@article{AbdaliYounasMafakherietal.2018,
  author    = {Abdali, Narges and Younas, Farhan and Mafakheri, Samaneh and Pothula, Karunakar R. and Kleinekath{\"o}fer, Ulrich and Tauch, Andreas and Benz, Roland},
  title     = {Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109},
  series = {BMC Biochemistry},
  volume    = {19},
  journal   = {BMC Biochemistry},
  doi       = {10.1186/s12858-018-0093-9},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-226959},
  year      = {2018},
  abstract  = {Background: Corynebacterium urealyticum, a pathogenic, multidrug resistant member of the mycolata, is known as causative agent of urinary tract infections although it is a bacterium of the skin flora. This pathogenic bacterium shares with the mycolata the property of having an unusual cell envelope composition and architecture, typical for the genus Corynebacterium. The cell wall of members of the mycolata contains channel-forming proteins for the uptake of solutes. Results: In this study, we provide novel information on the identification and characterization of a pore-forming protein in the cell wall of C. urealyticum DSM 7109. Detergent extracts of whole C. urealyticum cultures formed in lipid bilayer membranes slightly cation-selective pores with a single-channel conductance of 1.75 nS in 1 M KCl. Experiments with different salts and non-electrolytes suggested that the cell wall pore of C. urealyticum is wide and water-filled and has a diameter of about 1.8 nm. Molecular modelling and dynamics has been performed to obtain a model of the pore. For the search of the gene coding for the cell wall pore of C. urealyticum we looked in the known genome of C. urealyticum for a similar chromosomal localization of the porin gene to known porH and porA genes of other Corynebacterium strains. Three genes are located between the genes coding for GroEL2 and polyphosphate kinase (PKK2). Two of the genes (cur_1714 and cur_1715) were expressed in different constructs in C. glutamicum Delta porA Delta porH and in porin-deficient BL21 DE3 Omp8 E. coli strains. The results suggested that the gene cur_1714 codes alone for the cell wall channel. The cell wall porin of C. urealyticum termed PorACur was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 4 kDa on tricine-containing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Conclusions: Biophysical characterization of the purified protein (PorACur) suggested indeed that cur_1714 is the gene coding for the pore-forming protein in C. urealyticum because the protein formed in lipid bilayer experiments the same pores as the detergent extract of whole cells. The study is the first report of a cell wall channel in the pathogenic C. urealyticum.},
  language  = {en}
}
@article{AbdelhafezFawzyFahimetal.2018,
  author    = {Abdelhafez, Omnia Hesham and Fawzy, Michael Atef and Fahim, John Refaat and Desoukey, Samar Yehia and Krischke, Markus and Mueller, Martin J. and Abdelmohsen, Usama Ramadan},
  title     = {Hepatoprotective potential of Malvaviscus arboreus against carbon tetrachloride-induced liver injury in rats},
  series = {PLoS ONE},
  volume    = {13},
  journal   = {PLoS ONE},
  number    = {8},
  doi       = {10.1371/journal.pone.0202362},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177243},
  pages     = {e0202362},
  year      = {2018},
  abstract  = {Malvaviscus arboreus Cav. is a medicinal plant belonging to family Malvaceae with both ethnomedical and culinary value; however, its phytochemical and biological profiles have been scarcely studied. Accordingly, this work was designed to explore the chemical composition and the hepatoprotective potential of M. arboreus against carbon tetrachloride (CCl\(_4\))-induced hepatotoxicity. The total extract of the aerial parts and its derived fractions (petroleum ether, dichloromethane, ethyl acetate, and aqueous) were orally administered to rats for six consecutive days, followed by injection of CCl\(_4\) (1:1 v/v, in olive oil, 1.5 ml/kg, i.p.) on the next day. Results showed that the ethyl acetate and dichloromethane fractions significantly alleviated liver injury in rats as indicated by the reduced levels of alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), total bilirubin (TB), and malondialdehyde (MDA), along with enhancement of the total antioxidant capacities of their livers, with the maximum effects were recorded by the ethyl acetate fraction. Moreover, the protective actions of both fractions were comparable to those of silymarin (100 mg/kg), and have been also substantiated by histopathological evaluations. On the other hand, liquid chromatography-high resolution electrospray ionization mass spectrometry (LC‒HR‒ESI‒MS) metabolomic profiling of the crude extract of M. arboreus aerial parts showed the presence of a variety of phytochemicals, mostly phenolics, whereas the detailed chemical analysis of the most active fraction (i.e. ethyl acetate) resulted in the isolation and identification of six compounds for the first time in the genus, comprising four phenolic acids; β-resorcylic, caffeic, protocatechuic, and 4-hydroxyphenylacetic acids, in addition to two flavonoids; trifolin and astragalin. Such phenolic principles, together with their probable synergistic antioxidant and liver-protecting properties, seem to contribute to the observed hepatoprotective potential of M. arboreus.},
  language  = {en}
}
@article{AbtErdmenger2018,
  author    = {Abt, Raimond and Erdmenger, Johanna},
  title     = {Properties of modular Hamiltonians on entanglement plateaux},
  series = {Journal of High Energy Physics},
  volume    = {11},
  journal   = {Journal of High Energy Physics},
  number    = {2},
  doi       = {10.1007/JHEP11(2018)002},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-227693},
  pages     = {1-22},
  year      = {2018},
  abstract  = {The modular Hamiltonian of reduced states, given essentially by the logarithm of the reduced density matrix, plays an important role within the AdS/CFT correspondence in view of its relation to quantum information. In particular, it is an essential ingredient for quantum information measures of distances between states, such as the relative entropy and the Fisher information metric. However, the modular Hamiltonian is known explicitly only for a few examples. For a family of states rho(lambda) that is parametrized by a scalar lambda, the first order contribution in (lambda) over tilde = lambda-lambda(0) of the modular Hamiltonian to the relative entropy between rho(lambda) and a reference state rho(lambda 0) is completely determined by the entanglement entropy, via the first law of entanglement. For several examples, e.g. for ball-shaped regions in the ground state of CFTs, higher order contributions are known to vanish. In these cases the modular Hamiltonian contributes to the Fisher information metric in a trivial way. We investigate under which conditions the modular Hamiltonian provides a non-trivial contribution to the Fisher information metric, i.e. when the contribution of the modular Hamiltonian to the relative entropy is of higher order in (lambda) over tilde. We consider one-parameter families of reduced states on two entangling regions that form an entanglement plateau, i.e. the entanglement entropies of the two regions saturate the Araki-Lieb inequality. We show that in general, at least one of the relative entropies of the two entangling regions is expected to involve (lambda) over tilde contributions of higher order from the modular Hamiltonian. Furthermore, we consider the implications of this observation for prominent AdS/CFT examples that form entanglement plateaux in the large N limit.},
  language  = {en}
}
@article{AdamDeimelPardoMedinaetal.2018,
  author    = {Adam, Alexander and Deimel, Stephan and Pardo-Medina, Javier and Garc{\´i}a-Mart{\´i}nez, Jorge and Konte, Tilen and Lim{\´o}n, M. Carmen and Avalos, Javier and Terpitz, Ulrich},
  title     = {Protein activity of the \(Fusarium\) \(fujikuroi\) rhodopsins CarO and OpsA and their relation to fungus-plant interaction},
  series = {International Journal of Molecular Sciences},
  volume    = {19},
  journal   = {International Journal of Molecular Sciences},
  number    = {1},
  issn      = {1422-0067},
  doi       = {10.3390/ijms19010215},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-285125},
  year      = {2018},
  abstract  = {Fungi possess diverse photosensory proteins that allow them to perceive different light wavelengths and to adapt to changing light conditions in their environment. The biological and physiological roles of the green light-sensing rhodopsins in fungi are not yet resolved. The rice plant pathogen Fusarium fujikuroi exhibits two different rhodopsins, CarO and OpsA. CarO was previously characterized as a light-driven proton pump. We further analyzed the pumping behavior of CarO by patch-clamp experiments. Our data show that CarO pumping activity is strongly augmented in the presence of the plant hormone indole-3-acetic acid and in sodium acetate, in a dose-dependent manner under slightly acidic conditions. By contrast, under these and other tested conditions, the Neurospora rhodopsin (NR)-like rhodopsin OpsA did not exhibit any pump activity. Basic local alignment search tool (BLAST) searches in the genomes of ascomycetes revealed the occurrence of rhodopsin-encoding genes mainly in phyto-associated or phytopathogenic fungi, suggesting a possible correlation of the presence of rhodopsins with fungal ecology. In accordance, rice plants infected with a CarO-deficient F. fujikuroi strain showed more severe bakanae symptoms than the reference strain, indicating a potential role of the CarO rhodopsin in the regulation of plant infection by this fungus.},
  language  = {en}
}
@article{AkhrifRomanosDomschkeetal.2018,
  author    = {Akhrif, Atae and Romanos, Marcel and Domschke, Katharina and Schmitt-Boehrer, Angelika and Neufang, Susanne},
  title     = {Fractal Analysis of BOLD Time Series in a Network Associated With Waiting Impulsivity},
  series = {Frontiers in Physiology},
  volume    = {9},
  journal   = {Frontiers in Physiology},
  issn      = {1664-042X},
  doi       = {10.3389/fphys.2018.01378},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-189191},
  pages     = {1378},
  year      = {2018},
  abstract  = {Fractal phenomena can be found in numerous scientific areas including neuroscience. Fractals are structures, in which the whole has the same shape as its parts. A specific structure known as pink noise (also called fractal or 1/f noise) is one key fractal manifestation, exhibits both stability and adaptability, and can be addressed via the Hurst exponent (H). FMRI studies using H on regional fMRI time courses used fractality as an important characteristic to unravel neural networks from artificial noise. In this fMRI-study, we examined 103 healthy male students at rest and while performing the 5-choice serial reaction time task. We addressed fractality in a network associated with waiting impulsivity using the adaptive fractal analysis (AFA) approach to determine H. We revealed the fractal nature of the impulsivity network. Furthermore, fractality was influenced by individual impulsivity in terms of decreasing fractality with higher impulsivity in regions of top-down control (left middle frontal gyrus) as well as reward processing (nucleus accumbens and anterior cingulate cortex). We conclude that fractality as determined via H is a promising marker to quantify deviations in network functions at an early stage and, thus, to be able to inform preventive interventions before the manifestation of a disorder.},
  language  = {en}
}
@phdthesis{AlBaidhani2018,
  author    = {Al-Baidhani, Mohammed},
  title     = {Spectroscopy as a tool to investigate the high energy optical properties of nanostructured magnetically doped topological insulator},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157221},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {In this dissertation the electronic and high-energy optical properties of thin nanoscale films of the magnetic topological insulator (MTI) (V,Cr)y(BixSb1-x)2-yTe3 are studied by means of X-ray photoelectron spectroscopy (XPS) and electron energy-loss spectroscopy (EELS). Magnetic topological insulators are presently of broad interest as the combination of ferromagnetism and spin-orbit coupling in these materials leads to a new topological phase, the quantum anomalous Hall state (QAHS), with dissipation less conduction channels. Determining and controlling the physical properties of these complex materials is therefore desirable for a fundamental understanding of the QAHS and for their possible application in spintronics. EELS can directly probe the electron energy-loss function of a material from which one can obtain the complex dynamic dielectric function by means of the Kramers-Kronig transformation and the Drude-Lindhard model of plasmon oscillations. The XPS core-level spectra in (V,Cr)y(BixSb1-x)2-yTe3 are analyzed in detail with regards to inelastic background contributions. It is shown that the spectra can be accurately described based on the electron energy-loss function obtained from an independent EELS measurement. This allows for a comprehensive and quantitative analysis of the XPS data, which will facilitate future core-level spectroscopy studies in this class of topological materials. From the EELS data, furthermore, the bulk and surface optical properties were estimated, and compared to ab initio calculations based on density functional theory (DFT) performed in the GW approximation for Sb2Te3. The experimental results show a good agreement with the calculated complex dielectric function and the calculated energy-loss function. The positions of the main plasmon modes reported here are expected to be generally similar in other materials in this class of nanoscale TI films. Hence, the present work introduces EELS as a powerful method to access the high-energy optical properties of TI thin films. Based on the presented results it will be interesting to explore more systematically the effects of stoichiometry, magnetic doping, film thickness and surface morphology on the electron-loss function, potentially leading to a better understanding of the complex interplay of structural, electronic, magnetic and optical properties in MTI nanostructures.},
  subject      = {Topologischer Isolator},
  language  = {en}
}
@phdthesis{Albert2018,
  author    = {Albert, Julian},
  title     = {Quantum Studies on Low-Dimensional Coupled Electron-Nuclear Dynamics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-161512},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {In the context of quantum mechanical calculations, the properties of non-adiabatic coupling in a small system, the Shin-Metiu model, is investigated. The transition from adiabatic to non-adiabatic dynamics is elucidated in modifying the electron-nuclear interaction. This allows the comparison of weakly correlated electron-nuclear motion with the case where the strong correlations determine the dynamics. The studies of the model are extended to include spectroscopical transitions being present in two-dimensional and degenerate four-wave mixing spectroscopy. Furthermore, the quantum and classical time-evolution of the coupled motion in the complete electron-nuclear phase space is compared for the two coupling cases. Additionally, the numerically exact electron flux within the weak coupling case is compared to the Born-Oppenheimer treatment. In the last part of the thesis, the model is extended to two dimensions. The system then possesses potential energy surfaces which exhibit a typical 'Mexican hat'-like structure and a conical intersection in the adiabatic representation. Thus, it is possible to map properties of the system onto a vibronic coupling (Jahn-Teller) hamiltonian. Exact wave-packet propagations as well as nuclear wave-packet dynamics in the adiabatic and diabatic representation are performed.},
  subject      = {Theoretische Chemie},
  language  = {en}
}
@article{AlbrechtClassenVollstaedtetal.2018,
  author    = {Albrecht, J{\"o}rg and Classen, Alice and Vollst{\"a}dt, Maximilian G.R. and Mayr, Antonia and Mollel, Neduvoto P. and Schellenberger Costa, David and Dulle, Hamadi I. and Fischer, Markus and Hemp, Andreas and Howell, Kim M. and Kleyer, Michael and Nauss, Thomas and Peters, Marcell K. and Tschapka, Marco and Steffan-Dewenter, Ingolf and B{\"o}hning-Gaese, Katrin and Schleuning, Matthias},
  title     = {Plant and animal functional diversity drive mutualistic network assembly across an elevational gradient},
  series = {Nature Communications},
  volume    = {9},
  journal   = {Nature Communications},
  doi       = {10.1038/s41467-018-05610-w},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221056},
  pages     = {1-10},
  year      = {2018},
  abstract  = {Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.},
  language  = {en}
}
@article{AllertFoersterSvenssonetal.2018,
  author    = {Allert, Stefanie and F{\"o}rster, Toni M. and Svensson, Carl-Magnus and Richardson, Jonathan P. and Pawlik, Tony and Hebecker, Betty and Rudolphi, Sven and Juraschitz, Marc and Schaller, Martin and Blagojevic, Mariana and Morschh{\"a}user, Joachim and Figge, Marc Thilo and Jacobsen, Ilse D. and Naglik, Julian R. and Kasper, Lydia and Mogavero, Selene and Hube, Bernhard},
  title     = {\(Candida\) \(albicans\)-Induced Epithelial Damage Mediates Translocation through Intestinal Barriers},
  series = {mBio},
  volume    = {9},
  journal   = {mBio},
  number    = {3},
  doi       = {10.1128/mBio.00915-18},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221084},
  pages     = {1-20},
  year      = {2018},
  abstract  = {Life-threatening systemic infections often occur due to the translocation of pathogens across the gut barrier and into the bloodstream. While the microbial and host mechanisms permitting bacterial gut translocation are well characterized, these mechanisms are still unclear for fungal pathogens such as Candida albicans, a leading cause of nosocomial fungal bloodstream infections. In this study, we dissected the cellular mechanisms of translocation of C. albicans across intestinal epithelia in vitro and identified fungal genes associated with this process. We show that fungal translocation is a dynamic process initiated by invasion and followed by cellular damage and loss of epithelial integrity. A screen of >2,000 C. albicans deletion mutants identified genes required for cellular damage of and translocation across enterocytes. Correlation analysis suggests that hypha formation, barrier damage above a minimum threshold level, and a decreased epithelial integrity are required for efficient fungal translocation. Translocation occurs predominantly via a transcellular route, which is associated with fungus-induced necrotic epithelial damage, but not apoptotic cell death. The cytolytic peptide toxin of C. albicans, candidalysin, was found to be essential for damage of enterocytes and was a key factor in subsequent fungal translocation, suggesting that transcellular translocation of C. albicans through intestinal layers is mediated by candidalysin. However, fungal invasion and low-level translocation can also occur via non-transcellular routes in a candidalysin-independent manner. This is the first study showing translocation of a human-pathogenic fungus across the intestinal barrier being mediated by a peptide toxin. IMPORTANCE Candida albicans, usually a harmless fungus colonizing human mucosae, can cause lethal bloodstream infections when it manages to translocate across the intestinal epithelium. This can result from antibiotic treatment, immune dysfunction, or intestinal damage (e.g., during surgery). However, fungal processes may also contribute. In this study, we investigated the translocation process of C. albicans using in vitro cell culture models. Translocation occurs as a stepwise process starting with invasion, followed by epithelial damage and loss of epithelial integrity. The ability to secrete candidalysin, a peptide toxin deriving from the hyphal protein Ece1, is key: C. albicans hyphae, secreting candidalysin, take advantage of a necrotic weakened epithelium to translocate through the intestinal layer.},
  language  = {en}
}
@phdthesis{AlvarezLoeblich2018,
  author    = {Alvarez Loeblich, Paul Sebastian},
  title     = {Not Here, Not Now!
 - Situational Appropriateness, Negative Affect and the Experience of (Remote) Embarrassment. A Process Model.},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-161354},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Fremdsch{\"a}men or Fremdscham, a negative emotion which arises while observing someone behave inappropriately, comes to fame after the turn of the millennium in german speaking countries. There, they name it literally „other's shame" and it becomes obvious that this emotion happens most commonly while watching TV: reality shows, talent shows and bad comedies. The word even makes it to the dictionaries starting 2009, as its use increases unstoppably in everyday language, starting to get used in more and more situations, seemingly as a synonym of embarrassing or shameful. Still, a look in the emotional research on the subject returns exactly zero results as of 2011, leaving open the question as of what this emotion might be, and what it is not. The present wort aims at explaining not only the phenomenon of Fremdsch{\"a}men, but also the Emotion behind it - Embarrassment -, at a process level.},
  subject      = {Sozialpsychologie},
  language  = {en}
}
@article{AnanyKreckelFuellsacketal.2018,
  author    = {Anany, Mohamed A. and Kreckel, Jennifer and F{\"u}llsack, Simone and Rosenthal, Alevtina and Otto, Christoph and Siegmund, Daniela and Wajant, Harald},
  title     = {Soluble TNF-like weak inducer of apoptosis (TWEAK) enhances poly(I:C)-induced RIPK1-mediated necroptosis},
  series = {Cell Death \& Disease},
  volume    = {9},
  journal   = {Cell Death \& Disease},
  doi       = {10.1038/s41419-018-1137-1},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221104},
  year      = {2018},
  abstract  = {TNF-like weak inducer of apoptosis (TWEAK) and inhibition of protein synthesis with cycloheximide (CHX) sensitize for poly(I:C)-induced cell death. Notably, although CHX preferentially enhanced poly(I:C)-induced apoptosis, TWEAK enhanced primarily poly(I:C)-induced necroptosis. Both sensitizers of poly(I:C)-induced cell death, however, showed no major effect on proinflammatory poly(I:C) signaling. Analysis of a panel of HeLa-RIPK3 variants lacking TRADD, RIPK1, FADD, or caspase-8 expression revealed furthermore similarities and differences in the way how poly(I:C)/TWEAK, TNF, and TRAIL utilize these molecules for signaling. RIPK1 turned out to be essential for poly(I:C)/TWEAK-induced caspase-8-mediated apoptosis but was dispensable for this response in TNF and TRAIL signaling. TRADD-RIPK1-double deficiency differentially affected poly(I:C)-triggered gene induction but abrogated gene induction by TNF completely. FADD deficiency abrogated TRAIL- but not TNF- and poly(I:C)-induced necroptosis, whereas TRADD elicited protective activity against all three death inducers. A general protective activity against poly(I:C)-, TRAIL-, and TNF-induced cell death was also observed in FLIPL and FLIPS transfectrants.},
  language  = {en}
}
@article{AndratschkeAlheidAllgaeueretal.2018,
  author    = {Andratschke, N. and Alheid, H. and Allg{\"a}uer, M. and Becker, G. and Blanck, O. and Boda-Heggemann, J. and Brunner, T. and Duma, M. and Gerum, S. and Guckenberger, M. and Hildebrandt, G. and Klement, R. J. and Lewitzki, V. and Ostheimer, C. and Papachristofilou, A. and Petersen, C. and Schneider, T. and Semrau, R. and Wachter, S. and Habermehl, D.},
  title     = {The SBRT database initiative of the German Society for Radiation Oncology (DEGRO): patterns of care and outcome analysis of stereotactic body radiotherapy (SBRT) for liver oligometastases in 474 patients with 623 metastases},
  series = {BMC Cancer},
  volume    = {18},
  journal   = {BMC Cancer},
  doi       = {10.1186/s12885-018-4191-2},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221116},
  year      = {2018},
  abstract  = {Background The intent of this pooled analysis as part of the German society for radiation oncology (DEGRO) stereotactic body radiotherapy (SBRT) initiative was to analyze the patterns of care of SBRT for liver oligometastases and to derive factors influencing treated metastases control and overall survival in a large patient cohort. Methods From 17 German and Swiss centers, data on all patients treated for liver oligometastases with SBRT since its introduction in 1997 has been collected and entered into a centralized database. In addition to patient and tumor characteristics, data on immobilization, image guidance and motion management as well as dose prescription and fractionation has been gathered. Besides dose response and survival statistics, time trends of the aforementioned variables have been investigated. Results In total, 474 patients with 623 liver oligometastases (median 1 lesion/patient; range 1-4) have been collected from 1997 until 2015. Predominant histologies were colorectal cancer (n = 213 pts.; 300 lesions) and breast cancer (n = 57; 81 lesions). All centers employed an SBRT specific setup. Initially, stereotactic coordinates and CT simulation were used for treatment set-up (55\%), but eventually were replaced by CBCT guidance (28\%) or more recently robotic tracking (17\%). High variance in fraction (fx) number (median 1 fx; range 1-13) and dose per fraction (median: 18.5 Gy; range 3-37.5 Gy) was observed, although median BED remained consistently high after an initial learning curve. Median follow-up time was 15 months; median overall survival after SBRT was 24 months. One- and 2-year treated metastases control rate of treated lesions was 77\% and 64\%; if maximum isocenter biological equivalent dose (BED) was greater than 150 Gy EQD2Gy, it increased to 83\% and 70\%, respectively. Besides radiation dose colorectal and breast histology and motion management methods were associated with improved treated metastases control. Conclusion After an initial learning curve with regards to total cumulative doses, consistently high biologically effective doses have been employed translating into high local tumor control at 1 and 2 years. The true impact of histology and motion management method on treated metastases control deserve deeper analysis. Overall survival is mainly influenced by histology and metastatic tumor burden.},
  language  = {en}
}
@article{AnelliOrdasKneitzetal.2018,
  author    = {Anelli, Viviana and Ordas, Anita and Kneitz, Susanne and Sagredo, Leonel Munoz and Gourain, Victor and Schartl, Manfred and Meijer, Annemarie H. and Mione, Marina},
  title     = {Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression},
  series = {Frontiers in Genetics},
  volume    = {9},
  journal   = {Frontiers in Genetics},
  number    = {675},
  issn      = {1664-8021},
  doi       = {10.3389/fgene.2018.00675},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-196963},
  year      = {2018},
  abstract  = {Ras genes are among the most commonly mutated genes in human cancer; yet our understanding of their oncogenic activity at the molecular mechanistic level is incomplete. To identify downstream events that mediate ras-induced cellular transformation in vivo, we analyzed global microRNA expression in three different models of Ras-induction and tumor formation in zebrafish. Six microRNAs were found increased in Ras-induced melanoma, glioma and in an inducible model of ubiquitous Ras expression. The upregulation of the microRNAs depended on the activation of the ERK and AKT pathways and to a lesser extent, on mTOR signaling. Two Ras-induced microRNAs (miR-146a and 193a) target Jmjd6, inducing downregulation of its mRNA and protein levels at the onset of Ras expression during melanoma development. However, at later stages of melanoma progression, jmjd6 levels were found elevated. The dynamic of Jmjd6 levels during progression of melanoma in the zebrafish model suggests that upregulation of the microRNAs targeting Jmjd6 may be part of an anti-cancer response. Indeed, triple transgenic fish engineered to express a microRNA-resistant Jmjd6 from the onset of melanoma have increased tumor burden, higher infiltration of leukocytes and shorter melanoma-free survival. Increased JMJD6 expression is found in several human cancers, including melanoma, suggesting that the up-regulation of Jmjd6 is a critical event in tumor progression. The following link has been created to allow review of record GSE37015: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=jjcrbiuicyyqgpc\&acc=GSE37015.},
  language  = {en}
}
@phdthesis{Ankenbrand2018,
  author    = {Ankenbrand, Markus Johannes},
  title     = {Squeezing more information out of biological data - development and application of bioinformatic tools for ecology, evolution and genomics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156344},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {New experimental methods have drastically accelerated the pace and quantity at which biological data is generated. High-throughput DNA sequencing is one of the pivotal new technologies. It offers a number of novel applications in various fields of biology, including ecology, evolution, and genomics. However, together with those opportunities many new challenges arise. Specialized algorithms and software are required to cope with the amount of data, often requiring substantial training in bioinformatic methods. Another way to make those data accessible to non-bioinformaticians is the development of programs with intuitive user interfaces. In my thesis I developed analyses and programs to tackle current problems with high-throughput data in biology. In the field of ecology this covers the establishment of the bioinformatic workflow for pollen DNA meta-barcoding. Furthermore, I developed an application that facilitates the analysis of ecological communities in the context of their traits. Information from multiple public databases have been aggregated and can now be mapped automatically to existing community tables for interactive inspection. In evolution the new data are used to reconstruct phylogenetic trees from multiple genes. I developed the tool bcgTree to automate this process for bacteria. Many plant genomes have been sequenced in current years. Sequencing reads of those projects also contain data from the chloroplasts. The tool chloroExtractor supports the targeted extraction and analysis of the chloroplast genome. To compare the structure of multiple genomes specialized software is required for calculation and visualization of the relationships. I developed AliTV to address this. In contrast to existing programs for this task it allows interactive adjustments of produced graphics. Thus, facilitating the discovery of biologically relevant information. Another application I developed helps to analyze transcriptomes even if no reference genome is present. This is achieved by aggregating the different pieces of information, like functional annotation and expression level, for each transcript in a web platform. Scientists can then search, filter, subset, and visualize the transcriptome. Together the methods and tools expedite insights into biological systems that were not possible before.},
  language  = {en}
}
@article{ArnholdtKamawalHolzapfeletal.2018,
  author    = {Arnholdt, J{\"o}rg and Kamawal, Yama and Holzapfel, Boris Michael and Ripp, Axel and Rudert, Maximilian and Steinert, Andre Friedrich},
  title     = {Evaluation of implant fit and frontal plane alignment after bi-compartmental knee arthroplasty using patient-specific instruments and implants},
  series = {Archives of Medical Science},
  volume    = {14},
  journal   = {Archives of Medical Science},
  number    = {6},
  doi       = {10.5114/aoms.2018.79007},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-159668},
  pages     = {1424-1431},
  year      = {2018},
  abstract  = {Introduction The goals of successful bi-compartmental knee arthroplasty are to achieve correct fit and positioning of the implant, while appropriately correcting the mechanical alignment of the leg after surgery. As these requirements are not always reliably fulfilled using off-the-shelf implant systems, newer approaches for bi-compartmental resurfacing have been explored. Material and methods In this article we report the radiographic results of 30 patients with anteromedial osteoarthritis (OA) who were treated with a novel patient-specific fixed-bearing bi-compartmental knee resurfacing system using custom-made implants and instruments. Utilizing standardized pre- and postoperative radiographic analyses (based on anterior-posterior and lateral, anterior-posterior weight-bearing full-length radiographs, patella skyline views and preoperative computed tomography (CT) scanning) implant fit and positioning as well as correction of the mechanical axis (hip-knee-ankle angle, HKA) were determined. Results On average, HKA was corrected from 173.4 ±3.47° preoperatively to 179.4 ±2.85° postoperatively. The coronal femoro-tibial angle was corrected on average 5.61°. The preoperative tibial slope measured on lateral views was 6.38 ±2.4°, while the average slope in the CT-based planning protocol (iView) was 6.14 ±2.40°. Postoperative lateral tibial slope was determined to be 5.77 ±1.97°. The thickness of the posterior femoral cuts was measured intraoperatively and, in all cases, corresponded well to the targeted thickness of the cuts provided by the iView. The joint line was preserved in all cases and the average Insall-Salvati index was 1.078 ±0.11 pre- and 1.072 ±0.11 postoperatively. The fit of the implant components measured by over- or underhang was excellent throughout (< 1.01 mm). Conclusions Custom-made bicompartmental knee arthroplasty can ensure optimized fitting and positioning of the implant with restoration of the leg axis. These implants could be considered as an alternative primary solution for knee surgeons treating bi-compartmental disease.},
  language  = {en}
}
@unpublished{ArrowsmithMattockBoehnkeetal.2018,
  author    = {Arrowsmith, Merle and Mattock, James D. and B{\"o}hnke, Julian and Krummenacher, Ivo and Vargas, Alfredo and Braunschweig, Holger},
  title     = {Direct access to a cAAC-supported dihydrodiborene and its dianion},
  series = {Chemical Communications},
  journal   = {Chemical Communications},
  doi       = {10.1039/C8CC01580E},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164276},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@unpublished{AuerhammerArrowsmithBoehnkeetal.2018,
  author    = {Auerhammer, Dominic and Arrowsmith, Merle and B{\"o}hnke, Julian and Braunschweig, Holger and Dewhurst, Rian D. and Kupfer, Thomas},
  title     = {Brothers from Another Mother: a Borylene and its Dimer are Non-Interconvertible but Connected through Reactivity},
  series = {Chemical Science},
  journal   = {Chemical Science},
  doi       = {10.1039/C7SC04789D},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-157125},
  year      = {2018},
  abstract  = {The self-stabilizing, tetrameric cyanoborylene [(cAAC)B(CN)]4 (I, cAAC = 1-(2,6-diisopropylphenyl)-3,3,5,5-tetramethylpyrrolidin-2-ylidene) and its diborene relative, [(cAAC)(CN)B=B(CN)(cAAC)] (II), both react with disulfides and diselenides to yield the corresponding cAAC-supported cyanoboron bis(chalcogenides). Furthermore, reactions of I or II with elemental sulfur and selenium in various stoichiometries provided access to a variety of cAAC- stabilized cyanoboron-chalcogen heterocycles, including a unique dithiaborirane, a diboraselenirane, 1,3-dichalcogena-2,4-diboretanes, 1,3,4-trichalcogena- 2,5-diborolanes and a rare six-membered 1,2,4,5-tetrathia-3,6-diborinane. Stepwise addition reactions and solution stability studies provided insights into the mechanism of these reactions and the subtle differences in reactivity observed between I and II.},
  language  = {en}
}
@phdthesis{Auerhammer2018,
  author    = {Auerhammer, Nina A.},
  title     = {Energy Transfer and Excitonic Interactions in Conjugated Chromophore Arrangements of Bodipys and Pyrenes and Squaraines},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-166721},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {In this work the energy transfer and excitonic coupling in different chromophore arrangements were investigated. A difference in the coupling strength was introduced by varring the connecting unit and the spacial orientation relative to each other. The synthesis of the 2,7-substituted pyrene compounds could be optimised and good yields of HAB 1 and HAB 2 and small amounts of HAB 2 could be achieved by cobalt-catalysed trimerisation or Diels Alder reaction in the end. Absorption and fluorescence spectra reveal strong intramolecular interactions between the pyrene molecules in the HAB 1. Excitation spectra recorded at the high and low energy fluorescence suggest the contribution of two components to the spectra. One being similar to the ground state aggregate and a second species similar to undisturbed pyrene. All these feature can be accounted to two different fluorescent states which are due to electronical decoupling in the excited state. Due to the strong intramolecular coupling already in the ground state of the molecule, no energy transfer could be studied, as the six pyrene units cannot be seen as separate spectroscopic entities between which energy could be transferred. In the second part of this thesis dye conjugates of different size and alignment were synthesised to study the interaction of the transition-dipole moments. Therefore a systematic investigation of Sonogashira conditions was performed in order to obtain good yields of the desired compounds and keep dehalogenation at a minimum level. Nevertheless only the symmetrical triads could be purified as the asymmeric triads and pentades proved to decompose during purification. The pyrene containing triads Py2B and Py2SQB show small interactions already in the ground state represented by red shifts of the spectra and a broadening of the bands. Nevertheless, these interactions are in the weak coupling regime and energy transfer between the constituents is possible. On the contrary in the TA spectra it is obvious that always the whole triad, at least to some extend is excited. To question if the excitation of the high energy state is deactivated by energy transfer or rather IC in a superchromophore could not be distinguished in the course of this work. At present additional time-dependent calculations of the dynamics are in progress to get a deeper understanding of the photophysical processes taking place in the triads. The dye conjugates B2SQB-3 and (SQB)2B-4 can be assigned to the strong interaction range and hence are describable by exciton theory. The transition-dipole moments proved to be more than additive and increase for both compounds from absorption to fluorescence. This can be explained by an enhancement of the coupling in the relaxed excited state compared to the absorption into the Franck-Condon state due to a more steep potential energy surface in the excited state and hence smaller fluctuations. In the last part of this thesis the influence of disrupting electronical communication by implementing a rigid non-conjugated bridge in a bichromophoric trans-squaraine system was tested. While the flexible linked squaraines show complex spectra due to different conformers the SQA2Anth compound is rigified and no rotation is possible. This change in flexibility is represented in the steady-state spectra where just one main absorption and fluorescence band is present due to a single allowed excitonic state. The system proves to own an excited state that is completely delocalised over the whole molecule.},
  subject      = {Chromophor},
  language  = {en}
}
@phdthesis{Aufmkolk2018,
  author    = {Aufmkolk, Sarah},
  title     = {Super-Resolution Microscopy of Synaptic Proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151976},
  school      = {Universit{\"a}t W{\"u}rzburg},
  pages     = {X, 97},
  year      = {2018},
  abstract  = {The interaction of synaptic proteins orchestrate the function of one of the most complex organs, the brain. The multitude of molecular elements influencing neurological correlations makes imaging processes complicated since conventional fluorescence microscopy methods are unable to resolve structures beyond the diffraction-limit. The implementation of super-resolution fluorescence microscopy into the field of neuroscience allows the visualisation of the fine details of neural connectivity. The key element of my thesis is the super-resolution technique dSTORM (direct Stochastic Optical Reconstruction Microscopy) and its optimisation as a multi-colour approach. Capturing more than one target, I aim to unravel the distribution of synaptic proteins with nanometer precision and set them into a structural and quantitative context with one another. Therefore dSTORM specific protocols are optimized to serve the peculiarities of particular neural samples. In one project the brain derived neurotrophic factor (BDNF) is investigated in primary, hippocampal neurons. With a precision beyond 15 nm, preand post-synaptic sites can be identified by staining the active zone proteins bassoon and homer. As a result, hallmarks of mature synapses can be exhibited. The single molecule sensitivity of dSTORM enables the measurement of endogenous BDNF and locates BDNF granules aligned with glutamatergic pre-synapses. This data proofs that hippocampal neurons are capable of enriching BDNF within the mature glutamatergic pre-synapse, possibly influencing synaptic plasticity. The distribution of the metabotropic glutamate receptor mGlu4 is investigated in physiological brain slices enabling the analysis of the receptor in its natural environment. With dual-colour dSTORM, the spatial arrangement of the mGlu4 receptor in the pre-synaptic sites of parallel fibres in the molecular layer of the mouse cerebellum is visualized, as well as a four to six-fold increase in the density of the receptor in the active zone compared to the nearby environment. Prior functional measurements show that metabotropic glutamate receptors influence voltage-gated calcium channels and proteins that are involved in synaptic vesicle priming. Corresponding dSTORM data indeed suggests that a subset of the mGlu4 receptor is correlated with the voltage-gated calcium channel Cav2.1 on distances around 60 nm. These results are based on the improvement of the direct analysis of localisation data. Tools like coordinated based correlation analysis and nearest neighbour analysis of clusters centroids are used complementary to map protein connections of the synapse. Limits and possible improvements of these tools are discussed to foster the quantitative analysis of single molecule localisation microscopy data. Performing super-resolution microscopy on complex samples like brain slices benefits from a maximised field of view in combination with the visualisation of more than two targets to set the protein of interest in a cellular context. This challenge served as a motivation to establish a workflow for correlated structured illumination microscopy (SIM) and dSTORM. The development of the visualisation software coSIdSTORM promotes the combination of these powerful super-resolution techniques even on separated setups. As an example, synapses in the cerebellum that are affiliated to the parallel fibres and the dendrites of the Purkinje cells are identified by SIM and the protein bassoon of those pre-synapses is visualised threedimensionally with nanoscopic precision by dSTORM. In this work I placed emphasis on the improvement of multi-colour super-resolution imaging and its analysing tools to enable the investigation of synaptic proteins. The unravelling of the structural arrangement of investigated proteins supports the building of a synapse model and therefore helps to understand the relation between structure and function in neural transmission processes.},
  subject      = {Hochaufl{\"o}sende Mikroskopie},
  language  = {en}
}
@phdthesis{Aulbach2018,
  author    = {Aulbach, Julian},
  title     = {Gold-Induced Atomic Wires on Terraced Silicon Surfaces: Formation and Interactions of Silicon Spin Chains},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-169347},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {Atomic nanowires formed by self-assembled growth on semiconducting surfaces represent a feasible physical realization of quasi-1D electron systems and can be used to study fascinating 1D quantum phenomena. The system in the focus of this thesis, Si(553)-Au, is generated by Au adsorption onto a stepped silicon surface. It features two different chain types, interspersed with each other: A Au chain on the terrace, and a honeycomb chain of graphitic silicon located at the step edge. The silicon atoms at the exposed edges of the latter are predicted to be spin-polarized and charge-ordered [1], leading to an ordered array of local magnetic moments referred to as ``spin chains''. The present thesis puts this spin chain proposal to an experimental test. A detailed scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) scrutiny reveals a distinct unoccupied density of states (DOS) feature localized at every third Si step-edge atom, which aligns perfectly with the density functional theory (DFT) prediction. This finding provides strong evidence for the formation of spin chains at the Si(553)-Au step edges, and simultaneously rules out the interpretation of previous studies which attributed the x3 step-edge superstructure to a Peierls instability. To study the formation of spin chains in further detail, an additional member of the so-called Si(hhk)-Au family -- Si(775)-Au -- is analyzed. Based on DFT modeling (performed by S.C. Erwin, Naval Research Laboratory, USA) and detailed STM and STS experiments, a new structure model for this surface is developed, and the absence of spin chains at the Si(775)-Au step edges is demonstrated. The different step-edge charge distributions of all known Si(hhk)-Au surfaces are traced back to an electron transfer between the terrace and the step edge. Accordingly, an unintentional structure defect should create a localized spin at the Si(775)-Au step edge. This prediction is verified experimentally, and suggest that surface chemistry can be used to create and destroy Si spin chains. Having clarified why spin chains form on some Si(hhk)-Au surfaces but not on others, various interaction effects of the Si(553)-Au spin chains are inspected. A collaborative analysis by SPA-LEED (M. Horn-von Hoegen group, University of Duisburg-Essen, Germany), DFT (S.C. Erwin), and STM reveals strong lateral coupling between adjacent spin chains, bearing interesting implications for their magnetic ordering. The centered geometry uncovered leads to magnetic frustration, and may stabilize a 2D quantum spin liquid. Moreover, a complex interplay between neighboring Au and Si chains is detected. Specifically, the interaction is found effectively ``one-way'', i.e., the Si step edges respond to the Au chains but not vice versa. This unidirectional effect breaks the parity of the Si chains, and creates two different configurations of step edges with opposite directionality. In addition to the static properties of the Si(553)-Au surface mentioned above, the occurrence of solitons in both wire types is witnessed in real space by means of high-resolution STM imaging. The solitons are found to interact with one another such that both move in a coupled fashion along the chains. Likewise, STM experiments as a function of the tunneling current suggest an excitation of solitons along the step edge by the STM tunneling tip. Solitons are also found to play an essential role in the temperature-dependent behavior of the Si(553)-Au step edges. It is an accepted fact that the distinct x3 superstructure of the Si(553)-Au step edges vanishes upon heating to room temperature. As a first step in exploring this transition in detail over a large temperature range, a previously undetected, occupied electronic state associated with the localized step-edge spins is identified by means of angle-resolved photoemission spectroscopy (ARPES). A tracking of this state as a function of temperature reveals an order-disorder-type transition. Complementary STM experiments attribute the origin of this transition to local, thermally activated spin site hops, which correspond to soliton-anitsoliton pairs. Finally, a manipulation of the Si(553)-Au atomic wire array is achieved by the stepwise adsorption of potassium atoms. This does not only increase the filling of the Au-induced surface bands culminating in a metal-insulator transition (MIT), but also modifies the Si step-edge charge distribution, as indicated by STM and ARPES experiments. [1] S. C. Erwin and F. Himpsel, Intrinsic magnetism at silicon surfaces, Nat. Commun. 1, 58 (2010).},
  subject      = {Rastertunnelmikroskopie},
  language  = {en}
}