| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 3. |
- Adewumi, Oluseun, et al.
(författare)
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Characterization of human embryonic stem cell lines by the International Stem Cell Initiative
- 2007
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 25:7, s. 803-816
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Tidskriftsartikel (refereegranskat)abstract
- The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue- nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.
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| 4. |
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| 5. |
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| 6. |
- Kohler, Annegret, et al.
(författare)
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists.
- 2015
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 47:4, s. 176-410
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Tidskriftsartikel (refereegranskat)abstract
- To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall-degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7-38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.
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| 7. |
- Morioka, Naoya, et al.
(författare)
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Spin-controlled generation of indistinguishable and distinguishable photons from silicon vacancy centres in silicon carbide
- 2020
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Quantum systems combining indistinguishable photon generation and spin-based quantum information processing are essential for remote quantum applications and networking. However, identification of suitable systems in scalable platforms remains a challenge. Here, we investigate the silicon vacancy centre in silicon carbide and demonstrate controlled emission of indistinguishable and distinguishable photons via coherent spin manipulation. Using strong off-resonant excitation and collecting zero-phonon line photons, we show a two-photon interference contrast close to 90% in Hong-Ou-Mandel type experiments. Further, we exploit the systems intimate spin-photon relation to spin-control the colour and indistinguishability of consecutively emitted photons. Our results provide a deep insight into the systems spin-phonon-photon physics and underline the potential of the industrially compatible silicon carbide platform for measurement-based entanglement distribution and photonic cluster state generation. Additional coupling to quantum registers based on individual nuclear spins would further allow for high-level network-relevant quantum information processing, such as error correction and entanglement purification. Defects in silicon carbide can act as single photon sources that also have the benefit of a host material that is already used in electronic devices. Here the authors demonstrate that they can control the distinguishability of the emitted photons by changing the defect spin state.
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| 8. |
- Münch, Andreas, et al.
(författare)
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Budesonide as induction therapy for incomplete microscopic colitis : A randomised, placebo-controlled multicentre trial
- 2021
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Ingår i: United European Gastroenterology journal. - : Sage Publications. - 2050-6406 .- 2050-6414. ; 9:7, s. 837-847
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Tidskriftsartikel (refereegranskat)abstract
- Background and aims: Incomplete microscopic colitis (MCi) is a subtype of microscopic colitis (MC). Budesonide is recommended as a first-line treatment for MC. However, randomised trials on efficacy of treatment in MCi are missing. We therefore performed a randomised, placebo-controlled trial to evaluate budesonide as induction therapy for MCi.Methods: Patients with active MCi were randomly assigned to either budesonide 9 mg once daily or placebo for 8 weeks in a double-blind, double-dummy design. The primary endpoint was clinical remission, defined as a mean of <3 stools/day and a mean of <1 watery stool/day in the 7 days before week 8.Results: Due to insufficient patient recruitment, the trial was discontinued prematurely. The intention-to-treat analysis included 44 patients (21 budesonide and 23 placebo). The primary endpoint of clinical remission at week 8 was obtained by 71.4% on budesonide and 43.5% on placebo (p = 0.0582). All clinical secondary endpoints were in favour of budesonide. Budesonide decreased the number of soft or watery stools (16.3 vs. 7.7, p = 0.0186) and improved health-related quality of life for all four dimensions of the short health scale. Adverse events with a suspected relation to study drug were reported in one patient in the budesonide group and two patients in the placebo group. Neither serious nor severe adverse events occurred during the double-blind phase.Conclusions: Budesonide decreased the frequency of soft or watery stools and improved the patients' quality of life significantly in MCi, but the primary endpoint was not met due to the low sample size (type 2 error). Budesonide was safe and well tolerated during the 8-weeks treatment course.
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| 9. |
- Nagy, Roland, et al.
(författare)
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High-fidelity spin and optical control of single silicon-vacancy centres in silicon carbide
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Scalable quantum networking requires quantum systems with quantum processing capabilities. Solid state spin systems with reliable spin-optical interfaces are a leading hardware in this regard. However, available systems suffer from large electron-phonon interaction or fast spin dephasing. Here, we demonstrate that the negatively charged silicon-vacancy centre in silicon carbide is immune to both drawbacks. Thanks to its (4)A(2) symmetry in ground and excited states, optical resonances are stable with near-Fourier-transform-limited linewidths, allowing exploitation of the spin selectivity of the optical transitions. In combination with millisecond-long spin coherence times originating from the high-purity crystal, we demonstrate high-fidelity optical initialization and coherent spin control, which we exploit to show coherent coupling to single nuclear spins with similar to 1 kHz resolution. The summary of our findings makes this defect a prime candidate for realising memory-assisted quantum network applications using semiconductor-based spin-to-photon interfaces and coherently coupled nuclear spins.
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| 10. |
- Nagy, Roland, et al.
(författare)
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Narrow inhomogeneous distribution of spin-active emitters in silicon carbide
- 2021
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Ingår i: Applied Physics Letters. - : AMER INST PHYSICS. - 0003-6951 .- 1077-3118. ; 118:14
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Tidskriftsartikel (refereegranskat)abstract
- Optically active solid-state spin registers have demonstrated their unique potential in quantum computing, communication, and sensing. Realizing scalability and increasing application complexity require entangling multiple individual systems, e.g., via photon interference in an optical network. However, most solid-state emitters show relatively broad spectral distributions, which hinders optical interference experiments. Here, we demonstrate that silicon vacancy centers in semiconductor silicon carbide (SiC) provide a remarkably small natural distribution of their optical absorption/emission lines despite an elevated defect concentration of approximate to 0.43 mu m - 3. In particular, without any external tuning mechanism, we show that only 13 defects have to be investigated until at least two optical lines overlap within the lifetime-limited linewidth. Moreover, we identify emitters with overlapping emission profiles within diffraction-limited excitation spots, for which we introduce simplified schemes for the generation of computationally relevant Greenberger-Horne-Zeilinger and cluster states. Our results underline the potential of the CMOS-compatible SiC platform toward realizing networked quantum technology applications.
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| 11. |
- Nagy, Roland, et al.
(författare)
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Quantum Properties of Dichroic Silicon Vacancies in Silicon Carbide
- 2018
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Ingår i: Physical Review Applied. - 2331-7019. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- Although various defect centers have displayed promise as either quantum sensors, single photon emitters, or light-matter interfaces, the search for an ideal defect with multifunctional ability remains open. In this spirit, we study the dichroic silicon vacancies in silicon carbide that feature two well-distinguishable zero-phonon lines and analyze the quantum properties in their optical emission and spin control. We demonstrate that this center combines 40% optical emission into the zero-phonon lines showing the contrasting difference in optical properties with varying temperature and polarization, and a 100% increase in the fluorescence intensity upon the spin resonance, and long spin coherence time of their spin-3/2 ground states up to 0.6 ms. These results single out this defect center as a promising system for spin-based quantum technologies.
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