TY - INPR A1 - Odenwald, Johanna A1 - Gabiatti, Bernardo A1 - Braune, Silke A1 - Shen, Siqi A1 - Zoltner, Martin A1 - Kramer, Susanne T1 - Beyond BioID: Streptavidin outcompetes antibody fluorescence signals in protein localization and readily visualises targets evading immunofluorescence detection T2 - eLife N2 - Immunofluorescence is a common method to localise proteins within their cellular context via fluorophore labelled antibodies and for some applications without alternative. However, some protein targets evade detection due to low protein abundance or accessibility issues. In addition, some imaging methods require a massive reduction in antigen density thus impeding detection of even medium-abundant proteins.Here, we show that the fusion of the target protein to TurboID, a biotin ligase labelling lysine residues in close proximity, and subsequent detection of biotinylation by fluorescent streptavidin offers an “all in one” solution to the above-mentioned restrictions. For a wide range of target proteins tested, the streptavidin signal was significantly stronger than an antibody signal, markedly improving the imaging sensitivity in expansion microscopy and correlative light and electron microscopy, with no loss in resolution. Importantly, proteins within phase-separated regions, such as the central channel of the nuclear pores, the nucleolus or RNA granules, were readily detected with streptavidin, while most antibodies fail to label proteins in these environments. When TurboID is used in tandem with an HA epitope tag, co-probing with streptavidin and anti-HA can be used to map antibody-accessibility to certain cellular regions. As a proof of principle, we mapped antibody access to all trypanosome nuclear pore proteins (NUPs) and found restricted antibody labelling of all FG NUPs of the central channel that are known to be phase-separated, while most non-FG Nups could be labelled. Lastly, we show that streptavidin imaging can resolve dynamic, temporally and spatially distinct sub-complexes and, in specific cases, reveal a history of dynamic protein interaction.In conclusion, streptavidin imaging has major advantages for the detection of lowly abundant or inaccessible proteins and in addition, can provide information on protein interactions and biophysical environment. KW - BioID KW - Streptavidin KW - antibody fluorescence signals KW - protein localization KW - immunofluorescence detection Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-360704 ER - TY - INPR A1 - Brenner, Marian A1 - Zink, Christoph A1 - Witzinger, Linda A1 - Keller, Angelika A1 - Hadamek, Kerstin A1 - Bothe, Sebastian A1 - Neuenschwander, Martin A1 - Villmann, Carmen A1 - von Kries, Jens Peter A1 - Schindelin, Hermann A1 - Jeanclos, Elisabeth A1 - Gohla, Antje T1 - 7,8-Dihydroxyflavone is a direct inhibitor of pyridoxal phosphatase T2 - eLife N2 - Vitamin B6 deficiency has been linked to cognitive impairment in human brain disorders for decades. Still, the molecular mechanisms linking vitamin B6 to these pathologies remain poorly understood, and whether vitamin B6 supplementation improves cognition is unclear as well. Pyridoxal phosphatase (PDXP), an enzyme that controls levels of pyridoxal 5’-phosphate (PLP), the co-enzymatically active form of vitamin B6, may represent an alternative therapeutic entry point into vitamin B6-associated pathologies. However, pharmacological PDXP inhibitors to test this concept are lacking. We now identify a PDXP and age-dependent decline of PLP levels in the murine hippocampus that provides a rationale for the development of PDXP inhibitors. Using a combination of small molecule screening, protein crystallography and biolayer interferometry, we discover and analyze 7,8-dihydroxyflavone (7,8-DHF) as a direct and potent PDXP inhibitor. 7,8-DHF binds and reversibly inhibits PDXP with low micromolar affinity and sub-micromolar potency. In mouse hippocampal neurons, 7,8-DHF increases PLP in a PDXP-dependent manner. These findings validate PDXP as a druggable target. Of note, 7,8-DHF is a well-studied molecule in brain disorder models, although its mechanism of action is actively debated. Our discovery of 7,8-DHF as a PDXP inhibitor offers novel mechanistic insights into the controversy surrounding 7,8-DHF-mediated effects in the brain. KW - 7,8-dihydroxyflavone (7,8-DHF) KW - pyridoxal phosphatase (PDXP) KW - vitamin B6 KW - PDXP inhibitors Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-350446 ER - TY - INPR A1 - Dandekar, Thomas T1 - How do qubits interact? Implications for fundamental physics N2 - Proteins fold in water and achieve a clear structure despite a huge parameter space. Inside a (protein) crystal you have everywhere the same symmetries as there is everywhere the same unit cell. We apply this to qubit interactions to do fundamental physics: We modify cosmological inflation: we replace the big bang by a condensation event in an eternal all-encompassing ocean of free qubits. Rare interactions of qubits in the ocean provide a nucleus or seed for a new universe (domain), as the qubits become decoherent and freeze-out into defined bit ensembles. Next, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth). The crystal unit cell guarantees same symmetries (and laws of nature) everywhere inside the crystal, no inflation scenario is needed. Interacting qubits solidify, quantum entropy decreases in the crystal, but increases outside in the ocean. The interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After this very early modified steps, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements. Applying the Hurwitz theorem to qubits we prove that initiation of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. We describe a six-bit-ensemble toy model of qubit interaction and the repulsive forces of qubits for ultra-short distances. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below Planck´s quantum is liquidity left). The E8 symmetry of heterotic string theory has six curled-up, small dimensions. These keep the qubit crystal together and never expand. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit crystal formation. Implications are fundamental answers, e.g. why there is fine-tuning for life-friendliness, why there is string theory with rolled-up dimension and so many free parameters. We explain by cosmological crystallization instead of inflation the early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: the unit cell of our crystal universe has a matter handedness avoiding anti-matter. Importantly, crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. Vacuum energy gets appropriate low inside the crystal by its qubit binding energy, outside it is 10**20 higher. Scalar fields for color interaction/confinement and gravity could be derived from the qubit-interaction field. KW - protein folding KW - qubit interaction KW - early cosmology KW - qubit KW - modified inflation KW - crystallization KW - decoherence Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-357435 ER - TY - INPR A1 - Seitz, Florian A1 - Jungnickel, Tina A1 - Kleiber, Nicole A1 - Kretschmer, Jens A1 - Dietzsch, Julia A1 - Adelmann, Juliane A1 - Bohnsack, Katherine E. A1 - Bohnsack, Markus T. A1 - Höbartner, Claudia T1 - Atomic mutagenesis of N\(^6\)-methyladenosine reveals distinct recognition modes by human m\(^6\)A reader and eraser proteins T2 - Journal of the American Chemical Society N2 - N\(^6\)-methyladenosine (m\(^6\)A) is an important modified nucleoside in cellular RNA associated with multiple cellular processes and is implicated in diseases. The enzymes associated with the dynamic installation and removal of m\(^6\)A are heavily investigated targets for drug research, which requires detailed knowledge of the recognition modes of m\(^6\)A by proteins. Here, we use atomic mutagenesis of m\(^6\)A to systematically investigate the mechanisms of the two human m\(^6\)A demethylase enzymes FTO and ALKBH5 and the binding modes of YTH reader proteins YTHDF2/DC1/DC2. Atomic mutagenesis refers to atom-specific changes that are introduced by chemical synthesis, such as the replacement of nitrogen by carbon atoms. Synthetic RNA oligonucleotides containing site-specifically incorporated 1-deaza-, 3-deaza-, and 7-deaza-m\(^6\)A nucleosides were prepared by solid-phase synthesis and their RNA binding and demethylation by recombinant proteins were evaluated. We found distinct differences in substrate recognition and transformation and revealed structural preferences for the enzymatic activity. The deaza m\(^6\)A analogues introduced in this work will be useful probes for other proteins in m\(^6\)A research. KW - modified nucleosides KW - N6-methyladenosine (m6A) KW - atomic mutagenesis KW - YTH reader proteins KW - demethylase enzymes FTO and ALKBH5 Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-352376 ER - TY - INPR A1 - Dandekar, Thomas T1 - Protein folding and crystallization applied to qubit interactions and fundamental physics yields a modified inflation model for cosmology N2 - Protein folding achieves a clear solution structure in a huge parameter space (the so-called protein folding problem). Proteins fold in water, and get by this a highly ordered structure. Finally, inside a protein crystal for structure resolution, you have everywhere the same symmetries as there is everywhere the same unit cell. We apply this to qubit interactions to do fundamental physics: in a modified cosmology, we replace the big bang by a condensation event in an eternal all-encompassing ocean of free qubits. Interactions of qubits in the qubit ocean are quite rare but provide a nucleus or seed for a new universe (domain) as the qubits become decoherent and freeze-out into defined bit ensembles. Second, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth). The crystal unit cell guarantees same symmetries everywhere inside the crystal. The textbook inflation scenario to explain the same laws of nature in our domain is replaced by the unit cell of the crystal formed. Interacting qubits solidify, quantum entropy decreases (but increases in the ocean around). In a modified inflation scenario, the interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. Then standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements. We explain by cosmological crystallization instead of inflation: early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: the unit cell of our crystal universe has a matter handedness avoiding anti-matter. We prove initiation of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below Planck quantum there is liquidity left). The E8 symmetry of heterotic string theory has six curled-up, small dimensions which help to keep the qubit crystal together and will never expand. Mathematics focusses on the Hurwitz proof applied to qubit interaction, a toy model of qubit interaction and repulsive forces of qubits. Vacuum energy gets appropriate low inside the crystal. We give first energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction/confinement and gravity are derived from the qubit-interaction field. KW - protein folding KW - crystallization KW - qubit interaction KW - decoherence KW - modified inflation Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-346156 ER - TY - INPR A1 - Saal, Fridolin A1 - Swain, Asim A1 - Schmiedel, Alexander A1 - Holzapfel, Marco A1 - Lambert, Christoph A1 - Ravat, Prince T1 - Push-Pull [7]Helicene Diimide: Excited-State Charge Transfer and Solvatochromic Circularly Polarised Luminescence N2 - In this communication we describe a helically chiral push-pull molecule named 9,10-dimethoxy-[7]helicene diimide, displaying fluorescence (FL) and circularly polarised luminescence (CPL) over nearly the entire visible spectrum dependent on solvent polarity. The synthesised molecule exhibits an unusual solvent polarity dependence of FL quantum yield and nonradiative rate constant, as well as remarkable gabs and glum values along with high configurational stability. KW - Helicene diimide Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-345207 UR - https://doi.org/10.1039/D3CC04470J ET - submitted version ER - TY - INPR A1 - Warmdt, Julia A1 - Frisch, Henrik A1 - Ratz, Christoph A1 - Pohlmann-Rother, Sanna T1 - Digital lesen und erzählen. Eine Projektwoche für den inklusiven Anfangsunterricht T2 - Fördermagazin Grundschule N2 - Das Digital Storytelling bietet Schüler:innen im inklusiven Anfangsunterricht vielfältige Möglichkeiten der Teilhabe am Unterricht. Lesen Sie in diesem Beitrag, wie die Kinder eine digitale Geschichte auf unterschiedliche Art rezipieren und weitererzählen können. KW - Bilderbuch KW - Medienkompetenz KW - Inklusiver Unterricht KW - Anfangsunterricht KW - Erzählen KW - Digital Storytelling Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-328443 ET - accepted version ER - TY - INPR A1 - Neitz, Hermann A1 - Höbartner, Claudia T1 - A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker T2 - Chemical Communications N2 - We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detectio of a specific DNA sequence. KW - Tolane-Modified Fluorescent Nucleosides KW - Photoresponsive DNA Crosslinker Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-328255 ET - submitted version ER - TY - INPR A1 - Dietzsch, Julia A1 - Jayachandran, Ajay A1 - Mueller, Stefan A1 - Höbartner, Claudia A1 - Brixner, Tobias T1 - Excitonic coupling of RNA-templated merocyanine dimer studied by higher-order transient absorption spectroscopy T2 - Chemical Communications N2 - We report the synthesis and spectroscopic analysis of RNA containing the barbituric acid merocyanine rBAM2 as a nucleobase surrogate. Incorporation into RNA strands by solid-phase synthesis leads to fluorescence enhancement compared to the free chromophore. In addition, linear absorption studies show the formation of an excitonically coupled H-type dimer in the hybridized duplex. Ultrafast third- and fifth-order transient absorption spectroscopy of this non-fluorescent dimer suggests immediate (sub-200 fs) exciton transfer and annihilation due to the proximity of the rBAM2 units. KW - Barbituric Acid Merocyanines KW - Nucleobase Surrogate Incorporation KW - Higher-order Transient Absorption Spectroscopy KW - rBAM2-labeled RNA strands Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-327772 ET - submitted version ER - TY - INPR A1 - Heidenreich, Julius F. A1 - Gassenmaier, Tobias A1 - Ankenbrand, Markus J. A1 - Bley, Thorsten A. A1 - Wech, Tobias T1 - Self-configuring nnU-net pipeline enables fully automatic infarct segmentation in late enhancement MRI after myocardial infarction N2 - Purpose To fully automatically derive quantitative parameters from late gadolinium enhancement (LGE) cardiac MR (CMR) in patients with myocardial infarction and to investigate if phase sensitive or magnitude reconstructions or a combination of both results in best segmentation accuracy. Methods In this retrospective single center study, a convolutional neural network with a U-Net architecture with a self-configuring framework (“nnU-net”) was trained for segmentation of left ventricular myocardium and infarct zone in LGE-CMR. A database of 170 examinations from 78 patients with history of myocardial infarction was assembled. Separate fitting of the model was performed, using phase sensitive inversion recovery, the magnitude reconstruction or both contrasts as input channels. Manual labelling served as ground truth. In a subset of 10 patients, the performance of the trained models was evaluated and quantitatively compared by determination of the Sørensen-Dice similarity coefficient (DSC) and volumes of the infarct zone compared with the manual ground truth using Pearson’s r correlation and Bland-Altman analysis. Results The model achieved high similarity coefficients for myocardium and scar tissue. No significant difference was observed between using PSIR, magnitude reconstruction or both contrasts as input (PSIR and MAG; mean DSC: 0.83 ± 0.03 for myocardium and 0.72 ± 0.08 for scars). A strong correlation for volumes of infarct zone was observed between manual and model-based approach (r = 0.96), with a significant underestimation of the volumes obtained from the neural network. Conclusion The self-configuring nnU-net achieves predictions with strong agreement compared to manual segmentation, proving the potential as a promising tool to provide fully automatic quantitative evaluation of LGE-CMR. KW - Deep learning KW - CMR KW - Segmentation KW - Myocardial infarction KW - Scar KW - nnU-net Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-323418 UR - https://doi.org/10.1016/j.ejrad.2021.109817 ET - accepted version ER - TY - INPR A1 - Dandekar, Thomas T1 - A modified inflation cosmology relying on qubit-crystallization: rare qubit interactions trigger qubit ensemble growth and crystallization into “real” bit-ensembles and emergent time N2 - In a modified inflation scenario we replace the “big bang” by a condensation event in an eternal all-compassing big ocean of free qubits in our modified cosmology. Interactions of qubits in the qubit ocean are rare. If they happen, they provide a nucleus for a new universe as the qubits become decoherent and freeze-out into defined bit ensembles. Second, we replace inflation by a crystallization event triggered by the nucleus of interacting qubits to which rapidly more and more qubits attach (like in everyday crystal growth) – the crystal unit cell guarantees same symmetries everywhere. Hence, the textbook inflation scenario to explain the same laws of nature in our domain is replaced by the crystal unit cell of the crystal formed. We give here only the perspective or outline of this modified inflation theory, as the detailed mathematical physics behind this has still to be formulated and described. Interacting qubits solidify, quantum entropy decreases (but increases in the ocean around). The interacting qubits form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, but more importantly can explain well by such a type of cosmological crystallization instead of inflation the early creation of large-scale structure of voids and filaments, supercluster formation, galaxy formation, and the dominance of matter: no annihilation of antimatter necessary, rather the unit cell of our crystal universe has a matter handedness avoiding anti-matter. We prove a triggering of qubit interactions can only be 1,2,4 or 8-dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. The phase space of the crystal agrees with the standard model of the basic four forces for n quanta. It includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. However, this means that in our four dimensions there is only one bit overlap to neighbor states left (almost solid, only below h dash liquidity left). However, the E8 symmetry of heterotic string theory has six rolled-up, small dimensions which help to keep the qubit crystal together and will never expand. Finally, we give first energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field in the crystal. Hence, vacuum energy gets low inside the qubit crystal. Condensed mathematics may advantageously help to model free (many states denote the same qubit) and bound qubits in phase space. KW - qubit KW - cosmology KW - decoherence KW - crystallization KW - emergent time Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-321777 ER - TY - INPR A1 - Fersch, Daniel A1 - Malý, Pavel A1 - Rühe, Jessica A1 - Lisinetskii, Victor A1 - Hensen, Matthias A1 - Würthner, Frank A1 - Brixner, Tobias T1 - Single-Molecule Ultrafast Fluorescence-Detected Pump–Probe Microscopy N2 - We introduce fluorescence-detected pump–probe microscopy by combining a wavelength-tunable ultrafast laser with a confocal scanning fluorescence microscope, enabling access to the femtosecond time scale on the micrometer spatial scale. In addition, we obtain spectral information from Fourier transformation over excitation pulse-pair time delays. We demonstrate this new approach on a model system of a terrylene bisimide (TBI) dye embedded in a PMMA matrix and acquire the linear excitation spectrum as well as time-dependent pump–probe spectra simultaneously. We then push the technique towards single TBI molecules and analyze the statistical distribution of their excitation spectra. Furthermore, we demonstrate the ultrafast transient evolution of several individual molecules, highlighting their different behavior in contrast to the ensemble due to their individual local environment. By correlating the linear and nonlinear spectra, we assess the effect of the molecular environment on the excited-state energy. KW - Fluoreszenz KW - Ultrafast spectroscopy KW - Single-molecule microscopy Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-313485 ER - TY - INPR A1 - Neitz, Hermann A1 - Bessi, Irene A1 - Kuper, Jochen A1 - Kisker, Caroline A1 - Höbartner, Claudia T1 - Programmable DNA interstrand crosslinking by alkene-alkyne [2+2] photocycloaddition T2 - Journal of the American Chemical Society N2 - Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2’-deoxyuridine (\(^{Phe}\)dU). The crosslinking ability of \(^{Phe}\)dU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2+2] cycloaddition within the DNA duplex, resulting in efficient formation of a \(^{Phe}\)dU-dimer after short irradiation times of a few seconds. A \(^{Phe}\)dU dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology. KW - light-induced interstrand DNA crosslinking KW - alkene-alkyne [2+2] photocycloaddition KW - DNA-based nanostructures KW - DNA-processing enzymes Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-311822 N1 - This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Journal of the American Chemical Society, copyright © 2023 The Authors. Published by American Chemical Society. after peer review. To access the final edited and published work see https://doi.org/10.1021/jacs.3c01611. ET - submitted version ER - TY - INPR A1 - Dandekar, Thomas T1 - Analysing the phase space of the standard model and its basic four forces from a qubit phase transition perspective: implications for large-scale structure generation and early cosmological events N2 - The phase space for the standard model of the basic four forces for n quanta includes all possible ensemble combinations of their quantum states m, a total of n**m states. Neighbor states reach according to transition possibilities (S-matrix) with emergent time from entropic ensemble gradients. We replace the “big bang” by a condensation event (interacting qubits become decoherent) and inflation by a crystallization event – the crystal unit cell guarantees same symmetries everywhere. Interacting qubits solidify and form a rapidly growing domain where the n**m states become separated ensemble states, rising long-range forces stop ultimately further growth. After that very early events, standard cosmology with the hot fireball model takes over. Our theory agrees well with lack of inflation traces in cosmic background measurements, large-scale structure of voids and filaments, supercluster formation, galaxy formation, dominance of matter and life-friendliness. We prove qubit interactions to be 1,2,4 or 8 dimensional (agrees with E8 symmetry of our universe). Repulsive forces at ultrashort distances result from quantization, long-range forces limit crystal growth. Crystals come and go in the qubit ocean. This selects for the ability to lay seeds for new crystals, for self-organization and life-friendliness. We give energy estimates for free qubits vs bound qubits, misplacements in the qubit crystal and entropy increase during qubit decoherence / crystal formation. Scalar fields for color interaction and gravity derive from the permeating qubit-interaction field. Hence, vacuum energy gets low only inside the qubit crystal. Condensed mathematics may advantageously model free / bound qubits in phase space. KW - phase space KW - cosmology KW - emergent time KW - qubit KW - phase transition KW - bit Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-298580 ER - TY - INPR A1 - Scheitl, Carolin P. M. A1 - Mieczkowski, Mateusz A1 - Schindelin, Hermann A1 - Höbartner, Claudia T1 - Structure and mechanism of the methyltransferase ribozyme MTR1 T2 - Nature Chemical Biology N2 - RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m\(^1\)A) in RNA, using O\(^6\)-methylguanine (m\(^6\)G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution. KW - Methyltransferase Ribozyme MTR1 KW - Crystal structure of MTR1 KW - RNA-catalyzed RNA methylation KW - X-ray crystallography KW - RNA Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-272170 ET - submitted version ER - TY - INPR A1 - Hennig, Thomas A1 - Prusty, Archana B. A1 - Kaufer, Benedikt A1 - Whisnant, Adam W. A1 - Lodha, Manivel A1 - Enders, Antje A1 - Thomas, Julius A1 - Kasimir, Francesca A1 - Grothey, Arnhild A1 - Herb, Stefanie A1 - Jürges, Christopher A1 - Meister, Gunter A1 - Erhard, Florian A1 - Dölken, Lars A1 - Prusty, Bhupesh K. T1 - Selective inhibition of microRNA processing by a herpesvirus-encoded microRNA triggers virus reactivation from latency N2 - Herpesviruses have mastered host cell modulation and immune evasion to augment productive infection, life-long latency and reactivation thereof 1,2. A long appreciated, yet elusively defined relationship exists between the lytic-latent switch and viral non-coding RNAs 3,4. Here, we identify miRNA-mediated inhibition of miRNA processing as a novel cellular mechanism that human herpesvirus 6A (HHV-6A) exploits to disrupt mitochondrial architecture, evade intrinsic host defense and drive the latent-lytic switch. We demonstrate that virus-encoded miR-aU14 selectively inhibits the processing of multiple miR-30 family members by direct interaction with the respective pri-miRNA hairpin loops. Subsequent loss of miR-30 and activation of miR-30/p53/Drp1 axis triggers a profound disruption of mitochondrial architecture, which impairs induction of type I interferons and is necessary for both productive infection and virus reactivation. Ectopic expression of miR-aU14 was sufficient to trigger virus reactivation from latency thereby identifying it as a readily drugable master regulator of the herpesvirus latent-lytic switch. Our results show that miRNA-mediated inhibition of miRNA processing represents a generalized cellular mechanism that can be exploited to selectively target individual members of miRNA families. We anticipate that targeting miR-aU14 provides exciting therapeutic options for preventing herpesvirus reactivations in HHV-6-associated disorders like myalgic encephalitis/chronic fatigue syndrome (ME/CFS) and Long-COVID. KW - Herpesvirus KW - HHV-6 KW - miRNA processing KW - miR-30 KW - mitochondria KW - fusion and fission KW - type I interferon KW - latency KW - virus reactivation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-267858 UR - https://doi.org/10.21203/rs.3.rs-820696/v1 ET - submitted version ER - TY - INPR A1 - Dandekar, Thomas T1 - Qubit transition into defined Bits: A fresh perspective for cosmology and unifying theories N2 - In this view point we do not change cosmology after the hot fireball starts (hence agrees well with observation), but the changed start suggested and resulting later implications lead to an even better fit with current observations (voids, supercluster and galaxy formation; matter and no antimatter) than the standard model with big bang and inflation: In an eternal ocean of qubits, a cluster of qubits crystallizes to defined bits. The universe does not jump into existence (“big bang”) but rather you have an eternal ocean of qubits in free super-position of all their quantum states (of any dimension, force field and particle type) as permanent basis. The undefined, boiling vacuum is the real “outside”, once you leave our everyday universe. A set of n Qubits in the ocean are “liquid”, in very undefined state, they have all their m possibilities for quantum states in free superposition. However, under certain conditions the qubits interact, become defined, and freeze out, crystals form and give rise to a defined, real world with all possible time series and world lines. GR holds only within the crystal. In our universe all n**m quantum possibilities are nicely separated and crystallized out to defined bit states: A toy example with 6 qubits each having 2 states illustrates, this is completely sufficient to encode space using 3 bits for x,y and z, 1 bit for particle type and 2 bits for its state. Just by crystallization, space, particles and their properties emerge from the ocean of qubits, and following the arrow of entropy, time emerges, following an arrow of time and expansion from one corner of the toy universe to everywhere else. This perspective provides time as emergent feature considering entropy: crystallization of each world line leads to defined world lines over their whole existence, while entropy ensures direction of time and higher representation of high entropy states considering the whole crystal and all slices of world lines. The crystal perspective is also economic compared to the Everett-type multiverse, each qubit has its m quantum states and n qubits interacting forming a crystal and hence turning into defined bit states has only n**m states and not more states. There is no Everett-type world splitting with every decision but rather individual world trajectories reside in individual world layers of the crystal. Finally, bit-separated crystals come and go in the qubit ocean, selecting for the ability to lay seeds for new crystals. This self-organizing reproduction selects over generations also for life-friendliness. Mathematical treatment introduces quantum action theory as a framework for a general lattice field theory extending quantum chromo dynamics where scalar fields for color interaction and gravity have to be derived from the permeating qubit-interaction field. Vacuum energy should get appropriately low by the binding properties of the qubit crystal. Connections to loop quantum gravity, string theory and emergent gravity are discussed. Standard physics (quantum computing; crystallization, solid state physics) allow validation tests of this perspective and will extend current results. KW - qubit KW - cosmology KW - phase transition KW - unified theories KW - crystallization KW - emergent gravity Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-266418 ER - TY - INPR A1 - Sednev, Maksim V. A1 - Liaqat, Anam A1 - Höbartner, Claudia T1 - High-Throughput Activity Profiling of RNA-Cleaving DNA Catalysts by Deoxyribozyme Sequencing (DZ-seq) T2 - Journal of the American Chemical Society N2 - RNA-cleaving deoxyribozymes have found broad application as useful tools for RNA biochemistry. However, tedious in vitro selection procedures combined with laborious characterization of individual candidate catalysts hinder the discovery of novel catalytic motifs. Here, we present a new high-throughput sequencing method, DZ-seq, which directly measures activity and localizes cleavage sites of thousands of deoxyribozymes. DZ-seq exploits A-tailing followed by reverse transcription with an oligo-dT primer to capture the cleavage status and sequences of both deoxyribozyme and RNA substrate. We validated DZ-seq by conventional analytical methods and demonstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA targets or the analysis of RNA modification states. KW - RNA-Cleaving Deoxyribozymes KW - High-Throughput Sequencing Method, DZ-seq KW - Analysis of RNA Modifications Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-258520 ER - TY - INPR A1 - Händel, Barbara A1 - Schölvinck, Marieke T1 - The brain during free movement – what can we learn from the animal model T2 - Brain Research N2 - Animals, just like humans, can freely move. They do so for various important reasons, such as finding food and escaping predators. Observing these behaviors can inform us about the underlying cognitive processes. In addition, while humans can convey complicated information easily through speaking, animals need to move their bodies to communicate. This has prompted many creative solutions by animal neuroscientists to enable studying the brain during movement. In this review, we first summarize how animal researchers record from the brain while an animal is moving, by describing the most common neural recording techniques in animals and how they were adapted to record during movement. We further discuss the challenge of controlling or monitoring sensory input during free movement. However, not only is free movement a necessity to reflect the outcome of certain internal cognitive processes in animals, it is also a fascinating field of research since certain crucial behavioral patterns can only be observed and studied during free movement. Therefore, in a second part of the review, we focus on some key findings in animal research that specifically address the interaction between free movement and brain activity. First, focusing on walking as a fundamental form of free movement, we discuss how important such intentional movements are for understanding processes as diverse as spatial navigation, active sensing, and complex motor planning. Second, we propose the idea of regarding free movement as the expression of a behavioral state. This view can help to understand the general influence of movement on brain function. Together, the technological advancements towards recording from the brain during movement, and the scientific questions asked about the brain engaged in movement, make animal research highly valuable to research into the human “moving brain”. KW - free movement KW - animal research KW - virtual reality KW - recording methods KW - brain activity Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-251406 ET - accepted manuscript ER - TY - INPR A1 - Brych, Mareike A1 - Händel, Barbara T1 - Disentangling top-down and bottom-up influences on blinks in the visual and auditory domain T2 - International Journal of Psychophysiology N2 - Sensory input as well as cognitive factors can drive the modulation of blinking. Our aim was to dissociate sensory driven bottom-up from cognitive top-down influences on blinking behavior and compare these influences between the auditory and the visual domain. Using an oddball paradigm, we found a significant pre-stimulus decrease in blink probability for visual input compared to auditory input. Sensory input further led to an early post-stimulus blink increase in both modalities if a task demanded attention to the input. Only visual input caused a pronounced early increase without a task. In case of a target or the omission of a stimulus (as compared to standard input), an additional late increase in blink rate was found in the auditory and visual domain. This suggests that blink modulation must be based on the interpretation of the input, but does not need any sensory input at all to occur. Our results show a complex modulation of blinking based on top-down factors such as prediction and attention in addition to sensory-based influences. The magnitude of the modulation is mainly influenced by general attentional demands, while the latency of this modulation allows to dissociate general from specific top-down influences that are independent of the sensory domain. KW - eye blinks KW - attention KW - auditory KW - visual KW - visual domain KW - auditory domain KW - oddball Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-246590 SN - 1872-7697 SN - 0167-8760 N1 - accepted version ER - TY - INPR A1 - Schaefer, Natascha A1 - Janzen, Dieter A1 - Bakirci, Ezgi A1 - Hrynevich, Andrei A1 - Dalton, Paul D. A1 - Villmann, Carmen T1 - 3D Electrophysiological Measurements on Cells Embedded within Fiber-Reinforced Matrigel T2 - Advanced Healthcare Materials N2 - 2D electrophysiology is often used to determine the electrical properties of neurons, while in the brain, neurons form extensive 3D networks. Thus, performing electrophysiology in a 3D environment provides a closer situation to the physiological condition and serves as a useful tool for various applications in the field of neuroscience. In this study, we established 3D electrophysiology within a fiber-reinforced matrix to enable fast readouts from transfected cells, which are often used as model systems for 2D electrophysiology. Using melt electrowriting (MEW) of scaffolds to reinforce Matrigel, we performed 3D electrophysiology on a glycine receptor-transfected Ltk-11 mouse fibroblast cell line. The glycine receptor is an inhibitory ion channel associated when mutated with impaired neuromotor behaviour. The average thickness of the MEW scaffold was 141.4 ± 5.7µm, using 9.7 ± 0.2µm diameter fibers, and square pore spacings of 100 µm, 200 µm and 400 µm. We demonstrate, for the first time, the electrophysiological characterization of glycine receptor-transfected cells with respect to agonist efficacy and potency in a 3D matrix. With the MEW scaffold reinforcement not interfering with the electrophysiology measurement, this approach can now be further adapted and developed for different kinds of neuronal cultures to study and understand pathological mechanisms under disease conditions. KW - 3D cultures Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-244194 ER - TY - INPR A1 - Wolf, Norbert Richard T1 - Der Duden, die Genera und die Geschlechter T2 - Vestnik of Samara University. History, pedagogics, philology T2 - ВЕСТНИК САМАРСКОГО УНИВЕРСИТЕТА. ИСТОРИЯ, ПЕДАГОГИКА, ФИЛОЛОГИЯ N2 - Anlass für diesen Aufsatz ist die Tatsache, dass die Duden-Redaktion bei zahlreichen Personenbezeichnungen das sog. ‚generische Maskulinum‘ wegdefiniert hat. Das Anfang 2021 erschienene online Wörterbuch gibt als Bedeutungserklärung des Substantiv Arzt folgende Beschreibung an: „männliche Person, die nach Medizinstudium und klinischer Ausbildung die staatliche Zulassung (Approbation) erhalten hat, Kranke zu behandeln (Berufsbezeichnung)“. Demgegenüber hieß es im Duden Universalwörterbuch von 2015: „jemand, der nach Medizinstudium und klinischer Ausbildung die staatliche Zulassung (Approbation) erhalten hat, Kranke zu behandeln (Berufsbezeichnung)“ Der Aufsatz versucht, wieder einmal zu überprüfen, ob es das generische Maskulinum als geschlechtsübergreifende oder besser: geschlechtsneutrale Bezeichnung gibt oder ob es, nicht zuletzt aufgrund des jahrhundertelangen Einflusses des Patriarchats auf die Sprachentwicklung, sich doch um den Ausdruck männlicher Vormacht handelt. Dabei werden sowohl das Problem ‚Genus‘ als auch der Begriff ‚generisch‘ untersucht und auf seine Bezeichnungsfunktion hin getestet. Schließlich soll auch überprüft werden, ob die Sprache tatsächlich die Wirklichkeit widerspiegelt und ob die Sprache wirklich alle Phänomene in der außersprachlichen Realität benennen muss. Dazu kommt natürlich auch die Frage, ob die Duden-Redaktion ihre Kompetenzen richtig interpretiert (hat). KW - Duden KW - Genus KW - Sexus KW - lexikalische Bedeutung Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-241571 UR - https://journals.ssau.ru/hpp/ ER - TY - INPR A1 - Dandekar, Thomas T1 - Our universe may have started by Qubit decoherence N2 - Our universe may have started by Qubit decoherence: In quantum computers, qubits have all their states undefined during calculation and become defined as output (“decoherence”). We study the transition from an uncontrolled, chaotic quantum vacuum (“before”) to a clearly interacting “real world”. In such a cosmology, the Big Bang singularity is replaced by a condensation event of interacting strings. This triggers a crystallization process. This avoids inflation, not fitting current observations: increasing long-range interactions limit growth and crystal symmetries ensure the same laws of nature and basic symmetries over the whole crystal. Tiny mis-arrangements provide nuclei of superclusters and galaxies and crystal structure allows arrangement of dark (halo regions) and normal matter (galaxy nuclei) for galaxy formation. Crystals come and go: an evolutionary cosmology is explored: entropic forces from the quantum soup “outside” of the crystal try to dissolve it. This corresponds to dark energy and leads to a “big rip” in 70 Gigayears. Selection for best growth and condensation events over generations of crystals favors multiple self-organizing processes within the crystal including life or even conscious observers in our universe. Philosophically this theory shows harmony with nature and replaces absurd perspectives of current cosmology. Independent of cosmology, we suggest that a “real world” (so our everyday macroscopic world) happens only inside a crystal. “Outside” there is wild quantum foam and superposition of all possibilities. In our crystallized world the vacuum no longer boils but is cooled down by the crystallization event, space-time exists and general relativity holds. Vacuum energy becomes 10**20 smaller, exactly as observed in our everyday world. We live in a “solid” state, within a crystal, the n quanta which build our world have all their different m states nicely separated. There are only nm states available for this local “multiverse”. The arrow of entropy for each edge of the crystal forms one fate, one world-line or clear development of our world, while layers of the crystal are different system states. Mathematical leads from loop quantum gravity (LQG) point to required interactions and potentials. Interaction potentials for strings or loop quanta of any dimension allow a solid, decoherent state of quanta challenging to calculate. However, if we introduce here the heuristic that any type of physical interaction of strings corresponds just to a type of calculation, there is already since 1898 the Hurwitz theorem showing that then only 1D, 2D, 4D and 8D (octonions) allow complex or hypercomplex number calculations. No other hypercomplex numbers and hence dimensions or symmetries are possible to allow calculations without yielding divisions by zero. However, the richest solution allowed by the Hurwitz theorem, octonions, is actually the observed symmetry of our universe, E8. Standard physics such as condensation, crystallization and magnetization but also solid-state physics and quantum computing allow us to show an initial mathematical treatment of our new theory by LQG to describe the cosmological state transformations by equations, and, most importantly, point out routes to parametrization of free parameters looking at testable phenomena, experiments and formulas that describe processes of crystallization, protein folding, magnetization, solid-state physics and quantum computing. This is presented here for LQG, for string theory it would be more elegant but was too demanding to be shown here. Note: While my previous Opus server preprint “A new cosmology of a crystallization process (decoherence) from the surrounding quantum soup provides heuristics to unify general relativity and quantum physics by solid state physics” (https://doi.org/10.25972/OPUS-23076) deals with the same topics and basic formulas, this new version is improved: clearer in title, better introduction, more stringent in its mathematics and improved discussion of the implications including quantum computing, hints for parametrization and connections to LQG and other current cosmological efforts. This 5th of June 2021 version is again an OPUS preprint, but this will next be edited for Archives https://arxiv.org. KW - cosmology KW - quantum computing KW - loop quantum gravity KW - qubit KW - decoherence KW - crystallization Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-239181 ER - TY - INPR A1 - Schmidt, Uwe A1 - Fantuzzi, Felipe A1 - Arrowsmith, Merle A1 - Hermann, Alexander A1 - Prieschl, Dominic A1 - Rempel, Anna A1 - Engels, Bernd A1 - Braunschweig, Holger T1 - Tuneable reduction of cymantrenylboranes to diborenes or borylene-derived boratafulvenes T2 - Chemical Communications N2 - Whereas the reduction of N-heterocyclic carbene (NHC)-stabilised cymantrenyldibromoboranes, (NHC)BBr\(_2\)Cym, in benzene results in formation of the corresponding diborenes (NHC)\(_2\)B\(_2\)Cym\(_2\), a change of solvent to THF yields a borylene of the form (NHC)\(_2\)BCym, stabilised through its boratafulvene resonance form. KW - Borylene KW - Diborene KW - Boranes Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-222149 ER - TY - INPR A1 - Scheitl, Carolin P.M. A1 - Ghaem Maghami, Mohammad A1 - Lenz, Ann-Kathrin A1 - Höbartner, Claudia T1 - Site-specific RNA methylation by a methyltransferase ribozyme T2 - Nature N2 - Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification including RNA methylation. Methylated nucleotides belong to the evolutionarily most conserved features of tRNA and rRNA.1,2 Many contemporary methyltransferases use the universal cofactor S-adenosylmethionine (SAM) as methyl group donor. This and other nucleotide-derived cofactors are considered as evolutionary leftovers from an RNA World, in which ribozymes may have catalysed essential metabolic reactions beyond self-replication.3 Chemically diverse ribozymes seem to have been lost in Nature, but may be reconstructed in the laboratory by in vitro selection. Here, we report a methyltransferase ribozyme that catalyses the site-specific installation of 1-methyladenosine (m1A) in a substrate RNA, utilizing O6-methylguanine (m6G) as a small-molecule cofactor. The ribozyme shows a broad RNA sequence scope, as exemplified by site-specific adenosine methylation in tRNAs. This finding provides fundamental insights into RNA’s catalytic abilities, serves a synthetic tool to install m1A in RNA, and may pave the way to in vitro evolution of other methyltransferase and demethylase ribozymes. KW - Methyltransferase Ribozyme KW - RNA Enzymes KW - position-specific installation of m1A in RNA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-218687 ER - TY - INPR A1 - Ott, Christine T1 - Geschlechterstereotypen auf der Spur. Ein Plädoyer für mehr Linguistik in der Bildungsforschung T2 - Bildung und Differenz. Historische Analysen zu einem aktuellen Problem N2 - Kein Abstract verfügbar. KW - Geschlechterforschung KW - Stereotype KW - Schulbuch Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-210503 ER - TY - INPR A1 - Wohlgemuth, Matthias A1 - Mitric, Roland T1 - Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping T2 - Physical Chemistry Chemical Physics N2 - Absorption of ultraviolet light is known as a major source of carcinogenic mutations of DNA. The underlying processes of excitation energy dissipation are yet not fully understood. In this work we provide a new and generally applicable route for studying the excitation energy transport in multi-chromophoric complexes at an atomistic level. The surface-hopping approach in the frame of the extended Frenkel exciton model combined with QM/MM techniques allowed us to simulate the photodynamics of the alternating (dAdT)10 : (dAdT)10 double-stranded DNA. In accordance with recent experiments, we find that the excited state decay is multiexponential, involving a long and a short component which are due to two distinct mechanisms: formation of long-lived delocalized excitonic and charge transfer states vs. ultrafast decaying localized states resembling those of the bare nucleobases. Our simulations explain all stages of the ultrafast photodynamics including initial photoexcitation, dynamical evolution out of the Franck-Condon region, excimer formation and nonradiative relaxation to the ground state. KW - Photodynamics KW - DNA Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-209467 ET - submitted version ER - TY - INPR A1 - Hermann, Alexander A1 - Arrowsmith, Merle A1 - Trujillo-Gonzalez, Daniel A1 - Jiménez-Halla, J. Oscar C. A1 - Vargas, Alfredo A1 - Braunschweig, Holger T1 - Trapping of a Borirane Intermediate in the Reductive Coupling of an Arylborane to a Diborene T2 - Journal of the American Chemical Society N2 - The reductive coupling of an NHC-stabilized aryldibromoborane yields a mixture of trans- and cis-diborenes in which the aryl groups are coplanar with the diborene core. Under dilute reduction conditions two diastereomers of a borirane-borane intermediate are isolated, which upon further reduction give rise to the aforementioned diborene mixture. DFT calculations suggest a mechanism proceeding via nucleophilic attack of a dicoordinate borylene intermediate on the aryl ring and subsequent intramolecular B-B bond formation. KW - boron KW - reactive intermediates KW - reductive coupling Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-203140 N1 - This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of the American Chemical Society, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/jacs.0c02306 ER - TY - INPR A1 - Breitenbach, Tim A1 - Borzì, Alfio T1 - On the SQH scheme to solve non-smooth PDE optimal control problems T2 - Numerical Functional Analysis and Optimization N2 - A sequential quadratic Hamiltonian (SQH) scheme for solving different classes of non-smooth and non-convex PDE optimal control problems is investigated considering seven different benchmark problems with increasing difficulty. These problems include linear and nonlinear PDEs with linear and bilinear control mechanisms, non-convex and discontinuous costs of the controls, L\(^1\) tracking terms, and the case of state constraints. The SQH method is based on the characterisation of optimality of PDE optimal control problems by the Pontryagin's maximum principle (PMP). For each problem, a theoretical discussion of the PMP optimality condition is given and results of numerical experiments are presented that demonstrate the large range of applicability of the SQH scheme. KW - SQH method KW - non-smooth optimization KW - Pontryagin maximum principle KW - nonconvex optimization Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180936 N1 - This is an Accepted Manuscript of an article published by Taylor & Francis in Numerical Functional Analysis and Optimization on 27.04.2019, available online: http://www.tandfonline.com/10.1080/01630563.2019.1599911. ER - TY - INPR A1 - Humeniuk, Alexander A1 - Bužančić, Margarita A1 - Hoche, Joscha A1 - Cerezo, Javier A1 - Mitric, Roland A1 - Santoro, Fabrizio A1 - Bonačić-Koutecky, Vlasta T1 - Predicting fluorescence quantum yields for molecules in solution: A critical assessment of the harmonic approximation and the choice of the lineshape function T2 - The Journal of Chemical Physics N2 - For the rational design of new fluorophores, reliable predictions of fluorescence quantum yields from first principles would be of great help. However, efficient computational approaches for predicting transition rates usually assume that the vibrational structure is harmonic. While the harmonic approximation has been used successfully to predict vibrationally resolved spectra and radiative rates, its reliability for non-radiative rates is much more questionable. Since non-adiabatic transitions convert large amounts of electronic energy into vibrational energy, the highly excited final vibrational states deviate greatly from harmonic oscillator eigenfunctions. We employ a time-dependent formalism to compute radiative and non-radiative rates for transitions and study the dependence on model parameters. For several coumarin dyes we compare different adiabatic and vertical harmonic models (AS, ASF, AH, VG, VGF, VH), in order to dissect the importance of displacements, frequency changes and Duschinsky rotations. In addition we analyze the effect of different broadening functions (Gaussian, Lorentzian or Voigt). Moreover, to assess the qualitative influence of anharmonicity on the internal conversion rate, we develop a simplified anharmonic model. We adress the reliability of these models considering the potential errors introduced by the harmonic approximation and the phenomenological width of the broadening function. KW - fluorescence quantum yield Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-199305 UR - https://doi.org/10.1063/1.5143212 N1 - Accepted Manuscript. N1 - This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in A. Humeniuk et al. J. Chem. Phys. 152, 054107 (2020); https://doi.org/10.1063/1.5143212 and may be found at https://doi.org/10.1063/1.5143212. ER - TY - INPR A1 - Lindner, Joachim O. A1 - Sultangaleeva, Karina A1 - Röhr, Merle I. S. A1 - Mitric, Roland T1 - metaFALCON: A program package for automatic sampling of conical intersection seams using multistate metadynamics T2 - Journal of Chemical Theory and Computation N2 - The multistate metadynamics for automatic exploration of conical intersection seams and systematic location of minimum energy crossing points in molecular systems and its implementation into the software package metaFALCON is presented. Based on a locally modified energy gap between two Born–Oppenheimer electronic states as a collective variable, multistate metadynamics trajectories are driven toward an intersection point starting from an arbitrary ground state geometry and are subsequently forced to explore the conical intersection seam landscape. For this purpose, an additional collective variable capable of distinguishing structures within the seam needs to be defined and an additional bias is introduced into the off-diagonal elements of an extended (multistate) electronic Hamiltonian. We demonstrate the performance of the algorithm on the examples of the 1,3-butadiene, benzene, and 9H-adenine molecules, where multiple minimum energy crossing points could be systematically located using the Wiener number or Cremer–Pople parameters as collective variables. Finally, with the example of 9H-adenine, we show that the multistate metadynamics potential can be used to obtain a global picture of a conical intersection seam. Our method can be straightforwardly connected with any ab initio or semiempirical electronic structure theory that provides energies and gradients of the respective electronic states and can serve for systematic elucidation of the role of conical intersections in the photophysics and photochemistry of complex molecular systems, thus complementing nonadiabatic dynamics simulations. KW - Computational Chemistry KW - Metadynamics KW - Hydrogen KW - Hydrocarbons KW - Chemical Structure Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-199258 UR - https://doi.org/10.1021/acs.jctc.9b00029 N1 - This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see Journal of Chemical Theory and Computation 2019, 15, 6, 3450-3460. https://doi.org/10.1021/acs.jctc.9b00029. ER - TY - INPR A1 - Titov, Evgenii A1 - Humeniuk, Alexander A1 - Mitric, Roland T1 - Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections T2 - Chemical Physics N2 - We assess the performance of two different types of basis sets for nonadiabatic quantum dynamics at conical intersections. The basis sets of both types are generated using Ehrenfest trajectories of nuclear coherent states. These trajectories can either serve as a moving (time-dependent) basis or be employed to sample a fixed (time-independent) basis. We demonstrate on the example of two-state two-dimensional and three-state five-dimensional models that both basis set types can yield highly accurate results for population transfer at intersections, as compared with reference quantum dynamics. The details of wave packet evolutions are discussed for the case of the two-dimensional model. The fixed basis is found to be superior to the moving one in reproducing nonlocal spreading and maintaining correct shape of the wave packet upon time evolution. Moreover, for the models considered, the fixed basis set outperforms the moving one in terms of computational efficiency. KW - Nonadiabatic quantum dynamics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-199225 UR - https://doi.org/10.1016/j.chemphys.2019.110526 N1 - Submitted version ER - TY - INPR A1 - Titov, Evgenii A1 - Humeniuk, Alexander A1 - Mitric, Roland T1 - Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections T2 - Chemical Physics N2 - We assess the performance of two different types of basis sets for nonadiabatic quantum dynamics at conical intersections. The basis sets of both types are generated using Ehrenfest trajectories of nuclear coherent states. These trajectories can either serve as a moving (time-dependent) basis or be employed to sample a fixed (time-independent) basis. We demonstrate on the example of two-state two-dimensional and three-state five-dimensional models that both basis set types can yield highly accurate results for population transfer at intersections, as compared with reference quantum dynamics. The details of wave packet evolutions are discussed for the case of the two-dimensional model. The fixed basis is found to be superior to the moving one in reproducing true nonlocal spreading and maintaining correct shape of the wave packet upon time evolution. Moreover, for the models considered, the fixed basis set outperforms the moving one in terms of computational efficiency. KW - Nonadiabatic quantum dynamics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-198699 UR - https://doi.org/10.1016/j.chemphys.2019.110526 N1 - Accepted manuscript ER - TY - INPR A1 - Lisinetskaya, Polina G. A1 - Mitric, Roland T1 - Collective Response in DNA-Stabilized Silver Cluster Assemblies from First-Principles Simulations T2 - The Journal of Physical Chemistry Letters N2 - We investigate fluorescence resonant energy transfer and concurrent electron dynamics in a pair of DNA-stabilized silver clusters. For this purpose we introduce a methodology for the simulation of collective optoelectronic properties of coupled molecular aggregates starting from first-principles quantum chemistry, which can be further applied to a broad range of coupled molecular systems to study their electro-optical response. Our simulations reveal the existence of low-energy coupled excitonic states, which enable ultrafast energy transport between subunits, and give insight into the origin of the fluorescence signal in coupled DNA-stabilized silver clusters, which have been recently experimentally detected. Hence, we demonstrate the possibility of constructing ultrasmall energy transmission lines and optical converters based on these hybrid molecular systems. KW - Metal clusters Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-198729 UR - https://doi.org/10.1021/acs.jpclett.9b03136 N1 - This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Physical Chemistry A, copyright © American Chemical Society after peer review. To access the final edited and published work see The Journal of Physical Chemistry Letters 2019, 10, 24, 7884-7889. https://doi.org/10.1021/acs.jpclett.9b03136. ER - TY - INPR A1 - Auerhammer, Nina A1 - Schulz, Alexander A1 - Schmiedel, Alexander A1 - Holzapfel, Marco A1 - Hoche, Joscha A1 - Röhr, Merle I. S. A1 - Mitric, Roland A1 - Lambert, Christoph T1 - Dynamic exciton localisation in a pyrene-BODIPY-pyrene dye conjugate T2 - Physical Chemistry Chemical Physics N2 - The photophysics of a molecular triad consisting of a BODIPY dye and two pyrene chromophores attached in 2-position are investigated by steady state and fs-time resolved transient absorption spectroscopy as well as by field induced surface hopping (FISH) simulations. While the steady state measurements indicate moderate chromophore interactions within the triad, the time resolved measurements show upon pyrene excitation a delocalised excited state which localises onto the BODIPY chromophore with a time constant of 0.12 ps. This could either be interpreted as an internal conversion process within the excitonically coupled chromophores or as an energy transfer from the pyrenes to the BODIPY dye. The analysis of FISH-trajectories reveals an oscillatory behaviour where the excitation hops between the pyrene units and the BODIPY dye several times until finally they become localised on the BODIPY chromophore within 100 fs. This is accompanied by an ultrafast nonradiative relaxation within the excitonic manifold mediated by the nonadiabatic coupling. Averaging over an ensemble of trajectories allowed us to simulate the electronic state population dynamics and determine the time constants for the nonradiative transitions that mediate the ultrafast energy transfer and exciton localisation on BODIPY. KW - Exciton localization dynamics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-198718 UR - https://doi.org/10.1039/C9CP00908F N1 - Accepted manuscript ER - TY - INPR A1 - Titov, Evgenii A1 - Humeniuk, Alexander A1 - Mitric, Roland T1 - Exciton localization in excited-state dynamics of a tetracene trimer: A surface hopping LC-TDDFTB study T2 - Physical Chemistry Chemical Physics N2 - Excitons in the molecular aggregates of chromophores are key participants in important processes such as photosynthesis or the functioning of organic photovoltaic devices. Therefore, the exploration of exciton dynamics is crucial. Here we report on exciton localization during excited-state dynamics of the recently synthesized tetracene trimer [Liu et al., Org. Lett., 2017, 19, 580]. We employ the surface hopping approach to nonadiabatic molecular dynamics in conjunction with the long-range corrected time-dependent density functional tight binding (LC-TDDFTB) method [Humeniuk and Mitrić, Comput. Phys. Commun., 2017, 221, 174]. Utilizing a set of descriptors based on the transition density matrix, we perform comprehensive analysis of exciton dynamics. The obtained results reveal an ultrafast exciton localization to a single tetracene unit of the trimer during excited-state dynamics, along with exciton transfer between units. KW - Exciton dynamics Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-198680 UR - https://doi.org/10.1039/C8CP05240A N1 - Accepted Manuscript ER - TY - INPR A1 - Röder, Anja A1 - Petersen, Jens A1 - Issler, Kevin A1 - Fischer, Ingo A1 - Mitric, Roland A1 - Poisson, Lionel T1 - Exploring the Excited-State Dynamics of Hydrocarbon Radicals, Biradicals and Carbenes using Time-Resolved Photoelectron Spectroscopy and Field-Induced Surface Hopping Simulations T2 - The Journal of Physical Chemistry A N2 - Reactive hydrocarbon molecules like radicals, biradicals and carbenes are not only key players in combustion processes and interstellar and atmospheric chemistry, but some of them are also important intermediates in organic synthesis. These systems typically possess many low-lying, strongly coupled electronic states. After light absorption, this leads to rich photodynamics characterized by a complex interplay of nuclear and electronic motion, which is still not comprehensively understood and not easy to investigate both experimentally and theoretically. In order to elucidate trends and contribute to a more general understanding, we here review our recent work on excited-state dynamics of open-shell hydrocarbon species using time-resolved photoelectron spectroscopy and field-induced surface hopping simulations, and report new results on the excited-state dynamics of the tropyl and the 1-methylallyl radical. The different dynamics are compared, and the difficulties and future directions of time-resolved photoelectron spectroscopy and excited state dynamics simulations of open-shell hydrocarbon molecules are discussed. KW - Excited state dynamics KW - Hydrocarbon radicals KW - time-resolved photoelectron spectroscopy KW - field-induced surface hopping Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-198734 UR - https://doi.org/10.1021/acs.jpca.9b06346 N1 - This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of Physical Chemistry A, copyright © American Chemical Society after peer review. To access the final edited and published work see Journal of Physical Chemistry A 2019, 123, 50, 10643-10662. https://doi.org/10.1021/acs.jpca.9b06346. ER - TY - INPR A1 - Maghami, Mohammad Ghaem A1 - Scheitl, Carolin P. M. A1 - Höbartner, Claudia T1 - Direct in vitro selection of trans-acting ribozymes for posttranscriptional, site-specific, and covalent fluorescent labeling of RNA T2 - Journal of the American Chemical Society N2 - General and efficient tools for site-specific fluorescent or bioorthogonal labeling of RNA are in high demand. Here, we report direct in vitro selection, characterization, and application of versatile trans-acting 2'-5' adenylyl transferase ribozymes for covalent and site-specific RNA labeling. The design of our partially structured RNA pool allowed for in vitro evolution of ribozymes that modify a predetermined nucleotide in cis (i.e. intramolecular reaction), and were then easily engineered for applications in trans (i.e. in an intermolecular setup). The resulting ribozymes are readily designed for specific target sites in small and large RNAs and accept a wide variety of N6-modified ATP analogues as small molecule substrates. The most efficient new ribozyme (FH14) shows excellent specificity towards its target sequence also in the context of total cellular RNA. KW - covalent and site-specific RNA labeling KW - trans-acting 2'-5' adenylyl transferase ribozymes KW - in vitro selection from a structured RNA library KW - Ribozyme-catalyzed RNA labeling KW - intermolecular applications of ribozymes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-192333 N1 - This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of the American Chemical Society, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/jacs.9b10531. ER - TY - INPR A1 - Huber, Bernhard A1 - Pres, Sebastian A1 - Wittmann, Emanuel A1 - Dietrich, Lysanne A1 - Lüttig, Julian A1 - Fersch, Daniel A1 - Krauss, Enno A1 - Friedrich, Daniel A1 - Kern, Johannes A1 - Lisinetskii, Victor A1 - Hensen, Matthias A1 - Hecht, Bert A1 - Bratschitsch, Rudolf A1 - Riedle, Eberhard A1 - Brixner, Tobias T1 - Space- and time-resolved UV-to-NIR surface spectroscopy and 2D nanoscopy at 1 MHz repetition rate N2 - We describe a setup for time-resolved photoemission electron microscopy (TRPEEM) with aberration correction enabling 3 nm spatial resolution and sub-20 fs temporal resolution. The latter is realized by our development of a widely tunable (215–970 nm) noncollinear optical parametric amplifier (NOPA) at 1 MHz repetition rate. We discuss several exemplary applications. Efficient photoemission from plasmonic Au nanoresonators is investigated with phase-coherent pulse pairs from an actively stabilized interferometer. More complex excitation fields are created with a liquid-crystal-based pulse shaper enabling amplitude and phase shaping of NOPA pulses with spectral components from 600 to 800 nm. With this system we demonstrate spectroscopy within a single plasmonic nanoslit resonator by spectral amplitude shaping and investigate the local field dynamics with coherent two-dimensional (2D) spectroscopy at the nanometer length scale (“2D nanoscopy”). We show that the local response varies across a distance as small as 33 nm in our sample. Further, we report two-color pump–probe experiments using two independent NOPA beamlines. We extract local variations of the excited-state dynamics of a monolayered 2D material (WSe2) that we correlate with low-energy electron microscopy (LEEM) and reflectivity (LEER) measurements. Finally, we demonstrate the in-situ sample preparation capabilities for organic thin films and their characterization via spatially resolved electron diffraction and dark-field LEEM. KW - Photoemission electron microscopy PEEM KW - Low energy electron microscopy LEEM KW - Spatially resolved 2D spectroscopy KW - Two-color pump-probe spectroscopy KW - Time-resolved photoemission electron microscopy Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-191906 SN - 0034-6748 N1 - This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Review of Scientific Instruments 90, 113103 (2019); https://doi.org/10.1063/1.5115322 and may be found at https://doi.org/10.1063/1.5115322. ER - TY - INPR A1 - Werner, Rudolf A. A1 - Bundschuh, Ralph A. A1 - Bundschuh, Lena A1 - Javadi, Mehrbod S. A1 - Leal, Jeffrey P. A1 - Higuchi, Takahiro A1 - Pienta, Kenneth J. A1 - Buck, Andreas K. A1 - Pomper, Martin G. A1 - Gorin, Michael A. A1 - Lapa, Constantin A1 - Rowe, Steven P. T1 - Interobserver Agreement for the Standardized Reporting System PSMA-RADS 1.0 on \(^{18}\)F-DCFPyL PET/CT Imaging T2 - Journal of Nuclear Medicine N2 - Objectives: Recently, the standardized reporting and data system for prostate-specific membrane antigen (PSMA)-targeted positron emission tomography (PET) imaging studies, termed PSMA-RADS version 1.0, was introduced. We aimed to determine the interobserver agreement for applying PSMA-RADS to imaging interpretation of 18F-DCFPyL PET examinations in a prospective setting mimicking the typical clinical work-flow at a prostate cancer referral center. Methods: Four readers (two experienced readers (ER, > 3 years of PSMA-targeted PET interpretation experience) and two inexperienced readers (IR, < 1 year of experience)), who had all read the initial publication on PSMA-RADS 1.0, assessed 50 18F-DCFPyL PET/computed tomography (CT) studies independently. Per scan, a maximum of 5 target lesions were selected by the observers and a PSMA-RADS score for every target lesion was recorded. No specific pre-existing conditions were placed on the selection of the target lesions, although PSMA-RADS 1.0 suggests that readers focus on the most highly avid or largest lesions. An overall scan impression based on PSMA-RADS was indicated and interobserver agreement rates on a target lesion-based, on an organ-based, and on an overall PSMA-RADS score-based level were computed. Results: The number of target lesions identified by each observer were as follows: ER 1, 123; ER 2, 134; IR 1, 123; and IR 2, 120. Among those selected target lesions, 125 were chosen by at least two individual observers (all four readers selected the same target lesion in 58/125 (46.4%) instances, three readers in 40/125 (32%) and two observers in 27/125 (21.6%) instances). The interobserver agreement for PSMA-RADS scoring among identical target lesions was good (intraclass correlation coefficient (ICC) for four, three and two identical target lesions, ≥0.60, respectively). For lymph nodes, an excellent interobserver agreement was derived (ICC=0.79). The interobserver agreement for an overall scan impression based on PSMA-RADS was also excellent (ICC=0.84), with a significant difference for ER (ICC=0.97) vs. IR (ICC=0.74, P=0.005). Conclusions: PSMA-RADS demonstrates a high concordance rate in this study, even among readers with different levels of experience. This suggests that PSMA-RADS can be effectively used for communication with clinicians and can be implemented in the collection of data for large prospective trials. KW - 18F-DCFPyL KW - Positronen-Emissions-Tomografie KW - PSMA-RADS KW - interreader KW - interobserver KW - PSMA KW - prostate cancer KW - RADS KW - reporting and data system KW - PET Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-167788 SN - 0161-5505 N1 - This research was originally published in JNM. Rudolf A. Werner, Ralph A. Bundschuh, Lena Bundschuh, Mehrbod S. Javadi, Jeffrey P. Leal, Takahiro Higuchi, Kenneth J. Pienta, Andreas K. Buck, Martin G. Pomper, Michael A. Gorin, Constantin Lapa and Steven P. Rowe. Interobserver Agreement for the Standardized Reporting System PSMA-RADS 1.0 on 18F-DCFPyL PET/CT Imaging. J Nucl Med 2018;59:1857-1864 © SNMMI. ER - TY - INPR A1 - Brückner, Tobias A1 - Stennett, Tom E. A1 - Heß, Merlin A1 - Braunschweig, Holger T1 - Single and Double Hydroboration of B-B Triple Bonds and Conver- gent Routes to a Cationic Tetraborane T2 - Journal of the American Chemical Society N2 - A compound with a boron-boron triple bond is shown to undergo stepwise hydroboration reactions with catecholborane to yield an unsymmetrical hydro(boryl)diborene and a 2,3-dihydrotetraborane. Abstraction of H– from the latter compound produces an unusual cationic, planar tetraborane with a hydrogen atom bridging the central B2 moiety. Spectroscopic and crystallographic data and DFT calculations support a ‘protonated diborene’ structure for this compound, which can also be accessed via direct protonation of the corresponding diborene. KW - boron KW - multiple bonding KW - hydroboration Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-188632 N1 - This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in Journal of the American Chemical Society, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/jacs.9b07991. ER - TY - INPR A1 - Légaré, Marc-André A1 - Pranckevicius, Conor A1 - Braunschweig, Holger T1 - Metallomimetic Chemistry of Boron T2 - Chemical Reviews N2 - The study of main-group molecules that behave and react similarly to transition-metal (TM) complexes has attracted significant interest in recent decades. Most notably, the attractive idea of replacing the all-too-often rare and costly metals from catalysis has motivated efforts to develop main-group-element-mediated reactions. Main-group elements, however, lack the electronic flexibility of TM complexes that arises from combinations of empty and filled d orbitals and that seem ideally suited to bind and activate many substrates. In this review, we look at boron, an element that despite its nonmetal nature, low atomic weight, and relative redox staticity has achieved great milestones in terms of TM-like reactivity. We show how in interelement cooperative systems, diboron molecules, and hypovalent complexes the fifth element can acquire a truly metallomimetic character. As we discuss, this character is powerfully demonstrated by the reactivity of boron-based molecules with H2, CO, alkynes, alkenes and even with N2. KW - boron KW - small-molecule activation KW - catalysis KW - low-valent main group chemistry Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-186317 N1 - This document is the unedited Author’sv ersion of a Submitted Work that was subsequently accepted for publication in Chemical Reviews,copyright ©American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/acs.chemrev.8b00561. ER - TY - INPR A1 - Englert, Lukas A1 - Stoy, Andreas A1 - Arrowsmith, Merle A1 - Müssig, Jonas H. A1 - Thaler, Melanie A1 - Deißenberger, Andrea A1 - Häfner, Alena A1 - Böhnke, Julian A1 - Hupp, Florian A1 - Seufert, Jens A1 - Mies, Jan A1 - Damme, Alexander A1 - Dellermann, Theresa A1 - Hammond, Kai A1 - Kupfer, Thomas A1 - Radacki, Krzysztof A1 - Thiess, Torsten A1 - Braunschweig, Holger T1 - Stable Lewis Base Adducts of Tetrahalodiboranes: Synthetic Methods and Structural Diversity T2 - Chemistry - A European Journal N2 - A series of 22 new bis(phosphine), bis(carbene) and bis(isonitrile) tetrahalodiborane adducts has been synthesized, either by direct adduct formation with highly sensitive B2X4 precursors (X = Cl, Br, I) or by ligand exchange at stable B2X4(SMe2)2 precursors (X = Cl, Br) with labile dimethylsulfide ligands. The isolated compounds have been fully characterized using NMR spectroscopic, (C,H,N)- elemental and, for 20 of these compounds, X-ray crystallographic analysis, revealing an unexpected variation in the bonding motifs. Besides the classical B2X4L2 diborane(6) adducts, some of the more sterically demanding carbene ligands induce a halide displacement leading to the first halide-bridged monocationic diboron species, [B2X3L2]A (A = BCl4, Br, I). Furthermore, low-temperature 1:1 reactions of B2Cl4 with sterically demanding N-heterocyclic carbenes led to the formation of kinetically unstable mono-adducts, one of which was structurally characterized. A comparison of the NMR and structural data of new and literature-known bis-adducts shows several trends pertaining to the nature of the halides and the stereoelectronic properties of the Lewis bases employed. KW - diborane(6) KW - Lewis-base adducts KW - ligand exchange KW - crystallography KW - NMR spectroscopy Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-184888 N1 - This is the pre-peer reviewed version of the following article: L. Englert, A. Stoy, M. Arrowsmith, J. H. Muessig, M. Thaler, A. Deißenberger, A. Häfner, J. Böhnke, F. Hupp, J. Seufert, J. Mies, A. Damme, T. Dellermann, K. Hammond, T. Kupfer, K. Radacki, T. Thiess, H. Braunschweig, Chem. Eur. J. 2019, 25, 8612. https://doi.org/10.1002/chem.201901437, which has been published in final form at https://doi.org/10.1002/chem.201901437. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. ER - TY - INPR A1 - Brückner, Tobias A1 - Arrowsmith, Merle A1 - Heß, Merlin A1 - Hammond, Kai A1 - Müller, Marcel A1 - Braunschweig, Holger T1 - Synthesis of fused B,N-heterocycles by alkyne cleavage, NHC ring-expansion and C-H activation at a diboryne T2 - Chemical Communications N2 - The addition of alkynes to a staturated N-heterocyclic carbene (NHC)-supported diboryne results in spontaneous cycloaddition, with complete B≡B and C≡C triple bond cleavage, NHC ring- expansion and activation of a variety of C-H bonds, leading to the formation of complex mixtures of fused B,N-heterocycles. KW - heterocycles KW - alkynes KW - boron KW - carbenes Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-184899 N1 - This is the pre-peer reviewed version of the following article: Chem. Commun., 2019,55, 6700-6703, which has been published in final form at doi:10.1039/C9CC02657F ER - TY - INPR A1 - Arrowsmith, Merle A1 - Dömling, Michael A1 - Schmidt, Uwe A1 - Werner, Luis A1 - Castro, Abril C. A1 - Jiménez-Halla, J. Oscar C. A1 - Müssig, Jonas A1 - Prieschl, Dominic A1 - Braunschweig, Holger T1 - Spontaneous trans‐Selective Transfer Hydrogenation of Apolar B=B Double Bonds T2 - Angewandte Chemie, International Edition N2 - The transfer hydrogenation of NHC-supported diborenes with dimethylamine borane proceeds with high selectivity for the trans-1,2-dihydrodiboranes(6). DFT calculations suggest a stepwise proton-first-hydride-second reaction mechanism via an intermediate μ-hydrodiboronium dimethylaminoborate ion pair. KW - transfer hydrogenation KW - diborene KW - amine borane dehydrocoupling KW - diboranes KW - DFT mechanism Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-184874 N1 - This is the pre-peer reviewed version of the following article: M. Dömling, M. Arrowsmith, U. Schmidt, L. Werner, A. C. Castro, J. O. C. Jiménez-Halla, R. Bertermann, J. Müssig, D. Prieschl, H. Braunschweig, Angew. Chem. Int. Ed. 2019, 58, 9782. doi:10.1002/anie.201902656, which has been published in final form at https://doi.org/10.1002/anie.201902656. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. ER - TY - INPR A1 - Dandekar, Thomas T1 - Biological heuristics applied to cosmology suggests a condensation nucleus as start of our universe and inflation cosmology replaced by a period of rapid Weiss domain-like crystal growth N2 - Cosmology often uses intricate formulas and mathematics to derive new theories and concepts. We do something different in this paper: We look at biological processes and derive from these heuristics so that the revised cosmology agrees with astronomical observations but does also agree with standard biological observations. We show that we then have to replace any type of singularity at the start of the universe by a condensation nucleus and that the very early period of the universe usually assumed to be inflation has to be replaced by a period of rapid crystal growth as in Weiss magnetization domains. Impressively, these minor modifications agree well with astronomical observations including removing the strong inflation perturbations which were never observed in the recent BICEP2 experiments. Furthermore, looking at biological principles suggests that such a new theory with a condensation nucleus at start and a first rapid phase of magnetization-like growth of the ordered, physical laws obeying lattice we live in is in fact the only convincing theory of the early phases of our universe that also is compatible with current observations. We show in detail in the following that such a process of crystal creation, breaking of new crystal seeds and ultimate evaporation of the present crystal readily leads over several generations to an evolution and selection of better, more stable and more self-organizing crystals. Moreover, this explains the “fine-tuning” question why our universe is fine-tuned to favor life: Our Universe is so self-organizing to have enough offspring and the detailed physics involved is at the same time highly favorable for all self-organizing processes including life. This biological theory contrasts with current standard inflation cosmologies. The latter do not perform well in explaining any phenomena of sophisticated structure creation or self-organization. As proteins can only thermodynamically fold by increasing the entropy in the solution around them we suggest for cosmology a condensation nucleus for a universe can form only in a “chaotic ocean” of string-soup or quantum foam if the entropy outside of the nucleus rapidly increases. We derive an interaction potential for 1 to n-dimensional strings or quantum-foams and show that they allow only 1D, 2D, 4D or octonion interactions. The latter is the richest structure and agrees to the E8 symmetry fundamental to particle physics and also compatible with the ten dimensional string theory E8 which is part of the M-theory. Interestingly, any other interactions of other dimensionality can be ruled out using Hurwitz compositional theorem. Crystallization explains also extremely well why we have only one macroscopic reality and where the worldlines of alternative trajectories exist: They are in other planes of the crystal and for energy reasons they crystallize mostly at the same time, yielding a beautiful and stable crystal. This explains decoherence and allows to determine the size of Planck´s quantum h (very small as separation of crystal layers by energy is extremely strong). Ultimate dissolution of real crystals suggests an explanation for dark energy agreeing with estimates for the “big rip”. The halo distribution of dark matter favoring galaxy formation is readily explained by a crystal seed starting with unit cells made of normal and dark matter. That we have only matter and not antimatter can be explained as there may be right handed mattercrystals and left-handed antimatter crystals. Similarly, real crystals are never perfect and we argue that exactly such irregularities allow formation of galaxies, clusters and superclusters. Finally, heuristics from genetics suggest to look for a systems perspective to derive correct vacuum and Higgs Boson energies. KW - heuristics KW - inflation KW - cosmology KW - crystallization KW - crystal growth KW - E8 symmetry KW - Hurwitz theorem KW - evolution KW - Lee Smolin Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-183945 ER - TY - INPR A1 - Yin, Yafu A1 - Werner, Rudolf A. A1 - Higuchi, Takahiro A1 - Lapa, Constantin A1 - Pienta, Kenneth J. A1 - Pomper, Martin G. A1 - Gorin, Michael A. A1 - Rowe, Steven P. T1 - Follow-Up of Lesions with Equivocal Radiotracer Uptake on PSMA-Targeted PET in Patients with Prostate Cancer: Predictive Values of the PSMA-RADS-3A and PSMARADS- 3B Categories T2 - Journal of Nuclear Medicine N2 - Purpose: Prostate-specific membrane antigen (PSMA)-targeted positron emission tomography (PET) imaging has become commonly utilized in patients with prostate cancer (PCa). The PSMA reporting and data system version 1.0 (PSMA-RADS version 1.0) categorizes lesions on the basis of the likelihood of PCa involvement, with PSMA-RADS-3A (soft tissue) and PSMA-RADS-3B (bone) lesions being indeterminate for the presence of disease. We retrospectively reviewed the imaging follow-up of such lesions to determine the rate at which they underwent changes suggestive of underlying PCa. Methods: PET/CT imaging with \(^{18}\)F-DCFPyL was carried out in 110 patients with PCa and lesions were categorized according to PSMA-RADS Version 1.0. 56/110 (50.9%) patients were determined to have indeterminate PSMA-RADS-3A or PSMA-RADS-3B lesions and 22/56 (39.3%) patients had adequate follow-up to be included in the analysis. The maximum standardized uptake values (SUV\(_{max}\)) of the lesions were obtained and the ratios of SUV\(_{max}\) of the lesions to SUV\(_{mean}\) of blood pool (SUV\(_{max}\)-lesion/SUV\(_{mean}\)-bloodpool) were calculated. Pre-determined criteria were used to evaluate the PSMA-RADS-3A and PSMA-RADS-3B lesions on follow-up imaging to determine if they demonstrated evidence of underlying malignancy. Results: A total of 46 lesions in 22 patients were considered indeterminate for PCa (i.e. PSMA-RADS-3A (32 lesions) or PSMA-RADS-3B (14 lesions)) and were evaluable on follow-up imaging. 27/46 (58.7%) lesions demonstrated changes on follow-up imaging consistent with the presence of underlying PCa at baseline. These lesions included 24/32 (75.0%) PSMA-RADS-3A lesions and 3/14 (21.4%) lesions categorized as PSMA-RADS-3B. The ranges of SUVmax and SUVmax-lesion/SUVmean-bloodpool overlapped between those lesions demonstrating changes consistent with malignancy on follow-up imaging and those lesions that remained unchanged on follow-up. Conclusion: PSMA-RADS-3A and PSMA-RADS-3B lesions are truly indeterminate in that proportions of findings in both categories demonstrate evidence of malignancy on follow-up imaging. Overall, PSMA-RADS-3A lesions are more likely than PSMA-RADS-3B lesions to represent sites of PCa and this information should be taken into when guiding patient therapy. KW - PSMA-RADS-3B KW - Positronen-Emissions-Tomografie KW - prostate-specific membrane antigen KW - prostate cancer KW - PSMA-targeted PET KW - PSMA-RADS-3A Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-167594 SN - 0161-5505 N1 - This research was originally published in JNM. Yafu Yin, Rudolf A. Werner, Takahiro Higuchi, Constantin Lapa, Kenneth J. Pienta, Martin G. Pomper, Michael A. Gorin, Steven P. Rowe. Follow-Up of Lesions with Equivocal Radiotracer Uptake on PSMA-Targeted PET in Patients with Prostate Cancer: Predictive Values of the PSMA-RADS-3A and PSMA-RADS-3B Categories. J Nucl Med. 2019;60:511-516 © SNMMI. ER - TY - INPR A1 - Stennett, Tom E. A1 - Bissinger, Philipp A1 - Griesbeck, Stefanie A1 - Ullrich, Stefan A1 - Krummenacher, Ivo A1 - Auth, Michael A1 - Sperlich, Andreas A1 - Stolte, Matthias A1 - Radacki, Krzysztof A1 - Yao, Chang-Jiang A1 - Würthner, Frank A1 - Steffen, Andreas A1 - Marder, Todd B. A1 - Braunschweig, Holger T1 - Near-Infrared Quadrupolar Chromophores Combining Three-Coordinate Boron-Based Superdonor and Superacceptor Units T2 - Angewandte Chemie, International Edition N2 - In this work, two new quadrupolar A-π-D-π-A chromophores have been prepared featuring a strongly electron- donating diborene core and strongly electron-accepting dimesitylboryl F(BMes2) and bis(2,4,6-tris(trifluoromethyl)phenyl)boryl (BMes2) end groups. Analysis of the compounds by NMR spectroscopy, X-ray crystallography, cyclic voltammetry and UV-vis-NIR absorption and emission spectroscopy indicated that the compounds possess extended conjugated π-systems spanning their B4C8 cores. The combination of exceptionally potent π-donor (diborene) and π- acceptor (diarylboryl) groups, both based on trigonal boron, leads to very small HOMO-LUMO gaps, resulting in strong absorption in the near-IR region with maxima in THF at 840 and 1092 nm, respectively, and very high extinction coefficients of ca. 120,000 M-1cm-1. Both molecules also display weak near-IR fluorescence with small Stokes shifts. KW - boron KW - near-IR chromophores KW - conjugation KW - low-valent compounds KW - synthesis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180391 N1 - This is the pre-peer reviewed version of the following article: T. E. Stennett, P. Bissinger, S. Griesbeck, S. Ullrich, I. Krummenacher, M. Auth, A. Sperlich, M. Stolte, K. Radacki, C.-J. Yao, F. Wuerthner, A. Steffen, T. B. Marder, H. Braunschweig, Angew. Chem. Int. Ed. 2019, 58, 6449. , which has been published in final form at https://doi.org/10.1002/anie.201900889. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. ER - TY - INPR A1 - Lermann, Dr. Matthias T1 - Das Druckbild des Cartellverbands. Versuch über die Typographiegeschichte der Academia T2 - Festschrift 125 Jahre Academia N2 - Die vorliegende Untersuchung gilt der Mikro- und Makrotypografie der seit 125 Jahren erscheinenden katholischen Verbandszeitschrift "Academia". Für die graphologischen und paläographischen Besonderheiten wird eine Hermeneutik vorgeschlagen. Das hier erforschte Druckbild repräsentiert mit einer Auflage von 30.000 Exemplaren im achtwöchigen Erscheinungsrhythmus den Cartellverband der Katholischen Deutschen Studentenverbindungen (CV). So illustriert und visualisiert dieses Druckbild mit seiner typografischen Performance zugleich den mitgliederstärksten Akademikerverband Europas. KW - Cartellverband KW - Cartellverband der Katholischen Deutschen Studentenverbindungen KW - Buchdruck KW - Katholische Zeitschrift KW - Academia (Zeitschrift, Bad Honnef) KW - Drucktechnik KW - CV KW - Academia KW - Layout KW - Offset KW - Lithographie Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-180351 ER - TY - INPR A1 - Werner, Rudolf A. A1 - Bundschuh, Ralph A. A1 - Bundschuh, Lena A1 - Fanti, Stefano A1 - Javadi, Mehrbod S. A1 - Higuchi, Takahiro A1 - Weich, A. A1 - Pienta, Kenneth J. A1 - Buck, Andreas K. A1 - Pomper, Martin G. A1 - Gorin, Michael A. A1 - Herrmann, Ken A1 - Lapa, Constantin A1 - Rowe, Steven P. T1 - Novel Structured Reporting Systems for Theranostic Radiotracers T2 - Journal of Nuclear Medicine N2 - Standardized reporting is more and more routinely implemented in clinical practice and such structured reports have a major impact on a large variety of medical fields, e.g. laboratory medicine, pathology, and, recently, radiology. Notably, the field of nuclear medicine is constantly evolving, as novel radiotracers for numerous clinical applications are developed. Thus, framework systems for standardized reporting in this field may a) increase clinical acceptance of new radiotracers, b) allow for inter- and intra-center comparisons for quality assurance, and c) may be used in (global) multi-center studies to ensure comparable results and enable efficient data abstraction. In the last two years, several standardized framework systems for positron emission tomography (PET) radiotracers with potential theranostic applications have been proposed. These include systems for prostate-specific membrane antigen (PSMA)-targeted PET agents for the diagnosis and treatment of prostate cancer (PCa) and somatostatin receptor (SSTR)-targeted PET agents for the diagnosis and treatment of neuroendocrine neoplasias. In the present review, those standardized framework systems for PSMA- and SSTR-targeted PET will be briefly introduced followed by an overview of their advantages and limitations. In addition, potential applications will be defined, approaches to validate such concepts will be proposed, and future perspectives will be discussed. KW - standardized reporting KW - Positronen-Emissions-Tomografie KW - prostate cancer KW - neuroendocrine neoplasia KW - 68Ga-DOTATATE KW - 68Ga-DOTATOC KW - 68Ga-DOTANOC KW - somatostatin receptor KW - SSTR KW - prostate-specific membrane antigen KW - PSMA KW - RADS KW - PSMA-RADS KW - SSTR-RADS KW - MI-RADS KW - PROMISE Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-174629 SN - 0161-5505 N1 - This research was originally published in JNM. Authors: Rudolf A. Werner, Ralph A. Bundschuh, Lena Bundschuh, Stefano Fanti, Mehrbod S. Javadi, Takahiro Higuchi, A. Weich, Kenneth J. Pienta, Andreas K. Buck, Martin G. Pomper, Michael A. Gorin, Ken Herrmann, Constantin Lapa, Steven P. Rowe. Novel Structured Reporting Systems for Theranostic Radiotracers. J Nucl Med May 1, 2019 vol. 60 no. 5 577-584 © SNMMI. ER -