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- Marschall, Tobias, et al.
(författare)
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Computational pan-genomics : status, promises and challenges
- 2018
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Ingår i: Briefings in Bioinformatics. - : Oxford University Press (OUP). - 1467-5463 .- 1477-4054. ; 19:1, s. 118-135
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Tidskriftsartikel (refereegranskat)abstract
- Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
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- Horio, M., et al.
(författare)
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Oxide Fermi liquid universality revealed by electron spectroscopy
- 2020
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Ingår i: Physical Review B. - 2469-9969 .- 2469-9950. ; 102:24
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Tidskriftsartikel (refereegranskat)abstract
- We present a combined soft x-ray and high-resolution vacuum-ultraviolet angle-resolved photoemission spectroscopy study of the electron-overdoped cuprate Pr1.3-xLa0.7CexCuO4 (PLCCO). Demonstration of its highly two-dimensional band structure enabled precise determination of the in-plane self-energy dominated by electron-electron scattering. Through analysis of this self-energy and the Fermi liquid cut-off energy scale, we find-in contrast to hole-doped cuprates-a momentum isotropic and comparatively weak electron correlation in PLCCO. Yet, the self-energies extracted from multiple oxide systems combine to demonstrate a logarithmic divergent relation between the quasiparticle scattering rate and mass. This constitutes a spectroscopic version of the Kadowaki-Woods relation with an important merit-the demonstration of Fermi liquid quasiparticle lifetime and mass being set by a single energy scale.
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- Jacquet, J M, et al.
(författare)
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Safety and immunogenicity of a combined DTPa-IPV vaccine administered as a booster from 4 years of age : a review
- 2006
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Ingår i: Vaccine. - : Elsevier BV. - 0264-410X .- 1873-2518. ; 24:13, s. 2440-2448
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Tidskriftsartikel (refereegranskat)abstract
- A combined DTPa-IPV booster vaccine was administered as a 4th or 5th dose after DTPa or DTPw priming. Over 99% vaccines developed antibody levels considered to be protective to diphtheria, tetanus and poliovirus, and >95% mounted a response to acellular pertussis antigens. Rectal temperature >39.5 degrees C was observed in at most 3.2% of vaccinees. Swelling >50 mm occurred in 24% of DTPa-primed compared to 5.5% of DTPw-primed children. Large swelling involving the entire upper arm (extending to involve the elbow joint) was reported for up to 1.2% of DTPa-primed subjects, which is consistent with literature reports for other DTPa vaccines.
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- Lekki, J., et al.
(författare)
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On the follicular pathway of percutaneous uptake of nanoparticles: Ion microscopy and autoradiography studies
- 2007
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Ingår i: Nuclear Instruments & Methods in Physics Research. Section B: Beam Interactions with Materials and Atoms. - : Elsevier BV. - 0168-583X. ; 260:1, s. 174-177
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Tidskriftsartikel (refereegranskat)abstract
- We report on the visualization of the penetration of sunscreen formulations containing TiO2 nanoparticles (about 20 nm primary particle size) into hair follicles of both human and porcine skin using the complementary methods of ion microscopy (PIXE, RBS, STIM) and autoradiography. Particles were found as deep as approx. 400 pin in the follicle, obviously introduced mechanically rather than by a diffusive process. No particles were observed in vital tissue nor in sebaceous glands. (c) 2007 Elsevier B.V. All rights reserved.
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| 7. |
- Meyer, F., et al.
(författare)
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"Building Block Picture" of the Electronic Structure of Aqueous Cysteine Derived from Resonant Inelastic Soft X-ray Scattering
- 2014
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 118:46, s. 13142-13150
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of the amino acid l-cysteine in an aqueous environment was studied using resonant inelastic soft X-ray scattering (RIXS) in a 2D map representation and analyzed in the framework of a building block approach. The element selectivity of RIXS allows a local investigation of the electronic structure of the three functional groups of cysteine, namely, the carboxyl, amino, and thiol groups, by measuring at the O K, N K, and S L-2,L-3 edges, respectively. Variation of the pH value allows an investigation of molecules with protonated and deprotonated functional groups, which can then be compared with simple reference molecules that represent the isolated functional groups. We find that such building blocks can provide an excellent description of X-ray emission spectroscopy (XES) and RIXS spectra, but only if all nearest-neighbor atoms are included. This finding is analogous to the building block principle commonly used in X-ray absorption spectroscopy. The building blocks show a distinct spectral character (fingerprint) and allow a comprehensive interpretation of the cysteine spectra. This simple approach opens the path to investigate the electronic structure of more complex biological molecules in aqueous solutions using XES and RIXS.
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- Tremblin, P., et al.
(författare)
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Site testing for submillimetre astronomy at Dome C, Antarctica
- 2011
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 535:A112
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Tidskriftsartikel (refereegranskat)abstract
- Aims. Over the past few years a major effort has been put into the exploration of potential sites for the deployment of submillimetre astronomical facilities. Amongst the most important sites are Dome C and Dome A on the Antarctic Plateau, and the Chajnantor area in Chile. In this context, we report on measurements of the sky opacity at 200 mu m over a period of three years at the French-Italian station, Concordia, at Dome C, Antarctica. We also present some solutions to the challenges of operating in the harsh polar environment.Methods. The 200-mu m atmospheric opacity was measured with a tipper. The forward atmospheric model MOLIERE (Microwave Observation LIne Estimation and REtrieval) was used to calculate the atmospheric transmission and to evaluate the precipitable water vapour content (PWV) from the observed sky opacity. These results have been compared with satellite measurements from the Infrared Atmospheric Sounding Interferometer (IASI) on Metop-A, with balloon humidity sondes and with results obtained by a ground-based microwave radiometer (HAMSTRAD). In addition, a series of experiments has been designed to study frost formation on surfaces, and the temporal and spatial evolution of thermal gradients in the low atmosphere.Results. Dome C offers exceptional conditions in terms of absolute atmospheric transmission and stability for submillimetre astronomy. Over the austral winter the PWV exhibits long periods during which it is stable and at a very low level (0.1 to 0.3 mm). Higher values (0.2 to 0.8 mm) of PWV are observed during the short summer period. Based on observations over three years, a transmission of around 50% at 350 mu m is achieved for 75% of the time. The 200-mu m window opens with a typical transmission of 10% to 15% for 25% of the time.Conclusions. Dome C is one of the best accessible sites on Earth for submillimetre astronomy. Observations at 350 or 450 mu m are possible all year round, and the 200-mu m window opens long enough and with a sufficient transparency to be useful. Although the polar environment severely constrains hardware design, a permanent observatory with appropriate technical capabilities is feasible. Because of the very good astronomical conditions, high angular resolution and time series (multi-year) observations at Dome C with a medium size single dish telescope would enable unique studies to be conducted, some of which are not otherwise feasible even from space.
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