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  • 1.
    Aghdam, Araz Sheibani
    et al.
    Sabanci Univ, Fac Engn & Nat Sci, TR-34956 Istanbul, Turkey..
    Ghorbani, Morteza
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems. Sabanci Univ, Fac Engn & Nat Sci, Mechatron Engn Program, TR-34956 Istanbul, Turkey;Sabanci Univ, Ctr Excellence Funct Surfaces & Interfaces NanoDi, TR-34956 Istanbul, Turkey..
    Deprem, Gokberk
    Sabanci Univ, Fac Engn & Nat Sci, Mechatron Engn Program, TR-34956 Istanbul, Turkey..
    Cebeci, Fevzi Cakmak
    Sabanci Univ, Fac Engn & Nat Sci, TR-34956 Istanbul, Turkey.;Sabanci Univ, SUNUM Nanotechnol Res & Applicat Ctr, TR-34956 Istanbul, Turkey..
    Kosar, Ali
    Sabanci Univ, Fac Engn & Nat Sci, Mechatron Engn Program, TR-34956 Istanbul, Turkey.;Sabanci Univ, Ctr Excellence Funct Surfaces & Interfaces NanoDi, TR-34956 Istanbul, Turkey.;Sabanci Univ, SUNUM Nanotechnol Res & Applicat Ctr, TR-34956 Istanbul, Turkey..
    A New Method for Intense Cavitation Bubble Generation on Layer-by-Layer Assembled SLIPS2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 11600Article in journal (Refereed)
    Abstract [en]

    The importance of surface topology for the generation of cavitating flows in micro scale has been emphasized during the last decade. In this regard, the utilization of surface roughness elements is not only beneficial in promoting mass transportation mechanisms, but also in improving the surface characteristics by offering new interacting surface areas. Therefore, it is possible to increase the performance of microfluidic systems involving multiphase flows via modifying the surface. In this study, we aim to enhance generation and intensification of cavitating flows inside microfluidic devices by developing artificial roughness elements and trapping hydrophobic fluorinated lubricants. For this, we employed different microfluidic devices with various hydraulic diameters, while roughness structures with different lengths were formed on the side walls of microchannel configurations. The surface roughness of these devices was developed by assembling various sizes of silica nanoparticles using the layer-by-layer technique (D2). In addition, to compare the cavitating flow intensity with regular devices having plain surfaces (D1), highly fluorinated oil was trapped within the pores of the existing thin films in the configuration D2 via providing the Slippery Liquid-Infused Porous Surface (D3). The microfluidic devices housing the short microchannel and the extended channel were exposed to upstream pressures varying from 1 to 7.23 MPa. Cavitation inception and supercavitation condition occured at much lower upstream pressures for the configurations of D2 and D3. Interestingly, hydraulic flip, which rarely appears in the conventional conical nozzles at high pressures, was observed at moderate upstream pressures for the configuration D2 proving the air passage existence along one side of the channel wall.

  • 2.
    Ahmadi, Khadijeh
    et al.
    Shahid Beheshti Univ, Dept Phys, Tehran 19839, Iran.;Univ Tehran, Coll Engn, Adv Magnet Mat Res Ctr, Sch Met & Mat, Tehran 111554563, Iran..
    Mahfouzi, Farzad
    Calif State Univ Northridge, Dept Phys & Astron, Northridge, CA 91330 USA..
    Jamilpanah, Loghman
    Shahid Beheshti Univ, Dept Phys, Tehran 19839, Iran..
    Mohseni, Morteza
    Tech Univ Kaiserslautern, Fachbereich Phys & Landesforschungszentrum OPTIMA, D-67663 Kaiserslautern, Germany..
    Boettcher, Tobias
    Tech Univ Kaiserslautern, Fachbereich Phys & Landesforschungszentrum OPTIMA, D-67663 Kaiserslautern, Germany..
    Pirro, Philipp
    Tech Univ Kaiserslautern, Fachbereich Phys & Landesforschungszentrum OPTIMA, D-67663 Kaiserslautern, Germany..
    Kioussis, Nicholas
    Calif State Univ Northridge, Dept Phys & Astron, Northridge, CA 91330 USA..
    Åkerman, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. ;Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Ebrahimi, S. A. Seyyed
    Univ Tehran, Coll Engn, Adv Magnet Mat Res Ctr, Sch Met & Mat, Tehran 111554563, Iran..
    Mohseni, Seyed Majid
    Shahid Beheshti Univ, Dept Phys, Tehran 19839, Iran..
    Inducing Dzyaloshinskii-Moriya interaction in symmetrical multilayers using post annealing2022In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 11877Article in journal (Refereed)
    Abstract [en]

    The interfacial Dzyaloshinskii-Moriya Interaction (iDMI) is an antisymmetric exchange interaction that is induced by the broken inversion symmetry at the interface of, e.g., a ferromagnet/heavy metal. Thus, the presence of iDMI is not expected in symmetrical multilayer stacks of such structures. Here, we use thermal annealing to induce the iDMI in a [Py/Pt](x10) symmetrical multilayer stack. Brillouin light scattering spectroscopy is used to directly evidence the iDMI induction in the annealed sample. Structural characterizations highlight the modified crystallinity as well as a higher surface roughness of the sample after annealing. First principles electronic structure calculations demonstrate a monotonic increase of the iDMI with the interfacial disorder due to the interdiffusion of atoms, depicting the possible origin of the induced iDMI. The presented method can be used to tune the iDMI strength in symmetric multilayers, which are the integral part of racetrack memories, magnonic devices as well as spin-orbitronic elements.

  • 3.
    Alam, Mohammad Ayaz
    et al.
    Univ Santiago De Chile, Fac Ingn, Dept Ingn Geoespacial & Ambiental, Enr Kirberg Baltiansky n 03, Estn Cent, Santiago, Metropolitana, Chile..
    Mukherjee, Abhijit
    Indian Inst Technol Kharagpur, Dept Geol & Geophys, Kharagpur, W Bengal, India..
    Bhattacharya, Prosun
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Water and Environmental Engineering.
    Bundschuh, Jochen
    Univ Southern Queensland, Fac Hlth Engn & Sci, Sch Engn, West St, Toowoomba, Qld, Australia..
    An appraisal of the principal concerns and controlling factors for Arsenic contamination in Chile2023In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1Article in journal (Refereed)
    Abstract [en]

    Although geogenic Arsenic (As) contamination is well-recognized in northern Chile, it is not restricted to this part of the country, as the geological conditions favoring As release to the human environment exist across the country as well, although not at the same level, based on comparatively fewer studies in central and southern Chile. The present work provides a critical evaluation of As sources, pathways, and controls with reports and case studies from across the country based on an exhaustive bibliographic review of its reported geogenic sources and processes that affect its occurrence, systematization, and critical revision of this information. Arc magmatism and associated geothermal activities, identified as the primary As sources, are present across the Chilean Andes, except for the Pampean Flat Slab and Patagonian Volcanic Gap. Metal sulfide ore zones, extending from the country's far north to the south-central part, are the second most important geogenic As source. While natural leaching of As-rich mineral deposits contaminates the water in contact, associated mining, and metallurgical activities result in additional As release into the human environment through mining waste and tailings. Moreover, crustal thickness has been suggested as a principal controlling factor for As release, whose southward decrease has been correlated with lower As values.

  • 4.
    Albertsson, Dagur Ingi
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Electronics and Embedded systems.
    Rusu, Ana
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Electronics and Embedded systems.
    Highly reconfigurable oscillator-based Ising Machine through quasiperiodic modulation of coupling strength2023In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1, article id 4005Article in journal (Refereed)
    Abstract [en]

    Ising Machines (IMs) have the potential to outperform conventional Von-Neuman architectures in notoriously difficult optimization problems. Various IM implementations have been proposed based on quantum, optical, digital and analog CMOS, as well as emerging technologies. Networks of coupled electronic oscillators have recently been shown to exhibit characteristics required for implementing IMs. However, for this approach to successfully solve complex optimization problems, a highly reconfigurable implementation is needed. In this work, the possibility of implementing highly reconfigurable oscillator-based IMs is explored. An implementation based on quasiperiodically modulated coupling strength through a common medium is proposed and its potential is demonstrated through numerical simulations. Moreover, a proof-of-concept implementation based on CMOS coupled ring oscillators is proposed and its functionality is demonstrated. Simulation results show that our proposed architecture can consistently find the Max-Cut solution and demonstrate the potential to greatly simplify the physical implementation of highly reconfigurable oscillator-based IMs.

  • 5.
    Albertsson, Ingrid
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Svante Arrhenius Vag 16C, SE-10691 Stockholm, Sweden..
    Sjöholm, Johannes
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    ter Beek, Josy
    Stockholm Univ, Dept Biochem & Biophys, Svante Arrhenius Vag 16C, SE-10691 Stockholm, Sweden.;Umea Univ, Dept Med Biochem & Biophys, SE-90187 Umea, Sweden..
    Watmough, Nicholas J.
    Univ East Anglia, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England..
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Adelroth, Pia
    Stockholm Univ, Dept Biochem & Biophys, Svante Arrhenius Vag 16C, SE-10691 Stockholm, Sweden..
    Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 17234Article in journal (Refereed)
    Abstract [en]

    Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd(1) nitrite reductase (cd(1)NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd(1)NiR, presumably because cd(1)NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd(1)NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd(1)NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd(1)NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.

  • 6.
    Alibakhshikenari, Mohammad
    et al.
    Univ Carlos III Madrid, Dept Signal Theory & Commun, Madrid 28911, Spain..
    Virdee, Bal S.
    London Metropolitan Univ, Ctr Commun Technol, Sch Comp & Digital Media, London N7 8DB, England..
    Benetatos, Harry
    London Metropolitan Univ, Ctr Commun Technol, Sch Comp & Digital Media, London N7 8DB, England..
    Ali, Esraa Mousa
    Amman Arab Univ, Fac Aviat Sci, Amman 11953, Jordan..
    Soruri, Mohammad
    Univ Birjand, Tech Fac Ferdows, Birjand 9717434765, Iran..
    Dalarsson, Mariana
    KTH, School of Electrical Engineering and Computer Science (EECS), Electrical Engineering, Electromagnetic Engineering.
    Naser-Moghadasi, Mohammad
    Islamic Azad Univ, Dept Elect & Comp Engn, Sci & Res Branch, Tehran 1477893855, Iran..
    See, Chan Hwang
    Edinburgh Napier Univ, Sch Engn & Built Environm, 10 Colinton Rd, Edinburgh EH10 5DT, Midlothian, Scotland..
    Pietrenko-Dabrowska, Anna
    Gdansk Univ Technol, Fac Elect Telecommun & Informat, PL-80233 Gdansk, Poland..
    Koziel, Slawomir
    Gdansk Univ Technol, Fac Elect Telecommun & Informat, PL-80233 Gdansk, Poland.;Reykjavik Univ, Engn Optimizat & Modeling Ctr, IS-101 Reykjavik, Iceland..
    Szczepanski, Stanislaw
    Gdansk Univ Technol, Fac Elect Telecommun & Informat, PL-80233 Gdansk, Poland..
    Limiti, Ernesto
    Univ Roma Tor Vergata, Elect Engn Dept, Via Politecn 1, I-00133 Rome, Italy..
    An innovative antenna array with high inter element isolation for sub-6 GHz 5G MIMO communication systems2022In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 7907Article in journal (Refereed)
    Abstract [en]

    A novel technique is shown to improve the isolation between radiators in antenna arrays. The proposed technique suppresses the surface-wave propagation and reduces substrate loss thereby enhancing the overall performance of the array. This is achieved without affecting the antenna's footprint. The proposed approach is demonstrated on a four-element array for 5G MIMO applications. Each radiating element in the array is constituted from a 3 x 3 matrix of interconnected resonant elements. The technique involves (1) incorporating matching stubs within the resonant elements, (2) framing each of the four-radiating elements inside a dot-wall, and (3) defecting the ground plane with dielectric slots that are aligned under the dot-walls. Results show that with the proposed approach the impedance bandwidth of the array is increased by 58.82% and the improvement in the average isolation between antennas #1&2, #1&3, #1&4 are 8 dB, 14 dB, 16 dB, and 13 dB, respectively. Moreover, improvement in the antenna gain is 4.2% and the total radiation efficiency is 23.53%. These results confirm the efficacy of the technique. The agreement between the simulated and measured results is excellent. Furthermore, the manufacture of the antenna array using the proposed approach is relatively straightforward and cost effective.

  • 7.
    Alinejadian, Navid
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science. Department of Mechanical and Industrial Engineering, Tallinn University of Technology, Tallinn, 19086, Estonia.
    Kazemi, Sayed Habib
    Inst Adv Studies Basic Sci, Dept Chem, Zanjan 4513766731, Iran..
    Odnevall Wallinder, Inger
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Surface and Corrosion Science. AIMES-Center for the Advancement of Integrated Medical and Engineering Sciences; Department of Neuroscience, Karolinska Institutet, Stockholm, 171 77, Sweden.
    SLM-processed MoS2/Mo2S3 nanocomposite for energy conversion/storage applications2022In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 5030Article in journal (Refereed)
    Abstract [en]

    MoS2-based nanocomposites have been widely processed by a variety of conventional and 3D printing techniques. In this study, selective laser melting (SLM) has for the first time successfully been employed to tune the crystallographic structure of bulk MoS2 to a 2H/1T phase and to distribute Mo2S3 nanoparticles in-situ in MoS2/Mo2S3 nanocomposites used in electrochemical energy conversion/storage systems (EECSS). The remarkable results promote further research on and elucidate the applicability of laser-based powder bed processing of 2D nanomaterials for a wide range of functional structures within, e.g., EECSS, aerospace, and possibly high-temperature solid-state EECSS even in space.

  • 8. 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, 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.

  • 9.
    Amorebieta, Josu
    et al.
    Univ Basque Country, UPV EHU, Dept Commun Engn, Bilbao 48013, Spain..
    Pereira, Joao
    RISE Res Inst Sweden, Fiber Opt, S-16440 Stockholm, Sweden..
    Durana, Gaizka
    Univ Basque Country, UPV EHU, Dept Commun Engn, Bilbao 48013, Spain..
    Franciscangelis, Carolina
    RISE Res Inst Sweden, Fiber Opt, S-16440 Stockholm, Sweden..
    Ortega-Gomez, Angel
    Univ Basque Country, UPV EHU, Dept Commun Engn, Bilbao 48013, Spain..
    Zubia, Joseba
    Univ Basque Country, UPV EHU, Dept Commun Engn, Bilbao 48013, Spain..
    Villatoro, Joel
    Univ Basque Country, UPV EHU, Dept Commun Engn, Bilbao 48013, Spain.;Basque Fdn Sci, Ikerbasque, Bilbao 48011, Spain..
    Margulis, Walter
    KTH, School of Engineering Sciences (SCI), Applied Physics, Laser Physics. RISE Res Inst Sweden, Fiber Opt, S-16440 Stockholm.
    Twin-core fiber sensor integrated in laser cavity2022In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 11797Article in journal (Refereed)
    Abstract [en]

    In this work, we report on a twin-core fiber sensor system that provides improved spectral efficiency, allows for multiplexing and gives low level of crosstalk. Pieces of the referred strongly coupled multicore fiber are used as sensors in a laser cavity incorporating a pulsed semiconductor optical amplifier (SOA). Each sensor has its unique cavity length and can be addressed individually by electrically matching the periodic gating of the SOA to the sensor's cavity roundtrip time. The interrogator acts as a laser and provides a narrow spectrum with high signal-to-noise ratio. Furthermore, it allows distinguishing the response of individual sensors even in the case of overlapping spectra. Potentially, the number of interrogated sensors can be increased significantly, which is an appealing feature for multipoint sensing.

  • 10. Ananthaseshan, S.
    et al.
    Bojakowski, K.
    Sacharczuk, M.
    Poznanski, P.
    Skiba, D. S.
    Prahl Wittberg, Lisa
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics, Tillämpad strömningsmekanik.
    MacKenzie, Jordan
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Szkulmowska, A.
    Berg, Niclas
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics, Tillämpad strömningsmekanik.
    Andziak, P.
    Menkens, H.
    Wojtkowski, M.
    Religa, D.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Guzik, T.
    Gaciong, Z.
    Religa, P.
    Red blood cell distribution width is associated with increased interactions of blood cells with vascular wall2022In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 13676Article in journal (Refereed)
    Abstract [en]

    The mechanism underlying the association between elevated red cell distribution width (RDW) and poor prognosis in variety of diseases is unknown although many researchers consider RDW a marker of inflammation. We hypothesized that RDW directly affects intravascular hemodynamics, interactions between circulating cells and vessel wall, inducing local changes predisposing to atherothrombosis. We applied different human and animal models to verify our hypothesis. Carotid plaques harvested from patients with high RDW had increased expression of genes and proteins associated with accelerated atherosclerosis as compared to subjects with low RDW. In microfluidic channels samples of blood from high RDW subjects showed flow pattern facilitating direct interaction with vessel wall. Flow pattern was also dependent on RDW value in mouse carotid arteries analyzed with Magnetic Resonance Imaging. In different mouse models of elevated RDW accelerated development of atherosclerotic lesions in aortas was observed. Therefore, comprehensive biological, fluid physics and optics studies showed that variation of red blood cells size measured by RDW results in increased interactions between vascular wall and circulating morphotic elements which contribute to vascular pathology.

  • 11.
    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, 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.

  • 12.
    Andreozzi, Emilio
    et al.
    Univ Naples Federico II, Dept Elect Engn & Informat Technol DIETI, Naples, Italy.;Ist Clin Sci Maugeri IRCCS, Dept Bioengn, Telese Terme Inst, Telese Terme, BN, Italy..
    Carannante, Ilaria
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    D'Addio, Giovanni
    Ist Clin Sci Maugeri IRCCS, Dept Bioengn, Telese Terme Inst, Telese Terme, BN, Italy..
    Cesarelli, Mario
    Univ Naples Federico II, Dept Elect Engn & Informat Technol DIETI, Naples, Italy.;Ist Clin Sci Maugeri IRCCS, Dept Bioengn, Telese Terme Inst, Telese Terme, BN, Italy..
    Balbi, Pietro
    Ist Clin Sci Maugeri IRCCS, Lab Computat Neurophysiol, Telese Terme Inst, Telese Terme, BN, Italy..
    Phenomenological models of Na(V)1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 17493Article in journal (Refereed)
    Abstract [en]

    Computational models of ion channels represent the building blocks of conductance-based, biologically inspired models of neurons and neural networks. Ion channels are still widely modelled by means of the formalism developed by the seminal work of Hodgkin and Huxley (HH), although the electrophysiological features of the channels are currently known to be better fitted by means of kinetic Markov-type models. The present study is aimed at showing why simplified Markov-type kinetic models are more suitable for ion channels modelling as compared to HH ones, and how a manual optimization process can be rationally carried out for both. Previously published experimental data of an illustrative ion channel (Na(V)1.5) are exploited to develop a step by step optimization of the two models in close comparison. A conflicting practical limitation is recognized for the HH model, which only supplies one parameter to model two distinct electrophysiological behaviours. In addition, a step by step procedure is provided to correctly optimize the kinetic Markov-type model. Simplified Markov-type kinetic models are currently the best option to closely approximate the known complexity of the macroscopic currents of ion channels. Their optimization can be achieved through a rationally guided procedure, and allows to obtain models with a computational burden that is comparable with HH models one.

  • 13. 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, 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.

  • 14.
    Armgarth, Astrid
    et al.
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden.;RISE Res Inst Sweden AB, Printed Elect, S-60221 Norrköping, Sweden..
    Pantzare, Sandra
    RISE Res Inst Sweden AB, Printed Elect, S-60221 Norrköping, Sweden..
    Arven, Patrik
    J2 Holding AB, Elect Engn, S-59533 Mjolby, Sweden..
    Lassnig, Roman
    RISE Res Inst Sweden AB, Printed Elect, S-60221 Norrköping, Sweden..
    Jinno, Hiroaki
    RIKEN, Ctr Emergent Matter Sci, 2-1 Hirosawa, Wako, Saitama 3510198, Japan.;Univ Tokyo, Elect & Elect Engn & Informat Syst, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan..
    Gabrielsson, Erik O.
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden..
    Kifle, Yonatan
    Linköping Univ, Dept Elect Engn, S-58183 Linköping, Sweden..
    Cherian, Dennis
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden..
    Sjostrom, Theresia Arbring
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden..
    Berthou, Gautier
    Res Inst Sweden AB, RISE SICS, Kista, Sweden..
    Dowling, Jim
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Software and Computer systems, SCS.
    Someya, Takao
    RIKEN, Ctr Emergent Matter Sci, 2-1 Hirosawa, Wako, Saitama 3510198, Japan.;Univ Tokyo, Elect & Elect Engn & Informat Syst, Bunkyo Ku, 7-3-1 Hongo, Tokyo 1138656, Japan..
    Wikner, J. Jacob
    Linköping Univ, Dept Elect Engn, S-58183 Linköping, Sweden..
    Gustafsson, Goran
    RISE Res Inst Sweden AB, Printed Elect, S-60221 Norrköping, Sweden..
    Simon, Daniel T.
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden..
    Berggren, Magnus
    Linköping Univ, Dept Sci & Technol, Lab Organ Elect, S-60174 Norrköping, Sweden..
    A digital nervous system aiming toward personalized IoT healthcare2021In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 1, article id 7757Article in journal (Refereed)
    Abstract [en]

    Body area networks (BANs), cloud computing, and machine learning are platforms that can potentially enable advanced healthcare outside the hospital. By applying distributed sensors and drug delivery devices on/in our body and connecting to such communication and decision-making technology, a system for remote diagnostics and therapy is achieved with additional autoregulation capabilities. Challenges with such autarchic on-body healthcare schemes relate to integrity and safety, and interfacing and transduction of electronic signals into biochemical signals, and vice versa. Here, we report a BAN, comprising flexible on-body organic bioelectronic sensors and actuators utilizing two parallel pathways for communication and decision-making. Data, recorded from strain sensors detecting body motion, are both securely transferred to the cloud for machine learning and improved decision-making, and sent through the body using a secure body-coupled communication protocol to auto-actuate delivery of neurotransmitters, all within seconds. We conclude that both highly stable and accurate sensing-from multiple sensors-are needed to enable robust decision making and limit the frequency of retraining. The holistic platform resembles the self-regulatory properties of the nervous system, i.e., the ability to sense, communicate, decide, and react accordingly, thus operating as a digital nervous system.

  • 15. 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, 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.

  • 16. 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, E-ISSN 2045-2322, Vol. 7, no 1, 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.

  • 17.
    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, 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.

  • 18.
    Ban, Yifang
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Urban Planning and Environment, Geoinformatics.
    Zhang, Puzhao
    KTH, School of Architecture and the Built Environment (ABE), Urban Planning and Environment, Geoinformatics.
    Nascetti, Andrea
    KTH, School of Architecture and the Built Environment (ABE), Urban Planning and Environment, Geoinformatics.
    Bevington, A. R.
    Wulder, M. A.
    Near Real-Time Wildfire Progression Monitoring with Sentinel-1 SAR Time Series and Deep Learning2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 1322Article in journal (Refereed)
    Abstract [en]

    In recent years, the world witnessed many devastating wildfires that resulted in destructive human and environmental impacts across the globe. Emergency response and rapid response for mitigation calls for effective approaches for near real-time wildfire monitoring. Capable of penetrating clouds and smoke, and imaging day and night, Synthetic Aperture Radar (SAR) can play a critical role in wildfire monitoring. In this communication, we investigated and demonstrated the potential of Sentinel-1 SAR time series with a deep learning framework for near real-time wildfire progression monitoring. The deep learning framework, based on a Convolutional Neural Network (CNN), is developed to detect burnt areas automatically using every new SAR image acquired during the wildfires and by exploiting all available pre-fire SAR time series to characterize the temporal backscatter variations. The results show that Sentinel-1 SAR backscatter can detect wildfires and capture their temporal progression as demonstrated for three large and impactful wildfires: the 2017 Elephant Hill Fire in British Columbia, Canada, the 2018 Camp Fire in California, USA, and the 2019 Chuckegg Creek Fire in northern Alberta, Canada. Compared to the traditional log-ratio operator, CNN-based deep learning framework can better distinguish burnt areas with higher accuracy. These findings demonstrate that spaceborne SAR time series with deep learning can play a significant role for near real-time wildfire monitoring when the data becomes available at daily and hourly intervals with the launches of RADARSAT Constellation Missions in 2019, and SAR CubeSat constellations.

  • 19.
    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, 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.

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  • 20.
    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, 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.

  • 21.
    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, 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.

  • 22. 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, 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.

  • 23. 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, 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.

  • 24.
    Bhuyan, Prabal Dev
    et al.
    St Xaviers Coll, Dept Phys & Elect, Computat Mat & Nanosci Grp, Ahmadabad 380009, Gujarat, India.;Gujarat Univ, Univ Sch Sci, Dept Phys, Ahmadabad 380009, Gujarat, India..
    Gupta, Sanjeev K.
    St Xaviers Coll, Dept Phys & Elect, Computat Mat & Nanosci Grp, Ahmadabad 380009, Gujarat, India..
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Properties. Uppsala Univ, Dept Phys & Astron, Condensed Matter Theory Grp, S-75120 Uppsala, Sweden..
    Gajjar, P. N.
    Gujarat Univ, Univ Sch Sci, Dept Phys, Ahmadabad 380009, Gujarat, India..
    Metallic one-dimensional heterostructure for gas molecule sensing2021In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 1, article id 433Article in journal (Refereed)
    Abstract [en]

    We have investigated a new metallic core-shell nanowire (NW) geometry of that could be obtained experimentally, that is silicon (Si) and germanium (Ge) NWs with cores constituted by group-10 elements palladium (Pd) and platinum (Pt). These NWs are optimized with two different diameters of 1.5 angstrom and 2.5 angstrom. The nanowires having diameter of 1.5 angstrom show semi-metallic nature with GGA-PBE calculation and metallic nature while spin orbit interaction (SOC) is included. The quantum conductance of the NWs increases with the diameter of the nanowire. We have investigated current-voltage (IV) characteristics for the considered NWs. It has been found that current values in accordance with applied voltage show strong dependence on the diameter of the NWs. The optical study of the NWs shows that absorption co-efficient peak moves to lower energies; due to quantum confinement effect. Furthermore, we have extensively studied optical response of Pd and Pt based core-shell NWs in O-2 and CO2 environment. Our study on Si and Ge based metallic core/shell NW show a comprehensive picture as possible electron connector in future nano-electronic devices as well as nano gas detector for detecting O-2 gas.

  • 25.
    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, 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.

  • 26.
    Blystad, I
    et al.
    Linköping Univ, Dept Radiol Linköping, Linköping, Sweden.;Linköping Univ, Dept Hlth Med & Caring Sci, Linköping, Sweden.;Linköping Univ, Ctr Med Image Sci & Visualizat CMIV, Linköping, Sweden..
    Warntjes, J. B. M.
    Linköping Univ, Ctr Med Image Sci & Visualizat CMIV, Linköping, Sweden.;Linköping Univ, Div Cardiovasc Med, Dept Hlth Med & Caring Sci, Linköping, Sweden..
    Smedby, Örjan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Medical Imaging. Linköping Univ, Dept Radiol Linköping, Linköping, Sweden.;Linköping Univ, Dept Hlth Med & Caring Sci, Linköping, Sweden.;Linköping Univ, Ctr Med Image Sci & Visualizat CMIV, Linköping, Sweden..
    Lundberg, P.
    Linköping Univ, Dept Hlth Med & Caring Sci, Linköping, Sweden.;Linköping Univ, Ctr Med Image Sci & Visualizat CMIV, Linköping, Sweden.;Linköping Univ, Dept Radiat Phys, Linköping, Sweden..
    Larsson, E-M
    Linköping Univ, Ctr Med Image Sci & Visualizat CMIV, Linköping, Sweden.;Uppsala Univ, Dept Surg Sci, Radiol, Uppsala, Sweden..
    Tisell, A.
    Linköping Univ, Dept Hlth Med & Caring Sci, Linköping, Sweden.;Linköping Univ, Ctr Med Image Sci & Visualizat CMIV, Linköping, Sweden.;Linköping Univ, Dept Radiat Phys, Linköping, Sweden..
    Quantitative MRI using relaxometry in malignant gliomas detects contrast enhancement in peritumoral oedema2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 17986Article in journal (Refereed)
    Abstract [en]

    Malignant gliomas are primary brain tumours with an infiltrative growth pattern, often with contrast enhancement on magnetic resonance imaging (MRI). However, it is well known that tumour infiltration extends beyond the visible contrast enhancement. The aim of this study was to investigate if there is contrast enhancement not detected visually in the peritumoral oedema of malignant gliomas by using relaxometry with synthetic MRI. 25 patients who had brain tumours with a radiological appearance of malignant glioma were prospectively included. A quantitative MR-sequence measuring longitudinal relaxation (R-1), transverse relaxation (R-2) and proton density (PD), was added to the standard MRI protocol before surgery. Five patients were excluded, and in 20 patients, synthetic MR images were created from the quantitative scans. Manual regions of interest (ROIs) outlined the visibly contrast-enhancing border of the tumours and the peritumoral area. Contrast enhancement was quantified by subtraction of native images from post GD-images, creating an R-1-difference-map. The quantitative R-1-difference-maps showed significant contrast enhancement in the peritumoral area (0.047) compared to normal appearing white matter (0.032), p = 0.048. Relaxometry detects contrast enhancement in the peritumoral area of malignant gliomas. This could represent infiltrative tumour growth.

  • 27. 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, 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.

  • 28.
    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, 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.

  • 29.
    Bovornratanaraks, Thiti
    et al.
    Chulalongkorn Univ, Fac Sci, Dept Phys, ECPRL, Bangkok 10330, Thailand.;Chulalongkorn Univ, Fac Sci, Dept Phys, PEMRU, Bangkok 10330, Thailand.;Commiss Higher Educ, Thailand Ctr Excellence Phys, 328 Si Ayutthaya Rd, Bangkok 10400, Thailand..
    Tsuppayakorn-aek, Prutthipong
    Chulalongkorn Univ, Fac Sci, Dept Phys, ECPRL, Bangkok 10330, Thailand.;Chulalongkorn Univ, Fac Sci, Dept Phys, PEMRU, Bangkok 10330, Thailand.;Commiss Higher Educ, Thailand Ctr Excellence Phys, 328 Si Ayutthaya Rd, Bangkok 10400, Thailand..
    Luo, Wei
    Uppsala Univ, Dept Phys & Astron, Condensed Matter Theory Grp, Box 516, S-75120 Uppsala, Sweden..
    Ahuja, Rajeev
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Ground-state structure of semiconducting and superconducting phases in xenon carbides at high pressure2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 2459Article in journal (Refereed)
    Abstract [en]

    The 'missing Xe paradox' is one of the phenomena at the Earth's atmosphere. Studying the 'missing Xe paradox' will provide insights into a chemical reaction of Xe with C. We search the ground-state structure candidates of xenon carbides using the Universal Structure Predictor: Evolutionary Xtallography (USPEX) code, which has been successfully applied to a variety of systems. We predict that XeC2 is the most stable among the convex hull. We find that the I((4) over bar)2m structure of XeC2 is the semiconducting phase. Accurate electronic structures of tetragonal XeC2 have been calculated using a hybrid density functionals HSE06, which gives larger more accurate band gap than a GGA-PBE exchange-correlation functional. Specifically, we find that the I((4) over bar)2m structure of XeC2 is a dynamically stable structure at high pressure. We also predict that the P6/mmm structure of XeC2 is the superconducting phase with a critical temperature of 38 K at 200 GPa. The ground-state structure of xenon carbides is of critical importance for understanding in the missing Xe. We discuss the inference of the stable structures of XeC2. The accumulation of electrons between Xe and C led to the stability by investigating electron localization function (ELF).

  • 30.
    Braganca, F. M. Serra
    et al.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Broomé, Michael
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Robotics, Perception and Learning, RPL.
    Rhodin, M.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Bjornsdottir, S.
    Agr Univ Iceland, Hvanneyri, Borgarnes, Iceland..
    Gunnarsson, V
    Holar Univ Coll, Dept Equine Sci, Holar, Iceland..
    Voskamp, J. P.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Persson-Sjödin, E.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Back, W.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands.;Univ Ghent, Fac Vet Med, Dept Surg & Anaesthesiol Domest Anim, B-9820 Merelbeke, Belgium..
    Lindgren, G.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium..
    Novoa-Bravo, M.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Genet Anim Colombia Ltda, Bogota, Colombia..
    Roepstorff, C.
    Univ Zurich, Vetsuisse Fac, Equine Dept, Winterthurerstr 260, CH-8057 Zurich, Switzerland..
    van der Zwaag, B. J.
    Inertia Technol BV, Enschede, Netherlands..
    Van Weeren, P. R.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Hernlund, E.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Improving gait classification in horses by using inertial measurement unit (IMU) generated data and machine learning2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 17785Article in journal (Refereed)
    Abstract [en]

    For centuries humans have been fascinated by the natural beauty of horses in motion and their different gaits. Gait classification (GC) is commonly performed through visual assessment and reliable, automated methods for real-time objective GC in horses are warranted. In this study, we used a full body network of wireless, high sampling-rate sensors combined with machine learning to fully automatically classify gait. Using data from 120 horses of four different domestic breeds, equipped with seven motion sensors, we included 7576 strides from eight different gaits. GC was trained using several machine-learning approaches, both from feature-extracted data and from raw sensor data. Our best GC model achieved 97% accuracy. Our technique facilitated accurate, GC that enables in-depth biomechanical studies and allows for highly accurate phenotyping of gait for genetic research and breeding. Our approach lends itself for potential use in other quadrupedal species without the need for developing gait/animal specific algorithms.

  • 31.
    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..
    Sjöberg, Ronald
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Affinity Proteomics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    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, 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.

  • 32.
    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, 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.

  • 33. 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, 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.

  • 34.
    Carlberg, Konstantin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Korotkova, Marina
    Karolinska Inst, Karolinska Univ Hosp, Dept Med Solna, Div Rheumatol, Stockholm, Sweden..
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Catrina, Anca, I
    Karolinska Inst, Karolinska Univ Hosp, Dept Med Solna, Div Rheumatol, Stockholm, Sweden..
    Ståhl, Patrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. Royal Inst Technol, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden..
    Malmström, Vivianne
    Karolinska Inst, Karolinska Univ Hosp, Dept Med Solna, Div Rheumatol, Stockholm, Sweden..
    Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 18975Article in journal (Refereed)
    Abstract [en]

    Lately it has become possible to analyze transcriptomic profiles in tissue sections with retained cellular context. We aimed to explore synovial biopsies from rheumatoid arthritis (RA) and spondyloarthritis (SpA) patients, using Spatial Transcriptomics (ST) as a proof of principle approach for unbiased mRNA studies at the site of inflammation in these chronic inflammatory diseases. Synovial tissue biopsies from affected joints were studied with ST. The transcriptome data was subjected to differential gene expression analysis (DEA), pathway analysis, immune cell type identification using Xcell analysis and validation with immunohistochemistry (IHC). The ST technology allows selective analyses on areas of interest, thus we analyzed morphologically distinct areas of mononuclear cell infiltrates. The top differentially expressed genes revealed an adaptive immune response profile and T-B cell interactions in RA, while in SpA, the profiles implicate functions associated with tissue repair. With spatially resolved gene expression data, overlaid on high-resolution histological images, we digitally portrayed pre-selected cell types in silico. The RA displayed an overrepresentation of central memory T cells, while in SpA effector memory T cells were most prominent. Consequently, ST allows for deeper understanding of cellular mechanisms and diversity in tissues from chronic inflammatory diseases.

  • 35. 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, 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.

  • 36.
    Cavalli, Marco
    et al.
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Baltzer, Nicholas
    Uppsala Univ, Dept Cell & Mol Biol Computat Biol & Bioinformat, Uppsala, Sweden..
    Umer, Husen M.
    Uppsala Univ, Dept Cell & Mol Biol Computat Biol & Bioinformat, Uppsala, Sweden..
    Grau, Jan
    Martin Luther Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany..
    Lemnian, Ioana
    Martin Luther Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany..
    Pan, Gang
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Wallerman, Ola
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Spalinskas, Rapolas
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Sahlén, Pelin
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Grosse, Ivo
    Martin Luther Univ Halle Wittenberg, Inst Comp Sci, Halle, Germany.;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany..
    Komorowski, Jan
    Uppsala Univ, Dept Cell & Mol Biol Computat Biol & Bioinformat, Uppsala, Sweden.;Polish Acad Sci, Inst Comp Sci, Warsaw, Poland..
    Wadelius, Claes
    Uppsala Univ, Dept Immunol Genet & Pathol, Sci Life Lab, Uppsala, Sweden..
    Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 2695Article in journal (Refereed)
    Abstract [en]

    Several Genome Wide Association Studies (GWAS) have reported variants associated to immune diseases. However, the identified variants are rarely the drivers of the associations and the molecular mechanisms behind the genetic contributions remain poorly understood. ChIP-seq data for TFs and histone modifications provide snapshots of protein-DNA interactions allowing the identification of heterozygous SNPs showing significant allele specific signals (AS-SNPs). AS-SNPs can change a TF binding site resulting in altered gene regulation and are primary candidates to explain associations observed in GWAS and expression studies. We identified 17,293 unique AS-SNPs across 7 lymphoblastoid cell lines. In this set of cell lines we interrogated 85% of common genetic variants in the population for potential regulatory effect and we identified 237 AS-SNPs associated to immune GWAS traits and 714 to gene expression in B cells. To elucidate possible regulatory mechanisms we integrated long-range 3D interactions data to identify putative target genes and motif predictions to identify TFs whose binding may be affected by AS-SNPs yielding a collection of 173 AS-SNPs associated to gene expression and 60 to B cell related traits. We present a systems strategy to find functional gene regulatory variants, the TFs that bind differentially between alleles and novel strategies to detect the regulated genes.

  • 37. 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, 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.

  • 38.
    Chang, Weipang
    et al.
    Karolinska Inst, Neurosci Dept, S-17177 Stockholm, Sweden..
    Pedroni, Andrea
    Karolinska Inst, Neurosci Dept, S-17177 Stockholm, Sweden..
    Koster, Reinhard W.
    Tech Univ Braunschweig, Cellular & Mol Neurobiol Zool Inst, Brunswick, ME USA..
    Giacomello, Stefania
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Ampatzis, Konstantinos
    Karolinska Inst, Neurosci Dept, S-17177 Stockholm, Sweden..
    Purkinje cells located in the adult zebrafish valvula cerebelli exhibit variable functional responses2021In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 1, article id 18408Article in journal (Refereed)
    Abstract [en]

    Purkinje cells are critically involved in processing the cerebellar functions by shaping and coordinating commands that they receive. Here, we demonstrate experimentally that in the adult zebrafish valvular part of the cerebellum, the Purkinje cells exhibited variable firing and functional responses and allowed the categorization into three firing classes. Compared with the Purkinje cells in the corpus cerebelli, the valvular Purkinje cells receive weak and occasional input from the inferior olive and are not active during locomotion. Together, our findings expand further the regional functional differences of the Purkinje cell population and expose their non-locomotor functionality.

  • 39.
    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, Miranda
    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, Mózsi
    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, 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". 

  • 40.
    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, 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.

  • 41. 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, 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.

  • 42. 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, 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.

  • 43. 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, 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.

  • 44. 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, 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.

  • 45. 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, 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.

  • 46.
    Cheng, Zhaoyang
    et al.
    Key Laboratory of Systems and Control, Academy of Mathematics and Systems Science, Beijing, 100190, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
    Chen, Guanpu
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Decision and Control Systems (Automatic Control).
    Hong, Yiguang
    Department of Control Science and Engineering, Tongji University, Shanghai, 201804, China; Shanghai Research Institute for Intelligent Autonomous Systems, Tongji University, Shanghai, 210201, China.
    Zero-determinant strategy in stochastic Stackelberg asymmetric security game2023In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, no 1, article id 11308Article in journal (Refereed)
    Abstract [en]

    In a stochastic Stackelberg asymmetric security game, the strong Stackelberg equilibrium (SSE) strategy is a popular option for the defender to get the highest utility against an attacker with the best response (BR) strategy. However, the attacker may be a boundedly rational player, who adopts a combination of the BR strategy and a fixed stubborn one. In such a condition, the SSE strategy may not maintain the defensive performance due to the stubbornness. In this paper, we focus on how the defender can adopt the unilateral-control zero-determinate (ZD) strategy to confront the boundedly rational attacker. At first, we verify the existence of ZD strategies for the defender. We then investigate the performance of the defender’s ZD strategy against a boundedly rational attacker, with a comparison of the SSE strategy. Specifically, when the attacker’s strategy is close to the BR strategy, the ZD strategy admits a bounded loss for the defender compared with the SSE strategy. Conversely, when the attacker’s strategy is close to the stubborn strategy, the ZD strategy can bring higher defensive performance for the defender than the SSE strategy does.

  • 47. 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, 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.

  • 48.
    Chondrogiannis, Georgios
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Khaliliazar, Shirin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Toldrà Filella, Anna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Reu, Pedro
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Hamedi, Mahiar
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Fibre Technology.
    Nitrocellulose-bound achromopeptidase for point-of-care nucleic acid tests2021In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 1, article id 6140Article in journal (Refereed)
    Abstract [en]

    Enzymes are the cornerstone of modern biotechnology. Achromopeptidase (ACP) is a well-known enzyme that hydrolyzes a number of proteins, notably proteins on the surface of Gram-positive bacteria. It is therefore used for sample preparation in nucleic acid tests. However, ACP inhibits DNA amplification which makes its integration difficult. Heat is commonly used to inactivate ACP, but it can be challenging to integrate heating into point-of-care devices. Here, we use recombinase polymerase amplification (RPA) together with ACP, and show that when ACP is immobilized on nitrocellulose paper, it retains its enzymatic function and can easily and rapidly be activated using agitation. The nitrocellulose-bound ACP does, however, not leak into the solution, preventing the need for deactivation through heat or by other means. Nitrocellulose-bound ACP thus opens new possibilities for paper-based Point-of-Care (POC) devices.

  • 49.
    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, 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.

  • 50. 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, 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.

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