| 1. |
- Naumov, V., et al.
(författare)
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COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity
- 2021
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Ingår i: Plos Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- Author summary This article introduces COVIDomic, a new integrative multi-omics online platform designed to facilitate the analysis of the large amount of health data collected from COVID-19 patients. The COVIDomic platform includes a user-friendly interface and provides a set of bioinformatics tools for the analysis of multi-modal metatranscriptomic data to determine the origin of the coronavirus strain and the expected severity of the disease. An analytical workflow includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification. These features allow studying the presence of common microbial organisms, their antibiotic resistance and the severity of the infection, as well as obtaining insights on the geographical locations from which the strain could have originated. Such openly distributed multi-modal platform will greatly accelerate the ongoing COVID-19 research and improve our readiness to respond to other infectious outbreaks. Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in December 2019 in Wuhan, China. It was quickly established that both the symptoms and the disease severity may vary from one case to another and several strains of SARS-CoV-2 have been identified. To gain a better understanding of the wide variety of SARS-CoV-2 strains and their associated symptoms, thousands of SARS-CoV-2 genomes have been sequenced in dozens of countries. In this article, we introduce COVIDomic, a multi-omics online platform designed to facilitate the analysis and interpretation of the large amount of health data collected from patients with COVID-19. The COVIDomic platform provides a comprehensive set of bioinformatic tools for the multi-modal metatranscriptomic data analysis of COVID-19 patients to determine the origin of the coronavirus strain and the expected severity of the disease. An integrative analytical workflow, which includes microbial pathogens community analysis, COVID-19 genetic epidemiology and patient stratification, allows to analyze the presence of the most common microbial organisms, their antibiotic resistance, the severity of the infection and the set of the most probable geographical locations from which the studied strain could have originated. The online platform integrates a user friendly interface which allows easy visualization of the results. We envision this tool will not only have immediate implications for management of the ongoing COVID-19 pandemic, but will also improve our readiness to respond to other infectious outbreaks.
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| 2. |
- Galkin, M. V., et al.
(författare)
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Thermal lens spectrometry for the synthesis and study of nanocomposites on the basis of silver salts absorbed by a polyacrylate matrix
- 2010
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Ingår i: Moscow University Chemistry Bulletin. - : Allerton Press. - 0027-1314 .- 1935-0260. ; 65:2, s. 91-97
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Tidskriftsartikel (refereegranskat)abstract
- Thermal lens spectrometry is applied to determine the absorption of transparent nanocomposite materials, which are produced by the thermal decomposition of silver salts absorbed in the bulk of a polymethacrylate matrix. The high spatial resolution of determination, corresponding to the size of laser beams, makes it possible to evaluate the homogeneity for the distribution of coloration in the matrix. The advantages of thermal lens spectrometry over spectrophotometry include the weak effect of sample scattering on the results of its absorption determination and a higher sensitivity of determination, which may exceed that of spectrophotometry by one or two orders of magnitude. The possibility of achieving local syntheses of nanosized particles in the bulk of the matrix by virtue of the photoinduced decomposition of silver salts in initial polyacrylate materials is shown. Thermal lens experiments also allow the combination of the synthesis of silver nanoparticles and control of the absorbance for the prepared structural units.
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| 3. |
- Mondal, I. C., et al.
(författare)
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Organosulfur/Selenium-Based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging
- 2022
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Ingår i: Chemistry - An Asian Journal. - : Wiley. - 1861-4728 .- 1861-471X. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- We present fluorogenic cationic organo chalcogens that are highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report the application of organoselenium and organosulfur-based cell-permeable red-emissive probes bearing a favorable cyclic sidearm for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interacting with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes.
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| 4. |
- Alekseev, A. Yu, et al.
(författare)
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Interplay between structural changes, surface states and quantum confinement effects in semiconducting Mg2Si and Ca2Si thin films
- 2023
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 25:29, s. 19952-19962
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio techniques have been used to investigate structural changes in semiconducting Mg2Si and Ca2Si thin films (from 17 nm down to 0.2 nm corresponding to the 2D structure) along with band-gap variations due to quantum confinement. Cubic Mg2Si(111) thin films being dynamically stable at thicknesses (d) larger than 0.3 nm displayed an indirect band gap, the reduction of which with increasing d could be reasonably well described by the simple effective mass approximation. Only 2D Mg2Si has a unique structure because of the orthorhombic distortion and the direct band gap. Since the surface energy of cubic Ca2Si(111) films was lower with respect to any surface of the orthorhombic phase, which is the ground state for the Ca2Si bulk, the metastable in-bulk cubic phase in the form of thin films turned out to be preferable in total energy than any orthorhombic Ca2Si thin film for d < 3 nm. Sizable structural distortion and the appearance of surface states in the gap region of Ca2Si thin films with d < 3 nm could be the reason for an odd dependence of the band-gap variation on d.
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| 5. |
- Cherepov, Sergiy, et al.
(författare)
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Core-Core Dynamics in Spin Vortex Pairs
- 2012
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 109:9, s. 097204-
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Tidskriftsartikel (refereegranskat)abstract
- We investigate nanopillars in which two thin ferromagnetic particles are separated by a nanometer thin nonmagnetic spacer and can be set into stable spin vortex-pair configurations. We find that the previously unexplored limit of strong vortex core-core coupling can dominate the spin dynamics in the system. We observe experimentally and explain analytically and numerically how the 0.2 GHz gyrational resonance modes of the individual vortices are transformed into a 2 GHz collective rotational resonance mode in the configurations where the two cores form a bound pair.
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| 6. |
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| 7. |
- Cherkasov, A. R., et al.
(författare)
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Correlation analysis in the chemistry of free radicals
- 2001
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Ingår i: Uspehi himii. - 0042-1308 .- 1817-5651. ; 70:1, s. 3-27
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Forskningsöversikt (refereegranskat)abstract
- Published data available by now on the use of correlation analysis in the free-radical chemistry are discussed systematically. The scales of <> sigma -constants of substituents proposed previously are analysed. It is shown that none of them is suitable as a general scale because almost in all cases, it is impossible to separate correctly the proper radical and polar contributions to the overall effect of substituents. A new approach to the quantitative estimation of the relationship between the structure and reactivity of molecules in free-radical processes is proposed and called r(-2)-analysis.
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| 8. |
- Rebrova, N. V., et al.
(författare)
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Crystal growth and characterization of Eu2+ doped Cs1-xRbxCaBr3
- 2020
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Ingår i: Journal of Alloys and Compounds. - : Elsevier BV. - 0925-8388 .- 1873-4669. ; 816
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Tidskriftsartikel (refereegranskat)abstract
- A series of Eu2+ doped Cs1-xRbxCaBr3 solid solutions were grown using the Bridgman-Stockbarger technique. Their photoluminescence and scintillation properties are studied. Upon optical and X-ray excitation, the Cs1-xRbxCaBr3 and Eu2+ activated samples show a band, which can be attributed to the 5d-4f transition in Eu2+. The decay time constants become shorter with increasing Rb content and lie in the range of 3-4 mu s. The scintillation performance of solid solutions Cs1-xRbxCa0. 95Eu0.05Br3 is improved compared with the end members (CsCa0.95Eu0.05Br3 and RbCa0.95Eu0.05Br3). The best energy resolution of 6.4% at 662 keV was determined for Cs0.2Rb0.8Ca0.95Eu0.05Br3 , and the best light yield, equal to 61.2% of Nal:TI, was demonstrated by Cs0.4Rb0.6Ca0.95Eu0.05Br3.
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| 9. |
- Frasca, Serena, et al.
(författare)
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Toward biomass-based organic electronics: Continuous flow synthesis and electropolymerization of N-substituted polypyrroles
- 2023
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Ingår i: ACS Spring meeting 2023. - Indianapolis.
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Konferensbidrag (refereegranskat)abstract
- Pyrroles are important building blocks in many areas of chemistry, pharmaceuticals and materials. Pyrroles are currently fossil-based and transition to renewable alternatives demands new synthetic pathways. The use of biomass is a very attractive option for more sustainable solutions and several bulk and fine chemical are already produced from biomass. 2,5-Dimethoxytetrahydrofuran is an example of fine chemical derived from carbohydrate fraction of biomass. Here we report the synthesis of N-substituted pyrroles through a modified Clauson-Kass protocol starting from 2,5-dimethoxytetrahydrofuran. The proposed method allows to obtain pyrroles under mild reaction conditions and it can be performed catalyst-free. The protocol works both in continuous flow and under batch conditions.. A wide range of anilines and sulphonamides are transformed to corresponding N-substituted pyrroles in good to excellent yields. Conductive films are achieved through electropolymerization and they show distinct redox activity. Current efforts entail the application of the material in sensors or energy storage devices. The proposed method opens the pathway to sustainable biomass-based organic electronics.
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| 10. |
- Galkin, Maxim V., et al.
(författare)
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Hydrogen-free catalytic fractionation of woody biomass
- 2016
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Ingår i: ChemSusChem. - : Wiley. - 1864-5631 .- 1864-564X. ; 9:23, s. 3280-3287
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Tidskriftsartikel (refereegranskat)abstract
- The pulping industry could become a biorefinery if the lignin and hemicellulose components of the lignocellulose are valorized. Conversion of lignin into well-defined aromatic chemicals is still a major challenge. Lignin depolymerization reactions often occur in parallel with irreversible condensation reactions of the formed fragments. Here, we describe a strategy that markedly suppresses the undesired condensation pathways and allows to selectively transform lignin into a few aromatic compounds. Notably, applying this strategy to woody biomass at organosolv pulping conditions, the hemicellulose, cellulose, and lignin were separated and in parallel the lignin was transformed into aromatic monomers. In addition, we were able to utilize a part of the lignocellulose as an internal source of hydrogen for the reductive lignin transformations. We hope that the presented methodology will inspire researchers in the field of lignin valorization as well as pulp producers to develop more efficient biomass fractionation processes in the future.
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