Refine
Has Fulltext
- yes (130)
Is part of the Bibliography
- yes (130)
Year of publication
Document Type
- Preprint (130) (remove)
Language
- English (107)
- German (19)
- French (2)
- Portuguese (2)
Keywords
- boron (20)
- Quran (8)
- diborenes (8)
- Koran (7)
- Text Mining (7)
- crystallization (6)
- carbenes (5)
- cosmology (5)
- qubit (5)
- Archäologie (4)
Institute
- Institut für Anorganische Chemie (30)
- Institut für deutsche Philologie (25)
- Institut für Physikalische und Theoretische Chemie (19)
- Institut für Organische Chemie (14)
- Theodor-Boveri-Institut für Biowissenschaften (13)
- Institut für Altertumswissenschaften (6)
- Klinik und Poliklinik für Nuklearmedizin (6)
- Rudolf-Virchow-Zentrum (5)
- Physikalisches Institut (4)
- Neuphilologisches Institut - Moderne Fremdsprachen (3)
Schriftenreihe
Sonstige beteiligte Institutionen
- Johns Hopkins School of Medicine (3)
- International Max Planck Research School Molecular Biology, University of Göttingen, Germany (2)
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany (1)
- Center for Nanosystems Chemistry (CNC), University of Würzburg (1)
- Center for Nanosystems Chemistry (CNC), Universität Würzburg (1)
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Am Hubland, 97074 Würzburg, Germany (1)
- Center of Excellence for Science and Technology - Integration of Mediterranean region (STIM), Faculty of Science, University of Split, Poljička cesta 35, 2100 Split, Croatia (1)
- Charles University, Faculty of Mathematics and Physics, Ke Karlovu 5, 121 16 Prague, Czech Republic (1)
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain (1)
- Department of Biomedical Imaging, National Cerebral and Cardiovascular Research Center, Suita, Japan (1)
Webservices composition is traditionally carried out using composition technologies such as Business Process Execution Language (BPEL) [1] and Web Service Choreography Interface (WSCI) [2]. The composition technology involves the process of web service discovery, invocation, and composition. However these technologies are not easy and flexible enough because they are mainly developer-centric. Moreover majority of websites have not yet embarked into the world of web service, although they have very important and useful information to offer. Is it because they have not understood the usefulness of web services or is it because of the costs? Whatever might be the answers to these questions, time and money are definitely required in order to create and offer web services. To avoid these expenditures, wrappers [7] to automatically generate webservices from websites would be a cheaper and easier solution. Mashups offer a different way of doing webservices composition. In web environment a Mashup is a web application that brings together data from several sources using webservices, APIs, wrappers and so on, in order to create entirely a new application that was not provided before. This paper presents first an overview of Mashups and the process of web service invocation and composition based on Mashup, then describes an example of a web-based simulator for navigation system in Germany.
This paper discusses the categorization of Quranic chapters by major phases of Prophet Mohammad’s messengership using machine learning algorithms. First, the chapters were categorized by places of revelation using Support Vector Machine and naïve Bayesian classifiers separately, and their results were compared to each other, as well as to the existing traditional Islamic and western orientalists classifications. The chapters were categorized into Meccan (revealed in Mecca) and Medinan (revealed in Medina). After that, chapters of each category were clustered using a kind of fuzzy-single linkage clustering approach, in order to correspond to the major phases of Prophet Mohammad’s life. The major phases of the Prophet’s life were manually derived from the Quranic text, as well as from the secondary Islamic literature e.g hadiths, exegesis. Previous studies on computing the places of revelation of Quranic chapters relied heavily on features extracted from existing background knowledge of the chapters. For instance, it is known that Meccan chapters contain mostly verses about faith and related problems, while Medinan ones encompass verses dealing with social issues, battles…etc. These features are by themselves insufficient as a basis for assigning the chapters to their respective places of revelation. In fact, there are exceptions, since some chapters do contain both Meccan and Medinan features. In this study, features of each category were automatically created from very few chapters, whose places of revelation have been determined through identification of historical facts and events such as battles, migration to Medina…etc. Chapters having unanimously agreed places of revelation were used as the initial training set, while the remaining chapters formed the testing set. The classification process was made recursive by regularly augmenting the training set with correctly classified chapters, in order to classify the whole testing set. Each chapter was preprocessed by removing unimportant words, stemming, and representation with vector space model. The result of this study shows that, the two classifiers have produced useable results, with an outperformance of the support vector machine classifier. This study indicates that, the proposed methodology yields encouraging results for arranging Quranic chapters by phases of Prophet Mohammad’s messengership.
In this research, an attempt to create a knowledge-based learning system for the Quranic text has been performed. The knowledge base is made up of the Quranic text along with detailed information about each chapter and verse, and some rules. The system offers the possibility to study the Quran through web-based interfaces, implementing novel visualization techniques for browsing, querying, consulting, and testing the acquired knowledge. Additionally the system possesses knowledge acquisition facilities for maintaining the knowledge base.
Computing Generic Causes of Revelation of the Quranic Verses Using Machine Learning Techniques
(2011)
Because many verses of the holy Quran are similar, there is high probability that, similar verses addressing same issues share same generic causes of revelation. In this study, machine learning techniques have been employed in order to automatically derive causes of revelation of Quranic verses. The derivation of the causes of revelation is viewed as a classification problem. Initially the categories are based on the verses with known causes of revelation, and the testing set consists of the remaining verses. Based on a computed threshold value, a naïve Bayesian classifier is used to categorize some verses. After that, using a decision tree classifier the remaining uncategorized verses are separated into verses that contain indicators (resultative connectors, causative expressions…), and those that do not. As for those verses having indicators, each one is segmented into its constituent clauses by identification of the linking indicators. Then a dominant clause is extracted and considered either as the cause of revelation, or post-processed by adding or subtracting some terms to form a causal clause that constitutes the cause of revelation. Concerning remaining unclassified verses without indicators, a naive Bayesian classifier is again used to assign each one of them to one of the existing classes based on features and topics similarity. As for verses that could not be classified so far, manual classification was made by considering each verse as a category on its own. The result obtained in this study is encouraging, and shows that automatic derivation of Quranic verses’ generic causes of revelation is achievable, and reasonably reliable for understanding and implementing the teachings of the Quran.
Learning a book in general involves reading it, underlining important words, adding comments, summarizing some passages, and marking up some text or concepts. Once deeper understanding is achieved, one would like to organize and manage her/his knowledge in such a way that, it could be easily remembered and efficiently transmitted to others. This paper discusses about modeling religious texts using semantic XML markup based on frame-based knowledge representation, with the purpose of assisting understanding, retention, and sharing of knowledge they contain. In this study, books organized in terms of chapters made up of verses are considered as the source of knowledge to model. Some metadata representing the multiple perspectives of knowledge modeling are assigned to each chapter and verse. Chapters and verses with their metadata form a meta-model, which is represented using frames, and published on a web mashup. An XML-based annotation and visualization system equipped with user interfaces for creating static and dynamic metadata, annotating chapters’ contents according to user selected semantics, and templates for publishing generated knowledge on the Internet, has been developed. The system has been applied to the Quran, and the result obtained shows that multiple perspectives of information modeling can be successfully applied to religious texts, in order to support analysis, understanding, and retention of the texts.
Given a collection of diverging documents about some lost original text, any person interested in the text would try reconstructing it from the diverging documents. Whether it is eclecticism, stemmatics, or copy-text, one is expected to explicitly or indirectly select one of the documents as a starting point or as a base text, which could be emended through comparison with remaining documents, so that a text that could be designated as the original document is generated. Unfortunately the process of giving priority to one of the documents also known as witnesses is a subjective approach. In fact even Cladistics, which could be considered as a computer-based approach of implementing stemmatics, does not present or recommend users to select a certain witness as a starting point for the process of reconstructing the original document. In this study, a computational method using a rule-based Bayesian classifier is used, to assist text scholars in their attempts of reconstructing a non-existing document from some available witnesses. The method developed in this study consists of selecting a base text successively and collating it with remaining documents. Each completed collation cycle stores the selected base text and its closest witness, along with a weighted score of their similarities and differences. At the end of the collation process, a witness selected more often by majority of base texts is considered as the probable base text of the collection. Witnesses’ scores are weighted using a weighting system, based on effects of types of textual modifications on the process of reconstructing original documents. Users have the possibility to select between baseless and base text collation. If a base text is selected, the task is reduced to ranking the witnesses with respect to the base text, otherwise a base text as well as ranking of the witnesses with respect to the base text are computed and displayed on a bar diagram. Additionally this study includes a recursive algorithm for automatically reconstructing the original text from the identified base text and ranked witnesses.
The question of why the Quran structure does not follow its chronology of revelation is a recurring one. Some Islamic scholars such as [1] have answered the question using hadiths, as well as other philosophical reasons based on internal evidences of the Quran itself. Unfortunately till today many are still wondering about this issue. Muslims believe that the Quran is a summary and a copy of the content of a preserved tablet called Lawhul-Mahfuz located in the heaven. Logically speaking, this suggests that the arrangement of the verses and chapters is expected to be similar to that of the Lawhul-Mahfuz. As for the arrangement of the verses in each chapter, there is unanimity that it was carried out by the Prophet himself under the guidance of Angel Gabriel with the recommendation of God. But concerning the ordering of the chapters, there are reports about some divergences [3] among the Prophet’s companions as to which chapter should precede which one. This paper argues that Quranic chapters might have been arranged according to months and seasons of revelation. In fact, based on some verses of the Quran, it is defendable that the Lawhul-Mahfuz itself is understood to have been structured in terms of the months of the year. In this study, philosophical and mathematical arguments for computing chapters’ months of revelation are discussed, and the result is displayed on an interactive scatter plot.
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.
A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker
(2023)
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.
Background: Recent developments in cellular reprogramming technology enable the production of virtually unlimited numbers of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). Although hiPSC-CM share various characteristic hallmarks with endogenous cardiomyocytes, it remains a question as to what extent metabolic characteristics are equivalent to mature mammalian cardiomyocytes. Here we set out to functionally characterize the metabolic status of hiPSC-CM in vitro by employing a radionuclide tracer uptake assay. Material and Methods: Cardiac differentiation of hiPSC was induced using a combination of well-orchestrated extrinsic stimuli such as WNT activation (by CHIR99021) and BMP signalling followed by WNT inhibition and lactate based cardiomyocyte enrichment. For characterization of metabolic substrates, dual tracer uptake studies were performed with \(^{18}\)F-2-fluoro-2-deoxy-D-glucose (\(^{18}\)F-FDG) and \(^{125}\)I-β-methyl-iodophenyl-pentadecanoic acid (\(^{125}\)I-BMIPP) as transport markers of glucose and fatty acids, respectively. Results: After cardiac differentiation of hiPSC, in vitro tracer uptake assays confirmed metabolic substrate shift from glucose to fatty acids that was comparable to those observed in native isolated human cardiomyocytes. Immunostaining further confirmed expression of fatty acid transport and binding proteins on hiPSC-CM. Conclusions: During in vitro cardiac maturation, we observed a metabolic shift to fatty acids, which are known as a main energy source of mammalian hearts, suggesting hi-PSC-CM as a potential functional phenotype to investigate alteration of cardiac metabolism in cardiac diseases. Results also highlight the use of available clinical nuclear medicine tracers as functional assays in stem cell research for improved generation of autologous differentiated cells for numerous biomedical applications.
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.
We have investigated the photodynamics of \(\beta\)-D-glucose employing our field-induced surface hopping method (FISH), which allows us to simulate the coupled electron-nuclear dynamics, including explicitly nonadiabatic effects and light-induced excitation. Our results reveal that from the initially populated S\(_{1}\) and S\(_{2}\) states, glucose returns nonradiatively to the ground state within about 200 fs. This takes place mainly via conical intersections (CIs) whose geometries
in most cases involve the elongation of a single O-H bond, while in some instances ring-opening due to dissociation of a C-O bond is observed. Experimentally, excitation to a distinct excited electronic state is improbable due to the presence of a dense manifold of states bearing similar oscillator strengths. Our FISH simulations explicitly including a UV laser pulse of 6.43 eV photon energy reveals that after initial excitation the population is almost equally spread over several close-lying electronic states. This is followed by a fast nonradiative decay on the time scale of 100-200 fs, with the final return to the ground state proceeding via the S\(_{1}\) state through the same types of CIs as observed in the field-free simulations.
The analysis presented in this paper applies to experimental situations where observers or objects to be studied, all at stationary positions, are located in environments the optical thickness of which is strongly different. Non-transparent media comprise thin metallic films, packed or fluidised beds, superconductors, the Earth’s crust, and even dark clouds and other cosmological objects. The analysis applies mapping functions that correlate physical events, e, in non-transparent media, with their images, f(e), tentatively located on standard physical time scale. The analysis demonstrates, however, that physical time, in its rigorous sense, does not exist under non-transparency conditions. A proof of this conclusion is attempted in three steps: i) the theorem “there is no time without space and events” is accepted, (ii) images f[e(s,t)] do not constitute a dense, uncountably infinite set, and (iii) sets of images that are not uncountably infinite do not create physical time but only time-like sequences. As a consequence, mapping f[e(s,t)] in non-transparent space does not create physical analogues to the mathematical structure of the ordered, dense half-set R+ of real numbers, and reverse mapping, f-1f[e(s,t)], the mathematical inverse problem, would not allow unique identification and reconstruction of original events from their images. In these cases, causality as well as invariance of physical processes under time reversal, might be violated. An interesting problem is whether temporal cloaking (a time hole) in a transparent medium, as very recently reported in the literature, can be explained by the present analysis. Existence of time holes could perhaps be possible, not in transparent but in non-transparent media, as follows from the sequence of images, f[e(s,t)], that is not uncountably infinite, in contrast to R+. Impacts are expected for understanding physical diffusion-like, radiative transfer processes and stability models to protect superconductors against quenchs. There might be impacts also in relativity, quantum mechanics, nuclear decay, or in systems close to their phase transitions. The analysis is not restricted to objects of laboratory dimensions.
The analysis presented in this paper applies to experimental situations where observers or objects to be studied (both stationary, with respect to each other) are located in environments the optical thickness of which is strongly different. By their large optical thickness, non-transparent media are clearly distinguished from their transparent counterparts. Non-transparent media comprise thin metallic films, packed or fluidised beds, the Earth’s crust, and even dark clouds and other cosmological objects. As a representative example, a non-transparent slab is subjected to transient disturbances, and a rigorous analysis is presented whether physical time reasonably could be constructed under such condition. The analysis incorporates mapping functions that correlate physical events, e, in non-transparent media, with their images, f(e), tentatively located on a standard physical time scale. The analysis demonstrates, however, that physical time, in its rigorous sense, does not exist under non-transparency conditions. A proof of this conclusion is attempted in three steps: i) the theorem “there is no time without space and events” is accepted, (ii) images f[e(s,t)] do not constitute a dense, uncountably infinite set, and (iii) sets of images that are not uncountably infinite do not create physical time but only time-like sequences. As a consequence, mapping f[e(s,t)] in non-transparent space does not create physical analogues to the mathematical structure of the ordered, dense half-set R+ of real numbers, and reverse mapping, f-1f[e(s,t)] would not allow unique identification and reconstruction of original events from their images. In these cases, causality and determinism, as well as invariance of physical processes under time reversal, might be violated. Existence of time holes could be possible, as follows from the sequence of images, f[e(s,t)], that is not uncountably infinite, in contrast to R+. Practical impacts are expected for understanding physical diffusion-like, radiative transfer processes, stability models to protect superconductors against quenchs or for description of their transient local pair density and critical currents. Impacts would be expected also in mathematical formulations (differential equations) of classical physics, in relativity and perhaps in quantum mechanics, all as far as transient processes in non-transparent space would be concerned. An interesting problem is whether temporal cloaking (a time hole) in a transparent medium, as very recently reported in the literature, can be explained by the present analysis. The analysis is not restricted to objects of laboratory dimensions: Because of obviously existing radiation transfer analogues, it is tempting to discuss consequences also for much larger structures in particular if an origin of time is postulated.
No abstract available.
No abstract available.
We present a joint experimental and computational study of the nonradiative deactivation of the benzyl radical, C\(_7\)H\(_7\) after UV excitation. Femtosecond time-resolved photoelectron imaging was applied to investigate the photodynamics of the radical. The experiments were accompanied by excited state dynamics simulations using surface hopping. Benzyl has been excited at 265 nm into the D-band (\(\pi\pi^*\)) and the dynamics was probed using probe wavelengths of 398 nm or 798 nm. With 398 nm probe a single time constant of around 70-80 fs was observed. When the dynamics was probed at 798 nm, a second time constant \(\tau_2\)=1.5 ps was visible. It is assigned to further non-radiative deactivation to the lower-lying D\(_1\)/D\(_2\) states.
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.
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.
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.
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.
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.
Mit diesem Beitrag ("Türkei") liegt Teil 3 der dreiteiligen Online-Publikation "Historische Aufnahmen aus dem Vorderen Orient" vor, die als Zeitdokumente Bilder und begleitende Texte von Reisen aus den Jahren 1968 bis 1979 in einige Länder des Nahen Ostens vorstellt. Die Bildauswahl zeigt v. a. Kunstobjekte und Landschafts- bzw. Architekturaufnahmen mit Bezug zur Archäologie und Kunstgeschichte.
Mit diesem Beitrag ("Iraq und Iran") liegt Teil 2 der dreiteiligen Online-Publikation "Historische Aufnahmen aus dem Vorderen Orient" vor, die als Zeitdokumente Bilder und begleitende Texte von Reisen aus den Jahren 1968 bis 1979 in einige Länder des Nahen Ostens vorstellt. Die Bildauswahl zeigt v. a. Kunstobjekte und Landschafts- bzw. Architekturaufnahmen mit Bezug zur Archäologie und Kunstgeschichte.
Mit diesem Beitrag ("Syrien und Jordanien") liegt Teil 1 der dreiteiligen Online-Publikation "Historische Aufnahmen aus dem Vorderen Orient" vor, die als Zeitdokumente Bilder und begleitende Texte von Reisen aus den Jahren 1968 bis 1979 in einige Länder des Nahen Ostens vorstellt. Die Bildauswahl zeigt v. a. Kunstobjekte und Landschafts- bzw. Architekturaufnahmen mit Bezug zur Archäologie und Kunstgeschichte.
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.
ΙΟΥΔΙΘ und IUDITH: Überlegungen zum Verhätlnis der Judit-Erzählung in der LXX und der Vulgata
(2012)
“Das Buch Judit ist in zwei wesentlich voneinander unterschiedenen Textformen überliefert: einerseits in der griechischen Fassung und den sich daran anschließenden alten Übersetzungen (vetus latina, syr., aeth., sah., arm.), zum anderen in der Fassung der lateinischen Vulgata und, mit dieser durchweg parallel laufend, in mittelalterlichen hebräischen Hss.” – so fasst Helmut Engel die Textsituation des Buches Judit prägnant zusammen. Damit liegen heute zwei unterschiedliche Textformen der Juditerzählung vor: Die griechische Juditerzählung in der Septuaginta und die lateinische Iuditherzählung in der Vulgata. Beide Textfassungen unterscheiden sich deutlich voneinander: Die Vulgata-Fassung ist gegenüber der LXX-Fassung um 20 Prozent kürzer; weil die Vulgata-Fassung aber auch umfangreiche Erweiterungen aufweist, teilen LXX und Vulgata nur ungefähr die Hälfte des Textbestandes. Lange ist man davon ausgegangen, dass hinter der Septuaginta- und der Vulgata-Fassung der Juditerzählung ein hebräischer “Ur”-Text gestanden habe. Diese Annahme, die die Forschung seit dem 19. Jh. prägt, gründet sich im Wesentlichen auf zwei Argumenten:
Erstens sei der griechische Text der Septuaginta so durchgehend von einem hebräischen Sprachduktus geprägt, dass man hier von einem hebräischen Originaltext, der recht wörtlich ins Griechische übertragen worden sei, ausgehen müsse.
Zweitens spreche Hieronymus (ca. 347–420) in seiner praefatio zu seiner lateinischen Übertragung von einem ihm vorliegenden “chaldäischen” Text, der ihm als Vorlage gedient habe.
Beide Argumente werden im Folgenden diskutiert: Im ersten Teil wird auf die in den letzten Jahren neu aufgerollte Frage nach der Originalsprache der LXX-Fassung der Juditerzählung eingegangen; der zweite Teil ist der Analyse der praefatio des Hieronymus gewidmet.
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.
Deoxyribozymes are synthetic enzymes made of DNA that can catalyze the cleavage or formation of phosphodiester bonds and are useful tools for RNA biochemistry. Here we report new RNA-cleaving deoxyribozymes to interrogate the methylation status of target RNAs, thereby providing an alternative method for the biochemical validation of RNA methylation sites containing N\(^6\)-methyladenosine, which is the most wide-spread and extensively investigated natural RNA modification. Using in vitro selection from random DNA, we developed deoxyribozymes that are sensitive to the presence of N\(^6\)-methyladenosine in RNA near the cleavage site. One class of these DNA enzymes shows faster cleavage of methylated RNA, while others are strongly inhibited by the modified nucleotide. The general applicability of the new deoxyribozymes is demonstrated for several examples of natural RNA sequences, including a lncRNA and a set of C/D box snoRNAs, which have been suggested to contain m\(^6\)A as a regulatory element that influences RNA folding and protein binding.
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.
Sterically unencumbered diborenes based on a benzylphosphine chelate undergo diboration reactions with bis(catecholato)diboron in the absence of a catalyst to yield tetraboranes. The symmetrical diborenes studied undergo 1,2- diborations, whereas an unsymmetrical derivative was found to yield a triborylborane-phosphine adduct as the result of a formal 1,1-diboration. A related borylborylene compound also underwent a 1,2-diboration to produce a borylene-borane adduct.
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.
A doubly base-stabilized diborane based on a benzylphosphine linker was prepared by a salt elimination reaction between 2-LiC\(_6\)H\(_4\)CH\(_2\)PCy\(_2\).Et\(_2\)O and B\(_2\)Br\(_4\). This compound was reduced with KC8 to its corresponding diborene, with the benzylphosphine forming a five-membered chelate. The diborene reacts with butadiene, 2-trimethylsiloxy-1,3-butadiene and isoprene to form 4,5-diboracyclohexenes, which interconvert between their 1,1- (geminal) and 1,2- (vicinal) chelated isomers. The 1,1-chelated diborene undergoes a halide-catalysed isomerisation into its thermodynamically favoured 1,2-isomer, which undergoes Diels-Alder reactions more slowly than the kinetic product.
Cyclic diboranes(4) based on a chelating monoanionic, benzylphosphine linker were prepared by boron-silicon exchange between arylsilanes and B\(_2\)Br\(_4\). Coordination of Lewis bases to the remaining sp\(^2\) boron atom yielded unsymmetrical sp\(^3\)-sp\(^3\) diboranes, which were reduced with KC\(_8\) to their corresponding trans-diborenes. These compounds were studied by a combination of spectroscopic methods, X-ray diffraction and DFT calculations. PMe\(_3\)-stabilized diborene 6 was found to undergo thermal rearrangement to gem- diborene 8. DFT calculations on 8 reveal a polar boron-boron bond, and indicate that the compound is best described as a borylborylene.
CO\(_2\) is found to undergo room-temperature, ambient- pressure reactions with two species containing boron-boron multiple bonds, leading to incorporation of either one or two CO\(_2\) molecules. In one case, a thermally-unstable intermediate was structurally characterized, indicating the operation of an initial 2+2 cycloaddition mechanism in the reaction.
We present a theoretical study on exciton–exciton annihilation (EEA) in a molecular dimer. This process is monitored using a fifth-order coherent two-dimensional (2D) spectroscopy as was recently proposed by Dostál et al. [Nat. Commun. 9, 2466 (2018)]. Using an electronic three-level system for each monomer, we analyze the different paths which contribute to the 2D spectrum. The spectrum is determined by two entangled relaxation processes, namely, the EEA and the direct relaxation of higher lying excited states. It is shown that the change of the spectrum as a function of a pulse delay can be linked directly to the presence of the EEA process.
Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections
(2020)
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.
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.
Comparison of moving and fixed basis sets for nonadiabatic quantum dynamics at conical intersections
(2020)
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.
Durch die systematische Sichtung des Fundmaterials des frühmittelalterlichen Burgwalls von Kopchin in der Oberlausitz konnten einige Keramikscherben identifiziert werden, die wohl älter als bisher angenommen sind und in die Völkerwanderungszeit datieren. Dies ist von besonderer Relevanz, da für Nordostdeutschland traditionell eine Besiedlungslücke im 5.–7. Jh. AD postuliert wird. Dieser Hiatus ist offenbar teils auch der schwierigen sicheren Datierung der oft recht unspezifischen Keramiktypen geschuldet. So konnten mit wachsendem Kenntnisstand dieser Keramiken in den letzten Jahren auch einige völkerwanderungszeitliche Fundstellen, besonders in Nordbrandenburg und im deutsch-polnischen Pommern lokalisiert werden. In Nordost-Sachsen sind die vorgestellten singulären Funde des 5.–6. Jhs. AD jedoch bisher ohne sichere Parallelen, auch wenn mittlerweile einige Fundstellen der Völkerwanderungszeit in der Region erkannt worden sind.
Der Begriff Germanen ist eine Fremdbezeichnung griechisch-römischer Autoren der Antike. Die so bezeichneten Gruppen hatten aber keine gemeinsame germanische Identität. Die Germanen wurden schon in der Antike als mächtige Gegner stilisiert, was wiederum im Mittelalter im Zuge der Staatenbildungen gerne in den schriftlichen Quellen aufgegriffen wurde. Retrospektiv kann keine "Ursprache" oder "Urheimat" der Germanen rekonstruiert werden. In der Archäologie gibt es jedoch aufgrund des Fundmaterials Kulturräume einer materiellen Kultur, die als germanisch interpretiert werden. Diese sind jedoch nicht mit einer "germanischen Ethnie" zu verwechseln.
Eisenproduktionswerkplätze der späten römischen Kaiserzeit (3.–5. Jh. AD) im inneren Barbaricum
(2012)
Durch systematische Prospektionen in Südbrandenburg wurden auch bei den devastierten Ortschaften Klein Görigk und Kausche zahlreiche bisher unbekannte Fundplatze entdeckt (vgl. Abb. 1). Diese verdeutlichen den Fundreichtum dieser kargen Landschaft als „archäologisches Fenster“ einer fallbeispielhaft intensiv erforschten Region. Die sehr zahlreichen Werkplätze der späten römischen Kaiserzeit (3.–5. Jh. AD) belegen eine massenhafte Eisenproduktion, die über den Eigenbedarf weit hinausging und die Grundlage für Handel darstellte. Interessanterweise sind im Eisenverhüttungszentrum des Niederlausitzer Grenzwalls keine zeitgleichen Siedlungen und Gräberfelder entdeckt worden. Diese liegen etwas weiter entfernt in den fruchtbareren Niederungs- und Beckenlandschaften der Umgebung. Die Werkplätze sind also nur temporär zur Eisenverhüttung aufgesucht worden. Die stereotyp errichteten Eisenproduktionsstätten wurden in unmittelbarer Nähe zum lokal vorkommenden „Raseneisenerz“ im waldreichen Gebiet errichtet. Durch die massenhafte Eisenproduktion, die äußerst viel Holzkohle benötigte, ist auch von negativen Folgen auf die prähistorische Umwelt auszugehen. Indizien einer mutmaßlichen „ökologischen Krise“ zum Ende der spätgermanischen Kultur (Mitte 5. Jh. AD) konnten jedoch bisher nicht sicher belegt werden.
Der Einsatz von Geographischen Informationssystemen (GIS) bietet auch für die Geisteswissenschaften zahlreiche Ansätze zur Generierung von neuem Wissen. Die GIS-Software ist jedoch unterschiedlich geeignet für geisteswissenschaftliche Fragestellungen. Getestet wurden daher zwei kommerzielle und vier Open Source GIS-Programme: MapInfo, ArcGIS, Quantum GIS, gvSIG, DIVA-GIS und SAGA. MapInfo zeichnet sich besonders für GIS-Anfänger durch seine große Benutzerfreundlichkeit aus. Jedoch sind die Anschaffungskosten recht hoch. ArcGIS weist den größten Nutzungsumfang auf, wobei jedoch keine oder kaum eine „intuitive“ Nutzung möglich ist. Zudem sind die laufenden Kosten durch aufwändige Abo-Lizenzverträge besonders hoch. Quantum GIS ist eine freie Software, die benutzerfreundlich ist und auch Anfängern einen leichten Einstieg ermöglicht. Hunderte Erweiterungen machen Quantum GIS sehr leistungsstark und universal einsetzbar. gvSIG ist nicht ganz leicht zu bedienen, da zudem die Dokumentation nur fragmentarisch vorliegt. Der große Funktionsumfang macht es jedoch zu einem vollwertigen GIS, wenn auch manch ergänzende Funktion fehlt. DIVA-GIS ermöglicht einen schnellen Einstieg durch seine gute Dokumentation. Man gelangt jedoch recht bald an die Grenzen des Nutzungsumfangs durch die eingeschränkte Funktionalität. SAGA hingegen erfüllte alle hier gestellten Anforderungen, sodass es, trotz der geringeren Anzahl von Erweiterungen, zusammen mit Quantum GIS als Open Source eine echte Alternative zu kommerziellen GIS-Programmen darstellt.
The diborene 1 was synthesized by reduction of a mixture of 1,2-di-9-anthryl-1,2-dibromodiborane(4) (6) and trimethylphosphine with potassium graphite. The X-ray structure of 1 shows the two anthryl rings to be parallel and their π(C\(_{14}\)) systems perpendicular to the diborene π(B=B) system. This twisted conformation allows for intercalation of the relatively high-lying π(B=B) orbital and the low-lying π* orbital of the anthryl moiety with no significant conjugation, resulting in a small HOMO-LUMO gap (HLG) and ultimately an unprecedented anthryl B–B bond hydroarylation. The HLG of 1 was estimated to be 1.57 eV from the onset of the long wavelength band in its UV–vis absorption spectrum (THF, λ\(_{onset}\) = 788 nm). The oxidation of 1 with elemental selenium afforded diboraselenirane 8 in quantitative yield. By oxidative abstraction of one phosphine ligand by another equivalent of elemental selenium, the B–B and C\(^1\)–H bonds of 8 were cleaved to give the cyclic 1,9-diboraanthracene 9.
Despite the prevalence of stable π-complexes of most d\(^{10}\) metals, such as Cu(I) and Ni(0), with ethylene and other olefins, complexation of d\(^{10}\) Zn(II) to simple olefins is too weak to form isolable complexes due to the metal ion's limited capacity for π-backdonation. By employing more strongly donating π- ligands, namely neutral diborenes with a high-lying π(B=B) or- bital, monomeric 16-electron M(II)-diborene (M = Zn, Cd) π- complexes were synthesized in good yields. Metal–B2 π- interactions in both the solid and solution state were confirmed by single-crystal X-ray analyses and their solution NMR and UV-vis absorption spectroscopy, respectively. The M(II) centers adopt a trigonal planar geometry and interact almost symmetrically with both boron atoms. The MB2 planes significantly twist out of the MX\(_2\) planes about the M-centroid(B–B) vector, with angles rang- ing from 47.0° to 85.5°, depending on the steric interactions be- tween the diborene ligand and the MX\(_2\) fragment.
Upon complexation to CuOTf, a PMe\(_3\)-stabilized bis(9-anthryl) diborene slowly undergoes an intramolecular hydroarylation reaction at room temperature. Subsequent triflation of the B–H bond with CuOTf, followed by a PMe\(_3\) transfer, finally yields a cyclic sp\(^2\)-sp\(^3\) boryl-substituted boronium triflate salt.