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  • 1. Abramowski, A.
    et al.
    Aharonian, F.
    Benkhali, F. Ait
    Akhperjanian, A. G.
    Anguener, E. O.
    Backes, M.
    Balzer, A.
    Becherini, Y.
    Tjus, J. Becker
    Berge, D.
    Bernhard, S.
    Bernloehr, K.
    Birsin, E.
    Blackwell, R.
    Boettcher, M.
    Boisson, C.
    Bolmont, J.
    Bordas, P.
    Bregeon, J.
    Brun, F.
    Brun, P.
    Bryan, M.
    Bulik, T.
    Carr, J.
    Casanova, S.
    Chakraborty, N.
    Chalme-Calvet, R.
    Chaves, R. C. G.
    Chen, A.
    Chretien, M.
    Colafrancesco, S.
    Cologna, G.
    Conrad, Jan
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Couturier, C.
    Cui, Y.
    Davids, I. D.
    Degrange, B.
    Deil, C.
    deWilt, P.
    Djannati-Ata, A.
    Domainko, W.
    Donath, A.
    Drury, L. O'C.
    Dubus, G.
    Dutson, K.
    Dyks, J.
    Dyrda, M.
    Edwards, T.
    Egberts, K.
    Eger, P.
    Ernenwein, J-P.
    Espigat, P.
    Farnier, Christian
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Fegan, S.
    Feinstein, F.
    Fernandes, M. V.
    Fernandez, D.
    Fiasson, A.
    Fontaine, G.
    Foerster, A.
    Fuessling, M.
    Gabici, S.
    Gajdus, M.
    Gallant, Y. A.
    Garrigoux, T.
    Giavitto, G.
    Giebels, B.
    Glicenstein, J. F.
    Gottschall, D.
    Goyal, A.
    Grondin, M-H.
    Grudzinska, M.
    Hadasch, D.
    Haeffner, S.
    Hahn, J.
    Hawkes, J.
    Heinzelmann, G.
    Henri, G.
    Hermann, G.
    Hervet, O.
    Hillert, A.
    Hinton, J. A.
    Hofmann, W.
    Hofverberg, P.
    Hoischen, C.
    Holler, M.
    Horns, D.
    Ivascenko, A.
    Jacholkowska, A.
    Jamrozy, M.
    Janiak, M.
    Jankowsky, F.
    Jung-Richardt, I.
    Kastendieck, M. A.
    Katarzynski, K.
    Katz, U.
    Kerszberg, D.
    Khelifi, B.
    Kieffer, M.
    Klepser, S.
    Klochkov, D.
    Kluzniak, W.
    Kolitzus, D.
    Komin, Nu.
    Kosack, K.
    Krakau, S.
    Krayzel, F.
    Krueger, P. P.
    Laffon, H.
    Lamanna, G.
    Lau, J.
    Lefaucheur, J.
    Lefranc, V.
    Lemiere, A.
    Lemoine-Goumard, M.
    Lenain, J-P.
    Lohse, T.
    Lopatin, A.
    Lu, C-C.
    Lui, R.
    Marandon, V.
    Marcowith, A.
    Mariaud, C.
    Marx, R.
    Maurin, G.
    Maxted, N.
    Mayer, M.
    Meintjes, P. J.
    Menzler, U.
    Meyer, Manuel
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Mitchell, A. M. W.
    Moderski, R.
    Mohamed, M.
    Morå, Knut
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Moulin, E.
    Murach, T.
    de Naurois, M.
    Niemiec, J.
    Oakes, L.
    Odaka, H.
    Oettl, S.
    Ohm, S.
    Opitz, B.
    Ostrowski, M.
    Oya, I.
    Panter, M.
    Parsons, R. D.
    Arribas, M. Paz
    Pekeur, N. W.
    Pelletier, G.
    Petrucci, P-O.
    Peyaud, B.
    Pita, S.
    Poon, H.
    Prokoph, H.
    Puehlhofer, G.
    Punch, M.
    Quirrenbach, A.
    Raab, S.
    Reichardt, I.
    Reimer, A.
    Reimer, O.
    Renaud, M.
    de los Reyes, R.
    Rieger, F.
    Romoli, C.
    Rosier-Lees, S.
    Rowell, G.
    Rudak, B.
    Rulten, C. B.
    Sahakian, V.
    Salek, D.
    Sanchez, D. A.
    Santangelo, A.
    Sasaki, M.
    Schlickeiser, R.
    Schuessler, F.
    Schulz, A.
    Schwanke, U.
    Schwemmer, S.
    Seyffert, A. S.
    Simoni, R.
    Sol, H.
    Spanier, F.
    Spengler, Gerrit
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Spies, F.
    Stawarz, L.
    Steenkamp, R.
    Stegmann, C.
    Stinzing, F.
    Stycz, K.
    Sushch, I.
    Tavernet, J-P.
    Tavernier, T.
    Taylor, A. M.
    Terrier, R.
    Tluczykont, M.
    Trichard, C.
    Tuffs, R.
    Valerius, K.
    van der Walt, J.
    van Eldik, C.
    van Soelen, B.
    Vasileiadis, G.
    Veh, J.
    Venter, C.
    Viana, A.
    Vincent, P.
    Vink, J.
    Voisin, F.
    Voelk, H. J.
    Vuillaume, T.
    Wagner, S. J.
    Wagner, P.
    Wagner, Roger M.
    Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Weidinger, M.
    Weitzel, Q.
    White, R.
    Wierzcholska, A.
    Willmann, P.
    Woernlein, A.
    Wouters, D.
    Yang, R.
    Zabalza, V.
    Zaborov, D.
    Zacharias, M.
    Zdziarski, A. A.
    Zech, A.
    Zefi, F.
    Zywucka, N.
    Acceleration of petaelectronvolt protons in the Galactic Centre2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 531, no 7595, p. 476-+Article in journal (Refereed)
    Abstract [en]

    Galactic cosmic rays reach energies of at least a few petaelectronvolts(1) (of the order of 1015 electronvolts). This implies that our Galaxy contains petaelectronvolt accelerators ('PeVatrons'), but all proposed models of Galactic cosmic-ray accelerators encounter difficulties at exactly these energies(2). Dozens of Galactic accelerators capable of accelerating particles to energies of tens of teraelectronvolts (of the order of 10(13) electronvolts) were inferred from recent gamma-ray observations(3). However, none of the currently known accelerators-not even the handful of shell-type supernova remnants commonly believed to supply most Galactic cosmic rays-has shown the characteristic tracers of petaelectronvolt particles, namely, power-law spectra of.-rays extending without a cut-off or a spectral break to tens of teraelectronvolts(4). Here we report deep.-ray observations with arcminute angular resolution of the region surrounding the Galactic Centre, which show the expected tracer of the presence of petaelectronvolt protons within the central 10 parsecs of the Galaxy. We propose that the supermassive black hole Sagittarius A* is linked to this PeVatron. Sagittarius A* went through active phases in the past, as demonstrated by X-ray outbursts(5) and an outflow from the Galactic Centre(6). Although its current rate of particle acceleration is not sufficient to provide a substantial contribution to Galactic cosmic rays, Sagittarius A* could have plausibly been more active over the last 10(6)-10(7) years, and therefore should be considered as a viable alternative to supernova remnants as a source of petaelectronvolt Galactic cosmic rays.

  • 2.
    Aili, Hans
    et al.
    Stockholm University, Faculty of Humanities, Department of Romance Studies and Classics.
    Pietsch, Theodore W
    University of Washington, Seattle.
    Jacob Theodor Klein's Critique of Peter Artedi's Ichthyologia (1738)2014In: Svenska Linnésällskapets årsskrift, ISSN 0375-2038, p. 39-84Article in journal (Refereed)
    Abstract [en]

    An anonymous critique of Peter Artedi’s (1705‒1735) Ichthyologia sive opera omnia de piscibus, the latter edited and published posthumously by Carolus Linnaeus (1707‒ 1778) in 1738, is shown to have been written by the Prussian jurist and naturalist Jacob Theodor Klein (1685‒1759), and sent to Hans Sloane (1660−1753) in London for his approval. The critique is transcribed and translated, and its contents assessed in light of Artedi’s contribution to Linnaean systematics. While in some ways highly critical of Artedi, Klein must have been well aware that by criticizing Artedi he was, by association, criticizing Linnaeus as well. Linnaeus’s editorial contributions to the Ichthyologia as well as his on-going antagonistic relationship with Klein are also discussed.

  • 3. Anderson, Bruce T.
    et al.
    Hassanzadeh, Pedram
    Caballero, Rodrigo
    Stockholm University, Faculty of Science, Department of Meteorology .
    Persistent anomalies of the extratropical Northern Hemisphere wintertime circulation as an initiator of El Nino/Southern Oscillation events2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 10145Article in journal (Refereed)
    Abstract [en]

    Climates across both hemispheres are strongly influenced by tropical Pacific variability associated with the El Nino/Southern Oscillation (ENSO). Conversely, extratropical variability also can affect the tropics. In particular, seasonal-mean alterations of near-surface winds associated with the North Pacific Oscillation (NPO) serve as a significant extratropical forcing agent of ENSO. However, it is still unclear what dynamical processes give rise to year-to-year shifts in these long-lived NPO anomalies. Here we show that intraseasonal variability in boreal winter pressure patterns over the Central North Pacific (CNP) imparts a significant signature upon the seasonal-mean circulations characteristic of the NPO. Further we show that the seasonal-mean signature results in part from year-to-year variations in persistent, quasi-stationary low-pressure intrusions into the subtropics of the CNP, accompanied by the establishment of persistent, quasi-stationary high-pressure anomalies over high latitudes of the CNP. Overall, we find that the frequency of these persistent extratropical anomalies (PEAs) during a given winter serves as a key modulator of intraseasonal variability in extratropical North Pacific circulations and, through their influence on the seasonal-mean circulations in and around the southern lobe of the NPO, the state of the equatorial Pacific 9-12 months later.

  • 4.
    Andersson, Ole
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Bengtsson, Ingemar
    Stockholm University, Faculty of Science, Department of Physics.
    Ericsson, Marie
    Sjöqvist, Erik
    Geometric phases for mixed states of the Kitaev chain2016In: Philosophical Transactions. Series A: Mathematical, physical, and engineering science, ISSN 1364-503X, E-ISSN 1471-2962, Vol. 374, no 2068, article id 20150231Article in journal (Refereed)
    Abstract [en]

    The Berry phase has found applications in building topological order parameters for certain condensed matter systems. The question whether some geometric phase for mixed states can serve the same purpose has been raised, and proposals are on the table. We analyse the intricate behaviour of Uhlmann's geometric phase in the Kitaev chain at finite temperature, and then argue that it captures quite different physics from that intended. We also analyse the behaviour of a geometric phase introduced in the context of interferometry. For the Kitaev chain, this phase closely mirrors that of the Berry phase, and we argue that it merits further investigation.

  • 5.
    Andersson, Sara
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Mapping supply and demand of ecosystem services in the Helge Å catchment area, Sweden2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Research on ecosystem services has accelerated the last few years, but there is a knowledge gap on how to integrate the concept into management in a way that is mindful of the complex, dynamic and non-linear dimensions of ecosystem services. Ecosystem services are often approached from a supply side, and more often than not services are approached individually without attempt to capture the trade-offs and synergies between services. The overall aim of this master’s thesis is to contribute to the operationalization of the ecosystem services concept, within a social-ecological systems framework. This is done through a case study of the Helge Å catchment in Southern Sweden, in which I use publically available data to map the supply and demand of a selection of locally relevant provisioning, regulating, and, to some extent, cultural ecosystem services. The thesis analyses some of the challenges of, as well as opportunities for, making tangible sense of this complex social-ecological concept in a way that can inform decision making on ecosystem services for sustainable development. The results show that mapping both supply and demand adds important dimensions to ecosystem service assessment that has value within management contexts. Especially important are the added social dimensions of ecosystem service provision, and the incorporation of societal demand as a factor in mapping. There are some obvious challenges still associated with this type of mapping, foremost associated with mapping of cultural ecosystem services and data availability, which have yet to be resolved through continued research efforts.

  • 6. Arcavi, Iair
    et al.
    Howell, D. Andrew
    Kasen, Daniel
    Bildsten, Lars
    Hosseinzadeh, Griffin
    McCully, Curtis
    Wong, Zheng Chuen
    Katz, Sarah Rebekah
    Gal-Yam, Avishay
    Sollerman, Jesper
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Taddia, Francesco
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Leloudas, Giorgos
    Fremling, Christoffer
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Nugent, Peter E.
    Horesh, Assaf
    Mooley, Kunal
    Rumsey, Clare
    Cenko, S. B. Radley
    Graham, Melissa L.
    Perley, Daniel A.
    Nakar, Ehud
    Shaviv, Nir J.
    Bromberg, Omer
    Shen, Ken J.
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Ofek, Eran O.
    Cao, Yi
    Wang, Xiaofeng
    Huang, Fang
    Rui, Liming
    Zhang, Tianmeng
    Li, Wenxiong
    Li, Zhitong
    Zhang, Jujia
    Valenti, Stefano
    Guevel, David
    Shappee, Benjamin
    Kochanek, Christopher S.
    Holoien, Thomas W. -S.
    Filippenko, Alexei V.
    Fender, Rob
    Nyholm, Anders
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Yaron, Ofer
    Kasliwal, Mansi M. .
    Sullivan, Mark
    Lagorodnova, Nadja B.
    Walters, Richard S.
    Lunnan, Ragnhild
    Khazov, Danny
    Andreoni, Igor
    Laher, Russ R.
    Konidaris, Nick
    Wozniak, Przemek
    Bue, Brian
    Energetic eruptions leading to a peculiar hydrogen-rich explosion of a massive star2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 551, no 7679, p. 210-213Article in journal (Refereed)
    Abstract [en]

    Every supernova so far observed has been considered to be the terminal explosion of a star. Moreover, all supernovae with absorption lines in their spectra show those lines decreasing in velocity over time, as the ejecta expand and thin, revealing slower-moving material that was previously hidden. In addition, every supernova that exhibits the absorption lines of hydrogen has one main light-curve peak, or a plateau in luminosity, lasting approximately 100 days before declining(1). Here we report observations of iPTF14hls, an event that has spectra identical to a hydrogen-rich core-collapse supernova, but characteristics that differ extensively from those of known supernovae. The light curve has at least five peaks and remains bright for more than 600 days; the absorption lines show little to no decrease in velocity; and the radius of the line-forming region is more than an order of magnitude bigger than the radius of the photosphere derived from the continuum emission. These characteristics are consistent with a shell of several tens of solar masses ejected by the progenitor star at supernova-level energies a few hundred days before a terminal explosion. Another possible eruption was recorded at the same position in 1954. Multiple energetic pre-supernova eruptions are expected to occur in stars of 95 to 130 solar masses, which experience the pulsational pair instability(2-5). That model, however, does not account for the continued presence of hydrogen, or the energetics observed here. Another mechanism for the violent ejection of mass in massive stars may be required.

  • 7. Artiglia, Luca
    et al.
    Edebeli, Jacinta
    Orlando, Fabrizio
    Chen, Shuzhen
    Lee, Ming-Tao
    Stockholm University, Faculty of Science, Department of Physics. Paul Scherrer Institut, Switzerland.
    Arroyo, Pablo Corral
    Gilgen, Anina
    Bartels-Rausch, Thorsten
    Kleibert, Armin
    Vazdar, Mario
    Carignano, Marcelo Andres
    Francisco, Joseph S.
    Shepson, Paul B.
    Gladich, Ivan
    Ammann, Markus
    A surface-stabilized ozonide triggers bromide oxidation at the aqueous solution-vapour interface2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 700Article in journal (Refereed)
    Abstract [en]

    Oxidation of bromide in aqueous environments initiates the formation of molecular halogen compounds, which is important for the global tropospheric ozone budget. In the aqueous bulk, oxidation of bromide by ozone involves a [Br center dot OOO-] complex as intermediate. Here we report liquid jet X-ray photoelectron spectroscopy measurements that provide direct experimental evidence for the ozonide and establish its propensity for the solution-vapour interface. Theoretical calculations support these findings, showing that water stabilizes the ozonide and lowers the energy of the transition state at neutral pH. Kinetic experiments confirm the dominance of the heterogeneous oxidation route established by this precursor at low, atmospherically relevant ozone concentrations. Taken together, our results provide a strong case of different reaction kinetics and mechanisms of reactions occurring at the aqueous phase-vapour interface compared with the bulk aqueous phase.

  • 8. Baeza-Delgado, Carlos
    et al.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Marti-Renom, Marc A.
    Mingarro, Ismael
    Biological insertion of computationally designed short transmembrane segments2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 23397Article in journal (Refereed)
    Abstract [en]

    The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design.

  • 9.
    Balk, Lennart
    et al.
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Hägerroth, Per-Åke
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Gustavsson, Hanna
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Sigg, Lisa
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Åkerman, Gun
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Ruiz Munoz, Yolanda
    Honeyfield, Dale C.
    Tjärnlund, Ulla
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Oliveira, Kenneth
    Ström, Karin
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    McCormick, Stephen D.
    Karlsson, Simon
    Ström, Marika
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Karolinska Institutet, Sweden.
    van Manen, Mathijs
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. Utrecht University, Germany.
    Berg, Anna-Lena
    Halldorsson, Halldor P.
    Strömquist, Jennie
    Collier, Tracy K.
    Börjeson, Hans
    Mörner, Torsten
    Hansson, Tomas
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Widespread episodic thiamine deficiency in Northern Hemisphere wildlife2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 38821Article in journal (Refereed)
    Abstract [en]

    Many wildlife populations are declining at rates higher than can be explained by known threats to biodiversity. Recently, thiamine (vitamin B-1) deficiency has emerged as a possible contributing cause. Here, thiamine status was systematically investigated in three animal classes: bivalves, ray-finned fishes, and birds. Thiamine diphosphate is required as a cofactor in at least five life-sustaining enzymes that are required for basic cellular metabolism. Analysis of different phosphorylated forms of thiamine, as well as of activities and amount of holoenzyme and apoenzyme forms of thiaminedependent enzymes, revealed episodically occurring thiamine deficiency in all three animal classes. These biochemical effects were also linked to secondary effects on growth, condition, liver size, blood chemistry and composition, histopathology, swimming behaviour and endurance, parasite infestation, and reproduction. It is unlikely that the thiamine deficiency is caused by impaired phosphorylation within the cells. Rather, the results point towards insufficient amounts of thiamine in the food. By investigating a large geographic area, by extending the focus from lethal to sublethal thiamine deficiency, and by linking biochemical alterations to secondary effects, we demonstrate that the problem of thiamine deficiency is considerably more widespread and severe than previously reported.

  • 10. Belton, Lydia E.
    et al.
    Cameron, Elissa Z.
    Dalerum, Fredrik
    Stockholm University, Faculty of Science, Department of Zoology. University of Pretoria, South Africa; University of Oviedo, Spa.
    Spotted hyaena space use in relation to human infrastructure inside a protected area2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2596Article in journal (Refereed)
    Abstract [en]

    Increasing human population growth has led to elevated levels of human-carnivore conflict. However, some carnivore populations have adapted to urban environments and the resources they supply. Such associations may influence carnivore ecology, behaviour and life-history. Pockets of urbanisation sometimes occur within protected areas, so that anthropogenic influences on carnivore biology are not necessarily confined to unprotected areas. In this study we evaluated associations between human infrastructure and related activity and space use of spotted hyaenas within one of the largest protected areas in South Africa, the Kruger National Park. Home range size was smaller for the dominant female of a clan living in close proximity to humans than that of the dominant female of a clan without direct access to human infrastructure. The home range including human infrastructure was also used less evenly during the night, presumably when the animals were active. Within this home range, a village area was preferred during the night, when the least modified areas within the village were preferred and administration and highly modified areas were avoided. During the day, however, there were no preference or avoidance of the village area, but all habitats except unmodified habitats within the village area were avoided. We suggest that human infrastructure and associated activity influenced hyaena space use, primarily through alterations in the spatial distribution of food. However, these effects may have been indirectly caused by habitat modification that generated favourable hunting habitat rather than a direct effect caused by access to human food such as garbage. Because of the often pivotal effects of apex predators in terrestrial ecosystems, we encourage further work aimed to quantify how human presence influences large carnivores and associated ecosystem processes within protected areas.

  • 11. Bergh, Johan
    et al.
    Zetterstrom, Per
    Andersen, Peter M.
    Brannstrom, Thomas
    Graffmo, Karin S.
    Jonsson, P. Andreas
    Lang, Lisa
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Danielsson, Jens
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Oliveberg, Mikael
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Marklund, Stefan L.
    Structural and kinetic analysis of protein-aggregate strains in vivo using binary epitope mapping2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 14, p. 4489-4494Article in journal (Refereed)
    Abstract [en]

    Despite considerable progress in uncovering the molecular details of protein aggregation in vitro, the cause and mechanism of protein-aggregation disease remain poorly understood. One reason is that the amount of pathological aggregates in neural tissue is exceedingly low, precluding examination by conventional approaches. We present here a method for determination of the structure and quantity of aggregates in small tissue samples, circumventing the above problem. The method is based on binary epitope mapping using anti-peptide antibodies. We assessed the usefulness and versatility of the method in mice modeling the neurodegenerative disease amyotrophic lateral sclerosis, which accumulate intracellular aggregates of superoxide dismutase-1. Two strains of aggregates were identified with different structural architectures, molecular properties, and growth kinetics. Both were different from superoxide dismutase-1 aggregates generated in vitro under a variety of conditions. The strains, which seem kinetically under fragmentation control, are associated with different disease progressions, complying with and adding detail to the growing evidence that seeding, infectivity, and strain dependence are unifying principles of neurodegenerative disease.

  • 12. Berthelsen, Hanne
    et al.
    Hakanen, Jari J.
    Westerlund, Hugo
    Stockholm University, Faculty of Social Sciences, Stress Research Institute.
    Copenhagen Psychosocial Questionnaire - A validation study using the Job Demand-Resources model2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 4, article id e0196450Article in journal (Refereed)
    Abstract [en]

    Aim

    This study aims at investigating the nomological validity of the Copenhagen Psychosocial Questionnaire (COPSOQ II) by using an extension of the Job Demands-Resources (JD-R) model with aspects of work ability as outcome.

    Material and methods

    The study design is cross-sectional. All staff working at public dental organizations in four regions of Sweden were invited to complete an electronic questionnaire (75% response rate, n = 1345). The questionnaire was based on COPSOQ II scales, the Utrecht Work Engagement scale, and the one-item Work Ability Score in combination with a proprietary item. The data was analysed by Structural Equation Modelling.

    Results

    This study contributed to the literature by showing that: A) The scale characteristics were satisfactory and the construct validity of COPSOQ instrument could be integrated in the JD-R framework; B) Job resources arising from leadership may be a driver of the two processes included in the JD-R model; and C) Both the health impairment and motivational processes were associated with WA, and the results suggested that leadership may impact WA, in particularly by securing task resources.

    Conclusion

    In conclusion, the nomological validity of COPSOQ was supported as the JD-R model can be operationalized by the instrument. This may be helpful for transferral of complex survey results and work life theories to practitioners in the field.

  • 13.
    Blasiak, Robert
    et al.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. The University of Tokyo, Japan.
    Jouffray, Jean-Baptiste
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Royal Swedish Academy of Sciences, Sweden.
    Wabnitz, Colette C. C.
    Sundström, Emma
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Österblom, Henrik
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Corporate control and global governance of marine genetic resources2018In: Science Advances, ISSN 0036-8156, E-ISSN 2375-2548, Vol. 4, no 6, article id eaar5237Article in journal (Refereed)
    Abstract [en]

    Who owns ocean biodiversity? This is an increasingly relevant question, given the legal uncertainties associated with the use of genetic resources from areas beyond national jurisdiction, which cover half of the Earth's surface. We accessed 38 million records of genetic sequences associated with patents and created a database of 12,998 sequences extracted from 862 marine species. We identified >1600 sequences from 91 species associated with deepsea and hydrothermal vent systems, reflecting commercial interest in organisms from remote ocean areas, as well as a capacity to collect and use the genes of such species. A single corporation registered 47% of all marine sequences included in gene patents, exceeding the combined share of 220 other companies (37%). Universities and their commercialization partners registered 12%. Actors located or headquartered in 10 countries registered 98% of all patent sequences, and 165 countries were unrepresented. Our findings highlight the importance of inclusive participation by all states in international negotiations and the urgency of clarifying the legal regime around access and benefit sharing of marine genetic resources. We identify a need for greater transparency regarding species provenance, transfer of patent ownership, and activities of corporations with a disproportionate influence over the patenting of marine biodiversity. We suggest that identifying these key actors is a critical step toward encouraging innovation, fostering greater equity, and promoting better ocean stewardship.

  • 14. Brand, Stephen K.
    et al.
    Schmidt, Joel E.
    Deem, Michael W.
    Daeyaert, Frits
    Ma, Yanhang
    Terasaki, Osamu
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). ShanghaiTech University, China.
    Orazov, Marat
    Davis, Mark E.
    Enantiomerically enriched, polycrystalline molecular sieves2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 20, p. 5101-5106Article in journal (Refereed)
    Abstract [en]

    Zeolite and zeolite-like molecular sieves are being used in a large number of applications such as adsorption and catalysis. Achievement of the long-standing goal of creating a chiral, polycrystalline molecular sieve with bulk enantioenrichment would enable these materials to perform enantioselective functions. Here, we report the synthesis of enantiomerically enriched samples of a molecular sieve. Enantiopure organic structure directing agents are designed with the assistance of computational methods and used to synthesize enantioenriched, polycrystalline molecular sieve samples of either enantiomer. Computational results correctly predicted which enantiomer is obtained, and enantiomeric enrichment is proven by high-resolution transmission electron microscopy. The enantioenriched and racemic samples of the molecular sieves are tested as adsorbents and heterogeneous catalysts. The enantioenriched molecular sieves show enantioselectivity for the ring opening reaction of epoxides and enantioselective adsorption of 2-butanol (the R enantiomer of the molecular sieve shows opposite and approximately equal enantioselectivity compared with the S enantiomer of the molecular sieve, whereas the racemic sample of the molecular sieve shows no enantioselectivity).

  • 15. Burlacu, Elena
    et al.
    Lackmann, Fredrik
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Aguilar, Lisbeth-Carolina
    Belikov, Sergey
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    van Nues, Rob
    Trahan, Christian
    Hector, Ralph D.
    Dominelli-Whiteley, Nicholas
    Cockroft, Scott L.
    Wieslander, Lars
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Oeffinger, Marlene
    Granneman, Sander
    High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 714Article in journal (Refereed)
    Abstract [en]

    While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein-rRNA interactions, providing intriguing insights into the temporal order of protein-rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis.

  • 16. Bögli, Sabine
    et al.
    Brown, B. Malcolm
    Marletta, Marco
    Tretter, Christiane
    Stockholm University, Faculty of Science, Department of Mathematics. Universität Bern, Switzerland.
    Wagenhofer, Markus
    Guaranteed resonance enclosures and exclosures for atoms and molecules2014In: Proceedings of the Royal Society. Mathematical, Physical and Engineering Sciences, ISSN 1364-5021, E-ISSN 1471-2946, Vol. 470, no 2171, article id 20140488Article in journal (Refereed)
    Abstract [en]

    In this paper, we confirm, with absolute certainty, a conjecture on a certain oscillatory behaviour of higher auto-ionizing resonances of atoms and molecules beyond a threshold. These results not only definitely settle a more than 30 year old controversy in Rittby et al. (1981 Phys. Rev. A 24, 1636-1639 (doi: 10.1103/PhysRevA.24.1636)) and Korsch et al. (1982 Phys. Rev. A 26, 1802-1803 (doi:10.1103/PhysRevA.26.1802)), but also provide new and reliable information on the threshold. Our interval-arithmetic-based method allows one, for the first time, to enclose and to exclude resonances with guaranteed certainty. The efficiency of our approach is demonstrated by the fact that we are able to show that the approximations in Rittby et al. (1981 Phys. Rev. A 24, 1636-1639 (doi:10.1103/PhysRevA.24.1636)) do lie near true resonances, whereas the approximations of higher resonances in Korsch et al. (1982 Phys. Rev. A 26, 1802-1803 (doi:10.1103/PhysRevA.26.1802)) do not, and further that there exist two new pairs of resonances as suggested in Abramov et al. (2001 J. Phys. A 34, 57-72 (doi:10.1088/0305-4470/34/1/304)).

  • 17.
    Campennì, Marco
    et al.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Schino, Gabriele
    Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e1812Article in journal (Refereed)
    Abstract [en]

    Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-baseds model of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by', agents adopting symmetry-based reciprocity showed differentiated social relationships and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to from stand competition alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions.

  • 18.
    Cannon, Barbara
    et al.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Nedergaard, Jan
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Cell biology: Neither brown nor white.2012In: Nature, ISSN 1476-4687, Vol. 488, no 7411, p. 286-287Article in journal (Refereed)
  • 19.
    Cannon, Barbara
    et al.
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Nedergaard, Jan
    Stockholm University, Faculty of Science, The Wenner-Gren Institute.
    Yes, even human brown fat is on fire!2012In: Journal of Clinical Investigation, ISSN 0021-9738, E-ISSN 1558-8238, Vol. 122, no 2, p. 486-489Article in journal (Refereed)
    Abstract [en]

    That adult humans possess brown fat is now accepted - but is the brown fat metabolically active? Does human brown fat actually combust fat to release heat? In this issue of the JCI, Ouellet et al. demonstrate that metabolism in brown fat really is increased when adult humans are exposed to cold. This boosts the possibility that calorie combustion in brown fat may be of significance for our metabolism and, correspondingly, that the absence of brown fat may increase our proneness to obesity - provided that brown fat becomes activated not only by cold but also through food-related stimuli.

  • 20. Carpenter, Stephen R.
    et al.
    Brock, William A.
    Folke, Carl
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Royal Swedish Academy of Sciences, Sweden.
    van Nes, Egbert H.
    Scheffer, Marten
    Allowing variance may enlarge the safe operating space for exploited ecosystems2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 46, p. 14384-14389Article in journal (Refereed)
    Abstract [en]

    Variable flows of food, water, or other ecosystem services complicate planning. Management strategies that decrease variability and increase predictability may therefore be preferred. However, actions to decrease variance over short timescales (2-4 y), when applied continuously, may lead to long-term ecosystem changes with adverse consequences. We investigated the effects of managing short-term variance in three well-understood models of ecosystem services: lake eutrophication, harvest of a wild population, and yield of domestic herbivores on a rangeland. In all cases, actions to decrease variance can increase the risk of crossing critical ecosystem thresholds, resulting in less desirable ecosystem states. Managing to decrease short-term variance creates ecosystem fragility by changing the boundaries of safe operating spaces, suppressing information needed for adaptive management, cancelling signals of declining resilience, and removing pressures that may build tolerance of stress. Thus, the management of variance interacts strongly and inseparably with the management of resilience. By allowing for variation, learning, and flexibility while observing change, managers can detect opportunities and problems as they develop while sustaining the capacity to deal with them.

  • 21. Carreras-Puigvert, Jordi
    et al.
    Zitnik, Marinka
    Jemth, Ann-Sofie
    Carter, Megan
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Unterlass, Judith E.
    Hallström, Björn
    Loseva, Olga
    Karem, Zhir
    Calderón-Montaño, José Manuel
    Lindskog, Cecilia
    Edqvist, Per-Henrik
    Matuszewski, Damian J.
    Blal, Hammou Ait
    Berntsson, Ronnie P. A.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Häggblad, Maria
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Martens, Ulf
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Studham, Matthew
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lundgren, Bo
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Wählby, Carolina
    Sonnhammer, Erik L. L.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Lundberg, Emma
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Zupan, Blaz
    Helleday, Thomas
    A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 1541Article in journal (Refereed)
    Abstract [en]

    The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.

  • 22.
    Carter, Megan
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Jemth, Ann-Sofie
    Hagenkort, Anna
    Page, Brent D. G.
    Gustafsson, Robert
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Griese, Julia J.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gad, Helge
    Valerie, Nicholas C. K.
    Desroses, Matthieu
    Boström, Johan
    Berglund, Ulrika Warpman
    Helleday, Thomas
    Stenmark, Pål
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH22015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7871Article in journal (Refereed)
    Abstract [en]

    Deregulated redox metabolism in cancer leads to oxidative damage to cellular components including deoxyribonucleoside triphosphates (dNTPs). Targeting dNTP pool sanitizing enzymes, such as MTH1, is a highly promising anticancer strategy. The MTH2 protein, known as NUDT15, is described as the second human homologue of bacterial MutT with 8-oxo-dGTPase activity. We present the first NUDT15 crystal structure and demonstrate that NUDT15 prefers other nucleotide substrates over 8-oxo-dGTP. Key structural features are identified that explain different substrate preferences for NUDT15 and MTH1. We find that depletion of NUDT15 has no effect on incorporation of 8-oxo-dGTP into DNA and does not impact cancer cell survival in cell lines tested. NUDT17 and NUDT18 were also profiled and found to have far less activity than MTH1 against oxidized nucleotides. We show that NUDT15 is not a biologically relevant 8-oxo-dGTPase, and that MTH1 is the most prominent sanitizer of the cellular dNTP pool known to date.

  • 23. Cebula, Marcus
    et al.
    Turan, Ilke Simsek
    Sjödin, Birgitta
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Thulasingam, Madhuranayaki
    Brock, Joseph
    Chmyrov, Volodymyr
    Widengren, Jerker
    Abe, Hiroshi
    Mannervik, Bengt
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Haeggström, Jesper Z.
    Rinaldo-Matthis, Agnes
    Akkaya, Engin U.
    Morgenstern, Ralf
    Catalytic Conversion of Lipophilic Substrates by Phase constrained Enzymes in the Aqueous or in the Membrane Phase2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 38316Article in journal (Refereed)
    Abstract [en]

    Both soluble and membrane-bound enzymes can catalyze the conversion of lipophilic substrates. The precise substrate access path, with regard to phase, has however, until now relied on conjecture from enzyme structural data only (certainly giving credible and valuable hypotheses). Alternative methods have been missing. To obtain the first experimental evidence directly determining the access paths (of lipophilic substrates) to phase constrained enzymes we here describe the application of a BODIPY-derived substrate (PS1). Using this tool, which is not accessible to cytosolic enzymes in the presence of detergent and, by contrast, not accessible to membrane embedded enzymes in the absence of detergent, we demonstrate that cytosolic and microsomal glutathione transferases (GSTs), both catalyzing the activation of PS1, do so only within their respective phases. This approach can serve as a guideline to experimentally validate substrate access paths, a fundamental property of phase restricted enzymes. Examples of other enzyme classes with members in both phases are xenobiotic-metabolizing sulphotransferases/UDP-glucuronosyl transferases or epoxide hydrolases. Since specific GSTs have been suggested to contribute to tumor drug resistance, PS1 can also be utilized as a tool to discriminate between phase constrained members of these enzymes by analyzing samples in the absence and presence of Triton X-100.

  • 24. Chen, Geng
    et al.
    Aharon, Nati
    Sun, Yong-Nan
    Zhang, Zi-Huai
    Zhang, Wen-Hao
    He, De-Yong
    Tang, Jian-Shun
    Xu, Xiao-Ye
    Kedem, Yaron
    Stockholm University, Faculty of Science, Department of Physics.
    Li, Chuan-Feng
    Guo, Guang-Can
    Heisenberg-scaling measurement of the single-photon Kerr non-linearity using mixed states2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 93Article in journal (Refereed)
    Abstract [en]

    Improving the precision of measurements is a significant scientific challenge. Previous works suggest that in a photon-coupling scenario the quantum fisher information shows a quantum-enhanced scaling of N-2, which in theory allows a better-than-classical scaling in practical measurements. In this work, utilizing mixed states with a large uncertainty and a post-selection of an additional pure system, we present a scheme to extract this amount of quantum fisher information and experimentally attain a practical Heisenberg scaling. We performed a measurement of a single-photon's Kerr non-linearity with a Heisenberg scaling, where an ultra-small Kerr phase of. 6 x 10(-8) rad was observed with a precision of similar or equal to 3.6 x 10(-10) rad. From the use of mixed states, the upper bound of quantum fisher information is improved to 2N(2). Moreover, by using an imaginary weak-value the scheme is robust to noise originating from the self-phase modulation.

  • 25. Chernobrovkin, Alexey
    et al.
    Marin-Vicente, Consuelo
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Karolinska Institutet, Sweden .
    Visa, Neus
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Zubarev, Roman A.
    Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 11176Article in journal (Refereed)
    Abstract [en]

    Phenomenological screening of small molecule libraries for anticancer activity yields potentially interesting candidate molecules, with a bottleneck in the determination of drug targets and the mechanism of anticancer action. We have found that, for the protein target of a small-molecule drug, the abundance change in late apoptosis is exceptional compared to the expectations based on the abundances of co-regulated proteins. Based on this finding, a novel method to drug target deconvolution is proposed. In a proof of principle experiment, the method yielded known targets of several common anticancer agents among a few (often, just one) likely candidates identified in an unbiased way from cellular proteome comprising more than 4,000 proteins. A validation experiment with a different set of cells and drugs confirmed the findings. As an additional benefit, mapping most specifically regulated proteins on known protein networks highlighted the mechanism of drug action. The new method, if proven to be general, can significantly shorten drug target identification, and thus facilitate the emergence of novel anticancer treatments.

  • 26. Cho, Hae Sung
    et al.
    Deng, Hexiang
    Miyasaka, Keiichi
    Dong, Zhiyue
    Cho, Minhyung
    Neimark, Alexander V.
    Kang, Jeung Ku
    Yaghi, Omar M.
    Terasaki, Osamu
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Graduate School of Energy, Environment, Water and Sustainability, South Korea.
    Extra adsorption and adsorbate superlattice formation in metal-organic frameworks2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 527, no 7579, p. 503-U193Article in journal (Refereed)
    Abstract [en]

    Metal-organic frameworks (MOFs) have a high internal surface area and widely tunable composition(1,2), which make them useful for applications involving adsorption, such as hydrogen, methane or carbon dioxide storage(3-9). The selectivity and uptake capacity of the adsorption process are determined by interactions involving the adsorbates and their porous host materials. But, although the interactions of adsorbate molecules with the internal MOF surface(10-17) and also amongst themselves within individual pores(18-22) have been extensively studied, adsorbate-adsorbate interactions across pore walls have not been explored. Here we show that local strain in the MOF, induced by pore filling, can give rise to collective and long-range adsorbate-adsorbate interactions and the formation of adsorbate superlattices that extend beyond an original MOF unit cell. Specifically, we use in situ small-angle X-ray scattering to track and map the distribution and ordering of adsorbate molecules in five members of the mesoporous MOF-74 series along entire adsorption-desorption isotherms. We find in all cases that the capillary condensation that fills the pores gives rise to the formation of 'extra adsorption domains'-that is, domains spanning several neighbouring pores, which have a higher adsorbate density than non-domain pores. In the case of one MOF, IRMOF-74-V-hex, these domains form a superlattice structure that is difficult to reconcile with the prevailing view of pore-filling as a stochastic process. The visualization of the adsorption process provided by our data, with clear evidence for initial adsorbate aggregation in distinct domains and ordering before an even distribution is finally reached, should help to improve our understanding of this process and may thereby improve our ability to exploit it practically.

  • 27.
    Cottman, Petter
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Cykelolyckor, orsaksfaktorer och samband: Ett metodtest i GIS för att hitta ett eventuellt samband mellan cykelolyckor och platsen där de sker2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
  • 28. Cova, Ilaria
    et al.
    Clerici, Francesca
    Rossi, Annalia
    Cucumo, Valentina
    Ghiretti, Roberta
    Maggiore, Laura
    Pomati, Simone
    Galimberti, Daniela
    Scarpini, Elio
    Mariani, Claudio
    Caracciolo, Barbara
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI).
    Weight Loss Predicts Progression of Mild Cognitive Impairment to Alzheimer's Disease2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0151710Article in journal (Refereed)
    Abstract [en]

    Background Weight loss is common in people with Alzheimer's disease (AD) and it could be a marker of impending AD in Mild Cognitive Impairment (MCI) and improve prognostic accuracy, if accelerated progression to AD would be shown.

    Aims To assess weight loss as a predictor of dementia and AD in MCI.

    Methods One hundred twenty-five subjects with MCI (age 73.8 +/- 7.1 years) were followed for an average of 4 years. Two weight measurements were carried out at a minimum time interval of one year. Dementia was defined according to DSM-IV criteria and AD according to NINCDS-ADRDA criteria. Weight loss was defined as a >= 4% decrease in baseline weight.

    Results Fifty-three (42.4%) MCI progressed to dementia, which was of the AD-type in half of the cases. Weight loss was associated with a 3.4-fold increased risk of dementia (95% CI = 1.5-6.9) and a 3.2-fold increased risk of AD (95% CI = 1.4-8.3). In terms of years lived without disease, weight loss was associated to a 2.3 and 2.5 years earlier onset of dementia and AD.

    Conclusions Accelerated progression towards dementia and AD is expected when weight loss is observed in MCI patients. Weight should be closely monitored in elderly with mild cognitive impairment.

  • 29.
    Dahlin, Paul
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Royal Institute of Technology (KTH), Sweden.
    Srivastava, Vaibhav
    Ekengren, Sophia
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Royal Institute of Technology (KTH), Sweden.
    Mckee, Lauren S.
    Bulone, Vincent
    Comparative analysis of sterol acquisition in the oomycetes Saprolegnia parasitica and Phytophthora infestans2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 2, article id e0170873Article in journal (Refereed)
    Abstract [en]

    The oomycete class includes pathogens of animals and plants which are responsible for some of the most significant global losses in agriculture and aquaculture. There is a need to replace traditional chemical means of controlling oomycete growth with more targeted approaches, and the inhibition of sterol synthesis is one promising area. To better direct these efforts, we have studied sterol acquisition in two model organisms: the sterol-autotrophic Saprolegnia parasitica, and the sterol-heterotrophic Phytophthora infestans. We first present a comprehensive reconstruction of a likely sterol synthesis pathway for S. parasitica, causative agent of the disease saprolegniasis in fish. This pathway shows multiple potential routes of sterol synthesis, and draws on several avenues of new evidence: bioinformatic mining for genes with sterol-related functions, expression analysis of these genes, and analysis of the sterol profiles in mycelium grown in different media. Additionally, we explore the extent to which P. infestans, which causes the late blight in potato, can modify exogenously provided sterols. We consider whether the two very different approaches to sterol acquisition taken by these pathogens represent any specific survival advantages or potential drug targets.

  • 30.
    Daley, Daniel O.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Skoglund, Ulf
    Söderström, Bill
    FtsZ does not initiate membrane constriction at the onset of division2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 33138Article in journal (Refereed)
    Abstract [en]

    The source of constriction required for division of a bacterial cell remains enigmatic. FtsZ is widely believed to be a key player, because in vitro experiments indicate that it can deform liposomes when membrane tethered. However in vivo evidence for such a role has remained elusive as it has been challenging to distinguish the contribution of FtsZ from that of peptidoglycan-ingrowth. To differentiate between these two possibilities we studied the early stages of division in Escherichia coli, when FtsZ is present at the division site but peptidoglycan synthesizing enzymes such as FtsI and FtsN are not. Our approach was to use correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) to monitor the localization of fluorescently labeled FtsZ, FtsI or FtsN correlated with the septal ultra-structural geometry in the same cell. We noted that the presence of FtsZ at the division septum is not sufficient to deform membranes. This observation suggests that, although FtsZ can provide a constrictive force, the force is not substantial at the onset of division. Conversely, the presence of FtsN always correlated with membrane invagination, indicating that allosteric activation of peptidoglycan ingrowth is the trigger for constriction of the cell envelope during cell division in E. coli.

  • 31. Dall'Osto, M.
    et al.
    Beddows, D. C. S.
    Asmi, A.
    Poulain, L.
    Hao, L.
    Freney, E.
    Allan, J. D.
    Canagaratna, M.
    Crippa, M.
    Bianchi, F.
    de Leeuw, G.
    Eriksson, A.
    Swietlicki, E.
    Hansson, Hans Christen
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Henzing, J. S.
    Granier, C.
    Zemankova, K.
    Laj, P.
    Onasch, T.
    Prevot, A.
    Putaud, J. P.
    Sellegri, K.
    Vidal, M.
    Virtanen, A.
    Simo, R.
    Worsnop, D.
    O'Dowd, C.
    Kulmala, M.
    Harrison, Roy M.
    Novel insights on new particle formation derived from a pan-european observing system2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 1482Article in journal (Refereed)
    Abstract [en]

    The formation of new atmospheric particles involves an initial step forming stable clusters less than a nanometre in size (<similar to 1 nm), followed by growth into quasi-stable aerosol particles a few nanometres (similar to 1-10 nm) and larger (>similar to 10 nm). Although at times, the same species can be responsible for both processes, it is thought that more generally each step comprises differing chemical contributors. Here, we present a novel analysis of measurements from a unique multi-station ground-based observing system which reveals new insights into continental-scale patterns associated with new particle formation. Statistical cluster analysis of this unique 2-year multi-station dataset comprising size distribution and chemical composition reveals that across Europe, there are different major seasonal trends depending on geographical location, concomitant with diversity in nucleating species while it seems that the growth phase is dominated by organic aerosol formation. The diversity and seasonality of these events requires an advanced observing system to elucidate the key processes and species driving particle formation, along with detecting continental scale changes in aerosol formation into the future.

  • 32.
    Daume, Stefan
    et al.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Georg-August-University Göttingen, Germany; Swedish Museum of Natural History, Sweden.
    Galaz, Victor
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Anyone Know What Species This Is? - Twitter Conversations as Embryonic Citizen Science Communities2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0151387Article in journal (Refereed)
    Abstract [en]

    Social media like blogs, micro-blogs or social networks are increasingly being investigated and employed to detect and predict trends for not only social and physical phenomena, but also to capture environmental information. Here we argue that opportunistic biodiversity observations published through Twitter represent one promising and until now unexplored example of such data mining. As we elaborate, it can contribute to real-time information to traditional ecological monitoring programmes including those sourced via citizen science activities. Using Twitter data collected for a generic assessment of social media data in ecological monitoring we investigated a sample of what we denote biodiversity observations with species determination requests (N = 191). These entail images posted as messages on the micro-blog service Twitter. As we show, these frequently trigger conversations leading to taxonomic determinations of those observations. All analysed Tweets were posted with species determination requests, which generated replies for 64% of Tweets, 86% of those contained at least one suggested determination, of which 76% were assessed as correct. All posted observations included or linked to images with the overall image quality categorised as satisfactory or better for 81% of the sample and leading to taxonomic determinations at the species level in 71% of provided determinations. We claim that the original message authors and conversation participants can be viewed as implicit or embryonic citizen science communities which have to offer valuable contributions both as an opportunistic data source in ecological monitoring as well as potential active contributors to citizen science programmes.

  • 33. Davies, Gail
    et al.
    Lam, Max
    Harris, Sarah E.
    Trampush, Joey W.
    Luciano, Michelle
    Hill, W. David
    Hagenaars, Saskia P.
    Ritchie, Stuart J.
    Marioni, Riccardo E.
    Fawns-Ritchie, Chloe
    Liewald, David C. M.
    Okely, Judith A.
    Ahola-Olli, Ari V.
    Barnes, Catriona L. K.
    Bertram, Lars
    Bis, Joshua C.
    Burdick, Katherine E.
    Christoforou, Andrea
    DeRosse, Pamela
    Djurovic, Srdjan
    Espeseth, Thomas
    Giakoumaki, Stella
    Giddaluru, Sudheer
    Gustavson, Daniel E.
    Hayward, Caroline
    Hofer, Edith
    Ikram, M. Arfan
    Karlsson, Robert
    Knowles, Emma
    Lahti, Jari
    Leber, Markus
    Li, Shuo
    Mather, Karen A.
    Melle, Ingrid
    Morris, Derek
    Oldmeadow, Christopher
    Palviainen, Teemu
    Payton, Antony
    Pazoki, Raha
    Petrovic, Katja
    Reynolds, Chandra A.
    Sargurupremraj, Muralidharan
    Scholz, Markus
    Smith, Jennifer A.
    Smith, Albert V.
    Terzikhan, Natalie
    Thalamuthu, Anbupalam
    Trompet, Stella
    van der Lee, Sven J.
    Ware, Erin B.
    Windham, B. Gwen
    Wright, Margaret J.
    Yang, Jingyun
    Yu, Jin
    Ames, David
    Amin, Najaf
    Amouyel, Philippe
    Andreassen, Ole A.
    Armstrong, Nicola J.
    Assareh, Amelia A.
    Attia, John R.
    Attix, Deborah
    Avramopoulos, Dimitrios
    Bennett, David A.
    Boehmer, Anne C.
    Boyle, Patricia A.
    Brodaty, Henry
    Campbell, Harry
    Cannon, Tyrone D.
    Cirulli, Elizabeth T.
    Congdon, Eliza
    Conley, Emily Drabant
    Corley, Janie
    Cox, Simon R.
    Dale, Anders M.
    Dehghan, Abbas
    Dick, Danielle
    Dickinson, Dwight
    Eriksson, Johan G.
    Evangelou, Evangelos
    Faul, Jessica D.
    Ford, Ian
    Freimer, Nelson A.
    Gao, He
    Giegling, Ina
    Gillespie, Nathan A.
    Gordon, Scott D.
    Gottesman, Rebecca F.
    Griswold, Michael E.
    Gudnason, Vilmundur
    Harris, Tamara B.
    Hartmann, Annette M.
    Hatzimanolis, Alex
    Heiss, Gerardo
    Holliday, Elizabeth G.
    Joshi, Peter K.
    Kahonen, Mika
    Kardia, Sharon L. R.
    Karlsson, Ida
    Kleineidam, Luca
    Knopman, David S.
    Kochan, Nicole A.
    Konte, Bettina
    Kwok, John B.
    Le Hellard, Stephanie
    Lee, Teresa
    Lehtimaki, Terho
    Li, Shu-Chen
    Liu, Tian
    Koini, Marisa
    London, Edythe
    Longstreth, Will T.
    Lopez, Oscar L.
    Loukola, Anu
    Luck, Tobias
    Lundervold, Astri J.
    Lundquist, Anders
    Lyytikainen, Leo-Pekka
    Martin, Nicholas G.
    Montgomery, Grant W.
    Murray, Alison D.
    Need, Anna C.
    Noordam, Raymond
    Nyberg, Lars
    Ollier, William
    Papenberg, Göran
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI). Max Planck Institute for Human Development, Germany.
    Pattie, Alison
    Polasek, Ozren
    Poldrack, Russell A.
    Psaty, Bruce M.
    Reppermund, Simone
    Riedel-Heller, Steffi G.
    Rose, Richard J.
    Rotter, Jerome I.
    Roussos, Panos
    Rovio, Suvi P.
    Saba, Yasaman
    Sabb, Fred W.
    Sachdev, Perminder S.
    Satizabal, Claudia L.
    Schmid, Matthias
    Scott, Rodney J.
    Scult, Matthew A.
    Simino, Jeannette
    Slagboom, P. Eline
    Smyrnis, Nikolaos
    Soumare, Aicha
    Stefanis, Nikos C.
    Stott, David J.
    Straub, Richard E.
    Sundet, Kjetil
    Taylor, Adele M.
    Taylor, Kent D.
    Tzoulaki, Ioanna
    Tzourio, Christophe
    Uitterlinden, Andre
    Vitart, Veronique
    Voineskos, Aristotle N.
    Kaprio, Jaakko
    Wagner, Michael
    Wagner, Holger
    Weinhold, Leonie
    Wen, K. Hoyan
    Widen, Elisabeth
    Yang, Qiong
    Zhao, Wei
    Adams, Hieab H. H.
    Arking, Dan E.
    Bilder, Robert M.
    Bitsios, Panos
    Boerwinkle, Eric
    Chiba-Falek, Ornit
    Corvin, Aiden
    De Jager, Philip L.
    Debette, Stephanie
    Donohoe, Gary
    Elliott, Paul
    Fitzpatrick, Annette L.
    Gill, Michael
    Glahn, David C.
    Hagg, Sara
    Hansell, Narelle K.
    Hariri, Ahmad R.
    Ikram, M. Kamran
    Jukema, J. Wouter
    Vuoksimaa, Eero
    Keller, Matthew C.
    Kremen, William S.
    Launer, Lenore
    Lindenberger, Ulman
    Palotie, Aarno
    Pedersen, Nancy L.
    Pendleton, Neil
    Porteous, David J.
    Raikkonen, Katri
    Raitakari, Olli T.
    Ramirez, Alfredo
    Reinvang, Ivar
    Rudan, Igor
    Rujescu, Dan
    Schmidt, Reinhold
    Schmidt, Helena
    Schofield, Peter W.
    Schofield, Peter R.
    Starr, John M.
    Steen, Vidar M.
    Trollor, Julian N.
    Turner, Steven T.
    Van Duijn, Cornelia M.
    Villringer, Arno
    Weinberger, Daniel R.
    Weir, David R.
    Wilson, James F.
    Malhotra, Anil
    McIntosh, Andrew M.
    Gale, Catharine R.
    Seshadri, Sudha
    Mosley, Thomas H.
    Bressler, Jan
    Lencz, Todd
    Deary, Ian J.
    Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 2098Article in journal (Refereed)
    Abstract [en]

    General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N = 300,486; age 16-102) and find 148 genome-wide significant independent loci (P < 5 x 10(-8)) associated with general cognitive function. Within the novel genetic loci are variants associated with neurodegenerative and neurodevelopmental disorders, physical and psychiatric illnesses, and brain structure. Gene-based analyses find 709 genes associated with general cognitive function. Expression levels across the cortex are associated with general cognitive function. Using polygenic scores, up to 4.3% of variance in general cognitive function is predicted in independent samples. We detect significant genetic overlap between general cognitive function, reaction time, and many health variables including eyesight, hypertension, and longevity. In conclusion we identify novel genetic loci and pathways contributing to the heritability of general cognitive function.

  • 34.
    de Gysser, Isabell
    Stockholm University, Faculty of Science, Department of Mathematics and Science Education.
    Språkstödjande undervisning i de naturorienterade ämnena: En studie i grundskolans år 4-6 utifrån lärares perspektiv på undervisning2016Student paper second term, 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Syftet med den här studien är att belysa och tillföra ämnesdidaktisk kunskap kring språkstödjande undervisning i de naturorienterade ämnena i grundskolans årskurser 4-6. Studien ställer upp tre forskningsfrågor som handlar om hur några lärare beskriver sin undervisning i de naturorienterade ämnena utifrån ett språkligt förhållningssätt, vilka praktiska tillvägagångssätt de väljer att använda samt hur dessa val syftar till att skapa förståelse för ämnesspecifikt innehåll hos eleverna. Studien har således ett perspektiv på undervisning utifrån en lärarhorisont och grundar sig på sex kvalitativa semistrukturerade lärarintervjuer. Insamlat material har analyserats och resulterat i fem teman som strukturerar informanternas utsagor om deras språkinriktade undervisning: mötet med ämnesspråket, svårigheter och signifikant svårare områden, metoder och aktiviteter, synlig kunskapsutveckling samt framgångsfaktorer. Studien visar i likhet med tidigare empirisk forskning kring det naturvetenskapliga språkets särdrag att det skolspråk eleverna möter i NO-undervisningen i årskurs 4-6 har komplexa beståndsdelar. Undervisningen handlar mycket om att stötta eleverna i den språkligt och innehållsligt abstrakta världen genom metoder och aktiviteter som kopplar nytt ämnesstoff till en för eleverna välkänd kontext. När lärarna beskriver didaktiska val handlar det i stor utsträckning om sådana som kontextualiserar ämnesinnehållet, gör eleverna delaktiga i kommunikativa sammanhang samt ställer upp ett stödjande ramverk kring språket. Utifrån studiens resultat och teoretiska bakgrund kan lärarstudenter, lärare, skolledare eller annan personal verksam i svensk skola finna belägg för vikten av att ställa upp kunskapsmål och språkliga mål. Diskussionen i studien leder fram till ett förslag på vidare studier som handlar om de, från tidigare forskning uppställda tre kännetecken för en funktionell språkinriktad undervisning; kontextualisering, interaktion samt språkstöttning, skulle kunna utökas till att även omfatta en aspekt som handlar om vikten av repetition i undervisningen. I den här studien blev denna fjärde aspekt framträdande tillsammans med de tre övriga. 

  • 35. de lavergne, C.
    et al.
    Madec, G.
    Roquet, Fabien
    Stockholm University, Faculty of Science, Department of Meteorology .
    Holmes, R. M.
    McDougall, T. J.
    Abyssal ocean overturning shaped by seafloor distribution2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 551, no 7679, p. 181-186Article in journal (Refereed)
    Abstract [en]

    The abyssal ocean is broadly characterized by northward flow of the densest waters and southward flow of less-dense waters above them. Understanding what controls the strength and structure of these interhemispheric flows-referred to as the abyssal overturning circulation-is key to quantifying the ocean's ability to store carbon and heat on timescales exceeding a century. Here we show that, north of 32 degrees S, the depth distribution of the seafloor compels dense southernorigin waters to flow northward below a depth of about 4 kilometres and to return southward predominantly at depths greater than 2.5 kilometres. Unless ventilated from the north, the overlying mid-depths (1 to 2.5 kilometres deep) host comparatively weak mean meridional flow. Backed by analysis of historical radiocarbon measurements, the findings imply that the geometry of the Pacific, Indian and Atlantic basins places a major external constraint on the overturning structure.

  • 36. de Vries, Paul S.
    et al.
    Sabater-Lleal, Maria
    Chasman, Daniel I.
    Trompet, Stella
    Ahluwalia, Tarunveer S.
    Teumer, Alexander
    Kleber, Marcus E.
    Chen, Ming-Huei
    Wang, Jie Jin
    Attia, John R.
    Marioni, Riccardo E.
    Steri, Maristella
    Weng, Lu-Chen
    Pool, Rene
    Grossmann, Vera
    Brody, Jennifer A.
    Venturini, Cristina
    Tanaka, Toshiko
    Rose, Lynda M.
    Oldmeadow, Christopher
    Mazur, Johanna
    Basu, Saonli
    Frånberg, Mattias
    Stockholm University, Faculty of Science, Numerical Analysis and Computer Science (NADA). Karolinska Institutet, Sweden.
    Yang, Qiong
    Ligthart, Symen
    Hottenga, Jouke J.
    Rumley, Ann
    Mulas, Antonella
    de Craen, Anton J. M.
    Grotevendt, Anne
    Taylor, Kent D.
    Delgado, Graciela E.
    Kifley, Annette
    Lopez, Lorna M.
    Berentzen, Tina L.
    Mangino, Massimo
    Bandinelli, Stefania
    Morrison, Alanna C.
    Hamsten, Anders
    Tofler, Geoffrey
    de Maat, Moniek P. M.
    Draisma, Harmen H. M.
    Lowe, Gordon D.
    Zoledziewska, Magdalena
    Sattar, Naveed
    Lackner, Karl J.
    Voelker, Uwe
    McKnight, Barbara
    Huang, Jie
    Holliday, Elizabeth G.
    McEvoy, Mark A.
    Starr, John M.
    Hysi, Pirro G.
    Hernandez, Dena G.
    Guan, Weihua
    Rivadeneira, Fernando
    McArdle, Wendy L.
    Slagboom, P. Eline
    Zeller, Tanja
    Psaty, Bruce M.
    Uitterlinden, Andre G.
    de Geus, Eco J. C.
    Stott, David J.
    Binder, Harald
    Hofman, Albert
    Franco, Oscar H.
    Rotter, Jerome I.
    Ferrucci, Luigi
    Spector, Tim D.
    Deary, Ian J.
    Maerz, Winfried
    Greinacher, Andreas
    Wild, Philipp S.
    Cucca, Francesco
    Boomsma, Dorret I.
    Watkins, Hugh
    Tang, Weihong
    Ridker, Paul M.
    Jukema, Jan W.
    Scott, Rodney J.
    Mitchell, Paul
    Hansen, Torben
    O'Donnell, Christopher J.
    Smith, Nicholas L.
    Strachan, David P.
    Dehghan, Abbas
    Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 1, article id e0167742Article in journal (Refereed)
    Abstract [en]

    An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5x10(-8) is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5x10(-8)), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.

  • 37. Del Giudice, Marco
    et al.
    Bosia, Carla
    Grigolon, Silvia
    Bo, Stefano
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Stochastic sequestration dynamics: a minimal model with extrinsic noise for bimodal distributions and competitors correlation2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 10387Article in journal (Refereed)
    Abstract [en]

    Many biological processes are known to be based on molecular sequestration. This kind of dynamics involves two types of molecular species, namely targets and sequestrants, that bind to form a complex. In the simple framework of mass-action law, key features of these systems appear to be threshold-like profiles of the amounts of free molecules as a function of the parameters determining their possible maximum abundance. However, biochemical processes are probabilistic and take place in stochastically fluctuating environments. How these different sources of noise affect the final outcome of the network is not completely characterised yet. In this paper we specifically investigate the effects induced by a source of extrinsic noise onto a minimal stochastic model of molecular sequestration. We analytically show how bimodal distributions of the targets can appear and characterise them as a result of noise filtering mediated by the threshold response. We then address the correlations between target species induced by the sequestrant and discuss how extrinsic noise can turn the negative correlation caused by competition into a positive one. Finally, we consider the more complex scenario of competitive inhibition for enzymatic kinetics and discuss the relevance of our findings with respect to applications.

  • 38. Didion, John P.
    et al.
    Martin, Marcel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Collins, Francis S.
    Atropos: specific, sensitive, and speedy trimming of sequencing reads2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3720Article in journal (Refereed)
    Abstract [en]

    A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leadingedge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github. com/jdidion/atropos.

  • 39.
    Díez, Beatriz
    et al.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Pontificia Universidad Católica de Chile, Chile; Center for Climate Change and Resilience Research (CR)2, Chile.
    Nylander, Johan A. A.
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Swedish Museum of Natural History, Sweden.
    Ininbergs, Karolina
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Dupont, Christopher L.
    Allen, Andrew E.
    Yooseph, Shibu
    Rusch, Douglas B.
    Bergman, Birgitta
    Stockholm University, Science for Life Laboratory (SciLifeLab). Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5, article id e0155757Article in journal (Refereed)
    Abstract [en]

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 mu m to 20 mu m and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial lightharvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

  • 40.
    Ebert, Karin
    et al.
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Axelsson, Leona
    Stockholm University.
    Harbor, Jon
    Stockholm University, Faculty of Science, Department of Physical Geography. Purdue University, USA.
    Opportunities and challenges for building alumni networks in Sweden: a case study of Stockholm University2015In: Journal of Higher Education Policy and Management, ISSN 1360-080X, E-ISSN 1469-9508, Vol. 37, no 2, p. 252-262Article in journal (Refereed)
    Abstract [en]

    Because of the potential value of alumni involvement for student success, for connections to society and as a base for future philanthropy, there is growing interest in developing university alumni relations programmes in countries that do not have a long tradition in this area. This case study of Stockholm University describes the goals, strategies, barriers and successes of building an alumni programme in an environment that lacks a tradition of alumni relations and aims to provide perspectives and ideas that can help other universities worldwide with their work towards building alumni programmes that fit their cultural contexts and goals.

  • 41. Ericsson, Malin
    et al.
    Lundholm, Cecilia
    Fors, Stefan
    Stockholm University, Faculty of Social Sciences, Aging Research Center (ARC), (together with KI).
    Dahl Aslan, Anna K.
    Zavala, Catalina
    Reynolds, Chandra A.
    Pedersen, Nancy L.
    Childhood social class and cognitive aging in the Swedish Adoption/Twin Study of Aging2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 27, p. 7001-7006Article in journal (Refereed)
    Abstract [en]

    In this report we analyzed genetically informative data to investigate within-person change and between-person differences in late-life cognitive abilities as a function of childhood social class. We used data from nine testing occasions spanning 28 y in the Swedish Adoption/Twin Study of Aging and parental social class based on the Swedish socioeconomic index. Cognitive ability included a general factor and the four domains of verbal, fluid, memory, and perceptual speed. Latent growth curve models of the longitudinal data tested whether level and change in cognitive performance differed as a function of childhood social class. Between-within twin-pair analyses were performed on twins reared apart to assess familial confounding. Childhood social class was significantly associated with mean-level cognitive performance at age 65 y, but not with rate of cognitive change. The association decreased in magnitude but remained significant after adjustments for level of education and the degree to which the rearing family was supportive toward education. A between-pair effect of childhood social class was significant in all cognitive domains, whereas within-pair estimates were attenuated, indicating genetic confounding. Thus, childhood social class is important for cognitive performance in adulthood on a population level, but the association is largely attributable to genetic influences.

  • 42.
    Eriksson, Jenny
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    EU:s gemensamma jordbrukspolitikoch dess effekter på lantbrukaresbeslut samt landskapet: En fältstudie i Bettna, Södermanlands Län2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    Sverige har varit medlemmar i EU sedan 1995. Sedan dess har stora förändringar skettbåde i EU:s gemensamma jordbrukspolitik (GJP) och inom Sveriges jordbruk. Tidigarestudier har undersökt de ekologiska och ekonomiska effekterna av GJP med kvantitativametoder och modellering. Denna studie undersöker hur GJP har påverkat lantbrukaresbeslut i deras jordbruksverksamhet samt hur detta påverkar landskapet i samhälletBettna, Södermanlands län. Empirin som ligger till grund för uppsatsen har samlats ingenom semistrukturerade intervjuer med boende i Bettna som är involverade ijordbruket som heltids- eller deltidslantbrukare. De slutsatser som har framkommit äratt GJP inte haft särskilt stor påverkan på lantbrukarnas beslut i hur de driver sinjordbruksverksamhet. Detta trots att majoriteten av heltidslantbrukarna och vissadeltidslantbrukare var ekonomiskt beroende av stöden. Landskapet i Bettna har till vissdel förändrats till följd av GJP, dels genom att det förs ett mer extensivt jordbruk medökad vallodling, samt restaurering av betesmarker.

  • 43.
    Eriksson, Kimmo
    et al.
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for the Study of Cultural Evolution. Mälardalen University, Sweden.
    Cownden, Daniel
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for the Study of Cultural Evolution. INgrooves, Canada.
    Strimling, Pontus
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for the Study of Cultural Evolution. Institute for Futures Studies, Sweden.
    Social learning may lead to population level conformity without individual level frequency bias2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 17341Article in journal (Refereed)
    Abstract [en]

    A requirement of culture, whether animal or human, is some degree of conformity of behavior within populations. Researchers of gene-culture coevolution have suggested that population level conformity may result from frequency-biased social learning: individuals sampling multiple role models and preferentially adopting the majority behavior in the sample. When learning from a single role model, frequency-bias is not possible. We show why a population-level trend, either conformist or anticonformist, may nonetheless be almost inevitable in a population of individuals that learn through social enhancement, that is, using observations of others' behavior to update their own probability of using a behavior in the future. The exact specification of individuals' updating rule determines the direction of the trend. These results offer a new interpretation of previous findings from simulations of social enhancement in combination with reinforcement learning, and demonstrate how results of dynamical models may strongly depend on seemingly innocuous choices of model specifications, and how important it is to obtain empirical data on which to base such choices.

  • 44. Faranda, Davide
    et al.
    Messori, Gabriele
    Stockholm University, Faculty of Science, Department of Meteorology .
    Yiou, Pascal
    Dynamical proxies of North Atlantic predictability and extremes2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 41278Article in journal (Refereed)
    Abstract [en]

    Atmospheric flows are characterized by chaotic dynamics and recurring large-scale patterns. These two characteristics point to the existence of an atmospheric attractor defined by Lorenz as: the collection of all states that the system can assume or approach again and again, as opposed to those that it will ultimately avoid. The average dimension D of the attractor corresponds to the number of degrees of freedom sufficient to describe the atmospheric circulation. However, obtaining reliable estimates of D has proved challenging. Moreover, D does not provide information on transient atmospheric motions, such as those leading to weather extremes. Using recent developments in dynamical systems theory, we show that such motions can be classified through instantaneous rather than average properties of the attractor. The instantaneous properties are uniquely determined by instantaneous dimension and stability. Their extreme values correspond to specific atmospheric patterns, and match extreme weather occurrences. We further show the existence of a significant correlation between the time series of instantaneous stability and dimension and the mean spread of sea-level pressure fields in an operational ensemble weather forecast at lead times of over two weeks. Instantaneous properties of the attractor therefore provide an efficient way of evaluating and informing operational weather forecasts.

  • 45.
    Fetzer, Ingo
    et al.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Helmholtz Centre for Environmental Research–UFZ, Germany.
    Johst, Karin
    Schaewe, Robert
    Banitz, Thomas
    Harms, Hauke
    Chatzinotas, Antonis
    The extent of functional redundancy changes as species' roles shift in different environments2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 48, p. 14888-14893Article in journal (Refereed)
    Abstract [en]

    Assessing the ecological impacts of environmental change requires knowledge of the relationship between biodiversity and ecosystem functioning. The exact nature of this relationship can differ considerably between ecosystems, with consequences for the efficacy of species diversity as a buffer against environmental change. Using a microbial model system, we show that the relationship can vary depending on environmental conditions. Shapes suggesting functional redundancy in one environment can change, suggesting functional differences in another environment. We find that this change is due to shifting species roles and interactions. Species that are functionally redundant in one environment may become pivotal in another. Thus, caution is advised in drawing conclusions about functional redundancy based on a single environmental situation. It also implies that species richness is important because it provides a pool of species with potentially relevant traits. These species may turn out to be essential performers or partners in new interspecific interactions after environmental change. Therefore, our results challenge the generality of functional redundancy.

  • 46.
    Florêncio, Cláudia
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Learning to bridge conservation and development: A case study of the Environmental Monitors Programme in Kruger to Canyons Biosphere Reserve2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    We live in a world that faces several social and environmental problems and achieving sustainable development in contexts where it is necessary to alleviate poverty without eroding the capacity of the ecosystems to support future generations is challenging. Therefore, fostering sustainable development requires enabling both society and environment to cope with disturbances, adapt to and shape change (resilience).

    Literature suggests that adaptive co-management practices are appropriate for building resilience and fostering sustainable development. Additionally, studies have highlighted the role of bridging organizations in coordinating and facilitating adaptive co-management. However, adaptive co-management has not been studied in poverty contexts.

    This thesis aims to understand what the main tasks of bridging organizations are, and how they facilitate and stimulate adaptive co-management in poverty contexts and their role in nurturing sustainability.

    The Environmental Monitors Programme of the Kruger to Canyons Biosphere Reserve was chosen as a case-study. Biosphere reserves are considered learning sites for sustainable development. The programme was studied through the lenses of a bridging organization.

    Semi-structured interviews and participatory observation with stakeholders identified: 1) the importance of existing networks and collaborations; 2) monitoring contribution to the identification of social and environmental issues, experimentation contribution to the implementation of sustainable harvesting practices; 3) environmental education combined with social learning lead to community empowerment and adaptive responses that e.g. address erosion; 4) environmental monitors have a crucial role in linking organizations and communities; 5) challenges related to low income settings include communities’ basic needs.

    This study illustrates the need to address both social and ecological problems in a concerted manner, by capacitating and empowering communities while conserving the environment. Additionally, points out the need of studying alternative co-management strategies that give focus on different priorities regarding stakeholders’ interests and the influence of power in decision-making in poverty contexts.

  • 47.
    Forselius, Ellen
    Stockholm University, Faculty of Science, Department of Physical Geography.
    Spatial patterns of pollution associated with creosote treated poles in Mälardalen2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Creosote is a product name given to a mixture of several hundred compounds, which is often used to protect wooden poles from rot and insect damage, however it has also been linked to causing cancer in humans. Alternative materials for power poles include concrete, steel, composite and non-treated wooden poles. This report looks at Mälarenergi Elnät ABs 17,000 creosote coated poles and their patterns of pollution. GIS analyses in ArcGIS were used to evaluate which creosote poles are most critical to replace by implementing a system of "penalty points" based on the spatial distribution of the poles. 15 of the creosote poles were selected for a field study to investigate how much creosote is leaked to the ground.1,000 of the power poles were assigned penalty points of 10 or higher which could be a starting point in pole replacement, although the penalty points system could be used in many different ways for this purpose. Of the 15 power poles investigated during the field work, 5 showed higher leakage than recommended by Naturvårdsverkets guidelines for sensitive ground use. These 15 poles only make up 0,1% of Mälarenergi Elnät ABs total creosote coated poles, but the results are considered alarming enough to at least merit further studies of the creosote leakage.

  • 48. Frantz, Laurent A. F.
    et al.
    Mullin, Victoria E.
    Pionnier-Capitan, Maud
    Lebrasseur, Ophélie
    Ollivier, Morgane
    Perri, Angela
    Linderholm, Anna
    Mattiangeli, Valeria
    Teasdale, Matthew D.
    Dimopoulos, Evangelos A.
    Tresset, Anne
    Duffraisse, Marilyne
    McCormick, Finbar
    Bartosiewicz, László
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies.
    Gál, Erika
    Nyerges, Éva A.
    Sablin, Mikhail V.
    Bréhard, Stéphanie
    Mashkour, Marjan
    Balaşescu, Adrian
    Gillet, Benjamin
    Hughes, Sandrine
    Chassaing, Olivier
    Hitte, Christophe
    Vigne, Jean-Denis
    Dobney, Keith
    Hänni, Catherine
    Bradley, Daniel G.
    Larson, Greger
    Genomic and archaeological evidence suggests a dual origin of domestic dogs2016In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6290, p. 1228-1231Article in journal (Refereed)
    Abstract [en]

    The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to similar to 4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (similar to 14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.

  • 49.
    Fremling, Christoffer
    Stockholm University, Faculty of Science, Department of Astronomy.
    PTF12os and iPTF13bvn: Two stripped-envelope supernovae discovered by the Palomar Transient Factory2016Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is based on research made by the intermediate Palomar Transient Factory [(i)PTF], and it is particularly closely tied to the still ongoing research on the stripped-envelope (SE) supernova (SN), iPTF13bvn (Type Ib), that occurred in the nearby galaxy NGC 5806. This SN was initially thought to have been the explosion of a very massive Wolf-Rayet (WR) star, but I have shown that this is very likely not the case. I suggest instead that the most likely scenario is that iPTF13bvn originated from a binary system where the envelope was stripped off from the SN progenitor by tidal forces from a companion star, in a similar way as for the very well studied Type IIb SN 2011dh. I have also investigated another SE SN, PTF12os (Type IIb), that occurred in the same galaxy as iPTF13bvn, with the conclusion that PTF12os and iPTF13bvn are very similar amongst themselves, and that both of them are also remarkably similar to SN 2011dh, in terms of all of the available observations (light-curves, spectra). Hydrodynamical models have been used to constrain the explosion parameters of iPTF13bvn, PTF12os and SN 2011dh; finding 56Ni masses in the range 0.063 − 0.075 M⊙, ejecta masses in the range 1.85 − 1.91 M⊙. Using the 56Ni-masses derived from our hydrodynamical modeling in combination with nebular models and late-time spectroscopy we were able to constrain the Zero-Age Main Sequence (ZAMS) mass to ∼ 12 M⊙ for iPTF13bvn and ≲ 15 M⊙ for PTF12os. In current stellar evolution models, stars with these masses on the ZAMS cannot lose their hydrogen envelopes and become SE SNe without binary interactions.

  • 50.
    Fryers Hellquist, Katharina
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Exploring Change Agents in Watershed Governance: The Case of Lake Mälaren, Sweden.2016Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    The world is changing rapidly and it has become increasingly important to build resilience, through adaptation and transformation, to maintain the ecosystem services that watersheds provide. The importance of change agents to prepare for and navigate the transformation, as well as build resilience in the new state has been highlighted by scholars, however not in a comprehensive way, but rather as a final conclusion. This study investigates the role and perceptions of change agents around Lake Mälaren, Sweden. Through in-depth interviews, it explores incentives for change, visions, and strategies to reach those visions. The findings show that many actors without holistic and overarching governance creates dissatisfaction among change agent. Components of their visions are shared: well-functioning ecosystems that provide ecosystem services in the future, and to achieve legislated goals. Their strategy on how to reach their vision diverge: powerful political decisions and stricter steering, or changes in values and the inclusion of local knowledge of citizens. This study adds nuance to visions, highlights the importance of a common strategy and that collaboration is key to maintain the future provision of the essential ecosystem services watersheds provide.

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