| 1. |
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| 2. |
- Fomalont, E. B., et al.
(författare)
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THE 2014 ALMA LONG BASELINE CAMPAIGN: AN OVERVIEW
- 2015
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 808:1
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Tidskriftsartikel (refereegranskat)abstract
- A major goal of the Atacama Large Millimeter/submillimeter Array (ALMA) is to make accurate images with resolutions of tens of milliarcseconds, which at submillimeter (submm) wavelengths requires baselines up to similar to 15 km. To develop and test this capability, a Long Baseline Campaign (LBC) was carried out from 2014 September to late November, culminating in end-to-end observations, calibrations, and imaging of selected Science Verification (SV) targets. This paper presents an overview of the campaign and its main results, including an investigation of the short-term coherence properties and systematic phase errors over the long baselines at the ALMA site, a summary of the SV targets and observations, and recommendations for science observing strategies at long baselines. Deep ALMA images of the quasar 3C 138 at 97 and 241 GHz are also compared to VLA 43 GHz results, demonstrating an agreement at a level of a few percent. As a result of the extensive program of LBC testing, the highly successful SV imaging at long baselines achieved angular resolutions as fine as 19 mas at similar to 350 GHz. Observing with ALMA on baselines of up to 15 km is now possible, and opens up new parameter space for submm astronomy.
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| 3. |
- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 4. |
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| 5. |
- Dell'Angela, M., et al.
(författare)
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Real-Time Observation of Surface Bond Breaking with an X-ray Laser
- 2013
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 339:6125, s. 1302-1305
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Tidskriftsartikel (refereegranskat)abstract
- We used the Linac Coherent Light Source free-electron x-ray laser to probe the electronic structure of CO molecules as their chemisorption state on Ru(0001) changes upon exciting the substrate by using a femtosecond optical laser pulse. We observed electronic structure changes that are consistent with a weakening of the CO interaction with the substrate but without notable desorption. A large fraction of the molecules (30%) was trapped in a transient precursor state that would precede desorption. We calculated the free energy of the molecule as a function of the desorption reaction coordinate using density functional theory, including van der Waals interactions. Two distinct adsorption wells-chemisorbed and precursor state separated by an entropy barrier-explain the anomalously high prefactors often observed in desorption of molecules from metals.
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| 6. |
- Xin, H., et al.
(författare)
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Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and Ab Initio Simulations
- 2015
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 114:15
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Tidskriftsartikel (refereegranskat)abstract
- We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5 sigma and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.
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| 7. |
- Öberg, Henrik, et al.
(författare)
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Optical laser-induced CO desorption from Ru(0001) monitored with a free-electron X-ray laser : DFT prediction and X-ray confirmation of a precursor state
- 2015
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Ingår i: Surface Science. - : Elsevier BV. - 0039-6028 .- 1879-2758. ; 640, s. 80-88
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Tidskriftsartikel (refereegranskat)abstract
- We present density functional theory modeling of time-resolved optical pump/X-ray spectroscopic probe data of CO desorption from Ru(0001). The BEEF van der Waals functional predicts a weakly bound state as a precursor to desorption. The optical pump leads to a near-instantaneous (<100 fs) increase of the electronic temperature to nearly 7000 K. The temperature evolution and energy transfer between electrons, substrate phonons and adsorbate is described by the two-temperature model and found to equilibrate on a timescale of a few picoseconds to an elevated local temperature of similar to 2000K. Estimating the free energy based on the computed potential of mean force along the desorption path, we find an entropic barrier to desorption (and by time-reversal also to adsorption). This entropic barrier separates the chemisorbed and precursor states, and becomes significant at the elevated temperature of the experiment (similar to 1.4 eV at 2000 K). Experimental pump-probe X-ray absorption/X-ray emission spectroscopy indicates population of a precursor state to desorption upon laser-excitation of the system (Dell'Angela et al., 2013). Computing spectra along the desorption path confirms the picture of a weakly bound transient state arising from ultrafast heating of the metal substrate.
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| 8. |
- Östrom, Henrik, et al.
(författare)
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Probing the transition state region in catalytic CO oxidation on Ru
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 347:6225, s. 978-982
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Tidskriftsartikel (refereegranskat)abstract
- Femtosecond x-ray laser pulses are used to probe the carbon monoxide (CO) oxidation reaction on ruthenium (Ru) initiated by an optical laser pulse. On a time scale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and oxygen (O) on the surface, allowing the reactants to collide, and, with a transient close to a picosecond (ps), new electronic states appear in the OK-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond formation between CO and O with a distribution of OC-O bond lengths close to the transition state (TS). After 1 ps, 10% of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.
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| 9. |
- Beye, M., et al.
(författare)
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Selective Ultrafast Probing of Transient Hot Chemisorbed and Precursor States of CO on Ru(0001)
- 2013
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 110:18
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process.
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| 10. |
- Madanian, H., et al.
(författare)
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The Dynamics of a High Mach Number Quasi-perpendicular Shock : MMS Observations
- 2021
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 908:1
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Tidskriftsartikel (refereegranskat)abstract
- Shock parameters at Earth's bow shock in rare instances can approach the Mach numbers predicted at supernova remnants. We present our analysis of a high Alfven Mach number (M-A = 27) shock utilizing multipoint measurements from the Magnetospheric Multiscale spacecraft during a crossing of Earth's quasi-perpendicular bow shock. We find that the shock dynamics are mostly driven by reflected ions, perturbations that they generate, and nonlinear amplification of the perturbations. Our analyses show that reflected ions create modest magnetic enhancements upstream of the shock, which evolve in a nonlinear manner as they traverse the shock foot. They can transform into proto-shocks that propagate at small angles to the magnetic field and toward the bow shock. The nonstationary bow shock shows signatures of both reformation and surface ripples. Our observations indicate that although shock reformation occurs, the main shock layer never disappears. These observations are at high plasma beta, a parameter regime that has not been well explored by numerical models.
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| 11. |
- Dell'Angela, M., et al.
(författare)
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Vacuum space charge effects in sub-picosecond soft X-ray photoemission on a molecular adsorbate layer
- 2015
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:2
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Tidskriftsartikel (refereegranskat)abstract
- Vacuum space charge induced kinetic energy shifts of O 1s and Ru 3d core levels in femtosecond soft X-ray photoemission spectra (PES) have been studied at a free electron laser (FEL) for an oxygen layer on Ru(0001). We fully reproduced the measurements by simulating the in-vacuum expansion of the photoelectrons and demonstrate the space charge contribution of the high-order harmonics in the FEL beam. Employing the same analysis for 400 nm pump-X-ray probe PES, we can disentangle the delay dependent Ru 3d energy shifts into effects induced by space charge and by lattice heating from the femtosecond pump pulse.
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| 12. |
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| 13. |
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| 14. |
- Katayama, T., et al.
(författare)
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Ultrafast soft X-ray emission spectroscopy of surface adsorbates using an X-ray free electron laser
- 2013
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 187, s. 9-14
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Tidskriftsartikel (refereegranskat)abstract
- We report on an experimental system designed to probe chemical reactions on solid surfaces on a sub-picosecond timescale using soft X-ray emission spectroscopy at the Linac Coherent Light Source (LCLS) free electron laser (FEL) at the SLAC National Accelerator Laboratory. We analyzed the O 1s X-ray emission spectra recorded from atomic oxygen adsorbed on a Ru(0001) surface at a synchrotron beamline (SSRL, BL13-2) and an FEL beamline (LCLS, SXR). We have demonstrated conditions that provide negligible amount of FEL induced damage of the sample. In addition we show that the setup is capable of tracking the temporal evolution of electronic structure during a surface reaction of submonolayer quantities of CO molecules desorbing from the surface.
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| 15. |
- LaRue, Jerry, et al.
(författare)
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Real-Time Elucidation of Catalytic Pathways in CO Hydrogenation on Ru
- 2017
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8:16, s. 3820-3825
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Tidskriftsartikel (refereegranskat)abstract
- The direct elucidation of the reaction pathways in heterogeneous catalysis has been challenging due to the short-lived nature of reaction intermediates. Here, we directly measured on ultrafast time scales the initial hydrogenation steps of adsorbed CO on a Ru catalyst surface, which is known as the bottleneck reaction in syngas and CO2 reforming processes. We initiated the hydrogenation of CO with an ultrafast laser temperature jump and probed transient changes in the electronic structure using real-time X-ray spectroscopy. In combination with theoretical simulations, we verified the formation of CHO during CO hydrogenation.
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| 16. |
- Nilsson, Anders, et al.
(författare)
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Catalysis in real time using X-ray lasers
- 2017
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614 .- 1873-4448. ; 675, s. 145-173
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Tidskriftsartikel (refereegranskat)abstract
- We describe how the unique temporal and spectral characteristics of X-ray free-electron lasers (XFEL) can be utilized to follow chemical transformations in heterogeneous catalysis in real time. We highlight the systematic study of CO oxidation on Ru(0001), which we initiate either using a femtosecond pulse from an optical laser or by activating only the oxygen atoms using a THz pulse. We find that CO is promoted into an entropy-controlled precursor state prior to desorbing when the surface is heated in the absence of oxygen, whereas in the presence of oxygen, CO desorbs directly into the gas phase. We monitor the activation of atomic oxygen explicitly by the reduced split between bonding and antibonding orbitals as the oxygen comes out of the strongly bound hollow position. Applying these novel XFEL techniques to the full oxidation reaction resulted in the surprising observation of a significant fraction of the reactants at the transition state through the electronic signature of the new bond formation.
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| 17. |
- Nisson, D.M., et al.
(författare)
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Hydrogeochemical and isotopic signatures elucidate deep subsurface hypersaline brine formation through radiolysis driven water-rock interaction
- 2023
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier. - 0016-7037 .- 1872-9533. ; 340, s. 65-84
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Tidskriftsartikel (refereegranskat)abstract
- Geochemical and isotopic fluid signatures from a 2.9–3.2 km deep, 45–55 °C temperature, hypersaline brine from Moab Khotsong gold and uranium mine in the Witwatersrand Basin of South Africa were combined with radiolytic and water–rock isotopic exchange models to delineate brine evolution over geologic time, and to explore brine conditions for habitability. The Moab Khotsong brines were hypersaline (Ca-Na-Cl) with 215–246 g/L TDS, and Cl− concentrations up to 4 mol/L suggesting their position as a hypersaline end-member significantly more saline than any previously sampled Witwatersrand Basin fluids. The brines revealed low DIC (∼0.266–∼1.07 mmol/L) with high (∼8.49–∼23.6 mmol/L) DOC pools, and several reduced gaseous species (up to 46 % by volume H2) despite microoxic conditions (Eh = 135–161 mV). Alpha particle radiolysis of water to H2, H2O2, and O2 along with anhydrous-silicate-to-clay alteration reactions predicted 4 mol/L Cl− brine concentration and deuterium enrichment in the fracture waters over a period > 1.00 Ga, consistent with previously reported 40Ar noble gas-derived residence times of 1.20 Ga for this system. In addition, radiolytic production of 7–26 nmol/(L × yr) H2, 3–11 nmol/(L × yr) O2, and 1–8 nmol/(L × yr) H2O2 was predicted for 1–100 g/g 238U dosage scenarios, supporting radiolysis as a significant source of H2 and oxidant species to deep brines over time that are available to a low biomass system (102–103 cells/mL). The host rock lithology was predominately Archaean quartzite, with minerals exposed on fracture surfaces that included calcite, pyrite, and chlorite. Signatures of 18Ocalcite, 13Ccalcite, Δ33Spyrite, 34Spyrite and 87Sr/86Sr obtained from secondary ion mass spectrometry (SIMS) microanalyses suggest several discrete fluid events as the basin cooled from peak greenschist conditions to equilibrium with present-day brine temperatures. The brine physiochemistry, geochemistry, and cellular abundances were significantly different from those of a younger, shallower, low salinity dolomitic fluid in the same mine, and both were different from the mine service water. These results indicate the discovery of one of few long-isolated systems that supports subsurface brine formation via extended water–rock interaction, and an example of a subsurface brine system where abiotic geochemistry may support a low biomass microbial community.
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| 18. |
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| 19. |
- Schiros, Theanne, et al.
(författare)
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Unique water-water coordination tailored by a metal surface
- 2013
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 138:23, s. 234708-
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Tidskriftsartikel (refereegranskat)abstract
- At low coverage of water on Cu(110), substrate-mediated electrostatics lead to zigzagging chains along [001] as observed with STM [T. Yamada, S. Tamamori, H. Okuyama, and T. Aruga, Anisotropic water chain growth on Cu(110) observed with scanning tunneling microscopy Phys. Rev. Lett. 96, 036105 (2006)]. Using x-ray absorption spectroscopy we find an anomalous low-energy resonance at similar to 533.1 eV which, based on density functional theory spectrum simulations, we assign to an unexpected configuration of water units whose uncoordinated O-H bonds directly face those of their neighbors; this interaction repeats over trough sites with enhanced electron density and is analogous to the case of a hydrated electron.
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| 20. |
- Yamamoto, S., et al.
(författare)
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Water adsorption on α-Fe2O3 (0001) at near ambient conditions
- 2010
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:5, s. 2256-2266
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated hydroxylation and water adsorption on α Fe 2O3(0001) at water vapor pressures up to 2 Torr and temperatures ranging from 277 to 647 K (relative humidity (RH)
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| 21. |
- Abramson, JS, et al.
(författare)
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Lisocabtagene maraleucel as second-line therapy for large B-cell lymphoma: primary analysis of the phase 3 TRANSFORM study
- 2023
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Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 141:14, s. 1675-1684
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Tidskriftsartikel (refereegranskat)abstract
- This global, phase 3 study compared lisocabtagene maraleucel (liso-cel) with standard of care (SOC) as second-line therapy for primary refractory or early relapsed (≤12 months) large B-cell lymphoma (LBCL). Adults eligible for autologous stem cell transplantation (ASCT) were randomized 1:1 to liso-cel (100×106 CAR+ T cells) or SOC (3 cycles of platinum-based immunochemotherapy followed by high-dose chemotherapy and ASCT in responders). The primary end point was event-free survival (EFS) by independent review. A total of 184 patients were randomized. In this primary analysis with a median follow-up of 17.5 months, median EFS was not reached (NR) for liso-cel versus 2.4 months for SOC (hazard ratio [HR] = 0.356; 95% confidence interval [CI]: 0.243‒0.522). Complete response (CR) rate was 74% for liso-cel versus 43% for SOC (P < .0001) and median progression-free survival (PFS) was NR for liso-cel versus 6.2 months for SOC (HR = 0.400; 95% CI: 0.261‒0.615; P < .0001). Median overall survival was NR for liso-cel versus 29.9 months for SOC (HR = 0.724; 95% CI: 0.443‒1.183; P = .0987). When adjusted for crossover from SOC to liso-cel, median overall survival was NR for liso-cel and SOC (HR = 0.415; 95% CI: 0.251‒0.686). Grade 3 cytokine release syndrome and neurological events occurred in 1% and 4% of patients in the liso-cel arm, respectively (no grade 4/5 events). These data show significant improvements in EFS, CR rate, and PFS for liso-cel over SOC and support liso-cel as a preferred second-line treatment compared with SOC in patients with primary refractory or early relapsed LBCL. (ClinicalTrials.gov; NCT03575351.)
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| 22. |
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| 23. |
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| 24. |
- Andersson, Klas J., et al.
(författare)
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Preparation, Structure, and Orientation of Pyrite FeS2{100} Surfaces : Anisotropy, Sulfur Monomers, Dimer Vacancies, and a Possible FeS Surface Phase
- 2014
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:38, s. 21896-21903
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Tidskriftsartikel (refereegranskat)abstract
- Sulfur dimer (S-2(2-)) terminated pyrite FeS2{100} surfaces with a low energy electron diffraction (LEED) pattern of 2 x 1 symmetry are reported. The 2 X 1 symmetry correlates with the orientation of the anisotropic surface structure and external symmetry of macroscopic striations on the pyrite cube face. The basic condition to form these surfaces is a mild 200 V Ne+ sputter-cleaning procedure followed by a 570 K anneal of the sample in a 10(-7) Ton S-2(g) atmosphere. Controlled amounts of surface sulfur monomers (S2-) can be introduced by mild sputtering of the sulfur dimer terminated surfaces. At low monomer concentrations the surface displays the same characteristic 1 x 1 LEED pattern as that for fracture-generated surfaces. With increasing sulfur depletion, a (1/ root 2 x 1/ root 2)R45 degrees LEED pattern emerges, and soft X-ray photoelectron spectroscopy (XPS) results show a sulfur dinner deficient near-surface region and a new high binding energy sulfur spectral component suggesting the presence of local coordination environments where sulfur monomers are coordinated by four Fe ions compared to three as in the pyrite structure. The plausible formation of a defective FeS-like surface phase where monomeric sulfurs are coordinated by four Fe ions, and bond counting energetics favoring surface sulfur monomer recombination around Fe vacancy sites on pyrite FeS2{100}, both imply surface sulfur dimer vacancy sites with unique adsorption and reactivity properties. Taken together, our results suggest a very rich and dynamic defect structural landscape at pyrite FeS2{100} surfaces with direct implications for its surface chemical activity.
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| 25. |
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