| 1. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 2. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
-
Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
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| 5. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 6. |
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| 7. |
- Arvizu, Dan, et al.
(författare)
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Technical Summary
- 2011
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Ingår i: IPCC Special Report on Renewable Energy Sources and Climate Change Mitigation.
-
Bokkapitel (refereegranskat)
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| 8. |
- Claussnitzer, Melina, et al.
(författare)
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Leveraging cross-species transcription factor binding site patterns: from diabetes risk Loci to disease mechanisms.
- 2014
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Ingår i: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 156:1-2, s. 343-358
-
Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility. We show that integrative computational analysis of phylogenetic conservation with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify cis-regulatory variants and elucidate their mechanistic role in disease. Analysis of established type 2 diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele that triggers PRRX1 binding. Thus, cross-species conservation analysis at the level of co-occurring TFBS provides a valuable contribution to the translation of genetic association signals to disease-related molecular mechanisms.
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| 9. |
- Engert, Andreas, et al.
(författare)
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The European Hematology Association Roadmap for European Hematology Research : a consensus document
- 2016
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Ingår i: Haematologica. - Pavia, Italy : Ferrata Storti Foundation (Haematologica). - 0390-6078 .- 1592-8721. ; 101:2, s. 115-208
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Tidskriftsartikel (refereegranskat)abstract
- The European Hematology Association (EHA) Roadmap for European Hematology Research highlights major achievements in diagnosis and treatment of blood disorders and identifies the greatest unmet clinical and scientific needs in those areas to enable better funded, more focused European hematology research. Initiated by the EHA, around 300 experts contributed to the consensus document, which will help European policy makers, research funders, research organizations, researchers, and patient groups make better informed decisions on hematology research. It also aims to raise public awareness of the burden of blood disorders on European society, which purely in economic terms is estimated at (sic)23 billion per year, a level of cost that is not matched in current European hematology research funding. In recent decades, hematology research has improved our fundamental understanding of the biology of blood disorders, and has improved diagnostics and treatments, sometimes in revolutionary ways. This progress highlights the potential of focused basic research programs such as this EHA Roadmap. The EHA Roadmap identifies nine 'sections' in hematology: normal hematopoiesis, malignant lymphoid and myeloid diseases, anemias and related diseases, platelet disorders, blood coagulation and hemostatic disorders, transfusion medicine, infections in hematology, and hematopoietic stem cell transplantation. These sections span 60 smaller groups of diseases or disorders. The EHA Roadmap identifies priorities and needs across the field of hematology, including those to develop targeted therapies based on genomic profiling and chemical biology, to eradicate minimal residual malignant disease, and to develop cellular immunotherapies, combination treatments, gene therapies, hematopoietic stem cell treatments, and treatments that are better tolerated by elderly patients.
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| 10. |
- Esteve-Codina, Anna, et al.
(författare)
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Gender specific airway gene expression in COPD sub-phenotypes supports a role of mitochondria and of different types of leukocytes
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Chronic obstructive pulmonary disease (COPD) is a destructive inflammatory disease and the genes expressed within the lung are crucial to its pathophysiology. We have determined the RNAseq transcriptome of bronchial brush cells from 312 stringently defined ex-smoker patients. Compared to healthy controls there were for males 40 differentially expressed genes (DEGs) and 73 DEGs for females with only 26 genes shared. The gene ontology (GO) term "response to bacterium" was shared, with several different DEGs contributing in males and females. Strongly upregulated genes TCN1 and CYP1B1 were unique to males and females, respectively. For male emphysema (E)-dominant and airway disease (A)-dominant COPD (defined by computed tomography) the term "response to stress" was found for both sub-phenotypes, but this included distinct up-regulated genes for the E-sub-phenotype (neutrophil-related CSF3R, CXCL1, MNDA) and for the A-sub-phenotype (macrophage-related KLF4, F3, CD36). In E-dominant disease, a cluster of mitochondria-encoded (MT) genes forms a signature, able to identify patients with emphysema features in a confirmation cohort. The MT-CO2 gene is upregulated transcriptionally in bronchial epithelial cells with the copy number essentially unchanged. Both MT-CO2 and the neutrophil chemoattractant CXCL1 are induced by reactive oxygen in bronchial epithelial cells. Of the female DEGs unique for E- and A-dominant COPD, 88% were detected in females only. In E-dominant disease we found a pronounced expression of mast cell-associated DEGs TPSB2, TPSAB1 and CPA3. The differential genes discovered in this study point towards involvement of different types of leukocytes in the E- and A-dominant COPD sub-phenotypes in males and females.
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| 11. |
- Kaschina, Elena, et al.
(författare)
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Angiotensin II type 2 receptor stimulation : a novel option of therapeutic interference with the renin-angiotensin system in myocardial infarction?
- 2008
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Ingår i: Circulation. - 0009-7322 .- 1524-4539. ; 118:24, s. 2523-32
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: This study is the first to examine the effect of direct angiotensin II type 2 (AT(2)) receptor stimulation on postinfarct cardiac function with the use of the novel nonpeptide AT(2) receptor agonist compound 21 (C21). METHODS AND RESULTS: Myocardial infarction (MI) was induced in Wistar rats by permanent ligation of the left coronary artery. Treatment with C21 (0.01, 0.03, 0.3 mg/kg per day IP) was started 24 hours after MI and was continued until euthanasia (7 days after MI). Infarct size was assessed by magnetic resonance imaging, and hemodynamic measurements were performed via transthoracic Doppler echocardiography and intracardiac Millar catheter. Cardiac tissues were analyzed for inflammation and apoptosis markers with immunoblotting and real-time reverse transcription polymerase chain reaction. C21 significantly improved systolic and diastolic ventricular function. Scar size was smallest in the C21-treated rats. In regard to underlying mechanisms, C21 diminished MI-induced Fas-ligand and caspase-3 expression in the peri-infarct zone, indicating an antiapoptotic effect. Phosphorylation of the p44/42 and p38 mitogen-activated protein kinases, both involved in the regulation of cell survival, was strongly reduced after MI but almost completely rescued by C21 treatment. Furthermore, C21 decreased MI-induced serum monocyte chemoattractant protein-1 and myeloperoxidase as well as cardiac interleukin-6, interleukin-1beta, and interleukin-2 expression, suggesting an antiinflammatory effect. CONCLUSIONS: Direct AT(2) receptor stimulation may be a novel therapeutic approach to improve post-MI systolic and diastolic function by antiapoptotic and antiinflammatory mechanisms.
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| 12. |
- Aad, G., et al.
(författare)
-
- 2010
-
swepub:Mat__t
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| 13. |
- Arvizu, Dan, et al.
(författare)
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Summary for Policy Makers: Intergovernmental Panel on Climate Change Special Report Renewable Energy Sources (SRREN)
- 2011
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The Working Group III Special Report on Renewable Energy Sources and Climate Change Mitigation (SRREN) presents an assessment of the literature on the scientific, technological, environmental, economic and social aspects of the contribution of six renewable energy (RE) sources to the mitigation of climate change. It is intended to provide policy relevant information to governments, intergovernmental processes and other interested parties. This Summary for Policymakers provides an overview of the SRREN, summarizing the essential findings. The SRREN consists of 11 chapters. Chapter 1 sets the context for RE and climate change; Chapters 2 through 7 provide information on six RE technologies, and Chapters 8 through 11 address integrative issues.
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| 14. |
- Björklund, Henrik, 1973-, et al.
(författare)
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Efficient incremental evaluation of succinct regular expressions
- 2015
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Ingår i: Proceedings of the 24th ACM International on Conference on Information and Knowledge Management. - New York, NY, USA : Association for Computing Machinery (ACM). - 9781450337946 ; , s. 1541-1550
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Konferensbidrag (refereegranskat)abstract
- Regular expressions are omnipresent in database applications. They form the structural core of schema languages for XML, they are a fundamental ingredient for navigational queries in graph databases, and are being considered in languages for upcoming technologies such as schema- and transformation languages for tabular data on the Web. In this paper we study the usage and effectiveness of the counting operator (or: limited repetition) in regular expressions. The counting operator is a popular extension which is part of the POSIX standard and therefore also present in regular expressions in grep, Java, Python, Perl, and Ruby. In a database context, expressions with counting appear in XML Schema and languages for querying graphs such as SPARQL 1.1 and Cypher.We first present a practical study that suggests that counters are extensively used in practice. We then investigate evaluation methods for such expressions and develop a new algorithm for efficient incremental evaluation. Finally, we conduct an extensive benchmark study that shows that exploiting counting operators can lead to speed-ups of several orders of magnitude in a wide range of settings: normal and incremental evaluation on synthetic and real expressions.
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| 15. |
- Blåbäck, Johan, et al.
(författare)
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(Anti-)brane backreaction beyond perturbation theory
- 2012
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Ingår i: Journal of High Energy Physics (JHEP). - 1126-6708 .- 1029-8479. ; 2012:2, s. 025-
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Tidskriftsartikel (refereegranskat)abstract
- We improve on the understanding of the backreaction of anti-D6-branes in a flux background that is mutually BPS with D6-branes. This setup is analogous to the study of the backreaction of anti-D3-branes inserted in the KS throat, but does not require us to smear the anti-branes or do a perturbative analysis around the BPS background. We solve the full equations of motion near the anti-D6-branes and show that only two boundary conditions are consistent with the equations of motion. Upon invoking a topological argument we eliminate the boundary condition with regular H flux since it cannot lead to a solution that approaches the right kind of flux away from the anti-D6-branes. This leaves us with a boundary condition which has singular, but integrable, H flux energy density.
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| 16. |
- Blåbäck, Johan, et al.
(författare)
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Smeared versus localised sources in flux compactifications
- 2010
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Ingår i: Journal of High Energy Physics (JHEP). - 1126-6708 .- 1029-8479. ; :12, s. 043-
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Tidskriftsartikel (refereegranskat)abstract
- We investigate whether vacuum solutions in flux compactifications that are obtained with smeared sources (orientifolds or D-branes) still survive when the sources are localised. This seems to rely on whether the solutions are BPS or not. First we consider two sets of BPS solutions that both relate to the GKP solution through T-dualities: (p + 1)-dimensional solutions from spacetime-filling Op-planes with a conformally Ricci-flat internal space, and p-dimensional solutions with Op-planes that wrap a 1-cycle inside an everywhere negatively curved twisted torus. The relation between the solution with smeared orientifolds and the localised version is worked out in detail. We then demonstrate that a class of non-BPS AdS(4) solutions that exist for IASD fluxes and with smeared D3-branes (or analogously for ISD fluxes with anti-D3-branes) does not survive the localisation of the (anti) D3-branes. This casts doubts on the stringy consistency of non-BPS solutions that are obtained in the limit of smeared sources.
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| 17. |
- Blåbäck, Johan, et al.
(författare)
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The problematic backreaction of SUSY-breaking branes
- 2011
-
Ingår i: Journal of High Energy Physics (JHEP). - 1126-6708 .- 1029-8479. ; :8, s. 105-
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we investigate the localisation of SUSY-breaking branes which, in the smeared approximation, support specific non-BPS vacua. We show, for a wide class of boundary conditions, that there is no flux vacuum when the branes are described by a genuine delta-function. Even more, we find that the smeared solution is the unique solution with a regular brane profile. Our setup consists of a non-BPS AdS(7) solution in massive IIA supergravity with smeared anti-D6-branes and fluxes T-dual to ISD fluxes in IIB supergravity.
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| 18. |
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| 19. |
- Danielsson, Ulf H., et al.
(författare)
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De Sitter hunting in a classical landscape
- 2011
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Ingår i: Fortschritte der Physik. - : Wiley. - 0015-8208 .- 1521-3978. ; 59:9
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Tidskriftsartikel (refereegranskat)abstract
- We elaborate on the construction of de Sitter solutions from IIA orientifolds of SU(3)-structure manifolds that solve the 10-dimensional equations of motion at tree-level in the approximation of smeared sources. First we classify geometries that are orbifolds of a group manifold covering space which, upon the proper inclusion of O6 planes, can be described within the framework of N=1 supergravity in 4D. Then we scan systematically for de Sitter solutions, obtained as critical points of an effective 4D potential. Apart from finding many new solutions we emphasize the challenges in constructing explicit classical de Sitter vacua, which have sofar not been met. These challenges are interesting avenues for further research and include finding solutions that are perturbatively stable, satisfy charge and flux quantization, and have genuine localized (versus smeared) orientifold sources. This paper intends to be self-contained and pedagogical, and thus can serve as a guide to the necessary technical tools required for this line of research. In an appendix we explain how to study flux and charge quantization in the presence of a non-trivial H-field using twisted homology.
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| 20. |
- Egorov, Dmitrii, et al.
(författare)
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Near-Edge Soft X-ray Absorption Mass Spectrometry of Protonated Melittin
- 2018
-
Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305. ; 29:11, s. 2138-2151
-
Tidskriftsartikel (refereegranskat)abstract
- We have investigated the photoionization and photofragmentation yields of gas-phase multiply protonated melittin cations for photon energies at the K-shell absorption edges of carbon, nitrogen, and oxygen. Two similar experimental approaches were employed. In both experiments, mass selected [melittin+qH]q+ (q=2–4) ions were accumulated in radiofrequency ion traps. The trap content was exposed to intense beams of monochromatic soft X-ray photons from synchrotron beamlines and photoproducts were analyzed by means of time-of-flight mass spectrometry. Mass spectra were recorded for fixed photon energies, and partial ion yield spectra were recorded as a function of photon energy. The combination of mass spectrometry and soft X-ray spectroscopy allows for a direct correlation of protein electronic structure with various photoionization channels. Non-dissociative single and double ionization are used as a reference. The contribution of both channels to various backbone scission channels is quantified and related to activation energies and protonation sites. Soft X-ray absorption mass spectrometry combines fast energy deposition with single and double ionization and could complement established activation techniques. [Figure not available: see fulltext.].
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| 21. |
- Gerber, Timm, et al.
(författare)
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CO-Induced Smoluchowski Ripening of Pt Cluster Arrays on the Graphene/Ir(111) Moire
- 2013
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 7:3, s. 2020-2031
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Tidskriftsartikel (refereegranskat)abstract
- Regular Pt cluster arrays grown on the moire template formed by graphene on Ir(111) were tested for their stability with respect to CO gas exposure. Cluster stability and adsorption-Induced processes were analyzed as a function of cluster size, with In situ scanning tunneling microscopy and X-ray photoelectron spectroscopy. Small clusters containing fewer than 10 atoms were unstable upon CO adsorption. They sintered through Smoluchowski ripening-cluster diffusion and coalescence rather than the frequently reported Ostwald ripening mediated by metal-adsorbate complexes. Larger dusters remained immobile upon CO adsorption but became more three-dimensional. Careful analysis of the experimental data complemented by ab initio density functional theory calculations provides insight Into the origin of the CO-induced Pt cluster ripening and shape transformations.
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| 22. |
- Grånäs, Elin, et al.
(författare)
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CO Intercalation of Graphene on Ir(111) in the Millibar Regime
- 2013
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 117:32, s. 16438-16447
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Tidskriftsartikel (refereegranskat)abstract
- Here we show that it is possible to intercalate CO under graphene grown on Ir(111) already at room temperature when CO pressures in the millibar regime are used. From the interplay of X-ray photoelectron spectroscopy and scanning tunneling microscopy we conclude that the intercalated CO adsorption structure is similar to the (3 root 3 X 3 root 3)R30 degrees) adsorption structure that is formed on Ir(111) upon exposure to similar to 1 mbar of CO. Further, density functional theory calculations reveal that the structural and electronic properties of CO-intercalated graphene are similar to p-doped freestanding graphene. Finally we characterize nonintercalated stripes and islands that we always observe in the CO-intercalated graphene. We observe these nonintercalated areas predominately in HCP and FCC areas near step edges and suggest that stress release in graphene is the driving force for their formation, while the weak chemical bonds in HCP and FCC areas are the reason for their area selectivity.
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| 23. |
- Grånäs, Elin, et al.
(författare)
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Hydrogen intercalation under graphene on Ir(111)
- 2016
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Ingår i: Surface Science. - : Elsevier BV. - 0039-6028. ; 651, s. 57-61
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Tidskriftsartikel (refereegranskat)abstract
- Using high resolution X-ray photoelectron spectroscopy and scanning tunneling microscopy we study the intercalation of hydrogen under graphene/Ir(111). The hydrogen intercalated graphene is characterized by a component in C 1s that is shifted −0.10 to −0.18 eV with respect to pristine graphene and a component in Ir 4f at 60.54 eV. The position of this Ir 4f component is identical to that of the Ir(111) surface layer with hydrogen atoms adsorbed, indicating that the atomic hydrogen adsorption site on bare Ir(111) and beneath graphene is the same. Based on co-existence of fully- and non-intercalated graphene, and the inability to intercalate a closed graphene film covering the entire Ir(111) surface, we conclude that hydrogen dissociatively adsorbs at bare Ir(111) patches, and subsequently diffuses rapidly under graphene. A likely entry point for the intercalating hydrogen atoms is identified to be where graphene crosses an underlying Ir(111) step.
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| 24. |
- Grånäs, Elin, et al.
(författare)
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Oxygen Intercalation under Graphene on Ir(111): Energetics, Kinetics, and the Role of Graphene Edges.
- 2012
-
Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851.
-
Tidskriftsartikel (refereegranskat)abstract
- Using X-ray photoemission spectroscopy (XPS) and scanning tunneling microscopy (STM) we resolve the temperature-, time-, and flake size-dependent intercalation phases of oxygen underneath graphene on Ir(111) formed upon exposure to molecular oxygen. Through the applied pressure of molecular oxygen the atomic oxygen created on the bare Ir terraces is driven underneath graphene flakes. The importance of substrate steps and of the unbinding of graphene flake edges from the substrate for the intercalation is identified. With the use of CO titration to selectively remove oxygen from the bare Ir terraces the energetics of intercalation is uncovered. Cluster decoration techniques are used as an efficient tool to visualize intercalation processes in real space.
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| 25. |
- Grånäs, Elin, et al.
(författare)
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Water Chemistry beneath Graphene : Condensation of a Dense OH-H2O Phase under Graphene
- 2022
-
Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 126:9, s. 4347-4354
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Tidskriftsartikel (refereegranskat)abstract
- Room temperature oxygen hydrogenation below graphene flakes supported by Ir(111) is investigated through a combination of X-ray photoelectron spectroscopy, scanning tunneling microscopy, and density functional theory calculations using an evolutionary search algorithm. We demonstrate how the graphene cover and its doping level can be used to trap and characterize dense mixed O-OH-H2O phases that otherwise would not exist. Our study of these graphene-stabilized phases and their response to oxygen or hydrogen exposure reveals that additional oxygen can be dissolved into them at room temperature creating mixed O-OH-H2O phases with an increased areal coverage underneath graphene. In contrast, additional hydrogen exposure converts the mixed O-OH-H2O phases back to pure OH-H2O with a reduced areal coverage underneath graphene.
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| 26. |
- Haitjema, Jarich, et al.
(författare)
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Soft X-ray absorption and fragmentation of tin-oxo cage photoresists
- 2024
-
Ingår i: Physical Chemistry Chemical Physics. - 1463-9076. ; 26:7, s. 5986-5998
-
Tidskriftsartikel (refereegranskat)abstract
- “Tin-oxo cage” organometallic compounds are considered as photoresists for extreme ultraviolet (EUV) photolithography. To gain insight into their electronic structure and reactivity to ionizing radiation, we trapped bare gas-phase n-butyltin-oxo cage dications [(BuSn)12O14(OH)6]2+ in an ion trap and investigated their fragmentation upon soft X-ray photoabsorption by means of mass spectrometry. In complementary experiments, the tin-oxo cages with hydroxide and trifluoroacetate counter-anions were cast in thin films and studied using X-ray transmission spectroscopy. Quantum-chemical calculations were used to interpret the observed spectra. At the carbon K-edge, a distinct pre-edge absorption band can be attributed to transitions in which electrons are promoted from C1s orbitals to the lowest unoccupied molecular orbitals, which are delocalized orbitals with strong antibonding (Sn-C ?*) character. At higher energies, the most prominent resonant transitions involve C-C and C-H ?* valence states and Rydberg (3s and 3p) states. In the solid state, the onset of continuum ionization is shifted by ?5 eV to lower energy with respect to the gas phase, due to the electrostatic effect of the counterions. The O K-edge also shows a pre-edge absorption, but it is devoid of any specific features, because there are many transitions from the different O1s orbitals to a large number of vacant orbitals. In the gas phase, formation of the parent [(BuSn)12O14(OH)6]3+ radical ion is not observed at the C K-edge nor at the O K-edge, because the loss of a butyl group from this species is very efficient. We do observe a number of triply charged photofragment ions, some of which have lost up to 5 butyl groups. Structures of these species are proposed based on quantum-chemical calculations, and pathways of formation are discussed. Our results provide insight into the electronic structure of alkyltin-oxo cages, which is a prerequisite for understanding their response to EUV photons and their performance as EUV photoresists.
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| 27. |
- Hecker, Andreas, et al.
(författare)
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Phosphocholine-Modified Macromolecules and Canonical Nicotinic Agonists Inhibit ATP-Induced IL-1 beta Release
- 2015
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Ingår i: Journal of Immunology. - : AMER ASSOC IMMUNOLOGISTS. - 0022-1767 .- 1550-6606. ; 195:5, s. 2325-2334
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Tidskriftsartikel (refereegranskat)abstract
- IL-1 beta is a potent proinflammatory cytokine of the innate immune system that is involved in host defense against infection. However, increased production of IL-1 beta plays a pathogenic role in various inflammatory diseases, such as rheumatoid arthritis, gout, sepsis, stroke, and transplant rejection. To prevent detrimental collateral damage, IL-1 beta release is tightly controlled and typically requires two consecutive danger signals. LPS from Gram-negative bacteria is a prototypical first signal inducing pro-IL-1 beta synthesis, whereas extracellular ATP is a typical second signal sensed by the ATP receptor P2X7 that triggers activation of the NLRP3-containing inflammasome, proteolytic cleavage of pro-IL-1 beta by caspase-1, and release of mature IL-1 beta. Mechanisms controlling IL-1 beta release, even in the presence of both danger signals, are needed to protect from collateral damage and are of therapeutic interest. In this article, we show that acetylcholine, choline, phosphocholine, phosphocholine-modified LPS from Haemophilus influenzae, and phosphocholine-modified protein efficiently inhibit ATP-mediated IL-1 beta release in human and rat monocytes via nicotinic acetylcholine receptors containing subunits alpha 7, alpha 9, and/or alpha 10. Of note, we identify receptors for phosphocholine-modified macromolecules that are synthesized by microbes and eukaryotic parasites and are well-known modulators of the immune system. Our data suggest that an endogenous anti-inflammatory cholinergic control mechanism effectively controls ATP-mediated release of IL-1 beta and that the same mechanism is used by symbionts and misused by parasites to evade innate immune responses of the host.
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| 28. |
- Hilt, Sabine, et al.
(författare)
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Response of submerged macrophyte communities to external and internal restoration measures in north temperate shallow lakes
- 2018
-
Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Submerged macrophytes play a key role in north temperate shallow lakes by stabilizing clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analyzed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterized by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterized by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallowareas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonization by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined.
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| 29. |
- Jones, Daniel O.B., et al.
(författare)
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Environment, ecology, and potential effectiveness of an area protected from deep-sea mining (Clarion Clipperton Zone, abyssal Pacific)
- 2021
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Ingår i: Progress in Oceanography. - : Elsevier BV. - 0079-6611. ; 197:September-October 2021
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Tidskriftsartikel (refereegranskat)abstract
- To protect the range of habitats, species, and ecosystem functions in the Clarion Clipperton Zone (CCZ), a region of interest for deep-sea polymetallic nodule mining in the Pacific, nine Areas of Particular Environmental Interest (APEIs) have been designated by the International Seabed Authority (ISA). The APEIs are remote, rarely visited and poorly understood. Here we present and synthesise all available observations made at APEI-6, the most north eastern APEI in the network, and assess its representativity of mining contract areas in the eastern CCZ. The two studied regions of APEI-6 have a variable morphology, typical of the CCZ, with hills, plains and occasional seamounts. The seafloor is predominantly covered by fine-grained sediments, and includes small but abundant polymetallic nodules, as well as exposed bedrock. The oceanographic parameters investigated appear broadly similar across the region although some differences in deep-water mass separation were evident between APEI-6 and some contract areas. Sediment biogeochemistry is broadly similar across the area in the parameters investigated, except for oxygen penetration depth, which reached >2 m at the study sites within APEI-6, deeper than that found at UK1 and GSR contract areas. The ecology of study sites in APEI-6 differs from that reported from UK1 and TOML-D contract areas, with differences in community composition of microbes, macrofauna, xenophyophores and metazoan megafauna. Some species were shared between areas although connectivity appears limited. We show that, from the available information, APEI-6 is partially representative of the exploration areas to the south yet is distinctly different in several key characteristics. As a result, additional APEIs may be warranted and caution may need to be taken in relying on the APEI network alone for conservation, with other management activities required to help mitigate the impacts of mining in the CCZ.
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| 30. |
- Jonsson, Erik G., et al.
(författare)
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DTNBP1, NRG1, DAOA, DAO and GRM3 Polymorphisms and Schizophrenia : An Association Study
- 2009
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Ingår i: Neuropsychobiology. - : S. Karger AG. - 0302-282X .- 1423-0224. ; 59:3, s. 142-150
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Tidskriftsartikel (refereegranskat)abstract
- Background: Several studies of the dystrobrevin-binding protein 1 gene (DTNBP1), neuregulin 1 (NRG1), D-amino-acid oxidase (DAO), DAO activator (DAOA, G72), and metabotropic glutamate receptor 3 (GRM3) genes have suggested an association between variants of these genes and schizophrenia. Methods: In a replication attempt, single-nucleotide polymorphisms of the DTNBP1, NRG1, DAO, DAOA, and GRM3 genes were analyzed in three independent Scandinavian schizophrenia case-control samples. Results: One DTNBP1 and three GRM3 single-nucleotide polymorphisms showed nominal significant associations to the disease. However, after correction for multiple testing, there were no statistically significant allele, genotype or haplotype case-control differences. Conclusions: The present Scandinavian results do not verify previous associations between the analyzed DTNBP1, NRG1, DAO, DAOA, and GRM3 gene polymorphisms and schizophrenia. Additional studies and meta-analyses are warranted to shed further light on these relationships. Copyright (C) 2009 S. Karger AG, Basel
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| 31. |
- Kawasaki, Jason K., et al.
(författare)
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Epitaxial growth and surface studies of the Half Heusler compound NiTiSn (001)
- 2013
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Ingår i: Journal of Vacuum Science and Technology B. - : American Vacuum Society. - 1520-8567. ; 31:4
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Tidskriftsartikel (refereegranskat)abstract
- The Half Heuslers are currently an attractive family of compounds for high temperature thermoelectrics research, and recently, there has been renewed interest since some of these compounds are proposed to be topological insulators. NiTiSn belongs to the family of 18 valence electron Half Heuslers that are predicted to be semiconducting, despite being composed entirely of metallic elements. The growth of the Half Heusler compound NiTiSn by molecular beam epitaxy is demonstrated. The NiTiSn films are epitaxial and single crystalline as observed by reflection high-energy electron diffraction and x-ray diffraction. Temperature dependent transport measurements suggest the films may be semiconducting, but with a high background carrier density indicative of a high density of electrically active defect states. Methods of protecting the sample surface for synchrotron-based photoemission measurements are explored. These methods may be applied to the study of surface electronic structure in unconventional materials. (C) 2013 American Vacuum Society.
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| 32. |
- Knudsen, Jan, et al.
(författare)
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Clusters binding to the graphene moire on Ir(111): X-ray photoemission compared to density functional calculations
- 2012
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 85:3
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Tidskriftsartikel (refereegranskat)abstract
- Our understanding of metal-atom cluster adsorption on graphene on Ir(111) is based on elementary chemical ideas, rehybridization, and buckling, supported by density functional theory (DFT) calculations. We tested the DFT picture by comparing calculated core level spectra to x-ray photoemission spectroscopy (XPS) measurements. For pristine graphene, which forms a gently undulating moire on Ir(111), DFT predicts a 140 meV modulation of C 1s core level shifts (CLS), consistent with the measured spectrum. With Pt clusters adsorbed, measured Pt 4f CLS of the adsorbed clusters also support the calculations. The modulation of the C 1s spectrum is strengthened with clusters adsorbed, and C-atom ionization potentials under and in the vicinity of the Pt clusters are shifted enough to be experimentally distinguished as a broad shoulder of positive C 1s CLSs. Furthermore, DFT calculations imply that sp(2) to sp(3) graphene rehybridization of C atoms below the Pt cluster induces a 1.1 eV CLS splitting between Pt- and Ir-bonded C atoms; this prediction is also consistent with the XPS data.
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| 33. |
- Mohr, Sebastian, et al.
(författare)
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Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia.
- 2017
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Ingår i: Cancer cell. - : Elsevier BV. - 1878-3686 .- 1535-6108. ; 31:4
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Tidskriftsartikel (refereegranskat)abstract
- The transcription factor Meis1 drives myeloid leukemogenesis in the context of Hox gene overexpression butis currently considered undruggable. We therefore investigated whether myeloid progenitor cells transformed by Hoxa9 and Meis1 become addicted to targetable signaling pathways. A comprehensive (phospho)proteomic analysis revealed that Meis1 increased Syk protein expression and activity. Syk upregulation occurs through a Meis1-dependent feedback loop. By dissecting this loop, we show that Syk is a direct target of miR-146a, whose expression is indirectly regulated by Meis1 through the transcription factor PU.1. In the context of Hoxa9 overexpression, Syk signaling induces Meis1, recapitulating several leukemogenic features of Hoxa9/Meis1-driven leukemia. Finally, Syk inhibition disrupts the identified regulatory loop, prolonging survival of mice with Hoxa9/Meis1-driven leukemia.
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| 34. |
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| 35. |
- Myadam, Rahul, et al.
(författare)
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Risk of Adverse Outcomes Associated With Cardiac Sarcoidosis Diagnostic Schemes
- 2023
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Ingår i: JACC: Clinical Electrophysiology. - 2405-500X. ; 9:8, s. 1719-1729
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Tidskriftsartikel (refereegranskat)abstract
- Background: Multiple cardiac sarcoidosis (CS) diagnostic schemes have been published. Objectives: This study aims to evaluate the association of different CS diagnostic schemes with adverse outcomes. The diagnostic schemes evaluated were 1993, 2006, and 2017 Japanese criteria and the 2014 Heart Rhythm Society criteria. Methods: Data were collected from the Cardiac Sarcoidosis Consortium, an international registry of CS patients. Outcome events were any of the following: all-cause mortality, left ventricular assist device placement, heart transplantation, and appropriate implantable cardioverter-defibrillator therapy. Logistic regression analysis evaluated the association of outcomes with each CS diagnostic scheme. Results: A total of 587 subjects met the following criteria: 1993 Japanese (n = 310, 52.8%), 2006 Japanese (n = 312, 53.2%), 2014 Heart Rhythm Society (n = 480, 81.8%), and 2017 Japanese (n = 112, 19.1%). Patients who met the 1993 criteria were more likely to experience an event than patients who did not (n = 109 of 310, 35.2% vs n = 59 of 277, 21.3%; OR: 2.00; 95% CI: 1.38-2.90; P < 0.001). Similarly, patients who met the 2006 criteria were more likely to have an event than patients who did not (n = 116 of 312, 37.2% vs n = 52 of 275, 18.9%; OR: 2.54; 95% CI: 1.74-3.71; P < 0.001). There was no statistically significant association between the occurrence of an event and whether a patient met the 2014 or the 2017 criteria (OR: 1.39; 95% CI: 0.85-2.27; P = 0.18 or OR: 1.51; 95% CI: 0.97-2.33; P = 0.067, respectively). Conclusions: CS patients who met the 1993 and the 2006 criteria had higher odds of adverse clinical outcomes. Future research is needed to prospectively evaluate existing diagnostic schemes and develop new risk models for this complex disease.
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| 36. |
- Savary, Agata, et al.
(författare)
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PARSEME Corpus Release 1.3
- 2023
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Ingår i: Proceedings of the 19th Workshop on Multiword Expressions (MWE 2023). - Stroudsburg : Association for Computational Linguistics. - 9781959429593 ; , s. 24-35
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Konferensbidrag (refereegranskat)abstract
- We present version 1.3 of the PARSEME multilingual corpus annotated with verbal multiword expressions. Since the previous version, new languages have joined the undertaking of creating such a resource, some of the already existing corpora have been enriched with new annotated texts, while others have been enhanced in various ways. The PARSEME multilingual corpus represents 26 languages now. All monolingual corpora therein use Universal Dependencies v.2 tagset. They are (re-)split observing the PARSEME v.1.2 standard, which puts impact on unseen VMWEs. With the current iteration, the corpus release process has been detached from shared tasks; instead, a process for continuous improvement and systematic releases has been introduced.
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| 37. |
- Schroeder, Ulrike A., et al.
(författare)
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Etching of graphene on Ir(111) with molecular oxygen
- 2016
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Ingår i: Carbon. - : Elsevier BV. - 0008-6223. ; 96, s. 320-331
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Tidskriftsartikel (refereegranskat)abstract
- The mechanisms for oxygen etching of graphene on Ir(111) are uncovered through a systematic variation of the graphene morphology - ranging from an impermeable graphene layer to graphene nanoflakes - and the application of complementary experimental methods, including scanning tunneling microscopy, X-ray photoelectron spectroscopy, and temperature programmed desorption. Associated with a strong variation in the onset temperature for etching, we find a fundamental difference in the onset of etching for an impermeable layer and for graphene flakes. For the impermeable graphene layer etching is shown to nucleate at graphene pentagon heptagon point defects through molecules impinging from the gas phase. For graphene flakes the nucleation problem is absent due to the existence of edges in contact with the metallic substrate. The substrate enables dissociative chemisorption of oxygen, which can then diffuse as atomic oxygen to the graphene edge. Our results show that intercalation of oxygen is neither a necessary condition nor of specific relevance for etching. Based on our analysis, a quantitative estimate for the activation energy and attempt frequency of the elementary etch process in flake etching on Ir(111) is provided. (C) 2015 Elsevier Ltd. All rights reserved.
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| 38. |
- Schröder, Ulrike A, et al.
(författare)
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Core level shifts of intercalated graphene
- 2017
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Ingår i: 2D Materials. - : IOP Publishing. - 2053-1583. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Through intercalation of metals and gases the Dirac cone of graphene on Ir(111) can be shifted with respect to the Fermi level without becoming destroyed by strong hybridization. Here, we use x-ray photoelectron spectroscopy to measure the C 1s core level shift (CLS) of graphene in contact with a number of structurally well-defined intercalation layers (O, H, Eu, and Cs). By analysis of our own and additional literature data for decoupled graphene, the C 1s CLS is found to be a non-monotonic function of the doping level. For small doping levels the shifts are well described by a rigid band model. However, at larger doping levels, a second effect comes into play which is proportional to the transferred charge and counteracts the rigid band shift. Moreover, not only the position, but also the C 1s peak shape displays a unique evolution as a function of doping level. Our conclusions are supported by intercalation experiments with Li, with which, due to the absence of phase separation, the doping level of graphene can be continuously tuned.
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| 39. |
- Schubert, Kaja, et al.
(författare)
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The electronic structure and deexcitation pathways of an isolated metalloporphyrin ion resolved by metal L-edge spectroscopy
- 2021
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 12:11, s. 3966-3976
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Tidskriftsartikel (refereegranskat)abstract
- The local electronic structure of the metal-active site and the deexcitation pathways of metalloporphyrins are crucial for numerous applications but difficult to access by commonly employed techniques. Here, we applied near-edge X-ray absorption mass spectrometry and quantum-mechanical restricted active space calculations to investigate the electronic structure of the metal-active site of the isolated cobalt(iii) protoporphyrin IX cation (CoPPIX+) and its deexcitation pathways upon resonant absorption at the cobalt L-edge. The experiments were carried out in the gas phase, thus allowing for control over the chemical state and molecular environment of the metalloporphyrin. The obtained mass spectra reveal that resonant excitations of CoPPIX+at the cobalt L3-edge lead predominantly to the formation of the intact radical dication and doubly charged fragments through losses of charged and neutral side chains from the macrocycle. The comparison between experiment and theory shows that CoPPIX+is in a3A2gtriplet ground state and that competing excitations to metal-centred non-bonding and antibonding σ* molecular orbitals lead to distinct deexcitation pathways.
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