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  • Public defence: 2017-03-30 09:15 Auditorium Minus, Uppsala
    Moberg, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    The Human Endometrium: Studies on Angiogenesis and Endometriosis2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Angiogenesis is thought to play a pivotal role in the cycling endometrium. Coordinated by oestrogen and progesterone, endometrial blood vessel development is primarily mediated by vascular endothelial growth factor-A (VEGF-A), which promotes endothelial cell (EC) proliferation and protects ECs from induced apoptosis. Studying changes at transcript level in human endometrial endothelial cells (HEECs) in response to mitogenic and inhibitory stimuli is one way towards understanding the regulation of physiological endometrial angiogenesis.

    Endometriosis, the presence of endometrial-like tissue outside the uterine cavity, is a common gynaecological disorder in women of reproductive age, often causing pelvic pain and reduced fertility. Chronic inflammation in the peritoneal environment and defective endometrial protein expression are some of the contributors to the complex pathophysiology of endometriosis. The aim of this work was to study the changes in the transcriptome induced by VEGF-A and partial serum deprivation in primary HEECs, and to investigate biochemical factors associated with subfertility and chronic pelvic pain in endometriosis patients.

    Exposing primary HEECs to VEGF-A, and serum withdrawal was found to regulate transcripts associated with survival, migration, apoptosis and progression through the cell cycle, when assessed using microarray technology and bioinformatic tools. A subset of 88 transcripts was reciprocally regulated under the two experimental conditions; thus probably important in HEEC biology.

    Higher endometrial epithelial staining scores of oestrogen receptor-α and reduced staining of progesterone receptors were seen in subfertile endometriosis patients. Lower levels of the receptivity biomarker leukaemia inhibitory factor (LIF) and its receptor, as well as signs of dysregulated αB-crystallin expression and increased peritoneal fluid concentrations of interleukin (IL)-1α and IL-6 were associated with reduced pregnancy rates.

    Endometriosis patients with chronic pelvic pain had higher levels of vasoactive intestinal peptide (VIP) in eutopic endometria and in endometriotic lesions compared with patients without chronic pain. The presence of chronic pelvic pain was also associated with increased concentrations of VIP and IL-6 in peritoneal fluid.

    The present results may constitute a basis for further investigation of regulatory pathways in endometrial angiogenesis as well as for studies of endometrial receptivity and pain in women with endometriosis.

    List of papers
    1. VEGF-A and Serum Withdrawal Induced Changes in the Transcript Profile in Human Endometrial Endothelial Cells
    Open this publication in new window or tab >>VEGF-A and Serum Withdrawal Induced Changes in the Transcript Profile in Human Endometrial Endothelial Cells
    2010 (English)In: Reproductive Sciences, ISSN 1933-7191, Vol. 17, no 6, 590-611 p.Article in journal (Refereed) Published
    Abstract [en]

    The changes in transcript profile induced by vascular endothelial growth factor (VEGF-A) and serum withdrawal in primary human endometrial endothelial cells (ECs) were investigated using microarrays, gene ontology and pathway analysis. Vascular endothelial growth factor A altered the levels of transcripts involved in angiogenesis, cell survival, and apoptosis, including up-and downregulation of AKT1, BAD, MIF, and IGFBP3 and ANGPT2, respectively. Serum deprivation induced downregulation of cell-cycle-related transcripts such as mitosis regulators CDC20 and SPC25. Of the transcripts regulated by both VEGF-A and partial serum deprivation, remarkably 88 of 89 showed reciprocal regulation (p < 1 x 10(-49)). These are predominantly cell-fate-associated transcripts and this novel observation suggests that endometrial ECs may be particularly dependant on the levels of these transcripts. Our results show that in addition to the known role of VEGF-A as an EC growth and survival promoter, it also regulates apoptosis-related messenger RNAs (mRNAs), many of which were reciprocally regulated following serum withdrawal.

    Keyword
    Angiogenesis, apoptosis, cell survival, endometrial endothelial cells, VEGF-A
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-136555 (URN)10.1177/1933719110364550 (DOI)000277534500011 ()20360594 (PubMedID)
    Available from: 2010-12-14 Created: 2010-12-13 Last updated: 2017-01-31Bibliographically approved
    2. Levels of oestrogen receptor, progesterone receptor and alpha B-crystallin in eutopic endometrium in relation to pregnancy in women with endometriosis
    Open this publication in new window or tab >>Levels of oestrogen receptor, progesterone receptor and alpha B-crystallin in eutopic endometrium in relation to pregnancy in women with endometriosis
    2015 (English)In: Human Fertility, ISSN 1464-7273, Vol. 18, no 1, 30-37 p.Article in journal (Refereed) Published
    Abstract [en]

    Endometriosis affects fertility in many women and may partly be due to decreased endometrial receptivity. Several mechanisms have been suggested, notably, progesterone resistance for which a number of candidate biomarkers have been suggested. Here we demonstrate aberrant levels of steroid hormone receptors and the small heat shock protein αB-crystallin in eutopic endometrial epithelium from 38 women with peritoneal endometriosis diagnosed during investigation for secondary infertility. Spontaneous pregnancies within 1 year after medical and surgical treatment for endometriosis were recorded and semi-quantitative immunohistochemistry data compared between women with endometriosis who did or did not become pregnant and healthy controls. Stronger immunostaining for ER-α was detected in luminal and glandular endometrial epithelium from women with endometriosis who did not become pregnant during the post-treatment observation period versus endometriosis patients who became pregnant and controls. Staining levels of PR and PR-B were lower in patients without subsequent pregnancies than in the two other groups. Endometrial levels of αB-crystallin in endometriosis patients similar to those in controls were strongly correlated with the chance of becoming pregnant, whereas higher or lower levels were not.

    National Category
    Obstetrics, Gynecology and Reproductive Medicine
    Research subject
    Obstetrics and Gynaecology
    Identifiers
    urn:nbn:se:uu:diva-238875 (URN)10.3109/14647273.2014.922705 (DOI)000351604500005 ()24945100 (PubMedID)
    Available from: 2014-12-16 Created: 2014-12-16 Last updated: 2017-01-31Bibliographically approved
    3. Endometrial expression of LIF and its receptor and peritoneal fluid levels of IL-1 alpha and IL-6 in women with endometriosis are associated with the probability of pregnancy
    Open this publication in new window or tab >>Endometrial expression of LIF and its receptor and peritoneal fluid levels of IL-1 alpha and IL-6 in women with endometriosis are associated with the probability of pregnancy
    2015 (English)In: Archives of Gynecology and Obstetrics, ISSN 0932-0067, E-ISSN 1432-0711, Vol. 292, no 2, 429-437 p.Article in journal (Refereed) Published
    Abstract [en]

    To investigate whether eutopic endometrial expression of leukaemia inhibitory factor (LIF), LIF receptor (LIFR) and glycoprotein 130 (gp130) in subfertile women with endometriosis and in healthy controls is related to the probability of spontaneous pregnancy. In addition, we aimed to study peritoneal fluid (PF) levels of interleukin (IL)-1 alpha and IL-6 in the same subsets of women. Eutopic endometrial biopsy and PF samples were taken from patients with rASRM stage I-II endometriosis and healthy controls undergoing laparoscopy. Endometrial LIF, LIFR and gp130 immunostaining and PF levels of IL-1 alpha and IL-6 were assessed. Endometrial biopsy samples were obtained again after postoperative goserelin acetate treatment and on-going pregnancies were registered during a 6-month follow-up period. Reduced endometrial staining of LIF, LIFR and gp130, unaffected by surgery and goserelin, was seen in endometriosis patients without a recorded pregnancy during the study. Elevated PF levels of IL-6 and, in particular, IL-1 alpha were detected in these patients. Reduced eutopic endometrial LIF, LIFR and gp130 protein expression may be associated with subfertility in women with minimal-mild endometriosis. Combined surgical and goserelin acetate treatment does not seem to restore the expression of these members of the IL-6 cytokine superfamily. Elevated peritoneal fluid levels of IL-1 alpha and IL-6 may further contribute to the difficulties of achieving pregnancy in these patients.

    Keyword
    Endometriosis, Endometrium, Interleukin, Leukaemia inhibitory factor, Peritoneal fluid, Infertility
    National Category
    Obstetrics, Gynecology and Reproductive Medicine
    Identifiers
    urn:nbn:se:uu:diva-256979 (URN)10.1007/s00404-015-3626-0 (DOI)000355864000030 ()25631342 (PubMedID)
    Available from: 2015-07-01 Created: 2015-06-29 Last updated: 2017-01-31Bibliographically approved
    4. Vasoactive intestinal peptide is upregulated in women with endometriosis and chronic pelvic pain
    Open this publication in new window or tab >>Vasoactive intestinal peptide is upregulated in women with endometriosis and chronic pelvic pain
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    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Endometriosis, the presence of endometrial-like tissue outside the uterine cavity, is a major cause of chronic pelvic pain in women of reproductive age. The underlying mechanisms of endometriosis-associated pain are mainly attributed to inflammation and an increased presence of sensory nerve fibers in the endometrium, as well as in and around endometriotic lesions. Vasoactive intestinal peptide (VIP), a neuropeptide with immunomodulating and angiogenic properties, is one of the neurotransmitters identified in these nerve fibers and in immune cells.

    In the present study, we investigated VIP mRNA and protein expression in the endometrium and in peritoneal endometriotic lesions from endometriosis patients, with and without chronic pelvic pain (CPP), and controls. Peritoneal fluid (PF) concentrations of VIP and interleukin (IL)-6 were also measured. Our results reveal increased VIP transcript and protein levels in endometrium from endometriosis patients compared with controls. The most pronounced VIP expression is seen in endometrium and ectopic lesions from patients with CPP. In addition, we document an increased microvessel density, a measurement of angiogenic activity, in the endometrium and in endometriosis lesions in the same subset of patients.

    The major finding of the study is the high levels of VIP in eutopic and ectopic endometrium, as well as in PF, in our population of women with endometriosis and CPP. The increased microvessel density and PF concentrations of IL-6 suggest an elevated inflammation in the pelvic microenvironment of these patients. Functional studies are needed to elucidate whether VIP plays a key role in the pathogenesis of endometriosis–associated pain.

    Keyword
    endometriosis, pain, inflammation, microvessel density, angiogenesis, neurotransmitter, endometrium, ectopic lesion, vasoactive intestinal peptide, VIP, interleukin, peritoneal fluid
    National Category
    Obstetrics, Gynecology and Reproductive Medicine
    Research subject
    Obstetrics and Gynaecology
    Identifiers
    urn:nbn:se:uu:diva-314225 (URN)
    Funder
    Swedish Research Council, 8683
    Available from: 2017-01-31 Created: 2017-01-31 Last updated: 2017-01-31
  • Public defence: 2017-03-30 13:15 B42, Uppsala
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Exploring genetic diversity in natural and domestic populations through next generation sequencing2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Studying genetic diversity in natural and domestic populations is of major importance in evolutionary biology. The recent advent of next generation sequencing (NGS) technologies has dramatically changed the scope of these studies, enabling researchers to study genetic diversity in a whole-genome context. This thesis details examples of studies using NGS data to: (i) characterize evolutionary forces shaping the genome of the Atlantic herring, (ii) detect the genetic basis of speciation and domestication in the rabbit, and, (iii) identify mutations associated with skeletal atavism in Shetland ponies.

    The Atlantic herring (Clupea harengus) is the most abundant teleost species inhabiting the North Atlantic. Herring has seasonal reproduction and is adapted to a wide range of salinity (3-35‰) throughout the Baltic Sea and Atlantic Ocean. By using NGS data and whole-genome screening of 20 populations, we revealed the underlying genetic architecture for both adaptive features. Our results demonstrated that differentiated genomic regions have evolved by natural selection and genetic drift has played a subordinate role.

    The European rabbit (Oryctolagus cuniculus) is native to the Iberian Peninsula, where two rabbit subspecies with partial reproductive isolation have evolved. We performed whole genome sequencing to characterize regions of reduced introgression. Our results suggest key role of gene regulation in triggering genetic incompatibilities in the early stages of reproductive isolation. Moreover, we studied gene expression in testis and found misregulation of many genes in backcross progenies that often show impaired male fertility. We also scanned whole genome of wild and domestic populations and identified differentiated regions that were enriched for non-coding conserved elements. Our results indicated that selection has acted on standing genetic variation, particularly targeting genes expressed in the central nervous system. This finding is consistent with the tame behavior present in domestic rabbits, which allows them to survive and reproduce under the stressful non-natural rearing conditions provided by humans.

    In Shetland ponies, abnormally developed ulnae and fibulae characterize a skeletal deformity known as skeletal atavism. To explore the genetic basis of this disease, we scanned the genome using whole genome resequencing data. We identified two partially overlapping large deletions in the pseudoautosomal region (PAR) of the sex chromosomes that remove the entire coding sequence of the SHOX gene and part of CRLF2 gene. Based on this finding, we developed a diagnostic test that can be used as a tool to eradicate this inherited disease in horses.

    List of papers
    1. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
    Open this publication in new window or tab >>Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
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    2012 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 47, 19345-19350 p.Article in journal (Refereed) Published
    Abstract [en]

    The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled amuscle transcriptome and then aligned genomic reads to the transcripts, creating an "exome assembly," capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F-ST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.

    Keyword
    Baltic herring, genetics, population biology
    National Category
    Natural Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-191049 (URN)10.1073/pnas.1216128109 (DOI)000311997200067 ()
    Available from: 2013-01-09 Created: 2013-01-09 Last updated: 2017-02-14Bibliographically approved
    2. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
    Open this publication in new window or tab >>The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
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    2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, e12081Article in journal (Refereed) Published
    National Category
    Genetics and Breeding Evolutionary Biology Genetics Fish and Aquacultural Science
    Identifiers
    urn:nbn:se:uu:diva-279967 (URN)10.7554/eLife.12081 (DOI)000387459700001 ()27138043 (PubMedID)
    Funder
    EU, European Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg Foundation
    Note

    Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan and Nima Rafati contributed equally to this work.

    Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2017-02-08Bibliographically approved
    3. The early stages of species formation revealed by a genomic map of clinal variation across the European rabbit hybrid zone
    Open this publication in new window or tab >>The early stages of species formation revealed by a genomic map of clinal variation across the European rabbit hybrid zone
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    (English)Manuscript (preprint) (Other academic)
    Keyword
    Speciation, reproductive isolation, expression, hybrid
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-314393 (URN)
    Funder
    EU, European Research Council, SFRH/BPD/65464/2009
    Available from: 2017-02-02 Created: 2017-02-02 Last updated: 2017-02-14
    4. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
    Open this publication in new window or tab >>Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
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    2014 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 345, no 6200, 1074-1079 p.Article in journal (Refereed) Published
    Abstract [en]

    The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-232593 (URN)10.1126/science.1253714 (DOI)000340870900046 ()
    Note

    De två sista författarna delar sistaförfattarskapet (Andersson och Lindblad-Toh)

    Available from: 2014-09-24 Created: 2014-09-22 Last updated: 2017-02-14Bibliographically approved
    5. Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
    Open this publication in new window or tab >>Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
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    2016 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, 2213-2223 p.Article in journal (Refereed) Published
    Abstract [en]

    Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. Read depth analysis at these loci revealed homozygosity or compound heterozygosity for two partially overlapping large deletions in the pseudoautosomal region (PAR) of chromosome X/Y in cases but not in the control pool. One of these deletions removes the entire coding region of the SHOX gene and both deletions remove parts of the CRLF2 gene located downstream of SHOX. The horse reference assembly of the PAR is highly fragmented, and in order to characterize this region we sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 1602180 kb and 60280 kb, respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. The result of the present study is consistent with previous studies in humans showing crucial importance of SHOX for normal skeletal development.

    Keyword
    SMRT sequencing, skeletal atavism, SHOX, PAR
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-300547 (URN)10.1534/g3.116.029645 (DOI)000379590200041 ()27207956 (PubMedID)
    Available from: 2016-08-10 Created: 2016-08-09 Last updated: 2017-02-14Bibliographically approved
  • Public defence: 2017-03-30 14:15 Ihresalen, 21-0011, Uppsala
    Nourzaei, Maryam
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Participant Reference in Three Balochi Dialects: Male and Female Narrations of Folktales and Biographical Tales2017Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The aim of the present study is to investigate how men and women in three Iranian Balochi dialects, Coastal Balochi, Koroshi Balochi and Sistani Balochi, refer to 3rd person participants in oral narratives of two genres: folktales and biographical tales. The stories that are analysed were recorded during several field trips to Iran and the approach used is that of Levinsohn (1994, 2015).

    The first part of the dissertation begins with an overview of the Balochi language and its dialects, including a brief presentation of its phonology, and then reviews previous studies of Balochi, before introducing the case system and types of alignment in the three dialects. Chapter 2 introduces the reader to the status of orality in the three dialects, before giving details about the corpus of texts that were analysed. Of particular note is the fact that each story in the corpus was told by both a man and a woman. Chapter 3 examines different approaches to the analysis of participant reference, before comparing those of Gundel et al. and Levinsohn in greater detail.

    The second part of the dissertation applies Levinsohn’s approach to texts in each of the three dialects in turn. Chapters 4–6 identify and analyse the different ways in which the participants in the stories are referred to when the subject remains the same and in three specific situations when the subject changes. This enables default encoding values to be established for each of the four situations. Motivations for over-encoding and, in some situations, under-encoding, are then identified. Chapters 7–9 investigate whether the gender of the storyteller (male versus female) and/or the genre of the story (folktale versus biographical tale) influence the way that the participants are referred to. This leads in chapter 10 to a gender- and genre-based comparison of participant reference across the present dialects.

    Conclusions are presented in chapter 11. In general, the participant reference strategy used was the same in all three dialects, regardless of the gender or the genre. The main exception involved reported conversations in Koroshi Balochi, where the additive enclitic ham was attached to the reference to a subject who responded in line with the contents of the speech reported in the previous sentence. Other variations appeared to depend on the degree to which the storyteller was proficient in his or her art.

    The dissertation concludes with four Appendices. Appendix A presents six texts that were interlinearised using the FLEx programme, while Appendix B consists of participant reference charts of the same texts following Levinsohn’s approach. Appendix C presents details of the case system and alignment for each of the three dialects. Finally, the chart in Appendix D compares the approaches of Levinsohn and of Gundel et al. to participant reference in a specific text. A CD with audio files of the six texts and some photos taken during fieldwork is also available.

  • Public defence: 2017-03-31 09:00 Polhemssalen, Uppsala
    Vorobyev, Alexey
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Applied Mechanics.
    Static and time-dependent mechanical behaviour of preserved archaeological wood: Case studies of the seventeenth century warship Vasa2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Wooden objects have been widely used in the history of humanity and play an important role in our cultural heritage. The preservation of such objects is of great importance and can be a challenging task. This thesis investigates the static and time-dependent mechanical behaviour of archaeological oak wood from the Vasa warship. Characterisation of mechanical properties is necessary for the formulation of a numerical model to design an improved support structure. The ship was impregnated with polyethylene glycol (PEG) for dimensional stabilisation. All elastic engineering constants of the Vasa oak have been identified and compared with those of recent oak by means of the static and dynamic testing. The experiments were done on samples with cubic geometry, which allowed obtaining all elastic constants from a single sample. The usage of cubic samples with orthotropic mechanical properties during compressive experiments was validated with finite-element simulations. The Young's moduli of the Vasa oak in all orthotropic directions were smaller than those for the recent oak. The shear moduli of Vasa oak was determined and verified with the resonant ultrasound spectroscopy. The time-dependent mechanical behaviour of the Vasa oak has been studied. Creep studies were performed in uniaxial compression on the cubic samples in all orthotropic directions. The samples loaded in the longitudinal direction were subjected to different stress levels. A stress level below 15% of the yield stress in the longitudinal direction did not result in non-linear creep with increasing creep rates within the time frame of the tests. The results of the studies in radial and tangential directions showed that creep was dominated by the effect of annual fluctuations in relative humidity and temperature. The weight changes based on annual fluctuations of relative humidity were measured for Vasa oak and recent oak. The Vasa oak showed higher variations due to an increased hygroscopicity which is the result of the impregnation with PEG. In conceiving a full-scale finite-element model of Vasa ship, not only the stress-strain relations of the material but also those of the structural joints are needed. Since the in-situ measurement of joints is not an option, a replica of a section of the ship hull was built and tested mechanically. The load-induced displacements were measured using 3D laser scanning which proved to have advantages to conventional point displacement measurements. The mechanical characteristics of the Vasa oak and joint information presented in this work can be used as input for a finite-element model of the Vasa ship for simulation of static and time-dependent behaviour on a larger scale.

    List of papers
    1. Characterisation of cubic oak specimens from the Vasa ship and recent wood by means of quasi-static loading and resonance ultrasound spectroscopy (RUS)
    Open this publication in new window or tab >>Characterisation of cubic oak specimens from the Vasa ship and recent wood by means of quasi-static loading and resonance ultrasound spectroscopy (RUS)
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    2016 (English)In: Holzforschung, ISSN 0018-3830, E-ISSN 1437-434X, Vol. 70, no 5, 457-465 p.Article in journal (Refereed) Published
    Abstract [en]

    The cylindrical orthotropy, inherent time-dependency response, and variation between and within samples make the stiffness characterisation of wood more challenging than most other structural materials. The purpose of the present study is to compare static loading with resonant ultrasound spectroscopy (RUS) and to investigate how to combine the advantages of each of these two methods to improve the estimation of the full set of elastic parameters of a unique sample. The behavior of wood as an orthotropic mechanical material was quantified by elastic engineering parameters, i.e. Poisson’s ratios and Young’s and shear moduli. Recent and waterlogged archaeological oak impregnated with polyethylene glycol (PEG) from the Vasa warship built in 1628 was in focus. The experimental results were compared, and the difference between RUS and static loading was studied. This study contributes additional information on the influence of PEG and degradation on the elastic engineering parameters of wood. Finally, the shear moduli and Poisson’s ratios were experimentally determined for Vasa archaeological oak for the first time.

    Keyword
    archaeological wood; compression test; cubic samples; elastic constants; oak wood; quasi-static loading; resonant ultrasound spectroscopy (RUS); Vasa ship
    National Category
    Other Materials Engineering
    Identifiers
    urn:nbn:se:uu:diva-264455 (URN)10.1515/hf-2015-0073 (DOI)000375131700009 ()
    External cooperation:
    Available from: 2015-10-12 Created: 2015-10-12 Last updated: 2017-02-01Bibliographically approved
    2. Effects of barrelling during axial compressive tests of cubic samples with isotropic, transversely isotropic and orthotropic elastic properties
    Open this publication in new window or tab >>Effects of barrelling during axial compressive tests of cubic samples with isotropic, transversely isotropic and orthotropic elastic properties
    2016 (English)In: Composites Science And Technology, ISSN 0266-3538, E-ISSN 1879-1050, Vol. 137, 1-8 p.Article in journal (Refereed) Published
    Abstract [en]

    For scarce materials, such as archaeological wood, cubic samples are often used instead of standardised prisms for mechanical tests, since the elasticity can be determined in all three directions within a single sample, but with such samples barrelling makes it difficult to identify the elastic properties. The purpose of the present study is firstly to numerically investigate the effects of barrelling in cubic samples during compressive testing; secondly to numerically investigate and compare barrelling on isotropic and transversely isotropic material parameters; thirdly to compare four strain measurement techniques using digital image correlation, strain gauges and direct readings from the testing machine and finally to estimate the error due to barrelling by implementing the experimentally obtained orthotropic material parameters to the numerical model. The presented relative errors provide information when the perturbation caused by barrelling is negligible or significant for various materials and strain measurements. As an example, the results of compressive tests on waterlogged archaeological oak impregnated with polyethylene glycol are discussed.

    Keyword
    Cubic samples, Compressive testing, Barrelling formation, Wood
    National Category
    Materials Engineering
    Identifiers
    urn:nbn:se:uu:diva-306193 (URN)10.1016/j.compscitech.2016.10.015 (DOI)000389292600001 ()
    Projects
    Vasa support structure
    Funder
    Swedish Research Council FormasVINNOVASwedish Research Council
    Available from: 2016-10-26 Created: 2016-10-26 Last updated: 2017-02-01Bibliographically approved
    3. Relations of density, polyethylene glycol treatment and moisture content with stiffness properties of Vasa oak samples
    Open this publication in new window or tab >>Relations of density, polyethylene glycol treatment and moisture content with stiffness properties of Vasa oak samples
    (English)In: HoltzforschungArticle in journal (Refereed) Accepted
    Abstract [en]

    Treatment with polyethylene glycol (PEG) is the preferred method for conservation of waterlogged archaeological wooden objects. However, PEG impregnation leads to softening and increased hygroscopicity of the material. The present study compiles experimental results concerning the full elastic properties of PEG impregnated archaeological wood from the Vasa ship in relation to its basic density, PEG content (PEGC) and moisture content (MC). The results show a correlation between a more porous microstructure and high PEGC, and consequently, higher MC. The PEG and moisture contribute to the mass of the wooden object as well as to softening of the material, which are undesired properties in a larger load-carrying wooden structure. A compromise between the improved dimensional stability and degradation of mechanical properties should therefore be considered in the conservation of wooden object treated with PEG.

    Keyword
    archaeological wood, PEG impregnation, moisture content (MC), computed tomography, elastic constants, Vasa ship, basic density, Quercus robur
    National Category
    Other Natural Sciences
    Research subject
    Materials Science
    Identifiers
    urn:nbn:se:uu:diva-314263 (URN)
    Projects
    Stötta Vasa
    Funder
    Swedish Research CouncilSwedish Research Council FormasVINNOVA
    Available from: 2017-02-01 Created: 2017-02-01 Last updated: 2017-02-01
    4. Orthotropic creep in polyethylene glycol impregnated archaeological oak from the Vasa ship: Results of creep experiments in a museum-like climate
    Open this publication in new window or tab >>Orthotropic creep in polyethylene glycol impregnated archaeological oak from the Vasa ship: Results of creep experiments in a museum-like climate
    (English)Article in journal (Refereed) Submitted
    Keyword
    Time dependent, Creep, Vasa ship, Cubic samples, Wood, Climate, Polyethylene glycol
    National Category
    Other Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-314264 (URN)
    Available from: 2017-02-01 Created: 2017-02-01 Last updated: 2017-02-01
    5. Evaluation of displacements by means of 3D laser scanning in a mechanically loaded replica of a hull section of the Vasa ship
    Open this publication in new window or tab >>Evaluation of displacements by means of 3D laser scanning in a mechanically loaded replica of a hull section of the Vasa ship
    Show others...
    (English)Article in journal (Refereed) Submitted
    Abstract [en]

    For development of full-scale finite-element models of large objects in culturalheritage it can be useful to mechanically test replicas of key parts toidentify structural properties which would otherwise not be available. Thispaper presents full scale tests on a replica of a section of the hull of the17th century warship Vasa in three load configurations. We focus on determiningdisplacement of the loaded replica from 3D laser measurements.Two measures were found useful, namely (i) 3D displacements at well-definedintersections of the wooden replica, and (ii) normal displacements of largersurfaces. Wood surfaces were preferred to steel parts of the rig since the lattershowed more scatter in displacement values in their point clouds caused bytheir reflective properties. The measurements were verified with draw-wire 

    sensors. Some of these sensors were attached to the steel rig supporting thereplica and, therefore, measured relative displacements. The scanning datawas also useful to quantify the absolute movement of the steel rig supportingthe replica, which improved the precision of the measurements of replicadeformation. Finally, it is discussed how the replica test results can be usedin a model of the complete museum ship.

    Keyword
    3D laser scanning, Structural analysis, Vasa, Wood, Shear
    National Category
    Other Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-314265 (URN)
    Available from: 2017-02-01 Created: 2017-02-01 Last updated: 2017-02-01
  • Public defence: 2017-03-31 09:00 Skoogsalen, Uppsala
    Norlander, Katarina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Otolaryngology and Head and Neck Surgery.
    Exercise-induced laryngeal obstruction: Prevalence, laryngeal findings and evaluation of treatment2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Exercise-induced laryngeal obstruction (EILO) is one of many different causes for adolescents to experience dyspnoea during exercise. Objective exercise-testing with continuous video laryngoscopy is crucial for a correct diagnosis since it is difficult to differentiate EILO from other exercise related conditions in the airways only on the symptomatology. The main symptom in EILO is inspiratory stridor arising from an obstruction at the laryngeal level during ongoing exercise which quickly resolves after the exercise has stopped. EILO is often misdiagnosed as exercise-induced bronchoconstriction (EIB), which is obstruction in the peripheral airways that typically arises after cessation of exercise.

    From a previous survey investigating self-reported exercise-induced dyspnoea in all 12-13-year-old adolescents in Uppsala (n=3,838, response rate 60.2%) a subset of 150 randomly selected adolescents (103 with dyspnoea and 47 controls) performed standardized treadmill exercise-tests for EIB and EILO.

    During the exercise-test for EIB the subjects breathed dry air according to the current recommended guidelines. EIB was defined as a decrease in FEV1 ≥10% from baseline. EILO was diagnosed during a continuous laryngoscopy exercise (CLE) test by use of the CLE-score method and was defined as an obstruction of grade 2 at either glottic or/and supraglottic laryngeal level. The estimated prevalence of EIB in the general population was 19.2% and the estimated prevalence of EILO was 5.7%. No gender differences were detected.

    A diagnostic software program for EILO, EILOMEA, was compared with the CLE-score and the methods were found to be compatible. EILOMEA was used to map and compare laryngeal response patterns in adolescents with exercise-induced dyspnoea (EIB and/or EILO), in adolescents with dyspnoea but without a diagnosis of EIB or EILO, and in healthy controls, all of whom had performed the CLE-test. No differences were seen between the healthy controls and the adolescents with dyspnoea without a diagnosis. Only adolescents diagnosed with EILO showed a significant different laryngeal response pattern which strongly suggests that the diagnostic procedure is reliable.

    In a follow-up study of patients referred for investigation of exercise-induced dyspnoea, we investigated the outcome of surgical vs. conservative treatment of EILO-positive subjects and subjects tested negative for the diagnosis, regarding the level of exercise-induced dyspnoea and physical activity. Surgically treated patients had less breathing problems and were more physically active than both conservatively treated patients and patients who were tested negative.

    List of papers
    1. Comparison between two assessment methods for exercise-induced laryngeal obstructions
    Open this publication in new window or tab >>Comparison between two assessment methods for exercise-induced laryngeal obstructions
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    2016 (English)In: European Archives of Oto-Rhino-Laryngology, ISSN 0937-4477, E-ISSN 1434-4726, Vol. 273, no 2, 425-430 p.Article in journal (Refereed) Published
    Abstract [en]

    Exercise-induced laryngeal obstructions (E-ILOs) are important differential diagnoses to exercise-induced asthma and are diagnosed by the continuous laryngoscopy exercise (CLE) test. There are two different methods for evaluating the severity of E-ILOs using recordings from the CLE test; the CLE score and EILOMEA. The aim of this study was to investigate the consistency between these methods. Using their respective method, the developers of each method evaluated 60 laryngoscopic recordings from patients with different subtypes and various levels of severity of E-ILOs. The CLE score evaluates glottic and supraglottic obstructions on a 4-grade scale. EILOMEA uses software to calculate the obstruction severity on continuous scales from a still frame of the larynx during maximal obstruction giving three parameters reflecting glottic and supraglottic obstruction. The means of the EILOMEA measures differed significantly for CLE score 1 vs. 2 and 2 vs. 3, but not for 0 vs. 1 for glottic as well as supraglottic obstructions. The EILOMEA method does not distinguish between CLE score 0 and 1, but otherwise the methods correlate. Since previous studies have suggested that only CLE scores of 2 and 3 reflect a severity of E-ILOs of clinical importance, this lack of the EILOMEA method is not crucial for a correct medical evaluation.

    Keyword
    E-ILO; Continuous laryngoscopy exercise test; CLE score; EILOMEA; Exercise-induced respiratory difficulties
    National Category
    Otorhinolaryngology
    Identifiers
    urn:nbn:se:uu:diva-266447 (URN)10.1007/s00405-015-3758-7 (DOI)000368990700022 ()26351037 (PubMedID)
    External cooperation:
    Available from: 2015-11-10 Created: 2015-11-10 Last updated: 2017-02-09Bibliographically approved
    2. Prevalence of exercise-induced bronchoconstriction and exercise-induced laryngeal obstruction in a general adolescent population
    Open this publication in new window or tab >>Prevalence of exercise-induced bronchoconstriction and exercise-induced laryngeal obstruction in a general adolescent population
    Show others...
    2015 (English)In: Thorax, ISSN 0040-6376, E-ISSN 1468-3296, Vol. 70, no 1, 57-63 p.Article in journal (Refereed) Published
    Abstract [en]

    Background Exercise-induced respiratory symptoms are common among adolescents. Exercise is a known stimulus for transient narrowing of the airways, such as exercise-induced bronchoconstriction (EIB) and exercise-induced laryngeal obstruction (EILO). Our aim was to investigate the prevalence of EIB and EILO in a general population of adolescents. Methods In this cross-sectional study, a questionnaire on exercise-induced dyspnoea was sent to all adolescents born in 1997 and 1998 in Uppsala, Sweden (n=3838). A random subsample of 146 adolescents (99 with self-reported exercise-induced dyspnoea and 47 without this condition) underwent standardised treadmill exercise tests for EIB and EILO. The exercise test for EIB was performed while breathing dry air; a positive test was defined as a decrease of >= 10% in FEV1 from baseline. EILO was investigated using continuous laryngoscopy during exercise. Results The estimated prevalence of EIB and EILO in the total population was 19.2% and 5.7%, respectively. No gender differences were found. In adolescents with exercise-induced dyspnoea, 39.8% had EIB, 6% had EILO and 4.8% had both conditions. In this group, significantly more boys than girls had neither EIB nor EILO (64.7% vs 38.8%; p=0.026). There were no significant differences in body mass index, lung function, diagnosed asthma or medication between the participants with exercise-induced dyspnoea who had or did not have a positive EIB or EILO test result. Conclusions Both EIB and EILO are common causes of exercise-induced dyspnoea in adolescents. EILO is equally common among girls and boys and can coexist with EIB.

    National Category
    Respiratory Medicine and Allergy
    Identifiers
    urn:nbn:se:uu:diva-241953 (URN)10.1136/thoraxjnl-2014-205738 (DOI)000346338300012 ()
    Note

    Henrik Johansson and Katarina Norlander have shared first authorship on this paper.

    Available from: 2015-01-20 Created: 2015-01-19 Last updated: 2017-02-09Bibliographically approved
    3. Laryngeal findings during exercise in healthy and dyspneic adolescents
    Open this publication in new window or tab >>Laryngeal findings during exercise in healthy and dyspneic adolescents
    (English)Manuscript (preprint) (Other academic)
    National Category
    Otorhinolaryngology
    Identifiers
    urn:nbn:se:uu:diva-315122 (URN)
    Available from: 2017-02-09 Created: 2017-02-09 Last updated: 2017-02-09
    4. Surgical treatment is effective in severe cases of exercise-induced laryngeal obstruction: A follow-up study
    Open this publication in new window or tab >>Surgical treatment is effective in severe cases of exercise-induced laryngeal obstruction: A follow-up study
    Show others...
    2015 (English)In: Acta Oto-Laryngologica, ISSN 0001-6489, E-ISSN 1651-2251, Vol. 135, no 11, 1152-1159 p.Article in journal (Refereed) Published
    Abstract [en]

    Conclusions: Surgery is an effective treatment in severe cases of supraglottic exercise-induced laryngeal obstruction (E-ILO). Conservatively treated subjects and subjects tested negative for E-ILO, who still experience breathing problems 1–3 years after diagnosis, tend to adjust their physical activity to a greater extent than surgically treated subjects. Objective: To investigate how symptoms and level of physical activity change over time in patients with E-ILO who have undergone surgery, patients with E-ILO treated conservatively and patients who tested negative for laryngeal obstruction at continuous laryngoscopy exercise-test (CLE-test). Methods: Patients referred for exercise-induced breathing difficulties answered questionnaires at diagnostic CLE-test and at follow-up. Questions regarded exercise-induced breathing problems, current physical activity level, and medical history of asthma and perennial allergy. Results: Out of 84 invited subjects, 59 (70%) answered both questionnaires. Surgically treated subjects had less breathing problems at follow-up compared with conservatively treated subjects and subjects who tested negative (p < 0.001). None of the surgically treated subjects were less physically active or had changed sport due to exercise-induced dyspnoea, whereas 41.7% of the conservatively treated subjects had made such adjustments (p < 0.001).

    Keyword
    Laryngoplasty; exercice-induced dyspnoea; vocal cord dysfunction; physical activity; E-ILO
    National Category
    Otorhinolaryngology
    Identifiers
    urn:nbn:se:uu:diva-264379 (URN)10.3109/00016489.2015.1062548 (DOI)000369936800010 ()26200564 (PubMedID)
    Available from: 2015-10-10 Created: 2015-10-10 Last updated: 2017-02-09Bibliographically approved
  • Public defence: 2017-03-31 09:15 Auditorium Minus, Gustavianum, Uppsala
    Barradas, Gonçalo
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Psychology.
    A Cross-Cultural Approach to Psychological Mechanisms Underlying Emotional Reactions to Music2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Music plays a crucial role in everyday life by enabling listeners to seek individual emotional experiences. To explain why such emotions occur, we must understand the underlying process that mediates between surface-level features of the music and aroused emotions. This thesis aimed to investigate how musical emotions are mediated by psychological mechanisms from a cross-cultural perspective.

    Study I manipulated four mechanisms by selecting ecologically valid pieces of music that featured information relevant for each mechanism. The results suggested that listeners’ emotions could be successfully predicted based on theoretically based manipulations of target mechanisms. However, Study I featured only listeners from a single culture, neglecting the possible role of contextual and individual factors.

    Study II investigated the prevalence of emotions, mechanisms, and listening motives in a web survey featuring listeners from both individualist and collectivist countries. Results indicated that patterns of prevalence of emotions and mechanisms were quite similar across cultures. Still, Study II found that certain emotions such as nostalgia and the mechanism episodic memory were more frequent in collectivist cultures. In contrast, sadness and the mechanism musical expectancy were more frequent in individualist cultures. Study II also suggested that listening motives were country-specific, rather than subject to the individualism-collectivism dimension.

    Study III explored how particular mechanisms are manifested within a collectivist cultural setting with great potential for deeply felt emotions: fado music in Portugal. Interviews with listeners provided in-depth information on how the cultural context might shape listening motives and emotions. The results revealed that listeners strived for musical experiences that would arouse culturally valued emotions. Music-evoked nostalgia and contextual factors were regarded as important and contributed to an enhanced sense of wellbeing.

    Study IV tested the influence of lyrics on the emotions induced by Swedish and Portuguese pieces of music. The results revealed cross-cultural differences in how lyrics influenced emotions. The differences were not related to the music’s origin, but to the listener’s origin, suggesting that the impact of lyrics depends on the cultural background of the listener.

    In conclusion, the thesis suggests that cultural factors serve as moderators of effects of biologically based mechanisms for emotion induction.

    List of papers
    1. From sound to significance: Exploring the mechanisms underlying emotional reactions to music
    Open this publication in new window or tab >>From sound to significance: Exploring the mechanisms underlying emotional reactions to music
    2015 (English)In: American Journal of Psychology, ISSN 0002-9556, E-ISSN 1939-8298, Vol. 128, no 3, 281-304 p.Article in journal (Refereed) Published
    Abstract [en]

    A common approach to studying emotional reactions to music is to attempt to obtain direct links between musical surface features such as tempo and a listener's responses. However, such an analysis ultimately fails to explain why emotions are aroused in the listener. In this article we explore an alternative approach, which aims to account for musical emotions in terms of a set of psychological mechanisms that are activated by different types of information in a musical event. This approach was tested in 4 experiments that manipulated 4 mechanisms (brain stem reflex, contagion, episodic memory, musical expectancy) by selecting existing musical pieces that featured information relevant for each mechanism. The excerpts were played to 60 listeners, who were asked to rate their felt emotions on 15 scales. Skin conductance levels and facial expressions were measured, and listeners reported subjective impressions of relevance to specific mechanisms. Results indicated that the target mechanism conditions evoked emotions largely as predicted by a multimechanism framework and that mostly similar effects occurred across the experiments that included different pieces of music. We conclude that a satisfactory account of musical emotions requires consideration of how musical features and responses are mediated by a range of underlying mechanisms.

    National Category
    Psychology
    Identifiers
    urn:nbn:se:uu:diva-261219 (URN)000359014200001 ()
    Funder
    Swedish Research Council
    Available from: 2015-09-08 Created: 2015-08-31 Last updated: 2017-02-07
    2. Prevalence of emotions, mechanisms, and motives in music listening: A comparison of individualist and collectivist cultures
    Open this publication in new window or tab >>Prevalence of emotions, mechanisms, and motives in music listening: A comparison of individualist and collectivist cultures
    2016 (English)In: Psychomusicology, ISSN 0275-3987, E-ISSN 2162-1535Article in journal (Refereed) Accepted
    National Category
    Psychology
    Identifiers
    urn:nbn:se:uu:diva-310598 (URN)
    Available from: 2016-12-16 Created: 2016-12-16 Last updated: 2017-02-07
    3. Understanding nostalgia and sadness in fado music: A qualitative approach to the psychological mechanisms underlying musical emotions
    Open this publication in new window or tab >>Understanding nostalgia and sadness in fado music: A qualitative approach to the psychological mechanisms underlying musical emotions
    (English)Article in journal (Other academic) Submitted
    Keyword
    Fado music, Nostalgia, Psychological mechanisms, Qualitative method, Sadness, Wellbeing
    National Category
    Psychology
    Identifiers
    urn:nbn:se:uu:diva-312498 (URN)
    Available from: 2017-01-27 Created: 2017-01-10 Last updated: 2017-02-07
    4. When words matter: Lyrics and their relationship to musical emotions in Portugal and Sweden
    Open this publication in new window or tab >>When words matter: Lyrics and their relationship to musical emotions in Portugal and Sweden
    (English)Manuscript (preprint) (Other academic)
    Keyword
    Cross-cultural comparison, Emotion, Lyrics, Mechanisms, Music
    National Category
    Psychology
    Identifiers
    urn:nbn:se:uu:diva-312500 (URN)
    Available from: 2017-01-27 Created: 2017-01-10 Last updated: 2017-02-07
  • Public defence: 2017-03-31 10:00 Lindahlsalen, Uppsala
    Chen, Donglei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The Origin of Tooth Replacement: Three-dimensional Synchrotron Histology Visualizes the Dental Development of Silurian Stem Osteichthyans2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Mechanisms of tooth replacement distribute incongruently among extant gnathostomes (jawed vertebrates): a permanent tooth-generating dental lamina exists in chondrichthyans (cartilaginous fish) and tetrapods but not teleosts, whereas tooth shedding by basal hard tissue resorption occurs in tetrapods and teleosts but not chondrichthyans. Theories about the evolution of tooth development have been biased towards the chondrichthyan conveyor-belt replacement, since there has been no fossil evidence for the origin of osteichthyan (bony fish and tetrapods) tooth replacement until now. 3D virtual dissections with submicron-scale resolution, based on propagation phase contrast synchrotron microtomography (PPC-SRµCT), reveal the growth history of the dentitions of Andreolepis and Lophosteus, 423-Myr-old Silurian stem osteichthyans close to the common ancestor of tetrapods and teleosts. Their marginal jawbones and “tooth cushions” (possible homologues of coronoids) shed teeth by in situ cyclic basal resorption, the earliest examples of osteichthyan-style tooth replacement. The replacement cycles were site-autonomic, and occurred in broad irregular multi-row tooth fields, including at sites separated from the margin of the bone by intervening teeth, showing that the production of replacement teeth did not occur in a single deep dental lamina, but in pockets associated with each tooth, as in many teleosts. It suggests that the functionally and anatomically similar laminae of chondrichthyans and tetrapods are convergent. The marginal jaw bones of both genera carry an initial non-shedding dentition arranged in alternate transverse files, labial to the shedding tooth field, overgrown by later dermal ornament and probably not belonging to the oral domain, but bearing in vivo biting damage showing that they functioned as teeth. The most lingual of these odontodes have been resorbed apically and are overlain by shedding teeth. The first-generation teeth on the tooth cushions display basal resorption in Andreolepis, but semi-basal resorption in Lophosteus. The latter leaves a basal dentine ring from each tooth, implying only odontoclasts are involved in the semi-basal resorption, which is probably the first step towards evolving a site-specific resorption. The polarized displacement of each generation of resorption surfaces reflects the fact that the cyclic replacement, as well as the sequential addition of tooth sites, is closely related to bone growth. Resorption surfaces and growth arrest surfaces also record the life history and the replacement rate. These data provide unique insights into the origin of osteichthyan tooth replacement.

    List of papers
    1. The stem osteichthyan Andreolepis and the origin of tooth replacement
    Open this publication in new window or tab >>The stem osteichthyan Andreolepis and the origin of tooth replacement
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    2016 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 539, no 7628, 237-+ p.Article in journal (Refereed) Published
    Abstract [en]

    The teeth of gnathostomes (jawed vertebrates) show rigidly patterned, unidirectional replacement that may or may not be associated with a shedding mechanism. These mechanisms, which are critical for the maintenance of the dentition, are incongruently distributed among extant gnathostomes. Although a permanent tooth-generating dental lamina is present in all chondrichthyans, many tetrapods and some teleosts, it is absent in the non-teleost actinopterygians. Tooth-shedding by basal hard tissue resorption occurs in most osteichthyans (including tetrapods) but not in chondrichthyans. Here we report a three-dimensional virtual dissection of the dentition of a 424-million-year-old stem osteichthyan, Andreolepis hedei, using propagation phase-contrast synchrotron microtomography, with a reconstruction of its growth history. Andreolepis, close to the common ancestor of all extant osteichthyans, shed its teeth by basal resorption but probably lacked a permanent dental lamina. This is the earliest documented instance of resorptive tooth shedding and may represent the primitive osteichthyan mode of tooth replacement.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-310754 (URN)10.1038/nature19812 (DOI)000387318500034 ()27750278 (PubMedID)
    Funder
    EU, European Research Council, 233111Knut and Alice Wallenberg Foundation
    Available from: 2016-12-20 Created: 2016-12-19 Last updated: 2017-02-22Bibliographically approved
    2. Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 
    Open this publication in new window or tab >>Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 
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    (English)In: Royal Society Open Science, E-ISSN 2054-5703Article in journal (Refereed) Accepted
    Abstract [en]

    The numerous cushion-shaped tooth-bearing plates attributed to the stem-group osteichthyan Lophosteus superbus, which are argued here to represent the ancient form of inner dental arcade, display a unique and presumably primitive way of tooth shedding by basal hard tissue resorption. They carry regularly spaced, recumbent, gently recurved teeth arranged in transverse tooth files that diverge towards the lingual margin of the cushion. Three-dimensional (3D) reconstruction from propagation phase contrast synchrotron microtomography (PPC-SRμCT) reveals remnants of the first-generation teeth embedded in the basal plate that have never been discerned in any taxa. These teeth were shed by semi-basal resorption with the periphery of their bases retained as dentine rings. The rings are highly overlapped, which evidences tooth shedding prior to adding the next first-generation tooth. Later teeth at the same sites underwent cyclical replacing and shedding through basal resorption, producing stacks of buried resorption surfaces separated by bone of attachment. The number and spatial arrangement of resorption surfaces elucidates that basal resorption of replacement teeth had taken place at the older tooth sites before the addition of the youngest first-generation teeth at the lingual margin. Thus the replacement tooth buds cannot have been generated by a single permanent dental lamina, but must have arisen either from successional dental laminae associated with the predecessor teeth, or directly from the dental epithelium of these teeth. The virtual histological dissection of these Late Silurian microfossils broadens our understanding of the development of the gnathostome dental systems and the acquisition of the osteichthyan-type of tooth replacement. 

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315882 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
    3. Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.
    Open this publication in new window or tab >>Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315883 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
    4. The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.
    Open this publication in new window or tab >>The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315884 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
  • Public defence: 2017-03-31 13:15 Häggsalen, Uppsala
    Ren, Yi
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Annealing of Cu2ZnSn(S,Se)4 Thin Films: A Study of Secondary Compounds and Their Effects on Solar Cells2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Kesterite Cu2ZnSnS4 (CZTS) is interesting as a sustainable photovoltaic technology due to its earth-abundant elements and suitable semiconducting properties. To date, a record efficiency of 12.6% has been achieved but further improvements are required to reach high efficiency for industrial implementation. Among the limiting issues is the understanding of the annealing process, which is crucial in promoting high material quality. In particular, the knowledge of the effects of segregated secondary compounds on solar cell performance is lacking.

    In contrast to formation of ZnS particles throughout CZTS film, it is notable that SnS forms and usually segregates on the CZTS top and rear surfaces. The influence of SnS on CZTS solar cells was studied by electron beam induced current measurements. It is found that SnS presence on the CZTS surfacecan introduce “dead area”, whereas it seems beneficial for solar cell current when accumulates on the CZTS rear. For SnS passivation and from investigation of the passivation effect from an Al2O3 thin layer at the CZTS rear, improvement in overall device performance could not be demonstrated, due to either poor CZTS bulk or non-optimal device structure. The limitation in CZTS bulk quality was shown from a thickness study where carrier collection saturated already about 700-1000 nm CZTS thickness.

    Formation of SnS alongside CZTS implies the anneal is limited by a deficient sulfur partial pressure (PS2). By looking into Sn-S phase transformations in SnS2 films after annealing, we find that PS2 drops rapidly over the annealing time, which could be well-correlated to a series of changes in CZTS material quality including secondary phase formations and defect modifications. It is shown that annealing CZTS under sufficiently high PS2 is critical for CZTS solar cells with high open circuit voltage (upto 783mV was reached), possibly due to the defect modification.

    Besides SnS, it is observed that NaxS compounds are also readily formed on CZTS surfaces, due to Na diffusion from the glass substrate during annealing. NaxS negatively affects the formation of the CdS/CZTS interface during chemical bath deposition. It can be removed by an oxidation process or wet chemical etching.

    List of papers
    1. Reactively sputtered films in the CuxS–ZnS–SnSy system: From metastability to equilibrium
    Open this publication in new window or tab >>Reactively sputtered films in the CuxS–ZnS–SnSy system: From metastability to equilibrium
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    2015 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 582, 208-214 p.Article in journal, Meeting abstract (Refereed) Published
    Abstract [en]

    Cu2ZnSnS4 is a promising photovoltaic absorber containing earth abundant elements. Using a two stage process, low temperature reactive co-sputtering followed by heat treatment, we have previously achieved a 7.9% efficient solar cell. Because the sputtered precursors contain non-equilibrium phases with unusual crystal structures, it is crucial to understand their nature and their conversion into Cu2ZnSnS4 (and secondary phases) during heat treatment. In this study, we report phase analysis of reactively sputtered binary and ternary sulfides in the CuxS–ZnS–SnSy system before and after annealing. In the as deposited films, Raman spectroscopy with 532 and 325 nm excitation wavelengths reveals expected phases for the binaries (CuS, ZnS and SnS2) and the ternary (Cu2SnS3), and unique metastable phases for the Cu–Zn–S and Zn–Sn–S precursors. Upon annealing, the non-equilibrium phases disappear, accompanied by additional chemical changes. Excess S content in the films is removed, and in the Sn–S and Zn–Sn–S films, further S loss from decomposition of SnSx (x > 1) and CuS respectively generates SnS and CuxS (x > 1). Due to the presence of SnS vapor, Cu2ZnSnS4 is generated from the Cu–Zn–S precursor. Additionally, the range of sulfur partial pressure in the annealing process is estimated according to the temperature–pressure phase diagram. This gives us useful insight allowing better control of annealing conditions.

    Keyword
    Copper zinc tin sulfide; Thin film solar cells; Reactive sputtering; Secondary phases; Raman scattering; X-ray diffraction; Kesterite
    National Category
    Other Materials Engineering Other Electrical Engineering, Electronic Engineering, Information Engineering
    Research subject
    Engineering Science with specialization in Electronics
    Identifiers
    urn:nbn:se:uu:diva-236734 (URN)10.1016/j.tsf.2014.10.076 (DOI)000352225900045 ()
    Funder
    EU, FP7, Seventh Framework Programme, 316488 (KESTCELLS)
    Available from: 2014-11-21 Created: 2014-11-21 Last updated: 2017-02-07Bibliographically approved
    2. Influence of the Cu2ZnSnS4 absorber thickness on thin film solar cells
    Open this publication in new window or tab >>Influence of the Cu2ZnSnS4 absorber thickness on thin film solar cells
    2015 (English)In: Physica status solidi. A, Applied research, ISSN 0031-8965, E-ISSN 1521-396XArticle in journal (Refereed) Published
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-265420 (URN)DOI: 10.1002/pssa.201532311 (DOI)
    Available from: 2015-10-28 Created: 2015-10-28 Last updated: 2017-02-07
    3. Investigation of the SnS/Cu2ZnSnS4 interfaces in Kesterite Thin Film Solar Cells
    Open this publication in new window or tab >>Investigation of the SnS/Cu2ZnSnS4 interfaces in Kesterite Thin Film Solar Cells
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-314941 (URN)
    Available from: 2017-02-07 Created: 2017-02-07 Last updated: 2017-02-07
    4. Rear Surface Optimization of CZTS Solar Cells by Use of a Passivation Layer With Nanosized Point Openings
    Open this publication in new window or tab >>Rear Surface Optimization of CZTS Solar Cells by Use of a Passivation Layer With Nanosized Point Openings
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    2016 (English)In: IEEE Journal of Photovoltaics, ISSN 2156-3381, E-ISSN 2156-3403, Vol. 6, no 1, 332-336 p.Article in journal (Refereed) Published
    Abstract [en]

    Previously, an innovative way to reduce rear interface recombination in Cu(In, Ga)(S, Se)(2) (CIGSSe) solar cells has been successfully developed. In this work, this concept is established in Cu-2(Zn, Sn)(S, Se)(4) (CZTSSe) cells to demonstrate its potential for other thin-film technologies. Therefore, ultrathin CZTS cells with an Al2O3 rear surface passivation layer having nanosized point openings are fabricated. The results indicate that introducing such a passivation layer can have a positive impact on open-circuit voltage (V-OC; +17% rel.), short-circuit current (J(SC); +5% rel.), and fill factor (FF; +9% rel.), compared with corresponding unpassivated cells. Hence, a promising efficiency improvement of 32% rel. is obtained for the rear passivated cells.

    Keyword
    Aluminum oxide, Cu(In, Ga)(S, Se)(2), Cu-2(Zn, Sn)(S, Se)(4), nanosized point contacts, solar cells, surface passivation layer, thin-film
    National Category
    Environmental Engineering
    Identifiers
    urn:nbn:se:uu:diva-274909 (URN)10.1109/JPHOTOV.2015.2496864 (DOI)000367251900048 ()
    Funder
    Swedish Research CouncilSwedish Energy AgencyEU, FP7, Seventh Framework Programme, 300998EU, FP7, Seventh Framework Programme, 327367
    Available from: 2016-01-27 Created: 2016-01-26 Last updated: 2017-02-07Bibliographically approved
    5. Evolution of Cu2ZnSnS4 in non-equilibrium thermal processing with Quasi-in-situ Monitoring of Sulfur Partial Pressure
    Open this publication in new window or tab >>Evolution of Cu2ZnSnS4 in non-equilibrium thermal processing with Quasi-in-situ Monitoring of Sulfur Partial Pressure
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-314940 (URN)
    Available from: 2017-02-07 Created: 2017-02-07 Last updated: 2017-02-07
    6. Evolution of Na-S(-O) compounds on the Cu2ZnSnS4 absorber surface and their effects on CdS thin film growth
    Open this publication in new window or tab >>Evolution of Na-S(-O) compounds on the Cu2ZnSnS4 absorber surface and their effects on CdS thin film growth
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    2016 (English)In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 8, no 28, 18600-18607 p.Article in journal (Refereed) Published
    Abstract [en]

    Formation of Na-containing surface compounds is an important phenomenon in the Cu2ZnSnS4 (CZTS) quaternary material synthesis for solar cell applications. Still, identification of these compounds and the understanding of their potential influence on buffer layer growth and device performance are scarce. In this work, we discovered that the evolution of Na-S(-O) compounds on the CZTS surface substantially affect the solution/CZTS interface during the chemical bath deposition of CdS buffer film. We showed that Na2S negatively affects the growth of CdS, and that this compound is likely to form on the CZTS surface after annealing. It was also demonstrated that the Na2S compound can be oxidized to Na2SO4 by air exposure of the annealed CZTS surface or be removed using water dipping instead of the commonly used KCN etching process, resulting in significantly better quality of the CdS layer. Lastly, 6.5% CZTS solar cells were fabricated with air exposure treatment without incorporation of the KCN etching process. This work provides new insight into the growth of the CdS/CZTS interface for solar cell applications and opens new possibilities for improving likewise Cd-free buffer materials that are grown with a similar chemical bath deposition process.

    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-298673 (URN)10.1021/acsami.6b04978 (DOI)000380298400096 ()27356214 (PubMedID)
    Funder
    EU, FP7, Seventh Framework Programme, 316488Knut and Alice Wallenberg FoundationSwedish Foundation for Strategic Research Swedish Research Council
    Available from: 2016-07-06 Created: 2016-07-06 Last updated: 2017-02-07Bibliographically approved
    7. Surface modification through air annealing Cu2ZnSn(S,Se)4 absorbers
    Open this publication in new window or tab >>Surface modification through air annealing Cu2ZnSn(S,Se)4 absorbers
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    2016 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731Article in journal (Refereed) In press
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-314952 (URN)
    Available from: 2017-02-07 Created: 2017-02-07 Last updated: 2017-02-07
  • Public defence: 2017-04-07 09:15 Friessalen, Uppsala
    Marklund, Maria H. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. School of Biological Sciences and The Environment Institute, University of Adelaide, North Terrace, SA 5005, Australia.
    The influence of trophic polymorphisms on habitat coupling in aquatic food webs2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Trophic cascades, together with other indirect interactions are important aspects in shaping the composition and abundance of species in the food web. Theoretically, movement of energy between systems, and coupling between habitats by mobile predators have been suggested as being important for food web stability and evenness. Individual diet specialisations have been shown to be widespread in many animal taxa. Although not widely studied, some studies have indicated that mobile predators that display individual specialisations, may have a reduced ability to couple habitats.

    In this thesis, by using field studies and an experimental study, my aim was to assess the individual specialisation displayed by Eurasian perch (Perca fluviatilis) and its influence on the ability of the perch to couple habitats. In the experiment, we also investigated the effect of habitat coupling, or the lack of habitat coupling, on the dynamics and stability of the resources in the ecosystem.

    We show that habitat diversity and resource availability influenced perch individual specialisation and morphological variation. We found that the perch total niche width decreased with decreasing habitat switching ability. We demonstrate asymmetrical habitat coupling ability in perch across pelagic and littoral habitats, providing evidence that not all individuals within a species respond in the same way when it comes to spatial coupling and thereby providing stability within a food web.

    Our results expand on previous work and suggest that habitat coupling ability can influence individual specialisations and niche width. Furthermore, we show the importance of individual specialisations in relation to habitat coupling. Finally, we provide evidence for the theory that a food web dominated by a food specialist should exhibit more variable resource dynamics than a food web dominated by a generalist predator by showing a greater indirect effect of predation on the phytoplankton levels when no habitat coupling occurs. While many models and theoretical concepts have proposed a stabilising effect of cross movement of energy and mobile predators, little empirical evidence exists that confirms this mechanism.

    In conclusion, my thesis gives some support for the theoretical predictions that habitats coupled by a generalist predator should be more stable.

    List of papers
    1. The influence of habitat accessibility on the dietary and morphological specialisation of an aquatic top predator
    Open this publication in new window or tab >>The influence of habitat accessibility on the dietary and morphological specialisation of an aquatic top predator
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-315718 (URN)
    Available from: 2017-02-20 Created: 2017-02-20 Last updated: 2017-02-20
    2. Habitat coupling mediates trophic cascades in an aquatic community
    Open this publication in new window or tab >>Habitat coupling mediates trophic cascades in an aquatic community
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-315717 (URN)
    Available from: 2017-02-20 Created: 2017-02-20 Last updated: 2017-02-20
    3. Combining resource use assessment techniques reveals trade-offs in trophic specialization of polymorphic perch
    Open this publication in new window or tab >>Combining resource use assessment techniques reveals trade-offs in trophic specialization of polymorphic perch
    2016 (English)In: Ecosphere, ISSN 2150-8925, E-ISSN 2150-8925, Vol. 7, no 8, e01387Article in journal (Refereed) Published
    Abstract [en]

    Trophic polymorphism has found to be common in many taxa and is a suggested mechanism of ecological speciation. To characterize the trophic linkages of specific morphotypes of organisms as well as a time-integrated niche use, several methods are available. In this study, we present data of multiple techniques to investigate the trophic divergence of Eurasian perch (Perca fluviatilis) that displays well-studied trophic polymorphism associated with littoral and pelagic habitats in lakes. We combined bulk stable isotope and fatty acid analyses on the muscle tissue of perch from three different lakes in Sweden with analyses of stomach content. By comparing the three methods, we aimed at providing a broad and highly resolved picture on the trophic divergence in freshwater fish. The degree in morphological divergence varied between perch caught in the three different lakes. Generally, perch caught in the pelagic zone were more streamlined compared to the ones caught in the littoral zone that had a deeper body, as shown by geometric morphometrics. The three diet assessment methods revealed different levels of information. Data on stomach content showed some preferences for specific dietary items in littoral and pelagic perch, but general trophic specialization could not be concluded due to the small sample size. Analyses of delta C-13 and delta N-15, however, confirmed these results as a long-term pattern connected to specific habitat use in two of the three lakes. Fatty acid signatures of perch reflected partly those of the prey items of the specific habitats. Although the proportions of the essential fatty acid 22:6n-3 were lower in littoral resources, the proportions in littoral fish were similar to the ones caught in the pelagic zone. We concluded that although a fundamental contribution from littoral resources exists in littoral phenotypes, a minor reliance on pelagic prey items is obviously needed to provide essential compounds. Thus, by combining the methods to characterize direct resource use (i.e., stomach analyses) with others that utilize trophic biomarkers (i.e., analyses of stable isotopes and fatty acids), we were able to illustrate the degree of variation in trophic divergence of perch but also shed some light on potential trade-offs that are related to resource specialization in freshwater fish.

    Keyword
    carbon stable isotopes; ecological speciation; fatty acid analysis; geometric morphometrics; Perca fluviatilis; resource polymorphism; Special Feature; Biomarkers in Trophic Ecology; stomach content analysis
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-264657 (URN)10.1002/ecs2.1387 (DOI)000387208900001 ()
    Available from: 2015-10-15 Created: 2015-10-15 Last updated: 2017-02-20Bibliographically approved
    4. Asymmetrical habitat coupling of a top predator
    Open this publication in new window or tab >>Asymmetrical habitat coupling of a top predator
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-315719 (URN)
    Available from: 2017-02-20 Created: 2017-02-20 Last updated: 2017-02-20
  • Public defence: 2017-04-07 09:15 B21, Uppsala
    Blixt, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Neuroscience.
    Keeping up with retinal photoreceptors and horizontal cells: Labelling and mapping of cells in the normal and diseased embryonic chicken retina2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The childhood eye cancer retinoblastoma originates from the retina and its development is initiated while the foetus is in the uterus. Retinoblastoma has a reported incidence of 1 in 15-18 000 live births, and approximately 90% of all patients are diagnosed before the age of 5. The occurrence of retinoblastoma is usually detected by the parents and the most frequent symptoms are leukocoria (white pupillary reflex), strabismus (squinting) or if the child complains of visual problems. Retinoblastoma is diagnosed by examination under anaesthesia and documentation by RetCam. It is treated with various cytostatic agents, or by laser. If the treatment is unsuccessful, or there is a risk that the tumour cells will spread and form metastases, the eye is removed.

    Previous studies have indicated that the cell type from which the tumour arises, the cell-of-origin, may be the cone photoreceptors and/or their immediate interneuron, the horizontal cells. Determining the cell-of-origin for retinoblastoma is an important goal, however, understanding the molecular mechanisms that distinguish the photoreceptors and the horizontal cells from the other retinal cells may prove just as important for understanding this disease.

    The aim of my project has been to develop, optimise and validate methods to label, map and target expression to photoreceptors and horizontal cells in the chicken embryonic retina. We have successfully established several methods that test the expression pattern of conserved, regulatory DNA sequences, and have performed short- and long-term expression of various genes that have been reported to be involved in cell cycle regulation and cell fate determination. One of my most important findings was that a region from the RXRγ gene allowed us to specifically target the photoreceptors and horizontal cells. Our previous knowledge, together with the newly established tools, puts us an important step closer towards understanding the development and behaviour of the retinal photoreceptors and horizontal cells, however, further studies are of course needed.

    List of papers
    1. Whole Retinal Explants from Chicken Embryos for Electroporation and Chemical Reagent Treatments
    Open this publication in new window or tab >>Whole Retinal Explants from Chicken Embryos for Electroporation and Chemical Reagent Treatments
    2015 (English)In: Journal of Visualized Experiments, ISSN 1940-087X, E-ISSN 1940-087X, no 103, e53202Article in journal (Refereed) Published
    Abstract [en]

    The retina is a good model for the developing central nervous system. The large size of the eye and most importantly the accessibility for experimental manipulations in ovo/in vivo makes the chicken embryonic retina a versatile and very efficient experimental model. Although the chicken retina is easy to target in ovo by intraocular injections or electroporation, the effective and exact concentration of the reagents within the retina may be difficult to fully control. This may be due to variations of the exact injection site, leakage from the eye or uneven diffusion of the substances. Furthermore, the frequency of malformations and mortality after invasive manipulations such as electroporation is rather high. This protocol describes an ex ovo technique for culturing whole retinal explants from chicken embryos and provides a method for controlled exposure of the retina to reagents. The protocol describes how to dissect, experimentally manipulate, and culture whole retinal explants from chicken embryos. The explants can be cultured for approximately 24 hr and be subjected to different manipulations such as electroporation. The major advantages are that the experiment is not dependent on the survival of the embryo and that the concentration of the introduced reagent can be varied and controlled in order to determine and optimize the effective concentration. Furthermore, the technique is rapid, cheap and together with its high experimental success rate, it ensures reproducible results. It should be emphasized that it serves as an excellent complement to experiments performed in ovo.

    Keyword
    Developmental Biology, Issue 103, Culture, explant, eye, inhibitors, in ovo, in vitro, plasmid
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-268713 (URN)10.3791/53202 (DOI)000364222300048 ()
    Funder
    Swedish Childhood Cancer Foundation, PR2013-0104Swedish Research Council, 12187-18-3
    Available from: 2015-12-09 Created: 2015-12-09 Last updated: 2017-02-17
    2. The p53 co-activator Zac1 neither induces cell cycle arrest nor apoptosis in chicken Lim1 horizontal progenitor cells
    Open this publication in new window or tab >>The p53 co-activator Zac1 neither induces cell cycle arrest nor apoptosis in chicken Lim1 horizontal progenitor cells
    2015 (English)In: Cell Death Discovery, ISSN 2058-7716, Vol. 1, 15023Article in journal (Refereed) Published
    Abstract [en]

    Chicken horizontal progenitor cells are able to enter their final mitosis even in the presence of DNA damage despite having a functional p53-p21 system. This suggests that they are resistant to DNA damage and that the regulation of the final cell cycle of horizontal progenitor cells is independent of the p53-p21 system. The activity of p53 is regulated by positive and negative modulators, including the zinc finger containing transcription factor Zac1 (zinc finger protein that regulates apoptosis and cell cycle arrest). Zac1 interacts with and enhances the activity of p53, thereby inducing cell cycle arrest and apoptosis. In this work, we use a gain-of-function assay in which mouse Zac1 (mZac1) is overexpressed in chicken retinal progenitor cells to study the effect on the final cell cycle of horizontal progenitor cells. The results showed that overexpression of mZac1 induced expression of p21 in a p53-dependent way and arrested the cell cycle as well as triggered apoptosis in chicken non-horizontal retinal progenitor cells. The negative regulation of the cell cycle by mZac1 is consistent with its proposed role as a tumour-suppressor gene. However, the horizontal cells were not affected by mZac1 overexpression. They progressed into S- and late G2/M-phase despite overexpression of mZac1. The inability of mZac1 to arrest the cell cycle in horizontal progenitor cells support the notion that the horizontal cells are less sensitive to events that triggers the p53 system during their terminal and neurogenic cell cycle, compared with other retinal cells. These properties are associated with a cell that has a propensity to become neoplastic and thus with a cell that may develop retinoblastoma.

    Place, publisher, year, edition, pages
    Nature Publishing Group, 2015
    National Category
    Neurology Developmental Biology
    Research subject
    Neurology
    Identifiers
    urn:nbn:se:uu:diva-279034 (URN)10.1038/cddiscovery.2015.23 (DOI)
    Available from: 2016-02-28 Created: 2016-02-28 Last updated: 2017-02-17Bibliographically approved
    3. The zinc finger gene Nolz1 is controlled by retinoic acid and regulates the formation of chicken retinal progenitors and Lim3 expressing bipolar cells
    Open this publication in new window or tab >>The zinc finger gene Nolz1 is controlled by retinoic acid and regulates the formation of chicken retinal progenitors and Lim3 expressing bipolar cells
    (English)Article in journal (Refereed) Submitted
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-315608 (URN)
    Available from: 2017-02-16 Created: 2017-02-16 Last updated: 2017-02-17
    4. A regulatory sequence from the retinoid X receptor gamma gene directs expression to horizontal cells and photoreceptors in the embryonic chicken retina
    Open this publication in new window or tab >>A regulatory sequence from the retinoid X receptor gamma gene directs expression to horizontal cells and photoreceptors in the embryonic chicken retina
    2016 (English)In: Molecular Vision, ISSN 1090-0535, E-ISSN 1090-0535, Vol. 22, 1405-1420 p.Article in journal (Refereed) Published
    Abstract [en]

    PURPOSE: Combining techniques of episomal vector gene-specific Cre expression and genomic integration using the piggyBac transposon system enables studies of gene expression-specific cell lineage tracing in the chicken retina. In this work, we aimed to target the retinal horizontal cell progenitors. METHODS: A 208 bp gene regulatory sequence from the chicken retinoid X receptor gammagene (RXRgamma208) was used to drive Cre expression. RXRgamma is expressed in progenitors and photoreceptors during development. The vector was combined with a piggyBac "donor" vector containing a floxed STOP sequence followed by enhanced green fluorescent protein (EGFP), as well as a piggyBac helper vector for efficient integration into the host cell genome. The vectors were introduced into the embryonic chicken retina with in ovo electroporation. Tissue electroporation targets specific developmental time points and in specific structures. RESULTS: Cells that drove Cre expression from the regulatory RXRgamma208 sequence excised the floxed STOP-sequence and expressed GFP. The approach generated a stable lineage with robust expression of GFP in retinal cells that have activated transcription from the RXRgamma208 sequence. Furthermore, GFP was expressed in cells that express horizontal or photoreceptor markers when electroporation was performed between developmental stages 22 and 28. Electroporation of a stage 12 optic cup gave multiple cell types in accordance with RXRgamma gene expression in the early retina. CONCLUSIONS: In this study, we describe an easy, cost-effective, and time-efficient method for testing regulatory sequences in general. More specifically, our results open up the possibility for further studies of the RXRgamma-gene regulatory network governing the formation of photoreceptor and horizontal cells. In addition, the method presents approaches to target the expression of effector genes, such as regulators of cell fate or cell cycle progression, to these cells and their progenitor.

    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:uu:diva-313804 (URN)000393909400001 ()28003731 (PubMedID)
    Funder
    Swedish Research Council, MH521.2013.3346Swedish Childhood Cancer Foundation
    Available from: 2017-01-24 Created: 2017-01-24 Last updated: 2017-03-17Bibliographically approved
    5. Overexpression of MYCN in the developing chicken retina increases the generation of photoreceptor cells
    Open this publication in new window or tab >>Overexpression of MYCN in the developing chicken retina increases the generation of photoreceptor cells
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-315611 (URN)
    Available from: 2017-02-16 Created: 2017-02-16 Last updated: 2017-02-17
  • Public defence: 2017-04-07 10:00 Hambergsalen, Uppsala
    Basirat, Farzad
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Process Models for CO2 Migration and Leakage: Gas Transport, Pore-Scale Displacement and Effects of Impurities2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Geological Carbon Storage (GCS) is considered as one of the key techniques to reduce the rate of atmospheric emissions of CO2 and thereby to contribute to controlling the global warming. A successful application of a GCS project requires the capability of the formation to trap CO2 for a long term. In this context, processes related to CO2 trapping and also possible leakage of CO2 to the near surface environment need to be understood. The overall aim of this thesis is to understand the flow and transport of CO2 through porous media in the context of geological storage of CO2. The entire range of scales, including the pore scale, the laboratory scale, the field experiment scale and the industrial scale of CO2 injection operation are addressed, and some of the key processes investigated by means of experiments and modeling.  First, a numerical model and laboratory experimental setup were developed to investigate the CO2 gas flow, mimicking the system in the near-surface conditions in case a leak from the storage formation should occur. The system specifically addressed the coupled flow and mass transport of gaseous CO2 both in the porous domain as well as the free flow domain above it. The comparison of experiments and modelling results showed a very good agreement indicating that the model developed can be applied to evaluate monitoring and surface detection of potential CO2 leakage. Second, the field scale CO2 injection test carried out in a shallow aquifer in Maguelone, France was analyzed and modeled. The results showed that Monte Carlo simulations accounting for the heterogeneity effects of the permeability field did capture the key observations of the monitoring data, while a homogeneous model could not represent them. Third, a numerical model based on phase-field method was developed and model simulations carried out addressing the effect of wettability on CO2-brine displacement at the pore-scale. The results show that strongly water-wet reservoirs provide a better potential for the dissolution trapping, due to the increase of interface between CO2 and brine with very low contact angles. The results further showed that strong water-wet conditions also imply a strong capillary effect, which is important for residual trapping of CO2. Finally, numerical model development and model simulations were carried out to address the large scale geological storage of CO2 in the presence of impurity gases in the CO2 rich phase. The results showed that impurity gases N2 and CH4 affected the spatial distribution of the gas (the supercritical CO2 rich phase), and a larger volume of reservoir is needed in comparison to the pure CO2 injection scenario. In addition, the solubility trapping significantly increased in the presence of N2 and CH4

    List of papers
    1. Experimental and modeling investigation of CO2 flow and transport in a coupled domain of porous media and free flow
    Open this publication in new window or tab >>Experimental and modeling investigation of CO2 flow and transport in a coupled domain of porous media and free flow
    2015 (English)In: International Journal of Greenhouse Gas Control, ISSN 1750-5836, E-ISSN 1878-0148, Vol. 42, 461-470 p.Article in journal (Refereed) Published
    Abstract [en]

    A solid understanding of the transport mechanisms of gaseous CO2 near the land surface is necessary for developing reliable monitoring techniques and predictive models for possible CO2 leakage from deep underground storage. The objective of this work has been to develop an experimental method along with a simulation model for gaseous CO2 flow and transport in a system including both the porous media and the free air space above it. The experimental system consisted of a two-dimensional bench scale rectangular sandbox containing homogenous sand with an open space of still air above it. Gaseous CO2 was injected in different modes and the CO2 breakthrough was measured on specified ports in the system by using CO2 concentration sensors. A numerical model combining the gas flow in the porous medium and the free flow region was developed and used to model the experimental data. In this quest, the Discontinuous One-Domain approach was selected for modeling transport between the free flow and porous regions. The observed and simulated CO2 breakthrough curves both in the dried sand and in the free flow matched very well in the case of uniform injection and satisfactorily even in the case of point injection. Consequently, it seems that the model reasonably matches the observed data in the cases where the boundary condition is well defined. In summary, our results show that the developed experimental setup provides capability to study gaseous CO2 flow and transport in a coupled porous medium - free flow system and that our modeling approach is able to predict the flow and transport in this system with good accuracy.

    Keyword
    Carbon dioxide flow and transport, Coupling conditions, Discontinuous One-Domain Approach, Experimental method, Free flow, Porous media
    National Category
    Energy Engineering
    Identifiers
    urn:nbn:se:uu:diva-274707 (URN)10.1016/j.ijggc.2015.08.024 (DOI)000366947400041 ()
    Funder
    EU, FP7, Seventh Framework Programme, 282900Swedish Research Council, 2010-3657
    Available from: 2016-02-02 Created: 2016-01-25 Last updated: 2017-02-23
    2. Numerical modelling of CO2 injection at small-scale field experimental site in Maguelone, France
    Open this publication in new window or tab >>Numerical modelling of CO2 injection at small-scale field experimental site in Maguelone, France
    Show others...
    2016 (English)In: International Journal of Greenhouse Gas Control, ISSN 1750-5836, E-ISSN 1878-0148, Vol. 54, 200-210 p.Article in journal (Refereed) Published
    Abstract [en]

    To evaluate the performance of downhole and surface geophysical monitoring methods, a series of shallow gas injection-monitoring experiments has been performed in a coastal saline aquifer at Maguelone, France. The recorded data include pressure measurements with a Westbay multilevel completion and CO2 saturation at an observation well derived from electrical resistivity with a modified Waxman-Smits (MWS) model. In this work, the aim is to develop a simulation model capturing the gas transport behavior and consistent with field data. For this purpose, the simulation of the CO2 injection experiment is carried out with two conceptual models, a homogeneous model and a heterogeneous model treated with multiple realization Monte Carlo simulations. Numerical simulator TOUGH2 with the equation of state module EOS7C is used for the simulations. Comparison of the model results with field data suggests that the pressure responses are captured with relatively good accuracy. Similarly, the model also provides an overall reasonable agreement and correct order of magnitude for predicted gas saturation values. However, as the heterogeneity pattern in the field data remains largely unknown, the model predictions can only be used to capture the mean behavior as well as to provide insights into how heterogeneity can influence the system behavior, by means of sensitivity analyses of the influence of heterogeneities on individual realizations.

    Keyword
    CO2 storage, CO2 injection, Shallow aquifer, Downhole and pressure monitoring, Numerical simulation, Heterogeneity, Electrical resistivity, Downhole geophysical monitoring
    National Category
    Geosciences, Multidisciplinary
    Identifiers
    urn:nbn:se:uu:diva-311204 (URN)10.1016/j.ijggc.2016.09.006 (DOI)000387781500015 ()
    Funder
    EU, FP7, Seventh Framework Programme, 227286 309367
    Available from: 2016-12-22 Created: 2016-12-22 Last updated: 2017-02-23
    3. Pore-scale modeling of wettability effects on CO2–brine displacement during geological storage
    Open this publication in new window or tab >>Pore-scale modeling of wettability effects on CO2–brine displacement during geological storage
    2017 (English)In: Advances in Water Resources, ISSN 0309-1708, E-ISSN 1872-9657Article in journal (Other academic) Submitted
    Place, publisher, year, edition, pages
    Elsevier, 2017
    National Category
    Oceanography, Hydrology, Water Resources
    Research subject
    Hydrology
    Identifiers
    urn:nbn:se:uu:diva-315304 (URN)
    Available from: 2017-02-14 Created: 2017-02-14 Last updated: 2017-02-14
    4. Numerical simulation of geological storage of CO2 with impurities in large scale saline aquifer
    Open this publication in new window or tab >>Numerical simulation of geological storage of CO2 with impurities in large scale saline aquifer
    (English)Manuscript (preprint) (Other academic)
    National Category
    Water Engineering Oceanography, Hydrology, Water Resources
    Identifiers
    urn:nbn:se:uu:diva-315303 (URN)
    Available from: 2017-02-14 Created: 2017-02-14 Last updated: 2017-02-14
  • Public defence: 2017-04-07 10:15 Geijersalen, Uppsala
    Holmqvist, Sam
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Literature.
    Transformationer: 1800-talets svenska translitteratur genom Lasse-Maja, C.J.L. Almqvist och Aurora Ljungstedt2017Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Literary descriptions of shifting from and transgressing assigned sex were common in 19th Century Sweden. This thesis forms a contribution to the larger project of writing a history of Swedish trans literature, and develops new interpretations of certain works of fiction by applying a transgender studies perspective. Through trans readings the thesis also examines what potential and possible implications literature might have for trans people beyond the literary realm. Trans readings are able to supplement earlier research by providing a nuanced understanding of the production of trans- and cisgenders. The theoretical perspectives used in the thesis are drawn for the most part from queer and transgender studies. The thesis adopts a conceptual understanding of trans as a movement, and aims to widen the scope of what may be considered relevant to a history of trans literature.

    The primary objects of analysis are the 1833 autobiography of widely known thief and cross-dresser Lasse-Maja (Lars Molin), C.J.L. Almqvist’s Drottningens juvelsmycke (1834), and Aurora Ljungstedt’s Moderna typer (1874). In closing, two texts from the fin-de-siècle are also closely read; Amanda Kerfstedt’s Reflexer (1901) and Frida Stéenhoff’s “Ett sällsamt öde” (1911). A wide range of other fiction is additionally studied in order to establish a contextual pattern of trans literary traditions.

    The thesis demonstrates that trans permeates all kinds of fiction, and that the characters analysed construct both trans and cis gender categories. It concludes that trans is done in a variety of ways, and with a variety of meanings in 19th and early 20th century literature. Trans is often depicted as a positive, fruitful and desirable act, through trans characters who are both themselves subjects of erotic desire and who become symbols of liberty and emancipation. Other trans figures however are often counter images of what are considered to be correct sexes, and are depicted as threatening and/or ridiculous. Both these negative and positive representations of trans affirm the gender binary. At the same time, they also break and destabilize that same binary, and the trans characters in the study both can and cannot be interpreted as transgressing cis- and heteronormativity respectively.

  • Public defence: 2017-04-07 10:15 Ihresalen, Engelska parken. Humanistiskt centrum, Uppsala
    Backman, Agnieszka
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Scandinavian Languages.
    Handskriftens materialitet: Studier i den fornsvenska samlingshandskriften Fru Elins bok (Codex Holmiensis D 3)2017Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This dissertation contains a study of the multitext manuscript Codex Holmiensis D 3 based in Material Philology and its focus on the material conditions underlying manuscripts. The aim of the investigation is to describe D 3 in order to increase understanding of its material conditions including content and circumstance of copying, as well as its use and purpose. 

    D 3 contains 14 text works in different genres, for example romances, chronicles, and edifying works. The paper manuscript in the format of a holster book has been dated through its watermarks to around 1487/1488. It was written for the noblewoman Elin Gustavsdotter (Sture).

    An older manuscript, Codex Holmiensis D 4a, has previously been identified as the exemplar of D 3. These manuscripts are very similar as regards language and content. However, it is shown here that D 4a could not have been the model for D 3 in the case of the romance Flores och Blanzeflor; nor can the manuscript as a whole be a copy of D 4a.

    There are few traces of use in D 3, but the first work, Herr Ivan Lejonriddaren, has several concluding texts before its final closing. These concluding texts suggest that parts of the work were being read while the rest was being copied. There are also dual quire signatures in this work, implying that the quires were in disarray, possibly because they were in use when the signatures were added.

    The purpose of D 3 was to educate and provide examples of good and bad behaviour for the nobility. Moreover, there is an owner-epilogue which also stresses courtly ideals and can be linked to the concept of exemplary behaviour. The contents can also be ordered thematically, with first a Carolingian connection, followed by one connected with Ireland and finally one focused on the Christian community. Codicological breaks divide the manuscript into two parts, which leads to the assumption of at least two common exemplars for D 3 and D 4a.

    An emphasis on the materiality of the manuscript reveals it to be not so much an unwieldy collection of unrelated text witnesses as a book created for a certain person and her time.

  • Public defence: 2017-04-07 13:00 Geijersalen, Engelska parken Hus 6, Uppsala
    Aronsson, August
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of History.
    Löfte, tvist och försoning: Politikens spelregler i 1300-talets Norden2017Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This thesis aims to explain how politics in 14th century Scandinavia were structured by a set of rules or norms of conduct – rules which were neither codified nor enforced by any outside agency, yet had a very real impact on the patterns by which political action was conducted. Taking inspiration from historical anthropology, the study sets out to analyze the ways in which political tensions and relationships, primarily within the royal elite, were negotiated in various situations. The source material – mainly letters of treaties, but also contemporary literary sources – are treated as remains of political communication within a common discursive framework.

    The findings of the study go against some established notions about politics in the 14th century that are prevalent in current Scandinavian research. On the whole, patterns of political behaviour during the period show great similarities to those of the earlier Middle Ages, despite the discontinuity implied by the idea of the 13th century as the era of "state formation" in Scandinavia. Rather, the kings and princes of the 14th century appear to have been ruled by quite similar norms of behaviour to those of their predecessors, albeit on a more complex scale.

    The concepts of peace and justice are shown to have been central to the way that political action was legitimized. No functional difference can be shown to have been made between "feudal" or personal relations, and those of the state. Peace was conceived as a state of harmony, which could only be achieved through the establishment of mutual positive bonds, and an active striving for justice. The latter was achieved, both with the aid of mediators and negotiators, and through the demonstration of force, in patterns largely similar to the practice of feuding. Likewise, acts of supplication and reconciliation are shown to have played an active part in the way that political relations were reified during the process of ending an armed conflict.

  • Public defence: 2017-04-07 13:15 Siegbahnsalen, Uppsala
    Zabzina, Natalia
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Mathematical modelling approach to collective decision-making2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In everyday situations individuals make decisions. For example, a tourist usually chooses a crowded or recommended restaurant to have dinner. Perhaps it is an individual decision, but the observed pattern of decision-making is a collective phenomenon. Collective behaviour emerges from the local interactions that give rise to a complex pattern at the group level. In our example, the recommendations or simple copying the choices of others make a crowded restaurant even more crowded. The rules of interaction between individuals are important to study. Such studies should be complemented by biological experiments. Recent studies of collective phenomena in animal groups help us to understand these rules and develop mathematical models of collective behaviour. The most important communication mechanism is positive feedback between group members, which we observe in our example. In this thesis, we use a generic experimentally validated model of positive feedback to study collective decision-making.

    The first part of the thesis is based on the modelling of decision-making associated to the selection of feeding sites. This has been extensively studied for ants and slime moulds. The main contribution of our research is to demonstrate how such aspects as "irrationality", speed and quality of decisions can be modelled using differential equations. We study bifurcation phenomena and describe collective patterns above critical values of a bifurcation points in mathematical and biological terms. In the second part, we demonstrate how the primitive unicellular slime mould Physarum Polycephalum provides an easy test-bed for theoretical assumptions and model predictions about decision-making. We study its searching strategies and model decision-making associated to the selection of food options. We also consider the aggregation model to investigate the fractal structure of Physarum Polycephalum plasmodia.

    List of papers
    1. Collective Irrationality and Positive Feedback
    Open this publication in new window or tab >>Collective Irrationality and Positive Feedback
    2011 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 6, no 4, e18901- p.Article in journal (Refereed) Published
    Abstract [en]

    Recent experiments on ants and slime moulds have assessed the degree to which they make rational decisions when presented with a number of alternative food sources or shelter. Ants and slime moulds are just two examples of a wide range of species and biological processes that use positive feedback mechanisms to reach decisions. Here we use a generic, experimentally validated model of positive feedback between group members to show that the probability of taking the best of n options depends crucially on the strength of feedback. We show how the probability of choosing the best option can be maximized by applying an optimal feedback strength. Importantly, this optimal value depends on the number of options, so that when we change the number of options the preference of the group changes, producing apparent "irrationalities''. We thus reinterpret the idea that collectives show "rational" or "irrational" preferences as being a necessary consequence of the use of positive feedback. We argue that positive feedback is a heuristic which often produces fast and accurate group decision-making, but is always susceptible to apparent irrationality when studied under particular experimental conditions.

    National Category
    Biological Sciences Mathematics
    Identifiers
    urn:nbn:se:uu:diva-153556 (URN)10.1371/journal.pone.0018901 (DOI)000290018400016 ()21541321 (PubMedID)
    Available from: 2011-05-16 Created: 2011-05-16 Last updated: 2017-02-27Bibliographically approved
    2. Six Predictions about the Decision Making of Animal and Human Groups
    Open this publication in new window or tab >>Six Predictions about the Decision Making of Animal and Human Groups
    2012 (English)In: Managerial and Decision Economics, Vol. 33, no 5-6, 295-309 p.Article in journal (Refereed) Published
    National Category
    Social Sciences
    Identifiers
    urn:nbn:se:uu:diva-192153 (URN)10.1002/mde.2553 (DOI)
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-02-27
    3. A gradient flow approach to the model of positive feedback in decision-making
    Open this publication in new window or tab >>A gradient flow approach to the model of positive feedback in decision-making
    2015 (English)In: Chaos, Solitons & Fractals, ISSN 0960-0779, E-ISSN 1873-2887, Vol. 77, 215-224 p.Article in journal (Refereed) Published
    Abstract [en]

    Recent studies on social dynamics have been done by using tools and methods of physics and economics.. The main idea is that the regularity observed on a global scale arises out of local interactions between the group members. We consider the model describing one of the major interaction mechanism, the model of positive feedback. We propose a geometrical reformulation of this model in terms of gradient flow equations on a Riemannian manifold. The benefit of this reformulation is that we introduce an alternative method to study phenomena of the well known model. We suggest the analogy with a particle moving on curved manifold. We believe that this analogy will allow us to extend powerful mathematical tools from analytical mechanics to the biological systems.

    Keyword
    Mathematical model of positive feedback in decision making, Gradient flow equations, Differential geometry
    National Category
    Mathematics
    Identifiers
    urn:nbn:se:uu:diva-261246 (URN)10.1016/j.chaos.2015.05.027 (DOI)000358970500022 ()
    Available from: 2015-09-07 Created: 2015-08-31 Last updated: 2017-02-27
    4. Symmetry Restoring Bifurcation in Collective Decision-Making
    Open this publication in new window or tab >>Symmetry Restoring Bifurcation in Collective Decision-Making
    Show others...
    2014 (English)In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 10, no 12, e1003960- p.Article in journal (Refereed) Published
    Abstract [en]

    How social groups and organisms decide between alternative feeding sites or shelters has been extensively studied both experimentally and theoretically. One key result is the existence of a symmetry-breaking bifurcation at a critical system size, where there is a switch from evenly distributed exploitation of all options to a focussed exploitation of just one. Here we present a decision-making model in which symmetry-breaking is followed by a symmetry restoring bifurcation, whereby very large systems return to an even distribution of exploitation amongst options. The model assumes local positive feedback, coupled with a negative feedback regulating the flow toward the feeding sites. We show that the model is consistent with three different strains of the slime mold Physarum polycephalum, choosing between two feeding sites. We argue that this combination of feedbacks could allow collective foraging organisms to react flexibly in a dynamic environment.

    National Category
    Mathematical Analysis
    Identifiers
    urn:nbn:se:uu:diva-312747 (URN)
    Funder
    EU, European Research Council, IDCAB 220/104702003
    Available from: 2017-01-12 Created: 2017-01-12 Last updated: 2017-02-07
    5. Fractal dimentions of the conformal diffusion-limited aggregation
    Open this publication in new window or tab >>Fractal dimentions of the conformal diffusion-limited aggregation
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Diffusion-limited aggregation (DLA) is an important and popular mathematical model of random cluster growth. Conformal DLA, in which a cluster is grown by successive applications of conformal maps, is relletavily new and unexplored version of DLA. We implement conformal DLA numerically and compute several fractal dimentions of DLA clusters. To test applicability of the model to biological systems, the dimentions are compared with the experimentally computed fractal dimentions of the slime mould Physarum Polycephalum.

    National Category
    Natural Sciences Mathematics
    Identifiers
    urn:nbn:se:uu:diva-314796 (URN)
    Available from: 2017-02-06 Created: 2017-02-06 Last updated: 2017-03-01Bibliographically approved
  • Public defence: 2017-04-07 13:15 A1:111a, Uppsala
    Digre, Andreas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Implications of Heparan Sulfate and Heparanase in Inflammatory Diseases2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Heparan sulfate (HS), an unbranched sulfated carbohydrate chain, and the HS-degrading enzyme heparanase play important roles in physiological and pathological processes during all stages of life, from early embryogenesis to ageing. Accumulated information shows that HS and heparanase are involved in inflammatory processes and associated diseases, e.g. rheumatoid arthritis (RA) and Alzheimer’s disease.

    In this thesis I have investigated the role of HS and heparanase (Hpa) in inflammatory-related pathologies. In the first project, Hpa overexpressing mice (Hpa-tg) were induced with a murine model of RA. We found a pro-inflammatory role of Hpa through enhancing the activity of T-cells and innate immune cells, which contributed to an augmented severity of clinical symptoms in the Hpa-tg mice.

    In my second project, we revealed co-current interaction of heparin with both ApoA1 and SAA of HDL isolated from plasma of inflamed mouse. Mass spectrometry analysis indicated close proximity of ApoA1 and SAA on the HDL surface, providing a molecular and structural mechanism for the simultaneous binding of heparin to apoA1 and SAA.

    In my third project, we investigated the role of Hpa in AA amyloid formation and resolution in mice in a model of AA-amyloidosis. We found a similar degree of amyloid formation in Hpa-KO mice compared to the wildtype control mice, but the resolution process was faster in Hpa-KO mice. The rapid clearance of deposited SAA in Hpa-KO mice was associated with upregulated expression of matrix metalloproteases. The results suggest an associated function of ECM proteases with heparanase in the process of AA amyloid resolution.

    In my fourth project, we found that overexpression of heparanase impaired inflammation associated beta amyloid (Aβ) clearance in the brain of an Alzheimer’s disease mouse model. Examination of the cytokine profile of brain lysates revealed an overall lower inflammatory reaction in the double transgenic (tgHpa*Swe) mice compared to single APP-tg (tg-Swe) mice in response to LPS-induced inflammation.

    List of papers
    1. Overexpression of heparanase enhances T lymphocyte activities and intensifies the inflammatory response in a model of murine rheumatoid arthritis
    Open this publication in new window or tab >>Overexpression of heparanase enhances T lymphocyte activities and intensifies the inflammatory response in a model of murine rheumatoid arthritis
    Show others...
    (English)Article in journal (Other academic) Submitted
    Abstract [en]

    Heparanase is an endo-glucuronidase that degrades heparan sulfate chains. The enzyme is expressed at a low level in normal organs; however, elevated expression of heparanase has been detected in several inflammatory conditions, e.g. in the synovial joints of rheumatoid arthritis (RA) patients. Herein, we have applied the model of collagen-induced arthritis (CIA) to transgenic mice overexpressing human heparanase (Hpa-tg) along with wildtype (WT) mice. About 50 % of the induced animals developed clinical symptoms, i.e. swelling of joints, and there were no differences between the Hpa-tg and WT mice in the incidence of disease. However, Hpa-tg mice displayed an earlier response and developed more severe symptoms. Examination of cells from thymus, spleen and lymph nodes revealed increased innate and adaptive immune responses of the Hpa-tg mice, reflected by increased proportions of macrophages, antigen presenting cells and plasmacytoid dendritic cells as well as Helios-positive CD4+ and CD8+ T cells. Furthermore, splenic lymphocytes from Hpa-tg mice showed higher proliferation activity. Our results suggest that elevated expression of heparanase augmented both the innate and adaptive immune system and propagated inflammatory reactions in the murine RA model.

    Keyword
    Collagen-induced arthritis, Heparanase, Heparan Sulfate, Flow cytometry, T cells
    National Category
    Immunology in the medical area
    Research subject
    Immunology; Medical Science
    Identifiers
    urn:nbn:se:uu:diva-315694 (URN)
    Funder
    Swedish Research Council, 2015-02595; K2012-56X-15046-09-4Swedish Research Council, 521-2011-3533Swedish Heart Lung Foundation, 20140131Swedish Cancer Society, 150815
    Note

    Submitted and revised manuscript

    Available from: 2017-02-20 Created: 2017-02-20 Last updated: 2017-02-20
    2. Heparin interactions with apoA1 and SAA in inflammation-associated HDL
    Open this publication in new window or tab >>Heparin interactions with apoA1 and SAA in inflammation-associated HDL
    2016 (English)In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 474, no 2, 309-314 p.Article in journal (Refereed) Published
    Abstract [en]

    Apolipoprotein A1 (apoA1) is the main protein component responsible for transportation of cholesterol on high-density lipoprotein (HDL). Serum amyloid A (SAA) is an acute phase protein associated with HDL. Apart from their physiological functions, both apoA1 and SAA have been identified as 'amyloidogenic peptides'. We report herein that the polysaccharide heparin interacts with both apoA1 and SAA in HDL isolated from plasma of inflamed mice. The reaction is rapid, forming complex aggregates composed of heparin, apoA1 and SAA as revealed by gel electrophoresis. This interaction is dependent on the size and concentration of added heparin. Mass spectrometry analysis of peptides derived from chemically crosslinked HDL-SAA particles detected multiple crosslinks between apoA1 and SAA, indicating close proximity (within 25 angstrom) of these two proteins on the HDL surface, providing a molecular and structural mechanism for the simultaneous binding of heparin to apoA1 and SAA.

    Keyword
    Heparan sulfate, Lipoproteins/receptors, Amyloid, Atherosclerosis, Proteoglycans, Mass spectrometry
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-298081 (URN)10.1016/j.bbrc.2016.04.092 (DOI)000376221700013 ()27105909 (PubMedID)
    Funder
    Swedish Research Council, K2012-67X-21128-04-4Swedish Heart Lung Foundation, 20140131
    Available from: 2016-06-30 Created: 2016-06-29 Last updated: 2017-02-20Bibliographically approved
    3. Accelerated resolution of AA amyloid in heparanase knockout mice is associated with matrix metalloproteases
    Open this publication in new window or tab >>Accelerated resolution of AA amyloid in heparanase knockout mice is associated with matrix metalloproteases
    Show others...
    2012 (English)In: PLoS ONE, ISSN 1932-6203, Vol. 7, no 7, e39899Article in journal (Refereed) Published
    Abstract [en]

    AA-amyloidosis is a disease characterized by abnormal deposition of serum A amyloid (SAA) peptide along with other components in various organs. The disease is a complication of inflammatory conditions that cause persistent high levels of the acute phase reactant SAA in plasma. In experimental animal models, the deposited amyloid is resolved when the inflammation is stopped, suggesting that there is an efficient clearance mechanism for the amyloid. As heparan sulfate (HS) is one of the major components in the amyloid, its metabolism is expected to affect the pathology of AA amyloidosis. In this study, we investigated the effect of heparanase, a HS degradation enzyme, in resolution of the AA amyloid. The transgenic mice deficient in heparanase (Hpa-KO) produced a similar level of SAA in plasma as the wildtype control (Ctr) mice upon induction by injection of AEF (amyloid enhancing factor) and inflammatory stimuli. The induction resulted in formation of SAA amyloid 7-days post treatment in the spleen that displayed a comparable degree of amyloid load in both groups. The amyloid became significantly less in the Hpa-KO spleen than in the Ctr spleen 10-days post treatment, and was completely resolved in the Hpa-KO spleen on day 21 post induction, while a substantial amount was still detected in the Ctr spleen. The rapid clearance of the amyloid in the Hpa-KO mice can be ascribed to upregulated matrix metalloproteases (MMPs) that are believed to contribute to degradation of the protein components in the AA amyloid. The results indicate that both heparanase and MMPs play important parts in the pathological process of AA amyloidosis.

    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-194442 (URN)10.1371/journal.pone.0039899 (DOI)000306355500015 ()22808071 (PubMedID)
    Funder
    Swedish Cancer SocietySwedish Research Council, K2009-67X-21128-01-3
    Available from: 2013-02-14 Created: 2013-02-14 Last updated: 2017-02-20Bibliographically approved
    4. Overexpression of heparanase interferes with inflammatory-associated amyloid-beta clearance in mice
    Open this publication in new window or tab >>Overexpression of heparanase interferes with inflammatory-associated amyloid-beta clearance in mice
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Heparan sulfate proteoglycans (HSPGs) constitutes a major component in the plaques of amyloid-beta (Aβ), and heparanase degradation of HSPGs modulates deposition of Aβ in transgenic mice overexpressing Aβ precursor protein (AβPP) harboring Swedish mutation (tgSwe). In this study, we examined implications of heparanase expression in resolving/clearance of deposited Aβ in the tgSwe mice using an inflammation model induced by LPS-stimulation. Immunohistological staining of Aβx-40 and Aβx-42 showed reduced Aβ-burden in the brain of LPS-stimulated tgSwe in comparison to vehicle treated tgSwe. This reduction of Aβ-burden was evidenced by a significant decrease in the SDS and formic acid soluble Aβ in the brain lysate. In comparison, LPS-treatment had a marginal effect on Aβ-burden in the double transgenic (tgHpa*Swe) mice overexpressing both human heparanase and human AβPP. An immunological array analysis revealed an overall lower level of the inflammatory cytokines examined in the brain lysates of tgHpa*Swe mice, suggesting that heparanase overexpression attenuated inflammatory-associated clearance of deposited Aβ.

    Keyword
    Alzheimer's disease, APP mouse, Heparanase, Heparan sulfate, Neuroinflammation, Amyloidosis, Clearance, A beta
    National Category
    Neurosciences
    Research subject
    Neurology
    Identifiers
    urn:nbn:se:uu:diva-315696 (URN)
    Funder
    Swedish Research Council
    Available from: 2017-02-20 Created: 2017-02-20 Last updated: 2017-02-20
  • Public defence: 2017-04-12 10:00 Axel Hambergsalen, Uppsala
    Wu, Lichuan
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL.
    Introducing Surface Gravity Waves into Earth System Models2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Surface gravity waves alter the turbulence of the bottom atmosphere and the upper ocean. Accordingly, they can affect momentum flux, heat fluxes, gas exchange and atmospheric mixing. However, in most state-of-the-art Earth System Models (ESMs), surface wave influences are not fully considered or even included. Here, applying surface wave influences into ESMs is investigated from different aspects.

    Tuning parameterisations for including instantaneous wave influences has difficulties to capture wave influences. Increasing the horizontal resolution of models intensifies storm simulations for both atmosphere-wave coupled (considering the influence of instantaneous wave-induced stress) and stand-alone atmospheric models. However, coupled models are more sensitive to the horizontal resolution than stand-alone atmospheric models.

    Under high winds, wave states have a big impact on the sea spray generation. Introducing a wave-state-dependent sea spray generation function and Charnock coefficient into a wind stress parameterisation improves the model performance concerning wind speed (intensifies storms). Adding sea spray impact on heat fluxes improves the simulation results of air temperature. Adding sea spray impact both on the wind stress and heat fluxes results in better model performance on wind speed and air temperature while compared to adding only one wave influence.

    Swell impact on atmospheric turbulence closure schemes should be taken into account through three terms: the atmospheric mixing length scale, the swell-induced momentum flux at the surface, and the profile of swell-induced momentum flux. Introducing the swell impact on the three terms into turbulence closure schemes shows a better performance than introducing only one of the influences.

    Considering all surface wave impacts on the upper-ocean turbulence (wave breaking, Stokes drift interaction with the Coriolis force, Langmuir circulation, and stirring by non-breaking waves), rather than just one effect, significantly improves model performance. The non-breaking-wave-induced mixing and Langmuir circulation are the most important terms when considering the impact of waves on upper-ocean mixing.

    Accurate climate simulations from ESMs are very important references for social and biological systems to adapt the climate change. Comparing simulation results with measurements shows that adding surface wave influences improves model performance. Thus, an accurate description of all important wave impact processes should be correctly represented in ESMs, which are important tools to describe climate and weather. Reducing the uncertainties of simulation results from ESMs through introducing surface gravity wave influences is necessary.

    List of papers
    1. Surface Wave Impact When Simulating Midlatitude Storm Development
    Open this publication in new window or tab >>Surface Wave Impact When Simulating Midlatitude Storm Development
    2017 (English)In: Journal of Atmospheric and Oceanic Technology, ISSN 0739-0572, E-ISSN 1520-0426, Vol. 34, no 1, 233-248 p.Article in journal, News item (Refereed) Published
    Abstract [en]

    Surface gravity waves, present at the air–sea interface, can affect the momentum flux and heat fluxes by modifying turbulence in the lower layers of the atmosphere. How to incorporate wave impacts into model parameterizations is still an open issue. In this study, the influence of a dynamic roughness length (considering instantaneous wave-induced stress), horizontal resolution, and the coupling time resolution between waves and the atmosphere on storm simulations are investigated using sensitivity experiments. Based on the sim- ulations of six midlatitude storms using both an atmosphere–wave coupled model and an atmospheric stand- alone model, the impacts are investigated. Adding the wave-induced stress weakens the storm intensity. Applying a roughness length tuned to an average friction velocity is not enough to capture the simulation results from ‘‘true’’ wave-related roughness length. High-horizontal-resolution models intensify the simula- tion of storms, which is valid for both coupled and uncoupled models. Compared with the atmospheric stand- alone model, the coupled model (considering the influence of dynamic roughness length) is more sensitive to the model horizontal resolution. During reasonable ranges, the coupling time resolution does not have a significant impact on the storm intensity based on the limited experiments used in this study. It is concluded that the dynamic wave influence (instantaneous wave influence) and the model resolution should be taken into account during the development of forecast and climate models.

    National Category
    Meteorology and Atmospheric Sciences
    Identifiers
    urn:nbn:se:uu:diva-313154 (URN)10.1175/JTECH-D-16-0070.1 (DOI)000391826300016 ()
    Funder
    Swedish Research Council, 2012-3902
    Available from: 2017-01-17 Created: 2017-01-17 Last updated: 2017-02-22Bibliographically approved
    2. The impact of waves and sea spray on modelling storm track and development
    Open this publication in new window or tab >>The impact of waves and sea spray on modelling storm track and development
    2015 (English)In: Tellus. Series A, Dynamic meteorology and oceanography, ISSN 0280-6495, E-ISSN 1600-0870, Vol. 67, 27967Article in journal (Refereed) Published
    Abstract [en]

    In high wind speed conditions, sea spray generated by intensely breaking waves greatly influences the wind stress and heat fluxes. Measurements indicate that the drag coefficient decreases at high wind speeds. The sea spray generation function (SSGF), an important term of wind stress parameterisation at high wind speeds, is usually treated as a function of wind speed/friction velocity. In this study, we introduce a wave-state-dependent SSGF and wave-age-dependent Charnock number into a high wind speed–wind stress parameterisation. The newly proposed wind stress parameterisation and sea spray heat flux parameterisation were applied to an atmosphere–wave coupled model to study the mid-latitude storm development of six storm cases. Compared with measurements from the FINO1 platform in the North Sea, the new wind stress parameterisation can reduce wind speed simulation errors in the high wind speed range. Considering only sea spray impact on wind stress (and not on heat fluxes) will intensify the storms (in terms of minimum sea level pressure and maximum wind speed), but has little effect on the storm tracks. Considering the impact of sea spray on heat fluxes only (not on wind stress) can improve the model performance regarding air temperature, but it has little effect on the storm intensity and storm track performance. If the impact of sea spray on both the wind stress and heat fluxes is taken into account, the model performs best in all experiments for minimum sea level pressure, maximum wind speed and air temperature.

    Keyword
    sea spray, wind stress, heat fluxes, storms
    National Category
    Earth and Related Environmental Sciences
    Identifiers
    urn:nbn:se:uu:diva-263091 (URN)10.3402/tellusa.v67.27967 (DOI)000361746300001 ()
    Funder
    Swedish Research Council
    Available from: 2015-09-25 Created: 2015-09-25 Last updated: 2017-02-06Bibliographically approved
    3. Swell impact on wind stress and atmospheric mixing in a regional coupled atmosphere-wave model
    Open this publication in new window or tab >>Swell impact on wind stress and atmospheric mixing in a regional coupled atmosphere-wave model
    2016 (English)In: Journal of Geophysical Research - Oceans, ISSN 2169-9275, E-ISSN 2169-9291, Vol. 121, no 7, 4633-4648 p.Article in journal (Refereed) Published
    Abstract [en]

    Over the ocean, the atmospheric turbulence can be significantly affected by swell waves. Change in the atmospheric turbulence affects the wind stress and atmospheric mixing over swell waves. In this study, the influence of swell on atmospheric mixing and wind stress is introduced into an atmosphere-wave-coupled regional climate model, separately and combined. The swell influence on atmospheric mixing is introduced into the atmospheric mixing length formula by adding a swell-induced contribution to the mixing. The swell influence on the wind stress under wind-following swell, moderate-range wind, and near-neutral and unstable stratification conditions is introduced by changing the roughness length. Five year simulation results indicate that adding the swell influence on atmospheric mixing has limited influence, only slightly increasing the near-surface wind speed; in contrast, adding the swell influence on wind stress reduces the near-surface wind speed. Introducing the wave influence roughness length has a larger influence than does adding the swell influence on mixing. Compared with measurements, adding the swell influence on both atmospheric mixing and wind stress gives the best model performance for the wind speed. The influence varies with wave characteristics for different sea basins. Swell occurs infrequently in the studied area, and one could expect more influence in high-swell-frequency areas (i.e., low-latitude ocean). We conclude that the influence of swell on atmospheric mixing and wind stress should be considered when developing climate models.

    Keyword
    air-sea interaction; swell waves; wind stress; atmospheric mixing
    National Category
    Oceanography, Hydrology, Water Resources Meteorology and Atmospheric Sciences
    Identifiers
    urn:nbn:se:uu:diva-302007 (URN)10.1002/2015JC011576 (DOI)000383468500013 ()
    Funder
    Swedish Research Council, 2012-3902
    Available from: 2016-08-27 Created: 2016-08-27 Last updated: 2017-02-06Bibliographically approved
    4. Atmospheric boundary layer turbulence closure scheme for wind-following swell conditions
    Open this publication in new window or tab >>Atmospheric boundary layer turbulence closure scheme for wind-following swell conditions
    (English)In: Journal of Atmospheric Sciences, ISSN 0022-4928, E-ISSN 1520-0469Article in journal (Refereed) Submitted
    National Category
    Meteorology and Atmospheric Sciences
    Identifiers
    urn:nbn:se:uu:diva-314757 (URN)
    Available from: 2017-02-06 Created: 2017-02-06 Last updated: 2017-02-15
    5. Upper-ocean mixing due to surface gravity waves
    Open this publication in new window or tab >>Upper-ocean mixing due to surface gravity waves
    2015 (English)In: Journal of Geophysical Research - Oceans, ISSN 2169-9275, E-ISSN 2169-9291, Vol. 120, no 12, 8210-8228 p.Article in journal (Refereed) Published
    Abstract [en]

    Surface gravity waves play an important role in the lower layer of the atmosphere and the upper layer of the ocean. Surface waves effect upper-ocean mixing mainly through four processes: wave breaking, Stokes drift interaction with the Coriolis force, Langmuir circulation, and stirring by nonbreaking waves. We introduce the impact of these four processes into a 1-D  ocean turbulence model. The parameterizations used are based mainly on existing investigations. Comparison of simulation results and measurements demonstrates that considering all the effects of waves, rather than just one effect, significantly improves model performance. The nonbreaking-wave-induced mixing and Langmuir turbulence are the most important terms when considering the impact of waves on upper-ocean mixing. Under high-wave conditions, the turbulent mixing induced by nonbreaking waves can be of the same order of magnitude as the viscosity induced by other terms at the surface. Nonbreaking waves contribute very little to shear production and their impact is negligible in the models. Sensitivity experiments demonstrate that the vertical profile of the Stokes drift calculated from the 2-D wave spectrum improves model performance significantly compared with other methods of introducing wave effects.

    Keyword
    ocean mixing; nonbreaking waves; Langmuir circulation; Coriolis-Stokes forcing; breaking waves
    National Category
    Meteorology and Atmospheric Sciences
    Identifiers
    urn:nbn:se:uu:diva-270913 (URN)10.1002/2015JC011329 (DOI)000369153200027 ()
    Funder
    Swedish Research Council, 2012-3902
    Available from: 2016-01-05 Created: 2016-01-05 Last updated: 2017-02-06Bibliographically approved
  • Public defence: 2017-05-06 14:00 Aula minus, Uppsala
    Poveda Guillén, Oriol
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Theology, Department of Theology, The Social Sciences of Religion, Sociology of Religions.
    According to whose will: The entanglements of gender & religion in the lives of transgender Jews with an Orthodox background2017Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This study, the first in its scope on transgender religiosity, is based on in-depth biographical interviews with 13 transgender participants with a Jewish Orthodox background (currently and formerly Orthodox). The primary aim of the study has been to elucidate the entanglements of gender and religion in three periods of the participants’ lives: pre-transition, transition and post-transition. One of the main topics investigated have been the ways participants negotiated gendered religious practices in those three periods. A secondary aim of this study has been to co-theorize, in dialogue with the participants, different possible paths for religious change; that is, the ways in which the larger Orthodox community might respond to the presence of openly transgender members in its midst.

    Concerning the findings, in the course of this study I have developed the themes of dislocations and reversal stories to explain how the participants negotiated the entanglements of gender and religion particularly in the transitional and post-transitional periods. The latter theme–reversal stories–has been of special relevance to explain how gendered religious practices, which were generally detrimental to the acceptance of the participants’ gender identities during the pre-transitional period, had the potential to become a powerful source for gender affirmation after transition. In this study I argue that this possibility and its related mode of agency are not contained within the binary resistance/subordination that feminist scholars have developed to account for the agency of women in traditionalist religions. In order to better conceptualize the notion of agency and explore the nature of the mutual entanglements of gender and religion, I deploy the body of theoretical work developed by Karen Barad known as agential realism. Lastly, I conclude by examining my initial commitments to social constructionism (in Peter Berger’s definition). In the final chapter, I describe how in the course of my study I have encountered three unexpected sites of resistance to social constructionism that have led me to reconsider my previous epistemological commitments and embrace posthumanism as a more satisfactory alternative.