| 1. |
- Allesøe, Rosa Lundbye, et al.
(författare)
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Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models
- 2023
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 41:3, s. 399-408
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Tidskriftsartikel (refereegranskat)abstract
- The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug–omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug–drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.
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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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| 4. |
- Abdellah, Mohamed, et al.
(författare)
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Drastic difference between hole and electron injection through the gradient shell of CdxSeyZn1−xS1−y quantum dots
- 2017
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3364 .- 2040-3372. ; 9:34, s. 12503-12508
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Tidskriftsartikel (refereegranskat)abstract
- Ultrafast fluorescence spectroscopy was used to investigate the hole injection in CdxSeyZn1-xS1-y gradient core-shell quantum dot (CSQD) sensitized p-type NiO photocathodes. A series of CSQDs with a wide range of shell thicknesses was studied. Complementary photoelectrochemical cell measurements were carried out to confirm that the hole injection from the active core through the gradient shell to NiO takes place. The hole injection from the valence band of the QDs to NiO depends much less on the shell thickness when compared to the corresponding electron injection to n-type semiconductor (ZnO). We simulate the charge carrier tunneling through the potential barrier due to the gradient shell by numerically solving the Schrodinger equation. The details of the band alignment determining the potential barrier are obtained from X-ray spectroscopy measurements. The observed drastic differences between the hole and electron injection are consistent with a model where the hole effective mass decreases, while the gradient shell thickness increases.
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| 5. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 6. |
- Belgrano, Andrea, et al.
(författare)
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Mapping and Evaluating Marine Protected Areas and Ecosystem Services: A Transdisciplinary Delphi Forecasting Process Framework
- 2021
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Marine Protected Areas (MPAs) are an important tool for management and conservation and play an increasingly recognised role in societal and human well-being. However, the assessment of MPAs often lacks a simultaneous consideration of ecological and socio-economic outcomes, and this can lead to misconceptions on the effectiveness of MPAs. In this perspective, we present a transdisciplinary approach based on the Delphi method for mapping and evaluating Marine Protected Areas for their ability to protect biodiversity while providing Ecosystem Services (ES) and related human well-being benefits – i.e., the ecosystem outputs from which people benefit. We highlight the need to include the human dimensions of marine protection in such assessments, given that the effectiveness of MPAs over time is conditional on the social, cultural and institutional contexts in which MPAs evolve. Our approach supports Ecosystem-Based Management and highlights the importance of MPAs in achieving restoration, conservation, and sustainable development objectives in relation to EU Directives such as the Marine Strategy Framework Directive (MSFD), the Maritime Spatial Planning Directive (MSPD), and the Common Fisheries Policy (CFP).
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| 7. |
- De Vico, Luca, et al.
(författare)
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Macrocycle ring deformation as the secondary design principle for light-harvesting complexes
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 115:39, s. 9051-9057
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Tidskriftsartikel (refereegranskat)abstract
- Natural light-harvesting is performed by pigment–protein complexes, which collect and funnel the solar energy at the start of photosynthesis. The identity and arrangement of pigments largely define the absorption spectrum of the antenna complex, which is further regulated by a palette of structural factors. Small alterations are induced by pigment–protein interactions. In light-harvesting systems 2 and 3 from Rhodoblastus acidophilus, the pigments are arranged identically, yet the former has an absorption peak at 850 nm that is blue-shifted to 820 nm in the latter. While the shift has previously been attributed to the removal of hydrogen bonds, which brings changes in the acetyl moiety of the bacteriochlorophyll, recent work has shown that other mechanisms are also present. Using computational and modeling tools on the corresponding crystal structures, we reach a different conclusion: The most critical factor for the shift is the curvature of the macrocycle ring. The bending of the planar part of the pigment is identified as the second-most important design principle for the function of pigment–protein complexes—a finding that can inspire the design of novel artificial systems.
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| 8. |
- Finkelstein-Shapiro, Daniel, et al.
(författare)
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Adiabatic elimination and subspace evolution of open quantum systems
- 2020
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Ingår i: Physical Review A. - 2469-9926. ; 101:4
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Tidskriftsartikel (refereegranskat)abstract
- Efficient descriptions of open quantum systems can be obtained by performing an adiabatic elimination of the fast degrees of freedom and formulating effective operators for the slow degrees of freedom in reduced dimensions. Here, we perform the construction of effective operators in frequency space, and using the final value theorem or alternatively the Keldysh theorem, we provide a correction for the trace of the density matrix which takes into account the non-trace-preserving character of the evolution. We illustrate our results with two different systems, one where the eliminated fast subspace is constituted by a continuous set of states and ones with discrete states. Furthermore, we show that the two models converge for very large dissipation and at coherent population trapping points. Our results also provide an intuitive picture of the correction to the trace of the density matrix as a detailed balance equation.
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| 9. |
- Finkelstein-Shapiro, Daniel, et al.
(författare)
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Classification of dark states in multilevel dissipative systems
- 2019
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Ingår i: Physical Review A. - 2469-9926. ; 99:5
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Tidskriftsartikel (refereegranskat)abstract
- Dark states are eigenstates or steady states of a system that are decoupled from the radiation. Their use, along with associated techniques such as stimulated Raman adiabatic passage, has extended from atomic physics, where it is an essential cooling mechanism, to more recent versions in the condensed phase where it can increase the coherence times of qubits. These states are often discussed in the context of unitary evolution and found with elegant methods exploiting symmetries, or via the Morris-Shore transformation. However, the link with dissipative systems is not always transparent, and distinctions between classes of coherent population trapping are not always clear. We present a detailed overview of the arguments to find stationary dark states in dissipative systems, and examine their dependence on the Hamiltonian parameters, their multiplicity, and purity. We evidence the class of dark states that depends not only on the detunings of the lasers but also on their relative intensities and phases. We illustrate the criteria with the more complex physical system of the hyperfine transitions of Rb87 and show how a knowledge of the dark-state manifold can guide the preparation of pure states.
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| 10. |
- Finkelstein-Shapiro, Daniel, et al.
(författare)
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Coherent two-dimensional spectroscopy of a Fano model
- 2016
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Ingår i: Physical Review B. - 1098-0121. ; 94:20
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Tidskriftsartikel (refereegranskat)abstract
- The Fano line shape arises from the interference of two excitation pathways to reach a continuum. Its generality has resulted in a tremendous success in explaining the line shapes of many one-dimensional spectroscopies - absorption, emission, scattering, conductance, photofragmentation - applied to very varied systems - atoms, molecules, semiconductors, and metals. Unraveling a spectroscopy into a second dimension reveals the relationship between states in addition to decongesting the spectra. Femtosecond-resolved two-dimensional electronic spectroscopy (2DES) is a four-wave mixing technique that measures the time evolution of the populations and coherences of excited states. It has been applied extensively to the dynamics of photosynthetic units, and more recently to materials with extended band structures. In this paper, we solve the full time-dependent third-order response, measured in 2DES, of a Fano model and give the system parameters that become accessible.
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| 11. |
- Finkelstein-Shapiro, Daniel, et al.
(författare)
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Two-dimensional Fano lineshapes : Excited-state absorption contributions
- 2018
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 148:18
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Tidskriftsartikel (refereegranskat)abstract
- Fano interferences in nanostructures are influenced by dissipation effects as well as many-body interactions. Two-dimensional coherent spectroscopies have just begun to be applied to these systems where the spectroscopic signatures of a discrete-continuum structure are not known. In this article, we calculate the excited-state absorption contribution for different models of higher lying excited states. We find that the characteristic asymmetry of one-dimensional spectroscopies is recovered from the many-body contributions and that the higher lying excited manifolds have distorted lineshapes that are not anticipated from discrete-level Hamiltonians. We show that the Stimulated Emission cannot have contributions from a flat continuum of states. This work completes the Ground-State Bleach and Stimulated Emission signals that were calculated previously [D. Finkelstein-Shapiro et al., Phys. Rev. B 94, 205137 (2016)]. The model reproduces the observations reported for molecules on surfaces probed by 2DIR.
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| 12. |
- Freitag, Daniel F., et al.
(författare)
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Cardiometabolic effects of genetic upregulation of the interleukin 1 receptor antagonist: a Mendelian randomisation analysis
- 2015
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Ingår i: The Lancet Diabetes & Endocrinology. - 2213-8595. ; 3:4, s. 243-253
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Tidskriftsartikel (refereegranskat)abstract
- Background To investigate potential cardiovascular and other effects of long-term pharmacological interleukin 1 (IL-1) inhibition, we studied genetic variants that produce inhibition of IL-1, a master regulator of inflammation. Methods We created a genetic score combining the effects of alleles of two common variants (rs6743376 and rs1542176) that are located upstream of IL1RN, the gene encoding the IL-1 receptor antagonist (IL-1Ra; an endogenous inhibitor of both IL-1 alpha and IL-1 beta); both alleles increase soluble IL-1Ra protein concentration. We compared effects on inflammation biomarkers of this genetic score with those of anakinra, the recombinant form of IL-1Ra, which has previously been studied in randomised trials of rheumatoid arthritis and other inflammatory disorders. In primary analyses, we investigated the score in relation to rheumatoid arthritis and four cardiometabolic diseases (type 2 diabetes, coronary heart disease, ischaemic stroke, and abdominal aortic aneurysm; 453 411 total participants). In exploratory analyses, we studied the relation of the score to many disease traits and to 24 other disorders of proposed relevance to IL-1 signalling (746 171 total participants). Findings For each IL1RN minor allele inherited, serum concentrations of IL-1Ra increased by 0.22 SD (95% CI 0.18-0.25; 12.5%; p=9.3 x 10(-33)), concentrations of interleukin 6 decreased by 0.02 SD (-0.04 to -0.01; -1,7%; p=3.5 x 10(-3)), and concentrations of C-reactive protein decreased by 0.03 SD (-0.04 to -0.02; -3.4%; p=7.7 x 10(-14)). We noted the effects of the genetic score on these inflammation biomarkers to be directionally concordant with those of anakinra. The allele count of the genetic score had roughly log-linear, dose-dependent associations with both IL-1Ra concentration and risk of coronary heart disease. For people who carried four IL-1Ra-raising alleles, the odds ratio for coronary heart disease was 1.15 (1.08-1.22; p=1.8 x 10(-6)) compared with people who carried no IL-1Ra-raising alleles; the per-allele odds ratio for coronary heart disease was 1.03 (1.02-1.04; p=3.9 x 10(-10)). Perallele odds ratios were 0.97 (0.95-0.99; p=9.9 x 10(-4)) for rheumatoid arthritis, 0.99 (0.97-1.01; p=0.47) for type 2 diabetes, 1.00 (0.98-1.02; p=0.92) for ischaemic stroke, and 1.08 (1.04-1.12; p=1.8 x 10(-5)) for abdominal aortic aneurysm. In exploratory analyses, we observed per-allele increases in concentrations of proatherogenic lipids, including LDL-cholesterol, but no clear evidence of association for blood pressure, glycaemic traits, or any of the 24 other disorders studied. Modelling suggested that the observed increase in LDL-cholesterol could account for about a third of the association observed between the genetic score and increased coronary risk. Interpretation Human genetic data suggest that long-term dual IL-1 alpha/beta inhibition could increase cardiovascular risk and, conversely, reduce the risk of development of rheumatoid arthritis. The cardiovascular risk might, in part, be mediated through an increase in proatherogenic lipid concentrations. Copyright (C) The Interleukin 1 Genetics Consortium. Open Access article distributed under the terms of CC-BY-NC-ND.
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| 13. |
- Hansen, Thorsten, et al.
(författare)
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A molecule wired: Electrostatic investigation
- 2005
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Ingår i: Chemical Physics Letters. - : Elsevier BV. - 0009-2614. ; 405:1-3, s. 118-122
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Tidskriftsartikel (refereegranskat)abstract
- We present calculations of ground state and excitation energies for ethene between metal electrodes. The model determines the effects of the electrodes by incorporating a heterogeneous and structured solvation model with the quantum mechanical description of the molecular system. The effects of the electrodes are of electrostatic origin and an external bias can be applied enabling a close connection to the actual physical process related to the measurements of charge transport in molecules located between electrodes.
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| 14. |
- Hansen, Thorsten, et al.
(författare)
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Nonlinear response theory on the Keldysh contour
- 2012
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Ingår i: Journal of Physics B: Atomic, Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 45:15
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Tidskriftsartikel (refereegranskat)abstract
- Following the work of Schwinger (1961 J. Math. Phys 2 407), we present a general method for deriving quantum response functions on a closed-loop contour in the complex time plane. We focus on optical response functions of linear to third order and demonstrate by projecting contour time onto the real axis how they connect to Liouville space pathways. This work highlights the close connection between the Keldysh contour and the double-sided Feynman diagrams used in nonlinear optical spectroscopy. In addition, we give a Keldysh contour derivation of the Marcus equation for electron transfer.
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| 15. |
- Hansen, Thorsten, et al.
(författare)
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Orbital Topology Controlling Charge Injection in Quantum-Dot-Sensitized Solar Cells
- 2014
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 5:7, s. 1157-1162
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Tidskriftsartikel (refereegranskat)abstract
- Quantum-dot-sensitized solar cells are emerging as a promising development of dye-sensitized solar cells, where photostable semiconductor quantum dots replace molecular dyes. Upon photoexcitation of a quantum dot, an electron is transferred to a high-band-gap metal oxide. Swift electron transfer is crucial to ensure a high overall efficiency of the solar cell. Using femtosecond time-resolved spectroscopy, we find the rate of electron transfer to be surprisingly sensitive to the chemical structure of the linker molecules that attach the quantum dots to the metal oxide. A rectangular barrier model is unable to capture the observed variation. Applying bridge-mediated electron-transfer theory, we find that the electron-transfer rates depend on the topology of the frontier orbital of the molecular linker. This promises the capability of fine tuning the electron-transfer rates by rational design of the linker molecules.
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| 16. |
- Hawkes, Jeffrey A., et al.
(författare)
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Efficient removal of recalcitrant deep-ocean dissolved organic matter during hydrothermal circulation
- 2015
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Ingår i: Nature Geoscience. - 1752-0894 .- 1752-0908. ; 8:11, s. 856-
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Tidskriftsartikel (refereegranskat)abstract
- Oceanic dissolved organic carbon (DOC) is an important carbon pool, similar in magnitude to atmospheric CO2, but the fate of its oldest forms is not well understood(1,2). Hot hydrothermal circulation may facilitate the degradation of otherwise un-reactive dissolved organic matter, playing an important role in the long-term global carbon cycle. The oldest, most recalcitrant forms of DOC, which make up most of oceanic DOC, can be recovered by solid-phase extraction. Here we present measurements of solid-phase extractable DOC from samples collected between 2009 and 2013 at seven vent sites in the Atlantic, Pacific and Southern oceans, along with magnesium concentrations, a conservative tracer of water circulation through hydrothermal systems. We find that magnesium and solid-phase extractable DOC concentrations are correlated, suggesting that solid-phase extractable DOC is almost entirely lost from solution through mineralization or deposition during circulation through hydrothermal vents with fluid temperatures of 212-401 degrees C. In laboratory experiments, where we heated samples to 380 degrees C for four days, we found a similar removal efficiency. We conclude that thermal degradation alone can account for the loss of solid-phase extractable DOC in natural hydrothermal systems, and that its maximum lifetime is constrained by the timescale of hydrothermal cycling, at about 40 million years(3).
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| 17. |
- Hawkes, Jeffrey A., et al.
(författare)
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Molecular alteration of marine dissolved organic matter under experimental hydrothermal conditions
- 2016
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Ingår i: Geochimica et Cosmochimica Acta. - : Elsevier BV. - 0016-7037 .- 1872-9533. ; 175, s. 68-85
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Tidskriftsartikel (refereegranskat)abstract
- Marine dissolved organic matter (DOM) is a large (660 Pg) pool of reduced carbon that is subject to thermal alteration in hydrothermal systems and sedimentary basins. In natural high-temperature hydrothermal systems, DOM is almost completely removed, but the mechanism and temperature dependence of this removal have not been studied to date. We investigated molecular-level changes to DOM that was solid-phase extracted (SPE-DOM) from the deep ocean of the North Pacific Ocean. This complex molecular mixture was experimentally exposed to temperatures between 100 and 380 degrees C over the course of two weeks in artificial seawater, and was then characterised on a molecular level via ultrahigh-resolution Fourier-transform ion cyclotron mass spectrometry (FT-ICR-MS). Almost 93% of SPE-DOM was removed by the treatment at 380 degrees C, and this removal was accompanied by a consistent pattern of SPE-DOM alteration across the temperatures studied. Higher molecular weight and more oxygen rich compounds were preferentially removed, suggesting that decarboxylation and dehydration of carboxylic acid and alcohol groups are the most rapid degradation mechanisms. Nitrogen containing compounds followed the same overall trends as those containing just C, H and O up to 300 degrees C. Above this temperature, the most highly altered samples contained very little of the original character of marine DOM, instead being mainly composed of very low intensity N- and S-containing molecules with a high H/C ratio (>1.5). Our results suggest that abiotic hydrothermal alteration of SPE-DOM may already occur at temperatures above 68 degrees C. Our experiments were conducted without a sedimentary or mineral phase, and demonstrate that profound molecular alteration and almost complete removal of marine SPE-DOM requires nothing more than heating in a seawater matrix.
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| 18. |
- Mentovich, Elad D., et al.
(författare)
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Gated-Controlled Rectification of a Self-Assembled Monolayer-Based Transistor
- 2013
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 117:16, s. 8468-8474
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Tidskriftsartikel (refereegranskat)abstract
- A vertical gate symmetrical molecular transistor is demonstrated. It includes self assembled monolayer of ferrocene molecules chemically bonded to be a flat Au source and Au nanoparticles drain electrodes while gated with the central gate electrode. Using this configuration, we show that negative differential resistance, symmetrical behavior, and rectification effects can be tuned by controlling the gate voltage. The I-V curves shift from symmetric to strongly rectifying over a gate voltage range of a few tenths of volts around a threshold value where the junction behaves symmetrically. This is due to charging of the nanoparticle contact, which modifies the spatial profile of the voltage across the junction, a fact that we have included in a simple theoretical model that explains our experimental results quite well. Our device design affords a new way to fine-tune the rectification of molecular devices in a way that does not necessarily involve the Coulomb charging of the wire.
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| 19. |
- Merder, Julian, et al.
(författare)
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ICBM-OCEAN : Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures
- 2020
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 92:10, s. 6832-6838
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Tidskriftsartikel (refereegranskat)abstract
- Untargeted molecular analyses of complex mixtures are relevant for many fields of research, including geochemistry, pharmacology, and medicine. Ultrahigh-resolution mass spectrometry is one of the most powerful tools in this context. The availability of open scripts and online tools for specific data processing steps such as noise removal or molecular formula assignment is growing, but an integrative tool where all crucial steps are reproducibly evaluated and documented is lacking. We developed a novel, server-based tool (ICBM-OCEAN, Institute for Chemistry and Biology of the Marine Environment, Oldenburg-complex molecular mixtures, evaluation & analysis) that integrates published and novel approaches for standardized processing of ultrahigh-resolution mass spectrometry data of complex molecular mixtures. Different from published approaches, we offer diagnostic and validation tools for all relevant steps. Among other features, we included objective and reproducible reduction of noise and systematic errors, spectra recalibration and alignment, and identification of likeliest molecular formulas. With 15 chemical elements, the tool offers high flexibility in formula attribution. Alignment of mass spectra among different samples prior to molecular formula assignment improves mass error and facilitates molecular formula confirmation with the help of isotopologues. The online tool and the detailed instruction manual are freely accessible at www.icbm.de/icbm-ocean.
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| 20. |
- Moslemi, Camous, et al.
(författare)
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A large cohort study of the effects of Lewis, ABO, 13 other blood groups, and secretor status on COVID-19 susceptibility, severity, and long COVID-19
- 2023
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Ingår i: Transfusion. - : Wiley. - 0041-1132 .- 1537-2995. ; 63:1, s. 47-58
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Tidskriftsartikel (refereegranskat)abstract
- Background: Previous studies have reported Blood type O to confer a lower risk of SARS-CoV-2 infection, while secretor status and other blood groups have been suspected to have a similar effect as well. Study design and methods: To determine whether any other blood groups influence testing positive for SARS-CoV-2, COVID-19 severity, or prolonged COVID-19, we used a large cohort of 650,156 Danish blood donors with varying available data for secretor status and blood groups ABO, Rh, Colton, Duffy, Diego, Dombrock, Kell, Kidd, Knops, Lewis, Lutheran, MNS, P1PK, Vel, and Yt. Of these, 36,068 tested positive for SARS-CoV-2 whereas 614,088 tested negative between 2020-02-17 and 2021-08-04. Associations between infection and blood groups were assessed using logistic regression models with sex and age as covariates. Results: The Lewis blood group antigen Lea displayed strongly reduced SARS-CoV-2 susceptibility OR 0.85 CI[0.79–0.93] p <.001. Compared to blood type O, the blood types B, A, and AB were found more susceptible toward infection with ORs 1.1 CI[1.06–1.14] p <.001, 1.17 CI[1.14–1.2] p <.001, and 1.2 CI[1.14–1.26] p <.001, respectively. No susceptibility associations were found for the other 13 blood groups investigated. There was no association between any blood groups and COVID-19 hospitalization or long COVID-19. No secretor status associations were found. Discussion: This study uncovers a new association to reduced SARS-CoV-2 susceptibility for Lewis type Lea and confirms the previous link to blood group O. The new association to Lea could be explained by a link between mucosal microbiome and SARS-CoV-2.
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| 21. |
- Moslemi, Camous, et al.
(författare)
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Genetic prediction of 33 blood group phenotypes using an existing genotype dataset
- 2023
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Ingår i: Transfusion. - 0041-1132. ; 63:12, s. 2297-2310
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Tidskriftsartikel (refereegranskat)abstract
- Background: Accurate blood type data are essential for blood bank management, but due to costs, few of 43 blood group systems are routinely determined in Danish blood banks. However, a more comprehensive dataset of blood types is useful in scenarios such as rare blood type allocation. We aimed to investigate the viability and accuracy of predicting blood types by leveraging an existing dataset of imputed genotypes for two cohorts of approximately 90,000 each (Danish Blood Donor Study and Copenhagen Biobank) and present a more comprehensive overview of blood types for our Danish donor cohort. Study Design and Methods: Blood types were predicted from genome array data using known variant determinants. Prediction accuracy was confirmed by comparing with preexisting serological blood types. The Vel blood group was used to test the viability of using genetic prediction to narrow down the list of candidate donors with rare blood types. Results: Predicted phenotypes showed a high balanced accuracy >99.5% in most cases: A, B, C/c, Coa/Cob, Doa/Dob, E/e, Jka/Jkb, Kna/Knb, Kpa/Kpb, M/N, S/s, Sda, Se, and Yta/Ytb, while some performed slightly worse: Fya/Fyb, K/k, Lua/Lub, and Vel ~99%–98% and CW and P1 ~96%. Genetic prediction identified 70 potential Vel negatives in our cohort, 64 of whom were confirmed correct using polymerase chain reaction (negative predictive value: 91.5%). Discussion: High genetic prediction accuracy in most blood groups demonstrated the viability of generating blood types using preexisting genotype data at no cost and successfully narrowed the pool of potential individuals with the rare Vel-negative phenotype from 180,000 to 70.
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| 22. |
- Oddsson, Asmundur, et al.
(författare)
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Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
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| 23. |
- Olsen, Stine T., et al.
(författare)
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A theoretical approach to molecular single-electron transistors
- 2011
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Ingår i: Theoretical Chemistry Accounts. - : Springer Science and Business Media LLC. - 1432-881X .- 1432-2234. ; 130:4-6, s. 839-850
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Tidskriftsartikel (refereegranskat)abstract
- We present theoretical methods and computational strategies of the effects of nanoparticles on linear optical properties of molecules. We present quantum mechanical-molecular mechanics response methods for calculating electromagnetic properties of molecules interacting with nanoparticles and we report strategies for calculating electronic and redox states of molecules sandwiched between gold nanoparticles.
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| 24. |
- Olsen, Stine T., et al.
(författare)
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Computational assignment of redox states to Coulomb blockade diamonds
- 2014
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084. ; 16:33, s. 17473-17478
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Tidskriftsartikel (refereegranskat)abstract
- With the advent of molecular transistors, electrochemistry can now be studied at the single-molecule level. Experimentally, the redox chemistry of the molecule manifests itself as features in the observed Coulomb blockade diamonds. We present a simple theoretical method for explicit construction of the Coulomb blockade diamonds of a molecule. A combined quantum mechanical/molecular mechanical method is invoked to calculate redox energies and polarizabilities of the molecules, including the screening effect of the metal leads. This direct approach circumvents the need for explicit modelling of the gate electrode. From the calculated parameters the Coulomb blockade diamonds are constructed using simple theory. We offer a theoretical tool for assignment of Coulomb blockade diamonds to specific redox states in particular, and a study of chemical details in the diamonds in general. With the ongoing experimental developments in molecular transistor experiments, our tool could find use in molecular electronics, electrochemistry, and electrocatalysis.
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| 25. |
- Olsen, Stine T., et al.
(författare)
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Dark Photoswitching Induces Coulomb Blockade Diamond Collapse
- 2015
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Ingår i: Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:27, s. 14829-14833
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Tidskriftsartikel (refereegranskat)abstract
- A derivative of the photochromic molecule dihydroazulene (DHA) undergoes bias-induced switching into its vinylheptafulvene (VHF) conformation when inserted into a silver junction. This dark switching mechanism, which induces a collapse of the Coulomb blockade diamonds, is explained by quantum calculations on the molecular transport junction. Analysis of the nonequilibrium populations of molecular redox states explains the observed bias threshold. Predictions are made that another DHA derivative will not, in future experiments, exhibit bias-induced switching. Thus, the dark switching mechanism depends on the structure of the photoswitch. The methodology applies to any molecular junction and offers a versatile tool for answering mechanistic questions.
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| 26. |
- Osipov, Vladimir Al, et al.
(författare)
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Nature of relaxation processes revealed by the action signals of intensity-modulated light fields
- 2016
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Ingår i: Physical Review A (Atomic, Molecular and Optical Physics). - 1050-2947. ; 94:5
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Tidskriftsartikel (refereegranskat)abstract
- We present a generalized theory and experimental results of the action signals induced by the absorption of two photons from two phase-modulated laser beams. In our experiment, the phases of the laser beams are modulated at the frequencies φ1 and φ2, respectively. Their collinear combination leads to the modulation of the total intensity at the frequency φ=φ2-φ1. The action signals, such as photoluminescence and photocurrent, which result from the absorption of two photons, are isolated at frequencies mφ, m{0,1,2,»}. We demonstrate that the ratio of the amplitudes of the secondary (m=2) and the primary (m=1) signals A2φ:Aφ is sensitive to the type of relaxation processes in the media. Such sensitivity originates from the cumulative effects of the nonequilibrated state of the matter between the pulses. When the cumulative effects are small, i.e., the relaxation time is much shorter than the laser repetition rate or the laser intensity is high enough to dominate the system behavior, the ratio achieves the reference value of 1:4. This ratio decreases monotonically as the relaxation time increases. Our experimental results from fluorescent molecules rhodamine 6G and rubrene support these theoretical findings. In the case of a second-order relaxation process, the ratio changes rapidly with the excitation intensity. When the recombination rate in the second-order process is significantly slower than the repetition rate of the laser, we observe nonmonotonic behavior of the ratio as a function of excitation population at low excitation intensity, and when the recombination rate and the excitation intensity are high, the ratio approaches the value of 1:4. We also use the model to determine the value of the recombination rate of charge carriers in a GaP photodiode.
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| 27. |
- Reuter, Matthew G., et al.
(författare)
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Understanding and Controlling Crosstalk between Parallel Molecular Wires
- 2011
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 2:14, s. 1667-1671
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Tidskriftsartikel (refereegranskat)abstract
- Cooperative effects between molecular wires affect conduction through the wires, and studies have yet to clarify the conditions under which these effects enhance (diminish) conduction. Using a simple but general model, we attribute this crosstalk to the duality of energetic splitting and phase interference between the wires' conduction channels. In most cases, crosstalk increases (decreases) conductance when the Fermi level is far from (close to) an isolated wire's resonance. Finally, we discuss strategies for controlling crosstalk between parallel molecular wires.
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| 28. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 29. |
- Schulze, Bastian, et al.
(författare)
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Inter-laboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysis
- 2021
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Ingår i: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Non-target analysis (NTA) employing high-resolution mass spectrometry is a commonly applied approach for the detection of novel chemicals of emerging concern in complex environmental samples. NTA typically results in large and information-rich datasets that require computer aided (ideally automated) strategies for their processing and interpretation. Such strategies do however raise the challenge of reproducibility between and within different processing workflows. An effective strategy to mitigate such problems is the implementation of inter-laboratory studies (ILS) with the aim to evaluate different workflows and agree on harmonized/standardized quality control procedures. Here we present the data generated during such an ILS. This study was organized through the Norman Network and included 21 participants from 11 countries. A set of samples based on the passive sampling of drinking water pre and post treatment was shipped to all the participating laboratories for analysis, using one pre-defined method and one locally (i.e. in-house) developed method. The data generated represents a valuable resource (i.e. benchmark) for future developments of algorithms and workflows for NTA experiments.
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| 30. |
- Seibt, Joachim, et al.
(författare)
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3D Spectroscopy of Vibrational Coherences in Quantum Dots: Theory.
- 2013
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 117:38, s. 11124-11133
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Tidskriftsartikel (refereegranskat)abstract
- In semiconductor nanocrystals, called quantum dots (QD), electronic transition energies, phonon frequencies, and electron-phonon coupling strengths are all reported to depend on the size of the crystals. The size dependencies of the transition energies and the mode frequencies are well characterized and understood. At the same time, the electron-phonon coupling dependence on size is controversial-even the sign of the change is not settled. In this article, third-order response functions of a model QD resembling CdSe are calculated. The longitudinal optical (LO) mode is included as a relatively narrow Lorentzian contribution to the spectral density. A novel version of electronic 2D spectroscopy is investigated where a third Fourier transform is taken over a so-called population time, leading to 3D spectral representation. The amplitude and phase of the 2D cuts of the 3D spectral body around the LO mode frequency are analyzed. The analytical power and sensitivity of the cuts in determining the possible Huang-Rhys factor (electron-phonon coupling strength) and the LO mode frequency dependence on the QD size are investigated. Peak structures in the cuts with a tilt relative to the diagonal are identified as sensitive signatures for the size dependencies. The study elucidates the 3D representation of the electronic 2D spectroscopy as a powerful tool for obtaining insight into otherwise hardly accessible characteristics of the system.
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| 31. |
- Skov, Anders B., et al.
(författare)
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Excited‐State Topology Modifications of the Dihydroazulene Photoswitch Through Aromaticity
- 2019
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Ingår i: ChemPhotoChem. - : Wiley. - 2367-0932. ; 3:8, s. 619-629
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Tidskriftsartikel (refereegranskat)abstract
- The gain and loss of aromaticity plays a key role in organic chemistry and in the prediction of rate‐determining steps. Herein, we explore the concept of aromaticity in photoisomerization reactions. Benzannulated derivatives of the dihydroazulene‐vinylheptafulvene (DHA‐VHF) photoswitch were investigated using transient absorption spectroscopy and time‐dependent density functional theory to elucidate the effect of built‐in aromaticity on the switching properties. We found that benzannulation hampered the switching ability by enhancing an already existing barrier on the excited state surface. This enhancement was found to arise from a significant loss of aromaticity in the DHA‐to‐VHF transition state on the excited state potential energy surface. The VHF was found to be highly aromatic on the excited state surface, showing a reversal of aromaticity compared to the ground state. The barrier was found to be dependent on the position of benzannulation, since one derivative was found to switch as fast as the non‐benzannulated molecule although with lower efficiency, whereas another derivative completely lost the ability to undergo reversible photoswitching. The findings herein provide novel principles for the design of molecular photoswitches, shedding new light on excited state aromaticity, as previous discussions have mainly considered excited state aromaticity to be beneficial to switching. Our findings show that this view must be reconsidered.
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| 32. |
- Westergaard, David, et al.
(författare)
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Genome-wide association meta-analysis identifies five loci associated with postpartum hemorrhage.
- 2024
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Ingår i: Nature genetics. - 1546-1718.
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Tidskriftsartikel (refereegranskat)abstract
- Bleeding in early pregnancy and postpartum hemorrhage (PPH) bear substantial risks, with the former closely associated with pregnancy loss and the latter being the foremost cause of maternal death, underscoring the severe impact on maternal-fetal health. We identified five genetic loci linked to PPH in a meta-analysis. Functional annotation analysis indicated candidate genes HAND2, TBX3 and RAP2C/FRMD7 at three loci and showed that at each locus, associated variants were located within binding sites for progesterone receptors. There were strong genetic correlations with birth weight, gestational duration and uterine fibroids. Bleeding in early pregnancy yielded no genome-wide association signals but showed strong genetic correlation with various human traits, suggesting a potentially complex, polygenic etiology. Our results suggest that PPH is related to progesterone signaling dysregulation, whereas early bleeding is a complex trait associated with underlying health and possibly socioeconomic status and may include genetic factors that have not yet been identified.
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| 33. |
- 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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