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  • Disputas: 2017-12-12 09:30 Polhemssalen, Uppsala
    Lindgren, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Observationell astrofysik.
    Metallicity determination of M dwarfs2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    M dwarfs constitute around 70% of all stars in the local Galaxy. Their multitude together with their long main-sequence lifetimes make them important for studies of global properties of the Galaxy such as the initial mass function or the structure and kinematics of stellar populations. In addition, the exoplanet community is showing an increasing interest for those small, cold stars. However, very few M dwarfs are well characterized, and in the case of exoplanetary systems the stellar parameters have a direct influence on the derived planet properties.

    Stellar parameters of M dwarfs are difficult to determine because of their low surface temperatures that result in an optical spectrum dominated by molecular lines. Most previous works have therefore relied on empirical calibrations. High-resolution spectrographs operating in the infrared, a wavelength region less affected by molecular lines, have recently opened up a new window for the investigation of M dwarfs. In the two first papers of this thesis we have shown that we can determine the metallicity, and in some cases the effective temperature, using synthetic spectral fitting with improved accuracy.

    This method is time consuming and therefore not practical or even feasible for studies of large samples of M dwarfs. When comparing our results from the high-resolution studies with available photometric calibrations we find systematic differences. In the third paper we therefore used our sample to determine a new photometric metallicity calibration. Compared to previous calibrations our new photometric calibration shows improved statistical characteristics, and our calibration gives similar results as spectroscopic calibrations. In a comparison with theoretical calculations we find a good agreement of the shapes and slopes of iso-metallicity lines with our empirical relation. Applying the photometric calibration to a sample of M dwarfs with confirmed exoplanets we find a possible giant planet-metallicity correlation for M dwarfs.

    Delarbeid
    1. Metallicity determination of M dwarfs: High-resolution infrared spectroscopy
    Åpne denne publikasjonen i ny fane eller vindu >>Metallicity determination of M dwarfs: High-resolution infrared spectroscopy
    2016 (engelsk)Inngår i: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 586, A100Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Context. Several new techniques to determine the metallicity of M dwarfs with better precision have been developed over the last decades. However, most of these studies were based on empirical methods. In order to enable detailed abundance analysis, standard methods established for warmer solar-like stars, i.e. model-dependent methods using fitting of synthetic spectra, still need to be used.

    Aims. In this work we continue the reliability confirmation and development of metallicity determinations of M dwarfs using high-resolution infrared spectra. The reliability was confirmed through analysis of M dwarfs in four binary systems with FGK dwarf companions and by comparison with previous optical studies of the FGK dwarfs.

    Methods. The metallicity determination was based on spectra taken in the J band (1.1-1.4 mu m) with the CRIRES spectrograph. In this part of the infrared, the density of stellar molecular lines is limited, reducing the amount of blends with atomic lines enabling an accurate continuum placement. Lines of several atomic species were used to determine the stellar metallicity.

    Results. All binaries show excellent agreement between the derived metallicity of the M dwarf and its binary companion. Our results are also in good agreement with values found in the literature. Furthermore, we propose an alternative way to determine the effective temperature of M dwarfs of spectral types later than M2 through synthetic spectral fitting of the FeH lines in our observed spectra.

    Conclusions. We have confirmed that a reliable metallicity determination of M dwarfs can be achieved using high-resolution infrared spectroscopy. We also note that metallicites obtained with photometric metallicity calibrations available for M dwarfs only partly agree with the results we obtain from high-resolution spectroscopy.

    Emneord
    stars: abundances, stars: low-mass, techniques: spectroscopic
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-281831 (URN)10.1051/0004-6361/201526602 (DOI)000369715900111 ()
    Forskningsfinansiär
    Swedish National Space Board
    Tilgjengelig fra: 2016-03-30 Laget: 2016-03-30 Sist oppdatert: 2017-10-24
    2. Metallicity determination of M dwarfs: Expanded parameter range in metallicity and effective temperature
    Åpne denne publikasjonen i ny fane eller vindu >>Metallicity determination of M dwarfs: Expanded parameter range in metallicity and effective temperature
    2017 (engelsk)Inngår i: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 604, A97Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Context. Reliable metallicity values for late K and M dwarfs are important for studies of the chemical evolution of the Galaxy and advancement of planet formation theory in low-mass environments. Historically it has been challenging to determine the stellar parameters of low-mass stars because of their low surface temperature, which causes several molecules to form in the photospheric layers. In our work we use the fact that infrared high-resolution spectrographs have opened up a new window for investigating M dwarfs. This enables us to use similar methods as for warmer solar-like stars.

    Aims. Metallicity determination with high-resolution spectra is more accurate than with low-resolution spectra, but it is rather time consuming. In this paper we expand our sample analyzed with this precise method both in metallicity and effective temperature to build a calibration sample for a future revised empirical calibration. Methods. Because of the relatively few molecular lines in the J band, continuum rectification is possible for high-resolution spectra, allowing the stellar parameters to be determined with greater accuracy than with optical spectra. We obtained high-resolution spectra with the CRIRES spectrograph at the Very Large Telescope (VLT). The metallicity was determined using synthetic spectral fitting of several atomic species. For M dwarfs that are cooler than 3575 K, the line strengths of FeH lines were used to determine the effective temperatures, while for warmer stars a photometric calibration was used.

    Results. We analyzed 16 targets with a range of effective temperature from 3350-4550 K. The resulting metallicities lie between -0.5 < [M/H] < +0.4. A few targets have previously been analyzed using low-resolution spectra and we find a rather good agreement with our values. A comparison with available photometric calibrations shows varying agreement and the spread within all empirical calibrations is large.

    Conclusions. Including the targets from our previous paper, we analyzed 28 M dwarfs with high-resolution infrared spectra. The targets spread approximately one dex in metallicity and 1400 K in effective temperature. For individual M dwarfs we achieve uncer- tainties of 0.05 dex and 100 K on average. 

    Emneord
    stars:low-mass–stars:abundances–techniques:spectroscopic
    HSV kategori
    Forskningsprogram
    Astronomi
    Identifikatorer
    urn:nbn:se:uu:diva-332015 (URN)10.1051/0004-6361/201730715 (DOI)000408480100099 ()
    Forskningsfinansiär
    Swedish National Space Board
    Tilgjengelig fra: 2017-10-22 Laget: 2017-10-22 Sist oppdatert: 2017-10-24bibliografisk kontrollert
    3. A photometric calibration for M dwarfs based on high-resolution infrared spectrscopy
    Åpne denne publikasjonen i ny fane eller vindu >>A photometric calibration for M dwarfs based on high-resolution infrared spectrscopy
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Context. M dwarfs are, by number, the dominant stellar population in the local Galaxy. We have previously shown that the stellar parameters of individual M dwarfs can be determined with good accuracy using high-resolution infrared spectroscopy. Since this method is time-consuming the use of empirical calibrations based on photometry or low-resolution spectra is preferable for studies of large samples. In earlier work we showed that available photometric calibrations for M dwarfs have offsets compared to our high- resolution metallicity results.

    Aims. We use a sample of 33 late K and M dwarfs with accurately determined metallicities to derive a new photometric calibration for M dwarfs. The aim is to achieve a calibration with lower uncertainty and better agreement with spectroscopic results.Methods. We explored the B, V, J, H, K, g, r, i magnitudes to find combinations that show a correlation between the metallicity and the position in a color-magnitude diagram. We used 5-fold cross-validation and the corrected Akaike information criterion to find a polynomial model that minimizes the information lost, exploring different polynomial degrees, with and without cross-terms. The coefficients were determined through a weighted least-squares solution against our calibration sample.

    Results. We present a new photometric metallicity calibration for M dwarfs, where the metallicity is given by a linear relation and onecross-termoftheMKSmagnitudeandtheV−(JHK) or B−(JHK) colors. The new calibration relations have root-mean-square deviation values with respect to the calibration sample of 0.11-0.12 dex, which is about 0.1 dex lower than for previous photometric calibrations, and we also achieve a substantial improvement of the value of the adjusted squared multiple correlation coefficient. We furthermore show that our calibration compares well with two spectroscopic calibrations. Comparing synthetic calculated iso- metallicity lines with our empirical calibration, we find a good agreement of the shapes and slopes.

    Conclusions. Compared to previous calibrations our new photometric calibration shows improvement in all statistical tests performed. Through our testing of several polynomials we conclude that the inclusion of a cross-term between absolute magnitude and color is important for the performance of the photometric calibration. Applying our photometric calibration to a sample of M dwarfs known to host planets points towards a possible giant planet-metallicity correlation for M dwarfs.

    Emneord
    Stars: low-mass - Techniques: photometric - Planets and satellites: formation
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332624 (URN)
    Forskningsfinansiär
    Swedish National Space Board
    Tilgjengelig fra: 2017-10-31 Laget: 2017-10-31 Sist oppdatert: 2017-11-01
  • Disputas: 2017-12-12 13:15 Hörsal 2, Uppsala
    Crawford, Jason
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Samhällsvetenskapliga fakulteten, Företagsekonomiska institutionen.
    Regulation's Influence on Risk Management and Management Control Systems in Banks2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Risk Management and Management Control Systems Integration in Banks: The Role of Regulation and Strategy
    Åpne denne publikasjonen i ny fane eller vindu >>Risk Management and Management Control Systems Integration in Banks: The Role of Regulation and Strategy
    2017 (engelsk)Konferansepaper, Oral presentation only (Fagfellevurdert)
    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. 

    Emneord
    Integration, management control systems, package, regulation, risk management, strategy
    HSV kategori
    Forskningsprogram
    Företagsekonomi
    Identifikatorer
    urn:nbn:se:uu:diva-309674 (URN)
    Konferanse
    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.
    Tilgjengelig fra: 2016-12-06 Laget: 2016-12-06 Sist oppdatert: 2017-10-23
    2. Accounting and control in banks: A literature review
    Åpne denne publikasjonen i ny fane eller vindu >>Accounting and control in banks: A literature review
    Vise andre…
    2017 (engelsk)Inngår i: Bank Regulation: Effects on Strategy, Financial Accounting, and Management Control / [ed] Anna-Karin Stockenstrand, Fredrik Nilsson, New York: Routledge, 2017, 1, 15-63 s.Kapittel i bok, del av antologi (Annet vitenskapelig)
    sted, utgiver, år, opplag, sider
    New York: Routledge, 2017 Opplag: 1
    Serie
    Routledge Studies in Accounting, 19
    Emneord
    Accounting regulation, bank lending, corporate governance, fair value accounting, management control, stakeholders in banking, task control
    HSV kategori
    Forskningsprogram
    Företagsekonomi
    Identifikatorer
    urn:nbn:se:uu:diva-312455 (URN)978-1-138-68050-0 (ISBN)978-1-315-56389-3 (ISBN)
    Merknad

    In press

    Tilgjengelig fra: 2017-01-09 Laget: 2017-01-09 Sist oppdatert: 2017-10-23
    3. A Prediction-Postdiction Model of Risk Regulation and Governance in Banking: Infusing a Perspective from Psychology Theory
    Åpne denne publikasjonen i ny fane eller vindu >>A Prediction-Postdiction Model of Risk Regulation and Governance in Banking: Infusing a Perspective from Psychology Theory
    2017 (engelsk)Konferansepaper, Oral presentation only (Fagfellevurdert)
    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.

    Emneord
    Accounting, Control, Regulation, Prediction, Postdiction, Risk
    HSV kategori
    Forskningsprogram
    Företagsekonomi
    Identifikatorer
    urn:nbn:se:uu:diva-242123 (URN)
    Konferanse
    40th European Annual Congress (EAA)
    Tilgjengelig fra: 2015-01-21 Laget: 2015-01-21 Sist oppdatert: 2017-10-31
    4. Controlling Bank's IT in the Wake of Increasing Regulatory Demands: A Swedish Perspective
    Åpne denne publikasjonen i ny fane eller vindu >>Controlling Bank's IT in the Wake of Increasing Regulatory Demands: A Swedish Perspective
    2017 (engelsk)Inngår i: Bank Regulation: Effects on Strategy, Financial Accounting and Management Control, Routledge, 2017, 206-230 s.Kapittel i bok, del av antologi (Fagfellevurdert)
    sted, utgiver, år, opplag, sider
    Routledge, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-312458 (URN)
    Tilgjengelig fra: 2017-01-09 Laget: 2017-01-09 Sist oppdatert: 2017-10-23
  • Disputas: 2017-12-13 13:00 Auditorium Minus, Uppsala
    Jha, Paridhi
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kvinnors och barns hälsa.
    ‘Two Sides of a Coin’: Quality of Childbirth Services in Indian Public Health Facilities, from the Perspectives of Women and their Care Providers2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Cashless childbirth, but at a cost: A grounded theory study on quality of intrapartum care in public health facilities in India
    Åpne denne publikasjonen i ny fane eller vindu >>Cashless childbirth, but at a cost: A grounded theory study on quality of intrapartum care in public health facilities in India
    Vise andre…
    2016 (engelsk)Inngår i: Midwifery, ISSN 0266-6138, E-ISSN 1532-3099, Vol. 39, 78-86 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    Birth experience, Institutional delivery, Abuse, Communication, Care providers, Grounded theory
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-299546 (URN)10.1016/j.midw.2016.04.012 (DOI)000377935800011 ()27321724 (PubMedID)
    Forskningsfinansiär
    Sida - Swedish International Development Cooperation Agency
    Tilgjengelig fra: 2016-07-25 Laget: 2016-07-22 Sist oppdatert: 2017-11-28bibliografisk kontrollert
    2. Fear of Childbirth and Depressive Symptoms among Postnatal Women: A Cross-sectional Survey from Chhattisgarh, India
    Åpne denne publikasjonen i ny fane eller vindu >>Fear of Childbirth and Depressive Symptoms among Postnatal Women: A Cross-sectional Survey from Chhattisgarh, India
    2017 (engelsk)Inngår i: Women and Birth, ISSN 1871-5192, E-ISSN 1878-1799Artikkel i tidsskrift (Fagfellevurdert) Epub ahead of print
    Emneord
    Depression/depressiveve symptoms; EPDS; Fear of Birth (phobic disorders); Institutional births; WDEQ Version B
    HSV kategori
    Forskningsprogram
    Hälso- och sjukvårdsforskning
    Identifikatorer
    urn:nbn:se:uu:diva-331599 (URN)10.1016/j.wombi.2017.07.003 (DOI)
    Forskningsfinansiär
    Sida - Swedish International Development Cooperation Agency
    Tilgjengelig fra: 2017-10-16 Laget: 2017-10-16 Sist oppdatert: 2017-10-18bibliografisk kontrollert
    3. Satisfaction with childbirth services provided in public health facilities: results from a cross-sectional survey among postnatal women in Chhattisgarh, India
    Åpne denne publikasjonen i ny fane eller vindu >>Satisfaction with childbirth services provided in public health facilities: results from a cross-sectional survey among postnatal women in Chhattisgarh, India
    2017 (engelsk)Inngår i: Global Health Action, ISSN 1654-9716, E-ISSN 1654-9880Artikkel i tidsskrift (Fagfellevurdert) Accepted
    sted, utgiver, år, opplag, sider
    Taylor & Francis Group, 2017
    Emneord
    Hindi-translated Scale for 30 Measuring Maternal Satisfaction; intrapartum care; institutional births; Caesarean section; quality of care
    HSV kategori
    Forskningsprogram
    Hälso- och sjukvårdsforskning
    Identifikatorer
    urn:nbn:se:uu:diva-331601 (URN)
    Forskningsfinansiär
    Sida - Swedish International Development Cooperation Agency
    Tilgjengelig fra: 2017-10-16 Laget: 2017-10-16 Sist oppdatert: 2017-10-18bibliografisk kontrollert
    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
    Åpne denne publikasjonen i ny fane eller vindu >>“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
    Vise andre…
    2017 (engelsk)Artikkel i tidsskrift (Fagfellevurdert) Submitted
    HSV kategori
    Forskningsprogram
    Hälso- och sjukvårdsforskning
    Identifikatorer
    urn:nbn:se:uu:diva-331602 (URN)
    Forskningsfinansiär
    Sida - Swedish International Development Cooperation Agency
    Tilgjengelig fra: 2017-10-16 Laget: 2017-10-16 Sist oppdatert: 2017-10-26bibliografisk kontrollert
  • Disputas: 2017-12-14 09:00 Skoogsalen, Uppsala
    Cederblad, Lena
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi.
    Aspects on Head and neck Cancer with special reference to Salivary Gland Tumours and Single Nucleotide Polymorphism2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    A thesis on Head and neck cancer focusing on dose planning, salivary gland carcinoma and Single nucleotide polymorphism.

    For dose planning PET/CT (Positron emissions tomography/computed tomography) with tracer gave more precise information in comparison dose planning with CT. More primary tumours and metastases were found with the acetate tracer than with glucose tracer. Acetate PET/CT also showed larger volume of tumours attributed to lipid metabolism.

    In a retrospective study salivary gland cancer 5-year overall survival (OS) was 53 %. Salivary gland carcinoma consists of many histopathological groups, the two largest groups being mucoepidermoid carcinoma (MEC) and adenoid cystic carcinoma (ASCC). For ACC, having the best 5-year OS, it was 70 percent. Facial palsy, advanced stage disease, lymph node metastases worsened prognosis. ACC and polymorphous low grade carcinoma (PLGA) expressed c-myc and cyclin D1 to a larger extent than MEC.

    In squamous cell carcinoma of the head and neck we examined the occurrence of Single Nucleotide polymorphism, SNP. We found that the SNPs in male and female patients differed from each other. In male patients the SNPs were associated with immune response while in female patients the association was to SNPs concerning inflammation. This means that different pathways were engaged in cancer development for men and women. We also found that the SNPs in patients were different from those expressed in the healthy controls.

    Delarbeid
    1. Cancer of the parotid gland; long-term follow-up: A single centre experience on recurrence and survival
    Åpne denne publikasjonen i ny fane eller vindu >>Cancer of the parotid gland; long-term follow-up: A single centre experience on recurrence and survival
    Vise andre…
    2009 (engelsk)Inngår i: Acta Oncologica, ISSN 0284-186X, E-ISSN 1651-226X, Vol. 48, nr 4, 549-555 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    BACKGROUND:

    The aim of the study was to investigate the results of treatment of malignant parotid gland tumours at a single centre during a 56 year period, focusing on tumour control and survival.

    PATIENTS AND METHODS:

    At Uppsala University Hospital, Sweden, 144 patients (73 male and 71 female) with parotid cancer were treated between 1948 and 2004. The mean and median ages were 62 and 65 years, respectively (range 16-89 years). Surgery was the primary treatment in 113 (78%) patients followed by radiotherapy in 81. Postoperative radiotherapy in doses of 64-66 Gy, where the intention was curative and delivered with either split course or not, was administered to a majority of patients after 1970. The split-course mode was practised between 1970 and 1989. The median follow-up time was 8.3 years for patients still alive. There were 57 (40%) relapses, of which 40 were local recurrences with 26 inside the treatment volume.

    RESULTS:

    The overall 5-year survival was 53%. The majority of tumour-related deaths appeared in the first 3-5 years after diagnosis. Age, co-morbidity, the presence of lymph node metastases, adenoid cystic carcinoma and extent of disease were important for outcome; gender, however, was not. We found no difference in the survival between patients following split course therapy versus continuous fractionation. No difference could be seen in the survival of patients treated in the 1970s versus the 1990s.

    CONCLUSIONS:

    Age, nodal engagement, a higher T-stage, adenoid cystic carcinoma histopathology, facial palsy and intercurrent disease worsen the outcome of patients, whereas gender does not. Treatment principles at our hospital have been surgery followed by radiotherapy since the early 1970s even though a split course technique was practised during a part of this period. Survival has not improved markedly. Thus, there is scope for improvement for this group of patients.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-105426 (URN)10.1080/02841860802680419 (DOI)000265272900009 ()19140053 (PubMedID)
    Tilgjengelig fra: 2009-06-03 Laget: 2009-06-03 Sist oppdatert: 2017-10-25bibliografisk kontrollert
    2. The Combined Effects of Single-Nucleotide Polymorphisms, Tobacco Products, and Ethanol on Normal Resting Blood Mononuclear Cells
    Åpne denne publikasjonen i ny fane eller vindu >>The Combined Effects of Single-Nucleotide Polymorphisms, Tobacco Products, and Ethanol on Normal Resting Blood Mononuclear Cells
    Vise andre…
    2013 (engelsk)Inngår i: Nicotine & tobacco research, ISSN 1462-2203, E-ISSN 1469-994X, Vol. 15, nr 5, 890-895 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Introduction: Tobacco and ethanol consumption are crucial factors in the development of various diseases including cancer. In this investigation, we evaluated the combined effects of a number of single nucleotide polymorphisms (SNPs), with ethanol and tobacco products on healthy individuals. Methods: Pure nicotine, cigarette smoke extract, and Swedish snuff (snus) extract were used. The effects were examined by means of in vitro cell cycle progression and cell death of peripheral blood mononuclear cells (PBMCs) obtained from healthy donors. Results: After 3 days, in vitro, resting PBMCs entered the S and G2 stage in the presence of 100 mu M nicotine. The PBMCs only proceeded to S stage, in the presence of 0.2% ethanol. The nicotine- and ethanol-induced normal cell cycle progression correlated to a number of SNPs in the IL12RB2, Rad 52, XRCC2, P53, CCND3, and ABCA1 genes. Certain SNPs in Caspases 8, IL12RB2, Rad 52, MMP2, and MDM2 genes appeared to significantly influence the effects of EtOH-, snus-, and snus + EtOH-induced cell death. Importantly, the highest degree of cell death was observed in the presence of smoke + EtOH. The amount of cell death under this treatment condition also correlated to specific SNPs, located in the MDM2, ABCA1, or GASC1 genes. Conclusions: Cigarette smoke in combination with ethanol strongly induced massive cell death. Long-term exposure to smoke and ethanol could provoke chronic inflammation, and this could be the initiation of disease including the development of cancer at various sites.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-200343 (URN)10.1093/ntr/nts207 (DOI)000317796500004 ()
    Tilgjengelig fra: 2013-05-28 Laget: 2013-05-27 Sist oppdatert: 2017-12-06bibliografisk kontrollert
    3. Expression of Cyclin D1 and c-myc in adenoid cystic carcinoma, mucoepidermoid carcinoma and polymorphous low grade carcinoma
    Åpne denne publikasjonen i ny fane eller vindu >>Expression of Cyclin D1 and c-myc in adenoid cystic carcinoma, mucoepidermoid carcinoma and polymorphous low grade carcinoma
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332191 (URN)
    Tilgjengelig fra: 2017-10-25 Laget: 2017-10-25 Sist oppdatert: 2017-10-25
    4. Single Nucleotide Polymorphism and Cancer Risk, Tumour Recurrence or Survival of Head & Neck Cancer Patients
    Åpne denne publikasjonen i ny fane eller vindu >>Single Nucleotide Polymorphism and Cancer Risk, Tumour Recurrence or Survival of Head & Neck Cancer Patients
    Vise andre…
    2017 (engelsk)Inngår i: OncologyArtikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    OBJECTIVE: This paper aims at studying the influence of single-nucleotide polymorphisms (SNPs) on cancer risk, tumor recurrence, and survival in head and neck (H&amp;N) cancer patients. METHODS: A total of 45 SNPs in 41 genes were investigated. A total of 174 Caucasian H&amp;N cancer patients and 245 healthy blood donors were enrolled in the study. RESULTS: Ten SNPs were associated with H&amp;N cancer risk, but the identified SNPs differed among males and females. Some of the SNPs were related to immune response genes. The immune response gene SNPs were also related to survival. In particular, we noted that the tumor necrosis factor alpha (TNFalpha) rs1800629 could have an influence on cancer risk, tumor recurrence as well as survival. CONCLUSION: Genetic variation of the TNFalpha rs1800629 might be useful as a biomarker in clinical decision-making since it was found to be related to cancer risk, tumor recurrence, and survival of H&amp;N cancer patients.

    sted, utgiver, år, opplag, sider
    karger, 2017
    Emneord
    Tumor recurrenceSurvival timeSingle-nucleotide polymorphismsHead and neck cancer
    HSV kategori
    Forskningsprogram
    Onkologi
    Identifikatorer
    urn:nbn:se:uu:diva-331352 (URN)10.1159/000452278 (DOI)
    Tilgjengelig fra: 2017-10-13 Laget: 2017-10-13 Sist oppdatert: 2017-10-25
    5. 1-[C-11]-acetate PET imaging in head and neck cancer - a comparison with F-18-FDG-PET: implications for staging and radiotherapy planning
    Åpne denne publikasjonen i ny fane eller vindu >>1-[C-11]-acetate PET imaging in head and neck cancer - a comparison with F-18-FDG-PET: implications for staging and radiotherapy planning
    Vise andre…
    2007 (engelsk)Inngår i: European Journal of Nuclear Medicine and Molecular Imaging, ISSN 1619-7070, E-ISSN 1619-7089, Vol. 34, nr 5, 651-657 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Purpose  The aim of this study was to evaluate the feasibility of using 1-[11C]-acetate positron emission tomography (ACE-PET) to detect and delineate the gross tumour volume of head and neck cancer before radiotherapy, and to compare the results with those obtained using 18F-fluoro-2-deoxy-D-glucose (FDG) PET. Methods  Ten patients with histologically verified squamous cell carcinoma were investigated by FDG-PET and dynamic ACE-PET prior to radiotherapy. The two scans were performed on the same day or on consecutive days, except in one patient in whom they were done 5 days apart. Diagnostic CT or MRI was performed in all patients. The image data sets were analysed both visually and semi-quantitatively. All primary tumours and metastases were delineated automatically by using the 50% threshold of maximum radioactivity corrected for background. The mean standardised uptake value (SUV) and the tumour volumes were evaluated and compared. Results  All ten primary tumours were detected by ACE-PET, while nine primaries were detected by FDG-PET and CT and/or MRI. The ACE SUV tended to be lower than the FDG SUV (5.3±2.7 vs 9.6±7.0, p=0.07). The tumour volumes delineated with ACE were on average 51% larger than the FDG volumes (p<0.05). ACE-PET identified 20/21 lymph node metastases, while only 13/21 lesions were detected by FDG-PET and 16/21 lesions by CT or MRI. Conclusion  ACE-PET appears promising for the staging of head and neck cancer. The biological information provided by both FDG and ACE must be carefully validated before it can be used in clinical routine for radiation treatment planning. More studies are needed to evaluate the differences in volumes and to confirm the clinical potential of both FDG and ACE-PET, especially in radiotherapy.

     

    Emneord
    11C-acetate, 18F-FDG, PET, Head and neck cancer, SUV
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-14998 (URN)10.1007/s00259-006-0298-9 (DOI)000246095900005 ()17146654 (PubMedID)
    Tilgjengelig fra: 2008-02-01 Laget: 2008-02-01 Sist oppdatert: 2017-12-11bibliografisk kontrollert
  • Disputas: 2017-12-14 09:15 A1:107a, Uppsala
    Lundstedt, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Development of Mild Methods for Selective Covalent Functionalization of Graphene2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Ozonolysis of triphenylene in acetone
    Åpne denne publikasjonen i ny fane eller vindu >>Ozonolysis of triphenylene in acetone
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Forskningsprogram
    Kemi med inriktning mot organisk kemi
    Identifikatorer
    urn:nbn:se:uu:diva-332003 (URN)
    Tilgjengelig fra: 2017-10-20 Laget: 2017-10-20 Sist oppdatert: 2017-10-24
    2. Ozonolysis of polycyclic aromatic hydrocarbons in participating solvents
    Åpne denne publikasjonen i ny fane eller vindu >>Ozonolysis of polycyclic aromatic hydrocarbons in participating solvents
    2017 (engelsk)Inngår i: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 7, nr 10, 6152-6159 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-316964 (URN)10.1039/c6ra26248a (DOI)000393754100073 ()
    Forskningsfinansiär
    Swedish Research CouncilKnut and Alice Wallenberg Foundation
    Tilgjengelig fra: 2017-03-08 Laget: 2017-03-08 Sist oppdatert: 2017-11-29bibliografisk kontrollert
    3. Edge oxidation of graphite using a combined hydrogen peroxide - ozone treatment under sonication conditions
    Åpne denne publikasjonen i ny fane eller vindu >>Edge oxidation of graphite using a combined hydrogen peroxide - ozone treatment under sonication conditions
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    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.

    Emneord
    Edge oxidation, Graphite, Graphene, Hydrogen peroxide, Ozone
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-327165 (URN)
    Tilgjengelig fra: 2017-08-06 Laget: 2017-08-06 Sist oppdatert: 2017-10-24
    4. Metal-free photochemical silylations and transfer hydrogenations of benzenoid hydrocarbons and graphene
    Åpne denne publikasjonen i ny fane eller vindu >>Metal-free photochemical silylations and transfer hydrogenations of benzenoid hydrocarbons and graphene
    Vise andre…
    2016 (engelsk)Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Artikkel i tidsskrift (Fagfellevurdert) 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.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-303639 (URN)10.1038/ncomms12962 (DOI)000385553900001 ()27708336 (PubMedID)
    Forskningsfinansiär
    Wenner-Gren FoundationsSwedish Research CouncilKnut and Alice Wallenberg FoundationÅForsk (Ångpanneföreningen's Foundation for Research and Development)Magnus Bergvall Foundation
    Tilgjengelig fra: 2016-09-21 Laget: 2016-09-21 Sist oppdatert: 2017-11-21bibliografisk kontrollert
    5. White-light photoassisted covalent functionalization of graphene using 2-propanol
    Åpne denne publikasjonen i ny fane eller vindu >>White-light photoassisted covalent functionalization of graphene using 2-propanol
    Vise andre…
    2017 (engelsk)Inngår i: Small Methods, ISSN 2366-9608, 1700214- s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    John Wiley & Sons, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-314171 (URN)10.1002/smtd.201700214 (DOI)
    Tilgjengelig fra: 2017-01-29 Laget: 2017-01-29 Sist oppdatert: 2017-10-24
  • Disputas: 2017-12-14 13:00 Konferensrummet Arbets- och miljömedicin, Uppsala
    Palm, Peter
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Arbets- och miljömedicin.
    Methods to assess physical load at work: With a focus on the neck and upper extremities2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    To prevent work-related musculoskeletal disorders (MSDs), useful, reliable and valid methods for assessing physical workload and risks for MSDs are needed. Ergonomists often assess work by short visual observations without a specific tool. A branch-specific tool was developed for assessing working technique during cash register work (BAsiK observation protocol).

    Inclinometers are an alternative for assessing upper arm postures - over several days. Ergonomists need guidelines explaining how to analyze and interpret such data.

    The aim was to examine and investigate methods for assessing physical load at work, with focus on the neck and upper extremities.

    In Paper:

    I, the reliability and criterion validity of the BAsIK observation protocol were assessed.

    II, the reliability of risk assessments of repetitive work, based on visual observations performed by 21 ergonomists without a specific tool, was assessed.

    III, whole-day inclinometer measurements of upper arm elevation were compared between work and leisure, across 13 different occupations – before and after arm elevations during sitting time was excluded.

    IV, the association between inclinometer-based upper arm elevation and neck/shoulder pain was assessed among 654 blue-collar workers.

     

    The intra-observer reliability of the BAsIK protocol was deemed acceptable, but only 3 of 10 questions in the protocol showed acceptable inter-observer reliability, and 3 showed acceptable criterion validity.

    Neither the inter- or intra-observer reliability of risk assessment without any specific method was acceptable for any upper body regions.

    None of the occupation groups, in paper III, had higher proportion of time with arm elevation during work than leisure. However, when arm elevation during sitting was excluded, 8 occupation groups had higher proportion of time with elevated arms during work than leisure.

    Whole-workday inclinometer-based upper arm elevation was not associated with neck/shoulder pain within the assessed population.

       The results indicate that, in most cases, a single visual observation of a work sequence is not a reliable means of assessing repetitive work. A large proportion of arm elevation may derive from sitting time. At low exposure levels, arm elevation per se may not be a risk factor for neck/shoulder pain.

    This must be taken into account when evaluating the risk for MSDs.

    Delarbeid
    1. Reliability and criterion validity of an observation protocol for working technique assessments in cash register work
    Åpne denne publikasjonen i ny fane eller vindu >>Reliability and criterion validity of an observation protocol for working technique assessments in cash register work
    2016 (engelsk)Inngår i: Ergonomics, ISSN 0014-0139, E-ISSN 1366-5847, Vol. 59, nr 6, 829-839 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    We evaluated the intra- and inter-observer reliability and criterion validity of an observation protocol, developed in an iterative process involving practicing ergonomists, for assessment of working technique during cash register work for the purpose of preventing upper extremity symptoms. Two ergonomists independently assessed 17 15-min videos of cash register work on two occasions each, as a basis for examining reliability. Criterion validity was assessed by comparing these assessments with meticulous video-based analyses by researchers. Intra-observer reliability was acceptable (i.e. proportional agreement >0.7 and kappa >0.4) for 10/10 questions. Inter-observer reliability was acceptable for only 3/10 questions. An acceptable inter-observer reliability combined with an acceptable criterion validity was obtained only for one working technique aspect, 'Quality of movements'. Thus, major elements of the cashiers' working technique could not be assessed with an acceptable accuracy from short periods of observations by one observer, such as often desired by practitioners. Practitioner Summary: We examined an observation protocol for assessing working technique in cash register work. It was feasible in use, but inter-observer reliability and criterion validity were generally not acceptable when working technique aspects were assessed from short periods of work. We recommend the protocol to be used for educational purposes only.

    Emneord
    Repetitivt arbete, muskeloskeletala besvär
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-276838 (URN)10.1080/00140139.2015.1098734 (DOI)000380150600010 ()26538287 (PubMedID)
    Forskningsfinansiär
    Swedish Retail and Wholesale Development Council, 2008:2
    Tilgjengelig fra: 2016-02-16 Laget: 2016-02-16 Sist oppdatert: 2017-10-19
    2. Inter- and intra-observer reliability of risk assessment of repetitive work without an explicit method
    Åpne denne publikasjonen i ny fane eller vindu >>Inter- and intra-observer reliability of risk assessment of repetitive work without an explicit method
    2017 (engelsk)Inngår i: Applied Ergonomics, ISSN 0003-6870, E-ISSN 1872-9126, Vol. 62, 1-8 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    A common way to conduct practical risk assessments is to observe a job and report the observed long term risks for musculoskeletal disorders. The aim of this study was to evaluate the inter- and intra-observer reliability of ergonomists' risk assessments without the support of an explicit risk assessment method. Twenty-one experienced ergonomists assessed the risk level (low, moderate, high risk) of eight upper body regions, as well as the global risk of 10 video recorded work tasks. Intra-observer reliability was assessed by having nine of the ergonomists repeat the procedure at least three weeks after the first assessment. The ergonomists made their risk assessment based on his/her experience and knowledge. The statistical parameters of reliability included agreement in %, kappa, linearly weighted kappa, intraclass correlation and Kendall's coefficient of concordance. The average inter-observer agreement of the global risk was 53% and the corresponding weighted kappa (K-w) was 0.32, indicating fair reliability. The intra-observer agreement was 61% and 0.41 (K-w). This study indicates that risk assessments of the upper body, without the use of an explicit observational method, have non-acceptable reliability. It is therefore recommended to use systematic risk assessment methods to a higher degree.

    Emneord
    Inter-observer reliability, Intra-observer reliability, Risk assessment, Observational methods
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-276859 (URN)10.1016/j.apergo.2017.02.004 (DOI)000401206600001 ()28411720 (PubMedID)
    Forskningsfinansiär
    Forte, Swedish Research Council for Health, Working Life and Welfare, 1212-1202
    Merknad

    Title in thesis list of papers: Inter- and intra-observer reliability of risk assessment of repetitive work without any specific method

    Tilgjengelig fra: 2016-02-16 Laget: 2016-02-16 Sist oppdatert: 2017-10-19bibliografisk kontrollert
    3. Exposure to upper arm elevation during work compared to leisure among 13 different occupations measured with tri-axial accelerometers
    Åpne denne publikasjonen i ny fane eller vindu >>Exposure to upper arm elevation during work compared to leisure among 13 different occupations measured with tri-axial accelerometers
    Vise andre…
    (engelsk)Inngår i: Annals of work exposures and health, ISSN 2398-7308Artikkel i tidsskrift (Fagfellevurdert) Submitted
    sted, utgiver, år, opplag, sider
    Oxford University Press
    Emneord
    ergonomics, leisure, occupation, arm elevation, inclinometer, measurement strategy, neck and shoulder load, risk assessment
    HSV kategori
    Forskningsprogram
    Arbets- och miljömedicin
    Identifikatorer
    urn:nbn:se:uu:diva-329790 (URN)
    Tilgjengelig fra: 2017-09-21 Laget: 2017-09-21 Sist oppdatert: 2017-10-19
    4. Whole workday measurements of arm elevation and associations with neck shoulder pain among blue-collar workers in the DPHACTO cohort
    Åpne denne publikasjonen i ny fane eller vindu >>Whole workday measurements of arm elevation and associations with neck shoulder pain among blue-collar workers in the DPHACTO cohort
    Vise andre…
    (engelsk)Inngår i: BMC Musculoskeletal Disorders, ISSN 1471-2474, E-ISSN 1471-2474Artikkel i tidsskrift (Fagfellevurdert) Submitted
    sted, utgiver, år, opplag, sider
    BioMed Central
    Emneord
    Neck and shoulder pain, arm elevation, inclinometer, occupational, work load, musculoskeletal disorders, cleaners, manufacturing workers, transportation workers
    HSV kategori
    Forskningsprogram
    Arbets- och miljömedicin
    Identifikatorer
    urn:nbn:se:uu:diva-329797 (URN)
    Forskningsfinansiär
    AFA Insurance, 150035
    Tilgjengelig fra: 2017-09-21 Laget: 2017-09-21 Sist oppdatert: 2017-11-29
  • Disputas: 2017-12-15 09:00 4101, Ångströmlaboratoriet, Uppsala
    Belova, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Matematiska institutionen.
    Computational dynamics – real and complex2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Rigorous enclosures of rotation numbers by interval methods.
    Åpne denne publikasjonen i ny fane eller vindu >>Rigorous enclosures of rotation numbers by interval methods.
    2016 (engelsk)Inngår i: Journal of Computational Dynamics, ISSN 2158-2491, Vol. 3, nr 1, 81-91 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    rotation number, circle map, rigorous computation, interval arithmetic, set-valued mathematics
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332153 (URN)10.3934/jcd.2016004 (DOI)
    Tilgjengelig fra: 2017-10-24 Laget: 2017-10-24 Sist oppdatert: 2017-10-26
    2. Critical points of the multiplier map for the quadratic family.
    Åpne denne publikasjonen i ny fane eller vindu >>Critical points of the multiplier map for the quadratic family.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Emneord
    multipliers, quadratic family
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332157 (URN)
    Tilgjengelig fra: 2017-10-24 Laget: 2017-10-24 Sist oppdatert: 2017-10-26
    3. Quadratic irrationals, generating functions and Lévy constants.
    Åpne denne publikasjonen i ny fane eller vindu >>Quadratic irrationals, generating functions and Lévy constants.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Emneord
    continued fractions, generating functions
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332158 (URN)
    Tilgjengelig fra: 2017-10-24 Laget: 2017-10-24 Sist oppdatert: 2017-10-26
    4. Finding all solutions of stationary Kuramoto-Sivashinsky equations.
    Åpne denne publikasjonen i ny fane eller vindu >>Finding all solutions of stationary Kuramoto-Sivashinsky equations.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332279 (URN)
    Tilgjengelig fra: 2017-10-26 Laget: 2017-10-26 Sist oppdatert: 2017-10-26
  • Disputas: 2017-12-15 09:15 Hall B:21, Uppsala
    Roslin, Sara
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för läkemedelskemi, Avdelningen för organisk farmaceutisk kemi.
    Exploring Palladium-Mediated 11C/12C-Carbonylation Reactions: PET Tracer Development Targeting the Vesicular Acetylcholine Transporter2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The work presented herein describes the utilization and exploration of palladium-mediated incorporations of carbon monoxide and/or [11C]carbon monoxide into compounds and structural motifs with biological relevance.

    The first part of the thesis describes the design, synthesis and 11C-labeling of prospective PET tracers for the vesicular acetylcholine transporter (VAChT), a target affected in several neurodegenerative diseases. Different parts of the benzovesamicol scaffold were modified in papers I and II to probe the binding to VAChT. The key motif was an amide functional group, which enabled the use of palladium-mediated 11C/12C-carbonylations to synthesize and evaluate two different sets of structurally related ligands.

    The second part of the thesis describes the exploration of different aspects of palladium-mediated 11C/12C-carbonylation reactions. The utilization of unactivated alkyl iodides and bromides as coupling partners in a carbonylative Suzuki-Miyaura reaction was described in paper III. The combination of palladium-catalysis together with visible light irradiation enabled their functionalization via an alkyl radical. The mild conditions, namely the ambient temperature and pressure of carbon monoxide, and the accessible reaction set-up further added to the utility of the method. A palladium(II)-mediated oxidative 11C-carbonylation for synthesis of 11C-labeled ureas was described in paper IV. Utilizing only amines in addition to a palladium-source and [11C]carbon monoxide, the method proved to be facile and robust, thus representing a simplification in relation to methods using other 11C-synthons for synthesis of 11C-labeled ureas. Finally, a palladium(0)-catalyzed carbonylation reaction for synthesis of acylamidines was presented in paper V. The versatility of the method was demonstrated by one-pot cyclizations to form oxadiazoles and triazoles together with the corresponding 11C-carbonylation reaction to produce 11C-labeled acylamidines and an oxadiazole.

    The work described herein has thus contributed structural information in the search for a PET tracer for VAChT and identified a viable lead structure for future investigations. Furthermore, investigation of reaction conditions that would allow use of either elusive or accessible substrates led to the development of methods for synthesis and/or 11C-labeling of various carbonylated compounds.

    Delarbeid
    1. Synthesis and Labelling of a Piperazine-Based Library of 11C-Labeled Ligands for Imaging of the Vesicular Acetylcholine Transporter
    Åpne denne publikasjonen i ny fane eller vindu >>Synthesis and Labelling of a Piperazine-Based Library of 11C-Labeled Ligands for Imaging of the Vesicular Acetylcholine Transporter
    Vise andre…
    2014 (engelsk)Inngår i: Journal of labelled compounds & radiopharmaceuticals, ISSN 0362-4803, E-ISSN 1099-1344, Vol. 57, nr 8, 525-532 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    The cholinergic system is involved in neurodegenerative diseases, and visualization of cholinergic innervations with positron emission tomography (PET) would be a useful tool in understanding these diseases. A ligand for the vesicular acetylcholine transporter (VAChT), acknowledged as a marker for cholinergic neurons, could serve as such a PET tracer. The aim was to find a VAChT PET tracer using a library concept to create a small but diverse library of labeled compounds. From the same precursor and commercially available aryl iodides 6a-f, six potential VAChT PET tracers, [C-11]-(+/-)5a-f, were C-11-labeled by a palladium (0)-mediated aminocarbonylation, utilizing a standard protocol. The labeled compounds [C-11]-(+/-)5a-f were obtained in radiochemical purities >95% with decay-corrected radiochemical yields and specific radioactivities between 4-25% and 124-597 GBq/mu mol, respectively. Autoradiography studies were then conducted to assess the compounds binding selectivity for VAChT. Labeled compounds [C-11]-(+/-)5d and [C-11]-(+/-)5e showed specific binding but not enough to permit further preclinical studies. To conclude, a general method for a facile synthesis and labeling of a small piperazine-based library of potential PET tracers for imaging of VAChT was shown, and in upcoming work, another scaffold will be explored using this approach.

    Emneord
    vesicular acetylcholine transporter, carbonylation, PET, library, C-11-labeling, vesamicol
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-231333 (URN)10.1002/jlcr.3208 (DOI)000340169500004 ()24991704 (PubMedID)
    Tilgjengelig fra: 2014-09-07 Laget: 2014-09-07 Sist oppdatert: 2017-10-26
    2. Synthesis and In Vitro Evaluation of 5-Substituted Benzovesamicol Analogs containing N-Substituted Amides as Potential Positron Emission Tomography Tracers for the Vesicular Acetylcholine Transporter
    Åpne denne publikasjonen i ny fane eller vindu >>Synthesis and In Vitro Evaluation of 5-Substituted Benzovesamicol Analogs containing N-Substituted Amides as Potential Positron Emission Tomography Tracers for the Vesicular Acetylcholine Transporter
    Vise andre…
    2017 (engelsk)Inngår i: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 25, nr 19, 5095-5106 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332288 (URN)
    Tilgjengelig fra: 2017-10-26 Laget: 2017-10-26 Sist oppdatert: 2017-11-30
    3. Palladium and Visible-Light Mediated Carbonylative Suzuki-Miyaura Coupling of Unactivated Alkyl Halides and Aryl Boronic Acids
    Åpne denne publikasjonen i ny fane eller vindu >>Palladium and Visible-Light Mediated Carbonylative Suzuki-Miyaura Coupling of Unactivated Alkyl Halides and Aryl Boronic Acids
    2017 (engelsk)Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 53, 6895-6898 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Herein, a simple and efficient method for the palladium-catalyzed carbonylation of aryl boronic acids with unactivated alkyl iodides and bromides under visible-light irradiation, ambient temperature and low CO-pressure is presented. Notably, the procedure uses readily available equipment and an inexpensive palladium catalyst to generate the key alkyl radical intermediate. These mild conditions enabled the synthesis of a range of functionalized aryl alkyl ketones including the antipsychotic drug, melperone.

    sted, utgiver, år, opplag, sider
    ROYAL SOC CHEMISTRY, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-329634 (URN)10.1039/c7cc02763j (DOI)000404282900021 ()
    Tilgjengelig fra: 2017-09-26 Laget: 2017-09-26 Sist oppdatert: 2017-10-26
    4. Synthesis of 11C-Labelled Ureas by Palladium(II)-Mediated Oxidative Carbonylation
    Åpne denne publikasjonen i ny fane eller vindu >>Synthesis of 11C-Labelled Ureas by Palladium(II)-Mediated Oxidative Carbonylation
    Vise andre…
    2017 (engelsk)Inngår i: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, nr 10, 1688- s.Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332289 (URN)
    Tilgjengelig fra: 2017-10-26 Laget: 2017-10-26 Sist oppdatert: 2017-11-30
    5. Acylamidines by Pd-Catalyzed Aminocarbonylation: One-Pot Cyclizations and 11C-Labeling
    Åpne denne publikasjonen i ny fane eller vindu >>Acylamidines by Pd-Catalyzed Aminocarbonylation: One-Pot Cyclizations and 11C-Labeling
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332292 (URN)
    Tilgjengelig fra: 2017-10-26 Laget: 2017-10-26 Sist oppdatert: 2017-10-26
  • Disputas: 2017-12-15 09:15 Polhemssalen, Uppsala
    Jönsson, Olof
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ultrafast Structural and Electron Dynamics in Soft Matter Exposed to Intense X-ray Pulses2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
    Åpne denne publikasjonen i ny fane eller vindu >>Ultrafast self-gating Bragg diffraction of exploding nanocrystals in an X-ray laser
    Vise andre…
    2015 (engelsk)Inngår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 23, nr 2, 1213-1231 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    Ultrafast lasers, UV, EUV, and X-ray lasers, X-ray imaging, Diffraction theory, Ultrafast phenomena
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-242136 (URN)10.1364/OE.23.001213 (DOI)000349166100061 ()
    Merknad

    De två första författarna delar förstaförfattarskapet.

    Tilgjengelig fra: 2015-01-21 Laget: 2015-01-21 Sist oppdatert: 2017-12-05bibliografisk kontrollert
    2. Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
    Åpne denne publikasjonen i ny fane eller vindu >>Simulations of radiation damage as a function of the temporal pulse profile in femtosecond X-ray protein crystallography
    Vise andre…
    2015 (engelsk)Inngår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, nr 2, 256-266 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    X-ray free-electron laser, serial femtosecond crystallography, radiation damage, plasma simulations
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-245210 (URN)10.1107/S1600577515002878 (DOI)000350641100007 ()
    Tilgjengelig fra: 2015-02-25 Laget: 2015-02-25 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    3. FreeDam 1.0 – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
    Åpne denne publikasjonen i ny fane eller vindu >>FreeDam 1.0 – A Webtool for Free-Electron Laser-Induced Damage in Femtosecond X-ray Crystallography
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    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. 

    Emneord
    FreeDam, non-local thermodynamic equilibrium, x-ray free-electron laser, radiation damage, serial femtosecond x-ray crystallography, Cretin, simulation, database
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-329499 (URN)
    Tilgjengelig fra: 2017-09-17 Laget: 2017-09-17 Sist oppdatert: 2017-10-25
    4. Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
    Åpne denne publikasjonen i ny fane eller vindu >>Indications of radiation damage in ferredoxin microcrystals using high-intensity X-FEL beams
    Vise andre…
    2015 (engelsk)Inngår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 22, nr 2, 225-238 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    free-electron laser, SFX, serial femtosecond crystallography, radiation damage, protein crystallography, metalloprotein
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-245011 (URN)10.1107/S1600577515002349 (DOI)000350641100004 ()
    Tilgjengelig fra: 2015-02-23 Laget: 2015-02-23 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    5. Ultrafast non-thermal heating of water initiated by an X-ray laser
    Åpne denne publikasjonen i ny fane eller vindu >>Ultrafast non-thermal heating of water initiated by an X-ray laser
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-294554 (URN)
    Merknad

    De två första författarna delar förstaförfattarskapet

    Tilgjengelig fra: 2016-05-24 Laget: 2016-05-24 Sist oppdatert: 2017-11-06
    6. Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    Åpne denne publikasjonen i ny fane eller vindu >>Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    2017 (engelsk)Inngår i: IUCrJ, Vol. 4, nr 6Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    hit detection, plasma emission spectra, serial femtosecond crystallography, protein structure
    HSV kategori
    Forskningsprogram
    Fysik med inriktning mot biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-331934 (URN)10.1107/S2052252517014154 (DOI)
    Tilgjengelig fra: 2017-10-25 Laget: 2017-10-25 Sist oppdatert: 2017-10-25
  • Disputas: 2017-12-15 10:00 Lindhalsalen, Uppsala
    Martinossi-Allibert, Ivain
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Sexual Selection and Adaptation to Novel Environments2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Sex-specific selection under environmental stress in seed beetles
    Åpne denne publikasjonen i ny fane eller vindu >>Sex-specific selection under environmental stress in seed beetles
    2017 (engelsk)Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 30, nr 1, 161-173 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    sted, utgiver, år, opplag, sider
    WILEY-BLACKWELL, 2017
    Emneord
    adaptation, Callosobruchus maculatus, environmental change, host plant, natural selection, population viability, sexual reproduction, sexual selection, stress, temperature
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331971 (URN)10.1111/jeb.12996 (DOI)
    Forskningsfinansiär
    EU, European Research Council, GENCON AdG-294333Swedish Research Council, 621-2010-5266 261-2014-4523
    Tilgjengelig fra: 2017-10-20 Laget: 2017-10-20 Sist oppdatert: 2017-10-24bibliografisk kontrollert
    2. Intralocus Sexual Conflict and the Tragedy of the Commons in Seed Beetles
    Åpne denne publikasjonen i ny fane eller vindu >>Intralocus Sexual Conflict and the Tragedy of the Commons in Seed Beetles
    Vise andre…
    2016 (engelsk)Inngår i: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 188, nr 4, E98-E112 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    sexual selection, adaptation, sexual antagonism, sexual dimorphism, genetic architecture, population demography
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-305304 (URN)10.1086/687963 (DOI)000383774400001 ()27622882 (PubMedID)
    Forskningsfinansiär
    Swedish Research CouncilEU, European Research Council, AdG-294333; AGINGSEXDIFF
    Tilgjengelig fra: 2016-10-18 Laget: 2016-10-14 Sist oppdatert: 2017-10-24bibliografisk kontrollert
    3. The consequences of sexual selection in well-adapted and amaladapted populations of bean beetles: Sexual selection in maladapted populations
    Åpne denne publikasjonen i ny fane eller vindu >>The consequences of sexual selection in well-adapted and amaladapted populations of bean beetles: Sexual selection in maladapted populations
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    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.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331970 (URN)
    Tilgjengelig fra: 2017-10-20 Laget: 2017-10-20 Sist oppdatert: 2017-10-24bibliografisk kontrollert
    4. The efficiency of purifying sexual selection under environmental change
    Åpne denne publikasjonen i ny fane eller vindu >>The efficiency of purifying sexual selection under environmental change
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    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.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332106 (URN)
    Tilgjengelig fra: 2017-10-24 Laget: 2017-10-24 Sist oppdatert: 2017-10-27bibliografisk kontrollert
  • Disputas: 2017-12-15 10:15 Sal X, Universitetshuset, Uppsala
    Elmerot, Åsa
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Juridiska fakulteten, Juridiska institutionen.
    Defining, Regulating and Balancing Rights: A Constitutional Law Study of Indigenous Peoples' Rights to Land and Natural Resources in the Russian Federation2017Doktoravhandling, monografi (Annet vitenskapelig)
    Abstract [en]

    Article 69 of the Russian Constitution proclaims that the Russian Federation shall guarantee the rights of indigenous minority peoples in accordance with generally recognized principles and norms of international law (in essence, customary international law), as well as international treaties of the Russian Federation. Furthermore, under Article 15(4) of the Constitution, international law is an integral part of the Russian legal system.

    The purpose of this study is to analyze the level of protection provided by the Constitution regarding indigenous peoples’ rights to use land and natural resources in Russia. Because the study aims for a wider approach than to simply address the rights of those peoples who are officially recognized as indigenous minority peoples, it is structured along two avenues: the potential for international law to provide protection of indigenous peoples’ rights in the Russian legal system; and the potential of the constitutional protection of the right to property and the freedom of economic activity to achieve the same purpose.

    Concretizing the constitutional provisions, the study addresses the preconditions according to which international law becomes applicable and enforceable law within the Russian legal system. Thereafter, it ascertains whether there are any rights in international law protecting indigenous peoples’ rights to land and natural resources that fulfil these requirements. Subsequently, the study evaluates the potential of international law to provide protection of indigenous rights in Russia.

    Regarding the potential of constitutional rights, the study determines whether the rights by which indigenous peoples use land and natural resources for pasture, hunting, and fishing could potentially be included within the protection of property and the freedom of economic activity, as interpreted by the Constitutional Court, and to what extent such inclusion constitutes protection. By structuring the reasoning of the Constitutional Court into the stages of defining, delineating, and balancing rights, the study concludes that, although there is a difference between how legal rights are treated, when compared to mere privileges to use land and natural resources, this difference is on the verge of being negligible due to the way the Constitutional Court makes use of the principle of proportionality.

  • Disputas: 2017-12-15 13:00 Humanistiska Teatern, Uppsala
    Börjesson, Lisa
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för ABM.
    Resources for scholarly documentation in professional service organizations: A study of Swedish development-led archaeology report writing2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

    Delarbeid
    1. Information Policy for (Digital) Information in Archaeology: current state and suggestions for development
    Åpne denne publikasjonen i ny fane eller vindu >>Information Policy for (Digital) Information in Archaeology: current state and suggestions for development
    2015 (engelsk)Inngår i: Internet Archaeology, ISSN 1363-5387, E-ISSN 1363-5387, nr 40Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    Digital humanities; cultural heritage sector; digital heritage; digital archaeology; digital museums; information policy; digital agendas; digitization
    HSV kategori
    Forskningsprogram
    Biblioteks- och informationsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-275630 (URN)10.11141/ia.40.4 (DOI)
    Prosjekter
    ARKDIS
    Forskningsfinansiär
    Swedish Research Council, 340-2012-5751
    Tilgjengelig fra: 2016-02-04 Laget: 2016-02-04 Sist oppdatert: 2017-11-30bibliografisk kontrollert
    2. Beyond information policy: Conflicting documentation ideals in extra-academic knowledge making practices
    Åpne denne publikasjonen i ny fane eller vindu >>Beyond information policy: Conflicting documentation ideals in extra-academic knowledge making practices
    2016 (engelsk)Inngår i: Journal of Documentation, ISSN 0022-0418, E-ISSN 1758-7379, Vol. 72, nr 4, 674-695 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    Archaeology, Information practices, Information policy, Controversy studies, Documentation ideals, Idea analysis, Knowledge making practices
    HSV kategori
    Forskningsprogram
    Biblioteks- och informationsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-277190 (URN)10.1108/JDOC-10-2015-0134 (DOI)000379787000004 ()
    Prosjekter
    ARKDIS
    Forskningsfinansiär
    Swedish Research Council, 340-2012-5751
    Tilgjengelig fra: 2016-02-17 Laget: 2016-02-17 Sist oppdatert: 2017-11-30bibliografisk kontrollert
    3. Grey literature – grey sources?: Nuancing the view on professional documentation: the case of Swedish archaeology
    Åpne denne publikasjonen i ny fane eller vindu >>Grey literature – grey sources?: Nuancing the view on professional documentation: the case of Swedish archaeology
    2015 (svensk)Inngår i: Journal of Documentation, ISSN 0022-0418, E-ISSN 1758-7379, Vol. 71, nr 6, 1158-1182 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    Documentation; Reports; Grey literature; Information sources; Information use: Referencing; Bibliometrics; Sociology of professions; Archaeology
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-246514 (URN)10.1108/JD-09-2014-0137 (DOI)000369171600003 ()
    Forskningsfinansiär
    Swedish Research Council, 340-2012-5751
    Tilgjengelig fra: 2015-03-08 Laget: 2015-03-08 Sist oppdatert: 2017-12-04bibliografisk kontrollert
    4. Research outside academia?: An analysis of resources in extra-academic report writing
    Åpne denne publikasjonen i ny fane eller vindu >>Research outside academia?: An analysis of resources in extra-academic report writing
    2016 (engelsk)Inngår i: Proceedings of the Association for Information Science and Technology, 2016Konferansepaper, Publicerat paper (Fagfellevurdert)
    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.

    Emneord
    Scholarly communication; Practitioner researchers; Grey literature; Archaeology; Practice theory
    HSV kategori
    Forskningsprogram
    Biblioteks- och informationsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-303766 (URN)
    Konferanse
    Annual Meeting of the Association for Information Science and Technology, Copenhagen, Denmark Oct. 14-18, 2016
    Prosjekter
    ARKDIS
    Forskningsfinansiär
    Swedish Research Council, 340-2012-5751
    Tilgjengelig fra: 2016-09-23 Laget: 2016-09-23 Sist oppdatert: 2017-10-20
  • Disputas: 2017-12-15 13:00 Room B7:101a, Uppsala
    Daurer, Benedikt J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Algorithms for Coherent Diffractive Imaging with X-ray Lasers2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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. 

    Delarbeid
    1. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
    Åpne denne publikasjonen i ny fane eller vindu >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
    Vise andre…
    2017 (engelsk)Inngår i: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, 251-262 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-328529 (URN)10.1107/S2052252517003591 (DOI)
    Prosjekter
    eSSENCE
    Tilgjengelig fra: 2017-04-07 Laget: 2017-08-25 Sist oppdatert: 2017-10-24bibliografisk kontrollert
    2. Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
    Åpne denne publikasjonen i ny fane eller vindu >>Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time
    2016 (engelsk)Inngår i: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, 1042-1047 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-287197 (URN)10.1107/S1600576716005926 (DOI)000377020600036 ()
    Prosjekter
    eSSENCE
    Tilgjengelig fra: 2016-04-18 Laget: 2016-04-22 Sist oppdatert: 2017-10-24bibliografisk kontrollert
    3. SHARP: a distributed GPU-based ptychographic solver
    Åpne denne publikasjonen i ny fane eller vindu >>SHARP: a distributed GPU-based ptychographic solver
    Vise andre…
    2016 (engelsk)Inngår i: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, 1245-1252 s.Artikkel i tidsskrift (Fagfellevurdert) 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.

    Emneord
    coherent X-ray diffractive imaging, ptychography, nanoscience, X-ray microscopy, phase-contrast X-ray imaging
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-300178 (URN)10.1107/S1600576716008074 (DOI)000382755900015 ()
    Forskningsfinansiär
    Swedish Research CouncilSwedish Foundation for Strategic Research
    Tilgjengelig fra: 2016-08-04 Laget: 2016-08-04 Sist oppdatert: 2017-10-24
    4. Nanosurveyor: a framework for real-time data processing
    Åpne denne publikasjonen i ny fane eller vindu >>Nanosurveyor: a framework for real-time data processing
    Vise andre…
    2017 (engelsk)Inngår i: Advanced Structural and Chemical Imaging, ISSN 2198-0926, Vol. 3, nr 7Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

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

    Results: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis.

    Conclusions: The pipeline provides throughput, compression, and resolution as well as rapid feedback to the micro-scope operators

    Emneord
    Streaming, Ptychography
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-317013 (URN)10.1186/s40679-017-0039-0 (DOI)000411110400001 ()28261545 (PubMedID)
    Forskningsfinansiär
    Swedish Research CouncilSwedish Foundation for Strategic Research
    Tilgjengelig fra: 2017-03-08 Laget: 2017-03-08 Sist oppdatert: 2017-12-08bibliografisk kontrollert
    5. Wavefront sensing of individual XFEL pulses using ptychography
    Åpne denne publikasjonen i ny fane eller vindu >>Wavefront sensing of individual XFEL pulses using ptychography
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    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. 

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-329011 (URN)
    Tilgjengelig fra: 2017-10-24 Laget: 2017-10-24 Sist oppdatert: 2017-10-24
  • Disputas: 2017-12-15 13:00 Häggsalen, Uppsala
    Ayub, Rabia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström.
    Excited State Aromaticity and Antiaromaticity: Fundamental Studies and Applications2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The central theme of this thesis is the ability to tune various molecular properties by controlling and utilizing aromaticity and antiaromaticity in the lowest electronically excited states. This investigation is based on qualitative theory, quantum chemical (QC) calculations and experimental work.

    Baird's rule tells that the π-electron count for aromaticity and antiaromaticity is reversed in the ππ* triplet (T1) state when compared to Hückel's rule for the singlet ground state. The excited state aromatic character of [4n]annulenes is probed by usage of two structural moieties, the cyclopropyl (cPr) group and the silacyclobutene (SCB) ring. The results of QC calculations and photoreactivity experiments showed that the cPr group and the SCB ring remained closed when attached to or fused with [4n]annulenes so as to preserve T1 aromatic stabilization. In contrast, both moieties ring-opened when attached to or fused with [4n+2]annulenes as a means for alleviation of T1 antiaromaticity. These two structural moieties are shown to indicate T1 aromatic character of [4n]annulenes except in a limited number of cases.

    The T1 antiaromatic character of compounds with 4n+2 π-electrons was utilized for photo(hydro)silylations and photohydrogenations. QC calculations showed that due to T1 antiaromaticity, benzene is able to abstract hydrogen atoms from trialkylsilanes. The photoreactions occurred under mild conditions for benzene and certain polycyclic aromatic hydrocarbons. In contrast, COT was found to be unreactive under similar conditions.

    It is further revealed that various properties of molecules can be tailored by rational design using Baird’s rule. Three modes of connectivity (linear, bent, and cyclic) of polycyclic conjugated hydrocarbons (PCH) were explored by DFT calculations. When the PCHs contain a central [4n]unit and 4nπ-electron perimeter, bent isomers have lower triplet state energies than linear ones due to increased T1 aromaticity in the bent isomers. With regard to the cyclic connectivity, macrocyclic compounds are designed by modifying the C20 monocycle through incorporation of monocyclic units (all-carbon as well as heterocyclic) and the impact of macrocyclic T1 aromaticity upon insertion of different units is examined through QC calculations. The results provide insights on excited state aromaticity in macrocyclic systems.

    Delarbeid
    1. Cyclopropyl group: An excited state aromaticity indicator?
    Åpne denne publikasjonen i ny fane eller vindu >>Cyclopropyl group: An excited state aromaticity indicator?
    2017 (engelsk)Inngår i: Chemistry - A European Journal, Vol. 23, 13684-13695 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332139 (URN)10.1002/chem.201701404 (DOI)
    Tilgjengelig fra: 2017-10-24 Laget: 2017-10-24 Sist oppdatert: 2017-10-27
    2. The silacyclobutene ring: An indicator of triplet state Baird-aromaticity
    Åpne denne publikasjonen i ny fane eller vindu >>The silacyclobutene ring: An indicator of triplet state Baird-aromaticity
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332402 (URN)
    Tilgjengelig fra: 2017-10-27 Laget: 2017-10-27 Sist oppdatert: 2017-10-27
    3. Metal-free photochemical silylations and transfer hydrogenations of benzenoid hydrocarbons and graphene
    Åpne denne publikasjonen i ny fane eller vindu >>Metal-free photochemical silylations and transfer hydrogenations of benzenoid hydrocarbons and graphene
    Vise andre…
    2016 (engelsk)Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Artikkel i tidsskrift (Fagfellevurdert) 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.

    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-303639 (URN)10.1038/ncomms12962 (DOI)000385553900001 ()27708336 (PubMedID)
    Forskningsfinansiär
    Wenner-Gren FoundationsSwedish Research CouncilKnut and Alice Wallenberg FoundationÅForsk (Ångpanneföreningen's Foundation for Research and Development)Magnus Bergvall Foundation
    Tilgjengelig fra: 2016-09-21 Laget: 2016-09-21 Sist oppdatert: 2017-11-21bibliografisk kontrollert
    4. Can Baird's and Clar's Rules Combined Explain Triplet State Energies of Polycyclic Conjugated Hydrocarbons with Fused 4n pi- and (4n+2)pi-Rings?
    Åpne denne publikasjonen i ny fane eller vindu >>Can Baird's and Clar's Rules Combined Explain Triplet State Energies of Polycyclic Conjugated Hydrocarbons with Fused 4n pi- and (4n+2)pi-Rings?
    Vise andre…
    2017 (engelsk)Inngår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, nr 12, 6327-6340 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Compounds that can be labeled as "aromatic chameleons" are pi-conjugated compounds that are able to adjust their pi-electron distributions so as to comply with the different rules of aromaticity in different electronic states. We used quantum chemical calculations to explore how the fusion of benzene rings onto aromatic chameleonic units represented by biphenylene, dibenbzocyclooctatetraene, and dibenzo[a,e]pentalene modifies the first triplet excited states (T-1) of the compounds. Decreases in T-1 energies are observed when going from isomers with linear connectivity of the fused benzene rings to those with cis- or transbent connectivities. The T-1 energies decreased down to those of the parent (isolated) 4n pi-electron units. Simultaneously, we observe an increased influence of triplet State aromaticity of the central 4n ring as given by Baird's rule and evidenced by geometric, magnetic, and electron density based aromaticity indices (HOMA, NICS-XY, ACID, and FLU). Because of an influence of,triplet state aromaticity in the central 4n pi-electron units,, the most stabilized, compounds, retain the triplet excitation in Baird pi-quartets or octets, enabling the outer benzene rings to adapt closed-shell singlet Clar pi-sextet character. Interestingly, the T-1 energies go down as the total number of aromatic cycles within a molecule in the T-1 state increases.

    sted, utgiver, år, opplag, sider
    AMER CHEMICAL SOC, 2017
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-329665 (URN)10.1021/acs.joc.7b00906 (DOI)000403854500031 ()28535673 (PubMedID)
    Forskningsfinansiär
    Swedish Research Council
    Tilgjengelig fra: 2017-09-20 Laget: 2017-09-20 Sist oppdatert: 2017-10-27bibliografisk kontrollert
    5. Relating the triplet state Baird-aromaticity of the monocycle to that of the macrocycle
    Åpne denne publikasjonen i ny fane eller vindu >>Relating the triplet state Baird-aromaticity of the monocycle to that of the macrocycle
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-332403 (URN)
    Tilgjengelig fra: 2017-10-27 Laget: 2017-10-27 Sist oppdatert: 2017-10-27
  • Disputas: 2017-12-15 13:00
    Amvrosiadi, Nino
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Luft-, vatten och landskapslära.
    The value of experimental data and modelling for exploration of hydrological functioning: The case of a till hillslope2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Successfully modeling one system response (e.g. hydrograph or solute transport) sometimes gives the false sense of well-characterizing the modeled system. This is partly because of the well-known equifinality issue; during the calibration process multiple parameter combinations can produce similarly good results. One step forward towards a better-defined system is using measured (at relevant scale) values for the model parameters, as well as using multiple conditions to constrain the model.

    But when not enough, or relevant, field measurements are available, virtual experiments (VE’s) can be used as a supplementary method to model calibration. The advantage of VE’s over model calibration is that they can also be used to explore assumptions both on the system hydrological processes, and on the model structure.

    One goal of this study was to utilize both field measurements and models for better characterization of the S-transect hillslope, located in Västrabäcken catchment, Northern Sweden. This included (a) characteristics in space: system vertical boundaries, hydraulic parameters, pore water velocity distribution, spatial correlation of flowpaths, soil water retention properties; (b) characteristic of system’s dynamic behavior: storage – discharge relationship, transit time distribution, turnover time; and (c) outputs’ sensitivity to external forcing, and to small scale structure assumptions. The second goal was to comment on the value of field measurements and virtual experiments for extracting information about the studied system.

    An intensely monitored study hillslope was chosen for this work. Although the hillslope has already been the subject of multiple field and modelling studies, there are still open questions regarding the characteristics listed above. The models used were the Vertical Equilibrium Model (VEM), and the Multiple Interacting Pathways (MIPs) model.

    It was found that the hillslope was well connected; from the near-stream areas up to the water divide the storage – discharge relationship could be described as an exponential function. Also, the dynamic storage (which controls the hydrograph dynamics) was much smaller comparing to the total hillslope storage. The unsaturated soil storage was found to be more sensitive to water table positions than vertical flux magnitude. The dynamic condition of external forcing (precipitation and evapotranspiration) affected the transit time distribution (TTD) shape. And, opposite to expectations, TTD was not sensitive to micro-scale structural assumptions tested here.

    Delarbeid
    1. Water storage dynamics in a till hillslope: the foundation for modeling flows and turnover times
    Åpne denne publikasjonen i ny fane eller vindu >>Water storage dynamics in a till hillslope: the foundation for modeling flows and turnover times
    2016 (engelsk)Inngår i: Hydrological Processes, ISSN 0885-6087, E-ISSN 1099-1085, Vol. 31, nr 1, 4-14 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Emneord
    flow pathways, storage, storage dynamics, turnover time
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331679 (URN)10.1002/hyp.11046 (DOI)
    Tilgjengelig fra: 2017-10-16 Laget: 2017-10-16 Sist oppdatert: 2017-11-14
    2. Soil moisture storage estimation based on steady vertical fluxes under equilibrium
    Åpne denne publikasjonen i ny fane eller vindu >>Soil moisture storage estimation based on steady vertical fluxes under equilibrium
    2017 (engelsk)Inngår i: Journal of Hydrology, Vol. 553, 798-804 s.Artikkel i tidsskrift (Fagfellevurdert) Published
    Emneord
    Volumetric soil water content, Vertical flux, VEM, Catchment water storage
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331688 (URN)10.1016/j.jhydrol.2017.08.042 (DOI)
    Tilgjengelig fra: 2017-10-16 Laget: 2017-10-16 Sist oppdatert: 2017-11-14
    3. Value of virtual experiments for a hillslope scale system understanding
    Åpne denne publikasjonen i ny fane eller vindu >>Value of virtual experiments for a hillslope scale system understanding
    Vise andre…
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331730 (URN)
    Tilgjengelig fra: 2017-10-17 Laget: 2017-10-17 Sist oppdatert: 2017-11-14
    4. Water age dependence on vertical flux assumptions
    Åpne denne publikasjonen i ny fane eller vindu >>Water age dependence on vertical flux assumptions
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331731 (URN)
    Tilgjengelig fra: 2017-10-17 Laget: 2017-10-17 Sist oppdatert: 2017-11-14
    5. Following tracer through the unsaturated zone using a Multiple Interacting Pathways model: implications from laboratory experiments
    Åpne denne publikasjonen i ny fane eller vindu >>Following tracer through the unsaturated zone using a Multiple Interacting Pathways model: implications from laboratory experiments
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    HSV kategori
    Identifikatorer
    urn:nbn:se:uu:diva-331732 (URN)
    Tilgjengelig fra: 2017-10-17 Laget: 2017-10-17 Sist oppdatert: 2017-11-14
  • Disputas: 2017-12-15 13:15 room B42, Uppsala Biomedical Centre (BMC), Uppsala
    Garmendia, Eva
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    A Unified Multitude: Experimental Studies of Bacterial Chromosome Organization2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Bacteria are many, old and varied; different bacterial species have been evolving for millions of years and show many disparate life-styles and types of metabolism. Nevertheless, some of the characteristics regarding how bacteria organize their chromosomes are relatively conserved, suggesting that they might be both ancient and important, and that selective pressures inhibit their modification. This thesis aims to study some of these characteristics experimentally, assessing how changes affect bacterial growth, and how, after changing conserved features, bacteria might evolve.

    First, we experimentally tested what are the constraints on the horizontal transfer of a gene highly important for bacterial growth. Second, we investigated the significance of the location and orientation of a highly expressed and essential operon; and we experimentally evolved strains with suboptimal locations and orientations to assess how bacteria could adapt to these changes. Thirdly, we sought to understand the accessibility of different regions of the bacterial chromosome to engage in homologous recombination. And lastly, we constructed bacterial strains with chromosomal inversions to assess what effect the inversions had on growth rate, and how bacteria carrying costly inversions could evolve to reduce these costs.

    The results provide evidence for different selective forces acting to conserve these chromosome organizational traits. Accordingly, we found that evolutionary distance, functional conservation, suboptimal expression and impaired network connectivity of a gene can affect the successful transfer of genes between bacterial species. We determined that relative location of an essential and highly expressed operon is critical for supporting fast growth rate, and that its location seems to be more important than its orientation. We also found that both the location, and relative orientation of separated duplicate sequences can affect recombination rates between these sequences in different regions of the chromosome. Finally, the data suggest that the importance of having the two arms of a circular bacterial chromosome approximately equal in size is a strong selective force acting against certain type of chromosomal inversions.

    Delarbeid
    1. Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs.
    Åpne denne publikasjonen i ny fane eller vindu >>Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs.
    Vise andre…
    2017 (engelsk)Inngår i: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 8, nr 4, e01276-17Artikkel i tidsskrift (Fagfellevurdert) Published
    Abstract [en]

    Genes encoding proteins that carry out essential informational tasks in the cell, in particular where multiple interaction partners are involved, are less likely to be transferable to a foreign organism. Here, we investigated the constraints on transfer of a gene encoding a highly conserved informational protein, translation elongation factor Tu (EF-Tu), by systematically replacing the endogenous tufA gene in the Escherichia coli genome with its extant and ancestral homologs. The extant homologs represented tuf variants from both near and distant homologous organisms. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 billion years ago (bya). Our results demonstrate that all of the foreign tuf genes are transferable to the E. coli genome, provided that an additional copy of the EF-Tu gene, tufB, remains present in the E. coli genome. However, when the tufB gene was removed, only the variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth which demonstrates the limited functional interchangeability of E. coli tuf with its homologs. Relative bacterial fitness correlated with the evolutionary distance of the extant tuf homologs inserted into the E. coli genome. This reduced fitness was associated with reduced levels of EF-Tu and reduced rates of protein synthesis. Increasing the expression of tuf partially ameliorated these fitness costs. In summary, our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.IMPORTANCE Horizontal gene transfer (HGT) is a fundamental driving force in bacterial evolution. However, whether essential genes can be acquired by HGT and whether they can be acquired from distant organisms are very poorly understood. By systematically replacing tuf with ancestral homologs and homologs from distantly related organisms, we investigated the constraints on HGT of a highly conserved gene with multiple interaction partners. The ancestral homologs represented phylogenetically resurrected tuf sequences dating from 0.7 to 3.6 bya. Only variants obtained from the gammaproteobacterial family (extant and ancestral) supported growth, demonstrating the limited functional interchangeability of E. coli tuf with its homologs. Our analysis suggests that the functional conservation of protein activity, the amount of protein expressed, and its network connectivity act to constrain the successful transfer of this essential gene into foreign bacteria.

    Emneord
    EF-Tu, ancient genes, horizontal gene transfer, proteobacteria, tuf
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot mikrobiologi; Biologi med inriktning mot molekylärbiologi; Biologi med inriktning mot evolutionär genetik
    Identifikatorer
    urn:nbn:se:uu:diva-330501 (URN)10.1128/mBio.01276-17 (DOI)28851849 (PubMedID)
    Tilgjengelig fra: 2017-10-02 Laget: 2017-10-02 Sist oppdatert: 2017-10-29
    2. Phenotypic and Genotypic Responses to Relocating a Highly-Expressed Bacterial Operon.
    Åpne denne publikasjonen i ny fane eller vindu >>Phenotypic and Genotypic Responses to Relocating a Highly-Expressed Bacterial Operon.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Emneord
    location & orientation, chromosomal organization, highly expressed genes, EF-Tu, tuf
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot mikrobiologi; Biologi med inriktning mot molekylärbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-332469 (URN)
    Tilgjengelig fra: 2017-10-27 Laget: 2017-10-27 Sist oppdatert: 2017-10-29
    3. Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination.
    Åpne denne publikasjonen i ny fane eller vindu >>Chromosomal Location Determines the Rate of Intrachromosomal Homologous Recombination.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Emneord
    Co-evolution, gene families, chromosome organization, gene orientation
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot mikrobiologi; Biologi med inriktning mot molekylärbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-332470 (URN)
    Tilgjengelig fra: 2017-10-27 Laget: 2017-10-27 Sist oppdatert: 2017-10-29
    4. The Selective Advantage of Replichore Balance in Salmonella Typhimurium.
    Åpne denne publikasjonen i ny fane eller vindu >>The Selective Advantage of Replichore Balance in Salmonella Typhimurium.
    (engelsk)Manuskript (preprint) (Annet vitenskapelig)
    Emneord
    chromosome organization, inversions, rearrangements, experimental evolution
    HSV kategori
    Forskningsprogram
    Biologi med inriktning mot mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-332484 (URN)
    Tilgjengelig fra: 2017-10-27 Laget: 2017-10-27 Sist oppdatert: 2017-10-29
  • Disputas: 2017-12-15 13:15 Auditorium minus, Uppsala
    Ander, Malin
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kvinnors och barns hälsa, Forskargrupper (Inst. för kvinnor och barns hälsa), Klinisk psykologi i hälso- och sjukvård.
    Cancer during adolescence: Psychological consequences and development of psychological treatment2017Doktoravhandling, med artikler (Annet vitenskapelig)
    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