sjösatta 1974, 1996 och 2009).

    I ett bakgrundsavsnitt diskuteras bristen på bra kulturstatistik. Obrutna serier med statistik som sträcker sig över olika kulturpolitiska perioder har saknats. För att kunna jämföra länsteatrarnas ekonomiska förhållanden under perioder märkta av olika kulturpolitiska ideal har statistik därför samlats in från olika arkiv och skarvats ihop för hela den nämnda 35-årsperioden.

    Rapportens första undersökande del visar att det har skett en resursmässig förstärkning av länsteatrarna över tid (mätt med konsumentprisindex). Utvecklingen har dock varit ojämn. Den följer bredare trender i samhällsekonomin. Den genomsnittliga länsteaterns intäkter ökade markant mellan 1980 och 1990 (1974 års kulturpolitiska epok), minskade påtagligt mellan 1990 och 1996 (90-talets ekonomiska kris), ökade kraftigt mellan 1996 och 2005 (1996 års kulturpolitiska era), minskade noterbart mellan 2005 och 2012 (det sena 00-talets ekonomiska kris) och ökade något mellan 2012 och 2015 (2009 års kulturpolitiska period). Vi visade också att de genomsnittliga utgifternas utveckling följer samma typ av cykliska förlopp som de genomsnittliga intäkternas.

    Rapportens andra del studerade finansieringens effekter på kärnverksamheten, exemplifierad av personalstyrkans storlek och sammansättning. Länsteatrarnas största utgiftspost utgörs av personalkostnader. För att undersöka om lönekostnadsutvecklingen undergrävt uppräkningen av de offentliga anslagen justerades beloppen med olika löneindex. Nu blev ett motsatt utvecklingsscenario synligt. Istället för den trendmässiga – förvisso försiktiga och periodvisa – ökningen av intäkterna som visades när anslagen räknades om med konsumentprisindex minskade anslagen över tid när de justerades med löneindex. Den genomsnittliga länsteatern kan inte i dag, trots den måttliga resursförstärkningen de senaste åren, köpa lika mycket personal som i början av undersökningsperioden.I en separat delstudie visade vi även att antalet arbetade timmar av anställd ”konstnärlig” personal på teatrarna minskade över tid, medan antalet årsverken för ”administrativ” personal ökade något.

    I en avslutande delstudie ställdes följdfrågor om personalsituationen. Vi visade på den något paradoxala situationen att länsteatrarna – trots lägre köpkraft (mätt med löneindex) och färre ersatta arbetstimmar utförda av anställd konstnärlig personal (årsverken) – lyckats enrollera fler personer. En delförklaring till denna utveckling ligger i att länsteatrarna under de senaste tio åren alltmer börjat befolkas av visstidsoch korttidsanställd personal (med A-skattsedel) och frivilliga eller ofrivilliga företagare (med F- och FA-skattsedel).

  • Public defence: 2017-12-15 13:00 Room B7:101a, Uppsala
    Daurer, Benedikt J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Algorithms for Coherent Diffractive Imaging with X-ray Lasers2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Coherent diffractive imaging (CDI) has become a very popular technique over the past two decades. CDI is a "lensless" imaging method which replaces the objective lens of a conventional microscope by a computational image reconstruction procedure. Its increase in popularity came together with the development of X-ray free-electron lasers (XFELs) which produce extremely bright and coherent X-rays. By facilitating these unique properties, CDI enables structure determination of non-crystalline samples at nanometre resolution and has many applications in structural biology, material science and X-ray optics among others. This work focuses on two specific CDI techniques, flash X-ray diffractive imaging (FXI) on biological samples and X-ray ptychography.

    While the first FXI demonstrations using soft X-rays have been quite promising, they also revealed remaining technical challenges. FXI becomes even more demanding when approaching shorter wavelengths to allow subnanometre resolution imaging. We described one of the first FXI experiments using hard X-rays and characterized the most critical components of such an experiment, namely the properties of X-ray focus, sample delivery and detectors. Based on our findings, we discussed experimental and computational strategies for FXI to overcome its current difficulties and reach its full potential. We deposited the data in the Coherent X-ray Database (CXIDB) and made our data analysis code available in a public repository. We developed algorithms targeted towards the needs of FXI experiments and implemented a software package which enables the analysis of diffraction data in real time.

    X-ray ptychography has developed into a very useful tool for quantitative imaging of complex materials and has found applications in many areas. However, it involves a computational reconstruction step which can be slow. Therefore, we developed a fast GPU-based ptychographic solver and combined it with a framework for real-time data processing which already starts the ptychographic reconstruction process while data is still being collected. This provides immediate feedback to the user and allows high-throughput ptychographic imaging.

    Finally, we have used ptychographic imaging as a method to study the wavefront of a focused XFEL beam under typical FXI conditions. 

    We are convinced that this work on developing strategies and algorithms for FXI and ptychography is a valuable contribution to the development of coherent diffractive imaging. 

    List of papers
    1. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
    Open this publication in new window or tab >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
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    2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, 251-262 p.Article in journal (Refereed) Published
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:uu:diva-328529 (URN)10.1107/S2052252517003591 (DOI)
    Projects
    eSSENCE
    Available from: 2017-04-07 Created: 2017-08-25 Last updated: 2017-10-24Bibliographically approved
    2. Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
    Open this publication in new window or tab >>Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
    2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, 1042-1047 p.Article in journal (Refereed) Published
    National Category
    Biophysics Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-287197 (URN)10.1107/S1600576716005926 (DOI)000377020600036 ()
    Projects
    eSSENCE
    Available from: 2016-04-18 Created: 2016-04-22 Last updated: 2017-10-24Bibliographically approved
    3. SHARP: a distributed GPU-based ptychographic solver
    Open this publication in new window or tab >>SHARP: a distributed GPU-based ptychographic solver
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    2016 (English)In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, 1245-1252 p.Article in journal (Refereed) Published
    Abstract [en]

    Ever brighter light sources, fast parallel detectors and advances in phase retrieval methods have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time-consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength-limited resolution, coupled with a large field of view. This article describes a set of algorithmic and computational methodologies used at the Advanced Light Source and US Department of Energy light sources. These are packaged as a CUDA-based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction-limited light sources.

    Keyword
    coherent X-ray diffractive imaging, ptychography, nanoscience, X-ray microscopy, phase-contrast X-ray imaging
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-300178 (URN)10.1107/S1600576716008074 (DOI)000382755900015 ()
    Funder
    Swedish Research CouncilSwedish Foundation for Strategic Research
    Available from: 2016-08-04 Created: 2016-08-04 Last updated: 2017-10-24
    4. Nanosurveyor: a framework for real-time data processing
    Open this publication in new window or tab >>Nanosurveyor: a framework for real-time data processing
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    2017 (English)In: Advanced Structural and Chemical Imaging, ISSN 2198-0926, Vol. 3, no 1Article in journal (Refereed) Published
    Abstract [en]

    The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality.

    National Category
    Computer Science
    Identifiers
    urn:nbn:se:uu:diva-317013 (URN)10.1186/s40679-017-0039-0 (DOI)
    Funder
    Swedish Research CouncilSwedish Foundation for Strategic Research
    Available from: 2017-03-08 Created: 2017-03-08 Last updated: 2017-10-24
    5. Wavefront sensing of individual XFEL pulses using ptychography
    Open this publication in new window or tab >>Wavefront sensing of individual XFEL pulses using ptychography
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The characterization of the wavefront dynamics is important for many X-ray free-electron laser (XFEL) experiments, in particular for coherent diffractive imaging (CDI), as the reconstructed image is always the product of the incoming wavefront with the object. An accurate understanding of the wavefront is also important for any experiment wishing to achieve peak power densities, making use of the tightest possible focal spots. With the use of ptychography we demonstrate high-resolution imaging of the Linac Coherent Light Source (LCLS) beam focused at the endstation for Atomic, Molecular and Optical (AMO) experiments, including its phase and intensity at every plane along its propagation axis, for each individual pulse. Using a mixed-state approach, we have reconstructed the most dominant beam components that constitute an ensemble of pulses, and from the reconstructed components determined their respective contribution in each of the individual pulses. This enabled us to obtain complete wavefront information about each individual pulse. We hope that our findings aid interpretation of data from past and future LCLS experiments and we propose this method to be used routinely for XFEL beam diagnostics. 

    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-329011 (URN)
    Available from: 2017-10-24 Created: 2017-10-24 Last updated: 2017-10-24
  • Hermanson, M.
    et al.
    Department of Clinical Sciences Lund, Orthopaedics, Lund University, Skåne University Hospital.
    Hägglund, G.
    Department of Clinical Sciences Lund, Orthopaedics, Lund University, Skåne University Hospital.
    Riad, J.
    Department of Clinical Sciences, Skaraborgs Hospital/Skövde.
    Rodby-Bousquet, Elisabet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Centre for Clinical Research, County of Västmanland.
    Inter- and intra-rater reliability of the head-shaft angle in children with cerebral palsy2017In: Journal of Children's Orthopaedics, ISSN 1863-2521, E-ISSN 1863-2548, Vol. 11, no 4, 256-262 p.Article in journal (Refereed)
    Abstract [en]

    Purpose Children with cerebral palsy (CP) are at increased risk for hip dislocation. This can be prevented in most cases using surveillance programmes that include radiographic examinations. Known risk factors for hip dislocation include young age, high Gross Motor Function Classification System (GMFCS) level and high migration percentage (MP). The head-shaft angle (HSA) has recently been described as an additional risk factor. The study aim was to determine inter- and intra-rater reliability of the HSA in a surveillance programme for children with CP.

    Methods We included hip radiographs from the CP surveillance programme CPUP in southern Sweden during the first half of 2016. Fifty radiographs were included from children at GMFCS levels II-V, with a mean age of 6.6 (SD 3.2) years. Three raters measured the HSA of one hip (left or right) at baseline and four weeks later; intraclass correlation coefficient (ICC) was used to estimate inter- and intra-rater reliability.

    Results Inter-and intra-rater reliability were excellent for the HSA, with ICC 0.92 (95% CI 0.87-0.96) and ICC 0.99 ( 95% CI 0.98-0.99), respectively.

    Conclusion The HSA showed excellent inter- and intra-rater reliability for children with CP, providing further evidence for use of the HSA as an additional factor for identifying risk for further hip displacement or dislocation.

  • Stawarz, J. E.
    et al.
    Department of Physics, Imperial College London.
    Eastwood, J.P.
    Department of Physics, Imperial College London.
    Varsani, A.
    Space Research Institute, Austrian Academy of Sciences.
    Ergun, R.E.
    Department of Astrophysical and Planetary Sciences, University of Colorado Boulder; Laboratory for Atmospheric and Space Physics, University of Colorado Boulder.
    Shay, M.A.
    Department of Physics and Astronomy, University of Delaware.
    Nakamura, R.
    pace Research Institute, Austrian Academy of Sciences.
    Phan, T.D.
    Space Sciences Laboratory, University of California.
    Burch, J. L.
    South West Research Institute.
    Gershman, D. J.
    NASA Goddard Space Flight Center.
    Giles, B. L.
    NASA Goddard Space Flight Center.
    Goodrich, K. A.
    Department of Astrophysical and Planetary Sciences, University of Colorado Boulder; Laboratory for Atmospheric and Space Physics, University of Colorado Boulder.
    Khotyaintsev, Yuri V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Swedish Institute of Space Physics, Uppsala Division.
    Lindqvist, P. -A
    School of Electrical Engineering, KTH Royal Institute of Technology.
    Russell, C. T.
    Department of Earth, Planetary, and Space Sciences, University of California.
    Strangeway, R. J.
    Department of Earth, Planetary, and Space Sciences, University of California.
    Torbert, R. B.
    Department of Physics, University of New Hampshire.
    Magnetospheric Multiscale analysis of intense field-aligned Poynting flux near the Earth's plasma sheet boundary2017In: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 44, no 14, 7106-7113 p.Article in journal (Refereed)
    Abstract [en]

    The Magnetospheric Multiscale mission is employed to examine intense Poynting flux directed along the background magnetic field toward Earth, which reaches amplitudes of nearly 2 mW/m(2). The event is located within the plasma sheet but likely near the boundary at a geocentric distance of 9 RE in association with bulk flow signatures. The fluctuations have wavelengths perpendicular to the magnetic field of 124-264 km (compared to an ion gyroradius of 280 km), consistent with highly kinetic Alfven waves. While the wave vector remains highly perpendicular to the magnetic field, there is substantial variation of the direction in the perpendicular plane. The field-aligned Poynting flux may be associated with kinetic Alfven waves released along the separatrix by magnetotail reconnection and/or the radiation of waves excited by bursty bulk flow braking and may provide a means through which energy released by magnetic reconnection is transferred to the auroral region.

  • Djurhuus, Sjurdur
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Theology, Department of Theology.
    Democracy Promotion through the Lens of Governmentality: The EU and Civil Society in Bosnia-Herzegovina and Kosovo2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • Yang, Shuo
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    The Design of a User Interface for the Mobile Virtual Reality Application2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    With the constant updating of mobile terminal hardware and the rapid developmentof mobile internet, people’s demand for mobile 3D graphics application is increasing. Therefore, for mobile terminal 3D remote rendering has become a research hotspot. In recent years, the research of remote rendering of mobile terminal can be dividedinto three aspects: rendering standardization, rendering engine design, and key technology research. Among them, the research of rendering engine design focus onrendering quality, efficiency and interactivity. Based on the existing DIBR rendering engine, this report designs and implements the interactive module for mobile terminal, in order to improves and expand the function of the engine. The module isto identify different types of interactive input instructions of mobile terminal users,then map it to interaction primitive sequence and transformed into coordinatechanges of viewpoint in 3D scene, the obtained information pass to other parts of the engine to complete the rendering.This report mainly completes the following work.Firstly, investigating and analyzing the needs of mobile terminal interaction, and combining with existing functions of engine, design the interaction module and dividedit into the primitive map sub module and user input submodule. Secondly, implement two submodules separately, including the definition of the interaction primitives andthe analysis of different input modes. Finally, integrate the interaction module into theDIBR engine, and the relevant running examples are given.

  • Tyrala, Krzysztof
    et al.
    Institute of Physics, Jan Kochanowski University.
    Wojtaszek, Klaudia
    Institute of Physics, Jan Kochanowski University.
    Pajek, Marek
    Institute of Physics, Jan Kochanowski University.
    Kayser, Yves
    Physikalisch-Technische Bundesanstalt (PTB).
    Milne, Christopher
    Paul Scherrer Institute.
    Sá, Jacinto
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Institute of Physical Chemistry, Polish Academy of Sciences.
    Szlachetko, Jakub
    Institute of Physics, Jan Kochanowski University; Institute of Physical Chemistry, Polish Academy of Sciences.
    State-Population Narrowing Effect in Two-Photon Absorption for Intense Hard X-ray Pulses2017In: Applied Sciences: APPS, ISSN 1454-5101, E-ISSN 1454-5101, Vol. 7, no 7, 653Article in journal (Refereed)
    Abstract [en]

    We report on studies of state-populations during the two-photon absorption process using intense X-ray pulses. The calculations were performed in a time-dependent manner using a simple three-level model expressed by coupled rate equations. We show that the proposed approach describes well the measured rates of X-rays excited in the one-photon and two-photon absorption processes, and allows detailed investigation of the state population dynamics during the course of the incident X-ray pulse. Finally, we demonstrate that the nonlinear interaction of X-ray pulses with atoms leads to a time-narrowing of state populations. This narrowing-effect is attributed to a quadratic incidence X-ray intensity dependence characteristic for nonlinear interactions of photons with matter.

  • Wenting, Jin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Feedback Compilation for Decoupled Access-Execute Techniques2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Software level optimization for compilers has become a major research field.Dynamic Voltage Frequency Scaling (DVFS) technology gives some options for optimization, such as tweaking the voltage or frequency. Improvements in voltage are quickly reaching their limits and hence this thesis work investigates approaches that are focused on dynamic frequency scaling. Finding an optimum with respect to two objectives: performance and energy, has been explored for Decoupled-Access-Execute(DAE) technology with iterative feedback compilations.The goal is to find a close-to-optimum output with a multi-versioned procedure within a limited budget and examine how well and on what aspect DAE can make improvements. This thesis work focuses on automating the compilation with DAE, including program instruction analysis for automatic selection of initial search parameters.

  • Stoyanova, Desislava
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    ANN for Optimization on Large-Scale Structural Acoustics Models2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Optimization of transformer design is a challenging task which defines the dimensionsof all the transformer parts, based on a given specification in order to achieve better operating performance. The mechanical force distributions, as a result of the transformer operation, make the structure vibrate at twice the network frequency,and ultimately lead to noise emission from the outer surface of the tank. In this paper,an artificial intelligence technique is proposed for transformer noise data prediction asan optimized alternative to the finite-element method with multi-physics capabilities. The technique uses a feedforward artificial neural network and the back propagation of error learning rule for predicting the noisy data, along with a finite-element modelfor computing a training data set. The method considers two well-known backpropagation algorithms, Levenberg–Marquardt and Bayesian Regularization, and while both of them appear to be extremely efficient when it comes to execution time, Bayesian Regularization presents considerably higher accuracy. The level of accuracyas well as the fast execution time makes the application of artificial neural networksfor finite-element model optimization a viable and efficient approach for industrial use.

  • Ravindran, Adithya
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Implementation of handwritten text recognition using density value of Delauney tessellation2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This paper presents a novel Word spotting technique for handwritten documentsusing density value of Delaunay triangulation. Delaunay tessellation is constructedfrom a set of data points on a query image and the density value is computed for eachdata point. This information is either directly used for training in a feed-forward neural network or used to compute the probability estimates of a class from Delaunay Tessellation Field Estimation and classification follows using naive Bayesian classifier. This paper discusses the performance of a Delaunay tessellation fieldestimation model and neural network model.

  • Rubensson, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Visualization of Music Designed for Children with Severe Disabilities2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The children participating in the MUMIn-project at the special school Årstagrundsärskola are already developing their learning skills and creativity through music.Although they have a problem. They have not used a program that visualizes the music played in a way that is understandable and rewarding. In order to furtherdevelop their skills in cause-effect relationships, such a program is highly sought after. By creating an application designed to be run on a computer at the same time as thechildren are playing music on MIDI-instruments connected to the same computer, theproblem could be solved. The visualizations would be shown on a projected screen and display animations that were designed to be as easy to understand as possible butstill have room for further exploration if they would be too simple for some of the children. Even though the children were on different skill levels, how they played music along with the visualizations showed that the created application both helps thechildren to connect cause-effect relationships and also help develop other skills like for example motor skills. The created application could because of these results be avery useful learning tool in further work in the MUMIn-project.

  • Rodriguez-Åkerstedt, Olof
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of ALM.
    "Hittar bättre artiklar nu": En studie av biblioteksundervisning i en högskolekontext2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The purpose of this study is to contribute to an increased understanding of the importance of user education in relation to undergraduates´ bachelor thesis. The secondary purpose of the study was to investigate how institutional impact is reflected in student text production. The starting point of the study is an observation of user education at Södertörn University Library, where students in the process of writing their bachelor thesis in tourism participated. This student group became the focus of the study.

            Through a survey, feedback was collected concerning what the students think the user education might have contributed to in relation to their thesis writing. Whether the importance of user education reflected in the papers has been investigated based on a comparative reference analysis that included bachelor theses in tourism science published between 2015 and 2017.

    The students' questionnaire answered in general in the support of the user education, where an increased focus on searching in databases and after scientific articles was emphasized. The comparative reference analysis also did not dispute what was expressed in the questionnaire survey although the difference was marginal to those who participated and those that did not.

    Based on Norman Fairclough's critical discourse analysis, it was investigated how institutional impact was reflected in selected papers. By analysing the user education and guidelines, it was possible to see how a certain type of academic discourse was reproduced in the theses.

    This study describes the importance of library education in several ways. The discourse analysis showed that library education has a role as a genre of governance where academic and disciplinary discourse is reproduced. The survey also showed that library education constitutes a cognitive authority towards the students, which correlated with the reference analysis.

  • Åberg, Emma
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Saccoccia, Fulvio
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Grabherr, Manfred
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ore, Wai Ying Josefin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hultqvist, Greta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Evolution of the p53-MDM2 pathway2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, 177Article in journal (Refereed)
    Abstract [en]

    Background: The p53 signalling pathway, which controls cell fate, has been extensively studied due to its prominent role in tumor development. The pathway includes the tumor supressor protein p53, its vertebrate paralogs p63 and p73, and their negative regulators MDM2 and MDM4. The p53/p63/p73-MDM system is ancient and can be traced in all extant animal phyla. Despite this, correct phylogenetic trees including both vertebrate and invertebrate species of the p53/p63/p73 and MDM families have not been published. Results: Here, we have examined the evolution of the p53/p63/p73 protein family with particular focus on the p53/ p63/p73 transactivation domain (TAD) and its co-evolution with the p53/p63/p73- binding domain (p53/p63/p73BD) of MDM2. We found that the TAD and p53/p63/p73BD share a strong evolutionary connection. If one of the domains of the protein is lost in a phylum, then it seems very likely to be followed by loss of function by the other domain as well, and due to the loss of function it is likely to eventually disappear. By focusing our phylogenetic analysis to p53/p63/ p73 and MDM proteins from phyla that retain the interaction domains TAD and p53/p63/p73BD, we built phylogenetic trees of p53/p63/p73 and MDM based on both vertebrate and invertebrate species. The trees follow species evolution and contain a total number of 183 and 98 species for p53/p63/p73 and MDM, respectively. We also demonstrate that the p53/p63/p73 and MDM families result from whole genome duplications. Conclusions: The signaling pathway of the TAD and p53/p63/p73BD in p53/p63/p73 and MDM, respectively, dates back to early metazoan time and has since then tightly co-evolved, or disappeared in distinct lineages.

  • Lionel Sagayaraj, Linushiya Ranjani
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Gene Expression Analysis of Loto-Type Toll Receptors in the Onychophoran Euperipatoides kanangrensis2017Independent thesis Advanced level (degree of Master (Two Years)), 180 HE creditsStudent thesis
    Abstract [en]

    The expression and role of Loto genes was previously investigated in arthropods and it was concluded that the morphogenetic functions of Loto genes were conserved in the last common ancestors of arthropods. In this paper, possible orthologs of Loto clade genes are analysed and it was found that they possibly play a conserved role in convergent extension of cells from the blastoderm stage to germ band extension stage. The differences and similarities in the number of and expression of Loto clade genes in arthropods and onychophorans are compared and analysed. Unlike in arthropods, the expression of Euperipatoides Loto is strongest in the head including part of the somewhat enigmatic frontal appendages (the onychophoran antennae). I also find a stripped segmental pattern of expression that is similar to that classic expression in transverse segmental stripes of Loto class genes as seen in arthropods. However, these stripes are only week and appear to be mesodermal rather than ectodermal, as in arthropods. These facts are discussed in regard to current hypothesis about the origin of segmentation in panarthropods.Insects, crustaceans and chelicerates each possess a set of several Loto class genes which are also involved in convergent extension. But the myriapod Strigamia only appears to possess one such gene.  I therefore investigated Loto genes in another distantly related myriapod, Glomeris. It appears to only have one Loto gene and this appears to be involved in convergent extension as well. Two Toll genes  of Glomeris (Gm-567 and Gm-596) were incomplete and could according to phylogenetic analysis represent Loto genes. I therefore checked their expression and found that they are not expressed like Loto genes. A third potential Glomeris Loto gene (Gm-399) could not be isolated via PCR.My data suggest a somewhat different role for onychophoran Loto than convergent extension, and that the ancestral set of panarthropod Loto genes may be one, rather than a set.

  • Evers, Kathinka
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Centre for Research Ethics and Bioethics.
    Giordano, James
    Departments of Neurology and Biochemistry, Neuroethics Studies Program-Pellegrino Center for Clinical Bioethics, Georgetown University Medical Center, Washington, DC, United States.
    The Utility- and Use–of Neurotechnology to Recover Consciousness: Technical and Neuroethical Considerations in Approaching the “Hard Question” of Neuroscience2017In: Frontiers in Human Neuroscience, ISSN 1662-5161, E-ISSN 1662-5161, Vol. 11, 1-3 p., 564Article in journal (Refereed)
  • Engström, Maria
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Modern Languages, Slavic Languages.
    Ikonens metamorfoser i det postsovjetiska Ryssland2014In: Med blicken österut: Hyllningsskrift till Per-Arne Bodin / [ed] Per Ambrosiani, Elisabeth Löfstrand, Ewa Teodorowicz-Hellman, Artos & Norma bokförlag, 2014, 67-78 p.Chapter in book (Refereed)
  • Arikan, Tuba
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Sociology.
    Kucukgöl, Ebru
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Sociology.
    Dubbelliv i hederns namn: En kvalitativ studie om HBT-personer i en hederskontext2017Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Abstract: It has been put on the spotlight and a known fact in Sweden, individuals who live in different honor cultures are exposed to different types of honor oppression. However, there is still very little information about HBT-individuals who live in an honor culture environment and are exposed to honor oppression. The purpose of this study is to create a profound understanding in the HBT-individuals’ experiences with honor and their experiences with identity as HBT-individuals in relation to the honor culture they live in. The study also looks at the possibilities and limitations these individuals mustface every day or at certain times as HBT-individuals in an honor environment. A qualitative method was used throughout the study and the empirical material is based on interviews we made with seven informers. We have used two different interview methods to receive empirical results. The first method is based on a face-to-face interview and the second method is based on chat interviews online. The analysis was examined along the theoretical efforts we used throughout this study such as, social control, honor culture, identity and many more. The results indicate that these informants are at a higher risk of being exposed to different things, such as for example being rejected by their family if they chose to come out and live openly about their sexual identity and not follow the hetero norm that is put in place.

  • Public defence: 2017-12-14 09:15 A1:107a, Uppsala
    Lundstedt, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Development of Mild Methods for Selective Covalent Functionalization of Graphene2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis discusses methods for the comparatively mild covalent functionalization of graphene. Several graphene models were investigated: polycyclic aromatic hydrocarbons (PAHs), chemical vapor deposition (CVD)-graphene on SiO2/Si substrate, graphite foil, graphite flakes, kish graphite and highly oriented pyrolytic graphite. The PAHs were viewed as graphene edge analogs with the following molecules representing different edge motifs: pyrene, perylene, benzo[a]pyrene, benzo[e]pyrene, triphenylene, acenapthylene, and anthracene.

    Ozone was used in combination with different solvents to functionalize PAHs, graphite, and CVD-graphene on SiO2/Si. Ozonation in water or methanol resulted in trapping of the carbonyl oxide intermediate that was formed in the reaction, producing a variety of functional groups. Ozonation in hydrogen peroxide solution with sonication promoted radical formation, possibly resulting in edge-oxidation of graphite. The regioselectivity for addition reactions (ozonolysis) and electrophilic aromatic substitution reactions with graphene edges is discussed.

    To achieve functionalization of the basal plane of graphite or graphene, white light irradiation was used in combination with several transfer hydrogenation reagents. Formic acid treatment under irradiation resulted in the expected hydrogenation, whereas iso-propanol treatment resulted in iso-propanol attachment to the graphene.

    The developed methods provide opportunities for graphene functionalization without the need for metal based reagents or harsh conditions.

    List of papers
    1. Ozonolysis of triphenylene in acetone
    Open this publication in new window or tab >>Ozonolysis of triphenylene in acetone
    (English)Manuscript (preprint) (Other academic)
    National Category
    Organic Chemistry
    Research subject
    Chemistry with specialization in Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-332003 (URN)
    Available from: 2017-10-20 Created: 2017-10-20 Last updated: 2017-10-24
    2. Ozonolysis of polycyclic aromatic hydrocarbons in participating solvents
    Open this publication in new window or tab >>Ozonolysis of polycyclic aromatic hydrocarbons in participating solvents
    2017 (English)In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, no 10, 6152-6159 p.Article in journal (Refereed) Published
    Abstract [en]

    Seven polycyclic aromatic hydrocarbon (PAH) compounds that can be considered small models for graphene edges have been treated with ozone in solution. The presence of participating solvents such as water or methanol had a pronounced influence on conversion and identity of the functional groups formed, whereas the regioselectivity of the ozonation remained unaffected. Six previously unreported compounds have been isolated from the ozonolysis of pyrene 1, perylene 2 and benzo[e] pyrene 4. Comparison of the experimental data with calculated local ionization energy surfaces (IES) shows a good correlation, and indicates that this computational tool would be useful to predict the regioselectivity of ozone also for larger PAHs, including graphene and graphene nanoribbons.

    National Category
    Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-316964 (URN)10.1039/c6ra26248a (DOI)000393754100073 ()
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg Foundation
    Available from: 2017-03-08 Created: 2017-03-08 Last updated: 2017-10-24Bibliographically approved
    3. Edge oxidation of graphite using a combined hydrogen peroxide - ozone treatment under sonication conditions
    Open this publication in new window or tab >>Edge oxidation of graphite using a combined hydrogen peroxide - ozone treatment under sonication conditions
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    A mild method for edge oxidation of graphite using ultrasonication in the presence of ozone and hydrogen peroxide is described. The method benefits from sustainable reagents - no metals or oxidising mineral acids are involved; and easy purification of the resulting material. Initial characterisation of the material and its dispersibility by spectroscopic methods and thermogravimetric analysis is presented.

    Keyword
    Edge oxidation, Graphite, Graphene, Hydrogen peroxide, Ozone
    National Category
    Materials Chemistry Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-327165 (URN)
    Available from: 2017-08-06 Created: 2017-08-06 Last updated: 2017-10-24
    4. Metal-free photochemical silylations and transfer hydrogenations of benzenoid hydrocarbons and graphene
    Open this publication in new window or tab >>Metal-free photochemical silylations and transfer hydrogenations of benzenoid hydrocarbons and graphene
    Show others...
    2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Article in journal (Refereed) Published
    Abstract [en]

    The first hydrogenation step of benzene, which is endergonic in the electronic ground state (S0), becomes exergonic in the first triplet state (T1). This is in line with Baird’s rule, which tells that benzene is antiaromatic and destabilized in its T1 state and also in its first singlet excited state (S1), opposite to S0, where it is aromatic and remarkably unreactive. Here we utilized this feature to show that benzene and several polycyclic aromatic hydrocarbons (PAHs) to various extents undergo metal-free photochemical (hydro)silylations and transfer-hydrogenations at mild conditions, with the highest yield for naphthalene (photosilylation: 21%). Quantum chemical computations reveal that T1-state benzene is excellent at H-atom abstraction, while COT, aromatic in the T1 and S1 states according to Baird’s rule, is unreactive. Remarkably, also CVD-graphene on SiO2 is efficiently transfer-photohydrogenated using formic acid/water mixtures together with white light or solar irradiation under metal-free conditions.

    National Category
    Chemical Sciences Chemical Engineering
    Identifiers
    urn:nbn:se:uu:diva-303639 (URN)10.1038/ncomms12962 (DOI)000385553900001 ()27708336 (PubMedID)
    Funder
    Wenner-Gren FoundationsSwedish Research CouncilKnut and Alice Wallenberg FoundationÅForsk (Ångpanneföreningen's Foundation for Research and Development)Magnus Bergvall Foundation
    Available from: 2016-09-21 Created: 2016-09-21 Last updated: 2017-11-21Bibliographically approved
    5. White-light photoassisted covalent functionalization of graphene using 2-propanol
    Open this publication in new window or tab >>White-light photoassisted covalent functionalization of graphene using 2-propanol
    Show others...
    2017 (English)In: Small Methods, ISSN 2366-9608, 1700214- p.Article in journal (Refereed) Published
    Abstract [en]

    Herein, a photochemical method for functionalization of graphene using 2-propanol is reported. The functionalization method which is catalyst-free operates at ambient temperature in neat 2-propanol under an inert atmosphere of argon. The equipment requirement is a white-light source for the irradiation. The same methodology when applied to kish graphite results in a novel material, exhibiting significantly higher wettability than the starting material according to water contact angle measurements. Furthermore, the materials generated from both graphene and kish graphite exhibit increased adhesion energy, attributed to the fixation of isopropyl alcohol fragments onto graphene and graphite, respectively. The presence of hydroxyl groups and the possibility for further reactions on the functionalized graphene material are demonstrated through a substitution reaction with thionyl chloride, where the hydroxyl groups are replaced with chlorides, as confirmed through X-ray photoelectron spectroscopy analysis.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2017
    National Category
    Materials Engineering Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-314171 (URN)10.1002/smtd.201700214 (DOI)
    Available from: 2017-01-29 Created: 2017-01-29 Last updated: 2017-10-24
  • Public defence: 2017-12-12 13:15 Hörsal 2, Uppsala
    Crawford, Jason
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Business Studies.
    Regulation's Influence on Risk Management and Management Control Systems in Banks2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This dissertation explores regulation’s influence on risk management and management control systems (MCS) in banks. The dissertation comprises of an introductory chapter, two published book chapters, one of which is an extensive literature review, and two working papers, presented at several European conferences. The overall objective of this dissertation is to explore how banks are responding to banking regulation in light of the 2007-08 financial crisis and what the implications of those responses are, particularly in relation to risk management and MCS, and their interactions. The overall research question is therefore: what influence does regulation have on risk management and management control systems in banks over time? The intended ambition is to contribute to existing knowledge on the relationship between bank regulation, risk management, and MCS by providing several practical and theoretical contributions. The dissertation employs an adapted theoretical framework and uses institutional theory and contingency theory to expose tensions between, the demands for uniformity residing in banking regulation, and the demands for uniqueness residing inside banks themselves as they seek to maintain control over the design and use of their organizational controls. The empirical material used in the longitudinal case study is gathered from a large European bank. The main findings of the dissertation are as follows. In Paper I, the findings show that banking regulation’s influence on risk management and management control is mixed, which in turn can influence risk management’s integration with MCS. The paper also finds that very little knowledge exists about regulation’s influence on risk management and MCS. In Paper II, the findings show that while regulatory influence in IT control has increased over time, banks continue to exercise significant influence over regulatory demands. In Paper III, the findings show how regulation’s influence varies considerably over time and that increased regulatory pressure can lead to a higher degree of integration between risk management and MCS across the three dimensions of integration. In Paper IV, the findings show how regulation’s influence is shaping the mental processes of management and employees, and can vary significantly based on several identified factors.

    List of papers
    1. Risk Management and Management Control Systems Integration in Banks: The Role of Regulation and Strategy
    Open this publication in new window or tab >>Risk Management and Management Control Systems Integration in Banks: The Role of Regulation and Strategy
    2017 (English)Conference paper, Oral presentation only (Refereed)
    Abstract [en]

    The rise and expansion of risk management in banks in the last two decades have had a profound impact. New processes, tools, and IT systems have been introduced aimed at enhancing internal control, information quality as well as reporting and disclosure practices. These regulatory derived developments would suggest that risk management’s relationship with management control systems as part of the ‘control package’ is strengthening. Despite the growing number of academic publications, we still know very little about the degree of risk management’s integration with management controls. This paper addresses this gap by examining how and why regulation and strategy influence the degree of risk management’s integration with management control over time and across three integrating dimensions first presented by Gond et al. (2012). Using empirical evidence from a case study of a large European bank, we show movements between control configurations as well as changes in the relationship between the three dimensions over time. In addition we offer the reader deep empirical descriptions of the challenges associated with integrating risk management as part of the wider control package in a banking context. Finally, we explain how our findings can be used in future research to further explore the integration of risk management and management control systems in light of continually evolving regulatory demands and strategic goals. 

    Keyword
    Integration, management control systems, package, regulation, risk management, strategy
    National Category
    Business Administration
    Research subject
    Business Studies
    Identifiers
    urn:nbn:se:uu:diva-309674 (URN)
    Conference
    Nordic Accounting Conference (NORAC), 2016, 17-18 November, Copenhagen Business School, Denmark, The 10th Conference on New Directions in Management Accounting, 2016, 14-16 December, EIASM, Brussels, Belgium, European Network for Research in Organisational and Accounting Change (ENROAC), 2017, 29-30 June, University of Naples "Federico II", Italy.
    Available from: 2016-12-06 Created: 2016-12-06 Last updated: 2017-10-23
    2. Accounting and control in banks: A literature review
    Open this publication in new window or tab >>Accounting and control in banks: A literature review
    Show others...
    2017 (English)In: Bank Regulation: Effects on Strategy, Financial Accounting, and Management Control / [ed] Anna-Karin Stockenstrand, Fredrik Nilsson, New York: Routledge, 2017, 1, 15-63 p.Chapter in book (Other academic)
    Place, publisher, year, edition, pages
    New York: Routledge, 2017 Edition: 1
    Series
    Routledge Studies in Accounting, 19
    Keyword
    Accounting regulation, bank lending, corporate governance, fair value accounting, management control, stakeholders in banking, task control
    National Category
    Business Administration
    Research subject
    Business Studies
    Identifiers
    urn:nbn:se:uu:diva-312455 (URN)978-1-138-68050-0 (ISBN)978-1-315-56389-3 (ISBN)
    Note

    In press

    Available from: 2017-01-09 Created: 2017-01-09 Last updated: 2017-10-23
    3. A Prediction-Postdiction Model of Risk Regulation and Governance in Banking: Infusing a Perspective from Psychology Theory
    Open this publication in new window or tab >>A Prediction-Postdiction Model of Risk Regulation and Governance in Banking: Infusing a Perspective from Psychology Theory
    2017 (English)Conference paper, Oral presentation only (Refereed)
    Abstract [en]

    After the 2007–08 financial crisis, risk management failures in banks have drawn increasing regulatory attention, in turn promoting increasing risk-governance development. Regulatory efforts to refine policy temporarily leads to increased confidence by politicians and society in the risk management concept, but when a failure occurs, public intolerance increases dramatically, threating the legitimacy of financial institutions. The cyclical nature of this empirical phenomenon would seem to be closely related to how events are interpreted, not just by individuals but by society in general. Borrowing a term used in psychology, our understanding of this cyclical process may be improved by using what we might call the prediction-postdiction model of risk regulation and governance. The cycle has been the basis for considerable debate in public hearings, amongst regulatory bodies and in academic publications. Much of that debate has focused on the further development of formal policies, structures, and processes with very little attention given to the significance of individual actors or acknowledging the complexity and variation of practices in individual banks. In that void, multiple assumptions fill a space in order that politicians, the media, and even regulatory authorities, can reconcile predictive and post-hoc accounts. By drawing on psychological theory (cf. Hall 2016) and using empirical evidence from a case study of a large European bank, I propose that a better understanding of the crisis-regulation cycle can be achieved by applying the prediction-postdiction model. This may help us to see how some of the actions undertaken may be ineffective or even dysfunctional, as they build on assumptions which are dubious or wrong. The model can aid us in examining how the operation and effects of risk-management practices influence individual mental processes and behaviors over time. In doing so I offer deep empirical descriptions from a wide variety of individual perspectives on risk management's influence on behavior and how in aggregate this, in turn, influences organizational outcomes. Finally, I explain how these tentative findings can be used in future research.

    Keyword
    Accounting, Control, Regulation, Prediction, Postdiction, Risk
    National Category
    Business Administration
    Research subject
    Business Studies
    Identifiers
    urn:nbn:se:uu:diva-242123 (URN)
    Conference
    40th European Annual Congress (EAA)
    Available from: 2015-01-21 Created: 2015-01-21 Last updated: 2017-10-31
    4. Controlling Bank's IT in the Wake of Increasing Regulatory Demands: A Swedish Perspective
    Open this publication in new window or tab >>Controlling Bank's IT in the Wake of Increasing Regulatory Demands: A Swedish Perspective
    2017 (English)In: Bank Regulation: Effects on Strategy, Financial Accounting and Management Control, Routledge, 2017, 206-230 p.Chapter in book (Refereed)
    Place, publisher, year, edition, pages
    Routledge, 2017
    National Category
    Social Sciences
    Identifiers
    urn:nbn:se:uu:diva-312458 (URN)
    Available from: 2017-01-09 Created: 2017-01-09 Last updated: 2017-10-23
  • Kulkarni, Yashraj S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Liao, Qinghua
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Petrovic, Dusan
    Forschungszentrum Julich, Inst Complex Syst Struct Biochem, D-52425 Julich, Germany..
    Krüger, Dennis M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Strodel, Birgit
    Forschungszentrum Julich, Inst Complex Syst Struct Biochem, D-52425 Julich, Germany.;Heinrich Heine Univ Dusseldorf, Inst Theoret & Computat Chem, Univ Str 1, D-40225 Dusseldorf, Germany..
    Amyes, Tina L.
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Richard, John P.
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Kamerlin, Shina C. L.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 30, 10514-10525 p.Article in journal (Refereed)
    Abstract [en]

    Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to D-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (1170 and L230), over the carboxylate side chain of E165. This is critical both for creating a hydrophobic pocket for the catalytic base and for maintaining correct active site architecture. Truncation of these residues to alanine causes significant falloffs in TIM's catalytic activity, but experiments have failed to provide a full description of the action of this clamp in promoting substrate deprotonation. We perform here detailed empirical valence bond calculations of the TIM-catalyzed deprotonation of DHAP and GAP by both wild type TIM and its 1170A, L230A, and 1170A/L230A mutants, obtaining exceptional quantitative agreement with experiment. Our calculations provide a linear free energy relationship, with slope 0.8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions. We conclude that these clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the effects on reaction driving force are largely expressed at the transition state for proton transfer. Our combined analysis of previous experimental and current computational results allows us to provide an overview of the breakdown of ground-state and transition state effects in enzyme catalysis in unprecedented detail, providing a molecular description of the operation of a hydrophobic clamp in triosephosphate isomerase.

  • Karlsson, Anna
    et al.
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden..
    Brunnström, Hans
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden.;Reg Labs Reg Skane, Dept Pathol, Lund, Sweden..
    Micke, Patrick
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Veerla, Srinivas
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden..
    Mattsson, Johanna Sofia Margareta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    La Fleur, Linnea
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Botling, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Jönsson, Mats
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden..
    Reuterswärd, Christel
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden..
    Planck, Maria
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden.;Skane Univ Hosp, Dept Resp Med & Allergol, Lund, Sweden..
    Staaf, Johan
    Lund Univ, Dept Clin Sci Lund, Div Oncol & Pathol, SE-22381 Lund, Sweden..
    Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification2017In: Journal of Thoracic Oncology, ISSN 1556-0864, E-ISSN 1556-1380, Vol. 12, no 8, 1257-1267 p.Article in journal (Refereed)
    Abstract [en]

    Introduction: Large cell lung cancer (LCLC) and large cell neuroendocrine carcinoma (LCNEC) constitute a small proportion of NSCLC. The WHO 2015 classification guidelines changed the definition of the debated histological subtype LCLC to be based on immunomarkers for adenocarcinoma and squamous cancer. We sought to determine whether these new guidelines also translate into the transcriptional landscape of lung cancer, and LCLC specifically.

    Methods: Gene expression profiling was performed by using Illumina V4 HT12 microarrays (Illumina, San Diego, CA) on samples from 159 cases (comprising all histological subtypes, including 10 classified as LCLC WHO 2015 and 14 classified as LCNEC according to the WHO 2015 guidelines), with complimentary mutational and immunohistochemical data. Derived transcriptional phenotypes were validated in 199 independent tumors, including six WHO 2015 LCLCs and five LCNECs.

    Results: Unsupervised analysis of gene expression data identified a phenotype comprising 90% of WHO 2015 LCLC tumors, with characteristics of poorly differentiated proliferatiVe cancer, a 90% tumor protein p53 gene (TP53) mutation rate, and lack of well-known NSCLC oncogene driver alterations. Validation in independent data confirmed aggregation of WHO 2015 LCLCs in the specific phenotype. For LCNEC tumors, the unsupervised gene expression analysis suggested two different transcriptional patterns corresponding to a proposed genetic division of LCNEC tumors into SCLC-like and NSCLC-like cancer on the basis of TP53 and retinoblastoma 1 gene (RB1) alteration patterns.

    Conclusions: Refined classification of LCLC has implications for diagnosis, prognostics, and therapy decisions. Our molecular analyses support the WHO 2015 classification of LCLC and LCNEC tumors, which herein follow different tumorigenic paths and can accordingly be stratified into different transcriptional subgroups, thus linking diagnostic immunohistochemical staining driven classification with the transcriptional landscape of lung cancer.

  • Högerås, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Batterimatning som reservdrift på mellanspänningsnätet2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The grid in the northern part of Sweden is characterized by long radial lines with just a few customers. To secure electricity supply it is necessary to have a redundant feeding alternative. A loop structured grid which is used in the more populated urban area is a poor solution in the rural areas both regarding economy and technology due to the long distances. To feed the northern grid in Sweden a battery energy storage system (BESS) is therefore a solution that could secure the power delivery. An important aspect to investigate is how the electric power quality changes with the new feeder, but more importantly to secure disconnection of supply at fault occurrence.

     

    This thesis investigates how a battery storage system installed at the end of a mid-voltage line affects the electric power quality and the protection system compared to a reference case which represents the line today. The mid-voltage line is an existing line in the northern grid and is a good representation of the general northern grid.  

     

    The results obtained from this study show that the loop impedance does not necessarily have to deteriorate with the new feeder, which means that the voltage quality in this aspect does