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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.
Among the numerous routes organic chemists have developed to synthesize benzene derivatives and heteroaro- matic compounds, transition-metal-catalyzed cycloaddition reactions are the most elegant. In contrast, cycloaddition reactions of heavier alkene and alkyne analogues, though limited in scope, proceed uncatalyzed. In this work we present the first spontaneous cycloaddition reactions of lighter alkene and alkyne analogues. Selective addition of unactivated alkynes to boron–boron multiple bonds under ambient con- ditions yielded diborocarbon equivalents of simple aromatic hydrocarbons, including the first neutral 6p-aromatic dibora- benzene compound, a 2 p-aromatic triplet biradical 1,3-dibor- ete, and a phosphine-stabilized 2 p-homoaromatic 1,3-dihydro- 1,3-diborete. DFT calculations suggest that all three com- pounds are aromatic and show frontier molecular orbitals matching those of the related aromatic hydrocarbons, C6H6 and C4H42+, and homoaromatic C4H5+.
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.
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.
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.
Advances in stem cell research have allowed the development of 3-dimensional (3D) primary cell cultures termed organoid cultures, as they closely mimic the in vivo organization of different cell lineages. Bridging the gap between 2-dimensional (2D) monotypic cancer cell lines and whole organisms, organoids are now widely applied to model development and disease. Organoids hold immense promise for addressing novel questions in host-microbe interactions, infectious diseases and the resulting inflammatory conditions. Researchers have started to use organoids for modeling infection with pathogens, such as Helicobacter pylori or Salmonella enteritica, gut- microbiota interactions and inflammatory bowel disease. Future studies will broaden the spectrum of microbes used and continue to establish organoids as a standard model for human host-microbial interactions. Moreover, they will increasingly exploit the unique advantages of organoids, for example to address patient-specific responses to microbes.
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.
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.
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.
Overlapping is a common word used to describe documents whose structural dimensions cannot be adequately represented using tree structure. For instance a quotation that starts in one verse and ends in another verse. The problem of overlapping hierarchies is a recurring one, which has been addressed by a variety of approaches. There are XML based solutions as well as Non-XML ones. The XML-based solutions are: multiple documents, empty elements, fragmentation, out-of-line markup, JITT and BUVH. And the Non-XML approaches comprise CONCUR/XCONCUR, MECS, LMNL ...etc. This paper presents shortly state-of-the-art in overlapping hierarchies, and introduces two variations on the TEI fragmentation markup that have several advantages.
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.
This article discusses web frameworks that are available to a software developer in Java language. It introduces MVC paradigm and some frameworks that implement it. The article presents an overview of Struts, Spring MVC, JSF Frameworks, as well as guidelines for selecting one of them as development environment.
Molecules containing multiple bonds between atoms—most often in the form of olefins—are ubiquitous in nature, commerce, and science, and as such have a huge impact on everyday life. Given their prominence, over the last few decades, frequent attempts have been made to perturb the structure and reactivity of multiply-bound species through bending and twisting. However, only modest success has been achieved in the quest to completely twist double bonds in order to homolytically cleave the associated π bond. Here, we present the isolation of double-bond-containing species based on boron, as well as their fully twisted diradical congeners, by the incorporation of attached groups with different electronic properties. The compounds comprise a structurally authenticated set of diamagnetic multiply-bound and diradical singly-bound congeners of the same class of compound.
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.
Singapore has a unique and proactive approach towards managing the national transport system. This article explores the integrative approach of carsharing into the overall transport system from an individual sustainable mobility perspective. The authors argue that for Singapore, taxi services are the strongest competitor for the establishment of free-floating carsharing systems. Low taxi fares and a high distribution rate provide easy access for consumers and show great advantages in correspondence with the prevalent transport measures. Furthermore, the Singaporean government considers taxi services as part of public transport that helps bridging public transportation gaps in door-to-door travel. The article draws on literature review and expert interviews to evaluate the current market conditions and analyse the pros and cons of carsharing systems and taxi services as integrated part of the public transport system. The authors conclude by stating that from a sustainable perspective, the goal is to replace private car ownership. Provision of multi modal choices and therefore co-existence of different individual transport opportunities is indispensable.
A series of NHC-supported 1,2-dithienyldiborenes was synthesized from the corresponding (dihalo)thienylborane NHC precursors. NMR and UV-vis spectroscopic data, as well as X-ray crystallographic analyses, were used to assess the electronic and steric influences on the B=B double bond of various NHCs and electron-donating substituents on the thienyl ligands. Crystallographic data showed that the degree of coplanarity of the diborene core and thienyl groups is highly dependent on the sterics of the substituents. Furthermore, any increase in the electron- donating ability of the substituents resulted in the destabilization of the HOMO and greater instability of the resulting diborenes.
Objective: To examine the effects of two different treatment approaches on the course of anorexia nervosa (AN) over time.
Methods: The subjects were 27 hospitalized AN patients (mean age: 14.91 years; mean BMI: 14.58; mean height: 163.56) . In our retrospective analysis we compared weight gain in two groups. While one group was treated with a standard oral refeeding protocol (historical control) through January 2013 (N=16), the second group (highly standardized refeeding protocol) received a high energy liquid nutrition and nutritional supplements including omega-3 fatty acids (N=11).
Results: On admission, the two groups were comparable in terms of height, weight, age and heart rate. At the end of our monitoring time frame of 25 days, weight gain was 121.4% higher in the highly standardized refeeding protocol group than in the historical control group (66.5 ±52.4 vs 147.3 ±55.7 grams/day; t-Test p=0.004; CI95%: 29.3-132.2). About 45% of our patients stated they were vegetarians at admission. However, we could not identify a vegetarian diet as a statistically significant negative prognostic factor for weight gain.
Discussion: The highly standardized refeeding protocol seems to be helpful in malnourished AN patients to improve weight gain without enhancing the risk of a refeeding syndrome. Because of an increasing energy turnover, caloric intake should be adjusted during refeeding.
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.
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.
The heteroarene 1,4-bis(CAAC)-1,4-diborabenzene (1; CAAC = cyclic (alkyl)(amino)carbene) reacts with [(MeCN)\(_3\)M(CO)\(_3\)] (M = Cr, Mo, W) to yield half-sandwich complexes of the form [(η\(^6\)-diborabenzene)M(CO)\(_3\)] (M = Cr (2), Mo (3), W (4)). Investigation of the new complexes with a combination of X-ray diffraction, spectroscopic methods and DFT calculations shows that ligand 1 is a remarkably strong electron donor. In particular, [(η\(^6\)-arene)M(CO)\(_3\)] complexes of this ligand display the lowest CO stretching frequencies yet observed for this class of complex. Cyclic voltammetry on complexes 2-4 revealed one reversi- ble oxidation and two reversible reduction events in each case, with no evidence of ring-slippage of the arene to the η\(^4\) binding mode. Treatment of 4 with lithium metal in THF led to identification of the paramagnetic complex [(1)W(CO)\(_3\)]Li·2THF (5). Compound 1 can also be reduced in the absence of a transition metal to its dianion 1\(^{2–}\), which possesses a quinoid-type structure.
Recent years have seen rapid advances in the chemistry of small molecules containing electron-precise boron-boron bonds. This review provides an overview of the latest methods for the controlled synthesis of B–B single and multiple bonds as well as the ever-expanding range of reactivity displayed by the latter.
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.
We demonstrate two-quantum (2Q) coherent two-dimensional (2D)electronic spectroscopy using a shot-to-shot-modulated pulse shaper and fluorescence detection. Broadband collinear excitation is realized with the supercontinuum output of an argon-filled hollow-core fiber, enabling us to excite multiple transitions simultaneously in the visible range. The 2Q contribution is extracted via a three-pulse sequence with 16-fold phase cycling and simulated employing cresyl violet as a model system. Furthermore, we report the first experimental realization of one-quantum−two-quantum (1Q-2Q) 2D spectroscopy, offering less congested spectra as compared with the 2Q implementation. We avoid scattering artifacts and nonresonant solvent contributions by using fluorescence as the observable. This allows us to extract quantitative information about doubly excited states that agree with literature expectations. The high sensitivity and background-free nature of fluorescence detection allow for a general applicability of this method to many other systems.
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.
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.
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.
Excitation energy transport in DNA modelled by multi-chromophoric field-induced surface hopping
(2020)
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.
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.
Energy Transfer Between Squaraine Polymer Sections: From helix to zig-zag and All the Way Back
(2015)
Joint experimental and theoretical study of the absorption spectra of squaraine polymers in solution provide evidence that two different conformations are present in solution: a helix and a zig-zag structure. This unique situation allows investigating ultrafast energy transfer processes between different structural segments within a single polymer chain in solution. The understanding of the underlying dynamics is of fundamental importance for the development of novel materials for light-harvesting and optoelectronic applications. We combine here femtosecond transient absorption spectroscopy with time-resolved 2D electronic spectroscopy showing that ultrafast energy transfer within the squaraine polymer chains proceeds from initially excited helix segments to zig-zag segments or vice versa, depending on the solvent as well as on the excitation wavenumber. These observations contrast other conjugated polymers such as MEH-PPV where much slower intrachain energy transfer was reported. The reason for the very fast energy transfer in squaraine polymers is most likely a close matching of the density of states between donor and acceptor polymer segments because of very small reorganization energy in these cyanine-like chromophores.
Empirical Study on Screen Scraping Web Service Creation: Case of Rhein-Main-Verkehrsverbund (RMV)
(2010)
Internet is the biggest database that science and technology have ever produced. The world wide web is a large repository of information that cannot be used for automation by many applications due to its limited target audience. One of the solutions to the automation problem is to develop wrappers. Wrapping is a process whereby unstructured extracted information is transformed into a more structured one such as XML, which could be provided as webservice to other applications. A web service is a web page whose content is well structured so that a computer program can consume it automatically. This paper describes steps involved in constructing wrappers manually in order to automatically generate web services.
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.
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.
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.
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.
The two-fold reduction of (cAAC)BHX\(_2\) (cAAC = 1-(2,6-diisopropylphenyl)-3,3,5,5-tetramethylpyrrolidin-2-ylidene; X = Cl, Br) provides a facile, high-yielding route to the dihydrodiborene (cAAC)\(_2\)B\(_2\)H\(_2\). The (chloro)hydroboryl anion reduction intermediate was successfully isolated using a crown ether. Overreduction of the diborene to its dianion [(cAAC)\(_2\)B\(_2\)H\(_2\)]\(^{2−}\) causes a decrease in the B–B bond order whereas the B–C bond orders increase.
sp\(^2\)–sp\(^3\) diborane species based on bis(catecholato)diboron and N-heterocyclic carbenes (NHCs) are subjected to catechol/bromide exchange selectively at the sp\(^3\) boron atom. The reduction of the resulting 1,1-dibromodiborane adducts led to reductive coupling and isolation of doubly NHC-stabilized 1,2-diboryldiborenes. These compounds are the first examples of molecules exhibiting pelectron delocalization over an all-boron chain.
Unsaturated bridges that link the two cyclopentadienyl ligands together in strained ansa metallocenes are rare and limited to carbon-carbon double bonds. The synthesis and isolation of a strained ferrocenophane containing an unsaturated two-boron bridge, isoelectronic with a C=C double bond, was achieved by reduction of a carbene-stabilized 1,1’-bis(dihaloboryl)ferrocene. A combination of spectroscopic and electrochemical measurements as well as density functional theory (DFT) calculations was used to assess the influence of the unprecedented strained cis configuration on the optical and electrochemical properties of the carbene-stabilized diborene unit. Initial reactivity studies show that the dibora[2]ferrocenophane is prone to boron-boron double bond cleavage reactions.
Design and Implementation of Architectures for Interactive Textual Documents Collation Systems
(2011)
One of the main purposes of textual documents collation is to identify a base text or closest witness to the base text, by analyzing and interpreting differences also known as types of changes that might exist between those documents. Based on this fact, it is reasonable to argue that, explicit identification of types of changes such as deletions, additions, transpositions, and mutations should be part of the collation process. The identification could be carried out by an interpretation module after alignment has taken place. Unfortunately existing collation software such as CollateX1 and Juxta2’s collation engine do not have interpretation modules. In fact they implement the Gothenburg model [1] for collation process which does not include an interpretation unit. Currently both CollateX and Juxta’s collation engine do not distinguish in their critical apparatus between the types of changes, and do not offer statistics about those changes. This paper presents a model for both integrated and distributed collation processes that improves the Gothenburg model. The model introduces an interpretation component for computing and distinguishing between the types of changes that documents could have undergone. Moreover two architectures implementing the model in order to solve the problem of interactive collation are discussed as well. Each architecture uses CollateX library, and provides on the one hand preprocessing functions for transforming input documents into CollateX input format, and on the other hand a post-processing module for enabling interactive collation. Finally simple algorithms for distinguishing between types of changes, and linking collated source documents with the collation results are also introduced.
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.
Most proteins work in aqueous solution and the interaction with water strongly affects their structure and function. However, experimentally the motion of a specific single water molecule is difficult to trace by conventional methods, because they average over the heterogeneous solvation structure of bulk water surrounding the protein. Here, we provide a detailed atomistic picture of the water rearrangement dynamics around the –CONH– peptide linkage in the two model systems formanilide and acetanilide, which simply differ by the presence of a methyl group at the peptide linkage. The combination of picosecond pump–probe time-resolved infrared spectroscopy and molecular dynamics simulations demonstrates that the solvation dynamics at the molecular level is strongly influenced by this small structural difference. The effective timescales for solvent migration triggered by ionization are mainly controlled by the efficiency of the kinetic energy redistribution rather than the shape of the potential energy surface. This approach provides a fundamental understanding of protein hydration and may help to design functional molecules in solution with tailored properties.
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.
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.
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.
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.
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.
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.
Collective Response in DNA-Stabilized Silver Cluster Assemblies from First-Principles Simulations
(2019)
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.
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.
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.