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  • 1. Aad, G
    et al.
    Bélanger-Champagne, Camille
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Brenner, Richard
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Buszello, Claus P.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Ekelöf, Tord
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Ellert, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Ferrari, Arnaud
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Hansen, C. J.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Zwalinski, L
    Measurement of the inelastic proton-proton cross-section at root s=7 TeV with the ATLAS detector2011In: Nature Communications, E-ISSN 2041-1723, Vol. 2, p. 463-Article in journal (Refereed)
    Abstract [en]

    The dependence of the rate of proton-proton interactions on the centre-of-mass collision energy, root s, is of fundamental importance for both hadron collider physics and particle astrophysics. The dependence cannot yet be calculated from first principles; therefore, experimental measurements are needed. Here we present the first measurement of the inelastic proton-proton interaction cross-section at a centre-of-mass energy, root s, of 7 TeV using the ATLAS detector at the Large Hadron Collider. Events are selected by requiring hits on scintillation counters mounted in the forward region of the detector. An inelastic crosssection of 60.3 +/- 2.1 mb is measured for xi > 5x10(-6), where xi is calculated from the invariant mass, M(X), of hadrons selected using the largest rapidity gap in the event. For diffractive events, this corresponds to requiring at least one of the dissociation masses to be larger than 15.7 GeV.

  • 2. Aad, G.
    et al.
    Grahn, Karl-Johan
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Lund-Jensen, Bengt
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Strandberg, Jonas
    University of Chicago.
    Lafaye, Remi
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Zwalinski, L.
    et al.,
    Measurement of the inelastic proton-proton cross-section at root s=7 TeV with the ATLAS detector2011In: Nature Communications, E-ISSN 2041-1723, Vol. 2, p. 463-Article in journal (Refereed)
    Abstract [en]

    The dependence of the rate of proton-proton interactions on the centre-of-mass collision energy, root s, is of fundamental importance for both hadron collider physics and particle astrophysics. The dependence cannot yet be calculated from first principles; therefore, experimental measurements are needed. Here we present the first measurement of the inelastic proton-proton interaction cross-section at a centre-of-mass energy, root s, of 7 TeV using the ATLAS detector at the Large Hadron Collider. Events are selected by requiring hits on scintillation counters mounted in the forward region of the detector. An inelastic crosssection of 60.3 +/- 2.1 mb is measured for xi > 5x10(-6), where xi is calculated from the invariant mass, M(X), of hadrons selected using the largest rapidity gap in the event. For diffractive events, this corresponds to requiring at least one of the dissociation masses to be larger than 15.7 GeV.

  • 3.
    Aaij, R.
    et al.
    Nikhef Natl Inst Subatom Phys, Amsterdam, Netherlands.
    Eklund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Nuclear Physics. Univ Glasgow, Sch Phys & Astron, Glasgow, Lanark, Scotland.
    Zunica, G.
    Univ Manchester, Dept Phys & Astron, Manchester, Lancs, England.
    Study of the doubly charmed tetraquark T-cc(+)2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 3351Article in journal (Refereed)
    Abstract [en]

    Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the (DD0)-D-0 pi(+) mass spectrum just below the D*+D-0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalar T-cc(+), tetraquark with a quark content of cc (u) over bar(d) over bar and spin-parity quantum numbers J(P) =1(+). Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D*(+) mesons is consistent with the observed D-0 pi(+) mass distribution. To analyse the mass of the resonance and its coupling to the DID system, a dedicated model is developed under the assumption of an isoscalar axial-vector T-cc(+), state decaying to the D*D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the T-cc(+), state. In addition, an unexpected dependence of the production rate on track multiplicity is observed.

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  • 4.
    Abbey-Lee, Robin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Max Planck Inst Ornithol, Germany.
    Dingemanse, Niels J.
    Ludwig Maximilians Univ Munchen, Germany.
    Adaptive individual variation in phenological responses to perceived predation levels2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 1601Article in journal (Refereed)
    Abstract [en]

    The adaptive evolution of timing of breeding (a component of phenology) in response to environmental change requires individual variation in phenotypic plasticity for selection to act upon. A major question is what processes generate this variation. Here we apply multi-year manipulations of perceived predation levels (PPL) in an avian predator-prey system, identifying phenotypic plasticity in phenology as a key component of alternative behavioral strategies with equal fitness payoffs. We show that under low-PPL, faster (versus slower) exploring birds breed late (versus early); the pattern is reversed under high-PPL, with breeding synchrony decreasing in conjunction. Timing of breeding affects reproductive success, yet behavioral types have equal fitness. The existence of alternative behavioral strategies thus explains variation in phenology and plasticity in reproductive behavior, which has implications for evolution in response to anthropogenic change.

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  • 5.
    Abdellah, Tebani
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Gummesson, Anders
    Zhong, Wen
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Koistinen, Ina Schuppe
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lakshmikanth, Tadepally
    Olsson, Lisa M.
    Boulund, Fredrik
    Neiman, Maja
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Stenlund, Hans
    Hellström, Cecilia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Karlsson, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arif, Muhammad
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Dodig-Crnkovic, Tea
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London, England.
    Lee, Sunjae
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Zhang, Cheng
    Chen, Yang
    Olin, Axel
    Mikes, Jaromir
    Danielsson, Hanna
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Jansson, Per-Anders
    Angerås, Oskar
    Huss, Mikael
    Kjellqvist, Sanela
    Odeberg, Jacob
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Edfors, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Tremaroli, Valentina
    Forsström, Björn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Schwenk, Jochen M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Nilsson, Peter
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Moritz, Thomas
    Bäckhed, Fredrik
    Engstrand, Lars
    Brodin, Petter
    Bergström, Göran
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Danish Tech Univ, Ctr Biosustainabil, Copenhagen, Denmark.
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Integration of molecular profiles in a longitudinal wellness profiling cohort2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4487Article in journal (Refereed)
  • 6. Aben, Ralf C. H.
    et al.
    Barros, Nathan
    van Donk, Ellen
    Frenken, Thijs
    Hilt, Sabine
    Kazanjian, Garabet
    Lamers, Leon P. M.
    Peeters, Edwin T. H. M.
    Roelofs, Jan G. M.
    de Senerpont Domis, Lisette N.
    Stephan, Susanne
    Velthuis, Mandy
    Van de Waal, Dedmer B.
    Wik, Martin
    Thornton, Brett F.
    Wilkinson, Jeremy
    DelSontro, Tonya
    Kosten, Sarian
    Cross continental increase in methane ebullition under climate change2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, no 1Article in journal (Refereed)
    Abstract [en]

    Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature–ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 °C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6–20% per 1 °C increase), contributing to global warming.

  • 7. Aben, Ralf C. H.
    et al.
    Barros, Nathan
    van Donk, Ellen
    Frenken, Thijs
    Hilt, Sabine
    Kazanjian, Garabet
    Lamers, Leon P. M.
    Peeters, Edwin T. H. M.
    Roelofs, Jan G. M.
    de Senerpont Domis, Lisette N.
    Stephan, Susanne
    Velthuis, Mandy
    Van de Waal, Dedmer B.
    Wik, Martin
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Thornton, Brett F.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Wilkinson, Jeremy
    DelSontro, Tonya
    Kosten, Sarian
    Cross continental increase in methane ebullition under climate change2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 1682Article in journal (Refereed)
    Abstract [en]

    Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature-ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 degrees C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6-20% per 1 degrees C increase), contributing to global warming.

  • 8.
    Abreu-Vieira, Gustavo
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Fischer, Alexander W.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. University of Hamburg, Germany.
    Mattsson, Charlotte
    de Jong, Jasper M. A.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Shabalina, Irina G.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Ryden, Mikael
    Laurencikiene, Jurga
    Arner, Peter
    Cannon, Barbara
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Nedergaard, Jan
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Petrovic, Natasa
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Cidea improves the metabolic profile through expansion of adipose tissue2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 7433Article in journal (Refereed)
    Abstract [en]

    In humans, Cidea (cell death-inducing DNA fragmentation factor alpha-like effector A) is highly but variably expressed in white fat, and expression correlates with metabolic health. Here we generate transgenic mice expressing human Cidea in adipose tissues (aP2-hCidea mice) and show that Cidea is mechanistically associated with a robust increase in adipose tissue expandability. Under humanized conditions (thermoneutrality, mature age and prolonged exposure to high-fat diet), aP2-hCidea mice develop a much more pronounced obesity than their wild-type littermates. Remarkably, the malfunctioning of visceral fat normally caused by massive obesity is fully overcome-perilipin 1 and Akt expression are preserved, tissue degradation is prevented, macrophage accumulation is decreased and adiponectin expression remains high. Importantly, the aP2-hCidea mice display enhanced insulin sensitivity. Our data establish a functional role for Cidea and suggest that, in humans, the association between Cidea levels in white fat and metabolic health is not only correlative but also causative.

  • 9.
    Adam, Iris
    et al.
    Department of Biology, University of Southern Denmark, Odense, Denmark.
    Riebel, Katharina
    Institute of Biology, Animal Sciences & Health, Leiden University, Leiden, Netherlands.
    Stål, Per
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Wood, Neil
    Department of Molecular Physiology and Biophysics, Larner College of Medicine, University of Vermont, NJ, Burlington, United States.
    Previs, Michael J.
    Department of Molecular Physiology and Biophysics, Larner College of Medicine, University of Vermont, NJ, Burlington, United States.
    Elemans, Coen P. H.
    Department of Biology, University of Southern Denmark, Odense, Denmark.
    Daily vocal exercise is necessary for peak performance singing in a songbird2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 7787Article in journal (Refereed)
    Abstract [en]

    Vocal signals, including human speech and birdsong, are produced by complicated, precisely coordinated body movements, whose execution is fitness-determining in resource competition and mate choice. While the acquisition and maintenance of motor skills generally requires practice to develop and maintain both motor circuitry and muscle performance, it is unknown whether vocal muscles, like limb muscles, exhibit exercise-induced plasticity. Here, we show that juvenile and adult zebra finches (Taeniopygia castanotis) require daily vocal exercise to first gain and subsequently maintain peak vocal muscle performance. Experimentally preventing male birds from singing alters both vocal muscle physiology and vocal performance within days. Furthermore, we find females prefer song of vocally exercised males in choice experiments. Vocal output thus contains information on recent exercise status, and acts as an honest indicator of past exercise investment in songbirds, and possibly in all vocalising vertebrates.

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  • 10. Adamczyk, Bartosz
    et al.
    Sietio, Outi-Maaria
    Strakoya, Petra
    Prommer, Judith
    Wild, Birgit
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry. University of Vienna, Austria; University of Gothenburg, Sweden.
    Hagner, Marleena
    Pihlatie, Mari
    Fritze, Hannu
    Richter, Andreas
    Heinonsalo, Jussi
    Plant roots increase both decomposition and stable organic matter formation in boreal forest soil2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 3982Article in journal (Refereed)
    Abstract [en]

    Boreal forests are ecosystems with low nitrogen (N) availability that store globally significant amounts of carbon (C), mainly in plant biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms controlling boreal C and N pools are not well understood. Here, using a three-year field experiment, we compare SOM decomposition and stabilization in the presence of roots, with exclusion of roots but presence of fungal hyphae and with exclusion of both roots and fungal hyphae. Roots accelerate SOM decomposition compared to the root exclusion treatments, but also promote a different soil N economy with higher concentrations of organic soil N compared to inorganic soil N accompanied with the build-up of stable SOM-N. In contrast, root exclusion leads to an inorganic soil N economy (i.e., high level of inorganic N) with reduced stable SOM-N buildup. Based on our findings, we provide a framework on how plant roots affect SOM decomposition and stabilization.

  • 11. Adami, C.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Erratum: Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything (Nature Communications (2013) 4:2193 DOI: 10.1038/ncomms3193)2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, article id 3764Article in journal (Refereed)
  • 12. Adami, C.
    et al.
    Hintze, Arend
    Michigan State University, East Lansing, United States.
    Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything2013In: Nature Communications, E-ISSN 2041-1723, Vol. 4, article id 2193Article in journal (Refereed)
    Abstract [en]

    Zero-determinant strategies are a new class of probabilistic and conditional strategies that are able to unilaterally set the expected payoff of an opponent in iterated plays of the Prisoner's Dilemma irrespective of the opponent's strategy (coercive strategies), or else to set the ratio between the player's and their opponent's expected payoff (extortionate strategies). Here we show that zero-determinant strategies are at most weakly dominant, are not evolutionarily stable, and will instead evolve into less coercive strategies. We show that zero-determinant strategies with an informational advantage over other players that allows them to recognize each other can be evolutionarily stable (and able to exploit other players). However, such an advantage is bound to be short-lived as opposing strategies evolve to counteract the recognition. © 2013 Macmillan Publishers Limited. All rights reserved.

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  • 13. Adderley, Jack D.
    et al.
    von Freyend, Simona John
    Jackson, Sarah A.
    Bird, Megan J.
    Burns, Amy L.
    Anar, Burcu
    Metcalf, Tom
    Semblat, Jean-Philippe
    Billker, Oliver
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.
    Wilson, Danny W.
    Doerig, Christian
    Analysis of erythrocyte signalling pathways during Plasmodium falciparum infection identifies targets for host-directed antimalarial intervention2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4015Article in journal (Refereed)
    Abstract [en]

    Intracellular pathogens mobilize host signaling pathways of their host cell to promote their own survival. Evidence is emerging that signal transduction elements are activated in a-nucleated erythrocytes in response to infection with malaria parasites, but the extent of this phenomenon remains unknown. Here, we fill this knowledge gap through a comprehensive and dynamic assessment of host erythrocyte signaling during infection with Plasmodium falciparum. We used arrays of 878 antibodies directed against human signaling proteins to interrogate the activation status of host erythrocyte phospho-signaling pathways at three blood stages of parasite asexual development. This analysis reveals a dynamic modulation of many host signalling proteins across parasite development. Here we focus on the hepatocyte growth factor receptor (c-MET) and the MAP kinase pathway component B-Raf, providing a proof of concept that human signaling kinases identified as activated by malaria infection represent attractive targets for antimalarial intervention.

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  • 14.
    Adhikari, Subash
    et al.
    Macquarie Univ, Dept Biomed Sci, Fac Med Hlth & Human Sci, N Ryde, NSW 2109, Australia..
    Nice, Edouard C.
    Macquarie Univ, Dept Biomed Sci, Fac Med Hlth & Human Sci, N Ryde, NSW 2109, Australia.;Monash Univ, Dept Biochem & Mol Biol, Fac Med Nursing & Hlth Sci, Melbourne, Vic 3800, Australia..
    Deutsch, Eric W.
    Inst Syst Biol, 401 Terry Ave North, Seattle, WA 98109 USA..
    Lane, Lydie
    Univ Geneva, SIB Swiss Inst Bioinformat, Fac Med, CMU, Michel Servet 1, CH-1211 Geneva, Switzerland.;Univ Geneva, Dept Microbiol & Mol Med, Fac Med, CMU, Michel Servet 1, CH-1211 Geneva, Switzerland..
    Omenn, Gilbert S.
    Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA..
    Pennington, Stephen R.
    Univ Coll Dublin, UCD Conway Inst Biomol & Biomed Res, Sch Med, Dublin, Ireland..
    Paik, Young-Ki
    Yonsei Proteome Res Ctr, Sudaemoon Ku, 50 Yonsei ro, Seoul 120749, South Korea..
    Overall, Christopher M.
    Univ British Columbia, Fac Dent, Vancouver, BC, Canada..
    Corrales, Fernando J.
    Ctr Nacl Biotecnol CSIC, Funct Prote Lab, Proteored ISCIII, Madrid 28049, Spain..
    Cristea, Ileana M.
    Princeton Univ, Dept Mol Biol, Princeton, NJ 08544 USA..
    Van Eyk, Jennifer E.
    Smidt Heart Inst, Cedars Sinai Med Ctr, Adv Clin Biosyst Res Inst, Los Angeles, CA 90048 USA..
    Uhlen, Mathias
    KTH Royal Inst Technol, Sch Engn Sci Chem, Sci Life Lab Biotechnol & Hlth, S-17121 Solna, Sweden..
    Lindskog, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical and experimental pathology.
    Chan, Daniel W.
    Johns Hopkins Univ, Dept Pathol & Oncol, Sch Med, Baltimore, MD 21224 USA..
    Bairoch, Amos
    Arizona State Univ, Biodesign Inst, Tempe, AZ USA..
    Waddington, James C.
    Justice, Joshua L.
    Arizona State Univ, Biodesign Inst, Tempe, AZ USA..
    LaBaer, Joshua
    Rodriguez, Henry
    NCI, Off Canc Clin Prote Res, NIH, Bethesda, MD 20892 USA..
    He, Fuchu
    Beijing Inst Life, Beijing Proteome Res Ctr, Natl Ctr Prot Sci Beijing, State Key Lab Prote, Beijing 102206, Peoples R China..
    Kostrzewa, Markus
    Bruker Daltonik GmbH, Microbiol & Diagnost, Fahrenheitstr, D-428359 Bremen, Germany..
    Ping, Peipei
    Univ Calif Los Angeles, David Geffen Sch Med, Dept Physiol, Cardiac Prote & Signaling Lab, Los Angeles, CA USA..
    Gundry, Rebekah L.
    Univ Nebraska Med Ctr, Div Cardiovasc Med, Cardiom Program, Ctr Heart & Vasc Res, Omaha, NE 68198 USA.;Univ Nebraska Med Ctr, Dept Cellular & Integrat Physiol, Cardiom Program, Ctr Heart & Vasc Res, Omaha, NE 68198 USA..
    Stewart, Peter
    Royal Prince Alfred Hosp, Dept Chem Pathol, Camperdown, NSW, Australia..
    Srivastava, Sanjeeva
    Indian Inst Technol, Powai 400076, Maharashtra, India..
    Srivastava, Sudhir
    Natl Canc Inst, Natl Inst Hlth, Canc Biomarkers Res Branch, Med Ctr Dr, Suite 5E136, Rockville, MD 20852 USA.;Fed Univ Rio Janeiro, Inst Chem, Lab Prote, Athos da Silveria Ramos,149, BR-21941909 Rio De Janeiro, RJ, Brazil..
    Nogueira, Fabio C. S.
    Fed Univ Rio Janeiro, Inst Chem, Prote Unit, Athos da Silveria Ramos,149, BR-21941909 Rio De Janeiro, RJ, Brazil.;Univ Grenoble Alpes, INSERM, CEA, IRIG BGE,U1038, F-38000 Grenoble, France..
    Domont, Gilberto B.
    Univ Grenoble Alpes, INSERM, CEA, IRIG BGE,U1038, F-38000 Grenoble, France..
    Vandenbrouck, Yves
    Univ Colorado, Dept Med Cardiol, Anschutz Med Campus, Aurora, CO USA.;Univ Colorado, Dept Biochem, Anschutz Med Campus, Aurora, CO USA.;Univ Colorado, Dept Mol Genet, Anschutz Med Campus, Aurora, CO USA..
    Lam, Maggie P. Y.
    Univ Colorado, Dept Med, Div Cardiol, Anschutz Med Campus, Aurora, CO USA.;European Bioinformat Inst, Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England..
    Wennersten, Sara
    Univ New South Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW, Australia..
    Vizcaino, Juan Antonio
    Univ Calif San Diego, Dept Comp Sci & Engn, 9500 Gilman Dr,Mail Code 0404, San Diego, CA 92093 USA..
    Wilkins, Marc
    Lund Univ, Dept Biomed Engn, Lund, Sweden..
    Schwenk, Jochen M.
    Lundberg, Emma
    Bandeira, Nuno
    Univ Texas Hlth Sci Ctr San Antonio, UT Hlth, Dept Biochem & Struct Biol, 7703 Floyd Curl Dr, San Antonio, TX 78229 USA..
    Marko-Varga, Gyorgy
    Univ Rennes, INSERM, EHESP, IREST,UMR S 1085, F-35042 Rennes, France..
    Weintraub, Susan T.
    Leiden Univ, Med Ctr, NL-2333 Leiden, Netherlands..
    Pineau, Charles
    Stanford Sch Med, Dept Genet, Stanford, CA 94305 USA..
    Kusebauch, Ulrike
    Moritz, Robert L.
    Ahn, Seong Beom
    Palmblad, Magnus
    Univ Rennes, INSERM, EHESP, IREST,UMR S 1085, F-35042 Rennes, France..
    Snyder, Michael P.
    Leiden Univ, Med Ctr, NL-2333 Leiden, Netherlands..
    Aebersold, Ruedi
    Stanford Sch Med, Dept Genet, Stanford, CA 94305 USA..
    Baker, Mark S.
    Macquarie Univ, Dept Biomed Sci, Fac Med Hlth & Human Sci, N Ryde, NSW 2109, Australia.;Leiden Univ, Med Ctr, NL-2333 Leiden, Netherlands.;Univ Zurich, Fac Sci, Zurich, Switzerland..
    A high-stringency blueprint of the human proteome2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5301Article in journal (Refereed)
    Abstract [en]

    The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases. The Human Proteome Project (HPP) was launched in 2010 to enhance accurate annotation of the genome-encoded proteome. Ten years later, the HPP releases its first blueprint of the human proteome, annotating 90% of all known proteins at high-stringency and discussing the implications of proteomics for precision medicine.

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  • 15. Adhikari, Subash
    et al.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Baker, Mark S.
    A high-stringency blueprint of the human proteome2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5301Article in journal (Refereed)
    Abstract [en]

    The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases. The Human Proteome Project (HPP) was launched in 2010 to enhance accurate annotation of the genome-encoded proteome. Ten years later, the HPP releases its first blueprint of the human proteome, annotating 90% of all known proteins at high-stringency and discussing the implications of proteomics for precision medicine.

  • 16. Aghion, S.
    et al.
    Ahlén, O.
    Amsler, C.
    Ariga, A.
    Ariga, T.
    Belov, A. S.
    Berggren, Karl
    Physics Department, European Organisation for Nuclear Research, Switzerland.
    Bonomi, G.
    Bräunig, P.
    Bremer, J.
    Brusa, R. S.
    Cabaret, L.
    Canali, C.
    Caravita, R.
    Castelli, F.
    Cerchiari, G.
    Cialdi, S.
    Comparat, D.
    Consolati, G.
    Derking, H.
    Di Domizio, S.
    Di Noto, L.
    Doser, M.
    Dudarev, A.
    Ereditato, A.
    Ferragut, R.
    Fontana, A.
    Genova, P.
    Giammarchi, M.
    Gligorova, A.
    Gninenko, S. N.
    Haider, S.
    Huse, T.
    Jordan, E.
    Jørgensen, L. V.
    Kaltenbacher, T.
    Kawada, J.
    Kellerbauer, A.
    Kimura, M.
    Knecht, A.
    Krasnický, D.
    Lagomarsino, V.
    Lehner, S.
    Magnani, A.
    Malbrunot, C.
    Mariazzi, S.
    Matveev, V. A.
    Moia, F.
    Nebbia, G.
    Nédélec, P.
    Oberthaler, M. K.
    Pacifico, N.
    Petràček, V.
    Pistillo, C.
    Prelz, F.
    Prevedelli, M.
    Regenfus, C.
    Riccardi, C.
    Røhne, O.
    Rotondi, A.
    Sandaker, H.
    Scampoli, P.
    Storey, J.
    Vasquez, M.A. Subieta
    Špaček, M.
    Testera, G.
    Vaccarone, R.
    Widmann, E.
    Zavatarelli, S.
    Zmeskal, J.
    A moiré deflectometer for antimatter2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, article id 2538Article in journal (Refereed)
    Abstract [en]

    The precise measurement of forces is one way to obtain deep insight into the fundamental interactions present in nature. In the context of neutral antimatter, the gravitational interaction is of high interest, potentially revealing new forces that violate the weak equivalence principle. Here we report on a successful extension of a tool from atom optics—the moiré deflectometer—for a measurement of the acceleration of slow antiprotons. The setup consists of two identical transmission gratings and a spatially resolving emulsion detector for antiproton annihilations. Absolute referencing of the observed antimatter pattern with a photon pattern experiencing no deflection allows the direct inference of forces present. The concept is also straightforwardly applicable to antihydrogen measurements as pursued by the AEgIS collaboration. The combination of these very different techniques from high energy and atomic physics opens a very promising route to the direct detection of the gravitational acceleration of neutral antimatter.

  • 17.
    Aguirre-Gutierrez, Jesus
    et al.
    Univ Oxford, Environm Change Inst, Sch Geog & Environm, Oxford, England.;Naturalis Biodivers Ctr, Biodivers Dynam, Leiden, Netherlands..
    Malhi, Yadvinder
    Univ Oxford, Environm Change Inst, Sch Geog & Environm, Oxford, England..
    Lewis, Simon L.
    Univ Leeds, Sch Geog, Ecol & Global Change, Leeds, W Yorkshire, England.;UCL, Dept Geog, London, England..
    Fauset, Sophie
    Univ Plymouth, Sch Geog Earth & Environm Sci, Plymouth, Devon, England..
    Adu-Bredu, Stephen
    KNUST, CSIR Forestry Res Inst Ghana, Univ Post Off, Kumasi, Ghana..
    Affum-Baffoe, Kofi
    Forestry Commiss Ghana, Mensurat Unit, Kumasi, Ghana..
    Baker, Timothy R.
    Univ Leeds, Sch Geog, Ecol & Global Change, Leeds, W Yorkshire, England..
    Gvozdevaite, Agne
    Univ Oxford, Environm Change Inst, Sch Geog & Environm, Oxford, England..
    Hubau, Wannes
    Univ Leeds, Sch Geog, Ecol & Global Change, Leeds, W Yorkshire, England.;Royal Museum Cent Africa, Serv Wood Biol, Tervuren, Belgium..
    Moore, Sam
    Univ Oxford, Environm Change Inst, Sch Geog & Environm, Oxford, England..
    Peprah, Theresa
    KNUST, CSIR Forestry Res Inst Ghana, Univ Post Off, Kumasi, Ghana..
    Zieminska, Kasia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Arnold Arboretum Harvard Univ, Boston, MA 02115 USA..
    Phillips, Oliver L.
    Univ Leeds, Sch Geog, Ecol & Global Change, Leeds, W Yorkshire, England..
    Oliveras, Imma
    Univ Oxford, Environm Change Inst, Sch Geog & Environm, Oxford, England..
    Long-term droughts may drive drier tropical forests towards increased functional, taxonomic and phylogenetic homogeneity2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1Article in journal (Refereed)
    Abstract [en]

    Tropical ecosystems adapted to high water availability may be highly impacted by climatic changes that increase soil and atmospheric moisture deficits. Many tropical regions are experiencing significant changes in climatic conditions, which may induce strong shifts in taxonomic, functional and phylogenetic diversity of forest communities. However, it remains unclear if and to what extent tropical forests are shifting in these facets of diversity along climatic gradients in response to climate change. Here, we show that changes in climate affected all three facets of diversity in West Africa in recent decades. Taxonomic and functional diversity increased in wetter forests but tended to decrease in forests with drier climate. Phylogenetic diversity showed a large decrease along a wet-dry climatic gradient. Notably, we find that all three facets of diversity tended to be higher in wetter forests. Drier forests showed functional, taxonomic and phylogenetic homogenization. Understanding how different facets of diversity respond to a changing environment across climatic gradients is essential for effective long-term conservation of tropical forest ecosystems. Different aspects of biodiversity may not necessarily converge in their response to climate change. Here, the authors investigate 25-year shifts in taxonomic, functional and phylogenetic diversity of tropical forests along a spatial climate gradient in West Africa, showing that drier forests are less stable than wetter forests.

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  • 18.
    Ah-King, Malin
    Stockholm University, Faculty of Humanities, Department of Ethnology, History of Religions and Gender Studies.
    The history of sexual selection research provides insights as to why females are still understudied2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, article id 6976Article in journal (Refereed)
    Abstract [en]

    While it is widely acknowledged that Darwin’s descriptions of females were gender-biased, gender bias in current sexual selection research is less recognized. An examination of the history of sexual selection research shows prevalent male precedence—that research starts with male-centered investigations or explanations and thereafter includes female-centered equivalents. In comparison, the incidence of female precedence is low. Furthermore, a comparison between the volume of publications focusing on sexual selection in males versus in females shows that the former far outnumber the latter. This bias is not only a historical pattern; sexual selection theory and research are still male-centered—due to conspicuous traits, practical obstacles, and continued gender bias. Even the way sexual selection is commonly defined contributes to this bias. This history provides an illustrative example by which we can learn to recognize biases and identify gaps in knowledge. I conclude with a call for the scientific community to interrogate its own biases and suggest strategies for alleviating biases in this field and beyond.

  • 19.
    Ahlberg, Martina
    et al.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Chung, Sunjae
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden.;Korea Natl Univ Educ, Dept Phys Educ, Cheongju 28173, South Korea..
    Jiang, Sheng
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Gothenburg, Dept Phys.
    Frisk, Andreas
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Khademi, Maha
    Shahid Beheshti Univ, Dept Phys, Tehran 1983969411, Iran..
    Khymyn, Roman
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Awad, Ahmad A.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Le, Quang Tuan
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Gothenburg, Dept Phys.
    Mazraati, Hamid
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. NanOsc AB, S-16440 Kista, Sweden..
    Mohseni, Majid
    KTH, School of Engineering Sciences (SCI), Applied Physics. Shahid Beheshti Univ, Dept Phys, Tehran 1983969411, Iran..
    Weigand, Markus
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Bykova, Iuliia
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Gross, Felix
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Goering, Eberhard
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Schutz, Gisela
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Grafe, Joachim
    Max Planck Inst Intelligent Syst, Stuttgart, Germany..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Gothenburg, Dept Phys.
    Freezing and thawing magnetic droplet solitons2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2462Article in journal (Refereed)
    Abstract [en]

    Magnetic droplets are a type of non-topological magnetic soliton, which are stabilised and sustained by spin-transfer torques for instance. Without this, they would collapse. Here Ahlberg et al show that by decreasing the applied magnetic field, droplets can be frozen, forming a static nanobubble Magnetic droplets are non-topological magnetodynamical solitons displaying a wide range of complex dynamic phenomena with potential for microwave signal generation. Bubbles, on the other hand, are internally static cylindrical magnetic domains, stabilized by external fields and magnetostatic interactions. In its original theory, the droplet was described as an imminently collapsing bubble stabilized by spin transfer torque and, in its zero-frequency limit, as equivalent to a bubble. Without nanoscale lateral confinement, pinning, or an external applied field, such a nanobubble is unstable, and should collapse. Here, we show that we can freeze dynamic droplets into static nanobubbles by decreasing the magnetic field. While the bubble has virtually the same resistance as the droplet, all signs of low-frequency microwave noise disappear. The transition is fully reversible and the bubble can be thawed back into a droplet if the magnetic field is increased under current. Whereas the droplet collapses without a sustaining current, the bubble is highly stable and remains intact for days without external drive. Electrical measurements are complemented by direct observation using scanning transmission x-ray microscopy, which corroborates the analysis and confirms that the bubble is stabilized by pinning.

  • 20. Ahmadi, M.
    et al.
    Alves, B. X. R.
    Baker, C. J.
    Bertsche, W.
    Butler, E.
    Capra, A.
    Carruth, C.
    Cesar, C. L.
    Charlton, M.
    Cohen, S.
    Collister, R.
    Eriksson, S.
    Evans, A.
    Evetts, N.
    Fajans, J.
    Friesen, T.
    Fujiwara, M. C.
    Gill, D. R.
    Gutierrez, A.
    Hangst, J. S.
    Hardy, W. N.
    Hayden, M. E.
    Isaac, C. A.
    Ishida, A.
    Johnson, M. A.
    Jones, S. A.
    Jonsell, Svante
    Stockholm University, Faculty of Science, Department of Physics.
    Kurchaninov, L.
    Madsen, N.
    Mathers, M.
    Maxwell, D.
    McKenna, J. T. K.
    Menary, S.
    Michan, J. M.
    Momose, T.
    Munich, J. J.
    Nolan, P.
    Olchanski, K.
    Olin, A.
    Pusa, P.
    Rasmussen, C. Ø.
    Robicheaux, F.
    Sacramento, R. L.
    Sameed, M.
    Sarid, E.
    Silveira, D. M.
    Stracka, S.
    Stutter, G.
    So, C.
    Tharp, T. D.
    Thompson, J. E.
    Thompson, R. I.
    van der Werf, D. P.
    Wurtele, J. S.
    Antihydrogen accumulation for fundamental symmetry tests2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 681Article in journal (Refereed)
    Abstract [en]

    Antihydrogen, a positron bound to an antiproton, is the simplest anti-atom. Its structure and properties are expected to mirror those of the hydrogen atom. Prospects for precision comparisons of the two, as tests of fundamental symmetries, are driving a vibrant programme of research. In this regard, a limiting factor in most experiments is the availability of large numbers of cold ground state antihydrogen atoms. Here, we describe how an improved synthesis process results in a maximum rate of 10.5 +/- 0.6 atoms trapped and detected per cycle, corresponding to more than an order of magnitude improvement over previous work. Additionally, we demonstrate how detailed control of electron, positron and antiproton plasmas enables repeated formation and trapping of antihydrogen atoms, with the simultaneous retention of atoms produced in previous cycles. We report a record of 54 detected annihilation events from a single release of the trapped anti-atoms accumulated from five consecutive cycles.

  • 21.
    Ahmed, Heba
    et al.
    RMIT Univ, Australia.
    Alijani, Hossein
    RMIT Univ, Australia.
    El Ghazaly, Ahmed
    Linköping University, Department of Physics, Chemistry and Biology, Materials design. Linköping University, Faculty of Science & Engineering.
    Halim, Joseph
    Linköping University, Department of Physics, Chemistry and Biology, Materials design. Linköping University, Faculty of Science & Engineering.
    Murdoch, Billy J.
    RMIT Univ, Australia.
    Ehrnst, Yemima
    RMIT Univ, Australia.
    Massahud, Emily
    RMIT Univ, Australia.
    Rezk, Amgad R.
    RMIT Univ, Australia.
    Rosén, Johanna
    Linköping University, Department of Physics, Chemistry and Biology, Materials design. Linköping University, Faculty of Science & Engineering.
    Yeo, Leslie Y.
    RMIT Univ, Australia.
    Recovery of oxidized two-dimensional MXenes through high frequency nanoscale electromechanical vibration2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3Article in journal (Refereed)
    Abstract [en]

    MXenes hold immense potential given their superior electrical properties. The practical adoption of these promising materials is, however, severely constrained by their oxidative susceptibility, leading to significant performance deterioration and lifespan limitations. Attempts to preserve MXenes have been limited, and it has not been possible thus far to reverse the materials performance. In this work, we show that subjecting oxidized micron or nanometer thickness dry MXene films-even those constructed from nanometer-order solution-dispersed oxidized flakes-to just one minute of 10 MHz nanoscale electromechanical vibration leads to considerable removal of its surface oxide layer, whilst preserving its structure and characteristics. Importantly, electrochemical performance is recovered close to that of their original state: the pseudocapacitance, which decreased by almost 50% due to its oxidation, reverses to approximately 98% of its original value, with good capacitance retention ( approximate to 93%) following 10,000 charge-discharge cycles at 10 A g(-1). These promising results allude to the exciting possibility for rejuvenating the material for reuse, therefore offering a more economical and sustainable route that improves its potential for practical translation. Despite their vast potential, the practical deployment of MXenes has been hampered by their tendency to be oxidized. Here, the authors show that simply vibrating MXene films in just a minute can remove the oxide layer formed and restore their electrochemical performance close to its original state.

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  • 22. Ahola, Virpi
    et al.
    Lehtonen, Rainer
    Somervuo, Panu
    Salmela, Leena
    Koskinen, Patrik
    Rastas, Pasi
    Valimaki, Niko
    Paulin, Lars
    Kvist, Jouni
    Wahlberg, Niklas
    Tanskanen, Jaakko
    Hornett, Emily A.
    Ferguson, Laura C.
    Luo, Shiqi
    Cao, Zijuan
    de Jong, Maaike A.
    Duplouy, Anne
    Smolander, Olli-Pekka
    Vogel, Heiko
    McCoy, Rajiv C.
    Qian, Kui
    Chong, Wong Swee
    Zhang, Qin
    Ahmad, Freed
    Haukka, Jani K.
    Joshi, Aruj
    Salojarvi, Jarkko
    Wheat, Christopher W.
    Stockholm University, Faculty of Science, Department of Zoology.
    Grosse-Wilde, Ewald
    Hughes, Daniel
    Katainen, Riku
    Pitkanen, Esa
    Ylinen, Johannes
    Waterhouse, Robert M.
    Turunen, Mikko
    Vaharautio, Anna
    Ojanen, Sami P.
    Schulman, Alan H.
    Taipale, Minna
    Lawson, Daniel
    Ukkonen, Esko
    Makinen, Veli
    Goldsmith, Marian R.
    Holm, Liisa
    Auvinen, Petri
    Frilander, Mikko J.
    Hanski, Ilkka
    The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 4737-Article in journal (Refereed)
    Abstract [en]

    Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

  • 23.
    Akhoudas, Camille Hayatte
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Sallée, Jean-Baptiste
    Reverdin, Gilles
    Haumann, F. Alexander
    Pauthenet, Etienne
    Chapman, Christopher C.
    Margirier, Félix
    Lo Monaco, Claire
    Metzl, Nicolas
    Meilland, Julie
    Stranne, Christian
    Stockholm University, Faculty of Science, Department of Geological Sciences. Stockholm University, Faculty of Science, The Bolin Centre for Climate Research (together with KTH & SMHI).
    Isotopic evidence for an intensified hydrological cycle in the Indian sector of the Southern Ocean2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, article id 2763Article in journal (Refereed)
    Abstract [en]

    The hydrological cycle is expected to intensify in a warming climate. However, observational evidence of such changes in the Southern Ocean is difficult to obtain due to sparse measurements and a complex superposition of changes in precipitation, sea ice, and glacial meltwater. Here we disentangle these signals using a dataset of salinity and seawater oxygen isotope observations collected in the Indian sector of the Southern Ocean. Our results show that the atmospheric water cycle has intensified in this region between 1993 and 2021, increasing the salinity in subtropical surface waters by 0.06 ± 0.07 g kg−1 per decade, and decreasing the salinity in subpolar surface waters by -0.02 ± 0.01 g kg−1 per decade. The oxygen isotope data allow to discriminate the different freshwater processes showing that in the subpolar region, the freshening is largely driven by the increase in net precipitation (by a factor two) while the decrease in sea ice melt is largely balanced by the contribution of glacial meltwater at these latitudes. These changes extend the growing evidence for an acceleration of the hydrological cycle and a melting cryosphere that can be expected from global warming.

  • 24.
    Albers, Suki
    et al.
    Univ Hamburg, Inst Biochem & Mol Biol, Hamburg, Germany..
    Beckert, Bertrand
    Univ Hamburg, Inst Biochem & Mol Biol, Hamburg, Germany..
    Matthies, Marco C.
    Univ Hamburg, Ctr Bioinformat, Hamburg, Germany..
    Mandava, Chandra Sekhar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Schuster, Raphael
    Univ Hamburg, Inst Organ Chem, Hamburg, Germany..
    Seuring, Carolin
    Ctr Struct & Syst Biol, Hamburg, Germany..
    Riedner, Maria
    Univ Hamburg, Inst Organ Chem, Hamburg, Germany..
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Torda, Andrew E.
    Univ Hamburg, Ctr Bioinformat, Hamburg, Germany..
    Wilson, Daniel N.
    Univ Hamburg, Inst Biochem & Mol Biol, Hamburg, Germany..
    Ignatova, Zoya
    Univ Hamburg, Inst Biochem & Mol Biol, Hamburg, Germany..
    Repurposing tRNAs for nonsense suppression2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, article id 3850Article in journal (Refereed)
    Abstract [en]

    Three stop codons (UAA, UAG and UGA) terminate protein synthesis and are almost exclusively recognized by release factors. Here, we design de novo transfer RNAs (tRNAs) that efficiently decode UGA stop codons in Escherichia coli. The tRNA designs harness various functionally conserved aspects of sense-codon decoding tRNAs. Optimization within the T Psi C-stem to stabilize binding to the elongation factor, displays the most potent effect in enhancing suppression activity. We determine the structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon in the A site at 2.9 angstrom resolution. In the context of the suppressor tRNA, the conformation of the UGA codon resembles that of a sense-codon rather than when canonical translation termination release factors are bound, suggesting conformational flexibility of the stop codons dependent on the nature of the A-site ligand. The systematic analysis, combined with structural insights, provides a rationale for targeted repurposing of tRNAs to correct devastating nonsense mutations that introduce a premature stop codon. Here, the authors report de novo design, optimization and characterization of tRNAs that decode UGA stop codons in E. coli. The structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon suggests that distinct A-site ligands (tRNAs versus release factors) induce distinct conformation of the stop codon within the mRNA in the decoding center.

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  • 25.
    Allum, Fiona
    et al.
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Hedman, Asa K.
    Karolinska Inst, Cardiovasc Med Unit, Dept Med Solna, S-17176 Stockholm, Sweden.
    Shaol, Xiaojian
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Cheung, Warren A.
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada;Childrens Mercy Hosp & Clin, Kansas City, MO 64108 USA.
    Vijay, Jinchu
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Guenard, Frederic
    Univ Laval, Inst Nutr & Funct Foods INAF, Quebec City, PQ G1V 0A6, Canada.
    Kwan, Tony
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Simon, Marie-Michelle
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Ge, Bing
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Moura, Cristiano
    McGill Univ, Dept Epidemiol, Montreal, PQ H3A 1A2, Canada.
    Boulier, Elodie
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    Rönnblom, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology.
    Bernatsky, Sasha
    McGill Univ, Dept Epidemiol, Montreal, PQ H3A 1A2, Canada.
    Lathropl, Mark
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada.
    McCarthy, Mark, I
    Univ Oxford, Churchill Hosp, Oxford Ctr Diabet Endocrinol & Metab, Old Rd, Oxford OX3 7LJ, England;Univ Oxford, Wellcome Ctr Human Genet, Roosevelt Dr, Oxford OX3 7BN, England;Oxford Univ Hosp NHS Fdn Trust, John Radcliffe Hosp, Oxford NIHR Biomed Res Ctr, Oxford OX3 9DU, England.
    Deloukas, Panos
    Queen Mary Univ London, William Harvey Res Inst, Barts & London Sch Med & Dent, Charterhouse Sq, London EC1M 6BQ, England.
    Tchernof, Andre
    Univ Laval, Quebec Heart & Lung Inst, Quebec City, PQ G1V 0A6, Canada.
    Pastinen, Tomi
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada;Childrens Mercy Hosp & Clin, Kansas City, MO 64108 USA.
    Vohl, Marie-Claude
    Univ Laval, Inst Nutr & Funct Foods INAF, Quebec City, PQ G1V 0A6, Canada.
    Grundberg, Elin
    McGill Univ, Dept Human Genet, Montreal, PQ H3A 0C7, Canada;McGill Univ, Montreal, PQ H3A 0G1, Canada;Genome Quebec Innovat Ctr, Montreal, PQ H3A 0G1, Canada;Childrens Mercy Hosp & Clin, Kansas City, MO 64108 USA.
    Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 1209Article in journal (Refereed)
    Abstract [en]

    Sparse profiling of CpG methylation in blood by microarrays has identified epigenetic links to common diseases. Here we apply methylC-capture sequencing (MCC-Seq) in a clinical population of similar to 200 adipose tissue and matched blood samples (N-total similar to 400), providing high- resolution methylation profiling (>1.3 M CpGs) at regulatory elements. We link methylation to cardiometabolic risk through associations to circulating plasma lipid levels and identify lipid-associated CpGs with unique localization patterns in regulatory elements. We show distinct features of tissue-specific versus tissue-independent lipid-linked regulatory regions by contrasting with parallel assessments in similar to 800 independent adipose tissue and blood samples from the general population. We follow-up on adipose-specific regulatory regions under (1) genetic and (2) epigenetic (environmental) regulation via integrational studies. Overall, the comprehensive sequencing of regulatory element methylomes reveals a rich landscape of functional variants linked genetically as well as epigenetically to plasma lipid traits.

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    FULLTEXT01
  • 26. Allum, Fiona
    et al.
    Shao, Xiaojian
    Guénard, Frédéric
    Simon, Marie-Michelle
    Busche, Stephan
    Caron, Maxime
    Lambourne, John
    Lessard, Julie
    Tandre, Karolina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology.
    Hedman, Åsa K
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular epidemiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kwan, Tony
    Ge, Bing
    Rönnblom, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Rheumatology.
    McCarthy, Mark I
    Deloukas, Panos
    Richmond, Todd
    Burgess, Daniel
    Spector, Timothy D
    Tchernof, André
    Marceau, Simon
    Lathrop, Mark
    Vohl, Marie-Claude
    Pastinen, Tomi
    Grundberg, Elin
    Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 7211Article in journal (Refereed)
    Abstract [en]

    Most genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS.

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    fulltext
  • 27.
    Almqvist, Helena
    et al.
    Laboratories for Chemical Biology Karolinska Institutet Science for Life Laboratory Stockholm, Division of Translational Medicine & Chemical Biology.
    Axelsson, Hanna
    Laboratories for Chemical Biology Karolinska Institutet Science for Life Laboratory Stockholm, Division of Translational Medicine & Chemical Biology.
    Jafari, Rozbeh
    Department of Medical Biochemistry & Biophysics, Division of Biophysics, Karolinska Institutet.
    Dan, Chen
    School of Biological Sciences, Nanyang Technological University.
    Mateus, André
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Haraldsson, Martin
    Laboratories for Chemical Biology Karolinska Institutet Science for Life Laboratory Stockholm, Division of Translational Medicine & Chemical Biology.
    Larsson, Andreas
    School of Biological Sciences, Nanyang Technological University.
    Martinez-Molina, Daniel
    Department of Medical Biochemistry & Biophysics, Division of Biophysics, Karolinska Institutet.
    Artursson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lundbäck, Thomas
    Laboratories for Chemical Biology Karolinska Institutet Science for Life Laboratory Stockholm, Division of Translational Medicine & Chemical Biology.
    Nordlund, Pär
    Department of Medical Biochemistry & Biophysics, Division of Biophysics, Karolinska Institutet.
    CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 11040Article in journal (Refereed)
    Abstract [en]

    Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.

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    fulltext
  • 28.
    Almstedt, Elin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Elgendy, Ramy
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Hekmati, Neda
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Rosén, Emil
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Wärn, Caroline
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Olsen, Thale Kristin
    Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden..
    Dyberg, Cecilia
    Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden..
    Doroszko, Milena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Larsson, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Sundström, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Arsenian Henriksson, Marie
    Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
    Påhlman, Sven
    Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden..
    Bexell, Daniel
    Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund, Sweden..
    Vanlandewijck, Michael
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Vascular Biology. Department of Medicine, Integrated Cardio-Metabolic Centre Single Cell Facility, Karolinska Institutet, Stockholm, Sweden..
    Kogner, Per
    Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
    Jörnsten, Rebecka
    Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden..
    Krona, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Nelander, Sven
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Neuro-Oncology.
    Integrative discovery of treatments for high-risk neuroblastoma2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 71Article in journal (Refereed)
    Abstract [en]

    Despite advances in the molecular exploration of paediatric cancers, approximately 50% of children with high-risk neuroblastoma lack effective treatment. To identify therapeutic options for this group of high-risk patients, we combine predictive data mining with experimental evaluation in patient-derived xenograft cells. Our proposed algorithm, TargetTranslator, integrates data from tumour biobanks, pharmacological databases, and cellular networks to predict how targeted interventions affect mRNA signatures associated with high patient risk or disease processes. We find more than 80 targets to be associated with neuroblastoma risk and differentiation signatures. Selected targets are evaluated in cell lines derived from high-risk patients to demonstrate reversal of risk signatures and malignant phenotypes. Using neuroblastoma xenograft models, we establish CNR2 and MAPK8 as promising candidates for the treatment of high-risk neuroblastoma. We expect that our method, available as a public tool (targettranslator.org), will enhance and expedite the discovery of risk-associated targets for paediatric and adult cancers.

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    fulltext
  • 29.
    Alvez, Maria Bueno
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Edfors, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Zwahlen, Martin
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Mardinoglu, Adil
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, SE1 9RT, UK.
    Edqvist, Per Henrik
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Sjöblom, Tobias
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Lundin, Emma
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Rameika, Natallia
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Enblad, Gunilla
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Lindman, Henrik
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Höglund, Martin
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Hesselager, Göran
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Stålberg, Karin
    Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden.
    Enblad, Malin
    Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
    Simonson, Oscar E.
    Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
    Häggman, Michael
    Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
    Axelsson, Tomas
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Åberg, Mikael
    Department of Medical Sciences, Clinical Chemistry and SciLifeLab Affinity Proteomics, Uppsala University, Uppsala, Sweden.
    Nordlund, Jessica
    Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Zhong, Wen
    Science for Life Laboratory, Department of Biomedical and Clinical Sciences (BKV), Linköping University, Linköping, Sweden.
    Karlsson, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gyllensten, Ulf
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Ponten, Fredrik
    Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
    Next generation pan-cancer blood proteome profiling using proximity extension assay2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4308Article in journal (Refereed)
    Abstract [en]

    A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.

  • 30.
    Alvez, Maria Bueno
    et al.
    KTH Royal Inst Technol, Sweden.
    Edfors, Fredrik
    KTH Royal Inst Technol, Sweden.
    von Feilitzen, Kalle
    KTH Royal Inst Technol, Sweden.
    Zwahlen, Martin
    KTH Royal Inst Technol, Sweden.
    Mardinoglu, Adil
    KTH Royal Inst Technol, Sweden; Kings Coll London, England.
    Edqvist, Per-Henrik
    Uppsala Univ, Sweden.
    Sjoblom, Tobias
    Uppsala Univ, Sweden.
    Lundin, Emma
    Uppsala Univ, Sweden.
    Rameika, Natallia
    Uppsala Univ, Sweden.
    Enblad, Gunilla
    Uppsala Univ, Sweden.
    Lindman, Henrik
    Uppsala Univ, Sweden.
    Hoglund, Martin
    Uppsala Univ, Sweden.
    Hesselager, Goran
    Uppsala Univ, Sweden.
    Stalberg, Karin
    Uppsala Univ, Sweden.
    Enblad, Malin
    Uppsala Univ, Sweden.
    Simonson, Oscar E.
    Uppsala Univ, Sweden.
    Haggman, Michael
    Uppsala Univ, Sweden.
    Axelsson, Tomas
    Uppsala Univ, Sweden.
    Aberg, Mikael
    Uppsala Univ, Sweden.
    Nordlund, Jessica
    Uppsala Univ, Sweden.
    Zhong, Wen
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Karlsson, Max
    KTH Royal Inst Technol, Sweden.
    Gyllensten, Ulf
    Uppsala Univ, Sweden.
    Ponten, Fredrik
    Uppsala Univ, Sweden.
    Fagerberg, Linn
    KTH Royal Inst Technol, Sweden.
    Uhlen, Mathias
    KTH Royal Inst Technol, Sweden; Karolinska Inst, Sweden.
    Next generation pan-cancer blood proteome profiling using proximity extension assay2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1Article in journal (Refereed)
    Abstract [en]

    Comprehensive and scalable proteomic profiling of plasma samples can improve the screening and diagnosis of cancer patients. Here, the authors use the Olink Proximity Extension Assay technology to characterise the plasma proteomes of 1477 patients across twelve cancer types, and use machine learning to obtain a protein panel for cancer classification. A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.

  • 31.
    Alvez, Maria Bueno
    et al.
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
    Edfors, Fredrik
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
    von Feilitzen, Kalle
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
    Zwahlen, Martin
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
    Mardinoglu, Adil
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden.;Kings Coll London, Fac Dent Oral & Craniofacial Sci, Ctr Host Microbiome Interact, London SE1 9RT, England..
    peedq227, Per-Henrik D
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Sjöblom, Tobias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Lundin, Emma
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Rameika, Natallia
    Enblad, Gunilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Lindman, Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Höglund, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Hesselager, Göran
    Stålberg, Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Enblad, Malin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences.
    Simonson, Oscar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences.
    Häggman, Michael
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences.
    Axelsson, Tomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala Univ, Dept Med Sci, Clin Chem & SciLifeLab Affin Prote, Uppsala, Sweden..
    Åberg, Mikael
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Chemistry.
    Nordlund, Jessica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Zhong, Wen
    Linköping Univ, Dept Biomed & Clin Sci BKV, Sci Life Lab, Linköping, Sweden..
    Karlsson, Max
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
    Gyllensten, Ulf B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala Univ, Dept Immunol Genet & Pathol, Uppsala, Sweden..
    Ponten, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Fagerberg, Linn
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden..
    Uhlen, Mathias
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, Stockholm, Sweden.;Karolinska Inst, Dept Neurosci, Stockholm, Sweden..
    Next generation pan-cancer blood proteome profiling using proximity extension assay2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, article id 08Article in journal (Refereed)
    Abstract [en]

    Comprehensive and scalable proteomic profiling of plasma samples can improve the screening and diagnosis of cancer patients. Here, the authors use the Olink Proximity Extension Assay technology to characterise the plasma proteomes of 1477 patients across twelve cancer types, and use machine learning to obtain a protein panel for cancer classification. A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.

    Download full text (pdf)
    FULLTEXT01
  • 32.
    Amann-Winkel, Katrin
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.;Johannes Gutenberg Univ Mainz, Max Planck Inst Polymer Res, D-55128 Mainz, Germany..
    Kim, Kyung Hwan
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Giovambattista, Nicolas
    CUNY Brooklyn Coll, Dept Phys, Brooklyn, NY 11210 USA.;CUNY, Grad Ctr, New York, NY 10016 USA..
    Ladd-Parada, Marjorie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Spaeh, Alexander
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Perakis, Fivos
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Pathak, Harshad
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Yang, Cheolhee
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Eklund, Tobias
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Lane, Thomas J.
    SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    You, Seonju
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Jeong, Sangmin
    POSTECH, Dept Chem, Pohang 37673, South Korea..
    Lee, Jae Hyuk
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Eom, Intae
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Kim, Minseok
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Park, Jaeku
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Chun, Sae Hwan
    Pohang Accelerator Lab, Pohang 37673, Gyeongbuk, South Korea..
    Poole, Peter H.
    St Francis Xavier Univ, Dept Phys, Antigonish, NS B2G2W5, Canada..
    Nilsson, Anders
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 442Article in journal (Refereed)
    Abstract [en]

    Recent experiments continue to find evidence for a liquid-liquid phase transition (LLPT) in supercooled water, which would unify our understanding of the anomalous properties of liquid water and amorphous ice. These experiments are challenging because the proposed LLPT occurs under extreme metastable conditions where the liquid freezes to a crystal on a very short time scale. Here, we analyze models for the LLPT to show that coexistence of distinct high-density and low-density liquid phases may be observed by subjecting low-density amorphous (LDA) ice to ultrafast heating. We then describe experiments in which we heat LDA ice to near the predicted critical point of the LLPT by an ultrafast infrared laser pulse, following which we measure the structure factor using femtosecond x-ray laser pulses. Consistent with our predictions, we observe a LLPT occurring on a time scale < 100 ns and widely separated from ice formation, which begins at times >1 mu s. Obtaining experimental evidence of a liquid-liquid phase transition in supercooled water is challenging due to the rapid crystallization. Here the authors drive low-density amorphous ice to the conditions of liquid-liquid coexistence using ultrafast laser heating and observe the liquid-liquid phase transition with femtosecond x-ray laser pulses.

  • 33.
    Amann-Winkel, Katrin
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Max Planck Institute for Polymer Research and Johannes Gutenberg University, Germany.
    Kim, Kyung Hwan
    Giovambattista, Nicolas
    Ladd-Parada, Marjorie
    Stockholm University, Faculty of Science, Department of Physics.
    Späh, Alexander
    Stockholm University, Faculty of Science, Department of Physics.
    Perakis, Fivos
    Stockholm University, Faculty of Science, Department of Physics.
    Pathak, Harshad
    Stockholm University, Faculty of Science, Department of Physics.
    Yang, Cheolhee
    Eklund, Tobias
    Stockholm University, Faculty of Science, Department of Physics.
    Lane, Thomas J.
    You, Seonju
    Jeong, Sangmin
    Lee, Jae Hyuk
    Eom, Intae
    Kim, Minseok
    Park, Jaeku
    Chun, Sae Hwan
    Poole, Peter H.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Liquid-liquid phase separation in supercooled water from ultrafast heating of low-density amorphous ice2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 442Article in journal (Refereed)
    Abstract [en]

    Recent experiments continue to find evidence for a liquid-liquid phase transition (LLPT) in supercooled water, which would unify our understanding of the anomalous properties of liquid water and amorphous ice. These experiments are challenging because the proposed LLPT occurs under extreme metastable conditions where the liquid freezes to a crystal on a very short time scale. Here, we analyze models for the LLPT to show that coexistence of distinct high-density and low-density liquid phases may be observed by subjecting low-density amorphous (LDA) ice to ultrafast heating. We then describe experiments in which we heat LDA ice to near the predicted critical point of the LLPT by an ultrafast infrared laser pulse, following which we measure the structure factor using femtosecond x-ray laser pulses. Consistent with our predictions, we observe a LLPT occurring on a time scale < 100 ns and widely separated from ice formation, which begins at times >1 μs.

  • 34. Amole, C.
    et al.
    Ashkezari, M. D.
    Baquero-Ruiz, M.
    Bertsche, W.
    Butler, E.
    Capra, A.
    Cesar, C. L.
    Charlton, M.
    Eriksson, S.
    Fajans, J.
    Friesen, T.
    Fujiwara, M. C.
    Gill, D. R.
    Gutierrez, A.
    Hangst, J. S.
    Hardy, W. N.
    Hayden, M. E.
    Isaac, C. A.
    Jonsell, Svante
    Stockholm University, Faculty of Science, Department of Physics.
    Kurchaninov, L.
    Little, A.
    Madsen, N.
    McKenna, J. T. K.
    Menary, S.
    Napoli, S. C.
    Nolan, P.
    Olchanski, K.
    Olin, A.
    Povilus, A.
    Pusa, P.
    Rasmussen, C. O.
    Robicheaux, F.
    Sarid, E.
    Silveira, D. M.
    So, C.
    Tharp, T. D.
    Thompson, R. I.
    van der Werf, D. P.
    Vendeiro, Z.
    Wurtele, J. S.
    Zhmoginov, A. I.
    Charman, A. E.
    An experimental limit on the charge of antihydrogen2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 3955-Article in journal (Refereed)
    Abstract [en]

    The properties of antihydrogen are expected to be identical to those of hydrogen, and any differences would constitute a profound challenge to the fundamental theories of physics. The most commonly discussed antiatom- based tests of these theories are searches for antihydrogen- hydrogen spectral differences (tests of CPT (charge- parity- time) invariance) or gravitational differences (tests of the weak equivalence principle). Here we, the ALPHA Collaboration, report a different and somewhat unusual test of CPT and of quantum anomaly cancellation. A retrospective analysis of the influence of electric fields on antihydrogen atoms released from the ALPHA trap finds a mean axial deflection of 4.1 +/- 3.4mm for an average axial electric field of 0.51Vmm1. Combined with extensive numerical modelling, this measurement leads to a bound on the charge Qe of antihydrogen of Q (+/- 1.3 +/- 1.1 +/- 0.4)10 8. Here, e is the unit charge, and the errors are from statistics and systematic effects.

  • 35.
    Amora-Nogueira, Leonardo
    et al.
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil.
    Sanders, Christian J.
    Southern Cross Univ, Australia.
    Enrich Prast, Alex
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Univ Fed Rio de Janeiro, Brazil.
    Monteiro Sanders, Luciana Silva
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil; Southern Cross Univ, Australia.
    Abuchacra, Rodrigo Coutinho
    Biomass & Water Management Res Ctr NAB UFF, Brazil; State Univ Rio de Janeiro UERJ FFP, Brazil.
    Moreira-Turcq, Patricia F.
    Inst Rech Dev IRD, France.
    Cordeiro, Renato Campello
    Fluminense Fed Univ, Brazil.
    Gauci, Vincent
    Univ Birmingham, England; Univ Birmingham, England.
    Moreira, Luciane Silva
    Fluminense Fed Univ, Brazil.
    Machado-Silva, Fausto
    Univ Toledo, OH 43606 USA; Univ Fed Rio de Janeiro, Brazil.
    Libonati, Renata
    Univ Fed Rio de Janeiro, Brazil; Univ Lisbon, Portugal; Univ Lisbon, Portugal.
    Fonseca, Thairiny
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil.
    Francisco, Cristiane Nunes
    Fluminense Fed Univ, Brazil.
    Marotta, Humberto
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil.
    Tropical forests as drivers of lake carbon burial2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4051Article in journal (Refereed)
    Abstract [en]

    A significant proportion of carbon (C) captured by terrestrial primary production is buried in lacustrine ecosystems, which have been substantially affected by anthropogenic activities globally. However, there is a scarcity of sedimentary organic carbon (OC) accumulation information for lakes surrounded by highly productive rainforests at warm tropical latitudes, or in response to land cover and climate change. Here, we combine new data from intensive campaigns spanning 13 lakes across remote Amazonian regions with a broad literature compilation, to produce the first spatially-weighted global analysis of recent OC burial in lakes (over ~50-100-years) that integrates both biome type and forest cover. We find that humid tropical forest lake sediments are a disproportionately important global OC sink of 7.4 Tg C yr−1 with implications for climate change. Further, we demonstrate that temperature and forest conservation are key factors in maintaining massive organic carbon pools in tropical lacustrine sediments.

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    fulltext
  • 36.
    Amora-Nogueira, Leonardo
    et al.
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil.
    Sanders, Christian J.
    Southern Cross Univ, Australia.
    Enrich Prast, Alex
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Inst Sea, Brazil; Univ Fed Rio de Janeiro, Brazil.
    Sanders, Luciana Silva Monteiro
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil; Southern Cross Univ, Australia.
    Abuchacra, Rodrigo Coutinho
    Biomass & Water Management Res Ctr NAB UFF, Brazil; State Univ Rio de Janeiro UERJ FFP, Brazil.
    Moreira-Turcq, Patricia F.
    IRD, France.
    Cordeiro, Renato Campello
    Fluminense Fed Univ, Brazil.
    Gauci, Vincent
    Univ Birmingham, England.
    Moreira, Luciane Silva
    Fluminense Fed Univ, Brazil.
    Machado-Silva, Fausto
    Univ Toledo, OH 43606 USA; Univ Fed Rio de Janeiro, Brazil.
    Libonati, Renata
    Univ Fed Rio de Janeiro, Brazil; Univ Lisbon, Portugal; Univ Lisbon, Portugal.
    Fonseca, Thairiny
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil.
    Francisco, Cristiane Nunes
    Fluminense Fed Univ, Brazil.
    Marotta, Humberto
    Biomass & Water Management Res Ctr NAB UFF, Brazil; Fluminense Fed Univ UFF, Brazil; Fluminense Fed Univ, Brazil.
    Correction: Tropical forests as drivers of lake carbon burial (vol 13, 4051, 2022)2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3282Article in journal (Other academic)
  • 37.
    Amselem, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Broadwater, Bo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Haevermark, Tora
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Johansson, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Elf, Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 1336Article in journal (Refereed)
    Abstract [en]

    Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.

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  • 38.
    Andermann, Tobias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Stromberg, Caroline A. E.
    Univ Washington, Dept Biol, Seattle, WA 98195 USA.;Univ Washington, Burke Museum Nat Hist & Culture, Seattle, WA 98195 USA..
    Antonelli, Alexandre
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Gothenburg, Sweden.;Univ Oxford, Dept Plant Sci, Oxford, England.;Royal Bot Gardens, Richmond, Surrey, England..
    Silvestro, Daniele
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.;Univ Gothenburg, Gothenburg Global Biodivers Ctr, Dept Biol & Environm Sci, Gothenburg, Sweden.;Univ Fribourg, Dept Biol, Fribourg, Switzerland.;Swiss Inst Bioinformat, Fribourg, Switzerland..
    The origin and evolution of open habitats in North America inferred by Bayesian deep learning models2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4833Article in journal (Refereed)
    Abstract [en]

    Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth's history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we present a Bayesian deep learning model that utilizes information from fossil evidence, geologic models, and paleoclimatic proxies to reconstruct paleovegetation, placing the emergence of open habitats in North America at around 23 million years ago. By the time of the onset of theQuaternary glacial cycles, open habitatswere coveringmore than 30% of North America and were expanding at peak rates, to eventually become the most prominent natural vegetation type today. Our entirely datadriven approach demonstrates how deep learning can harness unexplored signals fromcomplex data sets to provide insights into the evolution of Earth's biomes in time and space.

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  • 39.
    Andersson, Alma
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stenbeck, Linnea
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Salmén, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Hubrecht Inst KNAW Royal Netherlands Acad Arts &, Utrecht, Netherlands.;Univ Med Ctr Utrecht, Canc Genom Netherlands, Utrecht, Netherlands..
    Ehinger, Anna
    Dept Genet & Pathol, Lab Med Reg Sane, Lund, Sweden.;Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Wu, Sunny Z.
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Al-Eryani, Ghamdan
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Roden, Daniel
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Swarbrick, Alex
    Garvan Inst Med Res, Kinghorn Canc Ctr, Sydney, NSW, Australia.;St Vincents Clin Sch, Fac Med, Sydney, NSW, Australia..
    Borg, Ake
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Frisen, Jonas
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden..
    Engblom, Camilla
    Karolinska Inst, Dept Cell & Mol Biol, Stockholm, Sweden..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 6012Article in journal (Refereed)
    Abstract [en]

    In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases. While transcriptomics have enhanced our understanding for cancer, spatial transcriptomics enable the characterisation of cellular interactions. Here, the authors integrate single cell data with spatial information for HER2 + tumours and develop tools for the prediction of interactions between tumour-infiltrating cells.

  • 40.
    Andersson, David
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Norwegian University of Science and Technology (NTNU), Norway.
    de Wijn, Astrid S.
    Stockholm University, Faculty of Science, Department of Physics. Norwegian University of Science and Technology (NTNU), Norway.
    Understanding the friction of atomically thin layered materials2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 420Article in journal (Refereed)
    Abstract [en]

    Friction is a ubiquitous phenomenon that greatly affects our everyday lives and is responsible for large amounts of energy loss in industrialised societies. Layered materials such as graphene have interesting frictional properties and are often used as (additives to) lubricants to reduce friction and protect against wear. Experimental Atomic Force Microscopy studies and detailed simulations have shown a number of intriguing effects such as frictional strengthening and dependence of friction on the number of layers covering a surface. Here, we propose a simple, fundamental, model for friction on thin sheets. We use our model to explain a variety of seemingly contradictory experimental as well as numerical results. This model can serve as a basis for understanding friction on thin sheets, and opens up new possibilities for ultimately controlling their friction and wear protection.

  • 41.
    Andersson Ersman, Peter
    et al.
    RISE Acreo, Sweden.
    Lassnig, Roman
    RISE Acreo, Sweden.
    Strandberg, Jan
    RISE Acreo, Sweden.
    Tu, Deyu
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Keshmiri, Vahid
    Linköping University, Department of Electrical Engineering, Information Coding. Linköping University, Faculty of Science & Engineering.
    Forchheimer, Robert
    Linköping University, Department of Electrical Engineering, Information Coding. Linköping University, Faculty of Science & Engineering.
    Fabiano, Simone
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Gustafsson, Goran
    RISE Acreo, Sweden.
    Berggren, Magnus
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    All-printed large-scale integrated circuits based on organic electrochemical transistors2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 5053Article in journal (Refereed)
    Abstract [en]

    The communication outposts of the emerging Internet of Things are embodied by ordinary items, which desirably include all-printed flexible sensors, actuators, displays and akin organic electronic interface devices in combination with silicon-based digital signal processing and communication technologies. However, hybrid integration of smart electronic labels is partly hampered due to a lack of technology that (de)multiplex signals between silicon chips and printed electronic devices. Here, we report all-printed 4-to-7 decoders and seven-bit shift registers, including over 100 organic electrochemical transistors each, thus minimizing the number of terminals required to drive monolithically integrated all-printed electrochromic displays. These relatively advanced circuits are enabled by a reduction of the transistor footprint, an effort which includes several further developments of materials and screen printing processes. Our findings demonstrate that digital circuits based on organic electrochemical transistors (OECTs) provide a unique bridge between all-printed organic electronics (OEs) and low-cost silicon chip technology for Internet of Things applications.

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    fulltext
  • 42.
    Andersson Ersman, Peter
    et al.
    RISE - Research Institutes of Sweden (2017-2019), ICT, Acreo.
    Lassnig, Roman
    RISE - Research Institutes of Sweden (2017-2019), ICT, Acreo.
    Strandberg, Jan
    RISE - Research Institutes of Sweden (2017-2019), ICT, Acreo. RISE Research Institutes of Sweden, Digital Systems, Smart Hardware.
    Tu, Deyu
    Linköping University, Sweden.
    Keshmiri, Vahid
    Linköping University, Sweden.
    Forchheimer, Robert
    Linköping University, Sweden.
    Fabiano, Simone
    Linköping University, Sweden.
    Gustafsson, Göran
    RISE - Research Institutes of Sweden (2017-2019), ICT, Acreo.
    Berggren, Magnus
    Linköping University, Sweden.
    All-printed large-scale integrated circuits based on organic electrochemical transistors2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, no 1, article id 5053Article in journal (Refereed)
    Abstract [en]

    The communication outposts of the emerging Internet of Things are embodied by ordinary items, which desirably include all-printed flexible sensors, actuators, displays and akin organic electronic interface devices in combination with silicon-based digital signal processing and communication technologies. However, hybrid integration of smart electronic labels is partly hampered due to a lack of technology that (de)multiplex signals between silicon chips and printed electronic devices. Here, we report all-printed 4-to-7 decoders and seven-bit shift registers, including over 100 organic electrochemical transistors each, thus minimizing the number of terminals required to drive monolithically integrated all-printed electrochromic displays. These relatively advanced circuits are enabled by a reduction of the transistor footprint, an effort which includes several further developments of materials and screen printing processes. Our findings demonstrate that digital circuits based on organic electrochemical transistors (OECTs) provide a unique bridge between all-printed organic electronics (OEs) and low-cost silicon chip technology for Internet of Things applications. © 2019, The Author(s).

  • 43. Andersson, Sandra
    et al.
    Sundberg, Marten
    Pristovsek, Nusa
    Ibrahim, Ahmed
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Natl Res Ctr, Egypt.
    Jonsson, Philip
    Katona, Borbala
    Clausson, Carl-Magnus
    Zieba, Agata
    Ramstrom, Margareta
    Soderberg, Ola
    Williams, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Houston, USA; Karolinska Inst, Sweden.
    Asplund, Anna
    Insufficient antibody validation challenges oestrogen receptor beta research2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 15840Article in journal (Refereed)
    Abstract [en]

    The discovery of oestrogen receptor beta (ER beta/ESR2) was a landmark discovery. Its reported expression and homology with breast cancer pharmacological target ER alpha (ESR1) raised hopes for improved endocrine therapies. After 20 years of intense research, this has not materialized. We here perform a rigorous validation of 13 anti-ER beta antibodies, using well-characterized controls and a panel of validation methods. We conclude that only one antibody, the rarely used monoclonal PPZ0506, specifically targets ER beta in immunohistochemistry. Applying this antibody for protein expression profiling in 44 normal and 21 malignant human tissues, we detect ER beta protein in testis, ovary, lymphoid cells, granulosa cell tumours, and a subset of malignant melanoma and thyroid cancers. We do not find evidence of expression in normal or cancerous human breast. This expression pattern aligns well with RNA-seq data, but contradicts a multitude of studies. Our study highlights how inadequately validated antibodies can lead an exciting field astray.

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    fulltext
  • 44.
    Andersson, Sandra
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Sundberg, Mårten
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Pristovsek, Nusa
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Ibrahim, Ahmed
    KTH Royal Inst Technol, Sch Biotechnol, Div Prote & Nanotechnol, Sci Life Lab, S-17121 Solna, Sweden.;Natl Res Ctr, Div Pharmaceut Ind, Dokki 12622, Egypt..
    Jonsson, Philip
    Univ Houston, Dept Biol & Biochem, Houston, TX 77204 USA.;Mem Sloan Kettering Canc Ctr, Dept Epidemiol & Biostat, Human Oncol & Pathogenesis Program, New York, NY 10065 USA..
    Katona, Borbala
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Clausson, Carl-Magnus
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Zieba, Agata
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Ramström, Margareta
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Söderberg, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Williams, Cecilia
    KTH Royal Inst Technol, Sch Biotechnol, Div Prote & Nanotechnol, Sci Life Lab, S-17121 Solna, Sweden.;Univ Houston, Dept Biol & Biochem, Houston, TX 77204 USA.;Karolinska Inst, Dept Biosci & Nutr, S-14183 Stockholm, Sweden..
    Asplund, Anna
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Insufficient antibody validation challenges oestrogen receptor beta research2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 15840Article in journal (Refereed)
    Abstract [en]

    The discovery of oestrogen receptor beta (ER beta/ESR2) was a landmark discovery. Its reported expression and homology with breast cancer pharmacological target ER alpha (ESR1) raised hopes for improved endocrine therapies. After 20 years of intense research, this has not materialized. We here perform a rigorous validation of 13 anti-ER beta antibodies, using well-characterized controls and a panel of validation methods. We conclude that only one antibody, the rarely used monoclonal PPZ0506, specifically targets ER beta in immunohistochemistry. Applying this antibody for protein expression profiling in 44 normal and 21 malignant human tissues, we detect ER beta protein in testis, ovary, lymphoid cells, granulosa cell tumours, and a subset of malignant melanoma and thyroid cancers. We do not find evidence of expression in normal or cancerous human breast. This expression pattern aligns well with RNA-seq data, but contradicts a multitude of studies. Our study highlights how inadequately validated antibodies can lead an exciting field astray.

    Download full text (pdf)
    fulltext
  • 45. Andresen, Camilla S.
    et al.
    Karlsson, Nanna B.
    Straneo, Fiammetta
    Schmidt, Sabine
    Andersen, Thorbjørn J.
    Eidam, Emily F.
    Bjørk, Anders A.
    Dartiguemalle, Nicolas
    Dyke, Laurence M.
    Vermassen, Flor
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Gundel, Ida E.
    Sediment discharge from Greenland's marine-terminating glaciers is linked with surface melt2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1332Article in journal (Refereed)
    Abstract [en]

    Sediment discharged from the Greenland Ice Sheet delivers nutrients to marine ecosystems around Greenland and shapes seafloor habitats. Current estimates of the total sediment flux are constrained by observations from land-terminating glaciers only. Addressing this gap, our study presents a budget derived from observations at 30 marine-margin locations. Analyzing sediment cores from nine glaciated fjords, we assess spatial deposition since 1950. A significant correlation is established between mass accumulation rates, normalized by surface runoff, and distance down-fjord. This enables calculating annual sediment flux at any fjord point based on nearby marine-terminating outlet glacier melt data. Findings reveal a total annual sediment flux of 1.324 + /- 0.79 Gt yr-1 over the period 2010-2020 from all marine-terminating glaciers to the fjords. These estimates are valuable for studies aiming to understand the basal ice sheet conditions and for studies predicting ecosystem changes in Greenland's fjords and offshore areas as the ice sheet melts and sediment discharge increase. 

  • 46.
    Andrighetto, Giulia
    et al.
    Linköping University, Department of Management and Engineering, The Institute for Analytical Sociology, IAS. Linköping University, Faculty of Arts and Sciences. Natl Res Council Italy, Italy; Inst Futures Studies, Sweden.
    Szekely, Aron
    Natl Res Council Italy, Italy; Coll Carlo Alberto, Italy.
    Guido, Andrea
    Natl Res Council Italy, Italy; Inst Futures Studies, Sweden; Univ Bourgogne Franche Comte, France.
    Gelfand, Michele
    Stanford Univ, CA USA.
    Abemathy, Jered
    Univ South Carolina, SC USA.
    Arikan, Gizem
    Trinity Coll Dublin, Ireland.
    Aycan, Zeynep
    Koc Univ, Turkiye.
    Bankar, Shweta
    Ashoka Univ, India.
    Barrera, Davide
    Coll Carlo Alberto, Italy; Univ Turin, Italy.
    Basnight-Brown, Dana
    US Int Univ Africa, Kenya.
    Belaus, Anabel
    Consejo Nacl Invest Cient & Tecn CONICET, Argentina; Univ Nacl Cordoba, Argentina.
    Berezina, Elizaveta
    Sunway Univ, Malaysia.
    Blumen, Sheyla
    Pontificia Univ Catolica Peru, Peru.
    Boski, Pawel
    SWPS Univ, Poland.
    Bui, Huyen Thi Thu
    Hanoi Natl Univ Educ, Vietnam.
    Camilo Cardenas, Juan
    Univ Los Andes, Colombia; Univ Massachusetts Amherst, MA USA.
    Cekrlija, Dorde
    Univ Banja Luka, Bosnia & Herceg; Univ Greifswald, Germany.
    de Barra, Micheal
    Brunel Univ London, England.
    de Zoysa, Piyanjali
    Univ Colombo, Sri Lanka.
    Dorrough, Angela
    Univ Cologne, Germany.
    Engelmann, Jan B.
    Univ Amsterdam, Netherlands.
    Euh, Hyun
    Univ Illinois, IL USA.
    Fiedler, Susann
    Vienna Univ Econ & Business, Austria.
    Foster-Gimbel, Olivia
    NYU, NY USA.
    Freitas, Goncalo
    Univ Lisbon, Portugal.
    Fulop, Marta
    HUN REN Inst Cognit Neurosci & Psychol, Hungary; Karoli Gaspar Univ Reformed Churches, Hungary.
    Gardarsdottir, Ragna B.
    Univ Iceland, Iceland.
    Gill, Colin Mathew Hugues D.
    Sunway Univ, Malaysia; Universal Coll Bangladesh, Bangladesh.
    Gloeckner, Andreas
    Univ Cologne, Germany.
    Graf, Sylvie
    Czech Acad Sci, Czech Republic.
    Grigoryan, Ani
    Yerevan State Univ, Armenia.
    Growiec, Katarzyna
    SWPS Univ, Poland.
    Hashimoto, Hirofumi
    Osaka Metropolitan Univ, Japan.
    Hopthrow, Tim
    Univ Kent, England.
    Hrebickova, Martina
    Czech Acad Sci, Czech Republic.
    Imada, Hirotaka
    Royal Holloway Univ London, England.
    Kamijo, Yoshio
    Waseda Univ, Japan.
    Kapoor, Hansika
    Monk Prayogshala, India.
    Kashima, Yoshihisa
    Univ Melbourne, Australia.
    Khachatryan, Narine
    Yerevan State Univ, Armenia.
    Kharchenko, Natalia
    Kyiv Int Inst Sociol, Ukraine.
    Leon, Diana
    DeJusticia, Colombia.
    Leslie, Lisa M.
    NYU, NY USA.
    Li, Yang
    Nagoya Univ, Japan.
    Liik, Kadi
    Tallinn Univ, Estonia.
    Liuzza, Marco Tullio
    Magna Graecia Univ Catanzaro, Italy.
    Maitner, Angela T.
    Amer Univ Sharjah, U Arab Emirates.
    Mamidi, Pavan
    Ashoka Univ, India.
    McArdle, Michele
    Trinity Coll Dublin, Ireland.
    Medhioub, Imed
    Imam Mohammad Ibn Saud Islamic Univ, Saudi Arabia.
    Mendes Teixeira, Maria Luisa
    Presbyterian Mackenzie Univ, Brazil.
    Mentser, Sari
    Hebrew Univ Jerusalem, Israel.
    Morales, Francisco
    Univ Andes, Chile.
    Narayanan, Jayanth
    Northeastern Univ, MA USA.
    Nitta, Kohei
    Ritsumeikan Univ, Japan.
    Nussinson, Ravit
    Open Univ Israel, Israel; Univ Haifa, Israel.
    Onyedire, Nneoma G.
    Univ Nigeria, Nigeria.
    Onyishi, Ike E.
    Univ Nigeria, Nigeria.
    Osin, Evgeny
    HSE Univ, Russia.
    Ozden, Seniha
    Koc Univ, Turkiye.
    Panagiotopoulou, Penny
    Univ Patras, Greece.
    Pereverziev, Oleksandr
    POLLSTER, Ukraine.
    Perez-Floriano, Lorena R.
    Univ Diego Portales, Chile.
    Pirttila-Backman, Anna-Maija
    Univ Helsinki, Finland.
    Pogosyan, Marianna
    Univ Amsterdam, Netherlands.
    Raver, Jana
    Queens Univ, Canada.
    Reyna, Cecilia
    Consejo Nacl Invest Cient & Tecn CONICET, Argentina.
    Rodrigues, Ricardo Borges
    Inst Univ Lisboa ISCTE IUL, Portugal.
    Romano, Sara
    Univ Turin, Italy.
    Romero, Pedro P.
    Univ San Francisco Quito, Ecuador.
    Sakki, Inari
    Univ Helsinki, Finland.
    Sanchez, Angel
    Univ Carlos III Madrid, Spain; Univ Zaragoza, Spain.
    Sherbaji, Sara
    Amer Univ Sharjah, U Arab Emirates; UCL, England.
    Simpson, Brent
    Univ South Carolina, SC USA.
    Spadoni, Lorenzo
    Univ Cassino & Southern Lazio, Italy.
    Stamkou, Eftychia
    Univ Amsterdam, Netherlands.
    Travaglino, Giovanni A.
    Royal Holloway Univ London, England.
    Van Lange, Paul A. M.
    Vrije Univ, Netherlands.
    Winata, Fiona Fira
    Univ Airlangga, Indonesia.
    Zein, Rizqy Amelia
    Univ Airlangga, Indonesia.
    Zhang, Qing-peng
    Guangzhou Univ, Peoples R China.
    Eriksson, Kimmo
    Inst Futures Studies, Sweden; Stockholm Univ, Sweden; Malardalens Univ, Sweden.
    Changes in social norms during the early stages of the COVID-19 pandemic across 43 countries2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1436Article in journal (Refereed)
    Abstract [en]

    The emergence of COVID-19 dramatically changed social behavior across societies and contexts. Here we study whether social norms also changed. Specifically, we study this question for cultural tightness (the degree to which societies generally have strong norms), specific social norms (e.g. stealing, hand washing), and norms about enforcement, using survey data from 30,431 respondents in 43 countries recorded before and in the early stages following the emergence of COVID-19. Using variation in disease intensity, we shed light on the mechanisms predicting changes in social norm measures. We find evidence that, after the emergence of the COVID-19 pandemic, hand washing norms increased while tightness and punishing frequency slightly decreased but observe no evidence for a robust change in most other norms. Thus, at least in the short term, our findings suggest that cultures are largely stable to pandemic threats except in those norms, hand washing in this case, that are perceived to be directly relevant to dealing with the collective threat. Tightness-looseness theory predicts that social norms strengthen following threat. Here the authors test this and find that, after the emergence of the COVID-19 pandemic, hand washing norms increased, but no evidence was observed for a robust change in most other norms.

  • 47.
    Andrighetto, Giulia
    et al.
    Natl Res Council Italy, Inst Cognit Sci & Technol, Rome, Italy.;Inst Futures Studies, Stockholm, Sweden.;Linköping Univ, Inst Analyt Sociol, Linköping, Sweden..
    Szekely, Aron
    Natl Res Council Italy, Inst Cognit Sci & Technol, Rome, Italy.;Coll Carlo Alberto, Turin, Italy..
    Guido, Andrea
    Natl Res Council Italy, Inst Cognit Sci & Technol, Rome, Italy.;Inst Futures Studies, Stockholm, Sweden.;Univ Bourgogne Franche Comte, Burgundy Sch Business, CEREN EA 7477, Dijon, France..
    Gelfand, Michele
    Stanford Univ, Grad Sch Business, Stanford, CA USA.;Stanford Univ, Dept Psychol, Stanford, CA USA..
    Abemathy, Jered
    Univ South Carolina, Dept Sociol, Columbia, SC USA..
    Arikan, Gizem
    Trinity Coll Dublin, Dept Polit Sci, Dublin, Ireland..
    Aycan, Zeynep
    Koc Univ, Dept Psychol, Istanbul, Turkiye.;Koc Univ, Fac Management, Istanbul, Turkiye..
    Bankar, Shweta
    Ashoka Univ, Sonipat, India..
    Barrera, Davide
    Coll Carlo Alberto, Turin, Italy.;Univ Turin, Dept Culture Polit & Soc, Turin, Italy..
    Basnight-Brown, Dana
    US Int Univ Africa, Nairobi, Kenya..
    Belaus, Anabel
    Consejo Nacl Invest Cient & Tecn CONICET, Inst Invest Psicol IIPsi, Cordoba, Argentina.;Univ Nacl Cordoba, Fac Psicol, Cordoba, Argentina..
    Berezina, Elizaveta
    Sunway Univ, Bandar Sunway, Malaysia..
    Blumen, Sheyla
    Pontificia Univ Catolica Peru, Dept Psicol, Lima, Peru..
    Boski, Pawel
    SWPS Univ, Warsaw, Poland..
    Bui, Huyen Thi Thu
    Camilo Cardenas, Juan
    Univ Los Andes, Bogota, Colombia.;Univ Massachusetts Amherst, Amherst, MA USA..
    Cekrlija, Dorde
    Univ Banja Luka, Fac Philosophy, Banja Luka, Bosnia & Herceg.;Univ Greifswald, Inst Psychol, Greifswald, Germany..
    de Barra, Micheal
    Brunel Univ London, Ctr Culture & Evolut, Uxbridge, Middx, England..
    de Zoysa, Piyanjali
    Univ Colombo, Fac Med, Colombo, Sri Lanka..
    Dorrough, Angela
    Univ Cologne, Dept Psychol, Cologne, Germany..
    Engelmann, Jan B.
    Univ Amsterdam, Amsterdam Sch Econ, Ctr Res Expt Econ & Polit Decis Making CREED, Amsterdam, Netherlands..
    Euh, Hyun
    Univ Illinois, Gies Coll Business, Champaign, IL USA..
    Fiedler, Susann
    Vienna Univ Econ & Business, Vienna, Austria..
    Foster-Gimbel, Olivia
    NYU, Sch Business, New York, NY USA..
    Freitas, Goncalo
    Univ Lisbon, Inst Ciencias Sociais, Lisbon, Portugal..
    Fulop, Marta
    HUN REN Inst Cognit Neurosci & Psychol, Res Ctr Nat Sci, Budapest, Hungary.;Karoli Gaspar Univ Reformed Churches, Inst Psychol, Budapest, Hungary..
    Gardarsdottir, Ragna B.
    Univ Iceland, Fac Psychol, Reykjavik, Iceland..
    Gill, Colin Mathew Hugues D.
    Sunway Univ, Bandar Sunway, Malaysia.;Universal Coll Bangladesh, Dhaka, Bangladesh..
    Gloeckner, Andreas
    Univ Cologne, Dept Psychol, Cologne, Germany..
    Graf, Sylvie
    Czech Acad Sci, Inst Psychol, Brno, Czech Republic..
    Grigoryan, Ani
    Yerevan State Univ, Dept Personal Psychol, Yerevan, Armenia..
    Growiec, Katarzyna
    SWPS Univ, Warsaw, Poland..
    Hashimoto, Hirofumi
    Osaka Metropolitan Univ, Osaka, Japan..
    Hopthrow, Tim
    Univ Kent, Sch Psychol, Canterbury, Kent, England..
    Hrebickova, Martina
    Czech Acad Sci, Inst Psychol, Brno, Czech Republic..
    Imada, Hirotaka
    Royal Holloway Univ London, Egham, Surrey, England..
    Kamijo, Yoshio
    Waseda Univ, Tokyo, Japan..
    Kapoor, Hansika
    Monk Prayogshala, Dept Psychol, Mumbai, Maharashtra, India..
    Kashima, Yoshihisa
    Univ Melbourne, Melbourne Sch Psychol Sci, Melbourne, Vic, Australia..
    Khachatryan, Narine
    Yerevan State Univ, Dept Personal Psychol, Yerevan, Armenia..
    Kharchenko, Natalia
    Kyiv Int Inst Sociol, Kiev, Ukraine..
    Leon, Diana
    DeJusticia, Bogota, Colombia..
    Leslie, Lisa M.
    NYU, Sch Business, New York, NY USA..
    Li, Yang
    Nagoya Univ, Nagoya, Aichi, Japan..
    Liik, Kadi
    Tallinn Univ, Sch Nat Sci & Hlth, Tallinn, Estonia..
    Liuzza, Marco Tullio
    Magna Graecia Univ Catanzaro, Dept Med & Surg Sci, Catanzaro, Italy..
    Maitner, Angela T.
    Amer Univ Sharjah, Dept Psychol, Sharjah, U Arab Emirates..
    Mamidi, Pavan
    Ashoka Univ, Sonipat, India..
    McArdle, Michele
    Trinity Coll Dublin, Dept Polit Sci, Dublin, Ireland..
    Medhioub, Imed
    Imam Mohammad Ibn Saud Islamic Univ, Dept Finance & Investment, Riyadh, Saudi Arabia..
    Mendes Teixeira, Maria Luisa
    Presbyterian Mackenzie Univ, Sao Paulo, Brazil..
    Mentser, Sari
    Hebrew Univ Jerusalem, Jerusalem, Israel..
    Morales, Francisco
    Univ Andes, Santiago, Chile..
    Narayanan, Jayanth
    Northeastern Univ, Boston, MA USA..
    Nitta, Kohei
    Ritsumeikan Univ, Shiga, Japan..
    Nussinson, Ravit
    Open Univ Israel, Dept Educ & Psychol, Raanana, Israel.;Univ Haifa, IIPDM, Haifa, Israel..
    Onyedire, Nneoma G.
    Univ Nigeria, Dept Psychol, Nsukka, Nigeria..
    Onyishi, Ike E.
    Univ Nigeria, Dept Psychol, Nsukka, Nigeria..
    Osin, Evgeny
    HSE Univ, Moscow, Russia..
    Ozden, Seniha
    Koc Univ, Dept Psychol, Istanbul, Turkiye..
    Panagiotopoulou, Penny
    Univ Patras, Dept Educ & Social Work, Patras, Greece..
    Pereverziev, Oleksandr
    POLLSTER, Kiev, Ukraine..
    Perez-Floriano, Lorena R.
    Univ Diego Portales, Santiago, Chile..
    Pirttila-Backman, Anna-Maija
    Univ Helsinki, Fac Social Sci, Social Psychol, Helsinki, Finland..
    Pogosyan, Marianna
    Univ Amsterdam, Amsterdam Business Sch ABS, Leadership & Management, Amsterdam, Netherlands..
    Raver, Jana
    Queens Univ, Kingston, ON, Canada..
    Reyna, Cecilia
    Consejo Nacl Invest Cient & Tecn CONICET, Inst Invest Psicol IIPsi, Cordoba, Argentina..
    Rodrigues, Ricardo Borges
    Inst Univ Lisboa ISCTE IUL, Ctr Invest & Intervencao Social, Lisbon, Portugal..
    Romano, Sara
    Univ Turin, Dept Culture Polit & Soc, Turin, Italy..
    Romero, Pedro P.
    Univ San Francisco Quito, Sch Econ, Quito, Ecuador.;Univ San Francisco Quito, ECEL, Quito, Ecuador..
    Sakki, Inari
    Univ Helsinki, Fac Social Sci, Social Psychol, Helsinki, Finland..
    Sanchez, Angel
    Univ Carlos III Madrid, Dept Matemat, GISC, Leganes, Spain.;Univ Zaragoza, Inst Biocomputac & Fis Sistemas Complejos BIFI, Zaragoza, Spain..
    Sherbaji, Sara
    Amer Univ Sharjah, Dept Psychol, Sharjah, U Arab Emirates.;UCL, Dept Anthropol, London, England..
    Simpson, Brent
    Univ South Carolina, Dept Sociol, Columbia, SC USA..
    Spadoni, Lorenzo
    Univ Cassino & Southern Lazio, Dept Econ & Law, Cassino, FR, Italy..
    Stamkou, Eftychia
    Univ Amsterdam, Dept Psychol, Amsterdam, Netherlands..
    Travaglino, Giovanni A.
    Royal Holloway Univ London, Egham, Surrey, England..
    Van Lange, Paul A. M.
    Vrije Univ, Dept Expt & Appl Psychol, Amsterdam, Netherlands..
    Winata, Fiona Fira
    Univ Airlangga, Fac Psychol, Surabaya, Indonesia..
    Zein, Rizqy Amelia
    Univ Airlangga, Fac Psychol, Surabaya, Indonesia..
    Zhang, Qing-peng
    Guangzhou Univ, Guangzhou, Peoples R China..
    Eriksson, Kimmo
    Mälardalen University, School of Education, Culture and Communication, Educational Sciences and Mathematics. Inst Futures Studies, Stockholm, Sweden.;Stockholm Univ, Ctr Cultural Evolut, Stockholm.
    Changes in social norms during the early stages of the COVID-19 pandemic across 43 countries2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1436Article in journal (Refereed)
    Abstract [en]

    The emergence of COVID-19 dramatically changed social behavior across societies and contexts. Here we study whether social norms also changed. Specifically, we study this question for cultural tightness (the degree to which societies generally have strong norms), specific social norms (e.g. stealing, hand washing), and norms about enforcement, using survey data from 30,431 respondents in 43 countries recorded before and in the early stages following the emergence of COVID-19. Using variation in disease intensity, we shed light on the mechanisms predicting changes in social norm measures. We find evidence that, after the emergence of the COVID-19 pandemic, hand washing norms increased while tightness and punishing frequency slightly decreased but observe no evidence for a robust change in most other norms. Thus, at least in the short term, our findings suggest that cultures are largely stable to pandemic threats except in those norms, hand washing in this case, that are perceived to be directly relevant to dealing with the collective threat. Tightness-looseness theory predicts that social norms strengthen following threat. Here the authors test this and find that, after the emergence of the COVID-19 pandemic, hand washing norms increased, but no evidence was observed for a robust change in most other norms.

  • 48. Ao, Hong
    et al.
    Dupont-Nivet, Guillaume
    Rohling, Eelco J.
    Zhang, Peng
    Ladant, Jean-Baptiste
    Roberts, Andrew P.
    Licht, Alexis
    Liu, Qingsong
    Liu, Zhonghui
    Dekkers, Mark J.
    Coxall, Helen K.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Jin, Zhangdong
    Huang, Chunju
    Xiao, Guoqiao
    Poulsen, Christopher J.
    Barbolini, Natasha
    Meijer, Niels
    Sun, Qiang
    Qiang, Xiaoke
    Yao, Jiao
    An, Zhisheng
    Orbital climate variability on the northeastern Tibetan Plateau across the Eocene-Oligocene transition2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 5249Article in journal (Refereed)
    Abstract [en]

    The first major build-up of Antarctic glaciation occurred in two consecutive stages across the Eocene-Oligocene transition (EOT): the EOT-1 cooling event at similar to 34.1-33.9Ma and the Oi-1 glaciation event at similar to 33.8-33.6Ma. Detailed orbital-scale terrestrial environmental responses to these events remain poorly known. Here we present magnetic and geochemical climate records from the northeastern Tibetan Plateau margin that are dated precisely from similar to 35.5 to 31Ma by combined magneto- and astro-chronology. These records suggest a hydroclimate transition at similar to 33.7Ma from eccentricity dominated cycles to oscillations paced by a combination of eccentricity, obliquity, and precession, and confirm that major Asian aridification and cooling occurred at Oi-1. We conclude that this terrestrial orbital response transition coincided with a similar transition in the marine benthic delta O-18 record for global ice volume and deep-sea temperature variations. The dramatic reorganization of the Asian climate system coincident with Oi-1 was, thus, a response to coeval atmospheric CO2 decline and continental-scale Antarctic glaciation. Marine records indicate a greenhouse to icehouse climate transition at similar to 34 million years ago, but how the climate changed within continental interiors at this time is less well known. Here, the authors show an orbital climate response shift with aridification on the northeastern Tibetan Plateau during this time.

  • 49. Arabi, A.
    et al.
    Ullah, K.
    Branca, R. M. M.
    Johansson, J.
    Bandarra, D.
    Haneklaus, M.
    Fu, J.
    Ariës, I.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Den Boer, M. L.
    Pokrovskaja, K.
    Grandér, D.
    Xiao, G.
    Rocha, S.
    Lehtiö, J.
    Sangfelt, O.
    Proteomic screen reveals Fbw7 as a modulator of the NF-kappa B pathway2012In: Nature Communications, E-ISSN 2041-1723, Vol. 3, p. 976-Article in journal (Refereed)
    Abstract [en]

    Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-κB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3 2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-κB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-κB2 pathway stimulation.

  • 50. Aragão, Luiz E. O. C.
    et al.
    Anderson, Liana O.
    Fonseca, Marisa G.
    Rosan, Thais M.
    Vedovato, Laura B.
    Wagner, Fabien H.
    Silva, Camila V. J.
    Silva Junior, Celso H. L.
    Arai, Egidio
    Aguiar, Ana P.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. National Institute for Space Research, Brazil.
    Barlow, Jos
    Berenguer, Erika
    Deeter, Merritt N.
    Domingues, Lucas G.
    Gatti, Luciana
    Gloor, Manuel
    Malhi, Yadvinder
    Marengo, Jose A.
    Miller, John B.
    Phillips, Oliver L.
    Saatchi, Sassan
    21st Century drought-related fires counteract the decline of Amazon deforestation carbon emissions2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 536Article in journal (Refereed)
    Abstract [en]

    Tropical carbon emissions are largely derived from direct forest clearing processes. Yet, emissions from drought-induced forest fires are, usually, not included in national-level carbon emission inventories. Here we examine Brazilian Amazon drought impacts on fire incidence and associated forest fire carbon emissions over the period 2003-2015. We show that despite a 76% decline in deforestation rates over the past 13 years, fire incidence increased by 36% during the 2015 drought compared to the preceding 12 years. The 2015 drought had the largest ever ratio of active fire counts to deforestation, with active fires occurring over an area of 799,293 km(2). Gross emissions from forest fires (989 +/- 504 Tg CO2 year(-1)) alone are more than half as great as those from old-growth forest deforestation during drought years. We conclude that carbon emission inventories intended for accounting and developing policies need to take account of substantial forest fire emissions not associated to the deforestation process.

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