@article{LetunicKhedkarBork2021, author = {Letunic, Ivica and Khedkar, Supriya and Bork, Peer}, title = {SMART: recent updates, new developments and status in 2020}, series = {Nucleic Acids Research}, volume = {49}, journal = {Nucleic Acids Research}, number = {D1}, doi = {10.1093/nar/gkaa937}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-363816}, pages = {D458-D460}, year = {2021}, abstract = {SMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curatedmodels formore than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART's vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.}, language = {en} } @article{DenkSchmidtSchurretal.2021, author = {Denk, S. and Schmidt, S. and Schurr, Y. and Schwarz, G. and Schote, F. and Diefenbacher, M. and Armendariz, C. and Dejure, F. and Eilers, M. and Wiegering, Armin}, title = {CIP2A regulates MYC translation (via its 5′UTR) in colorectal cancer}, series = {International Journal of Colorectal Disease}, volume = {36}, journal = {International Journal of Colorectal Disease}, number = {5}, doi = {10.1007/s00384-020-03772-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-280092}, pages = {911-918}, year = {2021}, abstract = {Background Deregulated expression of MYC is a driver of colorectal carcinogenesis, suggesting that decreasing MYC expression may have significant therapeutic value. CIP2A is an oncogenic factor that regulates MYC expression. CIP2A is overexpressed in colorectal cancer (CRC), and its expression levels are an independent marker for long-term outcome of CRC. Previous studies suggested that CIP2A controls MYC protein expression on a post-transcriptional level. Methods To determine the mechanism by which CIP2A regulates MYC in CRC, we dissected MYC translation and stability dependent on CIP2A in CRC cell lines. Results Knockdown of CIP2A reduced MYC protein levels without influencing MYC stability in CRC cell lines. Interfering with proteasomal degradation of MYC by usage of FBXW7-deficient cells or treatment with the proteasome inhibitor MG132 did not rescue the effect of CIP2A depletion on MYC protein levels. Whereas CIP2A knockdown had marginal influence on global protein synthesis, we could demonstrate that, by using different reporter constructs and cells expressing MYC mRNA with or without flanking UTR, CIP2A regulates MYC translation. This interaction is mainly conducted by the MYC 5′UTR. Conclusions Thus, instead of targeting MYC protein stability as reported for other tissue types before, CIP2A specifically regulates MYC mRNA translation in CRC but has only slight effects on global mRNA translation. In conclusion, we propose as novel mechanism that CIP2A regulates MYC on a translational level rather than affecting MYC protein stability in CRC.}, language = {en} } @article{ReddersenGuellmarTonndorfMartinietal.2021, author = {Reddersen, Kirsten and G{\"u}llmar, Andr{\´e} and Tonndorf-Martini, Silke and Sigusch, Bernd W. and Ewald, Andrea and Dauben, Thomas J. and Martin, Karin and Wiegand, Cornelia}, title = {Critical parameters in cultivation of experimental biofilms using the example of Pseudomonas fluorescens}, series = {Journal of Materials Science: Materials in Medicine}, volume = {32}, journal = {Journal of Materials Science: Materials in Medicine}, number = {9}, issn = {0957-4530}, doi = {10.1007/s10856-021-06568-w}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-309911}, year = {2021}, abstract = {Formation and treatment of biofilms present a great challenge for health care and industry. About 80\% of human infections are associated with biofilms including biomaterial centered infections, like infections of prosthetic heart valves, central venous catheters, or urinary catheters. Additionally, biofilms can cause food and drinking water contamination. Biofilm research focusses on application of experimental biofilm models to study initial adherence processes, to optimize physico-chemical properties of medical materials for reducing interactions between materials and bacteria, and to investigate biofilm treatment under controlled conditions. Exploring new antimicrobial strategies plays a key role in a variety of scientific disciplines, like medical material research, anti-infectious research, plant engineering, or wastewater treatment. Although a variety of biofilm models exist, there is a lack of standardization for experimental protocols, and designing experimental setups remains a challenge. In this study, a number of experimental parameters critical for material research have been tested that influence formation and stability of an experimental biofilm using the non-pathogenic model strain of Pseudomonas fluorescens. These parameters include experimental time frame, nutrient supply, inoculum concentration, static and dynamic cultivation conditions, material properties, and sample treatment during staining for visualization of the biofilm. It was shown, that all tested parameters critically influence the experimental biofilm formation process. The results obtained in this study shall support material researchers in designing experimental biofilm setups.}, language = {en} } @article{GlinzŠleichrtKytyřetal.2021, author = {Glinz, Jonathan and Šleichrt, Jan and Kyt{\´y}ř, Daniel and Ayalur-Karunakaran, Santhosh and Zabler, Simon and Kastner, Johann and Senck, Sascha}, title = {Phase-contrast and dark-field imaging for the inspection of resin-rich areas and fiber orientation in non-crimp vacuum infusion carbon-fiber-reinforced polymers}, series = {Journal of Materials Science}, volume = {56}, journal = {Journal of Materials Science}, number = {16}, doi = {10.1007/s10853-021-05907-0}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-351581}, pages = {9712-9727}, year = {2021}, abstract = {In this work, we present a multimodal approach to three-dimensionally quantify and visualize fiber orientation and resin-rich areas in carbon-fiber-reinforced polymers manufactured by vacuum infusion. Three complementary image modalities were acquired by Talbot-Lau grating interferometer (TLGI) X-ray microcomputed tomography (XCT). Compared to absorption contrast (AC), TLGI-XCT provides enhanced contrast between polymer matrix and carbon fibers at lower spatial resolutions in the form of differential phase contrast (DPC) and dark-field contrast (DFC). Consequently, relatively thin layers of resin, effectively indiscernible from image noise in AC data, are distinguishable. In addition to the assessment of fiber orientation, the combination of DPC and DFC facilitates the quantification of resin-rich areas, e.g., in gaps between fiber layers or at binder yarn collimation sites. We found that resin-rich areas between fiber layers are predominantly developed in regions characterized by a pronounced curvature. In contrast, in-layer resin-rich areas are mainly caused by the collimation of fibers by binder yarn. Furthermore, void volume around two adjacent 90°-oriented fiber layers is increased by roughly 20\% compared to a random distribution over the whole specimen.}, language = {en} } @article{KanzowLechner2021, author = {Kanzow, Christian and Lechner, Theresa}, title = {Globalized inexact proximal Newton-type methods for nonconvex composite functions}, series = {Computational Optimization and Applications}, volume = {78}, journal = {Computational Optimization and Applications}, number = {2}, doi = {10.1007/s10589-020-00243-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-283715}, pages = {377-410}, year = {2021}, abstract = {Optimization problems with composite functions consist of an objective function which is the sum of a smooth and a (convex) nonsmooth term. This particular structure is exploited by the class of proximal gradient methods and some of their generalizations like proximal Newton and quasi-Newton methods. The current literature on these classes of methods almost exclusively considers the case where also the smooth term is convex. Here we present a globalized proximal Newton-type method which allows the smooth term to be nonconvex. The method is shown to have nice global and local convergence properties, and some numerical results indicate that this method is very promising also from a practical point of view.}, language = {en} } @article{LoosKraussLyonsetal.2021, author = {Loos, Jacqueline and Krauss, Jochen and Lyons, Ashley and F{\"o}st, Stephanie and Ohlendorf, Constanze and Racky, Severin and R{\"o}der, Marina and Hudel, Lennart and Herfert, Volker and Tscharntke, Teja}, title = {Local and landscape responses of biodiversity in calcareous grasslands}, series = {Biodiversity and Conservation}, volume = {30}, journal = {Biodiversity and Conservation}, number = {8-9}, issn = {0960-3115}, doi = {10.1007/s10531-021-02201-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-308595}, pages = {2415-2432}, year = {2021}, abstract = {Across Europe, calcareous grasslands become increasingly fragmented and their quality deteriorates through abandonment and land use intensification, both affecting biodiversity. Here, we investigated local and landscape effects on diversity patterns of several taxonomic groups in a landscape of highly fragmented calcareous grassland remnants. We surveyed 31 grassland fragments near G{\"o}ttingen, Germany, in spring and summer 2017 for vascular plants, butterflies and birds, with sampling effort adapted to fragment area. Through regression modelling, we tested relationships between species richness and fragment size (from 314 to 51,395 m\(^2\)), successional stage, habitat connectivity and the per cent cover of arable land in the landscape at several radii. We detected 283 plant species, 53 butterfly species and 70 bird species. Of these, 59 plant species, 19 butterfly species and 9 bird species were grassland specialists. Larger fragments supported twice the species richness of plants than small ones, and hosted more species of butterflies, but not of birds. Larger grassland fragments contained more grassland specialist plants, but not butterfly or bird specialists. Increasing amounts of arable land in the landscape from 20 to 90\% was related to the loss of a third of species of plants, and less so, of butterflies, but not of birds. Per cent cover of arable land negatively correlated to richness of grassland specialist plants and butterflies, but positively to grassland specialist birds. We found no effect by successional stages and habitat connectivity. Our multi-taxa approach highlights the need for conservation management at the local scale, complemented by measures at the landscape scale.}, language = {en} } @article{RighessoTerekhovGoetzetal.2021, author = {Righesso, L. A. R. and Terekhov, M. and G{\"o}tz, H. and Ackermann, M. and Emrich, T. and Schreiber, L. M. and M{\"u}ller, W. E. G. and Jung, J. and Rojas, J. P. and Al-Nawas, B.}, title = {Dynamic contrast-enhanced magnetic resonance imaging for monitoring neovascularization during bone regeneration — a randomized in vivo study in rabbits}, series = {Clinical Oral Investigations}, volume = {25}, journal = {Clinical Oral Investigations}, number = {10}, issn = {1432-6981}, doi = {10.1007/s00784-021-03889-6}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-307614}, pages = {5843-5854}, year = {2021}, abstract = {Objectives Micro-computed tomography (μ-CT) and histology, the current gold standard methods for assessing the formation of new bone and blood vessels, are invasive and/or destructive. With that in mind, a more conservative tool, dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), was tested for its accuracy and reproducibility in monitoring neovascularization during bone regeneration. Additionally, the suitability of blood perfusion as a surrogate of the efficacy of osteoplastic materials was evaluated. Materials and methods Sixteen rabbits were used and equally divided into four groups, according to the time of euthanasia (2, 3, 4, and 6 weeks after surgery). The animals were submitted to two 8-mm craniotomies that were filled with blood or autogenous bone. Neovascularization was assessed in vivo through DCE-MRI, and bone regeneration, ex vivo, through μ-CT and histology. Results The defects could be consistently identified, and their blood perfusion measured through DCE-MRI, there being statistically significant differences within the blood clot group between 3 and 6 weeks (p = 0.029), and between the former and autogenous bone at six weeks (p = 0.017). Nonetheless, no significant correlations between DCE-MRI findings on neovascularization and μ-CT (r =-0.101, 95\% CI [-0.445; 0.268]) or histology (r = 0.305, 95\% CI [-0.133; 0.644]) findings on bone regeneration were observed. Conclusions These results support the hypothesis that DCE-MRI can be used to monitor neovascularization but contradict the premise that it could predict bone regeneration as well.}, language = {en} } @article{JockelSchneiderSchlagenhaufPetsosetal.2021, author = {Jockel-Schneider, Yvonne and Schlagenhauf, Ulrich and Petsos, Hari and R{\"u}ttermann, Stefan and Schmidt, Jana and Ziebolz, Dirk and Wehner, Christian and Laky, Markus and Rott, Thea and Noack, Michael and Noack, Barbara and Lorenz, Katrin}, title = {Impact of 0.1\% octenidine mouthwash on plaque re-growth in healthy adults: a multi-center phase 3 randomized clinical trial}, series = {Clinical Oral Investigations}, volume = {25}, journal = {Clinical Oral Investigations}, number = {7}, issn = {1432-6981}, doi = {10.1007/s00784-021-03781-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-307629}, pages = {4681-4689}, year = {2021}, abstract = {Objectives To investigate plaque inhibition of 0.1\% octenidine mouthwash (OCT) vs. placebo over 5 days in the absence of mechanical plaque control. Materials and methods For this randomized, placebo-controlled, double-blind, parallel group, multi-center phase 3 study, 201 healthy adults were recruited. After baseline recording of plaque index (PI) and gingival index (GI), collection of salivary samples, and dental prophylaxis, subjects were randomly assigned to OCT or placebo mouthwash in a 3:1 ratio. Rinsing was performed twice daily for 30 s. Colony forming units in saliva were determined before and after the first rinse. At day 5, PI, GI, and tooth discoloration index (DI) were assessed. Non-parametric van Elteren tests were applied with a significance level of p < 0.05. Results Treatment with OCT inhibited plaque formation more than treatment with placebo (PI: 0.36 vs. 1.29; p < 0.0001). OCT reduced GI (0.04 vs. placebo 0.00; p = 0.003) and salivary bacterial counts (2.73 vs. placebo 0.24 lgCFU/ml; p < 0.0001). Tooth discoloration was slightly higher under OCT (DI: 0.25 vs. placebo 0.00; p = 0.0011). Mild tongue staining and dysgeusia occurred. Conclusions OCT 0.1\% mouthwash inhibits plaque formation over 5 days. It therefore can be recommended when regular oral hygiene is temporarily compromised. Clinical relevance When individual plaque control is compromised, rinsing with octenidine mouthwash is recommended to maintain healthy oral conditions while side effects are limited.}, language = {en} } @article{CampanaCiaramellaBorzi2021, author = {Campana, Francesca Cal{\`a} and Ciaramella, Gabriele and Borz{\`i}, Alfio}, title = {Nash Equilibria and Bargaining Solutions of Differential Bilinear Games}, series = {Dynamic Games and Applications}, volume = {11}, journal = {Dynamic Games and Applications}, number = {1}, doi = {10.1007/s13235-020-00351-2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-283897}, pages = {1-28}, year = {2021}, abstract = {This paper is devoted to a theoretical and numerical investigation of Nash equilibria and Nash bargaining problems governed by bilinear (input-affine) differential models. These systems with a bilinear state-control structure arise in many applications in, e.g., biology, economics, physics, where competition between different species, agents, and forces needs to be modelled. For this purpose, the concept of Nash equilibria (NE) appears appropriate, and the building blocks of the resulting differential Nash games are different control functions associated with different players that pursue different non-cooperative objectives. In this framework, existence of Nash equilibria is proved and computed with a semi-smooth Newton scheme combined with a relaxation method. Further, a related Nash bargaining (NB) problem is discussed. This aims at determining an improvement of all players' objectives with respect to the Nash equilibria. Results of numerical experiments successfully demonstrate the effectiveness of the proposed NE and NB computational framework.}, language = {en} } @article{PotreckMutkeWeylandetal.2021, author = {Potreck, Arne and Mutke, Matthias A. and Weyland, Charlotte S. and Pfaff, Johannes A. R. and Ringleb, Peter A. and Mundiyanapurath, Sibu and M{\"o}hlenbruch, Markus A. and Heiland, Sabine and Pham, Mirko and Bendszus, Martin and Hoffmann, Angelika}, title = {Combined Perfusion and Permeability Imaging Reveals Different Pathophysiologic Tissue Responses After Successful Thrombectomy}, series = {Translational Stroke Research}, volume = {12}, journal = {Translational Stroke Research}, number = {5}, issn = {1868-4483}, doi = {10.1007/s12975-020-00885-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-308946}, pages = {799-807}, year = {2021}, abstract = {Despite successful recanalization of large-vessel occlusions in acute ischemic stroke, individual patients profit to a varying degree. Dynamic susceptibility-weighted perfusion and dynamic T1-weighted contrast-enhanced blood-brain barrier permeability imaging may help to determine secondary stroke injury and predict clinical outcome. We prospectively performed perfusion and permeability imaging in 38 patients within 24 h after successful mechanical thrombectomy of an occlusion of the middle cerebral artery M1 segment. Perfusion alterations were evaluated on cerebral blood flow maps, blood-brain barrier disruption (BBBD) visually and quantitatively on ktrans maps and hemorrhagic transformation on susceptibility-weighted images. Visual BBBD within the DWI lesion corresponded to a median ktrans elevation (IQR) of 0.77 (0.41-1.4) min-1 and was found in all 7 cases of hypoperfusion (100\%), in 10 of 16 cases of hyperperfusion (63\%), and in only three of 13 cases with unaffected perfusion (23\%). BBBD was significantly associated with hemorrhagic transformation (p < 0.001). While BBBD alone was not a predictor of clinical outcome at 3 months (positive predictive value (PPV) = 0.8 [0.56-0.94]), hypoperfusion occurred more often in patients with unfavorable clinical outcome (PPV = 0.43 [0.10-0.82]) compared to hyperperfusion (PPV = 0.93 [0.68-1.0]) or unaffected perfusion (PPV = 1.0 [0.75-1.0]). We show that combined perfusion and permeability imaging reveals distinct infarct signatures after recanalization, indicating the severity of prior ischemic damage. It assists in predicting clinical outcome and may identify patients at risk of stroke progression.}, language = {en} }