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  • Zeleskov, Lilia
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Zeleskov, Lilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Mei, Hong
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Patientnära rond: Patientens och sjukvårdspersonalens perspektiv2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Background: The ward round is a team collaboration mainly between patient, nurse and physician. A good collaboration enhances the relationship between them. In addition, a successful round between the patient and the medical personnel is of great significance for the patient to have a safe and person-centered care. Therefore it is important to gain a deeper understanding of how patients and medical staff experience ward rounds, as well as of the importance of team work during the ward rounds.

    Aim: To shed light upon the effects of ward rounding on healthcare teams and to explore the experience of ward rounds from the perspectives of both patients and medical staff (nurses, physicians and medical students).

    Method: A literature study based on 14 scientific articles. Databases used in the study were PubMed, Cochrane Library, CINAHL, SBU and SveMed.

    Results: The results of this study indicate that both patients and medical personnel experience an increased satisfaction during ward rounds. Furthermore, the results show that ward rounds contribute in making medical personnel provide a proactive care to their patients, that cooperation between medical staff becomes more efficient, and that ward rounding benefits medical students’ development and increases students’ satisfaction with their education. A challenge that nurses experience during ward rounds is time limitation – mainly they experience that it takes time for nurses and physicians to synchronize and coordinate the meeting between patient and medical personnel, and also that the time for documentation is inadequate. Physicians also experience that their autonomy is reduced in relation to ward rounds.

    Conclusion: Overall, ward rounding can be an effective way to promote person-centered care. Ward rounds have a positive impact on teamwork between medical personnel and contribute to increased satisfaction among both patients and medical staff. However, there is need for further research on patients' perception of ward rounding and which specific measures that can be taken for the medical staff to be able to collaborate more efficiently.

  • Herbert-Read, James E.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics. Stockholm Univ, Dept Zool, SE-10691 Stockholm, Sweden..
    Herbert-Read, James E.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics. Stockholm Univ, Dept Zool, SE-10691 Stockholm, Sweden..
    Understanding how animal groups achieve coordinated movement2016In: ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, ISSN 2053-230X, Vol. 72, 2971-2983 p.Article, review/survey (Refereed)
    Abstract [en]

    Moving animal groups display remarkable feats of coordination. This coordination is largely achieved when individuals adjust their movement in response to their neighbours' movements and positions. Recent advancements in automated tracking technologies, including computer vision and GPS, now allow researchers to gather large amounts of data on the movements and positions of individuals in groups. Furthermore, analytical techniques from fields such as statistical physics now allow us to identify the precise interaction rules used by animals on the move. These interaction rules differ not only between species, but also between individuals in the same group. These differences have wide-ranging implications, affecting how groups make collective decisions and driving the evolution of collective motion. Here, I describe how trajectory data can be used to infer how animals interact in moving groups. I give examples of the similarities and differences in the spatial and directional organisations of animal groups between species, and discuss the rules that animals use to achieve this organisation. I then explore how groups of the same species can exhibit different structures, and ask whether this results from individuals adapting their interaction rules. I then examine how the interaction rules between individuals in the same groups can also differ, and discuss how this can affect ecological and evolutionary processes. Finally, I suggest areas of future research.

  • Borres, Magnus P.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Pediatrics.
    Borres, Magnus P.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Pediatrics.
    Maruyama, Nobuyuki
    Kyoto Univ, Grad Sch Agr, Lab Food Qual Design & Dev, Kyoto, Japan..
    Sato, Sakura
    Sagamihara Natl Hosp, Dept Allergy, Clin Res Ctr Allergol & Rheumatol, Sagamihara, Kanagawa, Japan..
    Ebisawa, Motohiro
    Sagamihara Natl Hosp, Dept Allergy, Clin Res Ctr Allergol & Rheumatol, Sagamihara, Kanagawa, Japan..
    Recent advances in component resolved diagnosis in food allergy2016In: Allergology International, ISSN 1323-8930, E-ISSN 1440-1592, Vol. 65, no 4, 378-387 p.Article, review/survey (Refereed)
    Abstract [en]

    Due to the high prevalence of food allergic diseases globally there are increasing demands in clinical practice for managing IgE-mediated conditions. During the last decade, component resolved diagnostics has been introduced into the field of clinical allergology, providing information that cannot be obtained from extract-based tests. Component resolved data facilitate more precise diagnosis of allergic diseases and identify sensitizations attributable to cross-reactivity. Furthermore it assists risk assessment in clinical practice as sensitization to some allergenic molecules is related to persistence of clinical symptoms and systemic rather than local reactions. The information may also aid the clinician in prescription of oral immunotherapy (OIT) in patients with severe symptoms, and in giving advice on food allergen avoidance or on the need to perform food challenges. The use of allergen components is rapidly evolving and increases our possibility to treat food allergic patients with a more individual approach. Using molecular allergology, we can already now better diagnose, prognose and grade the food allergy. In summary, daily routine molecular allergy diagnostics offers a number of benefits that give us a higher diagnostic precision and allow for better management of the patient.

  • Wang, Yu
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History.
    Wang, Yu
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History.
    The making of Environmental law in China: The making of Environmental law in China2015Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • Kretzschmar, Ann
    et al.
    Univ Lancaster, Lancaster Environm Ctr, Lancaster LA1 4YQ, England..
    Kretzschmar, Ann
    Univ Lancaster, Lancaster Environm Ctr, Lancaster LA1 4YQ, England..
    Tych, Wlodek
    Univ Lancaster, Lancaster Environm Ctr, Lancaster LA1 4YQ, England..
    Chappell, Nick
    Univ Lancaster, Lancaster Environm Ctr, Lancaster LA1 4YQ, England..
    Beven, Keith
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Univ Lancaster, Lancaster Environm Ctr, Lancaster LA1 4YQ, England..
    What really happens at the end of the rainbow?: - paying the price for reducing uncertainty (using reverse hydrology models)2016In: 12Th International Conference On Hydroinformatics (HIC 2016) - Smart Water For The Future / [ed] Kim, JH; Kim, HS; Yoo, DG; Jung, D; Song, CG, 2016, 1333-1340 p.Conference paper (Refereed)
    Abstract [en]

    Modelling of environmental processes is subject to a high degree of uncertainty due to the incorporation of random errors and a lack of knowledge about how processes operate at the scale of interest. Use of uncertain data when identifying and calibrating a model can lead to disinformative data being included in the procedure, resulting in uncertain parameter estimation and ambiguity in the outcomes. Rainfall-runoff modelling where a single rain-gauge is often assumed to be representative of the potentially highly variable (in both space and time) rainfall field is a good example. The noisy pattern of rainfall inputs is transformed by the catchment into streamflow. The streamflow pattern is dependent on the spatio-temporal pattern of rainfall and of the dominant processes operating within the catchment. Inverse modelling of the catchment dynamics, that is, inferring catchment rainfall from streamflow, provides a possible means of improving the estimated rainfall input because all rain falling on the catchment becomes streamflow, and thus, providing improved forecasts of the streamflow output. A combination of inverse modelling, time series analysis, spatial analysis and spectral analysis may also help to provide an insight into the complex processes operating within the catchment system. This paper applies a novel method for inferring true catchment rainfall from streamflow highlighting that the streamflow is better estimated using inferred rainfall than observed rainfall (from a single gauge) because a single gauge only gives a partial description of the rainfall field. However reducing uncertainty in this way comes at a price, in this case, the reduction in time-resolution of the inferred rainfall series.

  • Ulväng, Göran
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Economic History.
    Ulväng, Göran
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Economic History.
    Herrgårdsnytt 20162016Other (Other (popular science, discussion, etc.))
  • Westerlund, Hugo
    et al.
    Stockholm Univ, Stress Res Inst, S-10691 Stockholm, Sweden.
    Westerlund, Hugo
    Stockholm Univ, Stress Res Inst, S-10691 Stockholm, Sweden.
    Gustafsson, Per E.
    Umea Univ, Dept Publ Hlth & Clin Med, Umea, Sweden.
    Theorell, Tores
    Stockholm Univ, Stress Res Inst, S-10691 Stockholm, Sweden.
    Janlert, Urban
    Umea Univ, Dept Publ Hlth & Clin Med Epidemiol & Publ Hlth, Umea, Sweden.
    Hammarström, Anne
    Umea Univ, Dept Publ Hlth & Clin Med, Umea, Sweden.
    Social Adversity in Adolescence Increases the Physiological Vulnerability to Job Strain in Adulthood: A Prospective Population-Based Study2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 4, e35967Article in journal (Refereed)
    Abstract [en]

    Background: It has been argued that the association between job strain and health could be confounded by early life exposures, and studies have shown early adversity to increase individual vulnerability to later stress. We therefore investigated if early life exposure to adversity increases the individual's physiological vulnerability job strain in adulthood. Methodology/Principal Findings: In a population-based cohort (343 women and 330 men, 83% of the eligible participants), we examined the association between on the one hand exposure to adversity in adolescence, measured at age 16, and job strain measured at age 43, and on the other hand allostatic load at age 43. Adversity was operationalised as an index comprising residential mobility and crowding, parental loss, parental unemployment, and parental physical and mental illness (including substance abuse). Allostatic load summarised body fat, blood pressure, inflammatory markers, glucose, blood lipids, and cortisol regulation. There was an interaction between adversity in adolescence and job strain (B = 0.09, 95% CI 0.02 to 0.16 after adjustment for socioeconomic status), particularly psychological demands, indicating that job strain was associated with increased allostatic load only among participants with adversity in adolescence. Job strain was associated with lower allostatic load in men (beta = -0.20, 95% CI -0.35 to -0.06). Conclusions/Significance: Exposure to adversity in adolescence was associated with increased levels of biological stress among those reporting job strain in mid-life, indicating increased vulnerability to environmental stressors.

  • Wiklund, Maria
    et al.
    Department of Community Medicine and Rehabilitation, Physiotherapy, Umeå University, Umeå, Sweden; Umeå Centre for Gender Studies in Medicine, Umeå University, Umeå, Sweden; Department of Public Health and Clinical Medicine, Social Medicine, Umeå University, Umeå, Sweden.
    Wiklund, Maria
    Department of Community Medicine and Rehabilitation, Physiotherapy, Umeå University, Umeå, Sweden; Umeå Centre for Gender Studies in Medicine, Umeå University, Umeå, Sweden; Department of Public Health and Clinical Medicine, Social Medicine, Umeå University, Umeå, Sweden.
    Fjellman-Wiklund, Anncristine
    Umeå universitet, Fysioterapi.
    Stålnacke, Britt-Marie
    Umeå Centre for Gender Studies in Medicine, Umeå University, Umeå, Sweden; Department of Community Medicine and Rehabilitation, Rehabilitation Medicine, Umeå University, Umeå, Sweden.
    Hammarström, Anne
    Umeå Centre for Gender Studies in Medicine, Umeå University, Umeå, Sweden; Department of Public Health and Clinical Medicine, Social Medicine, Umeå University, Umeå, Sweden.
    Lehti, Arja
    Umeå Centre for Gender Studies in Medicine, Umeå University, Umeå, Sweden; Department of Clinical Sciences, Professional Development, Umeå University, Umeå, Sweden.
    Access to rehabilitation: patient perceptions of inequalities in access to specialty pain rehabilitation from a gender and intersectional perspective2016In: Global Health Action, ISSN 1654-9716, E-ISSN 1654-9880, Vol. 9, 31542Article in journal (Refereed)
    Abstract [en]

    Background: Long-term musculoskeletal pain is common, particularly among women. Pain conditions are a concern in primary health care, and people with severe and complex pain are referred to specialty health care. There is gender bias in access, counselling, assessment, and treatment of long-term pain.

    Objective: This study explores patient accounts and perceptions about important (social) factors for accessing specialised pain rehabilitation from gender and intersectional equality perspectives. We aimed to identify potential biases and inequalities in accessing rehabilitation resources at a specialised rehabilitation clinic.

    Design: Individual semi-structured interviews were conducted with 10 adults after an assessment or completion of a specialised rehabilitation programme in northern Sweden. Qualitative content analysis was used to explore patients’ perceptions of important factors for accessing rehabilitation.

    Results: One main theme was formulated as Access to rehab – not a given. Three categories of perceived inequality were demonstrated: power of gender, power of social status, and power of diagnosis. Participants perceived rehabilitation as a resource that is not equally available, but dependent on factors such as gender, socio-economic status, ability to work, ethnicity, or age, and more subtle aspects of social status and habitus (e.g. appearance, fitness, and weight). The character of diagnosis received (medical versus psychiatric or social) was also noted.

    Conclusions: It is crucial that professionals are aware of how potential inequalities related to gender, social status, and diagnosis, and their intersections, can be created, perceived, and have influence on the processes of assessment and treatment. Reduction of social determinants of health and biases remain important within global, national, and local contexts.

  • Rångtell, Frida H.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Rångtell, Frida H.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Ekstrand, Emelie
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Rapp, Linnea
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Lagermalm, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Liethof, Lisanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Bucaro, Marcela Olaya
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Lingfors, David H. S.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Jan-Erik, Broman
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Psychiatry, University Hospital.
    Schiöth, Helgi B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Benedict, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Two hours of evening reading on a self-luminous tablet vs. reading a physical book does not alter sleep after daytime bright light exposure2016In: Sleep Medicine, ISSN 1389-9457, E-ISSN 1878-5506, Vol. 23, 111-118 p.Article in journal (Refereed)
    Abstract [en]

    Background: The use of electronic devices emitting blue light during evening hours has been associated with sleep disturbances in humans, possibly due to the blue light-mediated suppression of the sleep promoting hormone melatonin. However, experimental results have been mixed. The present study therefore sought to investigate if reading on a self-luminous tablet during evening hours would alter sleepiness, melatonin secretion, nocturnal sleep, as well as electroencephalographic power spectral density during early slow-wave sleep. Methods: Following a constant bright light exposure over 6.5 hours (similar to 569 lux), 14 participants (six females) read a novel either on a tablet or as physical book for two hours (21:00-23:00). Evening concentrations of saliva melatonin were repeatedly measured. Sleep (23:15-07:15) was recorded by polysomnography. Sleepiness was assessed before and after nocturnal sleep. About one week later, experiments were repeated; participants who had read the novel on a tablet in the first experimental session continued reading the same novel in the physical book, and vice versa. Results: There were no differences in sleep parameters and pre-sleep saliva melatonin levels between the tablet reading and physical book reading conditions. Conclusions: Bright light exposure during daytime has previously been shown to abolish the inhibitory effects of evening light stimulus on melatonin secretion. Our results could therefore suggest that exposure to bright light during the day - as in the present study - may help combat sleep disturbances associated with the evening use of electronic devices emitting blue light. However, this needs to be validated by future studies with larger sample populations.

  • Abu Hamdeh, Sami
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurosurgery.
    Abu Hamdeh, Sami
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurosurgery.
    Marklund, Niklas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurosurgery.
    Lannsjö, Marianne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Rehabilitation Medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm, Centre for Research and Development, Gävleborg.
    Howells, Tim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurosurgery.
    Raininko, Raili
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology.
    Wikström, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology.
    Enblad, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurosurgery.
    Extended anatomical grading in diffuse axonal injury using MRI: Hemorrhagic lesions in the substantia nigra and mesencephalic tegmentum indicate poor long-term outcome2016In: Journal of Neurotrauma, ISSN 0897-7151, E-ISSN 1557-9042Article in journal (Refereed)
    Abstract [en]

    Clinical outcome after traumatic diffuse axonal injury (DAI) is difficult to predict. In this study, three magnetic resonance imaging (MRI) sequences were used to quantify the anatomical distribution of lesions, to grade DAI according to the Adams grading system, and to evaluate the value of lesion localization in combination with clinical prognostic factors to improve outcome prediction. Thirty patients (mean 31.2 years ±14.3 standard deviation) with severe DAI (Glasgow Motor Score [GMS] <6) examined with MRI within 1 week post-injury were included. Diffusion-weighted (DW), T2*-weighted gradient echo and susceptibility-weighted (SWI) sequences were used. Extended Glasgow outcome score was assessed after 6 months. Number of DW lesions in the thalamus, basal ganglia, and internal capsule and number of SWI lesions in the mesencephalon correlated significantly with outcome in univariate analysis. Age, GMS at admission, GMS at discharge, and low proportion of good monitoring time with cerebral perfusion pressure <60 mm Hg correlated significantly with outcome in univariate analysis. Multivariate analysis revealed an independent relation with poor outcome for age (p = 0.005) and lesions in the mesencephalic region corresponding to substantia nigra and tegmentum on SWI (p  = 0.008). We conclude that higher age and lesions in substantia nigra and mesencephalic tegmentum indicate poor long-term outcome in DAI. We propose an extended MRI classification system based on four stages (stage I—hemispheric lesions, stage II—corpus callosum lesions, stage III—brainstem lesions, and stage IV—substantia nigra or mesencephalic tegmentum lesions); all are subdivided by age (≥/<30 years).

  • Johnzon, Carl-Fredrik
    et al.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Johnzon, Carl-Fredrik
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Artursson, Karin
    Natl Vet Inst SVA, Uppsala, Sweden..
    Söderlund, Robert
    Natl Vet Inst SVA, Uppsala, Sweden..
    Guss, Bengt
    Swedish Univ Agr Sci, Dept Biomed Sci & Vet Publ Hlth, Uppsala, Sweden..
    Rönnberg, Elin
    Uppsala Univ, Dept Med Biochem & Microbiol, BMC, Uppsala, Sweden..
    Pejler, Gunnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden.
    Mastitis Pathogens with high Virulence in a Mouse Model Produce a Distinct cytokine Profile In Vivo2016In: Frontiers in Immunology, ISSN 1664-3224, E-ISSN 1664-3224, Vol. 7, 368Article in journal (Refereed)
    Abstract [en]

    Mastitis is a serious medical condition of dairy cattle. Here, we evaluated whether the degree of virulence of mastitis pathogens in a mouse model can be linked to the inflammatory response that they provoke. Clinical isolates of Staphylococcus aureus (S. aureus) (strain 556 and 392) and Escherichia coli (E. coli) (676 and 127), and laboratory control strains [8325-4 (S. aureus) and MG1655 (E. coli)], were injected i.p. into mice, followed by the assessment of clinical scores and inflammatory parameters. As judged by clinical scoring, E. coli 127 exhibited the largest degree of virulence among the strains. All bacterial strains induced neutrophil recruitment. However, whereas E. coli 127 induced high peritoneal levels of CXCL1, G-CSF, and CCL2, strikingly lower levels of these were induced by the less virulent bacterial strains. High concentrations of these compounds were also seen in blood samples taken from animals infected with E. coli 127, suggesting systemic inflammation. Moreover, the levels of CXCL1 and G-CSF, both in the peritoneal fluid and in plasma, correlated with clinical score. Together, these findings suggest that highly virulent clinical mastitis isolates produce a distinct cytokine profile that shows a close correlation with the severity of the bacterial infection.

  • Brosché, Johan
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Peace and Conflict Research.
    Brosché, Johan
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Peace and Conflict Research.
    Legnér, Mattias
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Art History.
    Kreutz, Joakim
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Peace and Conflict Research. Department of Political Science, Stockholm university, Stockholm, Sweden.
    Ijla, Akram
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Art History, Conservation.
    Heritage under Attack: motives for targeting cultural property during armed conflict2016In: International Journal of Heritage Studies (IJHS), ISSN 1352-7258, E-ISSN 1470-3610Article in journal (Refereed)
    Abstract [en]

    Although attacks on cultural property have caused international outcry,our understanding of this phenomenon is still limited. In particular, littleresearch has been directed towards exploring the motivations for suchattacks. Therefore, we ask: What are the motives for attacking sites, buildingsor objects representing cultural heritage? By combining insights from peaceand conflict research with findings from heritage studies we present atypology of motivations for attacking cultural property. We identify four,not mutually exclusive, broad groups of motives: (i) attacks related to conflictgoals, in which cultural property is targeted because it is connected to theissue the warring parties are fighting over (ii), military-strategic attacks, inwhich the main motivation is to win tactical advantages in the conflict (iii),signalling attacks, in which cultural property is targeted as a low-risk targetthat signals the commitment of the aggressor, and (iv) economic incentiveswhere cultural property provides funding for warring parties. Our typologyoffers a theoretical structure for research about why, when, and by whom,cultural property is targeted. This is not only likely to provide academicbenefits, but also to contribute to the development of more effective toolsfor the protection of cultural property during armed conflict.

  • Juuso, Nikolaus
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Juuso, Nikolaus
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Modelling the Wind Climate in Mountain Valleys Using the MIUU Mesoscale Model2002Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    High average wind speeds have been measured in many valleys. The reasons for these high winds are channelling effects of two physical origins, forced channelling and pressure driven channelling. In this study, the MIUU-model, a three-dimensional mesoscale model with a higher order closure, has been used to investigate these effects in idealised valleys. The simulations have been performed in both two- and three-dimensions with a multitude of conditions. The valley dimensions, as depth, width and length, have been changed in order to investigate the flow within the valley. The dependence of strength and direction of the geostrophic wind have also been examined. Most of the simulations are performed for wintertime conditions at high latitudes with low roughness. In addition, simulations representing summertime conditions are made to check the influence of the diurnal variation of incoming radiation and thermal stability.

    In the two-dimensional simulations the mean wind speed along the valley is found to be independent of the magnitude of the geostrophic wind (at least up to 10 ms-1) if the large-scale flow is perpendicular to the valley. In this case, only the pressure driven channelling effect is of importance. When the geostrophic wind is higher than10 ms-1, the valley winds are coupled to the ambient flow and gravity waves are affecting the results. The mean and maximum wind speeds are found to be a function of the valley depth. In a valley with a water body (a lake) at the bottom, the simulations gave higher within valley winds for lower water temperatures, which increases the stability.

    In the three-dimensional simulations, it is shown that the maximum valley winds are almost independent of the valley length. However, the mean valley wind speed is more affected. Furthermore, it was found that close to the area where the valley widens - towards the region with lower synoptic pressure - a wind maximum is found in all simulations.

    A simulation of the Torneträsk area was made to investigate the flow in a real topography. With geostrophic wind perpendicular to the valley, high wind speeds occur at low levels in accordance with measurements. For the conditions used, channelling effects dominated the within valley flow.

  • Jansson, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Jansson, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Evaluation of a New Lateral Boundary Condition in the MIUU Meso-Scale Model2002Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The MIUU meso-scale model has been used to evaluate a new lateral boundary condition. The new lateral boundary condition is a combination of two lateral boundary conditions used in regional models, the flow relaxation scheme and the tendency modification scheme. The impact of different lateral boundary formulations on meso-scale phenomena, such as convective boundary layers, nocturnal jets, sea breezes and mountain waves (Bora winds) has been studied.

    When, for instance, stably stratified air with a constant wind speed is advected through the lateral boundaries into a meso-scale model with a flat and homogenous land surface, the convective boundary layer is reduced in height and the nocturnal jet is reduced in magnitude up to a distance of 750 km from the inflow lateral boundary. This is the case, when the most common lateral boundary condition is used, namely the flow relaxation scheme, where the flow relaxation parameter is constant with height and a function of the horizontal grid points only. In the other tests a flow relaxation parameter is used that is very small up to a certain level above ground, increasing with height to a maximum value higher up, and being constant above this upper level. Then, the convective boundary layer and the nocturnal jet are fully developed already at 23 km from the inflow lateral boundary.

    When, for instance, islands are not represented in the large-scale model, due to the coarse grid resolution, but well represented in the meso-scale model, stably stratified air can be advected into the meso-scale model even during daytime. Then, artificial thermal circulations can arise at the lateral boundaries of the meso-scale model, and collide with a real sea-breeze circulation that develops at the coast-line. These artificial thermal circulations disappear only when the flow relaxation parameter is very small in the lowest levels.

    When mountain waves (Bora winds) are simulated in a relatively small model domain, the critical layer, i.e. the layer where the nonlinear large-amplitude mountain wave is generated and broken, is surprisingly displaced irrespective of the tested lateral boundary formulations.

    In many simulations large-scale fields have to be introduced into meso-scale models. If only the flow relaxation scheme is used, the flow relaxation parameter has to be “constant-in-height” and relatively large in order to introduce large-scale temperature and wind changes with the right time-scale at all levels. However, with the new lateral boundary condition, the flow relaxation parameter can be kept very small in the lowest kilometers above ground. A small value of the flow relaxation parameter means that the convective boundary layer and the nocturnal jet at the lateral boundaries are not affected by the boundary conditions, and furthermore, no artificial thermal circulations are created. At the same time, large-scale temperature and wind changes are correctly introduced at all heights during the prescribed time into the meso-scale model through the tendency modification scheme.

  • Höglund, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Höglund, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Statistisk studie av sambandet mellan geostrofisk vind och temperatur i södra Sverige2002Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Atmospheric circulation is important in determining the surface climate on both global and regional scale. To quantify its effect, different circulation indices are often used. Here the geostrophic wind equations are applied to obtain circulation information for the south of Sweden on a monthly basis. Monthly means of temperatures have also been used.

    In this work, the connection between the mean temperature in the south of Sweden and the large-scale circulation in the North Atlantic area is studied. It is shown that flows with a westerly component clearly favour higher temperatures. Moreover, the westerly component is well correlated with the temperature in the winter. The temperature does not correlate with the northerly component for the winter season. In the summer an opposite relationship between the westerly and the northerly components on one hand, and the temperature on the other, as shown.

    The derived circulation models were established via statistical models. Simple and multiple regressions were used to understand the relationship between temperature and circulation. The accuracy in the models was determined by the correlation coefficient and the residual variance. The accuracy of the models is good during the winter and worse for the rest of the year.

    Different regression models have been estimated from the two data sets of pressure and temperature using the geostrophic wind equations. The most interesting in this study is to find out if the circulation can explain the increasing temperatures during the latest 10-15 years. By applying the results from the regression models, calibrated on data for the period 1873-1975, to the latest 25 years of high temperatures, it is shown that positive residuals exist during the winter. During the spring the residuals are positive as well. Moreover, the results are significantly differing from zero according to a test of hypothesis. The conclusion of this is that changes on the circulation itself can probably not explain the higher temperatures during the winter and spring.

  • Hansson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Hansson, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    En enkel modell för beräkning av tjäldjup2002Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    Många aktiviteter vintertid kräver att man känner till snö- och tjälförhållanden. Försvarsmakten har sedan mitten av 1960- talet mätt tjäldjupet på ett 20- tal platser runt om i landet. Antalet stationer har under senare år minskat kraftigt trots att behovet av tjäldjupsuppgifter inte minskat. Syftet med detta arbete är att ta fram en enkel modell för att kunna uppskatta tjäldjupet på en plats då man känner tjäldjupet på en närliggande plats. Övriga parametrar i modellen är lufttemperaturen på två meters höjd samt snödjupet vilka mättes i direkt anslutning till tjäldjupsmätplatserna. Även jordarternas egenskaper på de båda platserna ska vara med i modellen. De införs genom jordartskonstanter som bestämdes för de olika platserna i en undersökning genomförd i början av 1980- talet. Resultaten varierar från plats till plats men generellt kan sägas att modellen inte ger rimliga resultat under senvintern och våren. Under intjälningsperioden och tidiga högvintern ger däremot modellen rimliga resultat. Under denna tid ligger felet nästan hela tiden inom intervallet ± 20 cm, ofta även inom ett snävare intervall.

  • Andersson, Ulrika
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Andersson, Ulrika
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Åska längs Sveriges kuster2002Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    Åskan har i alla tider påverkat livet på jorden med sin enorma kraft. Det har skapats och berättats många skrönor och historier angående olika budskap och bestraffningar i samband med åska. Inte förrän i modern tid har människan börjat att förstå uppkomsten och fysiken bakom åska, som inte än är helt förklarat i detalj. Sedan år 1987, då blixtpejlsystemet LLP (Lightning Location System) installerades i Sverige, har blixtnedslagen och deras egenskaper registrerats och sparats i stora databaser i Sverige. Detta kan ses som en milstolpe i åskforskningen, då mer information om ett blixtnedslag går att erhållas. Utbyggnader och effektivisering av LLP-systemet (blixtpejlsystemet) sker nu i samarbete med andra nordiska länder.

    Examensarbetet börjar med en introduktion om hur åska uppkommer samt dess elektriska uppladdningsprocesser för att sedan vidare gå in på blixtens fysik. Därefter följer en presentation av LLP-systemet, dess uppbyggnad och funktion.

    Fördelningen av blixtnedslag längs södra Sveriges kuster under olika förutsättningar, som tid på året, blixtens amplitud och nedslagsplats har studerats. Olika uppkomna effekter av blixtdensiteten längs kusterna till följd av meteorologiska faktorer, som land- och sjöbris, hävningseffekter samt konvektion har studerats. Studier visar att blixtnedslagens densitet är beroende av underlaget och dess egenskaper, som varierar under årstiderna. Sommartid observeras fler blixtnedslag in över land, medan för höstperioden förflyttas detta maximum ut över hav. Land- och sjöbris kan på västkusten ha en påverkande effekt, då ett intensitets-minimum observeras strax utanför kustbandet.

    En fallstudie av en åskfrontpassage, som passerade över södra och mellersta Sverige den 16 augusti 2001, har studerats med avseende på den uppkomna tråglinjen, så kallad ”squall line”, i samband med frontpassagen. Den genererade kraftig och intensiv blixtaktivitet innan själva frontens ankomst västerifrån.

    Här ovan har enbart meteorologiska effekter på uppkomsten av åska behandlats. Även den lokala mark- och havsytan kan ge upphov till elektriska fenomen, som har betydelse för uppkomsten av blixtar. Därför studerades de elektriska rymdladdningarna i atmosfären och olika effekter beroende på underlagets skrovlighet. De teoretiska studierna visar på en ökning av rymdladdningsdensiteten över områden med skrovligare underlag, som in över land, vid kraftiga konvektiva moln med höga elektriska fält. Lägre rymdladdningsdensitet över havsytor medför att över hav kan det förekomma mycket högre elektriska fältstyrkor än över ojämn mark. Däremot kan höga föremål ute till havs, som master och vindkraftverk, lätt utlösa blixturladdningar.

  • Olsen, Arvid
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Olsen, Arvid
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Snow or rain? - A matter of wet-bulb temperature2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Accurate precipitation-type forecasts are essential in many areas of our modern society andtherefore there is a need to develop proper working methods for this purpose. Focus of thiswork has been to study important physical processes decisive in deciding both the temperatureof the precipitation particles, hence affecting their phase, and the surrounding air. Two majorlatent heating effects have been emphasized, melting effect and cooling byevaporation/sublimation. Melting of the snow flakes subtracts heat from the surroundings andhence acts as a cooling agent. Phase transformation from solid/liquid into the gas phase alsoneeds heat which here results in a cooling tendency. These two mechanisms may sometimeshave a crucial influence for deciding the correct precipitation-type. The melting effect isdiscussed in a paper about a snow event in Tennessee in USA, and another paper describingan event in Japan showing the influence of the evaporation/sublimation process. In the lattercase the wet-bulb temperature, Tiw as a physical correct discriminator between snow and rainis obtained.

    A numerical weather prediction model (HIRLAM) is being used to study differentcondensation schemes during three weather situations occurring in Sweden. These areRasch/Kristjánsson condensation scheme, Sundqvist original condensation scheme and amodification of the latter scheme. In the modified Sundqvist condensation scheme the Tiw hasbeen implemented as a limit temperature between snow and rain. The results are showingdifferences between the two main schemes concerning the total precipitation (both snow andrain). Comparisons between Sundqvist condensation scheme and this modified version, calledSundqvist scheme with Tiw show that this latter version creates slightly more snow.Differences between them are largest in dryer areas. Differences in the snow accumulationincrease when the forecast length increases. That makes them harder to be compared to snowanalyses from MESAN (mesoscale analysis) because the analyses is partly based ondifferences in the snow depth and this cannot be directly compared to amount of newly fallensnow especially when surface air temperatures are above freezing. Deviations from the dataanalyses are obtained in both Sundqvist and Sundqvist scheme with Tiw but in some regionsthe latter is in better agreement with measurements. Further work is needed in precipitationtypestudies but the physical correct value with Tiw = 0 ºC as melting temperature used inSundqvist with Tiw scheme is an interesting project for the future in the field of precipitationtypeforecasting.

  • Karelid, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Karelid, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Stadsklimateffekter i Uppsala2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The studies of the local climate types in our cities become more and more important withfaster growing population and expanding cities. In this study, profile data and turbulence datacollected in Uppsala between 1974 and 1979 were analysed. Variables were compared atdifferent wind directions, especially for wind blowing over the city and when it comes fromthe surrounding rural areas.

    Profiles of the Richardson number showed an obvious difference between the two differentwind sectors used, first and foremost at night. With wind blowing from the city thestratification often became less stable and sometimes there was convection. Together with theRichardson number the MPT-index (MPT = Modified Pasquil-Turner) was also tested as ameasure of stability for lower heights and the agreement was very good. The index agreeswith the Richardson number up to at least 20 m. One advantage with the MPT-index is that itcontains just a few variables and has obvious limits between different stabilities.

    The internal boundary layers that build up over surfaces with different characteristics than thesurrounding area was discovered above Uppsala in a study with near neutral stratification.The surface of Uppsala is very rough compared to the surroundings. It was found that airblowing about 4000 m through Uppsala created an internal boundary layer of a height ofabout 110 m.

    In other studies, mostly in cities larger than Uppsala, it was found that the isotherms at nightcame much closer together and it was warmer than in the surrounding areas. This gives theisotherms the shape of the topographical isolines for an island. This gives the expression,urban heat island. In Uppsala this study showed some signs for a night-time urban heat islandalthough the city is quite small. The urban heat island was most obvious during winter and spring.

    Measurements of turbulence gave spectra for u, w, q and T with very different lowestfrequenciesfor the start of the inertial subrange. For higher frequencies inside the inertialsubrange the spectra for all stabilities are collapsing onto each other, satisfying the Monin-Obukhov similarity theory, although the introduction of local scaling. The division at lowerfrequencies gave the deviations between the spectra.

  • Sohlberg, Johan
    Sohlberg, Johan
    Stabilitetsindex – en stabil prognosmetod för åska?2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this work different stability indices have been tested to determine which one ofthem that should be given most attention in the forecasting of thunderstorms. Thestudy also includes a brief description of a number of stability indices and theirbackground.

    The investigation includes eight frequently used stability indices. The results areevaluated with the indices POD, FAR, Brier Score and Skill Score. When making asummary of the case studies the stability indices HH-index and Åskrisk give the bestresults, while the results for indices KO-index and CAPE are poor. The other stabilityindices give mediocre results.

    The bad results for the widely used KO-index and CAPE are surprising. The mostlikely cause for the bad result of KO-index is an inadequate translation from the indexvalue to risk of thunderstorm in percent. Studies like this should in the future beperformed during an entire season. The use of the ECMWF-model may be a source oferror because of gross resolution. A model with less spacing between the grid pointsis preferable when making this kind of studies. Finally, HH-index and Åskrisk givethe best results in this study and should therefore be given most attention whenforecasting thunderstorms.

  • Doshi, Jiten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. ETH Zurich.
    Doshi, Jiten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. ETH Zurich.
    A platform for Chinese hamster ovary (CHO) cell genome engineering2016Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The production of therapeutic recombinant proteins in heterologous systems has gained significance since the last decade. For recombinant proteins that require post-translational modifications (PTMs), mammalian systems are preferred. Chinese hamster ovary (CHO) cells are the mammalian cells of choice for production of recombinant proteins. This is because of their ability to provide correct protein-folding and post-translational modifications, displaying high productivity at large scale, ability to grow in suspension mode at high densities in a serum-free media, incapable of infection by most viruses and their history of regulatory approvals. There is an established state of the art technology for development of CHO cells for recombinant protein production. This technology relies on random integration of the gene of interest and gene amplification process for obtaining high expressing clones. There is a high degree of clonal heterogeneity and instability observed in the screened clones. To overcome the process of random integration, this report describes a lentivirus based screening for search of stable and high expressing integration sites in CHO cells. The integration sites are identified by using nrLAM-PCR (non-restrictive linear amplification mediated PCR) coupled with high throughput sequencing. Lentivirus are chosen as they preferentially integrate within the coding regions rendering the possibility of obtaining stable and high expressing clones. In addition, lentivirus vector is designed to possess landing pad for recombinase mediated cassette exchange of viral sequence with foreign DNA. The report describes a successful cassette exchange reaction but with low efficiency. Genome engineering technologies such as CRISPR/Cas, TALENs can used for targeted gene insertion at integration sites and thus establishing stable and efficient production of recombinant proteins in CHO cells. Additionally, an approach for designing synthetic promoters based on Ef1α promoter architecture has been shown. Synthetic promoters are useful for expression of multi-gene cassettes as they are short in length and provide comparable expression levels to the native mammalian promoter. 

  • Nilsson, Charlotta
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Nilsson, Charlotta
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Beräkning av turbulenta flödenenligt inertial dissipationsmetodenmed mätdata från enspecialkonstrueradlättviktsanemometer samtjämförelsemed turbulenta utbytesmetoden2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In order to evaluate a combined cup anemometer/wind vane profile instrument, measurementsfrom the instrument has been used in the so called inertial-dissipation method to derive itsability to measure turbulent fluxes. The result was compared to data from a sonic anemometercalculated with eddy-correlation method, which is assumed to be correct. Analysis of theresult was made from measurements at levels 8, 16 and 20 m. The profile instrument (inertialdissipationmethod) agreed well with the sonic anemometer (eddy-correlation method) duringnear neutral conditions and at high wind speed. The profile instrument also proved to be mostaccurate at conditions of growing sea, otherwise the result was affected by waves. In thereport there is also a recommendation for specific corrections when the profile instrument isused for calculating turbulent fluxes according to the inertial-dissipation method.

  • Lindholm, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Lindholm, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Methods for Estimating the Wind Climate Using The MIUU-model2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In the year 2002 the Swedish Energy Agency assigned the department of Earth science at Uppsala University a research assignment to make a detailed wind climatology mapping covering Sweden. A survey of the Swedish wind climate has been made earlier in some areas, using the Danish model WASP. In this study the MIUU-model is usedwhich is a mesoscale three dimensional numerical model with a turbulence closure scheme of level 2.5. The MIUU-model is computer time demanding. Therefore a method to minimize the total number of simulations is wanted, without negative effects on the result.

    In this thesis the main issue is to compare the sensitivities and differences between climatological wind calculations using runs with different forcing parameters, i.e. with different meteorological conditions. Primarily the climatological results received with different geostrophic wind forcing are studied and compared. The idea is to find combinations with as small deviations as possible. The parameters investigated, called flow forcing parameters, are; geostrophic wind (magnitude and direction), thermal wind and thermal stratification. To compare the calculations a reference run is used. In theruns studying the influence of the geostrophic wind, calculations where made with 1, 2, 3 and 6 geostrophic wind speeds and with 4, 8, 16 and 32 wind directions. All compared to the reference that is based on 3 wind speeds and 8 wind directions. The model has earlier been used without any thermal wind influence. Therefore radio sonde data have been used to calculate the geostrophic mean wind profile introduced in the model to make new runs. The thermal stratification has also been modified in April and October to find out the sensitivities in the model.

    The result shows that there are only a few possible shortcuts in the number of runs needed and in the verification of the parameters. The question is if it is worth searching for them, since they might not be valid in other areas with more complex terrain. To be on the safe side, runs like the reference runs should at least be used in order to get accurate results as regards the wind climate.

  • Carlsson, Björn
    Carlsson, Björn
    Evaluation of the Inertial Dissipation Methodover Land2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The focus was to evaluate the Inertial Dissipation Method (IDM) over land duringunstable conditions. This was done by comparing the friction velocity, u*, from theeddy-correlation method (ECM) with u* from IDM. The result can be used to see ifIDM can rely on its assumptions, since the surface-layer theory is more fulfilled overland, where we for example do not have wave influence. The measurements weretaken from the flat agricultural site Marsta, 8 km north of Uppsala, Sweden.

    The result shows that IDM works well over land (relative standard deviation of about 10 %). For weakly unstable stratification, it is enough to use an assumption of neutralconditions in the IDM calculations. If it is more unstable, one should include theinfluence of stability and also include an imbalance term. The imbalance term isintroduced implicitly by varying the effective Kolmogorov’s constant with stability.The effective Kolmogorov’s constant used here, varied from 0.50 up to above 0.80.

    To calculate u* using IDM, a first estimation of u* was calculated from aparameterised drag coefficient CD. Also, to imitate the measuring setup on a movingplatform on the sea, the stability parameter, z/L, was calculated using a bulkestimatedheat flux. The large scatter showed that it is important that theparameterisations of CD and the heat flux are good.

    One can conclude that the IDM as a method to determine turbulent fluxes over landworks satisfactory. The larger scatter over sea is probably an effect of sea waveinfluence, even though the sea surface is considered more homogeneous and theconditions more stationary.

  • Hansson, Ulrika
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Hansson, Ulrika
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Inverkan av det interna gränsskiktets höjd på turbulensstruktureni ytskiktet2003Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The aim of this study is to find out if and how the height of the internal boundary

    layer affects the structure of the turbulence in the surface layer. This has been done

    from measurements made 1984 and 1988 at Näsudden on the southwest part of

    Gotland. The wind direction has been chosen to get as long fetch over sea as possible.

    The height of the internal boundary layer is obtained from temperature profiles where

    the first inversion represents the height of the internal boundary layer. The Monin-

    Obukhov similarity theory has been used as a frame in this investigation.

     

    The study has shown that some turbulence features follow the Monin-Obukhov

    similarity better than others. The height of the internal boundary layer mostly affects

    the wind structure, but partly also the temperature structure. In some cases the

    characteristic velocity in the mixed layer also influences the turbulence in the surface

    layer. For example, it is better to normalize the horizontal wind variance with this

    velocity than the friction velocity as proposed in Monin-Obukhov theory. To

    normalize the vertical wind variance in the surface layer, it is possible to use both the

    friction velocity and the characteristic velocity in the mixed layer. This means the

    vertical wind variance can be normalized with both the height above ground and the

    height of the internal boundary layer.

  • Belking, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Belking, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    En ny metod för att beräkna impuls- och värmeflöden vid stabila förhållanden2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    De Bruin and Hartogensis have proposed a new method to determine momentum flux and sensible heat flux at stable conditions. When using this method the assumption is made that the standard deviations for the longitudinal wind component and temperature are approximately constant. Only the mean wind and the temperature and the standard deviations are necessary for the calculations.

    The method has been analyzed in this study with data from Labans kvarnar sited on Gotland in the Baltic Sea and Östergarnsholm which is situated 4 km outside Gotland. Labans kvarnar represents fluxes over land and Östergarnsholm represents fluxes over sea.

    The constants that De Bruin and Hartogensis found are the following:Cu=2.5 for wind speed and CT=2.3  for temperature, which shows very little scatter in the calculations of the fluxes. The data they used where measured in Kansas over a very flat grassland site.

    Different statistics measurements have been tested to receive values of the constants. In search of constants the mean value, median value and the modal value for respectively quantity have been calculated. For land conditions the values of the constants are a little bit higher, Cu=2.6 and CT=2.6, than the values De Bruin and Hartogensis received.

    When calculating the fluxes over ocean the wind direction is divided in to two intervals. The wind direction between 220- 300represents winds from Gotland and wind direction between  80o - 220o represents winds from open sea. For the open sea conditions the constants calculated for the momentum flux in this study are a little bit lower, Cu=2.2, than the value De Bruin and Hartogensis found. For winds from Gotland the constant for momentum flux was found to be: Cu=3.0. When calculating the sensible heat flux the constants are very difficult to find and do not give as good result as for the momentum flux over sea. The conditions for the sensible heat are much more complicated than it is for momentum flux. Firstly two constants are needed and secondly the temperature structure in the marine boundary layer does not follow Monin-Obukhov similarity theory.

  • Tisell, Camilla
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Tisell, Camilla
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    An investigation of the surface fluxes and other parameters inthe regional climate model RCA1 during ice conditions2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this study data from the regional climate model RCA1 is compared to measured data to investigate how good the model is during ice conditions and mainly how well the turbulent surface fluxes are described by the model. Comparisons of the sensible heat flux and the momentum flux as well as mean parameters are included. The measured data used are from the Bothnian Bay measured during the BASIS field experiment in February to March 1998. RCA1 (Rossby Centre regional Atmospheric model) is a regional climate model for Northern Europe based on HIRLAM and forced by ERA-40 data. Two different grid points of the RCA1 44 km grid have been chosen with geographical coordinates as close as possible to the two measuring sites. The first site is a small peninsula south of the town Umeå at the east coast of Sweden and the second one is the ship R/V Aranda anchored in the sea ice outside the Finnish west coast.

    The model presents generally too large negative (downward) sensible heat fluxes and too large momentum fluxes over ice. The largest difference between modelled and measured sensible heat fluxes are seen after warm front passages due to melting conditions. There are some uncertainties in the comparison of modelled fluxes and measured fluxes at Umeå due to a complex and varying ice cover around this measuring site.

    The vertical structure in the atmosphere has also been studied and modelled temperature, wind and humidity profiles were compared to radiosondes at the Umeå site. Two periods with on-ice flow and off-ice flow was analysed and one of the main differences was that for the on-ice situation an internal boundary layer was built up over the ice. Modelled profiles are generally smoother then measured profiles and inversions and other small-scale phenomena like low-level jets are almost never described correctly by the model but there are tendencies of the phenomena to occur.

  • Nilsson, Gabriella
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Nilsson, Gabriella
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    An investigation of the accuracy and long term trends of ERA-40 over the Baltic Sea2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Meteorological measurements from the research station at Östergarnsholm in the Baltic Sea between 1995 and 2001 are used to evaluate the ERA-40 data base over the Baltic Sea. This includes comparisons of mean parameters and turbulent fluxes. The statistics concern all the data available when the measuring site was exposed to open sea conditions, and includes about 1500 hours of data. Seasonal data is compared as well.

    Regarding all the mean parameters compared, ERA-40 is partly in line with the results from the measurements, with various scatter. Temperature is too warm, wind speed is lower as well as relative humidity and sea surface temperature is systematically overestimated. The heat fluxes are generally overestimated by ERA-40 when compared to heat fluxes calculated by the bulk formulae, sensible heat flux with a mean value of 5W/m2 and latent heat flux with 9W/m2. The overestimation is larger for high fluxes and during high wind speeds. Friction velocity is too large in ERA-40.

    There are indications that the ERA-40 data over the Baltic Sea is somewhat influenced by land.

    A second objective for this study is to detect possible trends occurring at Östergarnsholm over a long term perspective with the aid of the complete 44 year long data set. An increasing trend in temperature can be observed, which is in agreement with other long term temperature series in the region.

  • Lennartsson, Linda
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Lennartsson, Linda
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Influence of fog on stratification and turbulent fluxes over the ocean2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this thesis a case of advection fog over the Baltic Sea is studied. The period examined is from June 5th to 7th 1995.

    Data is taken from the instrumented mast, situated on the island Östergarnsholm, a small and flat island without trees outside of Gotland. From the measurements among others the heat flux, relative humidity and temperature are analyzed.

    In the evening June 5th 1995 the fog is advected in over Östergarnsholm. This can both be seen from the increasing relative humidity and the decreasing temperature. Before the fog arrived the boundary layer was stably stratified. This stratification quickly changed to neutral as the fog reaches Östergarnsholm. After careful evaluation the neutral stratification is shown not to be neutral at all. The stratification closest to the ground up to 15 meters is unstable and above the stratification is stable. From this the conclusion is made that the fog is low only 15 meters high during this period.

    At noon June 6th the air temperature decreases dramatically below the sea surface temperature at the same time as the relative humidity increases up to 100%. The fog is now thick enough to have most of the outgoing radiation coming from the top, which decreases the temperature a few degrees. As the stability is investigated it shows unstable stratification up to the highest level (28 meters). The assumption is made that the fog is at least 30 meters deep.

    Also the normalized standard deviations for temperature and vertical velocity are examined to find out if they behave as the variation in the undisturbed boundary layer.2

  • Larsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Larsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Can effects from global warming be seen in Swedish snow statistics?2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This study is a result from a major investigation about the snow conditions in Sweden since the beginning of the twentieth century. For this purpose, data were analysed with respect to the maximum snow depth and the number of days with snow cover every year from some more than forty selected stations. These stations were then divided into different regions and means were calculated for each series. The data are presented in the shape of different histograms in the four following categories; the whole period in request (1900-2003), the latest 43 years (1961-2003), consecutive mean values for every decade and time series with the highest frequented fluctuations equalized. To be able to detect any trends in the plotted time series two statistical methods, simple linear regression and Mann-Kendall’s test, were applied. The calculations belonging to these tests are showed in tables.

    To be able to answer the question if the global warming can be related to the latest 3-4 decades predominantly warm winters in the southern part of Sweden I have been studying correlations in snow data with respect to the northern hemispheres mean temperature for the winter season. Corresponding estimates of the correlation coefficients have also been made with respect to the Swedish winter mean temperature.

    The response of the tests shows that it has not been such dramatic change in the snow conditions in the long run. The magnitude of the slope for the adjusted regression lines implies that the maximum snow depth and the number of days with snow cover in average have been on a fairly constant level during the latest hundred years. When it comes to the maximum snow depth one can distinguish a tendency for a small rise in Götaland and northern Norrland. This is also the only cases which are statistical significant for the period in request (1905-2003).

    For the shorter period 1961-2003 however, the number of days with snow cover has decreased quite substantially in the southern part of Sweden corresponding to a decrease about 40% in Götaland and 20% in Svealand. The test based on simple linear regression gives significant results in both cases while Mann-Kendall only establishes the trend for Götaland.

    A closer view of the maximum snow depth for the shorter period (1961-2003) does not give the same response but there is at least evidence for a significant decrease in Svealand in the test with simple linear regression. It corresponds to a decrease of about 30% since 1960.

    One cannot immediately relate the changes in the Swedish snow climate to the global warming. Estimated values of the correlation coefficient do not even give significant results for the period 1961-2003 despite of the fact that the global mean temperature has raised quite considerably since 1970. The corresponding calculations for the Swedish winter mean temperature show that it plays a very important roll if the precipitation in Götaland and Svealand is coming as rain or snow while it does not matter at all in northern Norrland.

  • Knutsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Knutsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Sprite observations over France in relation to their parent thunderstorm system2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    As a part of the European research program CAL, sprite observations were carried out from the OMP observatory in the French Pyrenees during the summer 2003. Images of the sprites were taken by two remotely controlled CCD cameras. The 23 July was considered particularly interesting because we then had access to data concerning both cloud-to-ground and intracloud lightning activity. This day was therefore chosen as the object of the present study.

    A large thunderstorm with two convective cores, one to the north and the other to the south, developed over the South of France during the late afternoon, and about two hours after sunset, the first sprite was detected. During a little more than three hours, 13 sprites were observed, 7 over the northern system and 6 over the southern system. The images enabled us to determine the azimuth angle of each sprite from the OMP observatory. 12 of the 13 sprites could be associated to positive cloud-to-ground flashes, and by putting together the sprite directions and the locations of the associated flashes on the radar images, we managed to get a rough idea of the position of the sprites in the storm system, and also to estimate their vertical and horizontal extent. Satellite images were included at this point of the study, and it appeared clear that sprites tend to occur over the stratiform region of the storm system in the area with the coldest (highest) cloud tops. The associated positive flashes were also within or close to this portion of the storm.

    The sprite occurrences were studied in relation to the cloud-to-ground and to the intracloud activity. We found that sprites seem to occur in a late stage of each storm system, when the rate of negative cloud-to-ground flashes has considerably decreased, and when the ratio of positive cloud-to-ground flashes is much higher then during the most active phase of the storm. Globally, the intracloud activity is also low during the sprite-producing periods, but sudden "bursts" of intracloud lightning could frequently be observed at the moment of the sprite. The peak current of the positive flashes was found to be rather weakly correlated to their sprite-generating capacity. The available Schumann resonance measurements seem to indicate that the charge moment is a much more adequate parameter in this respect.

    The areal coverage of the radar echo was calculated. The result supports the idea that sprite events tend to appear almost exclusively over large thunderstorm systems.

  • Grunditz, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Grunditz, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Statistisk undersökning av prognosmetod för stratus efter snöfall2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The purpose of this thesis is to evaluate a local method of forecasting the formation of stratus clouds after persistent snowfall. The method was developed during the end of the 1970s and is based on the difference in vapour pressure between ice and water.

    The evaluation is made on statistical data from three places with different topographic conditions; Malmen, Frösön and Vidsel. The statistical data consists of SYNOP observations from all three stations, radio soundings from Frösön and sodar data from Vidsel.

    To calculate the cloud base it is necessary to have the height to the inversion that limits the boundary layer, a mixing height. This mixing height is either estimated from SYNOP telegrams, sounding data, sodar data or calculated. Then the calculated and observed cloud base are compared to see how well the method works.

    It is hard to show a single physical phenomenon (in this case the effect of the difference in vapour pressure between ice and water) only with a statistical study. The method does work when the necessary conditions are met. It is clear that the cloud base is affected by many other meteorological effects. The terrain largely affects the outcome.

    The value of the cloud base that is computed with this method should only be taken as a good hint of how low the cloud base can get and not as an absolute value.

  • Frost, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Frost, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Klassificering av Low Level Jets och analys av den termiska vinden över Östergarnsholm2004Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The aim of this study is to classify Low Level Jets (LLJ) and analyze the thermal wind over Östergarnsholm. Östergarnsholm is a small island that is situated 4 kilometres east of Gotland in the Baltic Sea. Pibal trackings and soundings from 1995 to 2001 and 2003 have been used in the study. The criteria that have been used to classify the LLJs is that there must be a maximum of the wind speed below 500 meters. Wind profiles from a specific day have been used to determine if the LLJs is caused by sea breeze. The shift of wind direction at ground level, during the day, compared to the geostrophic wind at 2000 meters has been analyzed.

    LLJs caused by internal oscillation have been analyzed. In the used method the geostrophic wind speed and wind direction have been analyzed to determine how the wind has blown and where a LLJ possibly could be formed. Only wind directions between 20º and 220º have been used to avoid that the wind should have passed Gotland. If the winds have passed Gotland the internal oscillation has been disturbed and no LLJ can appear. Measured wind speeds and directions have been compared to theoretical values from pressure measurements.

    103 wind profiles with LLJs were found from all pibal trackings. In 27 of these pibal trackings, from 12 days, were LLJs caused by sea breeze. It is difficult to say how many LLJs that are caused by an internal oscillation. This due to the different results obtained when using wind speeds and wind directions from pibal trackings or pressure measurements. Also using straight line trajectories or trajectories following the isobars gives different results. Totally 9 LLJs were found, caused by an internal oscillation. Probably this way of analyze the internal oscillations is a better method for measurements over land than over sea. This due to the difficulties in measuring the exact wind speed and wind direction over the whole traveling distance over sea.

    The thermal wind over the island has been analyzed by studying all pibal trackings, even those without LLJs. The pibal trackings have been compared to the geostrophic wind calculated from pressure measurements to determine if thermal winds occur over Östergarnsholm. A LLJ caused by thermal wind occur when the geostrophic wind decreese with height, i.e. negative thermal wind.

    There was no difference in the amount of negative thermal winds and cases with no thermal wind. There were a few more positive thermal winds and they had higher wind speeds than the negative ones. There is no connection in the shift of wind direction when there is a LLJ caused by thermal wind. But there is a significant connection between the u- and v-component of the negative thermal winds and the u- and v-component of the geostrophic wind. In both cases the geostrophic wind tends to decreese towards zero with height. 41 of all LLJs were caused by thermal winds. About 50% of both negative and positive thermal winds have a positive v-component and a negative u-component. This means that the warmer region is in the north east.

  • Edfors, Fredrik
    et al.
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Edfors, Fredrik
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Danielsson, Frida
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Hallström, Björn M.
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Käll, Lukas
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Lundberg, Emma
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Pontén, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Forsstrom, Björn
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden..
    Uhlen, Mathias
    KTH Royal Inst Technol, Sci Life Lab, Stockholm, Sweden.;Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, Horsholm, Denmark..
    Gene-specific correlation of RNA and protein levels in human cells and tissues2016In: Molecular Systems Biology, ISSN 1744-4292, E-ISSN 1744-4292, Vol. 12, no 10, 883Article in journal (Refereed)
    Abstract [en]

    An important issue for molecular biology is to establish whether transcript levels of a given gene can be used as proxies for the corresponding protein levels. Here, we have developed a targeted proteomics approach for a set of human non-secreted proteins based on parallel reaction monitoring to measure, at steady-state conditions, absolute protein copy numbers across human tissues and cell lines and compared these levels with the corresponding mRNA levels using transcriptomics. The study shows that the transcript and protein levels do not correlate well unless a gene-specific RNA-to-protein (RTP) conversion factor independent of the tissue type is introduced, thus significantly enhancing the predictability of protein copy numbers from RNA levels. The results show that the RTP ratio varies significantly with a few hundred copies per mRNA molecule for some genes to several hundred thousands of protein copies per mRNA molecule for others. In conclusion, our data suggest that transcriptome analysis can be used as a tool to predict the protein copy numbers per cell, thus forming an attractive link between the field of genomics and proteomics.

  • Mezheyeuski, Artur
    et al.
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden.;Belarusian State Med Univ, Dept Pathol, Minsk, Byelarus..
    Mezheyeuski, Artur
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden.;Belarusian State Med Univ, Dept Pathol, Minsk, Byelarus..
    Hrynchyk, Ina
    City Clin Pathologoanat Bur, Minsk, Byelarus..
    Karlberg, Mia
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Portyanko, Anna
    Belarusian State Med Univ, Dept Pathol, Minsk, Byelarus..
    Egevad, Lars
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Ragnhammar, Peter
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Edler, David
    Karolinska Univ Hosp Solna, Dept Mol Med & Surg, Stockholm, Sweden..
    Glimelius, Bengt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Experimental and Clinical Oncology.
    Östman, Arne
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Image analysis-derived metrics of histomorphological complexity predicts prognosis and treatment response in stage II-III colon cancer2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 36149Article in journal (Refereed)
    Abstract [en]

    The complexity of tumor histomorphology reflects underlying tumor biology impacting on natural course and response to treatment. This study presents a method of computer-aided analysis of tissue sections, relying on multifractal (MF) analyses, of cytokeratin-stained tumor sections which quantitatively evaluates of the morphological complexity of the tumor-stroma interface. This approach was applied to colon cancer collection, from an adjuvant treatment randomized study. Metrics obtained with the method acted as independent markers for natural course of the disease, and for benefit of adjuvant treatment. Comparative analyses demonstrated that MF metrics out-performed standard histomorphological features such as tumor grade, budding and configuration of invasive front. Notably, the MF analyses-derived "alpha(max)" -metric constitutes the first response-predictive biomarker in stage II-III colon cancer showing significant interactions with treatment in analyses using a randomized trial-derived study population. Based on these results the method appears as an attractive and easy-to-implement tool for biomarker identification.

  • Burchardt, Steffi
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics.
    Burchardt, Steffi
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics.
    Troll, Valentin R.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics.
    Schmeling, Harro
    Goethe Univ Frankfurt, Fac Earth Sci, Altenhoferallee 1, D-60438 Frankfurt, Germany..
    Koyi, Hemin
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics.
    Blythe, Lara
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Solid Earth Geology.
    Erupted frothy xenoliths may explain lack of country-rock fragments in plutons2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 34566Article in journal (Refereed)
    Abstract [en]

    Magmatic stoping is discussed to be a main mechanism of magma emplacement. As a consequence of stoping, abundant country-rock fragments should occur within, and at the bottom of, magma reservoirs as "xenolith graveyards", or become assimilated. However, the common absence of sufficient amounts of both xenoliths and crustal contamination have led to intense controversy about the efficiency of stoping. Here, we present new evidence that may explain the absence of abundant country-rock fragments in plutons. We report on vesiculated crustal xenoliths in volcanic rocks that experienced devolatilisation during heating and partial melting when entrained in magma. We hypothesise that the consequential inflation and density decrease of the xenoliths allowed them to rise and become erupted instead of being preserved in the plutonic record. Our thermomechanical simulations of this process demonstrate that early-stage xenolith sinking can be followed by the rise of a heated, partially-molten xenolith towards the top of the reservoir. There, remnants may disintegrate and mix with resident magma or erupt. Shallow-crustal plutons emplaced into hydrous country rocks may therefore not necessarily contain evidence of the true amount of magmatic stoping during their emplacement. Further studies are needed to quantify the importance of frothy xenolith in removing stoped material.

  • Hodik, Monika
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    Hodik, Monika
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    Skog, Oskar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    Lukinius, Agneta
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    Isaza-Correa, J. M.
    Univ Groningen, Univ Med Ctr Groningen, Dept Cell Biol, Groningen, Netherlands..
    Kuipers, J.
    Univ Groningen, Univ Med Ctr Groningen, Dept Cell Biol, Groningen, Netherlands..
    Giepmans, B. N. G.
    Univ Groningen, Univ Med Ctr Groningen, Dept Cell Biol, Groningen, Netherlands..
    Frisk, Gun
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology.
    Enterovirus infection of human islets of Langerhans affects beta-cell function resulting in disintegrated islets, decreased glucose stimulated insulin secretion and loss of Golgi structure2016In: BMJ OPEN DIABETES RESEARCH & CARE, ISSN 2052-4897, Vol. 4, no 1, e000179Article in journal (Refereed)
    Abstract [en]

    Aims/hypothesis: In type 1 diabetes (T1D), most insulin-producing beta cells are destroyed, but the trigger is unknown. One of the possible triggers is a virus infection and the aim of this study was to test if enterovirus infection affects glucose stimulated insulin secretion and the effect of virus replication on cellular macromolecules and organelles involved in insulin secretion. Methods: Isolated human islets were infected with different strains of coxsackievirus B (CVB) virus and the glucose-stimulated insulin release (GSIS) was measured in a dynamic perifusion system. Classical morphological electron microscopy, large-scale electron microscopy, so-called nanotomy, and immunohistochemistry were used to study to what extent virus-infected beta cells contained insulin, and real-time PCR was used to analyze virus induced changes of islet specific genes. Results: In islets infected with CVB, GSIS was reduced in correlation with the degree of virus-induced islet disintegration. The expression of the gene encoding insulin was decreased in infected islets, whereas the expression of glucagon was not affected. Also, in islets that were somewhat disintegrated, there were uninfected beta cells. Ultrastructural analysis revealed that virus particles and virus replication complexes were only present in beta cells. There was a significant number of insulin granules remaining in the virus-infected beta cells, despite decreased expression of insulin mRNA. In addition, no typical Golgi apparatus was detected in these cells. Exposure of islets to synthetic dsRNA potentiated glucose-stimulated insulin secretion. Conclusions/interpretation: Glucose-stimulated insulin secretion; organelles involved in insulin secretion and gene expression were all affected by CVB replication in beta cells.

  • Hansson, Mats G.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Centre for Research Ethics and Bioethics.
    Hansson, Mats G.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences, Centre for Research Ethics and Bioethics.
    Lochmuller, Hanns
    Newcastle Univ, Inst Med Genet, John Walton Muscular Dystrophy Res Ctr, Newcastle Upon Tyne, Tyne & Wear, England..
    Riess, Olaf
    Univ Tubingen, Rare Dis Ctr, Inst Med Genet & Appl Genom, Tubingen, Germany..
    Schaefer, Franz
    Heidelberg Univ, Ctr Pediat & Adolescent Med, Div Pediat Nephrol, Heidelberg, Germany..
    Orth, Michael
    Ulm Univ Hosp, Dept Neurol, Ulm, Germany..
    Rubinstein, Yaffa
    NIH, ORDR, Natl Ctr Adv Translat Sci, Bldg 10, Bethesda, MD 20892 USA..
    Molster, Caron
    Dept Hlth Govt Western Australia, Off Populat Hlth Genom, Publ Hlth & Clin Serv Div, Perth, WA, Australia..
    Dawkins, Hugh
    Dept Hlth Govt Western Australia, Off Populat Hlth Genom, Publ Hlth & Clin Serv Div, Perth, WA, Australia.;Murdoch Univ, Ctr Comparat Genom, Murdoch, WA, Australia.;Curtin Univ Technol, Ctr Populat Hlth Res, Bentley, WA, Australia.;Univ Western Australia, Sch Pathol & Lab Med, Nedlands, WA, Australia..
    Taruscio, Domenica
    Ist Super Sanita, Natl Ctr Rare Dis, Rome, Italy..
    Posada, Manuel
    SpainRDR, ISCIII, Inst rare Dis Res, Madrid, Spain.;CIBERER, Madrid, Spain..
    Woods, Simon
    Newcastle Univ, Policy Eth & Life Sci Res Ctr, Newcastle Upon Tyne, Tyne & Wear, England..
    The risk of re-identification versus the need to identify individuals in rare disease research2016In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 24, no 11, 1553-1558 p.Article in journal (Refereed)
    Abstract [en]

    There is a growing concern in the ethics literature and among policy makers that de-identification or coding of personal data and biospecimens is not sufficient for protecting research subjects from privacy invasions and possible breaches of confidentiality due to the possibility of unauthorized re-identification. At the same time, there is a need in medical science to be able to identify individual patients. In particular for rare disease research there is a special and well-documented need for research collaboration so that data and biosamples from multiple independent studies can be shared across borders. In this article, we identify the needs and arguments related to de-identification and re-identification of patients and research subjects and suggest how the different needs may be balanced within a framework of using unique encrypted identifiers.

  • Sundh, D.
    et al.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med & Clin Nutr, Geriatr Med, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Sundh, D.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med & Clin Nutr, Geriatr Med, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Mellstrom, D.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med & Clin Nutr, Geriatr Med, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Ljunggren, Östen
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Endocrinology and mineral metabolism.
    Karlsson, M. K.
    Lund Univ, Dept Clin Sci, Clin & Mol Osteoporosis Res Unit, Lund, Sweden.;Skane Univ Hosp, Dept Orthopaed, Malmo, Sweden..
    Ohlsson, C.
    Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Nilsson, M.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med & Clin Nutr, Geriatr Med, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Nilsson, A. G.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med & Clin Nutr, Geriatr Med, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Lorentzon, M.
    Univ Gothenburg, Sahlgrenska Acad, Dept Internal Med & Clin Nutr, Geriatr Med, Gothenburg, Sweden.;Univ Gothenburg, Sahlgrenska Acad, Ctr Bone & Arthrit Res, Inst Med, Gothenburg, Sweden..
    Low serum vitamin D is associated with higher cortical porosity in elderly men2016In: Journal of Internal Medicine, ISSN 0954-6820, E-ISSN 1365-2796, Vol. 280, no 5, 496-508 p.Article in journal (Refereed)
    Abstract [en]

    BackgroundBone loss at peripheral sites in the elderly is mainly cortical and involves increased cortical porosity. However, an association between bone loss at these sites and 25-hydroxyvitamin D has not been reported. ObjectiveTo investigate the association between serum levels of 25-hydroxyvitamin D, bone microstructure and areal bone mineral density (BMD) in elderly men. MethodsA population-based cohort of 444 elderly men (mean SD age 80.2 3.5 years) was investigated. Bone microstructure was measured by high-resolution peripheral quantitative computed tomography, areal BMD by dual-energy X-ray absorptiometry and serum 25-hydroxyvitamin D and parathyroid hormone levels by immunoassay. ResultsMean cortical porosity at the distal tibia was 14.7% higher (12.5 +/- 4.3% vs. 10.9 +/- 4.1%, P < 0.05) whilst cortical volumetric BMD, area, trabecular bone volume fraction and femoral neck areal BMD were lower in men in the lowest quartile of vitamin D levels compared to the highest. In men with vitamin D deficiency (<25 nmol L-1) or insufficiency [25-49 nmol L-1, in combination with an elevated serum level of parathyroid hormone (>6.8 pmol L-1)], cortical porosity was 17.2% higher than in vitamin D-sufficient men (P < 0.01). A linear regression model including age, weight, height, daily calcium intake, physical activity, smoking vitamin D supplementation and parathyroid hormone showed that 25-hydroxyvitamin D independently predicted cortical porosity (standardized = -0.110, R-2 = 1.1%, P = 0.024), area ( = 0.123, R-2 = 1.4%, P = 0.007) and cortical volumetric BMD ( = 0.125, R-2 = 1.4%, P = 0.007) of the tibia as well as areal BMD of the femoral neck ( = 0.102, R-2 = 0.9%, P = 0.04). ConclusionSerum vitamin D is associated with cortical porosity, area and density, indicating that bone fragility as a result of low vitamin D could be due to changes in cortical bone microstructure and geometry.

  • Vijay, Nagarjun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Zool Populat Genet, SE-10691 Stockholm, Sweden..
    Poelstra, Jelmer W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Weissensteiner, Matthias H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kryukov, Alexey P.
    Russian Acad Sci, Inst Biol & Soil Sci, Far East Branch, Lab Evolutionary Zool & Genet, Vladivostok 690022, Russia..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Munich, Div Evolutionary Biol, Grosshaderner St 2, D-82152 Planegg Martinsried, Germany..
    Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, 13195Article in journal (Refereed)
    Abstract [en]

    Uncovering the genetic basis of species diversification is a central goal in evolutionary biology. Yet, the link between the accumulation of genomic changes during population divergence and the evolutionary forces promoting reproductive isolation is poorly understood. Here, we analysed 124 genomes of crow populations with various degrees of genome-wide differentiation, with parallelism of a sexually selected plumage phenotype, and ongoing hybridization. Overall, heterogeneity in genetic differentiation along the genome was best explained by linked selection exposed on a shared genome architecture. Superimposed on this common background, we identified genomic regions with signatures of selection specific to independent phenotypic contact zones. Candidate pigmentation genes with evidence for divergent selection were only partly shared, suggesting context-dependent selection on a multigenic trait architecture and parallelism by pathway rather than by repeated single-gene effects. This study provides insight into how various forms of selection shape genome-wide patterns of genomic differentiation as populations diverge.

  • Kullinger, Merit
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Obstetrics and Gynaecology. Vastmanland Cty Hosp, Clin Res Ctr, Vasteras, Sweden.;Vastmanland Cty Hosp, Dept Obstet & Gynecol, Vasteras, Sweden..
    Kullinger, Merit
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Obstetrics and Gynaecology. Vastmanland Cty Hosp, Clin Res Ctr, Vasteras, Sweden.;Vastmanland Cty Hosp, Dept Obstet & Gynecol, Vasteras, Sweden..
    Haglund, Bengt
    Karolinska Inst, Ctr Pharmacoepidemiol CPE, Dept Med, Stockholm, Sweden..
    Kieler, Helle
    Karolinska Inst, Ctr Pharmacoepidemiol CPE, Dept Med, Stockholm, Sweden..
    Skalkidou, Alkistis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Obstetrics and Gynaecology.
    Effects of ultrasound pregnancy dating on neonatal morbidity in late preterm and early term male infants: a register-based cohort study2016In: BMC Pregnancy and Childbirth, ISSN 1471-2393, E-ISSN 1471-2393, Vol. 16, 335Article in journal (Refereed)
    Abstract [en]

    Background: Assessing gestational age by ultrasound can introduce a systematic bias due to sex differences in early growth. Methods: This cohort study included data on 1,314,602 births recorded in the Swedish Medical Birth Register. We compared rates of prematurity-related adverse outcomes in male infants born early term (gestational week 37-38) or late preterm (gestational week 35-36), in relation to female infants, between a time period when pregnancy dating was based on the last menstrual period (1973-1978), and a time period when ultrasound was used for pregnancy dating (1995-2010), in order to assess the method's influence on outcome by fetal sex. Results: As expected, adverse outcomes were lower in the later time period, but the reduction in prematurity-related morbidity was less marked for male than for female infants. After changing the pregnancy dating method, male infants born early term had, in relation to female infants, higher odds for pneumothorax (Cohort ratio [CR] 2. 05; 95 % confidence interval [CI] 1.33-3.16), respiratory distress syndrome of the newborn (CR 1.99; 95 % CI 1.33-2. 98), low Apgar score (CR 1.26; 5 % CI 1.08-1.47), and hyperbilirubinemia (CR 1.12; 95 % CI 1.06-1.19), when outcome was compared between the two time periods. A similar trend was seen for late preterm male infants. Conclusion: Misclassification of gestational age by ultrasound, due to size differences, can partially explain currently reported sex differences in early term and late preterm infants' adverse neonatal outcomes, and should be taken into account in clinical decisions and when interpreting study results related to fetal sex.

  • Mathew, Bini
    et al.
    Southern Res Inst, Drug Discovery Div, 2000 Ninth Ave South, Birmingham, AL 35205 USA..
    Mathew, Bini
    Southern Res Inst, Drug Discovery Div, 2000 Ninth Ave South, Birmingham, AL 35205 USA..
    Hobrath, Judith Varady
    Univ Dundee, Coll Life Sci, Drug Discovery Unit, Dundee DD1 5EH, Scotland..
    Ross, Larry
    Southern Res Inst, Drug Discovery Div, 2000 Ninth Ave South, Birmingham, AL 35205 USA..
    Connelly, Michele C.
    St Jude Childrens Res Hosp, Dept Chem Biol & Therapeut, 262 Danny Thomas Pl, Memphis, TN 38105 USA..
    Lofton, Hava
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Univ Texas Tyler, Hlth Sci Ctr, Tyler, TX 75708 USA..
    Rajagopalan, Malini
    Univ Texas Tyler, Hlth Sci Ctr, Tyler, TX 75708 USA..
    Guy, R. Kiplin
    St Jude Childrens Res Hosp, Dept Chem Biol & Therapeut, 262 Danny Thomas Pl, Memphis, TN 38105 USA..
    Reynolds, Robert C.
    Univ Alabama Birmingham, Dept Chem, Birmingham, AL 35294 USA.;Univ Alabama Birmingham, Div Hematol & Oncol, Birmingham, AL 35294 USA..
    Screening and Development of New Inhibitors of FtsZ from M-Tuberculosis2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, e0164100Article in journal (Refereed)
    Abstract [en]

    A variety of commercial analogs and a newer series of Sulindac derivatives were screened for inhibition of M. tuberculosis (Mtb) in vitro and specifically as inhibitors of the essential mycobacterial tubulin homolog, FtsZ. Due to the ease of preparing diverse analogs and a favorable in vivo pharmacokinetic and toxicity profile of a representative analog, the Sulindac scaffold may be useful for further development against Mtb with respect to in vitro bacterial growth inhibition and selective activity for Mtb FtsZ versus mammalian tubulin. Further discovery efforts will require separating reported mammalian cell activity from both antibacterial activity and inhibition of Mtb FtsZ. Modeling studies suggest that these analogs bind in a specific region of the Mtb FtsZ polymer that differs from human tubulin and, in combination with a pharmacophore model presented herein, future hybrid analogs of the reported active molecules that more efficiently bind in this pocket may improve antibacterial activity while improving other drug characteristics.

  • Kreuger, Johan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Kreuger, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    O'Callaghan, Paul
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, e0165012Article in journal (Refereed)
    Abstract [en]

    Here we report on a technical difficulty we encountered while optimizing genotyping strategies to identify mice derived from Exoc3l2(tm1a( KOMP)Wtsi) embryonic stem cells obtained from the Knockout Mouse Project Repository. The Exoc3l2(tm1a(KOMP)Wtsi) construct encodes a "knockout-first" design with loxP sites that confer conditional potential (KO1st). We designed primers that targeted wild-type sequences flanking the most downstream element of the construct, an 80 base pair synthetic loxP region, which BLAST alignment analysis reveals is an element common to over 10,000 conditional gene-targeting mouse models. As PCR products amplified from KO1st and wild-type templates would have different lengths (and different mobility in an agarose gel) this strategy was designed to determine the zygosity of individual mice from a single PCR. In parallel we performed PCR with a primer specifically targeting the synthetic loxP sequence. Unexpectedly, while the latter strategy detected the synthetic loxP region and correctly genotyped KO1st chimeric mice, the same individuals were genotyped as wild-type when using the primers that flanked the synthetic loxP region. We discuss the possibility that secondary DNA structures, formed due to the palindromic nature of the synthetic loxP region, may have caused the KO1st template to elude the PCR when using primers that flanked this region. This brief report aims to raise awareness regarding this potential source of false-negative genotype results, particularly for those who are devising genotyping strategies for similarly engineered animal models.

  • Abarenkov, Kessy
    et al.
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Adams, Rachel I.
    Univ Calif Berkeley, Plant & Microbial Biol, Berkeley, CA 94720 USA..
    Irinyi, Laszlo
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Agan, Ahto
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Ambrosio, Elia
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.;Via Calamandrei 2, I-53035 Siena, Italy..
    Antonelli, Alexandre
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.;Gothenburg Bot Garden, Carl Skottsbergs Gata 22A, S-41319 Gothenburg, Sweden..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Bengtsson-Palme, Johan
    Univ Gothenburg, Sahlgrenska Acad, Dept Infect Dis, Guldhedsgatan 10, S-41346 Gothenburg, Sweden..
    Bok, Gunilla
    SP Tech Res Inst Sweden, Box 857, S-50115 Boras, Sweden..
    Cangren, Patrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Coimbra, Victor
    Univ Fed Pernambuco UFPE, Dept Micol, CCB, Av Prof Nelson Chaves S-N, BR-50670901 Recife, PE, Brazil..
    Coleine, Claudia
    Univ Tuscia, Dept Ecol & Biol Sci, I-01100 Viterbo, Italy..
    Gustafsson, Claes
    Univ Gothenburg, Herbarium GB, Box 461, S-40530 Gothenburg, Sweden..
    He, Jinhong
    Chinese Acad Sci, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China..
    Hofmann, Tobias
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Kristiansson, Erik
    Chalmers, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Larsson, Tomas
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Liu, Yingkui
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Martinsson, Svante
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Meyer, Wieland
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Panova, Marina
    Univ Gothenburg, Dept Marine Sci Tjarno, S-45296 Stromstad, Sweden..
    Pombubpa, Nuttapon
    Univ Calif Riverside, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA.;Univ Calif Riverside, Inst Integrat Genome Biol, Riverside, CA 92521 USA..
    Ritter, Camila
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Scharn, Ruud
    Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden..
    Svensson, Ola
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Töpel, Mats
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Unterseher, Martin
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Soldmannstr 15, D-17487 Greifswald, Germany..
    Visagie, Cobus
    Agr & Agri Food Canada, Biodivers Mycol, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.;Univ Ottawa, Dept Biol, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Taylor, Andy F. S.
    James Hutton Inst, Aberdeen AB15 8QH, Scotland.;Univ Aberdeen, Inst Biol & Environm Sci, Cruickshank Bldg, Aberdeen AB24 3UU, Scotland..
    Köljalg, Urmas
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Schriml, Lynn
    Univ Maryland, Sch Med, Dept Epidemiol & Publ Hlth, Baltimore, MD 21201 USA.;Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard - a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 16, 1-15 p.Article in journal (Refereed)
    Abstract [en]

    Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data - for example, "retrieve all fungal sequences recovered from bathrooms" - a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http:// gensc.org/ mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http:// its. mycologylab.org).

  • Wurzbacher, Christian
    et al.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.;Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Wurzbacher, Christian
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.;Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Warthmann, Norman
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Australian Natl Univ, Res Sch Biol, Div Plant Sci, Canberra, ACT, Australia..
    Bourne, Elizabeth C.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany..
    Attermeyer, Katrin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.
    Allgaier, Martin
    Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany..
    Powell, Jeff R.
    Univ Western Sydney, Hawkesbury Inst Environm, Penrith, NSW, Australia..
    Detering, Harald
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Univ Vigo, Dept Biochem Genet & Immunol, Vigo, Spain..
    Mbedi, Susan
    Berlin Ctr Genom Biodivers Res, Berlin, Germany.;Leibniz Inst Evolut & Biodivers Sci, Museum Nat Kunde, Berlin, Germany..
    Grossart, Hans-Peter
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Expt Limnol, Stechlin, Germany.;Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany..
    Monaghan, Michael T.
    Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Ecosyst Res, Berlin, Germany.;Berlin Ctr Genom Biodivers Res, Berlin, Germany..
    High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 16, 17-44 p.Article in journal (Refereed)
    Abstract [en]

    Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body.

  • Wahlberg, Per
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wahlberg, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lundmark, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Nordlund, Jessica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Busche, Stephan
    McGill Univ, Dept Human Genet, Montreal, PQ, Canada.;Genome Quebec Innovat Ctr, Montreal, PQ, Canada..
    Raine, Amanda
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tandre, Karolina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology.
    Rönnblom, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology.
    Sinnett, Daniel
    St Justine Univ Hlth Ctr, Res Ctr, Montreal, PQ, Canada.;Univ Montreal, Dept Pediat, Montreal, PQ, Canada..
    Forestier, Erik
    Umea Univ, Dept Med Biosci, Umea, Sweden..
    Pastinen, Tomi
    McGill Univ, Dept Human Genet, Montreal, PQ, Canada.;Genome Quebec Innovat Ctr, Montreal, PQ, Canada..
    Lönnerholm, Gudmar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Pediatrics.
    Syvänen, Ann-Christine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands2016In: Epigenomics, ISSN 1750-1911, Vol. 8, no 10, 1367-1387 p.Article in journal (Refereed)
    Abstract [en]

    Aim: To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale. Materials & methods: Whole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set. Results: Compared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient. Differentially methylated regions are enriched to CpG poor regions, active enhancers and transcriptional start sites. We also identified approximately 8000 CpG islands with variable intermediate DNA methylation that seems to occur as a result of stochastic de novo methylation. Conclusion: WGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.

  • Ann-sofie, Helgsten
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Ann-sofie, Helgsten
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Miriam, Jenefeldt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Public Health and Caring Sciences.
    Förbereda barn med text- och bildmaterial inför hälsobesök på barnavårdscentral vid fem år2016Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
  • Levander, Sara
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Educational Sciences, Department of Education.
    Levander, Sara
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Educational Sciences, Department of Education.
    Riis, Ulla
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Educational Sciences, Department of Education.
    Assessing educational expertise in academic faculty promotion2016In: Nordic Journal of Studies in Educational Policy, ISSN 1654-2290, E-ISSN 2245-0157, Vol. 2, 33759Article in journal (Refereed)
    Abstract [en]

    During 19992010, eligible Swedish university lecturers had an unconditional right to apply for promotion tothe position of professor. Our aim was to discuss the motives of the reform and to problematise challenges inmaking qualitative assessments of educational expertise. We presented the results from an evaluation of thereform, and we focused on the weights that the peer reviewers in their assessment assign to the educationalcredentials of the applicants as opposed to those assigned to the research credentials. The empirical materialconsists of the dossiers from 294 cases of promotion. For research expertise and for educational expertise, wecreated one and three indices, respectively, where different types of credentials were given different weights.Changes over time were examined, as well as differences between disciplinary domains. In the assessment anddecision process, educational expertise was outweighed by research expertise, and mainly quantitative aspectsof the former were taken into account. There were signs that the peer review system underwent changes andthat its intended quality-promoting function diminished over time.

  • Hedman, Filip
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Hedman, Filip
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Improved Visualization of Rock Carvings2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Digitizing rock carvings is a way to archive historically important sites and to makethe data available for interpretation all around the world. Laser scanning has becomea very useful tool to capture the details of the rocks, and this thesis aim to answerhow we can use different filters on the captured 3D data to visualize patterns fromthe rock carvings, while minimizing the noise from the surrounding geometry.Different coloring methods are evaluated to accentuate the rock carvings, while amedian filter is implemented to reduce the noise of the renderings. The results showthat it is indeed possible to perform this kind of visualization, and that some methodsare more suitable for the task than others. The results of this thesis will hopefullymake the choice of method easier for other researchers in forthcoming projects.

  • Van den Berg, Ronald
    et al.
    Department of Mathematics and Computing Science and School of Behavioral and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands..
    Van den Berg, Ronald
    Department of Mathematics and Computing Science and School of Behavioral and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands..
    Roerdink, Jos B. T. M.
    Department of Mathematics and Computing Science and School of Behavioral and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands..
    Cornelissen, Frans W.
    Department of Mathematics and Computing Science and School of Behavioral and Cognitive Neurosciences, University of Groningen, Groningen, The Netherlands..
    On the generality of crowding: visual crowding in size, saturation, and hue compared to orientation2007In: Journal of Vision, ISSN 1534-7362, E-ISSN 1534-7362, Vol. 7, no 2Article in journal (Refereed)
    Abstract [en]

    Perception of peripherally viewed shapes is impaired when surrounded by similar shapes. This phenomenon is commonly referred to as "crowding". Although studied extensively for perception of characters (mainly letters) and, to a lesser extent, for orientation, little is known about whether and how crowding affects perception of other features. Nevertheless, current crowding models suggest that the effect should be rather general and thus not restricted to letters and orientation. Here, we report on a series of experiments investigating crowding in the following elementary feature dimensions: size, hue, and saturation. Crowding effects in these dimensions were benchmarked against those in the orientation domain. Our primary finding is that all features studied show clear signs of crowding. First, identification thresholds increase with decreasing mask spacing. Second, for all tested features, critical spacing appears to be roughly half the viewing eccentricity and independent of stimulus size, a property previously proposed as the hallmark of crowding. Interestingly, although critical spacings are highly comparable, crowding magnitude differs across features: Size crowding is almost as strong as orientation crowding, whereas the effect is much weaker for saturation and hue. We suggest that future theories and models of crowding should be able to accommodate these differences in crowding effects.