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  • 51.
    Elshaari, Ali W.
    et al.
    KTH, School of Electrical Engineering (EES).
    Zadeh, Iman Esmaeil
    Fognini, Andreas
    Reimer, Michael E.
    Dalacu, Dan
    Poole, Philip J.
    Zwiller, Val
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Electrical Engineering (EES).
    Jöns, Klaus D.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Nano Photonics.
    On-chip single photon filtering and multiplexing in hybrid quantum photonic circuits2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 379Article in journal (Refereed)
    Abstract [en]

    Quantum light plays a pivotal role in modern science and future photonic applications. Since the advent of integrated quantum nanophotonics different material platforms based on III-V nanostructures-, colour centers-, and nonlinear waveguides as on-chip light sources have been investigated. Each platform has unique advantages and limitations; however, all implementations face major challenges with filtering of individual quantum states, scalable integration, deterministic multiplexing of selected quantum emitters, and on-chip excitation suppression. Here we overcome all of these challenges with a hybrid and scalable approach, where single III-V quantum emitters are positioned and deterministically integrated in a complementary metal-oxide-semiconductor-compatible photonic circuit. We demonstrate reconfigurable on-chip single-photon filtering and wavelength division multiplexing with a foot print one million times smaller than similar table-top approaches, while offering excitation suppression of more than 95 dB and efficient routing of single photons over a bandwidth of 40 nm. Our work marks an important step to harvest quantum optical technologies' full potential.

  • 52.
    Englund, Elias
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). Joint BioEnergy Institute, Emeryville, CA, USA.
    Schmidt, Matthias
    Joint BioEnergy Institute, Emeryville, CA, USA; Institute of Applied Microbiology, Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA.
    Nava, Alberto A.
    Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
    Klass, Sarah
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
    Keiser, Leah
    Joint BioEnergy Institute, Emeryville, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
    Dan, Qingyun
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA.
    Katz, Leonard
    Joint BioEnergy Institute, Emeryville, CA, USA; QB3, University of California, Berkeley, Berkeley, CA, USA.
    Yuzawa, Satoshi
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan; Graduate school of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan.
    Keasling, Jay D.
    Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National laboratory, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA; QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Center for Biosustainability, Danish Technical University, Lyngby, Denmark; Center for Synthetic biochemistry, Institute for Synthetic biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
    Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4871Article in journal (Refereed)
    Abstract [en]

    Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.

  • 53.
    Etcheverry, Sebastian
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Faridi, Muhammad Asim
    KTH. mafaridi@kth.se.
    Ramachandraiah, Harisha
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Margulis, Walter
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Optical Fiber inertial focusing based micro FlowcytometerIn: Nature Communications, E-ISSN 2041-1723Article in journal (Refereed)
    Abstract [en]

    Flow cytometry is a powerful method for analysis of cells and particles. Fueled by the need for point of care diagnostic applications, a significant effort has been made to miniaturize flow cytometry. However, despite recent advances, current microflow cytometers remain less versatile and much slower than their large-scale counterparts. Here, we present a portable all-silica optofluidic device that integrates particle focusing in flow through cylindrical silica capillaries and light delivery in optical fibers to simultaneously measure fluorescence and scattering from cells and particles at a rate of 2500 particles/s – a throughput comparable to conventional cytometers. Precise 3D cell focusing and ordering is accomplished using extended elasto-inertial focusing (EEF), a key enabler for eliminating the sheath fluid commonly employed in flow cytometry with maintained high throughput. We demonstrate simultaneously two-color fluorescence and scattering measurement of different sized particles and cells. This robust and low-cost optofluidic device, assembled without the need of clean-room facilities, is ideal suited for point of care applications.

  • 54.
    Fan, Ke
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Chen, Hong
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Ji, Yongfei
    Huang, Hui
    Claesson, Per Martin
    Daniel, Quentin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Philippe, Bertrand
    Rensmo, Hakan
    Li, Fusheng
    Luo, Yi
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Nickel-vanadium monolayer double hydroxide for efficient electrochemical water oxidation2016In: Nature Communications, E-ISSN 2041-1723, Vol. 7, article id 11981Article in journal (Refereed)
    Abstract [en]

    Highly active and low-cost electrocatalysts for water oxidation are required due to the demands on sustainable solar fuels; however, developing highly efficient catalysts to meet industrial requirements remains a challenge. Herein, we report a monolayer of nickel-vanadium-layered double hydroxide that shows a current density of 27 mA cm(-2) (57 mA cm(-2) after ohmic-drop correction) at an overpotential of 350 mV for water oxidation. Such performance is comparable to those of the best-performing nickel-iron-layered double hydroxides for water oxidation in alkaline media. Mechanistic studies indicate that the nickel-vanadium-layered double hydroxides can provide high intrinsic catalytic activity, mainly due to enhanced conductivity, facile electron transfer and abundant active sites. This work may expand the scope of cost-effective electrocatalysts for water splitting.

  • 55.
    Forchheimer, Daniel
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Forchheimer, Robert
    Linköping University.
    Haviland, David B.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Improving image contrast and material discrimination with nonlinear response in bimodal atomic force microscopy2015In: Nature Communications, E-ISSN 2041-1723, Vol. 6, article id 6270Article in journal (Refereed)
    Abstract [en]

    Atomic force microscopy has recently been extented to bimodal operation, where increased image contrast is achieved through excitation and measurement of two cantilever eigenmodes. This enhanced material contrast is advantageous in analysis of complex heterogeneous materials with phase separation on the micro or nanometre scale. Here we show that much greater image contrast results from analysis of nonlinear response to the bimodal drive, at harmonics and mixing frequencies. The amplitude and phase of up to 17 frequencies are simultaneously measured in a single scan. Using a machine-learning algorithm we demonstrate almost threefold improvement in the ability to separate material components of a polymer blend when including this nonlinear response. Beyond the statistical analysis performed here, analysis of nonlinear response could be used to obtain quantitative material properties at high speeds and with enhanced resolution.

  • 56. Forsberg, Björn
    et al.
    Aibara, Shintaro
    Howard, R. J.
    Mortezaei, N.
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4667Article in journal (Refereed)
    Abstract [en]

    The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.

  • 57.
    Fougères, Chloé
    et al.
    Grand Accélérateur National d’Ions Lourds (GANIL), CEA/DRF-CNRS/IN2P3, Caen, France; Physics Division, Argonne National Laboratory, Lemont, IL 60439, USA.
    Cederwall, Bo
    KTH, School of Engineering Sciences (SCI), Physics, Nuclear Physics.
    Zielińska, Magdalena
    Irfu, CEA, Université Paris-Saclay, Gif-sur-Yvette, France.
    et al.,
    Search for 22Na in novae supported by a novel method for measuring femtosecond nuclear lifetimes2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4536Article in journal (Refereed)
    Abstract [en]

    Classical novae are thermonuclear explosions in stellar binary systems, and important sources of 26Al and 22Na. While γ rays from the decay of the former radioisotope have been observed throughout the Galaxy, 22Na remains untraceable. Its half-life (2.6 yr) would allow the observation of its 1.275 MeV γ-ray line from a cosmic source. However, the prediction of such an observation requires good knowledge of its nucleosynthesis. The 22Na(p, γ)23Mg reaction remains the only source of large uncertainty about the amount of 22Na ejected. Its rate is dominated by a single resonance on the short-lived state at 7785.0(7) keV in 23Mg. Here, we propose a combined analysis of particle-particle correlations and velocity-difference profiles to measure femtosecond nuclear lifetimes. The application of this method to the study of the 23Mg states, places strong limits on the amount of 22Na produced in novae and constrains its detectability with future space-borne observatories.

  • 58.
    Fredin Haslum, Johan
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab. Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
    Lardeau, Charles Hugues
    Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK.
    Karlsson, Johan
    Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
    Turkki, Riku
    Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
    Leuchowius, Karl Johan
    Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
    Smith, Kevin
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Müllers, Erik
    Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
    Cell Painting-based bioactivity prediction boosts high-throughput screening hit-rates and compound diversity2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 3470Article in journal (Refereed)
    Abstract [en]

    Identifying active compounds for a target is a time- and resource-intensive task in early drug discovery. Accurate bioactivity prediction using morphological profiles could streamline the process, enabling smaller, more focused compound screens. We investigate the potential of deep learning on unrefined single-concentration activity readouts and Cell Painting data, to predict compound activity across 140 diverse assays. We observe an average ROC-AUC of 0.744 ± 0.108 with 62% of assays achieving ≥0.7, 30% ≥0.8, and 7% ≥0.9. In many cases, the high prediction performance can be achieved using only brightfield images instead of multichannel fluorescence images. A comprehensive analysis shows that Cell Painting-based bioactivity prediction is robust across assay types, technologies, and target classes, with cell-based assays and kinase targets being particularly well-suited for prediction. Experimental validation confirms the enrichment of active compounds. Our findings indicate that models trained on Cell Painting data, combined with a small set of single-concentration data points, can reliably predict the activity of a compound library across diverse targets and assays while maintaining high hit rates and scaffold diversity. This approach has the potential to reduce the size of screening campaigns, saving time and resources, and enabling primary screening with more complex assays.

  • 59. Frye, M.
    et al.
    Taddei, A.
    Dierkes, C.
    Martinez-Corral, I.
    Fielden, Matthew
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Ortsäter, H.
    Kazenwadel, J.
    Calado, D. P.
    Ostergaard, P.
    Salminen, M.
    He, L.
    Harvey, N. L.
    Kiefer, F.
    Mäkinen, T.
    Matrix stiffness controls lymphatic vessel formation through regulation of a GATA2-dependent transcriptional program2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, no 1, article id 1511Article in journal (Refereed)
    Abstract [en]

    Tissue and vessel wall stiffening alters endothelial cell properties and contributes to vascular dysfunction. However, whether extracellular matrix (ECM) stiffness impacts vascular development is not known. Here we show that matrix stiffness controls lymphatic vascular morphogenesis. Atomic force microscopy measurements in mouse embryos reveal that venous lymphatic endothelial cell (LEC) progenitors experience a decrease in substrate stiffness upon migration out of the cardinal vein, which induces a GATA2-dependent transcriptional program required to form the first lymphatic vessels. Transcriptome analysis shows that LECs grown on a soft matrix exhibit increased GATA2 expression and a GATA2-dependent upregulation of genes involved in cell migration and lymphangiogenesis, including VEGFR3. Analyses of mouse models demonstrate a cell-autonomous function of GATA2 in regulating LEC responsiveness to VEGF-C and in controlling LEC migration and sprouting in vivo. Our study thus uncovers a mechanism by which ECM stiffness dictates the migratory behavior of LECs during early lymphatic development.

  • 60.
    Fulara, Himanshu
    et al.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Zahedinejad, Mohammad
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, Electrum 229, S-16440 Kista, Sweden..
    Khymyn, Roman
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Dvornik, Mykola
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, Electrum 229, S-16440 Kista, Sweden..
    Fukami, Shunsuke
    Tohoku Univ, Res Inst Elect Commun, Lab Nanoelect & Spintron, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, Ctr Spintron Res Network, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, Ctr Innovat Integrated Elect Syst, Aoba Ku, 468-1 Aramaki Aza Aoba, Sendai, Miyagi 9800845, Japan.;Tohoku Univ, Ctr Sci & Innovat Spintron, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, WPI Adv Inst Mat Res, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan..
    Kanai, Shun
    Tohoku Univ, Res Inst Elect Commun, Lab Nanoelect & Spintron, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, Ctr Spintron Res Network, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan..
    Ohno, Hideo
    Tohoku Univ, Res Inst Elect Commun, Lab Nanoelect & Spintron, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, Ctr Spintron Res Network, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, Ctr Innovat Integrated Elect Syst, Aoba Ku, 468-1 Aramaki Aza Aoba, Sendai, Miyagi 9800845, Japan.;Tohoku Univ, Ctr Sci & Innovat Spintron, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan.;Tohoku Univ, WPI Adv Inst Mat Res, Aoba Ku, 2-1-1 Katahira, Sendai, Miyagi 9808577, Japan..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, Electrum 229, S-16440 Kista, Sweden.;KTH Royal Inst Technol, Sch Engn Sci, Mat & Nanophys, Electrum 229, S-16440 Kista, Sweden..
    Giant voltage-controlled modulation of spin Hall nano-oscillator damping2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 4006Article in journal (Refereed)
    Abstract [en]

    Spin Hall nano-oscillators (SHNOs) are emerging spintronic devices for microwave signal generation and oscillator-based neuromorphic computing combining nano-scale footprint, fast and ultra-wide microwave frequency tunability, CMOS compatibility, and strong non-linear properties providing robust large-scale mutual synchronization in chains and two-dimensional arrays. While SHNOs can be tuned via magnetic fields and the drive current, neither approach is conducive to individual SHNO control in large arrays. Here, we demonstrate electrically gated W/CoFeB/MgO nano-constrictions in which the voltage-dependent perpendicular magnetic anisotropy tunes the frequency and, thanks to nano-constriction geometry, drastically modifies the spin-wave localization in the constriction region resulting in a giant 42% variation of the effective damping over four volts. As a consequence, the SHNO threshold current can be strongly tuned. Our demonstration adds key functionality to nano-constriction SHNOs and paves the way for energy-efficient control of individual oscillators in SHNO chains and arrays for neuromorphic computing. Spin Hall nano-oscillators can be tuned via magnetic fields and the drive current, but individual oscillator control in large arrays remains a challenge. Here, the authors provide individual control of the threshold current and the auto-oscillation frequency by voltage-controlled magnetic anisotropy.

  • 61.
    Fuldauer, Lena I.
    et al.
    Univ Oxford, Environm Change Inst, South Parks Rd, Oxford OX1 3QY, England..
    Thacker, Scott
    Univ Oxford, Environm Change Inst, South Parks Rd, Oxford OX1 3QY, England..
    Haggis, Robyn A.
    Univ Oxford, Environm Change Inst, South Parks Rd, Oxford OX1 3QY, England..
    Nerini, Francesco Fuso
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Energy Systems.
    Nicholls, Robert J.
    Univ East Anglia, Tyndall Ctr Climate Change Res, Norwich NR4 7TJ, Norfolk, England..
    Hall, Jim W.
    Univ Oxford, Environm Change Inst, South Parks Rd, Oxford OX1 3QY, England..
    Targeting climate adaptation to safeguard and advance the Sustainable Development Goals2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 3579Article in journal (Refereed)
    Abstract [en]

    The international community has committed to achieve 169 Sustainable Development Goal (SDG) targets by 2030 and to enhance climate adaptation under the Paris Agreement. Despite the potential for synergies, aligning SDG and climate adaptation efforts is inhibited by an inadequate understanding of the complex relationship between SDG targets and adaptation to impacts of climate change. Here we propose a framework to conceptualise how ecosystems and socio-economic sectors mediate this relationship, which provides a more nuanced understanding of the impacts of climate change on all 169 SDG targets. Global application of the framework reveals that adaptation of wetlands, rivers, cropland, construction, water, electricity, and housing in the most vulnerable countries is required to safeguard achievement of 68% of SDG targets from near-term climate risk by 2030. We discuss how our framework can help align National Adaptation Plans with SDG targets, thus ensuring that adaptation advances, rather than detracts from, sustainable development. Without targeted climate adaptation, impacts of climate change threaten achievement of all 169 SDG targets. Fuldauer et al. provide an actionable framework to assess these impacts and help systematically align national adaptation plans with the SDGs.

  • 62.
    Gandini, Rosaria
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Reichenbach, Tom
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Tan, Tien-Chye
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Structural basis for dolichylphosphate mannose biosynthesis2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, no 1, article id 120Article in journal (Refereed)
    Abstract [en]

    Protein glycosylation is a critical protein modification. In biogenic membranes of eukaryotes and archaea, these reactions require activated mannose in the form of the lipid conjugate dolichylphosphate mannose (Dol-P-Man). The membrane protein dolichylphosphate mannose synthase (DPMS) catalyzes the reaction whereby mannose is transferred from GDP-mannose to the dolichol carrier Dol-P, to yield Dol-P-Man. Failure to produce or utilize Dol-P-Man compromises organism viability, and in humans, several mutations in the human dpm1 gene lead to congenital disorders of glycosylation (CDG). Here, we report three high-resolution crystal structures of archaeal DPMS from Pyrococcus furiosus, in complex with nucleotide, donor, and glycolipid product. The structures offer snapshots along the catalytic cycle, and reveal how lipid binding couples to movements of interface helices, metal binding, and acceptor loop dynamics to control critical events leading to Dol-P-Man synthesis. The structures also rationalize the loss of dolichylphosphate mannose synthase function in dpm1-associated CDG.The generation of glycolipid dolichylphosphate mannose (Dol-P-Man) is a critical step for protein glycosylation and GPI anchor synthesis. Here the authors report the structure of dolichylphosphate mannose synthase in complex with bound nucleotide and donor to provide insight into the mechanism of Dol-P-Man synthesis.

  • 63.
    Garmroudi, Fabian
    et al.
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Parzer, Michael
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Riss, Alexander
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Ruban, Andrei V.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Structures. Mat Ctr Leoben Forsch GmbH, Leoben, Austria..
    Khmelevskyi, Sergii
    TU Wien, Ctr Computat Mat Sci & Engn, Vienna, Austria..
    Reticcioli, Michele
    Univ Wien, Ctr Computat Mat Sci, Fac Phys, Vienna, Austria..
    Knopf, Matthias
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Michor, Herwig
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Pustogow, Andrej
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Mori, Takao
    Natl Inst Mat Sci, Int Ctr Mat Nanoarchitecton, WPI MANA, Tsukuba, Ibaraki, Japan.;Univ Tsukuba, Grad Sch Pure & Appl Sci, Tsukuba, Ibaraki, Japan..
    Bauer, Ernst
    TU Wien, Inst Solid State Phys, Vienna, Austria..
    Anderson transition in stoichiometric Fe2VAl: high thermoelectric performance from impurity bands2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 3599Article in journal (Refereed)
    Abstract [en]

    The mathematical conditions for the best thermoelectric is well known but never realised in real materials. Here, the authors propose the Anderson transition in a narrow impurity band as a physical realisation of this seemingly unrealisable scenario. Discovered more than 200 years ago in 1821, thermoelectricity is nowadays of global interest as it enables direct interconversion of thermal and electrical energy via the Seebeck/Peltier effect. In their seminal work, Mahan and Sofo mathematically derived the conditions for 'the best thermoelectric'-a delta-distribution-shaped electronic transport function, where charge carriers contribute to transport only in an infinitely narrow energy interval. So far, however, only approximations to this concept were expected to exist in nature. Here, we propose the Anderson transition in a narrow impurity band as a physical realisation of this seemingly unrealisable scenario. An innovative approach of continuous disorder tuning allows us to drive the Anderson transition within a single sample: variable amounts of antisite defects are introduced in a controlled fashion by thermal quenching from high temperatures. Consequently, we obtain a significant enhancement and dramatic change of the thermoelectric properties from p-type to n-type in stoichiometric Fe2VAl, which we assign to a narrow region of delocalised electrons in the energy spectrum near the Fermi energy. Based on our electronic transport and magnetisation experiments, supported by Monte-Carlo and density functional theory calculations, we present a novel strategy to enhance the performance of thermoelectric materials.

  • 64.
    Gibson, Ursula J.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. Norwegian Univ Sci & Technol, Dept Phys, Trondheim, Norway..
    Wei, Lei
    Nanyang Technol Univ, Sch Elect & Elect Engn, Singapore, Singapore..
    Ballato, John
    Clemson Univ, Dept Mat Sci & Engn, Clemson, SC USA..
    Semiconductor core fibres: materials science in a bottle2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 3990Article, review/survey (Refereed)
    Abstract [en]

    Novel core fibers have a wide range of applications in optics, as sources, detectors and nonlinear response media. Optoelectronic, and even electronic device applications are now possible, due to the introduction of methods for drawing fibres with a semiconductor core. This review examines progress in the development of glass-clad, crystalline core fibres, with an emphasis on semiconducting cores. The underlying materials science and the importance of post-processing techniques for recrystallization and purification are examined, with achievements and future prospects tied to the phase diagrams of the core materials. The application space for optical fibers is growing, enabled by fibers built using special materials and processes. In this Review, the authors discuss the materials science behind producing crystalline core fibers for diverse applications and progress in the field.

  • 65.
    Goerlin, Mikaela
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden.;Uppsala Univ, Angstrom Lab, Dept Chem, Box 538, SE-75121 Uppsala, Sweden..
    Halldin Stenlid, Joakim
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Koroidov, Sergey
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Wang, Hsin-Yi
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Boerner, Mia
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Shipilin, Mikhail
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Kalinko, Aleksandr
    Univ Paderborn, Dept Chem, Warburger Str 100, D-33098 Paderborn, Germany.;Univ Paderborn, Ctr Sustainable Syst Design CSSD, Warburger Str 100, D-33098 Paderborn, Germany.;Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany..
    Murzin, Vadim
    Deutsch Elektronen Synchrotron DESY, Notkestr 85, D-22607 Hamburg, Germany.;Berg Univ Wuppertal, Gaussstr 20, D-42119 Wuppertal, Germany..
    Safonova, Olga V.
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland..
    Nachtegaal, Maarten
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland..
    Uheida, Abdusalam
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Dutta, Joydeep
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Bauer, Matthias
    Nilsson, Anders
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Diaz-Morales, Oscar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemical Engineering, Applied Electrochemistry. Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Key activity descriptors of nickel-iron oxygen evolution electrocatalysts in the presence of alkali metal cations2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 6181Article in journal (Refereed)
    Abstract [en]

    Efficient oxygen evolution reaction (OER) electrocatalysts are pivotal for sustainable fuel production, where the Ni-Fe oxyhydroxide (OOH) is among the most active catalysts for alkaline OER. Electrolyte alkali metal cations have been shown to modify the activity and reaction intermediates, however, the exact mechanism is at question due to unexplained deviations from the cation size trend. Our X-ray absorption spectroelectrochemical results show that bigger cations shift the Ni2+/(3+delta)+ redox peak and OER activity to lower potentials (however, with typical discrepancies), following the order CsOH>NaOH approximate to KOH>RbOH>LiOH. Here, we find that the OER activity follows the variations in electrolyte pH rather than a specific cation, which accounts for differences both in basicity of the alkali hydroxides and other contributing anomalies. Our density functional theory-derived reactivity descriptors confirm that cations impose negligible effect on the Lewis acidity of Ni, Fe, and O lattice sites, thus strengthening the conclusions of an indirect pH effect. It is commonly accepted that electrolyte alkali metal cations modify the catalytic activity for oxygen evolution reaction. Here the authors challenge this assumption, showing that the activity is actually affected by a change in the electrolyte pH rather than a specific alkali cation.

  • 66.
    Graham, D. B.
    et al.
    Swedish Inst Space Phys, Uppsala, Sweden..
    Khotyaintsev, Yu. V.
    Swedish Inst Space Phys, Uppsala, Sweden..
    Andre, M.
    Swedish Inst Space Phys, Uppsala, Sweden..
    Vaivads, Andris
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    Divin, A.
    St Petersburg State Univ, Earth Phys Dept, Fac Phys, St Petersburg, Russia..
    Drake, J. F.
    Univ Maryland, IREAP, College Pk, MD 20742 USA..
    Norgren, C.
    Univ Bergen, Dept Phys & Technol, Bergen, Norway..
    Le Contel, O.
    Sorbonne Univ, Lab Phys Plasmas UMR7648, Ecole Polytech, Observ Paris,CNRS, Paris, France..
    Lindqvist, Per-Arne
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    Rager, A. C.
    NASA Goddard Space Flight Ctr, Greenbelt, MD USA.;Catholic Univ Amer, Dept Phys, Washington, DC USA..
    Gershman, D. J.
    NASA Goddard Space Flight Ctr, Greenbelt, MD USA..
    Russell, C. T.
    Univ Calif Los Angeles, Dept Earth & Space Sci, Los Angeles, CA 90024 USA..
    Burch, J. L.
    Southwest Res Inst, San Antonio, TX USA..
    Hwang, K. -J
    Dokgo, K.
    Southwest Res Inst, San Antonio, TX USA..
    Direct observations of anomalous resistivity and diffusion in collisionless plasma2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2954Article in journal (Refereed)
    Abstract [en]

    Coulomb collisions provide plasma resistivity and diffusion but in many low-density astrophysical plasmas such collisions between particles are extremely rare. Scattering of particles by electromagnetic waves can lower the plasma conductivity. Such anomalous resistivity due to wave-particle interactions could be crucial to many processes, including magnetic reconnection. It has been suggested that waves provide both diffusion and resistivity, which can support the reconnection electric field, but this requires direct observation to confirm. Here, we directly quantify anomalous resistivity, viscosity, and cross-field electron diffusion associated with lower hybrid waves using measurements from the four Magnetospheric Multiscale (MMS) spacecraft. We show that anomalous resistivity is approximately balanced by anomalous viscosity, and thus the waves do not contribute to the reconnection electric field. However, the waves do produce an anomalous electron drift and diffusion across the current layer associated with magnetic reconnection. This leads to relaxation of density gradients at timescales of order the ion cyclotron period, and hence modifies the reconnection process. It is suggested that waves can provide both diffusion and resistivity that can potentially support the reconnection electric field in low-density astrophysical plasmas. Here, the authors show, using direct spacecraft measurements, that the waves contribute to anomalous diffusion but do not contribute to the reconnection electric field.

  • 67. Grapotte, Mathys
    et al.
    Forsberg, Mattias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Oksvold, Per
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sivertsson, Åsa
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Sjöstedt, Evelina
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    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.
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology. 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.
    et al,
    Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network2021In: Nature Communications, E-ISSN 2041-1723Article in journal (Refereed)
    Abstract [en]

    Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

  • 68.
    Gratz, Lukas
    et al.
    Karolinska Inst, Dept Physiol & Pharmacol, Sec Receptor Biol & Signaling, Biomed, S-17165 Stockholm, Sweden..
    Kowalski-Jahn, Maria
    Karolinska Inst, Dept Physiol & Pharmacol, Sec Receptor Biol & Signaling, Biomed, S-17165 Stockholm, Sweden..
    Scharf, Magdalena M.
    Karolinska Inst, Dept Physiol & Pharmacol, Sec Receptor Biol & Signaling, Biomed, S-17165 Stockholm, Sweden..
    Kozielewicz, Pawel
    Karolinska Inst, Dept Physiol & Pharmacol, Sec Receptor Biol & Signaling, Biomed, S-17165 Stockholm, Sweden..
    Jahn, Michael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Max Planck Unit Sci Pathogens, Bioinformat Platform, Charitepl 1, D-10117 Berlin, Germany..
    Bous, Julien
    Karolinska Inst, Dept Physiol & Pharmacol, Sec Receptor Biol & Signaling, Biomed, S-17165 Stockholm, Sweden..
    Lambert, Nevin A.
    Augusta Univ, Med Coll Georgia, Dept Pharmacol & Toxicol, Augusta, GA USA..
    Gloriam, David E.
    Univ Copenhagen, Dept Drug Design & Pharmacol, Copenhagen, Denmark..
    Schulte, Gunnar
    Karolinska Inst, Dept Physiol & Pharmacol, Sec Receptor Biol & Signaling, Biomed, S-17165 Stockholm, Sweden..
    Pathway selectivity in Frizzleds is achieved by conserved micro-switches defining pathway-determining, active conformations2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4573Article in journal (Refereed)
    Abstract [en]

    The class Frizzled of G protein-coupled receptors (GPCRs), consisting of ten Frizzled (FZD(1-10)) paralogs and Smoothened, remains one of the most enigmatic GPCR families. This class mediates signaling predominantly through Disheveled (DVL) or heterotrimeric G proteins. However, the mechanisms underlying pathway selection are elusive. Here we employ a structure-driven mutagenesis approach in combination with an extensive panel of functional signaling readouts to investigate the importance of conserved state-stabilizing residues in FZD(5) for signal specification. Similar data were obtained for FZD(4) and FZD(10) suggesting that our findings can be extrapolated to other members of the FZD family. Comparative molecular dynamics simulations of wild type and selected FZD(5) mutants further support the concept that distinct conformational changes in FZDs specify the signal outcome. In conclusion, we find that FZD(5) and FZDs in general prefer coupling to DVL rather than heterotrimeric G proteins and that distinct active state micro-switches in the receptor are essential for pathway selection arguing for conformational changes in the receptor protein defining transducer selectivity. Signaling pathway selectivity downstream of GPCRs is not fully understood. Here, authors perform functional analysis of Frizzled mutants to uncover state-stabilizing residues or 'micro-switches' mediating selectivity towards Disheveled over G proteins.

  • 69.
    Guo, Xin
    et al.
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Pu, Rui
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Zhu, Zhimin
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Qiao, Shuqian
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Liang, Yusen
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Huang, Bingru
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Liu, Haichun
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Labrador-Páez, Lucia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Kostiv, Uliana
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Zhao, Pu
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Wu, Qiusheng
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China..
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Zhan, Qiuqiang
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Natl Ctr Int Res Green Optoelect,Guangdong Prov K, Guangzhou 510006, Peoples R China.;South China Normal Univ, Coll Biophoton, MOE Key Lab, Guangzhou 510631, Peoples R China.;South China Normal Univ, Coll Biophoton, Guangdong Prov Key Lab Laser Life Sci, Guangzhou 510631, Peoples R China..
    Achieving low-power single-wavelength-pair nanoscopy with NIR-II continuous-wave laser for multi-chromatic probes2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2843Article in journal (Refereed)
    Abstract [en]

    The authors introduce stimulated-emission induced excitation depletion (STExD) nanoscopy using a single pair of low-power, near-infrared, continue-wave lasers. Emission of multichromatic probes is inhibited by cascade amplified depletion in lanthanide upconversion systems induced by manipulating their common sensitizer. Stimulated emission depletion (STED) microscopy is a powerful diffraction-unlimited technique for fluorescence imaging. Despite its rapid evolution, STED fundamentally suffers from high-intensity light illumination, sophisticated probe-defined laser schemes, and limited photon budget of the probes. Here, we demonstrate a versatile strategy, stimulated-emission induced excitation depletion (STExD), to deplete the emission of multi-chromatic probes using a single pair of low-power, near-infrared (NIR), continuous-wave (CW) lasers with fixed wavelengths. With the effect of cascade amplified depletion in lanthanide upconversion systems, we achieve emission inhibition for a wide range of emitters (e.g., Nd3+, Yb3+, Er3+, Ho3+, Pr3+, Eu3+, Tm3+, Gd3+, and Tb3+) by manipulating their common sensitizer, i.e., Nd3+ ions, using a 1064-nm laser. With NaYF4:Nd nanoparticles, we demonstrate an ultrahigh depletion efficiency of 99.3 +/- 0.3% for the 450 nm emission with a low saturation intensity of 23.8 +/- 0.4 kW cm(-2). We further demonstrate nanoscopic imaging with a series of multi-chromatic nanoprobes with a lateral resolution down to 34 nm, two-color STExD imaging, and subcellular imaging of the immunolabelled actin filaments. The strategy expounded here promotes single wavelength-pair nanoscopy for multi-chromatic probes and for multi-color imaging under low-intensity-level NIR-II CW laser depletion.

  • 70.
    Gyger, Samuel
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics. KTH Royal Inst Technol, Dept Appl Phys, Stockholm, Sweden..
    Zichi, Julien
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Schweickert, Lucas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Elshaari, Ali W.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Steinhauer, Stephan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    da Silva, Saimon F. Covre
    Johannes Kepler Univ Linz, Inst Semicond & Solid State Phys, Linz, Austria..
    Rastelli, Armando
    Johannes Kepler Univ Linz, Inst Semicond & Solid State Phys, Linz, Austria..
    Zwiller, Val
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Jöns, Klaus D.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Errando-Herranz, Carlos
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Reconfigurable photonics with on-chip single-photon detectors2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 1408Article in journal (Refereed)
    Abstract [en]

    Integrated quantum photonics offers a promising path to scale up quantum optics experiments by miniaturizing and stabilizing complex laboratory setups. Central elements of quantum integrated photonics are quantum emitters, memories, detectors, and reconfigurable photonic circuits. In particular, integrated detectors not only offer optical readout but, when interfaced with reconfigurable circuits, allow feedback and adaptive control, crucial for deterministic quantum teleportation, training of neural networks, and stabilization of complex circuits. However, the heat generated by thermally reconfigurable photonics is incompatible with heat-sensitive superconducting single-photon detectors, and thus their on-chip co-integration remains elusive. Here we show low-power microelectromechanical reconfiguration of integrated photonic circuits interfaced with superconducting single-photon detectors on the same chip. We demonstrate three key functionalities for photonic quantum technologies: 28 dB high-extinction routing of classical and quantum light, 90 dB high-dynamic range single-photon detection, and stabilization of optical excitation over 12 dB power variation. Our platform enables heat-load free reconfigurable linear optics and adaptive control, critical for quantum state preparation and quantum logic in large-scale quantum photonics applications. Integrated photonics are promising to scale up quantum optics. Here the authors combine low-power microelectromechanical control and superconducting single-photon detectors on the same chip and demonstrate routing, high-dynamic-range detection, and power stabilization.

  • 71. Haidar, Mohammad
    et al.
    Awad, Ahmad A.
    Dvornik, Mykola
    Khymyn, Roman
    Houshang, Afshin
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    A single layer spin-orbit torque nano-oscillator2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 2362Article in journal (Refereed)
    Abstract [en]

    Spin torque and spin Hall effect nano-oscillators generate high intensity spin wave auto-oscillations on the nanoscale enabling novel microwave applications in spintronics, magnonics, and neuromorphic computing. For their operation, these devices require externally generated spin currents either from an additional ferromagnetic layer or a material with a high spin Hall angle. Here we demonstrate highly coherent field and current tunable microwave signals from nano-constrictions in single 15-20 nm thick permalloy layers with oxide interfaces. Using a combination of spin torque ferromagnetic resonance measurements, scanning micro-Brillouin light scattering microscopy, and micromagnetic simulations, we identify the auto-oscillations as emanating from a localized edge mode of the nano-constriction driven by spin-orbit torques. Our results pave the way for greatly simplified designs of auto-oscillating nano-magnetic systems only requiring single ferromagnetic layers with oxide interfaces.

  • 72.
    Hao, Meng-Shu
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Mazurkewich, Scott
    Li, He
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Kvammen, Alma
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Saha, Srijani
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Protein Technology.
    Koskela, Salla
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Inman, Annie R.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Nakajima, Masahiro
    Tanaka, Nobukiyo
    Nakai, Hiroyuki
    Brändén, Gisela
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience.
    Larsbrink, Johan
    McKee, Lauren S.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Structural and biochemical analysis of family 92 carbohydrate-binding modules uncovers multivalent binding to β-glucans2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 3429Article in journal (Refereed)
    Abstract [en]

    Carbohydrate-binding modules (CBMs) are non-catalytic proteins found appended to carbohydrate-active enzymes. Soil and marine bacteria secrete such enzymes to scavenge nutrition, and they often use CBMs to improve reaction rates and retention of released sugars. Here we present a structural and functional analysis of the recently established CBM family 92. All proteins analysed bind preferentially to β−1,6-glucans. This contrasts with the diversity of predicted substrates among the enzymes attached to CBM92 domains. We present crystal structures for two proteins, and confirm by mutagenesis that tryptophan residues permit ligand binding at three distinct functional binding sites on each protein. Multivalent CBM families are uncommon, so the establishment and structural characterisation of CBM92 enriches the classification database and will facilitate functional prediction in future projects. We propose that CBM92 proteins may cross-link polysaccharides in nature, and might have use in novel strategies for enzyme immobilisation.

  • 73.
    He, Guiying
    et al.
    Department of Physics, Graduate Center, City University of New York, New York, NY, 10016, USA; Photonics Initiative, Advanced Science Research Center, City University of New York, New York, NY, 10031, USA.
    Churchill, Emily M.
    Department of Chemistry, Columbia University, New York, NY, 10027, USA.
    Parenti, Kaia R.
    Department of Chemistry, Columbia University, New York, NY, 10027, USA.
    Zhang, Jocelyn
    Department of Chemistry, Columbia University, New York, NY, 10027, USA.
    Narayanan, Pournima
    Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA; Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
    Namata, Faridah
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Coating Technology.
    Malkoch, Michael
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Coating Technology.
    Congreve, Daniel N.
    Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
    Cacciuto, Angelo
    Department of Chemistry, Columbia University, New York, NY, 10027, USA.
    Sfeir, Matthew Y.
    Department of Physics, Graduate Center, City University of New York, New York, NY, 10016, USA; Photonics Initiative, Advanced Science Research Center, City University of New York, New York, NY, 10031, USA.
    Campos, Luis M.
    Department of Chemistry, Columbia University, New York, NY, 10027, USA.
    Promoting multiexciton interactions in singlet fission and triplet fusion upconversion dendrimers2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 6080Article in journal (Refereed)
    Abstract [en]

    Singlet fission and triplet-triplet annihilation upconversion are two multiexciton processes intimately related to the dynamic interaction between one high-lying energy singlet and two low-lying energy triplet excitons. Here, we introduce a series of dendritic macromolecules that serve as platform to study the effect of interchromophore interactions on the dynamics of multiexciton generation and decay as a function of dendrimer generation. The dendrimers (generations 1–4) consist of trimethylolpropane core and 2,2-bis(methylol)propionic acid (bis-MPA) dendrons that provide exponential growth of the branches, leading to a corona decorated with pentacenes for SF or anthracenes for TTA-UC. The findings reveal a trend where a few highly ordered sites emerge as the dendrimer generation grows, dominating the multiexciton dynamics, as deduced from optical spectra, and transient absorption spectroscopy. While the dendritic structures enhance TTA-UC at low annihilator concentrations in the largest dendrimers, the paired chromophore interactions induce a broadened and red-shifted excimer emission. In SF dendrimers of higher generations, the triplet dynamics become increasingly dominated by pairwise sites exhibiting strong coupling (Type II), which can be readily distinguished from sites with weaker coupling (Type I) by their spectral dynamics and decay kinetics.

  • 74.
    Hildebrandt, Franziska
    et al.
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Svante Arrhenius Väg 20C, SE-10691 Stockholm, Sweden..
    Andersson, Alma
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Saarenpää, Sami
    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.
    Van Hul, Noemi
    Karolinska Inst Stockholm, Dept Cell & Mol Biol, SE-17177 Solna, Sweden..
    Kanatani, Sachie
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Svante Arrhenius Väg 20C, SE-10691 Stockholm, Sweden..
    Masek, Jan
    Karolinska Inst Stockholm, Dept Cell & Mol Biol, SE-17177 Solna, Sweden.;Charles Univ Prague, Dept Cell Biol, Fac Sci, Vinicna 7, Prague 12800 2, Czech Republic..
    Ellis, Ewa
    Karolinska Inst, Dept Clin Sci Intervent & Technol CLINTEC, S-14186 Stockholm, Sweden..
    Barragan, Antonio
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Svante Arrhenius Väg 20C, SE-10691 Stockholm, Sweden..
    Mollbrink, Annelie
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Andersson, Emma R.
    Karolinska Inst Stockholm, Dept Cell & Mol Biol, SE-17177 Solna, Sweden..
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Ankarklev, Johan
    Stockholm Univ, Wenner Gren Inst, Dept Mol Biosci, Svante Arrhenius Väg 20C, SE-10691 Stockholm, Sweden.;Uppsala Univ, Microbial Single Cell Genom Facil, SciLifeLab, Biomed Ctr BMC, SE-75123 Uppsala, Sweden..
    Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver2021In: Nature Communications, E-ISSN 2041-1723, Vol. 12, no 1, article id 7046Article in journal (Refereed)
    Abstract [en]

    Reconstruction of heterogeneity through single cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we apply Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology. Global transcriptional differences across lobular units in the liver remain unknown. Here the authors perform spatial transcriptomics of liver tissue to delineate transcriptional differences in physical space, confirm lobular zonation along transcriptional gradients and suggest the presence of previously uncharacterized structures within liver tissue.

  • 75.
    Holmes, Susannah
    et al.
    La Trobe Univ, Sch Engn Comp & Math Sci, Dept Math & Phys Sci, Melbourne, Vic 3086, Australia.;La Trobe Univ, La Trobe Inst Mol Sci, Melbourne, Vic 3086, Australia..
    Sellberg, Jonas A.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Abbey, Brian
    La Trobe Univ, Sch Engn Comp & Math Sci, Dept Math & Phys Sci, Melbourne, Vic 3086, Australia.;La Trobe Univ, La Trobe Inst Mol Sci, Melbourne, Vic 3086, Australia..
    Darmanin, Connie
    La Trobe Univ, Sch Engn Comp & Math Sci, Dept Math & Phys Sci, Melbourne, Vic 3086, Australia.;La Trobe Univ, La Trobe Inst Mol Sci, Melbourne, Vic 3086, Australia..
    Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4708Article in journal (Refereed)
    Abstract [en]

    The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 mu s, yield up to 2.1 angstrom resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX. Free-electron lasers are capable of high repetition rates and it is assumed that protein crystals often do not survive the first X-ray pulse. Here the authors address these issues with a demonstration of multi-hit serial crystallography in which multiple FEL pulses interact with the sample without destroying it.

  • 76.
    Horio, M.
    et al.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Matt, C. E.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland.;Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland.;Harvard Univ, Dept Phys, Cambridge, MA 02138 USA..
    Kramer, K.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Sutter, D.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Cook, A. M.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Sassa, Y.
    Uppsala Univ, Dept Phys & Astron, SE-75121 Uppsala, Sweden..
    Hauser, K.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Månsson, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Plumb, N. C.
    Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland..
    Shi, M.
    Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland..
    Lipscombe, O. J.
    Univ Bristol, HH Wills Phys Lab, Bristol BS8 1TL, Avon, England..
    Hayden, S. M.
    Univ Bristol, HH Wills Phys Lab, Bristol BS8 1TL, Avon, England..
    Neupert, T.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Chang, J.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Two-dimensional type-II Dirac fermions in layered oxides2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 3252Article in journal (Refereed)
    Abstract [en]

    Relativistic massless Dirac fermions can be probed with high-energy physics experiments, but appear also as low-energy quasi-particle excitations in electronic band structures. In condensed matter systems, their massless nature can be protected by crystal symmetries. Classification of such symmetry-protected relativistic band degeneracies has been fruitful, although many of the predicted quasi-particles still await their experimental discovery. Here we reveal, using angle-resolved photoemission spectroscopy, the existence of two-dimensional type-II Dirac fermions in the high-temperature superconductor La1.77Sr0.23CuO4. The Dirac point, constituting the crossing of d(x2-y2) and d(z2) bands, is found approximately one electronvolt below the Fermi level (E-F) and is protected by mirror symmetry. If spin-orbit coupling is considered, the Dirac point degeneracy is lifted and the bands acquire a topologically non-trivial character. In certain nickelate systems, band structure calculations suggest that the same type-II Dirac fermions can be realised near EF.

  • 77.
    Houshangh, A.
    et al.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, S-16440 Kista, Sweden..
    Khymyn, R.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Fulara, H.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Gangwar, A.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Haidar, M.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Etesami, S. R.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Ferreira, R.
    Int Iberian Nanotechnol Lab, P-4715330 Braga, Portugal..
    Freitas, P. P.
    Int Iberian Nanotechnol Lab, P-4715330 Braga, Portugal..
    Dvornik, M.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Dumas, R. K.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF. Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, S-16440 Kista, Sweden..
    Spin transfer torque driven higher-order propagating spin waves in nano-contact magnetic tunnel junctions2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, article id 4374Article in journal (Refereed)
    Abstract [en]

    Short wavelength exchange-dominated propagating spin waves will enable magnonic devices to operate at higher frequencies and higher data transmission rates. While giant magnetoresistance (GMR)-based magnetic nanocontacts are efficient injectors of propagating spin waves, the generated wavelengths are 2.6 times the nano-contact diameter, and the electrical signal strength remains too weak for applications. Here we demonstrate nano-contact-based spin wave generation in magnetic tunnel junctions and observe large-frequency steps consistent with the hitherto ignored possibility of second-and third-order propagating spin waves with wavelengths of 120 and 74 nm, i.e., much smaller than the 150-nm nanocontact. Mutual synchronization is also observed on all three propagating modes. These higher-order propagating spin waves will enable magnonic devices to operate at much higher frequencies and greatly increase their transmission rates and spin wave propagating lengths, both proportional to the much higher group velocity.

  • 78. Huang, M.
    et al.
    Bao, J.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Petranovic, D.
    Nielsen, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Efficient protein production by yeast requires global tuning of metabolism2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, no 1, article id 1131Article in journal (Refereed)
    Abstract [en]

    The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion.

  • 79.
    Huang, Po-Han
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Laakso, Miku
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Edinger, Pierre
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Hartwig, Oliver
    Univ Bundeswehr Munich, Inst Phys, Fac Elect Engn & Informat Technol, SENS Res Ctr, D-85577 Neubiberg, Germany..
    Duesberg, Georg S.
    Univ Bundeswehr Munich, Inst Phys, Fac Elect Engn & Informat Technol, SENS Res Ctr, D-85577 Neubiberg, Germany..
    Lai, Lee-Lun
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Mayer, Joachim
    Rhein Westfal TH Aachen, Cent Facil Electron Microscopy GFE, D-52074 Aachen, Germany..
    Nyman, Johan
    Linköping Univ, Dept Phys Chem & Biol IFM, S-58183 Linköping, Sweden..
    Errando-Herranz, Carlos
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Gylfason, Kristinn
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Niklaus, Frank
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Micro and Nanosystems.
    Three-dimensional printing of silica glass with sub-micrometer resolution2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3305Article in journal (Refereed)
    Abstract [en]

    Silica glass is a high-performance material used in many applications such as lenses, glassware, and fibers. However, modern additive manufacturing of micro-scale silica glass structures requires sintering of 3D-printed silica-nanoparticle-loaded composites at similar to 1200 degrees C, which causes substantial structural shrinkage and limits the choice of substrate materials. Here, 3D printing of solid silica glass with sub-micrometer resolution is demonstrated without the need of a sintering step. This is achieved by locally crosslinking hydrogen silsesquioxane to silica glass using nonlinear absorption of sub-picosecond laser pulses. The as-printed glass is optically transparent but shows a high ratio of 4-membered silicon-oxygen rings and photoluminescence. Optional annealing at 900 degrees C makes the glass indistinguishable from fused silica. The utility of the approach is demonstrated by 3D printing an optical microtoroid resonator, a luminescence source, and a suspended plate on an optical-fiber tip. This approach enables promising applications in fields such as photonics, medicine, and quantum-optics.

  • 80.
    Huang, Shuo
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Huang, He
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang, 621900, PR China.
    Li, Wei
    Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, SE-75120, Uppsala, Sweden.
    Kim, Dongyoo
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. Department of Physics, Pukyung National University, Busan, 608-737, Republic of Korea.
    Lu, Song
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Li, Xiaoqing
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Holmström, E.
    Kwon, S. K.
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Twinning in metastable high-entropy alloys2018In: Nature Communications, E-ISSN 2041-1723, Vol. 9, no 1, article id 2381Article in journal (Refereed)
    Abstract [en]

    Twinning is a fundamental mechanism behind the simultaneous increase of strength and ductility in medium- and high-entropy alloys, but its operation is not yet well understood, which limits their exploitation. Since many high-entropy alloys showing outstanding mechanical properties are actually thermodynamically unstable at ambient and cryogenic conditions, the observed twinning challenges the existing phenomenological and theoretical plasticity models. Here, we adopt a transparent approach based on effective energy barriers in combination with first-principle calculations to shed light on the origin of twinning in high-entropy alloys. We demonstrate that twinning can be the primary deformation mode in metastable face-centered cubic alloys with a fraction that surpasses the previously established upper limit. The present advance in plasticity of metals opens opportunities for tailoring the mechanical response in engineering materials by optimizing metastable twinning in high-entropy alloys. 

  • 81.
    Hueting, David A.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Coating Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Schriever, Karen
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Coating Technology.
    Sun, Rui
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Vlachiotis, Stelios
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Zuo, Fanglei
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Du, Likun
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Persson, Helena
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Drug Discovery and Development.
    Hofström, Camilla
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Drug Discovery and Development.
    Ohlin, Mats
    Karolinska Inst, Sci Life Lab, Solna, Sweden.;Lund Univ, Dept Immunotechnol, Lund, Sweden..
    Wallden, Karin
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Buggert, Marcus
    Karolinska Inst, Ctr Infect Med, Dept Med Huddinge, Stockholm, Sweden..
    Hammarstrom, Lennart
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Marcotte, Harold
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Pan-Hammarstroem, Qiang
    Karolinska Inst, Dept Med Biochem & Biophys, Div Vasc Biol, Stockholm, Sweden..
    Andrell, Juni
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.;Karolinska Inst, Dept Med Biochem & Biophys, Stockholm, Sweden..
    Syrén, Per-Olof
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Design, structure and plasma binding of ancestral β-CoV scaffold antigens2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 6527Article in journal (Refereed)
    Abstract [en]

    We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 angstrom) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma. Development of vaccines remains challenging because viral antigens can be unstable or aggregate. Here, authors present ancestral sequence reconstruction as a method to generate stable and soluble antigens using exclusively available sequence information.

  • 82.
    Håkansson, Karl
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Fall, Andreas
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Fibre Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Yu, Sun
    DESY, Hamburg Germany.
    Krywka, Christina
    Institute of experimental and applied physics. Kiel Germany.
    Roth, Stephan
    DESY, Hamburg Germany.
    Santoro, Gonzalo
    DESY, Hamburg Germany.
    Kvick, Mathias
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Prahl Wittberg, Lisa
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Wågberg, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Fibre Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Söderberg, Daniel
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Innventia AB, Stockholm Sweden.
    Hydrodynamic alignment and assembly of nanofibrils resulting in strong cellulose filaments2014In: Nature Communications, E-ISSN 2041-1723, Vol. 5, p. 4018-Article in journal (Refereed)
    Abstract [en]

    Cellulose nanofibrils can be obtained from trees and have considerable potential as a building block for biobased materials. In order to achieve good properties of these materials, the nanostructure must be controlled. Here we present a process combining hydrodynamic alignment with a dispersion-gel transition that produces homogeneous and smooth filaments from a low-concentration dispersion of cellulose nanofibrils in water. The preferential fibril orientation along the filament direction can be controlled by the process parameters. The specific ultimate strength is considerably higher than previously reported filaments made of cellulose nanofibrils. The strength is even in line with the strongest cellulose pulp fibres extracted from wood with the same degree of fibril alignment. Successful nanoscale alignment before gelation demands a proper separation of the timescales involved. Somewhat surprisingly, the device must not be too small if this is to be achieved.

  • 83.
    Hård, Joanna
    et al.
    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; ETH AI Center, ETH Zurich, Zurich, Switzerland.
    Mold, Jeff E.
    Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
    Eisfeldt, Jesper
    Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
    Tellgren-Roth, Christian
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Häggqvist, Susana
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Bunikis, Ignas
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Contreras-Lopez, Orlando
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Chin, Chen Shan
    GeneDX LLC, Stamford, CT, 06902, USA.
    Nordlund, Jessica
    Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
    Rubin, Carl Johan
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Feuk, Lars
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Michaëlsson, Jakob
    Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
    Ameur, Adam
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
    Long-read whole-genome analysis of human single cells2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 5164Article in journal (Refereed)
    Abstract [en]

    Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.

  • 84.
    Iglesias, Maria Jesus
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. Division of Internal Medicine, University Hospital of North Norway (UNN), PB100, 9038, Tromsø, Norway; Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway.
    Sanchez-Rivera, Laura
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Ibrahim-Kosta, Manal
    Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique—Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France, HemoVasc (CRB AP-HM HemoVasc).
    Naudin, Clément
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway.
    Munsch, Gaëlle
    University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France, ELEANOR.
    Goumidi, Louisa
    Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique—Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France, HemoVasc (CRB AP-HM HemoVasc).
    Farm, Maria
    Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden.
    Smith, Philip M.
    Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden; Theme of Emergency and Reparative Medicine, Karolinska University Hospital, Stockholm, Sweden.
    Thibord, Florian
    Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA; The Framingham Heart Study, Boston University, Framingham, MA, USA.
    Kral-Pointner, Julia Barbara
    Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria.
    Hong, Mun-Gwan
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Suchon, Pierre
    Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique—Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France, HemoVasc (CRB AP-HM HemoVasc).
    Germain, Marine
    University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France, ELEANOR; Laboratory of Excellence GENMED (Medical Genomics), Bordeaux, France.
    Schottmaier, Waltraud
    Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria.
    Dusart, Philip
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab. Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway.
    Boland, Anne
    Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France; Laboratory of Excellence GENMED (Medical Genomics), Evry, France.
    Kotol, David
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Edfors, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Koprulu, Mine
    MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK.
    Pietzner, Maik
    MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK; Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany; Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
    Langenberg, Claudia
    MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, CB2 0QQ, UK; Computational Medicine, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany; Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
    Damrauer, Scott M.
    Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA; Department of Surgery and Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
    Johnson, Andrew D.
    Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, MA, USA; The Framingham Heart Study, Boston University, Framingham, MA, USA.
    Klarin, Derek M.
    VA Palo Alto Healthcare System, Palo Alto, CA, USA; Department of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, USA.
    Smith, Nicholas L.
    Department of Epidemiology, University of Washington, Seattle, WA, USA; Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA; Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA.
    Smadja, David M.
    Hematology Department and Biosurgical Research Lab (Carpentier Foundation), European Georges Pompidou Hospital, Assistance Publique Hôpitaux de Paris, 20 rue Leblanc, Paris, 75015, France, 20 rue Leblanc; Innovative Therapies in Haemostasis, INSERM, Université de Paris, 4 avenue de l’Observatoire, Paris, 75270, France, 4 avenue de l’Observatoire.
    Holmström, Margareta
    Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden, SE-171 76.
    Magnusson, Maria
    Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden, SE-171 76; Department of Clinical Science, Intervention and Technology, Karolinska Institute, 171 77, Stockholm, Sweden, 171 77.
    Silveira, Angela
    Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Renné, Thomas
    Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, D-20246, Hamburg, Germany; Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, D-, 55131, Mainz, Germany; Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin 2, D02 YN77, Ireland.
    Martinez-Perez, Angel
    Genomics of Complex Diseases Group, Research Institute Hospital de la Santa Creu i Sant Pau. IIB Sant Pau, Barcelona, Spain.
    Emmerich, Joseph
    Department of vascular medicine, Paris Saint-Joseph Hospital Group, INSERM 1153-CRESS, University of Paris Cité, 185 rue Raymond Losserand, Paris, 75674, France, 185 rue Raymond Losserand.
    Deleuze, Jean Francois
    Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France; Laboratory of Excellence GENMED (Medical Genomics), Evry, France; Centre D’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France.
    Antovic, Jovan
    Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden.
    Soria Fernandez, Jose Manuel
    Genomics of Complex Diseases Group, Research Institute Hospital de la Santa Creu i Sant Pau. IIB Sant Pau, Barcelona, Spain.
    Assinger, Alice
    Center for Physiology and Pharmacology, Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria.
    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.
    Souto Andres, Joan Carles
    Unitat d’Hemostàsia i Trombosi. Hospital de la Santa Creu i Sant Pau and IIB-Sant Pau, Barcelona, Spain.
    Morange, Pierre Emmanuel
    Aix-Marseille Univ, INSERM, INRAE, C2VN, Laboratory of Haematology, CRB Assistance Publique—Hôpitaux de Marseille, HemoVasc (CRB AP-HM HemoVasc), Marseille, France, HemoVasc (CRB AP-HM HemoVasc).
    Butler, Lynn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway; Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Department of Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden.
    Trégouët, David Alexandre
    University of Bordeaux, INSERM, Bordeaux Population Health Research Center, UMR 1219, ELEANOR, Bordeaux, France, ELEANOR; Laboratory of Excellence GENMED (Medical Genomics), Bordeaux, France.
    Odeberg, Jacob
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. Division of Internal Medicine, University Hospital of North Norway (UNN), PB100, 9038, Tromsø, Norway; Translational Vascular Research, Department of Clinical Medicine, UiT The Arctic University of Norway, 9019, Tromsø, Norway; Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden; Coagulation Unit, Department of Haematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden, SE-171 76.
    Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3280Article in journal (Refereed)
    Abstract [en]

    Venous thromboembolism (VTE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. Here we show, using proteomics profiling to screen plasma from patients with suspected acute VTE, and several case-control studies for VTE, how Complement Factor H Related 5 protein (CFHR5), a regulator of the alternative pathway of complement activation, is a VTE-associated plasma biomarker. In plasma, higher CFHR5 levels are associated with increased thrombin generation potential and recombinant CFHR5 enhanced platelet activation in vitro. GWAS analysis of ~52,000 participants identifies six loci associated with CFHR5 plasma levels, but Mendelian randomization do not demonstrate causality between CFHR5 and VTE. Our results indicate an important role for the regulation of the alternative pathway of complement activation in VTE and that CFHR5 represents a potential diagnostic and/or risk predictive plasma biomarker.

  • 85.
    Jain, Yashvardhan
    et al.
    Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
    Godwin, Leah L.
    Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
    Joshi, Sripad
    Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
    Mandarapu, Shriya
    Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
    Le, Trang
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
    Lindskog, Cecilia
    Department of Immunology, Genetics and Pathology, Division of Cancer Precision Medicine, Uppsala University, Uppsala, Sweden.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA, 94305, USA.
    Börner, Katy
    Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
    Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 4656Article in journal (Refereed)
    Abstract [en]

    The development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the Hacking the Human Body machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We create a dataset containing 880 histology images with 12,901 segmented structures, engaging 1175 teams from 78 countries in community-driven, open-science development of machine learning models. Tissue variations in the dataset pose a major challenge to the teams which they overcome by using color normalization techniques and combining vision transformers with convolutional models. The best model will be productized in the HuBMAP portal to process tissue image datasets at scale in support of Human Reference Atlas construction.

  • 86.
    Jerzembeck, Fabian
    et al.
    Max Planck Inst Chem Phys Solids, Nothnitzer Str 40, D-01187 Dresden, Germany..
    Roising, Henrik S.
    NORDITA SU.
    Steppke, Alexander
    Max Planck Inst Chem Phys Solids, Nothnitzer Str 40, D-01187 Dresden, Germany..
    Rosner, Helge
    Max Planck Inst Chem Phys Solids, Nothnitzer Str 40, D-01187 Dresden, Germany..
    Sokolov, Dmitry A.
    Max Planck Inst Chem Phys Solids, Nothnitzer Str 40, D-01187 Dresden, Germany..
    Kikugawa, Naoki
    Natl Inst Mat Sci, Tsukuba, Ibaraki 3050003, Japan..
    Scaffidi, Thomas
    Univ Toronto, Dept Phys, Toronto, ON M5S 1A7, Canada.;Univ Calif Irvine, Dept Phys & Astron, Irvine, CA 92697 USA..
    Simon, Steven H.
    Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3PU, England..
    Mackenzie, Andrew P.
    Max Planck Inst Chem Phys Solids, Nothnitzer Str 40, D-01187 Dresden, Germany.;Univ St Andrews, Sch Phys & Astron, Scottish Univ Phys Alliance, St Andrews KY16 9SS, Fife, Scotland..
    Hicks, Clifford W.
    Max Planck Inst Chem Phys Solids, Nothnitzer Str 40, D-01187 Dresden, Germany.;Univ Birmingham, Sch Phys & Astron, Birmingham B15 2TT, W Midlands, England..
    The superconductivity of Sr2RuO4 under c-axis uniaxial stress2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 4596Article in journal (Refereed)
    Abstract [en]

    Applying in-plane uniaxial pressure to strongly correlated low-dimensional systems has been shown to tune the electronic structure dramatically. For example, the unconventional superconductor Sr2RuO4 can be tuned through a single Van Hove point, resulting in strong enhancement of both T-c and H-c2. Out-of-plane (c axis) uniaxial pressure is expected to tune the quasi-two-dimensional structure even more strongly, by pushing it towards two Van Hove points simultaneously. Here, we achieve a record uniaxial stress of 3.2 GPa along the c axis of Sr2RuO4. H-c2 increases, as expected for increasing density of states, but unexpectedly T-c falls. As a first attempt to explain this result, we present three-dimensional calculations in the weak interaction limit. We find that within the weak-coupling framework there is no single order parameter that can account for the contrasting effects of in-plane versus c-axis uniaxial stress, which makes this new result a strong constraint on theories of the superconductivity of Sr2RuO4. In the superconductor Sr2RuO4, in-plane strain is known to enhance both the superconducting transition temperature Tc and upper critical field Hc2, but the effect of out-of-plane strain has not been studied. Here, the authors find that Hc2 is enhanced under out-of-plane strain, but Tc unexpectedly decreases.

  • 87.
    Jia, Shi
    et al.
    Tech Univ Denmark, DTU Fotonik, DK-2800 Lyngby, Denmark..
    Lo, Mu-Chieh
    Zhang, Lu
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Communication Systems, CoS, Optical Network Laboratory (ON Lab). Zhejiang Univ, Coll Informat Sci & Elect Engn, Hangzhou 310027, Peoples R China..
    Ozolins, Oskars
    KTH, School of Engineering Sciences (SCI), Applied Physics, Photonics. RISE Res Inst Sweden, S-16440 Kista, Sweden.;Riga Tech Univ, Inst Telecommun, LV-1048 Riga, Latvia..
    Udalcovs, Aleksejs
    RISE Res Inst Sweden, S-16440 Kista, Sweden..
    Kong, Deming
    Tech Univ Denmark, DTU Fotonik, DK-2800 Lyngby, Denmark..
    Pang, Xiaodan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Photonics.
    Guzman, Robinson
    Univ Carlos III Madrid, Madrid 28911, Spain..
    Yu, Xianbin
    Zhejiang Univ, Coll Informat Sci & Elect Engn, Hangzhou 310027, Peoples R China..
    Xiao, Shilin
    Shanghai Jiao Tong Univ, Sch SE IEE, Shanghai 200240, Peoples R China..
    Popov, Sergei
    KTH, School of Engineering Sciences (SCI), Applied Physics, Photonics.
    Chen, Jiajia
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Communication Systems, CoS.
    Carpintero, Guillermo
    Univ Carlos III Madrid, Madrid 28911, Spain..
    Morioka, Toshio
    Tech Univ Denmark, DTU Fotonik, DK-2800 Lyngby, Denmark..
    Hu, Hao
    Tech Univ Denmark, DTU Fotonik, DK-2800 Lyngby, Denmark..
    Oxenlowe, Leif K.
    Tech Univ Denmark, DTU Fotonik, DK-2800 Lyngby, Denmark..
    Integrated dual-laser photonic chip for high-purity carrier generation enabling ultrafast terahertz wireless communications2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1388Article in journal (Refereed)
    Abstract [en]

    Photonic generation of Terahertz (THz) carriers displays high potential for THz communications with a large tunable range and high modulation bandwidth. While many photonics-based THz generations have recently been demonstrated with discrete bulky components, their practical applications are significantly hindered by the large footprint and high energy consumption. Herein, we present an injection-locked heterodyne source based on generic foundry-fabricated photonic integrated circuits (PIC) attached to a uni-traveling carrier photodiode generating high-purity THz carriers. The generated THz carrier is tunable within the range of 0-1.4 THz, determined by the wavelength spacing between the two monolithically integrated distributed feedback (DFB) lasers. This scheme generates and transmits a 131 Gbits(-1) net rate signal over a 10.7-m distance with -24 dBm emitted power at 0.4 THz. This monolithic dual-DFB PIC-based THz generation approach is a significant step towards fully integrated, cost-effective, and energy-efficient THz transmitters. A photonic Terahertz source based on injection-locking an integrated dual-laser chip generates and transmits a 131 Gbps THz signal over 10.7-m distance, showing great potential towards fully integrated and energy-efficient THz transmitters for 6G.

  • 88.
    Jiang, S.
    et al.
    School of Microelectronics, South China University of Technology, 511442, Guangzhou, China; Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden.
    Chung, S.
    Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden; Department of Physics Education, Korea National University of Education, 28173, Cheongju, Korea.
    Ahlberg, M.
    Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden.
    Frisk, A.
    Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden.
    Khymyn, R.
    Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden.
    Le, Quang Tuan
    KTH, School of Engineering Sciences (SCI), Applied Physics. Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden.
    Mazraati, Hamid
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Houshang, A.
    Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden.
    Heinonen, O.
    Materials Science Division, Argonne National Laboratory, 60439, Lemont, IL, USA; Seagate Technology, 7801 Computer Ave., 55435, Bloomington, MN, USA, 7801 Computer Ave..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Physics Department, University of Gothenburg, 412 96, Gothenburg, Sweden; Center for Science and Innovation in Spintronics, Tohoku University, 2-1-1 Katahira, 980-8577, Aoba-ku, Sendai, Japan, 2-1-1 Katahira, Sendai; Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, 980-8577, Aoba-ku, Sendai, Japan, 2-1-1 Katahira, Sendai.
    Magnetic droplet soliton pairs2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 2118Article in journal (Refereed)
    Abstract [en]

    We demonstrate magnetic droplet soliton pairs in all-perpendicular spin-torque nano-oscillators (STNOs), where one droplet resides in the STNO free layer (FL) and the other in the reference layer (RL). Typically, theoretical, numerical, and experimental droplet studies have focused on the FL, with any additional dynamics in the RL entirely ignored. Here we show that there is not only significant magnetodynamics in the RL, but the RL itself can host a droplet driven by, and coexisting with, the FL droplet. Both single droplets and pairs are observed experimentally as stepwise changes and sharp peaks in the dc and differential resistance, respectively. While the single FL droplet is highly stable, the coexistence state exhibits high-power broadband microwave noise. Furthermore, micromagnetic simulations reveal that the pair dynamics display periodic, quasi-periodic, and chaotic signatures controlled by applied field and current. The strongly interacting and closely spaced droplet pair offers a unique platform for fundamental studies of highly non-linear soliton pair dynamics.

  • 89. Jin, Chiming
    et al.
    Li, Zi-An
    Kovacs, Andras
    Caron, Jan
    Zheng, Fengshan
    Rybakov, Filipp N.
    KTH, School of Engineering Sciences (SCI), Physics, Statistical Physics. Ural federal university, Russian Federation.
    Kiselev, Nikolai S.
    Du, Haifeng
    Bluegel, Stefan
    Tian, Mingliang
    Zhang, Yuheng
    Farle, Michael
    Dunin-Borkowski, Rafal E.
    Control of morphology and formation of highly geometrically confined magnetic skyrmions2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, article id 15569Article in journal (Refereed)
    Abstract [en]

    The ability to controllably manipulate magnetic skyrmions, small magnetic whirls with particle-like properties, in nanostructured elements is a prerequisite for incorporating them into spintronic devices. Here, we use state-of-the-art electron holographic imaging to directly visualize the morphology and nucleation of magnetic skyrmions in a wedge-shaped FeGe nanostripe that has a width in the range of 45-150 nm. We find that geometrically-confined skyrmions are able to adopt a wide range of sizes and ellipticities in a nanostripe that are absent in both thin films and bulk materials and can be created from a helical magnetic state with a distorted edge twist in a simple and efficient manner. We perform a theoretical analysis based on a three-dimensional general model of isotropic chiral magnets to confirm our experimental results. The flexibility and ease of formation of geometrically confined magnetic skyrmions may help to optimize the design of skyrmion-based memory devices.

  • 90.
    Jin, Han
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Zhang, Cheng
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Zwahlen, Martin
    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.
    Karlsson, Max
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Shi, Mengnan
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Yuan, Meng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Song, Xiya
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Li, Xiangyu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Yang, Hong
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Turkez, Hasan
    Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey.
    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 Institute, Stockholm, Sweden.
    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, UK.
    Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, p. 5417-Article in journal (Refereed)
    Abstract [en]

    Cell lines are valuable resources as model for human biology and translational medicine. It is thus important to explore the concordance between the expression in various cell lines vis-à-vis human native and disease tissues. In this study, we investigate the expression of all human protein-coding genes in more than 1,000 human cell lines representing 27 cancer types by a genome-wide transcriptomics analysis. The cell line gene expression is compared with the corresponding profiles in various tissues, organs, single-cell types and cancers. Here, we present the expression for each cell line and give guidance for the most appropriate cell line for a given experimental study. In addition, we explore the cancer-related pathway and cytokine activity of the cell lines to aid human biology studies and drug development projects. All data are presented in an open access cell line section of the Human Protein Atlas to facilitate the exploration of all human protein-coding genes across these cell lines.

  • 91.
    Johansson, Henrik J.
    et al.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Socciarelli, Fabio
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Vacanti, Nathaniel M.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden.;Cornell Univ, Div Nutrit Sci, Ithaca, NY 14853 USA..
    Haugen, Mads H.
    Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0424 Oslo, Norway.;Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Zhu, Yafeng
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Siavelis, Ioannis
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Fernandez-Woodbridge, Alejandro
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Aure, Miriam R.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Sennblad, Bengt
    Uppsala Univ, Sci Life Lab, Dept Cell & Mol Biol, Natl Bioinformat Infrastruct Sweden, S-75237 Uppsala, Sweden..
    Vesterlund, Mattias
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Branca, Rui M.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Orre, Lukas M.
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Huss, Mikael
    Stockholm Univ, Sci Life Lab, Dept Biochem & Biophys, Natl Bioinformat Infrastruct Sweden, S-17121 Solna, Sweden..
    Fredlund, Erik
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Beraki, Elsa
    Oslo Univ Hosp, Dept Pathol, N-0424 Oslo, Norway..
    Garred, Oystein
    Oslo Univ Hosp, Dept Pathol, N-0424 Oslo, Norway..
    Boekel, Jorrit
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Sauer, Torill
    Akershus Univ Hosp, Dept Pathol, N-1478 Lorenskog, Norway.;Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway..
    Zhao, Wei
    Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Houston, TX 77230 USA..
    Nord, Silje
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Hoglander, Elen K.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Jans, Daniel C.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics. Karolinska Inst, Dept Womenss & Childrens Hlth, S-17121 Solna, Sweden..
    Haukaas, Tonje H.
    Norwegian Univ Sci & Technol NTNU, Dept Circulat & Med Imaging, N-7491 Trondheim, Norway..
    Bathen, Tone F.
    Norwegian Univ Sci & Technol NTNU, Dept Circulat & Med Imaging, N-7491 Trondheim, Norway..
    Schlichting, Ellen
    Oslo Univ Hosp, Dept Canc, Sect Breast & Endocrine Surg, Div Surg Canc & Transplantat Med, N-0424 Oslo, Norway..
    Naume, Bjorn
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Oslo Univ Hosp, Div Surg & Canc & Transplantat Med, Dept Oncol, N-0424 Oslo, Norway..
    Geisler, Juergen
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Akershus Univ Hosp, Dept Oncol, N-1478 Lorenskog, Norway.;Akershus Univ Hosp, Div Med, N-1478 Lorenskog, Norway..
    Hofvind, Solveig
    Canc Registry Norway, N-0379 Oslo, Norway.;Oslo & Akershus Univ, Coll Appl Sci, Fac Hlth Sci, N-0130 Oslo, Norway..
    Engebraten, Olav
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Oslo Univ Hosp, Div Surg & Canc & Transplantat Med, Dept Oncol, N-0424 Oslo, Norway.;Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0379 Oslo, Norway..
    Geitvik, Gry Aarum
    Oslo Univ Hosp, Norwegian Radium Hosp, Inst Canc Res, Dept Canc Genet, N-0379 Oslo, Norway..
    Langerod, Anita
    Oslo Univ Hosp, Norwegian Radium Hosp, Inst Canc Res, Dept Canc Genet, N-0379 Oslo, Norway..
    Karesen, Rolf
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Oslo Univ Hosp, Div Surg Canc & Transplantat, Dept Breast & Endocrine Surg, N-0379 Oslo, Norway..
    Maelandsmo, Gunhild Mari
    Oslo Univ Hosp, Inst Canc Res, Dept Tumor Biol, N-0379 Oslo, Norway.;Univ Tromso, Fac Hlth Sci, Dept Pharm, N-9010 Tromso, Norway..
    Sorlie, Therese
    Oslo Univ Hosp, Norwegian Radium Hosp, Inst Canc Res, Dept Canc Genet, N-0379 Oslo, Norway..
    Skjerven, Helle Kristine
    Vestre Viken Hosp Trust, Dept Breast & Endocrine Surg, Breast & Endocrine Surg, N-3004 Drammen, Norway..
    Park, Daehoon
    Vestre Viken Hosp Trust, Dept Pathol, N-3004 Drammen, Norway..
    Hartman-Johnsen, Olaf-Johan
    Ostfold Hosp, N-1714 Ostfold, Norway..
    Luders, Torben
    Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Akershus Univ Hosp, Div Med, Dept Clin Mol Biol & Lab Sci EpiGen, N-1478 Lorenskog, Norway..
    Borgen, Elin
    Oslo Univ Hosp, Dept Pathol, N-0424 Oslo, Norway..
    Kristensen, Vessela N.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway.;Akershus Univ Hosp, Div Med, Dept Clin Mol Biol & Lab Sci EpiGen, N-1478 Lorenskog, Norway..
    Russnes, Hege G.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway..
    Lingjaerde, Ole Christian
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Univ Oslo, Ctr Canc Biomed, N-0424 Oslo, Norway..
    Mills, Gordon B.
    Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Houston, TX 77230 USA..
    Sahlberg, Kristine K.
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Vestre Viken Hosp Trust, Dept Res, N-3004 Drammen, Norway..
    Borresen-Dale, Anne-Lise
    Oslo Univ Hosp, Inst Canc Res, Dept Canc Genet, N-0424 Oslo, Norway.;Univ Oslo, Inst Clin Med, N-0318 Oslo, Norway..
    Lehtio, Janne
    Karolinska Inst, Dept Oncol Pathol, Sci Life Lab, S-17121 Solna, Sweden..
    Breast cancer quantitative proteome and proteogenomic landscape2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, article id 1600Article in journal (Refereed)
    Abstract [en]

    In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.

  • 92.
    Jun, Seong-Hwan
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Rochester, Med Ctr, Dept Biostat & Computat Biol, Rochester, NY 14627 USA..
    Toosi, Hosein
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mold, Jeff
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Engblom, Camilla
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Chen, Xinsong
    Karolinska Inst, Dept Pathol & Oncol, Solna, Sweden..
    O'Flanagan, Ciara
    BC Canc, Dept Mol Oncol, Vancouver, BC, Canada..
    Hagemann-Jensen, Michael
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Sandberg, Rickard
    Karolinska Inst, Dept Cell & Mol Biol, Solna, Sweden..
    Aparicio, Samuel
    BC Canc, Dept Mol Oncol, Vancouver, BC, Canada.;Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC, Canada..
    Hartman, Johan
    Karolinska Inst, Dept Pathol & Oncol, Solna, Sweden.;Karolinska Univ Lab, Dept Clin Pathol & Cytol, Stockholm, Sweden..
    Roth, Andrew
    BC Canc, Dept Mol Oncol, Vancouver, BC, Canada.;Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC, Canada.;Univ British Columbia, Dept Comp Sci, Vancouver, BC, Canada..
    Lagergren, Jens
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 982Article in journal (Refereed)
    Abstract [en]

    Functional characterization of the cancer clones can shed light on the evolutionary mechanisms driving cancer's proliferation and relapse mechanisms. Single-cell RNA sequencing data provide grounds for understanding the functional state of cancer as a whole; however, much research remains to identify and reconstruct clonal relationships toward characterizing the changes in functions of individual clones. We present PhylEx that integrates bulk genomics data with co-occurrences of mutations from single-cell RNA sequencing data to reconstruct high-fidelity clonal trees. We evaluate PhylEx on synthetic and well-characterized high-grade serous ovarian cancer cell line datasets. PhylEx outperforms the state-of-the-art methods both when comparing capacity for clonal tree reconstruction and for identifying clones. We analyze high-grade serous ovarian cancer and breast cancer data to show that PhylEx exploits clonal expression profiles beyond what is possible with expression-based clustering methods and clear the way for accurate inference of clonal trees and robust phylo-phenotypic analysis of cancer. The functional changes of individual clones in single cell RNA sequencing (scRNA-seq) data remain elusive. Here, the authors develop PhylEx that integrates bulk genomics data with co-occurrences of mutations revealed by scRNA-seq data and apply it to high-grade serous ovarian cancer cell line and breast cancer datasets.

  • 93.
    Kayser, Yves
    et al.
    Phys Tech Bundesanstalt, Abbestr 2-12, D-10587 Berlin, Germany;Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Milne, Chris
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Juranic, Pavle
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Sala, Leonardo
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Czapla-Masztafiak, Joanna
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Follath, Rolf
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Kavcic, Matjaz
    Inst Jozef Stefan, Jamova 39, Ljubljana 1000, Slovenia.
    Knopp, Gregor
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Rehanek, Jens
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland;Adv Accelerator Technol AG, CH-5234 Villigen, Switzerland.
    Blachucki, Wojciech
    Polish Acad Sci, Inst Phys Chem, PL-01224 Warsaw, Poland.
    Delcey, Mickael G
    Uppsala universitet, Teoretisk kemi.
    Lundberg, Marcus
    Uppsala universitet, Teoretisk kemi.
    Tyrala, Krzysztof
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Zhu, Diling
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Alonso-Mori, Roberto
    SLAC Natl Accelerator Lab, LCLS, Menlo Pk, CA 94025 USA.
    Abela, Rafael
    Paul Scherrer Inst, CH-5232 Villigen, Switzerland.
    Sá, Jacinto
    Uppsala universitet, Fysikalisk kemi.
    Szlachetkc, Jakub
    Polish Acad Sci, Inst Nucl Phys, PL-31342 Krakow, Poland.
    Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, no 1, article id 4761Article in journal (Refereed)
    Abstract [en]

    Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.

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  • 94.
    Kazemzadeh, Amin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Eriksson, Anders
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Madou, Marc
    Univ Calif Irvine, Dept Mech & Aerosp Engn, Irvine, CA 92697 USA..
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A micro-dispenser for long-term storage and controlled release of liquids2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, no 1, article id 189Article in journal (Refereed)
    Abstract [en]

    The success of lab-on-a-chip systems may depend on a low-cost device that incorporates on-chip storage and fluidic operations. To date many different methods have been developed that cope separately with on-chip storage and fluidic operations e. g., hydrophobic and capillary valves pneumatic pumping and blister storage packages. The blister packages seem difficult to miniaturize and none of the existing liquid handling techniques despite their variety are capable of proportional repeatable dispensing. We report here on an inexpensive robust and scalable micro-dispenser that incorporates long-term storage and aliquoting of reagents on different microfluidics platforms. It provides long-term shelf-life for different liquids enables precise dispensing on lab-on-a-disc platforms and less accurate but proportional dispensing when operated by finger pressure. Based on this technology we introduce a method for automation of blood plasma separation and multi-step bioassay procedures. This micro-dispenser intends to facilitate affordable portable diagnostic devices and accelerate the commercialization of lab-on-a-chip devices.

  • 95. Kennedy, S. A.
    et al.
    Jarboui, M. -A
    Srihari, S.
    Raso, C.
    Bryan, K.
    Dernayka, L.
    Charitou, T.
    Bernal-Llinares, M.
    Herrera-Montavez, C.
    Krstic, A.
    Matallanas, D.
    Kotlyar, M.
    Jurisica, I.
    Curak, J.
    Wong, V.
    Stagljar, I.
    LeBihan, T.
    Imrie, L.
    Pillai, P.
    Lynn, M. A.
    Fasterius, Erik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Al-Khalili Szigyarto, Cristina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Breen, J.
    Kiel, C.
    Serrano, L.
    Rauch, N.
    Rukhlenko, O.
    Kholodenko, B. N.
    Iglesias-Martinez, L. F.
    Ryan, C. J.
    Pilkington, R.
    Cammareri, P.
    Sansom, O.
    Shave, S.
    Auer, M.
    Horn, N.
    Klose, F.
    Ueffing, M.
    Boldt, K.
    Lynn, D. J.
    Kolch, W.
    Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 499Article in journal (Refereed)
    Abstract [en]

    Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping &gt;6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.

  • 96. Kerr, A. G.
    et al.
    Wang, Zuoneng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems.
    Wang, N.
    Kwok, K. H. M.
    Jalkanen, J.
    Ludzki, A.
    Lecoutre, S.
    Langin, D.
    Bergo, M. O.
    Dahlman, I.
    Mim, Carsten
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Structural Biotechnology.
    Arner, P.
    Gao, H.
    The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 2958Article in journal (Refereed)
    Abstract [en]

    The pleiotropic function of long noncoding RNAs is well recognized, but their direct role in governing metabolic homeostasis is less understood. Here, we describe a human adipocyte-specific lncRNA, ADIPINT, that regulates pyruvate carboxylase, a pivotal enzyme in energy metabolism. We developed an approach, Targeted RNA-protein identification using Orthogonal Organic Phase Separation, which identifies that ADIPINT binds to pyruvate carboxylase and validated the interaction with electron microscopy. ADIPINT knockdown alters the interactome and decreases the abundance and enzymatic activity of pyruvate carboxylase in the mitochondria. Reduced ADIPINT or pyruvate carboxylase expression lowers adipocyte lipid synthesis, breakdown, and lipid content. In human white adipose tissue, ADIPINT expression is increased in obesity and linked to fat cell size, adipose insulin resistance, and pyruvate carboxylase activity. Thus, we identify ADIPINT as a regulator of lipid metabolism in human white adipocytes, which at least in part is mediated through its interaction with pyruvate carboxylase. 

  • 97.
    Kim, Gijeong
    et al.
    Korea Adv Inst Sci & Technol, Dept Biol Sci, Daejeon 34141, South Korea..
    Azmi, Liyana
    Univ Glasgow, Inst Infect Immun & Inflammat, Glasgow G12 8QQ, Lanark, Scotland..
    Jang, Seongmin
    Korea Adv Inst Sci & Technol, Dept Biol Sci, Daejeon 34141, South Korea..
    Jung, Taeyang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Structural Biotechnology. Korea Adv Inst Sci & Technol, Dept Biol Sci, Daejeon 34141, South Korea..
    Hebert, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Structural Biotechnology. Karolinska Inst, Dept Biosci & Nutr, S-14183 Huddinge, Sweden..
    Roe, Andrew J.
    Univ Glasgow, Inst Infect Immun & Inflammat, Glasgow G12 8QQ, Lanark, Scotland..
    Byron, Olwyn
    Univ Glasgow, Sch Life Sci, Glasgow G12 8QQ, Lanark, Scotland..
    Song, Ji-Joon
    Korea Adv Inst Sci & Technol, Dept Biol Sci, Daejeon 34141, South Korea..
    Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity2019In: Nature Communications, E-ISSN 2041-1723, Vol. 10, no 1, article id 4527Article in journal (Refereed)
    Abstract [en]

    Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 angstrom resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity.

  • 98.
    Kirchschlager, Florian
    et al.
    Physics and Astronomy, Ghent University, Krijgslaan 281-S9, 9000, Ghent, Belgium, Krijgslaan 281-S9; Physics and Astronomy, University College London, WC1E 6BT, Gower Street, London, UK, London.
    Mattsson, Lars
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm University, Hannes Alfvéns väg 12, SE-106, Stockholm, Sweden, Hannes Alfvéns väg 12.
    Gent, Frederick A.
    Nordita SU.
    Supernova dust destruction in the magnetized turbulent ISM2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1841Article in journal (Refereed)
    Abstract [en]

    Dust in the interstellar medium (ISM) is critical to the absorption and intensity of emission profiles used widely in astronomical observations, and necessary for star and planet formation. Supernovae (SNe) both produce and destroy ISM dust. In particular the destruction rate is difficult to assess. Theory and prior simulations of dust processing by SNe in a uniform ISM predict quite high rates of dust destruction, potentially higher than the supernova dust production rate in some cases. Here we show simulations of supernova-induced dust processing with realistic ISM dynamics including magnetic field effects and demonstrate how ISM inhomogeneity and magnetic fields inhibit dust destruction. Compared to the non-magnetic homogeneous case, the dust mass destroyed within 1 Myr per SNe is reduced by more than a factor of two, which can have a great impact on the ISM dust budget.

  • 99.
    Kitamura, N.
    et al.
    Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan.;Univ Tokyo, Grad Sch Sci, Dept Earth & Planetary Sci, Tokyo, Japan..
    Amano, T.
    Univ Tokyo, Grad Sch Sci, Dept Earth & Planetary Sci, Tokyo, Japan..
    Omura, Y.
    Kyoto Univ, Res Inst Sustainable Humanosphere, Uji, Japan..
    Boardsen, S. A.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA.;Univ Maryland Baltimore Cty, Goddard Planetary Heliophys Inst, Baltimore, MD 21228 USA..
    Gershman, D. J.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA..
    Miyoshi, Y.
    Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan..
    Kitahara, M.
    Tohoku Univ, Grad Sch Sci, Dept Geophys, Sendai, Miyagi, Japan..
    Katoh, Y.
    Tohoku Univ, Grad Sch Sci, Dept Geophys, Sendai, Miyagi, Japan..
    Kojima, H.
    Kyoto Univ, Res Inst Sustainable Humanosphere, Uji, Japan..
    Nakamura, S.
    Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan..
    Shoji, M.
    Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan..
    Saito, Y.
    Japan Aerosp Explorat Agcy, Inst Space & Astronaut Sci, Sagamihara, Kanagawa, Japan..
    Yokota, S.
    Osaka Univ, Grad Sch Sci, Dept Earth & Space Sci, Toyonaka, Osaka, Japan..
    Giles, B. L.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA..
    Paterson, W. R.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA..
    Pollock, C. J.
    Denali Sci, Fairbanks, AK USA..
    Barrie, A. C.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA.;Aurora Engn, Potomac, MD USA..
    Skeberdis, D. G.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA.;Ai Solut Inc, Lanham, MD USA..
    Kreisler, S.
    NASA, Goddard Space Flight Ctr, Greenbelt, MD USA.;Aurora Engn, Potomac, MD USA..
    Le Contel, O.
    Sorbonne Univ, Univ Paris Saclay, Lab Phys Plasmas,CNRS, Observ Paris,Ecole Polytech Inst Polytech Paris, Paris, France..
    Russell, C. T.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA..
    Strangeway, R. J.
    Univ Calif Los Angeles, Dept Earth Planetary & Space Sci, Los Angeles, CA USA..
    Lindqvist, Per-Arne
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Space and Plasma Physics.
    Ergun, R. E.
    Univ Colorado, Lab Atmospher & Space Phys, Boulder, CO 80309 USA..
    Torbert, R. B.
    Univ New Hampshire, Dept Phys, Durham, NH 03824 USA.;Southwest Res Inst, San Antonio, TX USA..
    Burch, J. L.
    Southwest Res Inst, San Antonio, TX USA..
    Direct observations of energy transfer from resonant electrons to whistler-mode waves in magnetosheath of Earth2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 6259Article in journal (Refereed)
    Abstract [en]

    Excitation of whistler-mode waves by cyclotron instability is considered as the likely generation process of the waves. Here, the authors show direct observational evidence for locally ongoing secular energy transfer from the resonant electrons to the whistler-mode waves in Earth's magnetosheath. Electromagnetic whistler-mode waves in space plasmas play critical roles in collisionless energy transfer between the electrons and the electromagnetic field. Although resonant interactions have been considered as the likely generation process of the waves, observational identification has been extremely difficult due to the short time scale of resonant electron dynamics. Here we show strong nongyrotropy, which rotate with the wave, of cyclotron resonant electrons as direct evidence for the locally ongoing secular energy transfer from the resonant electrons to the whistler-mode waves using ultra-high temporal resolution data obtained by NASA's Magnetospheric Multiscale (MMS) mission in the magnetosheath. The nongyrotropic electrons carry a resonant current, which is the energy source of the wave as predicted by the nonlinear wave growth theory. This result proves the nonlinear wave growth theory, and furthermore demonstrates that the degree of nongyrotropy, which cannot be predicted even by that nonlinear theory, can be studied by observations.

  • 100.
    Korosec, Chapin S.
    et al.
    Department of Physics, Simon Fraser University, V5A 1S6, Burnaby, BC, Canada; Department of Mathematics and Statistics, York University, M3J 1P3, Toronto, ON, Canada.
    Unksov, Ivan N.
    NanoLund and Solid State Physics, Lund University, Box 118, SE – 22100, Lund, Sweden, Box 118.
    Surendiran, Pradheebha
    NanoLund and Solid State Physics, Lund University, Box 118, SE – 22100, Lund, Sweden, Box 118.
    Lyttleton, Roman
    NanoLund and Solid State Physics, Lund University, Box 118, SE – 22100, Lund, Sweden, Box 118.
    Curmi, Paul M.G.
    School of Physics, University of New South Wales, 2052, Sydney, NSW, Australia.
    Angstmann, Christopher N.
    School of Mathematics and Statistics, University of New South Wales, 2052, Sydney, NSW, Australia.
    Eichhorn, Ralf
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm University, 106 91, Stockholm, Sweden.
    Linke, Heiner
    NanoLund and Solid State Physics, Lund University, Box 118, SE – 22100, Lund, Sweden, Box 118.
    Forde, Nancy R.
    Department of Physics, Simon Fraser University, V5A 1S6, Burnaby, BC, Canada.
    Motility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle2024In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 1511Article in journal (Refereed)
    Abstract [en]

    Inspired by biology, great progress has been made in creating artificial molecular motors. However, the dream of harnessing proteins – the building blocks selected by nature – to design autonomous motors has so far remained elusive. Here we report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor comprised of a spherical hub decorated with proteases. Its “burnt-bridge” motion is directed by cleavage of a peptide lawn, promoting motion towards unvisited substrate. We find that Lawnmowers exhibit directional motion with average speeds of up to 80 nm/s, comparable to biological motors. By selectively patterning the peptide lawn on microfabricated tracks, we furthermore show that the Lawnmower is capable of track-guided motion. Our work opens an avenue towards nanotechnology applications of artificial protein motors.

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