| 1. |
- Demichev, Vadim, et al.
(author)
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A time-resolved proteomic and prognostic map of COVID-19
- 2021
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In: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7
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Journal article (peer-reviewed)abstract
- COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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| 2. |
- Karpus, V., et al.
(author)
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Mg 2p shallow core-level and local atomic structure of i-ZnMgRE quasicrystals
- 2006
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In: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 252:15, s. 5411-5414
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Journal article (peer-reviewed)abstract
- We present a detailed analysis of the Mg 2p shallow core-levels measured on icosahedral single-grain ZnMgY, ZnMgHo, and ZnMgEr quasicrystals during a photoelectron microscopy study. The synchrotron radiation photoemission measurements were performed on in situ cleaved samples at a pressure of 10(-10) mbar and at low temperature, typically 90-150 K. The Mg 2p photoemission lines are essentially broadened as compared to those of the Mg 2p spin-orbit doublet recorded on the Zn2Mg crystalline Laves phase. The broadening is associated to the coordination shifts of the Mg 2p level due to the inequivalent magnesium sites in the quasicrystalline lattice. The coordination shifts are calculated on the basis of i-ZnMg(Ho, Y) atomic structure data, recently determined from the pair distribution function analysis. The coordination shifts obtained are up to 0.2 eV. The Mg 2p experimental spectral intensity is nicely reproduced by a superposition of coordination-shifted Mg 2p spin-orbit doublets.
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| 3. |
- Karpus, V., et al.
(author)
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Photoemission spectroscopy study of si-ZnMgHo quasicrystals
- 2008
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In: Optical materials (Amsterdam). - : Elsevier BV. - 0925-3467 .- 1873-1252. ; 30:5, s. 690-692
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Journal article (peer-reviewed)abstract
- The results of photoemission spectroscopy of the simple-icosahedral single-grain ZnMgHo quasicrystals are presented. Synchrotron radiation photoemission measurements were performed on in situ cleaved samples at 10(-10) mbar pressure and low, 160 K, temperature. The valence band photoemission spectra measured reveal a simple metal type valence band with a distinct Fermi edge and a sharp pseudogap feature, which originates from the van Hove singularities in the density of states. The photoemission spectra of the Mg 2p core level show the coordination shifts of Mg 2p, spin-orbit doublet due to inequivalent Mg sites in the quasicrystalline lattice.
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| 4. |
- Rollings, N., et al.
(author)
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Sperm telomere length correlates with blood telomeres and body size in red-sided garter snakes, Thamnophis sirtalis parietalis
- 2020
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In: Journal of Zoology. - : Wiley. - 0952-8369 .- 1469-7998. ; 312:1, s. 21-31
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Journal article (peer-reviewed)abstract
- Telomeres, tandem repeats of TTAGGG at the ends of chromosomes, are highly dynamic structures that shorten in response to a variety of factors, including organismal stress and tissue-specific growth rates. Cell turnover rates are frequently linked to their functions, resource availability and telomere dynamics. Using male red-sided garter snakes, Thamnophis sirtalis parietalis, as a model, we investigated the relationship between telomere length in sperm cells, blood cells telomere length and a growth proxy (age-adjusted body length and mass). This relationship is interesting because snakes exhibit indeterminate growth and because these garter snakes have a dissociated reproductive cycle where spermatogenesis occurs months prior to the mating season. In this study, we determined sperm telomere length (STL) and male age using qPCR and skeletochronology, respectively. Sperm telomere length correlated positively with snout-vent length (SVL) and with age-adjusted SVL as a proxy for growth rate (residuals of size against age regression, hereafter growth), but not with age. Although an individual's STL is correlated with blood telomere length (BTL), sperm telomeres are 60% longer than blood telomeres. In previous work, we have shown that BTL is shorter in older males and unrelated to SVL or any growth rate proxies. We hypothesized that STL is related to growth and SVL because growth and sperm production both occur during summer when resources are most abundant and stress lowest. This study is the first to compare telomere dynamics between cell types in a snake and supports growing evidence that telomere dynamics may be highly tissue-specific and driven by the life-history strategy of an organism.
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| 5. |
- Schöpf, Julia, et al.
(author)
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Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions
- 2024
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In: Nature Communications. - 2041-1723. ; 15, s. 1-17
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Journal article (peer-reviewed)abstract
- Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
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| 6. |
- Suchodolskis, A., et al.
(author)
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Indication of van Hove singularities in the density of states of ZnMg(Y,Ho) quasicrystals
- 2003
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In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 68:5
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Journal article (peer-reviewed)abstract
- We present a low-temperature synchrotron-radiation photoelectron microspectroscopy study of the valence bands of single-grain icosahedral ZnMgY and ZnMgHo quasicrystals. Their valence band photoemission spectra reveal in both cases a simple metal-type behavior with a clear metallic Fermi edge and a sharp pseudogap feature: the spectral intensity exhibits a maximum at approximate to0.7 eV below the chemical potential and a subsequent decrease as the Fermi level is approached. The analysis of the pseudogap feature, based on the band-structure hypothesis, shows that it corresponds to the van Hove singularities in the density of states (DOS), which originate from the intersections of the isoenergetic surface with the 222100 and 311111 Bragg planes. The reconstructed density of states agrees in general trends with the theoretical first-principles DOS of hexagonal ZnMgY approximants, and correctly reproduces the experimental value of i-ZnMgY electronic specific-heat coefficient.
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| 7. |
- Suchodolskis, A., et al.
(author)
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Photoemission and optical spectroscopy of i-ZnMgEr quasicrystal
- 2005
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In: Acta Physica Polonica. A. - 0587-4246 .- 1898-794X. ; 107:2, s. 412-419
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Journal article (peer-reviewed)abstract
- The results of photoemission and optical studies of icosahedral single-grain ZnMgEr quasicrystals are presented. Synchrotron radiation photoemission measurements were performed on in situ cleaved samples at 10(-10) mbar pressure and low, 140-150 K temperature. The valence band photoemission spectra measured reveal a simple metal-type valence band of icosahedral ZnMgEr with a distinct Fermi edge cut-off and with a sharp pseudogap feature. The photoemission spectra of shallow Mg 2p and Zn 3d core levels indicate a coordination shift of Mg 2p spin-orbit doublet and an oscillating dependence of Zn 3d photoemission line components on the photon energy within the hv = 20-160 eV range investigated. The optical response of icosahedral ZnMgEr, a dispersion of the dielectric function, was measured by the spectroscopic ellipsometry technique in the 0.5-5.0 eV spectral range. The optical spectra of the quasicrystal indicate the Drude-type optical response superimposed with a peak of interband optical transitions. The interband optical transitions can be modelled with the pseudogap parameters which agree with those deduced in an analysis of the photoemission valence band spectra.
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| 8. |
- Suchodolskis, A., et al.
(author)
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Pseudogap structure in icosahedral ZnMgY and ZnMgHo quasicrystals
- 2003
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In: Applied Surface Science. - 0169-4332 .- 1873-5584. ; 212, s. 485-490
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Journal article (peer-reviewed)abstract
- The results of a photoemission study of icosahedral single-grain ZnMg(Y, Ho) quasicrystals and their crystalline approximant Zn2Mg are presented. Synchrotron radiation photoemission measurements have been performed on in situ cleaved samples at low temperature of approximate to90 K and 10(-10) mbar pressure. The spectra obtained indicate simple metal-type valence bands (VB) with distinct Fermi edge cutoff. Analysis of the Fermi edge spectra reveals the presence of a pseudogap in i-ZnMg(Y, Ho) quasicrystals. The pseudogap corresponds to a rather sharp DOS dip at the Fermi level with th approximate to50% (of the normal DOS) depth and the approximate to0.8 eV width. The values of i-ZnMg(Y, Ho) pseudogap parameters are comparable with those of other quasicrystals.
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| 9. |
- Suchodolskis, A., et al.
(author)
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Valence band structure of i-ZnMgEr quasicrystal : photoemission study
- 2004
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In: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 16:50, s. 9137-9142
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Journal article (peer-reviewed)abstract
- The results of photoemission study of icosahedral single-grain ZnMgEr quasicrystals are presented. Synchrotron radiation photoemission measurements were performed on in situ cleaved samples at 10(-10) mbar pressure and low, 140-150 K, temperature. The valence band photoemission spectra measured reveal a simple-metal type valence band of i-ZnMgEr with a distinct Fermi edge cutoff and a spectral feature at 0.7 eV below epsilon(F). Analysis of the PE spectra shows that the spectral feature observed corresponds to the van Hove singularities in the density of states, which are due to intersections of the Fermi surface with the 222100 and 311111 Bragg planes.
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