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  • 1. Altfeder, Igor
    et al.
    Voevodin, Andrey A.
    Check, Michael H.
    Eichfeld, Sarah M.
    Robinson, Joshua A.
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Scanning Tunneling Microscopy Observation of Phonon Condensate2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 43214Article in journal (Refereed)
    Abstract [en]

    Using quantum tunneling of electrons into vibrating surface atoms, phonon oscillations can be observed on the atomic scale. Phonon interference patterns with unusually large signal amplitudes have been revealed by scanning tunneling microscopy in intercalated van der Waals heterostructures. Our results show that the effective radius of these phonon quasi-bound states, the real-space distribution of phonon standing wave amplitudes, the scattering phase shifts, and the nonlinear intermode coupling strongly depend on the presence of defect-induced scattering resonance. The observed coherence of these quasi-bound states most likely arises from phase-and frequency-synchronized dynamics of all phonon modes, and indicates the formation of many-body condensate of optical phonons around resonant defects. We found that increasing the strength of the scattering resonance causes the increase of the condensate droplet radius without affecting the condensate fraction inside it. The condensate can be observed at room temperature.

  • 2.
    Andersson, Richard L.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Ström, Valter
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Engineering Material Physics.
    Gedde, Ulf W.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Mallon, Peter E.
    Hedenqvist, Mikael S.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Olsson, Richard T.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Polymeric Materials.
    Micromechanics of ultra-toughened electrospun PMMA/PEO fibres as revealed by in-situ tensile testing in an electron microscope2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 6335-Article in journal (Refereed)
    Abstract [en]

    A missing cornerstone in the development of tough micro/nano fibre systems is an understanding of the fibre failure mechanisms, which stems from the limitation in observing the fracture of objects with dimensions one hundredth of the width of a hair strand. Tensile testing in the electron microscope is herein adopted to reveal the fracture behaviour of a novel type of toughened electrospun poly(methyl methacrylate)/poly(ethylene oxide) fibre mats for biomedical applications. These fibres showed a toughness more than two orders of magnitude greater than that of pristine PMMA fibres. The in-situ microscopy revealed that the toughness were not only dependent on the initial molecular alignment after spinning, but also on the polymer formulation that could promote further molecular orientation during the formation of micro/nano-necking. The true fibre strength was greater than 150 MPa, which was considerably higher than that of the unmodified PMMA (17 MPa). This necking phenomenon was prohibited by high aspect ratio cellulose nanocrystal fillers in the ultra-tough fibres, leading to a decrease in toughness by more than one order of magnitude. The reported necking mechanism may have broad implications also within more traditional melt-spinning research.

  • 3. Araujo, C. Moyses
    et al.
    Nagar, Sandeep
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Ramzan, Muhammad
    Shukla, R.
    Jayakumar, O. D.
    Tyagi, A. K.
    Liu, Yi-Sheng
    Chen, Jeng-Lung
    Glans, Per-Anders
    Chang, Chinglin
    Blomqvist, Andreas
    Lizarraga, Raquel
    Holmström, Erik
    Belova, Lyubov
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Engineering Material Physics.
    Guo, Jinghua
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Rao, K. Venkat
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Disorder-induced Room Temperature Ferromagnetism in Glassy Chromites2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 4686-Article in journal (Refereed)
    Abstract [en]

    We report an unusual robust ferromagnetic order above room temperature upon amorphization of perovskite [YCrO3] in pulsed laser deposited thin films. This is contrary to the usual expected formation of a spin glass magnetic state in the resulting disordered structure. To understand the underlying physics of this phenomenon, we combine advanced spectroscopic techniques and first-principles calculations. We find that the observed order-disorder transformation is accompanied by an insulator-metal transition arising from a wide distribution of Cr-O-Cr bond angles and the consequent metallization through free carriers. Similar results also found in YbCrO3-films suggest that the observed phenomenon is more general and should, in principle, apply to a wider range of oxide systems. The ability to tailor ferromagnetic order above room temperature in oxide materials opens up many possibilities for novel technological applications of this counter intuitive effect.

  • 4. Arslanov, Temirlan R.
    et al.
    Mollaev, Akhmedbek Yu.
    Kamilov, Ibragimkhan K.
    Arslanov, Rasul K.
    Kilanski, Lukasz
    Minikaev, Roman
    Reszka, Anna
    Lopez-Moreno, Sinhue
    Romero, Aldo H.
    Ramzan, Muhammad
    Panigrahi, Puspamitra
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Trukhan, Vladimir M.
    Chatterji, Tapan
    Marenkin, Sergey F.
    Shoukavaya, Tatyana V.
    Pressure control of magnetic clusters in strongly inhomogeneous ferromagnetic chalcopyrites2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, p. 7720-Article in journal (Refereed)
    Abstract [en]

    Room-temperature ferromagnetism in Mn-doped chalcopyrites is a desire aspect when applying those materials to spin electronics. However, dominance of high Curie-temperatures due to cluster formation or inhomogeneities limited their consideration. Here we report how an external perturbation such as applied hydrostatic pressure in CdGeP2:Mn induces a two serial magnetic transitions from ferromagnet to non-magnet state at room temperature. This effect is related to the unconventional properties of created MnP magnetic clusters within the host material. Such behavior is also discussed in connection with ab initio density functional calculations, where the structural properties of MnP indicate magnetic transitions as function of pressure as observed experimentally. Our results point out new ways to obtain controlled response of embedded magnetic clusters.

  • 5. Ashaduzzaman, Md.
    et al.
    Deshpande, Swapneel R.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mishra, Yogendra Kumar
    Turner, Anthony P. F.
    Tiwari, Ashutosh
    On/off-switchable LSPR nano-immunoassay for troponin-T2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44027Article in journal (Refereed)
    Abstract [en]

    Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature.

  • 6.
    Asp, Michaela
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology.
    Salmen, Fredrik
    KTH, School of Biotechnology (BIO), Gene Technology.
    Stahl, Patrik L.
    Vickovic, Sanja
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Felldin, Ulrika
    Lofling, Marie
    Navarro, Jose Fernandez
    Maaskola, Jonas
    Eriksson, Maria J.
    Persson, Bengt
    Corbascio, Matthias
    Persson, Hans
    Linde, Cecilia
    Lundeberg, Joakim
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Spatial detection of fetal marker genes expressed at low level in adult human heart tissue2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 12941Article in journal (Refereed)
    Abstract [en]

    Heart failure is a major health problem linked to poor quality of life and high mortality rates. Hence, novel biomarkers, such as fetal marker genes with low expression levels, could potentially differentiate disease states in order to improve therapy. In many studies on heart failure, cardiac biopsies have been analyzed as uniform pieces of tissue with bulk techniques, but this homogenization approach can mask medically relevant phenotypes occurring only in isolated parts of the tissue. This study examines such spatial variations within and between regions of cardiac biopsies. In contrast to standard RNA sequencing, this approach provides a spatially resolved transcriptome- and tissue-wide perspective of the adult human heart, and enables detection of fetal marker genes expressed by minor subpopulations of cells within the tissue. Analysis of patients with heart failure, with preserved ejection fraction, demonstrated spatially divergent expression of fetal genes in cardiac biopsies.

  • 7.
    Bass, Tarek
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Rosestedt, Maria
    Mitran, Bogdan
    Frejd, Fredrik Y.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Protein Technology.
    Tolmachev, Vladimir
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Orlova, Anna
    In vivo evaluation of a novel format of a bivalent HER3-targeting and albumin- binding therapeutic affibody construct2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 43118Article in journal (Refereed)
    Abstract [en]

    Overexpression of human epidermal growth factor receptor 3 (HER3) is involved in resistance to several therapies for malignant tumours. Currently, several anti-HER3 monoclonal antibodies are under clinical development. We introduce an alternative approach to HER3-targeted therapy based on engineered scaffold proteins, i.e. affibody molecules. We designed a small construct (22.5 kDa, denoted 3A3), consisting of two high-affinity anti-HER3 affibody molecules flanking an albumin-binding domain ABD, which was introduced for prolonged residence in circulation. In vitro, 3A3 efficiently inhibited growth of HER3-expressing BxPC-3 cells. Biodistribution in mice was measured using 3A3 that was site-specifically labelled with In-111 via a DOTA chelator. The residence time of In-111-DOTA-3A3 in blood was extended when compared with the monomeric affibody molecule. In-111-DOTA-3A3 accumulated specifically in HER3-expressing BxPC-3 xenografts in mice. However, In-111-DOTA-3A3 cleared more rapidly from blood than a size-matched control construct In-111-DOTA-TAT, most likely due to sequestering of 3A3 by mErbB3, the murine counterpart of HER3. Repeated dosing and increase of injected protein dose decreased uptake of In-111-DOTA-3A3 in mErbB3-expressing tissues. Encouragingly, growth of BxPC-3 xenografts in mice was delayed in an experimental (pilot-scale) therapy study using 3A3. We conclude that the 3A3 affibody format seems promising for treatment of HER3-overexpressing tumours.

  • 8.
    Belonoshko, Anatoly B.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Lukinov, Timofiy
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Rosengren, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory. KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. AlbaNova University Center, Sweden.
    Bryk, Taras
    Litasov, Konstantin D.
    Synthesis of heavy hydrocarbons at the core-mantle boundary2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 18382Article in journal (Refereed)
    Abstract [en]

    The synthesis of complex organic molecules with C-C bonds is possible under conditions of reduced activity of oxygen. We have found performing ab initio molecular dynamics simulations of the C-O-H- Fe system that such conditions exist at the core-mantle boundary (CMB). H2O and CO2 delivered to the CMB by subducting slabs provide a source for hydrogen and carbon. The mixture of H2O and CO2 subjected to high pressure (130 GPa) and temperature (4000 to 4500 K) does not lead to synthesis of complex hydrocarbons. However, when Fe is added to the system, C-C bonds emerge. It means that oil might be a more abundant mineral than previously thought.

  • 9.
    Belonoshko, Anatoly B.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Ramzan, Muhammad
    Mao, Ho-kwang
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Atomic Diffusion in Solid Molecular Hydrogen2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, p. 2340-Article in journal (Refereed)
    Abstract [en]

    We performed ab initio molecular dynamics simulations of the C2c and Cmca-12 phases of hydrogen at pressures from 210 to 350 GPa. These phases were predicted to be stable at 0 K and pressures above 200 GPa. However, systematic studies of temperature impact on properties of these phases have not been performed so far. Filling this gap, we observed that on temperature increase diffusion sets in the Cmca-12 phase, being absent in C2c. We explored the mechanism of diffusion and computed melting curve of hydrogen at extreme pressures. The results suggest that the recent experiments claiming conductive hydrogen at the pressure around 260 GPa and ambient temperature might be explained by the diffusion. The diffusion might also be the reason for the difference in Raman spectra obtained in recent experiments.

  • 10. Bergman, Anders
    et al.
    Hellsvik, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Bessarab, Pavel F.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. Univ Iceland, Iceland.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Spin relaxation signature of colossal magnetic anisotropy in platinum atomic chains2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 36872Article in journal (Refereed)
    Abstract [en]

    Recent experimental data demonstrate emerging magnetic order in platinum atomically thin nanowires. Furthermore, an unusual form of magnetic anisotropy-colossal magnetic anisotropy (CMA)-was earlier predicted to exist in atomically thin platinum nanowires. Using spin dynamics simulations based on first-principles calculations, we here explore the spin dynamics of atomically thin platinum wires to reveal the spin relaxation signature of colossal magnetic anisotropy, comparing it with other types of anisotropy such as uniaxial magnetic anisotropy (UMA). We find that the CMA alters the spin relaxation process distinctly and, most importantly, causes a large speed-up of the magnetic relaxation compared to uniaxial magnetic anisotropy. The magnetic behavior of the nanowire exhibiting CMA should be possible to identify experimentally at the nanosecond time scale for temperatures below 5 K. This time-scale is accessible in e.g., soft x-ray free electron laser experiments.

  • 11. Bessarab, Pavel F.
    et al.
    Mueller, Gideon P.
    Lobanov, Igor S.
    Rybakov, Filipp N.
    KTH, School of Engineering Sciences (SCI), Physics, Statistical Physics.
    Kiselev, Nikolai S.
    Jonsson, Hannes
    Uzdin, Valery M.
    Blugel, Stefan
    Bergqvist, Lars
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lifetime of racetrack skyrmions2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 3433Article in journal (Refereed)
    Abstract [en]

    The skyrmion racetrack is a promising concept for future information technology. There, binary bits are carried by nanoscale spin swirls-skyrmions-driven along magnetic strips. Stability of the skyrmions is a critical issue for realising this technology. Here we demonstrate that the racetrack skyrmion lifetime can be calculated from first principles as a function of temperature, magnetic field and track width. Our method combines harmonic transition state theory extended to include Goldstone modes, with an atomistic spin Hamiltonian parametrized from density functional theory calculations. We demonstrate that two annihilation mechanisms contribute to the skyrmion stability: At low external magnetic field, escape through the track boundary prevails, but a crossover field exists, above which the collapse in the interior becomes dominant. Considering a Pd/Fe bilayer on an Ir(111) substrate as a well-established model system, the calculated skyrmion lifetime is found to be consistent with reported experimental measurements. Our simulations also show that the Arrhenius pre-exponential factor of escape depends only weakly on the external magnetic field, whereas the pre-exponential factor for collapse is strongly field dependent. Our results open the door for predictive simulations, free from empirical parameters, to aid the design of skyrmion-based information technology.

  • 12.
    Bin Ashraf, Faisal
    et al.
    Univ Oulu, Water Resources & Environm Engn Res Unit, POB 4300, Oulu 90014, Finland..
    Haghighi, Ali Torabi
    Univ Oulu, Water Resources & Environm Engn Res Unit, POB 4300, Oulu 90014, Finland..
    Riml, Joakim
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Alfredsen, Knut
    Norwegian Univ Sci & Technol NTNU Vassbygget, 442 Valgrinda, Trondheim, Norway..
    Koskela, Jarkko J.
    Finnish Environm Inst SYKE, Mechelininkatu 34a,POB 140, Helsinki 00260, Finland..
    Klove, Bjorn
    Univ Oulu, Water Resources & Environm Engn Res Unit, POB 4300, Oulu 90014, Finland..
    Marttila, Hannu
    Univ Oulu, Water Resources & Environm Engn Res Unit, POB 4300, Oulu 90014, Finland..
    Changes in short term river flow regulation and hydropeaking in Nordic rivers2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 17232Article in journal (Refereed)
    Abstract [en]

    Quantifying short-term changes in river flow is important in understanding the environmental impacts of hydropower generation. Energy markets can change rapidly and energy demand fluctuates at sub-daily scales, which may cause corresponding changes in regulated river flow (hydropeaking). Due to increasing use of renewable energy, in future hydropower will play a greater role as a load balancing power source. This may increase current hydropeaking levels in Nordic river systems, creating challenges in maintaining a healthy ecological status. This study examined driving forces for hydropeaking in Nordic rivers using extensive datasets from 150 sites with hourly time step river discharge data. It also investigated the influence of increased wind power production on hydropeaking. The data revealed that hydropeaking is at high levels in the Nordic rivers and have seen an increase over the last decade and especially over the past few years. These results indicate that increased building for renewable energy may increase hydropeaking in Nordic rivers.

  • 13. Bora, Tanujjal
    et al.
    Zoepfl, David
    Dutta, Joydeep
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Importance of Plasmonic Heating on Visible Light Driven Photocatalysis of Gold Nanoparticle Decorated Zinc Oxide Nanorods2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 26913Article in journal (Refereed)
    Abstract [en]

    Herein we explore the role of localized plasmonic heat generated by resonantly excited gold (Au) NPs on visible light driven photocatalysis process. Au NPs are deposited on the surface of vertically aligned zinc oxide nanorods (ZnO NRs). The localized heat generated by Au NPs under 532 nm continuous laser excitation (SPR excitation) was experimentally probed using Raman spectroscopy by following the phonon modes of ZnO. Under the resonant excitation the temperature at the surface of the AuZnO NRs reaches up to about 300 degrees C, resulting in almost 6 times higher apparent quantum yield (AQY) for photocatalytic degradation of methylene blue (MB) compared to the bare ZnO NRs. Under solar light irradiation the Au-ZnO NRs demonstrated visible light photocatalytic activity twice that of what was achieved with bare ZnO NRs, while significantly reduced the activation energy required for the photocatalytic reactions allowing the reactions to occur at a faster rate.

  • 14.
    Boucly, Anthony
    et al.
    Sorbonne Univ, CNRS UMR 7614, Lab Chim Phys Matiere & Rayonnement, 4 Pl Jussieu, F-75252 Paris 05, France..
    Rochet, Francois
    Sorbonne Univ, CNRS UMR 7614, Lab Chim Phys Matiere & Rayonnement, 4 Pl Jussieu, F-75252 Paris 05, France.;Synchrotron SOLEIL, BP 48, F-91192 Gif Sur Yvette, France..
    Arnoux, Quentin
    Sorbonne Univ, CNRS UMR 7614, Lab Chim Phys Matiere & Rayonnement, 4 Pl Jussieu, F-75252 Paris 05, France..
    Gallet, Jean-Jacques
    Sorbonne Univ, CNRS UMR 7614, Lab Chim Phys Matiere & Rayonnement, 4 Pl Jussieu, F-75252 Paris 05, France.;Synchrotron SOLEIL, BP 48, F-91192 Gif Sur Yvette, France..
    Bournel, Fabrice
    Sorbonne Univ, CNRS UMR 7614, Lab Chim Phys Matiere & Rayonnement, 4 Pl Jussieu, F-75252 Paris 05, France.;Synchrotron SOLEIL, BP 48, F-91192 Gif Sur Yvette, France..
    Tissot, Heloise
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Sorbonne Univ, CNRS UMR 7614, Lab Chim Phys Matiere & Rayonnement, 4 Pl Jussieu, F-75252 Paris 05, France.;Synchrotron SOLEIL, BP 48, F-91192 Gif Sur Yvette, France.
    Marry, Virginie
    Sorbonne Univ, CNRS UMR 8234, Physicochim Electrolyses & Nanosyst Interfaciaux, 4 Pl Jussieu, F-75252 Paris 05, France..
    Dubois, Emmanuelle
    Sorbonne Univ, CNRS UMR 8234, Physicochim Electrolyses & Nanosyst Interfaciaux, 4 Pl Jussieu, F-75252 Paris 05, France..
    Michot, Laurent
    Sorbonne Univ, CNRS UMR 8234, Physicochim Electrolyses & Nanosyst Interfaciaux, 4 Pl Jussieu, F-75252 Paris 05, France..
    Soft X-ray Heterogeneous Radiolysis of Pyridine in the Presence of Hydrated Strontium-Hydroxyhectorite and its Monitoring by Near-Ambient Pressure Photoelectron Spectroscopy2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 6164Article in journal (Refereed)
    Abstract [en]

    The heterogeneous radiolysis of organic molecules in clays is a matter of considerable interest in astrochemistry and environmental sciences. However, little is known about the effects of highly ionizing soft X-rays. By combining monochromatized synchrotron source irradiation with in situ Near Ambient Pressure X-ray Photoelectron Spectroscopy (in the mbar range), and using the synoptic view encompassing both the gas and condensed phases, we found the water and pyridine pressure conditions under which pyridine is decomposed in the presence of synthetic Sr2+-hydroxyhectorite. The formation of a pyridine/water/Sr2+ complex, detected from the Sr 3d and N 1s core-level binding energies, likely presents a favorable situation for the radiolytic breaking of the O-H bond of water molecules adsorbed in the clay and the subsequent decomposition of the molecule. However, decomposition stops when the pyridine pressure exceeds a critical value. This observation can be related to a change in the nature of the active radical species with the pyridine loading. This highlights the fact that the destruction of the molecule is not entirely determined by the properties of the host material, but also by the inserted organic species. The physical and chemical causes of the present observations are discussed.

  • 15.
    Bremer, Hanna D.
    et al.
    Swedish Univ Agr Sci, Dept Clin Sci, SE-75007 Uppsala, Sweden..
    Landegren, Nils
    Karolinska Inst, Karolinska Univ Hosp, Dept Med Solna, CMM, L8 01, SE-17176 Stockholm, Sweden.;Uppsala Univ, Dept Med Sci, Sci Life Lab, Uppsala, Sweden..
    Sjoberg, Ronald
    KTH Royal Inst Technol, Sch Biotechnol, Affin Prote, SciLifeLab, SE-17121 Solna, Sweden..
    Hallgren, Asa
    Karolinska Inst, Karolinska Univ Hosp, Dept Med Solna, CMM, L8 01, SE-17176 Stockholm, Sweden..
    Renneker, Stefanie
    Euroimmun AG, D-23560 Lubeck, Germany..
    Lattwein, Erik
    Euroimmun AG, D-23560 Lubeck, Germany..
    Leonard, Dag
    Uppsala Univ, Rheumatol & Sci Life Lab, Dept Med Sci, SE-75185 Uppsala, Sweden..
    Eloranta, Maija-Leena
    Uppsala Univ, Rheumatol & Sci Life Lab, Dept Med Sci, SE-75185 Uppsala, Sweden..
    Ronnblom, Lars
    Uppsala Univ, Rheumatol & Sci Life Lab, Dept Med Sci, SE-75185 Uppsala, Sweden..
    Nordmark, Gunnel
    Uppsala Univ, Rheumatol & Sci Life Lab, Dept Med Sci, SE-75185 Uppsala, Sweden..
    Nilsson, Peter
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics.
    Andersson, Goran
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Lilliehook, Inger
    Swedish Univ Agr Sci, Dept Clin Sci, SE-75007 Uppsala, Sweden..
    Lindblad-Toh, Kerstin
    Broad Inst Harvard & MIT, Cambridge, MA 02142 USA.;Uppsala Univ, Sci Life Lab, IMBIM, SE-75123 Uppsala, Sweden..
    Kampe, Olle
    Karolinska Inst, Karolinska Univ Hosp, Dept Med Solna, CMM, L8 01, SE-17176 Stockholm, Sweden.;Uppsala Univ, Dept Med Sci, Sci Life Lab, Uppsala, Sweden.;Univ Bergen, Dept Clin Sci, N-5021 Bergen, Norway.;Univ Bergen, KG Jebsen Ctr Autoimmune Disorders, N-5021 Bergen, Norway.;Haukeland Hosp, Dept Med, N-5021 Bergen, Norway..
    Hansson-Hamlin, Helene
    Swedish Univ Agr Sci, Dept Clin Sci, SE-75007 Uppsala, Sweden..
    ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 4852Article in journal (Refereed)
    Abstract [en]

    Dogs can spontaneously develop complex systemic autoimmune disorders, with similarities to human autoimmune disease. Autoantibodies directed at self-antigens are a key feature of these autoimmune diseases. Here we report the identification of interleukin enhancer-binding factors 2 and 3 (ILF2 and ILF3) as autoantigens in canine immune-mediated rheumatic disease. The ILF2 autoantibodies were discovered in a small, selected canine cohort through the use of human protein arrays; a method not previously described in dogs. Subsequently, ILF3 autoantibodies were also identified in the same cohort. The results were validated with an independent method in a larger cohort of dogs. ILF2 and ILF3 autoantibodies were found exclusively, and at a high frequency, in dogs that showed a speckled pattern of antinuclear antibodies on immunofluorescence. ILF2 and ILF3 autoantibodies were also found at low frequency in human patients with SLE and Sjogren's syndrome. These autoantibodies have the potential to be used as diagnostic biomarkers for canine, and possibly also human, autoimmune disease.

  • 16.
    Burgos-Parra, E.
    et al.
    Univ Exeter, Coll Engn Math & Phys Sci, Exeter EX4 4QL, Devon, England..
    Bukin, N.
    Univ Exeter, Coll Engn Math & Phys Sci, Exeter EX4 4QL, Devon, England..
    Redjai Sani, Sohrab
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Figueroa, A. I.
    Diamond Light Source, Magnet Spect Grp, Didcot, Oxon, England..
    Beutier, G.
    Univ Grenoble Alpes, CNRS, Genoble INP, SIMaP, Grenoble, France..
    Dupraz, M.
    Univ Grenoble Alpes, CNRS, Genoble INP, SIMaP, Grenoble, France..
    Chung, Sunjae
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden.;Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Duerrenfeld, P.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Le, Q. Tuan
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden.;Uppsala Univ, Dept Phys & Astron, S-75120 Uppsala, Sweden..
    Mohseni, S. M.
    Shahid Beheshti Univ, Fac Phys, Tehran 19839, Iran..
    Houshang, A.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden.;NanOsc AB, Electrum 205, S-16440 Kista, Sweden..
    Cavill, S. A.
    Univ York, Dept Phys, York YO10 5DD, N Yorkshire, England..
    Hicken, R. J.
    Univ Exeter, Coll Engn Math & Phys Sci, Exeter EX4 4QL, Devon, England..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden.;NanOsc AB, Electrum 205, S-16440 Kista, Sweden..
    van der Laan, G.
    Diamond Light Source, Magnet Spect Grp, Didcot, Oxon, England..
    Ogrin, F. Y.
    Univ Exeter, Coll Engn Math & Phys Sci, Exeter EX4 4QL, Devon, England..
    Investigation of magnetic droplet solitons using x-ray holography with extended references2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11533Article in journal (Refereed)
    Abstract [en]

    A dissipative magnetic soliton, or magnetic droplet, is a structure that has been predicted to exist within a thin magnetic layer when non-linearity is balanced by dispersion, and a driving force counteracts the inherent damping of the spin precession. Such a soliton can be formed beneath a nano-contact (NC) that delivers a large spin-polarized current density into a magnetic layer with perpendicular magnetic anisotropy. Although the existence of droplets has been confirmed from electrical measurements and by micromagnetic simulations, only a few attempts have been made to directly observe the magnetic landscape that sustains these structures, and then only for a restricted set of experimental parameter values. In this work we use and x-ray holography technique HERALDO, to image the magnetic structure of the [ Co/ Ni] x4 multilayer within a NC orthogonal pseudo spin-valve, for different range of magnetic fields and injected electric currents. The magnetic configuration imaged at -33 mA and 0.3 T for devices with 90 nm NC diameter reveals a structure that is within the range of current where the droplet soliton exist based on our electrical measurements and have it is consistent with the expected size of the droplet (similar to 100 nm diameter) and its spatial position within the sample. We also report the magnetisation configurations observed at lower DC currents in the presence of fields (0-50 mT), where it is expected to observe regimes of the unstable droplet formation.

  • 17. Cappel, Ute B
    et al.
    Moia, Davide
    Bruno, Annalisa
    Vaissier, Valerie
    Haque, Saif A
    Barnes, Piers R F
    Evidence for photo-induced charge separation between dye molecules adsorbed to aluminium oxide surfaces.2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 21276Article in journal (Refereed)
    Abstract [en]

    Excited state dynamics and photo-induced charge transfer of dye molecules have been widely studied due to their relevance for organic and dye-sensitised solar cells. Herein, we present a femtosecond transient absorption spectroscopy study of the indolene dye D131 when adsorbed to inert Al2O3 substrates for different surface concentration of the dye. Surprisingly, we find that at high surface concentrations, the first singlet excited state of the dye is converted into a new state with an efficiency of about 80%. We assign the absorption features of this state to the oxidised dye and discuss the possibility of photo-induced charge separation between neighboring dye molecules. Our study is the first to show that this process can be highly efficient without the use of donor and acceptor molecules of different chemical structures.

  • 18. Caspeta, Luis
    et al.
    Chen, Yun
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 degrees C2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 27003Article in journal (Refereed)
    Abstract [en]

    Exposure to long-term environmental changes across >100s of generations results in adapted phenotypes, but little is known about how metabolic and transcriptional responses are optimized in these processes. Here, we show that thermotolerant yeast strains selected by adaptive laboratory evolution to grow at increased temperature, activated a constitutive heat stress response when grown at the optimal ancestral temperature, and that this is associated with a reduced growth rate. This preventive response was perfected by additional transcriptional changes activated when the cultivation temperature is increased. Remarkably, the sum of global transcriptional changes activated in the thermotolerant strains when transferred from the optimal to the high temperature, corresponded, in magnitude and direction, to the global changes observed in the ancestral strain exposed to the same transition. This demonstrates robustness of the yeast transcriptional program when exposed to heat, and that the thermotolerant strains streamlined their path to rapidly and optimally reach post-stress transcriptional and metabolic levels. Thus, long-term adaptation to heat improved yeasts ability to rapidly adapt to increased temperatures, but this also causes a trade-off in the growth rate at the optimal ancestral temperature.

  • 19. Cebula, Marcus
    et al.
    Turan, Ilke Simsek
    Sjodin, Birgitta
    Thulasingam, Madhuranayaki
    Brock, Joseph
    Chmyrov, Volodymyr
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Abe, Hiroshi
    Mannervik, Bengt
    Haeggstrom, Jesper Z.
    Rinaldo-Matthis, Agnes
    Akkaya, Engin U.
    Morgenstern, Ralf
    Catalytic Conversion of Lipophilic Substrates by Phase constrained Enzymes in the Aqueous or in the Membrane Phase2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 38316Article in journal (Refereed)
    Abstract [en]

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

  • 20.
    Chauvin, Maxime
    et al.
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Florén, H. -G
    Friis, M.
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Jackson, M.
    KTH, School of Engineering Sciences (SCI), Physics. Present address: School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3AA, UK.
    Kamae, T.
    Kataoka, J.
    Kawano, T.
    Kiss, M.
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Mikhalev, V.
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Mizuno, T.
    Ohashi, N.
    Stana, T.
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Tajima, H.
    Takahashi, H.
    Uchida, N.
    Pearce, Mark
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Correction: Shedding new light on the crab with polarized X-rays (Scientific Reports DOI: 10.1038/s41598-017-07390-7)2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, no 1, article id 7975Article in journal (Refereed)
    Abstract [en]

    This Article contains a typographical error in the legend of Figure 2. "Gaussian 1, 2 and 3& #x1D70E;" should read: "Gaussian 1, 2 and 3σ". 

  • 21.
    Chauvin, Maxime
    et al.
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Florén, H.-G.
    Friis, Mette
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Jackson, Miranda
    KTH, School of Engineering Sciences (SCI), Physics. School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3AA, UK.
    Kamae, T.
    Kataoka, J.
    Kawano, T.
    Kiss, Mózsi
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Mikhalev, Victor
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Mizuno, T.
    Ohashi, N.
    Stana, Theodor-Adrian
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Tajima, H.
    Takahashi, H.
    Uchida, N.
    Pearce, Mark
    KTH, School of Engineering Sciences (SCI), Physics. The Oskar Klein Centre for Cosmoparticle Physics, AlbaNova University Centre, 106 91, Stockholm, Sweden.
    Shedding new light on the Crab with polarized X-rays2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 7816, p. 1-6Article in journal (Refereed)
    Abstract [en]

    Strong magnetic fields, synchrotron emission, and Compton scattering are omnipresent in compactcelestial X-ray sources. Emissions in the X-ray energy band are consequently expected to be linearlypolarized. X-ray polarimetry provides a unique diagnostic to study the location and fundamentalmechanisms behind emission processes. The polarization of emissions from a bright celestial X-raysource, the Crab, is reported here for the first time in the hard X-ray band (~20–160 keV). The Crab isa complex system consisting of a central pulsar, a diffuse pulsar wind nebula, as well as structures inthe inner nebula including a jet and torus. Measurements are made by a purpose-built and calibratedpolarimeter, PoGO+. The polarization vector is found to be aligned with the spin axis of the pulsar for apolarization fraction, PF = (20.9 ± 5.0)%. This is higher than that of the optical diffuse nebula, implyinga more compact emission site, though not as compact as, e.g., the synchrotron knot. Contrary tomeasurements at higher energies, no significant temporal evolution of phase-integrated polarisationparameters is observed. The polarization parameters for the pulsar itself are measured for the first timein the X-ray energy band and are consistent with observations at optical wavelengths.

  • 22. Chen, J.
    et al.
    Yang, J.
    Sun, Xianqiang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wang, Z.
    Cheng, X.
    Lu, W.
    Cai, X.
    Hu, C.
    Shen, X.
    Cao, P.
    Allosteric inhibitor remotely modulates the conformation of the orthestric pockets in mutant IDH2/R140Q2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 1, article id 16458Article in journal (Refereed)
    Abstract [en]

    Neomorphic mutation R140Q in the metabolic enzyme isocitrate dehydrogenase 2 (IDH2) is found to be a driver mutation in cancers. Recent studies revealed that allosteric inhibitors could selectively inhibit IDH2/R140Q and induce differentiation of TF-1 erythroleukemia and primary human AML cells. However, the allosteric inhibition mechanism is not very clear. Here, we report the results from computational studies that AGI-6780 binds tightly with the divalent cation binding helices at the homodimer interface and prevents the transition of IDH2/R140Q homodimer to a closed conformation that is required for catalysis, resulting in the decrease of the binding free energy of NADPHs. If the allosteric inhibitor is removed, the original open catalytic center of IDH2/R140Q will gradually reorganize to a quasi-closed conformation and the enzymatic activity might recover. Unlike IDH2/R140Q, AGI-6780 locks one monomer of the wild-type IDH2 in an inactive open conformation and the other in a half-closed conformation, which can be used to explain the selectivity of AGI-6780. Our results suggest that conformational changes are the primary contributors to the inhibitory potency of the allosteric inhibitor. Our study will also facilitate the understanding of the inhibitory and selective mechanisms of AG-221 (a promising allosteric inhibitor that has been approved by FDA) for mutant IDH2.

  • 23. Chen, Rui-Pin
    et al.
    Chen, Zhaozhong
    Chew, Khian-Hooi
    Li, Pei-Gang
    Yu, Zhongliang
    Ding, Jianping
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Structured caustic vector vortex optical field: manipulating optical angular momentum flux and polarization rotation2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 10628Article in journal (Refereed)
    Abstract [en]

    A caustic vector vortex optical field is experimentally generated and demonstrated by a caustic-based approach. The desired caustic with arbitrary acceleration trajectories, as well as the structured states of polarization (SoP) and vortex orders located in different positions in the field cross-section, is generated by imposing the corresponding spatial phase function in a vector vortex optical field. Our study reveals that different spin and orbital angular momentum flux distributions (including opposite directions) in different positions in the cross-section of a caustic vector vortex optical field can be dynamically managed during propagation by intentionally choosing the initial polarization and vortex topological charges, as a result of the modulation of the caustic phase. We find that the SoP in the field cross-section rotates during propagation due to the existence of the vortex. The unique structured feature of the caustic vector vortex optical field opens the possibility of multi-manipulation of optical angular momentum fluxes and SoP, leading to more complex manipulation of the optical field scenarios. Thus this approach further expands the functionality of an optical system.

  • 24. Chen, Rui-Pin
    et al.
    Chew, Khian-Hooi
    He, Sailing
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering. KTH, School of Information and Communication Technology (ICT), Centres, Zhejiang-KTH Joint Research Center of Photonics, JORCEP.
    Dynamic Control of Collapse in a Vortex Airy Beam2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, p. 1406-Article in journal (Refereed)
    Abstract [en]

    Here we study systematically the self-focusing dynamics and collapse of vortex Airy optical beams in a Kerr medium. The collapse is suppressed compared to a non-vortex Airy beam in a Kerr medium due to the existence of vortex fields. The locations of collapse depend sensitively on the initial power, vortex order, and modulation parameters. The collapse may occur in a position where the initial field is nearly zero, while no collapse appears in the region where the initial field is mainly distributed. Compared with a non-vortex Airy beam, the collapse of a vortex Airy beam can occur at a position away from the area of the initial field distribution. Our study shows the possibility of controlling and manipulating the collapse, especially the precise position of collapse, by purposely choosing appropriate initial power, vortex order or modulation parameters of a vortex Airy beam.

  • 25. Chen, Xiaobin
    et al.
    Tian, Fuyang
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Persson, Clas
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling.
    Duan, Wenhui
    Chen, Nan-xian
    Interlayer interactions in graphites2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 3, p. 3046-Article in journal (Refereed)
    Abstract [en]

    Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Mobius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

  • 26. Cheng, J.
    et al.
    Sun, Xianqiang
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, W.
    Liu, G.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tang, Y.
    Molecular switches of the κ opioid receptor triggered by 6′-GNTI and 5′-GNTI2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 18913Article in journal (Refereed)
    Abstract [en]

    The κ opioid receptor (κOR) is a member of G-protein-coupled receptors, and is considered as a promising drug target for treating neurological diseases. κOR selective 6′-GNTI was proved to be a G-protein biased agonist, whereas 5′-GNTI acts as an antagonist. To investigate the molecular mechanism of how these two ligands induce different behaviors of the receptor, we built two systems containing the 5′-GNTI-κOR complex and the 6′-GNTI-κOR complex, respectively, and performed molecular dynamics simulations of the two systems. We observe that transmembrane (TM) helix 6 of the κOR rotates about 4.6° on average in the κOR-6′-GNTI complex. Detailed analyses of the simulation results indicate that E2976.58 and I2946.55 play crucial roles in the rotation of TM6. In the simulation of the κOR-5′-GNTI system, it is revealed that 5′-GNTI can stabilize TM6 in the inactive state form. In addition, the kink of TM7 is stabilized by a hydrogen bond between S3247.47 and the residue V691.42 on TM1.

  • 27. Ch'ng, Jun-Hong
    et al.
    Sirel, Madle
    Zandian, Arash
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Quintana, Maria del Pilar
    Chan, Sherwin Chun Leung
    Moll, Kirsten
    Tellgren-Roth, Asa
    Nilsson, IngMarie
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Qundos, Ulrika
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Wahlgren, Mats
    Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 43190Article in journal (Refereed)
    Abstract [en]

    Variable surface antigens of Plasmodium falciparum have been a major research focus since they facilitate parasite sequestration and give rise to deadly malaria complications. Coupled with its potential use as a vaccine candidate, the recent suggestion that the repetitive interspersed families of polypeptides (RIFINs) mediate blood group A rosetting and influence blood group distribution has raised the research profile of these adhesins. Nevertheless, detailed investigations into the functions of this highly diverse multigene family remain hampered by the limited number of validated reagents. In this study, we assess the specificities of three promising polyclonal anti-RIFIN antibodies that were IgG-purified from sera of immunized animals. Their epitope regions were mapped using a 175,000-peptide microarray holding overlapping peptides of the P. falciparum variable surface antigens. Through immunoblotting and immunofluorescence imaging, we show that different antibodies give varying results in different applications/assays. Finally, we authenticate the antibody-based detection of RIFINs in two previously uncharacterized non-rosetting parasite lines by identifying the dominant rif transcripts using RNA sequencing.

  • 28.
    Choong, Ferdinand X.
    et al.
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, SE-17177 Stockholm, Sweden..
    Back, Marcus
    Linkoping Univ, IFM, Dept Chem, SE-58183 Linkoping, Sweden..
    Schulz, Anette
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, SE-17177 Stockholm, Sweden..
    Nilsson, K. Peter. R.
    Linkoping Univ, IFM, Dept Chem, SE-58183 Linkoping, Sweden..
    Edlund, Ulrica
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Richter-Dahlfors, Agneta
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, SE-17177 Stockholm, Sweden..
    Stereochemical identification of glucans by oligothiophenes enables cellulose anatomical mapping in plant tissues2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 3108Article in journal (Refereed)
    Abstract [en]

    Efficient use of plant-derived materials requires enabling technologies for non-disruptive composition analysis. The ability to identify and spatially locate polysaccharides in native plant tissues is difficult but essential. Here, we develop an optical method for cellulose identification using the structure-responsive, heptameric oligothiophene h-FTAA as molecular fluorophore. Spectrophotometric analysis of h-FTAA interacting with closely related glucans revealed an exceptional specificity for beta-linked glucans. This optical, non-disruptive method for stereochemical differentiation of glycosidic linkages was next used for in situ composition analysis in plants. Multi-laser/multi-detector analysis developed herein revealed spatial localization of cellulose and structural cell wall features such as plasmodesmata and perforated sieve plates of the phloem. Simultaneous imaging of intrinsically fluorescent components revealed the spatial relationship between cell walls and other organelles, such as chloroplasts and lignified annular thickenings of the trachea, with precision at the sub-cellular scale. Our non-destructive method for cellulose identification lays the foundation for the emergence of anatomical maps of the chemical constituents in plant tissues. This rapid and versatile method will likely benefit the plant science research fields and may serve the biorefinery industry as reporter for feedstock optimization as well as in-line monitoring of cellulose reactions during standard operations.

  • 29. Choong, Ferdinand X.
    et al.
    Back, Marcus
    Steiner, Svava E.
    Melican, Keira
    Nilsson, K. Peter R.
    Edlund, Ulrica
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Richter-Dahlfors, Agneta
    Nondestructive, real-time determination and visualization of cellulose, hemicellulose and lignin by luminescent oligothiophenes2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 35578Article in journal (Refereed)
    Abstract [en]

    Enabling technologies for efficient use of the bio-based feedstock are crucial to the replacement of oil-based products. We investigated the feasibility of luminescent conjugated oligothiophenes (LCOs) for non-destructive, rapid detection and quality assessment of lignocellulosic components in complex biomass matrices. A cationic pentameric oligothiophene denoted p-HTEA (pentamer hydrogen thiophene ethyl amine) showed unique binding affinities to cellulose, lignin, hemicelluloses, and cellulose nanofibrils in crystal, liquid and paper form. We exploited this finding using spectrofluorometric methods and fluorescence confocal laser scanning microscopy, for sensitive, simultaneous determination of the structural and compositional complexities of native lignocellulosic biomass. With exceptional photostability, p-HTEA is also demonstrated as a dynamic sensor for real-time monitoring of enzymatic cellulose degradation in cellulolysis. These results demonstrate the use of p-HTEA as a non-destructive tool for the determination of cellulose, hemicellulose and lignin in complex biomass matrices, thereby aiding in the optimization of biomass-converting technologies.

  • 30. Clausson, Carl-Magnus
    et al.
    Arngarden, Linda
    Ishaq, Omer
    Klaesson, Axel
    Kuhnemund, Malte
    Grannas, Karin
    Koos, Bjorn
    Qian, Xiaoyan
    Ranefall, Petter
    Krzywkowski, Tomasz
    Brismar, Hjalmar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cell Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nilsson, Mats
    Wahlby, Carolina
    Soderberg, Ola
    Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 12317Article in journal (Refereed)
    Abstract [en]

    Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.

  • 31.
    Commowick, Olivier
    et al.
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France..
    Istace, Audrey
    Hosp Civils Lyon, Lyon Sud Hosp, Dept Radiol, Lyon, France..
    Kain, Michael
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France..
    Laurent, Baptiste
    Univ Brest, IBSAM, INSERM, LaTIM,UMR 1101, Brest, France..
    Leray, Florent
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France..
    Simon, Mathieu
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France..
    Pop, Sorina Camarasu
    Univ Claude Bernard Lyon 1, Univ Lyon,INSA Lyon, UJM St Etienne,CNRS,Inserm, CREATIS,UMR 5220,U1206, F-69621 Lyon, France..
    Girard, Pascal
    Univ Claude Bernard Lyon 1, Univ Lyon,INSA Lyon, UJM St Etienne,CNRS,Inserm, CREATIS,UMR 5220,U1206, F-69621 Lyon, France..
    Ameli, Roxana
    Hosp Civils Lyon, Lyon Sud Hosp, Dept Radiol, Lyon, France..
    Ferre, Jean-Christophe
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France.;CHU Rennes, Dept Neuroradiol, F-35033 Rennes, France..
    Kerbrat, Anne
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France.;CHU Rennes, Dept Neurol, F-35033 Rennes, France..
    Tourdias, Thomas
    CHU Bordeaux, Serv Neuroimagerie, Bordeaux, France..
    Cervenansky, Frederic
    Univ Claude Bernard Lyon 1, Univ Lyon,INSA Lyon, UJM St Etienne,CNRS,Inserm, CREATIS,UMR 5220,U1206, F-69621 Lyon, France..
    Glatard, Tristan
    Concordia Univ, Dept Comp Sci & Software Engn, Montreal, PQ, Canada..
    Beaumont, Jeremy
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France..
    Doyle, Senan
    Pixyl Med, Grenoble, France..
    Forbes, Florence
    Pixyl Med, Grenoble, France.;Inria Grenoble Rhone Alpes, Grenoble, France..
    Knight, Jesse
    Univ Guelph, Sch Engn, Image Anal Med Lab, Guelph, ON, Canada..
    Khademi, April
    Ryerson Univ, Image Anal Med Lab IAMLAB, Toronto, ON, Canada..
    Mahbod, Amirreza
    KTH, School of Technology and Health (STH).
    Wang, Chunliang
    KTH, School of Technology and Health (STH).
    McKinley, Richard
    Univ Bern, Dept Diagnost & Intervent Neuroradiol, Inselspital, Bern, Switzerland..
    Wagner, Franca
    Univ Bern, Dept Diagnost & Intervent Neuroradiol, Inselspital, Bern, Switzerland..
    Muschelli, John
    Johns Hopkins Bloomberg Sch Publ Hlth, Baltimore, MD USA..
    Sweeney, Elizabeth
    Johns Hopkins Bloomberg Sch Publ Hlth, Baltimore, MD USA..
    Roura, Eloy
    Univ Girona, Res Inst Comp Vis & Robot VICOROB, Girona, Spain..
    Llado, Xavier
    Univ Girona, Res Inst Comp Vis & Robot VICOROB, Girona, Spain..
    Santos, Michel M.
    Univ Fed Pernambuco, Ctr Informat, Recife, Brazil..
    Santos, Wellington P.
    Univ Fed Pernambuco, Dept Engn Biomed, Recife, Brazil..
    Silva-Filho, Abel G.
    Univ Fed Pernambuco, Ctr Informat, Recife, Brazil..
    Tomas-Fernandez, Xavier
    Childrens Hosp, Dept Radiol, Computat Radiol Lab, 300 Longwood Ave, Boston, MA 02115 USA..
    Urien, Helene
    Univ Paris Saclay, LTCI, Telecom ParisTech, Paris, France..
    Bloch, Isabelle
    Univ Paris Saclay, LTCI, Telecom ParisTech, Paris, France..
    Valverde, Sergi
    Univ Girona, Res Inst Comp Vis & Robot VICOROB, Girona, Spain..
    Cabezas, Mariano
    Univ Girona, Res Inst Comp Vis & Robot VICOROB, Girona, Spain..
    Javier Vera-Olmos, Francisco
    Univ Rey Juan Carlos, Med Image Anal Lab, Madrid, Spain..
    Malpica, Norberto
    Univ Rey Juan Carlos, Med Image Anal Lab, Madrid, Spain..
    Guttmann, Charles
    Brigham & Womens Hosp, Dept Radiol, Ctr Neurol Imaging, 75 Francis St, Boston, MA 02115 USA..
    Vukusic, Sandra
    Hosp Civils Lyon, Lyon Sud Hosp, Dept Radiol, Lyon, France..
    Edan, Gilles
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France.;CHU Rennes, Dept Neurol, F-35033 Rennes, France..
    Dojat, Michel
    Univ Grenoble Alpes, CHU Grenoble, GIN, Inserm,U1216, Grenoble, France..
    Styner, Martin
    Univ N Carolina, Dept Comp Sci, Chapel Hill, NC 27515 USA..
    Warfield, Simon K.
    Childrens Hosp, Dept Radiol, Computat Radiol Lab, 300 Longwood Ave, Boston, MA 02115 USA..
    Cotton, Francois
    Hosp Civils Lyon, Lyon Sud Hosp, Dept Radiol, Lyon, France..
    Barillot, Christian
    Univ Rennes 1, CNRS, INSERM, VISAGES,U1228,UMR6074, Rennes, France..
    Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 13650Article in journal (Refereed)
    Abstract [en]

    We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning,.), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.

  • 32. Conti, Luca
    et al.
    Renhorn, Jakob
    Gabrielsson, Anders
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Turesson, Fredrik
    Liin, Sara I.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. Stockholm University, Sweden.
    Elinder, Fredrik
    Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 27562Article in journal (Refereed)
    Abstract [en]

    Voltage-gated potassium channels open at depolarized membrane voltages. A prolonged depolarization causes a rearrangement of the selectivity filter which terminates the conduction of ions - a process called slow or C-type inactivation. How structural rearrangements in the voltage-sensor domain (VSD) cause alteration in the selectivity filter, and vice versa, are not fully understood. We show that pulling the pore domain of the Shaker potassium channel towards the VSD by a Cd2+ bridge accelerates C-type inactivation. Molecular dynamics simulations show that such pulling widens the selectivity filter and disrupts the K+ coordination, a hallmark for C-type inactivation. An engineered Cd2+ bridge within the VSD also affect C-type inactivation. Conversely, a pore domain mutation affects VSD gating-charge movement. Finally, C-type inactivation is caused by the concerted action of distant amino acid residues in the pore domain. All together, these data suggest a reciprocal communication between the pore domain and the VSD in the extracellular portion of the channel.

  • 33.
    Couto, Rafael C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Univ Fed Goias, Brazil.
    Guarise, Marco
    Nicolaou, Alessandro
    Jaouen, Nicolas
    Chiuzbaian, Gheorghe S.
    Luening, Jan
    Ekholm, Victor
    Rubensson, Jan-Erik
    Sathe, Conny
    Hennies, Franz
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Guimaraes, Freddy F.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Journel, Loic
    Simon, Marc
    Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 20947Article in journal (Refereed)
    Abstract [en]

    The unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12-14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of "dark" with "bright" final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past.

  • 34.
    Dahlberg, Carl F. O.
    et al.
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.), Solid Mechanics (Div.).
    Mitchell-Thomas, R. C.
    Quevedo-Teruel, Oscar
    KTH, School of Electrical Engineering (EES), Electromagnetic Engineering.
    Reducing the Dispersion of Periodic Structures with Twist and Polar Glide Symmetries2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 10136Article in journal (Refereed)
    Abstract [en]

    In this article, a number of guiding structures are proposed which take advantage of higher symmetries to vastly reduce the dispersion. These higher symmetries are obtained by executing additional geometrical operations to introduce more than one period into the unit cell of a periodic structure. The specific symmetry operations employed here are a combination of p-fold twist and polar glide. Our dispersion analysis shows that a mode in a structure possessing higher symmetries is less dispersive than in a conventional structure. It is also demonstrated that, similar to the previously studied Cartesian glide-symmetric structures, polar glide-symmetric structures also exhibit a frequency independent response. Promising applications of these structures are leaky-wave antennas which utilize the low frequency dependence.

  • 35.
    Del Giudice, Marco
    et al.
    Politecn Torino, Dept Appl Sci & Technol, Corso Duca Abruzzi 24, IT-10129 Turin, Italy.;Italian Inst Genom Med, Via Nizza 52, I-10126 Turin, Italy..
    Bosia, Carla
    Politecn Torino, Dept Appl Sci & Technol, Corso Duca Abruzzi 24, IT-10129 Turin, Italy.;Italian Inst Genom Med, Via Nizza 52, I-10126 Turin, Italy..
    Grigolon, Silvia
    Francis Crick Inst, 1 Midland Rd, London NW1 1AT, England..
    Bo, Stefano
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Stockholm Univ, Roslagstullsbacken 23, SE-10691 Stockholm, Sweden.
    Stochastic sequestration dynamics: a minimal model with extrinsic noise for bimodal distributions and competitors correlation2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 10387Article in journal (Refereed)
    Abstract [en]

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

  • 36.
    Dias, Jorge T
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Svedberg, Gustav
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Nystrand, Mats
    Andersson-Svahn, Helene
    Gantelius, Jesper
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rapid signal enhancement method for nanoprobe-based biosensing2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 6837Article in journal (Refereed)
    Abstract [en]

    The introduction of nanomaterials as detection reagents has enabled improved sensitivity and facilitated detection in a variety of bioanalytical assays. However, high nanoprobe densities are typically needed for colorimetric detection and to circumvent this limitation several enhancement protocols have been reported. Nevertheless, there is currently a lack of universal, enzyme-free and versatile methods that can be readily applied to existing as well as new biosensing strategies. The novel method presented here is shown to enhance the signal of gold nanoparticles enabling visual detection of a spot containing < 10 nanoparticles. Detection of Protein G on paper arrays was improved by a 100-fold amplification factor in under five minutes of assay time, using IgG-labelled gold, silver, silica and iron oxide nanoprobes. Furthermore, we show that the presented protocol can be applied to a commercial allergen microarray assay, ImmunoCAP ISAC sIgE 112, attaining a good agreement with fluorescent detection when analysing human clinical samples.

  • 37.
    Dias, Jorge T.
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Svedberg, Gustav
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nystrand, Mats
    Thermo Fisher Sci IDD, Global Res & Dev, Uppsala, Sweden..
    Svahn Andersson, Helene
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Gantelius, Jesper
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Rapid signal enhancement method for nanoprobe-based biosensing (vol 7, 2017)2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, no 1, article id 8184Article in journal (Refereed)
    Abstract [en]

    In the Methods section of this Article references 18 to 22 are incorrectly cited. The correct references were omitted from the reference list and appear below as references 1-5. References 18 to 22 are correctly cited in Introduction and Results and Discussion sections. "AuNPs of 10 nm in diameter were prepared following the protocol described by Bastus et al.18." should read: "AuNPs of 10 nm in diameter were prepared following the protocol described by Bastus et al.1." "AgNPs of 90 nm in diameter were prepared following the protocol described by Rivero et al.19." should read: "AgNPs of 90 nm in diameter were prepared following the protocol described by Rivero et al.2" "The size was determined by UV-Vis spectroscopy according to the AgNPs size theory demonstrated by Malynych20." should read: "The size was determined by UV-Vis spectroscopy according to the AgNPs size theory demonstrated by Malynych3." "The coupling of antibody to the NPs was prepared following a modified version of a protocol previously reported by Puertas et al.21." should read: "The coupling of antibody to the NPs was prepared following a modified version of a protocol previously reported by Puertas et al.4." "Microarrays were prepared as previously reported by our group22." should read: "Microarrays were prepared as previously reported by our group5.

  • 38. Ding, Fei
    et al.
    Dai, Jin
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Chen, Yiting
    Zhu, Jianfei
    Jin, Yi
    Bozhevolnyi, Sergey I.
    Broadband near-infrared metamaterial absorbers utilizing highly lossy metals2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 39445Article in journal (Refereed)
    Abstract [en]

    Radiation absorbers have increasingly been attracting attention as crucial components for controllable thermal emission, energy harvesting, modulators, etc. However, it is still challenging to realize thin absorbers which can operate over a wide spectrum range. Here, we propose and experimentally demonstrate thin, broadband, polarization-insensitive and omnidirectional absorbers working in the near-infrared range. We choose titanium (Ti) instead of the commonly used gold (Au) to construct nano-disk arrays on the top of a silicon dioxide (SiO2) coated Au substrate, with the quality (Q) factor of the localized surface plasmon (LSP) resonance being decreased due to the intrinsic high loss of Ti. The combination of this low-Q LSP resonance and the propagating surface plasmon (PSP) excitation resonance, which occur at different wavelengths, is the fundamental origin of the broadband absorption. The measured (at normal light incidence) absorption is over 90% in the wavelength range from 900 nm to 1825 nm, with high absorption persisting up to the incident angle of similar to 40 degrees. The demonstrated thin-film absorber configuration is relatively easy to fabricate and can be realized with other properly selected materials.

  • 39.
    Dong, Zhihua
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Schönecker, Stephan
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Li, Wei
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Chen, Dengfu
    Chongqing Univ, Coll Mat Sci & Engn, Chongqing 400030, Peoples R China..
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Thermal spin fluctuations in CoCrFeMnNi high entropy alloy2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 12211Article in journal (Refereed)
    Abstract [en]

    High entropy alloys based on 3d transition metals display rich and promising magnetic characteristics for various high-technology applications. Understanding their behavior at finite temperature is, however, limited by the incomplete experimental data for single-phase alloys. Here we use first-principles alloy theory to investigate the magnetic structure of polymorphic CoCrFeMnNi in the paramagnetic state by accounting for the longitudinal spin fluctuations (LSFs) as a function of temperature. In both face-centered cubic (fcc) and hexagonal close-packed (hcp) structures, the LSFs induce sizable magnetic moments for Co, Cr and Ni. The impact of LSFs is demonstrated on the phase stability, stacking fault energy and the fcc-hcp interfacial energy. The hcp phase is energetically preferable to the fcc one at cryogenic temperatures, which results in negative stacking fault energy at these conditions. With increasing temperature, the stacking fault energy increases, suppressing the formation of stacking faults and nano-twins. Our predictions are consistent with recent experimental findings.

  • 40.
    Dusart, Philip
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Fagerberg, Linn
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Perisic, L.
    Civelek, M.
    Struck, Eike
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hedin, U.
    Uhlén, Mathias
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO).
    Trégouët, D. -A
    Renné, T.
    Odeberg, Jacob
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO). Coagulation Unit, Centre for Hematology, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
    Butler, Lynn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO). Clinical Chemistry and Blood Coagulation, Department of Molecular Medicine and Surgery, Karolinska Institute, SE-171 76, Stockholm, Sweden Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, D-20246, Hamburg, Germany.
    A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, no 1, article id 14668Article in journal (Refereed)
    Abstract [en]

    The intermediate filament protein nestin is expressed during embryonic development, but considered largely restricted to areas of regeneration in the adult. Here, we perform a body-wide transcriptome and protein-profiling analysis to reveal that nestin is constitutively, and highly-selectively, expressed in adult human endothelial cells (EC), independent of proliferative status. Correspondingly, we demonstrate that it is not a marker for tumour EC in multiple malignancy types. Imaging of EC from different vascular beds reveals nestin subcellular distribution is shear-modulated. siRNA inhibition of nestin increases EC proliferation, and nestin expression is reduced in atherosclerotic plaque neovessels. eQTL analysis reveals an association between SNPs linked to cardiovascular disease and reduced aortic EC nestin mRNA expression. Our study challenges the dogma that nestin is a marker of proliferation, and provides insight into its regulation and function in EC. Furthermore, our systems-based approach can be applied to investigate body-wide expression profiles of any candidate protein. 

  • 41.
    Dyakov, S. A.
    et al.
    Skolkovo Inst Sci & Technol, Photon & Quantum Mat Ctr, Moscow 143025, Russia..
    Zhigunov, D. M.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia..
    Marinins, A.
    KTH, School of Electrical Engineering (EES).
    Shalygina, O. A.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia..
    Vabishchevich, P. P.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia..
    Shcherbakov, M. R.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia..
    Presnov, D. E.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia.;Skobeltsyn Inst Nucl Phys, Moscow 119991, Russia..
    Fedyanin, A. A.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia..
    Kashkarov, P. K.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia.;Natl Res Ctr Inst, Moscow 123182, Russia..
    Popov, S.
    KTH, School of Electrical Engineering (EES).
    Gippius, N. A.
    Skolkovo Inst Sci & Technol, Photon & Quantum Mat Ctr, Moscow 143025, Russia..
    Tikhodeev, S. G.
    Lomonosov Moscow State Univ, Fac Phys, Moscow 119991, Russia.;AM Prokhorov Gen Phys Inst, Moscow 119991, Russia..
    Plasmon induced modification of silicon nanocrystals photoluminescence in presence of gold nanostripes2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 4911Article in journal (Refereed)
    Abstract [en]

    We report on the results of theoretical and experimental studies of photoluminescense of silicon nanocrystals in the proximity to plasmonic modes of different types. In the studied samples, the type of plasmonic mode is determined by the filling ratio of a one-dimensional array of gold stripes which covers the thin film with silicon nanocrystals on a quartz substrate. We analyze the extinction, photoluminesce spectra and decay kinetics of silicon nanocrystals and show that the incident and emitted light is coupled to the corresponding plasmonic mode. We demonstrate the modification of the extinction and photoluminesce spectra under the transition from wide to narrow gold stripes. The experimental extinction and photoluminescense spectra are in good agreement with theoretical calculations performed by the rigorous coupled wave analysis. We study the contribution of individual silicon nanocrystals to the overall photoluminescense intensity, depending on their spacial position inside the structure.

  • 42.
    Edsgärd, Daniel
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Iglesias, Maria Jesus
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden .
    Reilly, Sarah-Jayne
    Hamsten, Anders
    Tornvall, Per
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab. Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden; .
    Emanuelsson, Olof
    KTH, School of Biotechnology (BIO). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 21134Article in journal (Refereed)
    Abstract [en]

    Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively.

  • 43. El-Sayed, Ramy
    et al.
    Bhattacharya, Kunal
    Gu, Zonglin
    Yang, Zaixing
    Weber, Jeffrey K.
    Li, Hu
    Leifer, Klaus
    Zhao, Yichen
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Toprak, Muhammet S.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Functional Materials, FNM.
    Zhou, Ruhong
    Fadeel, Bengt
    Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A42016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 21316Article in journal (Refereed)
    Abstract [en]

    We report a detailed computational and experimental study of the interaction of single-walled carbon nanotubes (SWCNTs) with the drug-metabolizing cytochrome P450 enzyme, CYP3A4. Dose-dependent inhibition of CYP3A4-mediated conversion of the model compound, testosterone, to its major metabolite, 6 beta-hydroxy testosterone was noted. Evidence for a direct interaction between SWCNTs and CYP3A4 was also provided. The inhibition of enzyme activity was alleviated when SWCNTs were pre-coated with bovine serum albumin. Furthermore, covalent functionalization of SWCNTs with polyethylene glycol (PEG) chains mitigated the inhibition of CYP3A4 enzymatic activity. Molecular dynamics simulations suggested that inhibition of the catalytic activity of CYP3A4 is mainly due to blocking of the exit channel for substrates/products through a complex binding mechanism. This work suggests that SWCNTs could interfere with metabolism of drugs and other xenobiotics and provides a molecular mechanism for this toxicity. Our study also suggests means to reduce this toxicity, eg., by surface modification.

  • 44.
    Ergül, Adem
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics. Stockholm University, Sweden.
    Weissl, Thomas
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Johansson, Jan
    Lidmar, Jack
    KTH, School of Engineering Sciences (SCI), Physics, Statistical Physics.
    Haviland, David B.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Spatial and temporal distribution of phase slips in Josephson junction chains2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 11447Article in journal (Refereed)
    Abstract [en]

    The Josephson effect, tunnelling of a supercurrent through a thin insulator layer between two superconducting islands, is a phenomena characterized by a spatially distributed phase of the superconducting condensate. In recent years, there has been a growing focus on Josephson junction devices particularly for the applications of quantum metrology and superconducting qubits. In this study, we report the development of Josephson junction circuit formed by serially connecting many Superconducting Quantum Interference Devices, SQUIDs. We present experimental measurements as well as numerical simulations of a phase-slip center, a SQUID with weaker junctions, embedded in a Josephson junction chain. The DC transport properties of the chain are the result of phase slips which we simulate using a classical model that includes linear external damping, terminating impedance, as well as internal nonlinear quasiparticle damping. We find good agreement between the simulated and the experimental current voltage characteristics. The simulations allow us to examine the spatial and temporal distribution of phase-slip events occurring across the chains and also the existence of travelling voltage pulses which reflect at the chain edges.

  • 45.
    Etcheverry, Sebastian
    et al.
    Center for optics and photonics,Univesity of Concepcion.
    Cañas, Gustavo
    S. Gomez, Esteban
    Nogueira, Wallon
    Saaveda, Carlos
    Xavier, Guilherme
    Lima, Gustavo
    Quantum key distribution session with 16-dimensional photonic states2013In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, no 3, p. 2316-Article in journal (Refereed)
    Abstract [en]

    The secure transfer of information is an important problem in modern telecommunications. Quantum key distribution (QKD) provides a solution to this problem by using individual quantum systems to generate correlated bits between remote parties, that can be used to extract a secret key. QKD with D-dimensional quantum channels provides security advantages that grow with increasing D. However, the vast majority of QKD implementations has been restricted to two dimensions. Here we demonstrate the feasibility of using higher dimensions for real-world quantum cryptography by performing, for the first time, a fully automated QKD session based on the BB84 protocol with 16-dimensional quantum states. Information is encoded in the single-photon transverse momentum and the required states are dynamically generated with programmable spatial light modulators. Our setup paves the way for future developments in the field of experimental high-dimensional QKD.

  • 46.
    Etcheverry, Sebastián
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. RISE Acreo AB, Sweden.
    Faridi, Muhammad Asim
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ramachandraiah, Harisha
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Kumar, T.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Margulis, Walter
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. RISE Acreo AB, Sweden.
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics.
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    High performance micro-flow cytometer based on optical fibres2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 5628Article in journal (Refereed)
    Abstract [en]

    Flow cytometry is currently the gold standard for analysis of cells in the medical laboratory and biomedical research. Fuelled by the need of point-of-care diagnosis, a significant effort has been made to miniaturize and reduce cost of flow cytometers. However, despite recent advances, current microsystems remain less versatile and much slower than their large-scale counterparts. In this work, an all-silica fibre microflow cytometer is presented that measures fluorescence and scattering from particles and cells. It integrates cell transport in circular capillaries and light delivery by optical fibres. Single-stream cell focusing is performed by Elasto-inertial microfluidics to guarantee accurate and sensitive detection. The capability of this technique is extended to high flow rates (up to 800 mu l/min), enabling a throughput of 2500 particles/s. The robust, portable and low-cost system described here could be the basis for a point-of-care flow cytometer with a performance comparable to commercial systems.

  • 47.
    Fasterius, Erik
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Systems Biology.
    Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11226Article in journal (Refereed)
    Abstract [en]

    Meta-analysis of datasets available in public repositories are used to gather and summarise experiments performed across laboratories, as well as to explore consistency of scientific findings. As data quality and biological equivalency across samples may obscure such analyses and consequently their conclusions, we investigated the comparability of 85 public RNA-seq cell line datasets. Thousands of pairwise comparisons of single nucleotide variants in 139 samples revealed variable genetic heterogeneity of the eight cell line populations analysed as well as variable data quality. The H9 and HCT116 cell lines were found to be remarkably stable across laboratories (with median concordances of 99.2% and 98.5%, respectively), in contrast to the highly variable HeLa cells (89.3%). We show that the genetic heterogeneity encountered greatly affects gene expression between same-cell comparisons, highlighting the importance of interrogating the biological equivalency of samples when comparing experimental datasets. Both the number of differentially expressed genes and the expression levels negatively correlate with the genetic heterogeneity. Finally, we demonstrate how comparing genetically heterogeneous datasets affect gene expression analyses and that high dissimilarity between same-cell datasets alters the expression of more than 300 cancer-related genes, which are often the focus of studies using cell lines.

  • 48. Fasterius, Erik
    et al.
    Szigyarto, Cristina Al-Khalili
    Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11226Article in journal (Refereed)
    Abstract [en]

    Meta-analysis of datasets available in public repositories are used to gather and summarise experiments performed across laboratories, as well as to explore consistency of scientific findings. As data quality and biological equivalency across samples may obscure such analyses and consequently their conclusions, we investigated the comparability of 85 public RNA-seq cell line datasets. Thousands of pairwise comparisons of single nucleotide variants in 139 samples revealed variable genetic heterogeneity of the eight cell line populations analysed as well as variable data quality. The H9 and HCT116 cell lines were found to be remarkably stable across laboratories (with median concordances of 99.2% and 98.5%, respectively), in contrast to the highly variable HeLa cells (89.3%). We show that the genetic heterogeneity encountered greatly affects gene expression between same-cell comparisons, highlighting the importance of interrogating the biological equivalency of samples when comparing experimental datasets. Both the number of differentially expressed genes and the expression levels negatively correlate with the genetic heterogeneity. Finally, we demonstrate how comparing genetically heterogeneous datasets affect gene expression analyses and that high dissimilarity between same-cell datasets alters the expression of more than 300 cancer-related genes, which are often the focus of studies using cell lines.

  • 49.
    Fleetwood, Filippa
    et al.
    KTH, School of Biotechnology (BIO), Protein Technology.
    Klint, Susanne
    Hanze, Martin
    KTH, School of Biotechnology (BIO), Protein Technology.
    Gunneriusson, Elin
    Frejd, Fredrik
    Ståhl, Stefan
    KTH, School of Biotechnology (BIO), Protein Technology.
    Löfblom, John
    KTH, School of Biotechnology (BIO), Protein Technology.
    Simultaneous targeting of two ligand-binding sites on VEGFR2 using biparatopic Affibody molecules results in dramatically improved affinity2014In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, p. 7518-Article in journal (Refereed)
    Abstract [en]

    Angiogenesis plays an important role in cancer and ophthalmic disorders such as age-related macular degeneration and diabetic retinopathy. The vascular endothelial growth factor (VEGF) family and corresponding receptors are regulators of angiogenesis and have been much investigated as therapeutic targets. The aim of this work was to generate antagonistic VEGFR2-specific affinity proteins having adjustable pharmacokinetic properties allowing for either therapy or molecular imaging. Two antagonistic Affibody molecules that were cross-reactive for human and murine VEGFR2 were selected by phage and bacterial display. Surprisingly, although both binders independently blocked VEGF-A binding, competition assays revealed interaction with non-overlapping epitopes on the receptor. Biparatopic molecules, comprising the two Affibody domains, were hence engineered to potentially increase affinity even further through avidity. Moreover, an albumin-binding domain was included for half-life extension in future in vivo experiments. The best-performing of the biparatopic constructs demonstrated up to 180-fold slower dissociation than the monomers. The new Affibody constructs were also able to specifically target VEGFR2 on human cells, while simultaneously binding to albumin, as well as inhibit VEGF-induced signaling. In summary, we have generated small antagonistic biparatopic Affibody molecules with high affinity for VEGFR2, which have potential for both future therapeutic and diagnostic purposes in angiogenesis-related diseases.

  • 50.
    Fogelqvist, Emelie
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Kördel, Mikael
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
    Carannante, Valentina
    Önfelt, Björn
    KTH, School of Engineering Sciences (SCI), Applied Physics, Cellular Biophysics.
    Hertz, Hans
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. Karolinska Institutet, Sweden.
    Laboratory cryo x-ray microscopy for 3D cell imaging2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 13433Article in journal (Refereed)
    Abstract [en]

    Water-window x-ray microscopy allows two-and three-dimensional (2D and 3D) imaging of intact unstained cells in their cryofixed near-native state with unique contrast and high resolution. Present operational biological water-window microscopes are based at synchrotron facilities, which limits their accessibility and integration with complementary methods. Laboratory-source microscopes have had difficulty addressing relevant biological tasks with proper resolution and contrast due to long exposure times and limited up-time. Here we report on laboratory cryo x-ray microscopy with the exposure time, contrast, and reliability to allow for routine high-spatial resolution 3D imaging of intact cells and cell-cell interactions. Stabilization of the laser-plasma source combined with new optics and sample preparation provide high-resolution cell imaging, both in 2D with ten-second exposures and in 3D with twenty-minute tomography. Examples include monitoring of the distribution of carbon-dense vesicles in starving HEK293T cells and imaging the interaction between natural killer cells and target cells.

1234 1 - 50 of 199
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