| 1. |
- Sundberg, Jill, et al.
(författare)
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Understanding the effects of sputter damage in W–S thin films by HAXPES
- 2014
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Ingår i: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 305, s. 203-213
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Tidskriftsartikel (refereegranskat)abstract
- WS2 is an excellent solid lubricant in dry conditions, and can be applied as thin films. The analysis of WS2 and WS2-based films by x-ray photoelectron spectroscopy (XPS) can be challenging, due to contaminationand oxidized material on the surface. The investigations have traditionally therefore included sputter etching by ion bombardment, which however leads to changes of the remaining material. In this study, hard x-ray photoelectron spectroscopy (HAXPES) has been used to study W–S films deposited bymagnetron sputtering. High-resolution reference measurements for crystalline WS2 and metallic W are also presented. The W–S films were analyzed before and after sputter cleaning by Ar+ ion bombardment, using photon energies of 3 and 6 keV. The as-deposited films were found to consist mainly of a WSx phase,similar to WS2 but with a broader range of chemical states. It is shown that ion bombardment of the surface not only removes the outermost oxidized material, but also leads to preferential sputtering of sulfur and the formation of metallic tungsten. The results are of strong interest for the analysis of WS2-based materials, as they demonstrate that spectra from sputter-cleaned films include effects of sputter damage,and may not be representative of the original sample.
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| 2. |
- Alfoeldi, Jessica, et al.
(författare)
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The genome of the green anole lizard and a comparative analysis with birds and mammals
- 2011
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 477:7366, s. 587-591
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Tidskriftsartikel (refereegranskat)abstract
- The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
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| 3. |
- Amemiya, Chris T., et al.
(författare)
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The African coelacanth genome provides insights into tetrapod evolution
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 496:7445, s. 311-316
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.
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| 4. |
- Arion, Tiberiu, et al.
(författare)
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New insight into the Auger decay process in O-2: The coincidence perspective
- 2012
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 185:8-9, s. 234-243
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Tidskriftsartikel (refereegranskat)abstract
- Photoelectron-Auger electron coincidence spectroscopy is a powerful tool for the investigation of Auger decay processes with different core-ionized intermediate states. In this paper we describe an investigation into the Auger decay of the O-2 molecule, with the purpose of bringing new insight into the dynamics of the core hole decay mechanism. Using a novel experimental approach to measuring such coincidence spectra we report the highest resolution Auger spectrum of O-2 recorded hitherto. In our approach, we have combined the advantages of these coincidence spectra with the high resolution and excellent signal-to-noise ratios of non-coincident Auger spectra and a state-of-the-art fit analysis. In this way we have derived information about the potential energy curves of the final states W-3 Delta(u), B-3 Pi(g), and B' (3)Sigma(-)(u) and concluded that the corresponding Auger transitions are formed to a large part by strongly overlapping vibrational progressions. The present findings are compared to earlier results reported in the literature confirming some theoretical predictions. (C) 2012 Elsevier B.V. All rights reserved.
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| 5. |
- Berg, Andreas, et al.
(författare)
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Cyanobacteria as a source of hydrogen for methane formation
- 2014
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Ingår i: World Journal of Microbiology & Biotechnology. - : Springer Verlag (Germany). - 0959-3993 .- 1573-0972. ; 30:2, s. 539-545
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Tidskriftsartikel (refereegranskat)abstract
- In a study during the 1970s co-variation of nitrogenase activity and methane formation associated with Sphagnum riparium was observed. This was suggested as evidence for a possible mechanism of hydrogen transfer from cyanobacteria to methanogens. We show experimentally that such a pathway is feasible. In a series of laboratory experiments, using a hydrogenase deficient strain of the heterocystous cyanobacterium Nostoc punctiforme and the hydrogenotrophic methanogen Methanospirillum hungateii in co-cultures, increasing light intensities resulted in elevated nitrogenase activity and methane production. The increase in methane production can be directly deduced from the nitrogenase activity of the N. punctiforme based on hydrogen balance calculations. These experimental results clearly suggest the possible existence of a novel photosynthetically regulated pathway for methane formation.
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| 6. |
- Fondell, Mattis, 1984-, et al.
(författare)
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An HAXPES study of Sn, SnS, SnO and SnO2
- 2014
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Mattis Fondell. - 0368-2048 .- 1873-2526. ; 195, s. 195-199
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Tidskriftsartikel (refereegranskat)abstract
- Hard X-ray photoelectron spectra have been recorded for Sn, SnO2, SnO and SnS. The binding energies of the core levels of elemental Sn from 2s up to, and including, 4d have been determined with least squares fitting and calibrated against an Au 4f standard. For the oxides and the sulphide data on Sn 3p, 3d core levels’ binding energies and relative intensities are presented together with the binding energies of O 1s, S 1s and 2p. This study thus serves as a picture of tin's core level spectra compared to those of some of its oxides and a sulphide taken at photon energies beyond Al Kα and Mg Kα.
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| 7. |
- Fondell, Mattis, 1984-, et al.
(författare)
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HAXPES study of Sn core levels and their plasmon loss features
- 2014
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Ingår i: Results in Physics. - : Elsevier BV. - 2211-3797. ; 4, s. 168-169
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Tidskriftsartikel (refereegranskat)abstract
- Hard X-ray Photoelectron spectra have been recorded for elemental Sn. Electron loss features, prominent in all core level spectra of the metal, are analyzed at several photo energies for the 3p core level. For higher photoelectron kinetic energies the intensity of the plasmonic features follows a simple exponential law. The data and models presented here will aid the modeling of spectra where tin is present and especially if its spectrum overlaps with those from other sources.
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| 8. |
- Fondell, Mattis, 1984-
(författare)
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Synthesis and Characterisation of Ultra Thin Film Oxides for Energy Applications
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis describes studies of materials which can be exploited for hydrogen production from water and sunlight. The materials investigated are maghemite (γ-Fe2O3), magnetite (Fe3O4) and especially hematite (α-Fe2O3), which is an iron oxide with most promising properties in this field. Hematite has been deposited using Atomic Layer Deposition (ALD) - a thin-film technique facilitating layer-by-layer growth with excellent thickness control and step coverage. The iron oxides were deposited using bis-cyclopentadienyl iron (Fe(Cp)2) or iron pentacarbonyl (Fe(CO)5) in combination with an O2 precursor. Since it is crucial to have good control of the deposition process, the influence of substrate, process temperature, precursor and carrier gas have been investigated systematically. By careful control of these deposition parameters, three polymorphs of iron oxide could be deposited: hematite (α-Fe2O3), maghemite (γ-Fe2O3) and magnetite (Fe3O4).The deposited materials were characterized using X-ray Diffraction, Raman and UV-VIS Spectroscopy, and Scanning Electron Microscopy. Hard X-ray Photoelectron Spectroscopy (HAXPES) was also used, since it is a non-destructive, chemically specific, surface sensitive technique – the surface sensitivity resulting from the short mean escape depth of the photoelectrons. The depth probed can be controlled by varying the excitation energy; higher photoelectron energies increasing the inelastic mean-free-path in the material.HAXPES studies of atomic diffusion from F-doped SnO2 substrates showed increased doping levels of Sn, Si and F in the deposited films. Diffusion from the substrate was detected at annealing temperatures between 550 °C and 800 °C. Films annealed in air exhibited improved photocatalytic behavior; a photocurrent of 0.23 mA/cm2 was observed for those films, while the as-deposited hematite films showed no photo-activity whatsoever.The optical properties of low-dimensional hematite were studied in a series of ultra-thin films (thicknesses in the 2-70 nm range). The absorption maxima were shifted to higher energies for films thinner than 20 nm, revealing a different electronic structure in thin films.
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| 9. |
- Grabherr, Manfred G, et al.
(författare)
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
- 2011
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 29:7, s. 644-652
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Tidskriftsartikel (refereegranskat)abstract
- Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.
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| 10. |
- Harnes, J., et al.
(författare)
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Size of Free Neutral CO(2) Clusters from Carbon 1s Ionization Energies
- 2011
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 115:38, s. 10408-10415
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Tidskriftsartikel (refereegranskat)abstract
- Free neutral CO(2) clusters were produced by adiabatic expansion and characterized by carbon 1s (C1s) photoelectron spectroscopy using synchrotron radiation. The shift in C1s ionization energy (IE) between the cluster and the monomer, i.e., Delta IE = IE(cluster) - IE(monomer), was found to vary systematically with the experimental conditions. A functional relationship is established between the mean cluster size in the beam, < N >, and Delta IE, in good agreement with theoretical calculations of shifts in ionization energy for model clusters. This makes it possible to use core-level photoelectron spectroscopy to monitor the mean cluster size and also to estimate < N > from expansion conditions.
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