TY - JOUR A1 - Letunic, Ivica A1 - Khedkar, Supriya A1 - Bork, Peer T1 - SMART: recent updates, new developments and status in 2020 JF - Nucleic Acids Research N2 - 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. KW - SMART KW - SMART version 9 KW - protein domains KW - protein domain architectures Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-363816 VL - 49 IS - D1 ER - TY - JOUR A1 - Denk, S. A1 - Schmidt, S. A1 - Schurr, Y. A1 - Schwarz, G. A1 - Schote, F. A1 - Diefenbacher, M. A1 - Armendariz, C. A1 - Dejure, F. A1 - Eilers, M. A1 - Wiegering, Armin T1 - CIP2A regulates MYC translation (via its 5′UTR) in colorectal cancer JF - International Journal of Colorectal Disease N2 - 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. KW - CIP2A KW - MYC KW - translation KW - colon cancer Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-280092 VL - 36 IS - 5 ER - TY - GEN A1 - Baur, Johannes A1 - Ramser, Michaela A1 - Keller, Nicola A1 - Muysoms, Filip A1 - Dörfer, Jörg A1 - Wiegering, Armin A1 - Eisner, Lukas A1 - Dietz, Ulrich A. T1 - Erratum to: Robotic hernia repair II. English version Robotic primary ventral and incisional hernia repair (rv-TAPP and r-Rives or r-TARUP). Video report and results of a series of 118 patients T2 - Der Chirurg N2 - No abstract available. KW - erratum Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-326357 VL - 92 IS - SUPPL 1 SP - S27 ER - TY - JOUR A1 - Reddersen, Kirsten A1 - Güllmar, André A1 - Tonndorf-Martini, Silke A1 - Sigusch, Bernd W. A1 - Ewald, Andrea A1 - Dauben, Thomas J. A1 - Martin, Karin A1 - Wiegand, Cornelia T1 - Critical parameters in cultivation of experimental biofilms using the example of Pseudomonas fluorescens JF - Journal of Materials Science: Materials in Medicine N2 - 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. KW - biomaterials KW - biomedical engineering and bioengineering KW - regenerative medicine/tissue engineering KW - polymer sciences KW - ceramics, glass, composites, natural materials KW - surfaces and interfaces, thin films Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-309911 SN - 0957-4530 SN - 1573-4838 VL - 32 IS - 9 ER - TY - JOUR A1 - Glinz, Jonathan A1 - Šleichrt, Jan A1 - Kytýř, Daniel A1 - Ayalur-Karunakaran, Santhosh A1 - Zabler, Simon A1 - Kastner, Johann A1 - Senck, Sascha T1 - 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 JF - Journal of Materials Science N2 - 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. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-351581 VL - 56 IS - 16 ER - TY - GEN A1 - Kanzow, Christian A1 - Lechner, Theresa T1 - Correction to: Globalized inexact proximal Newton-type methods for nonconvex composite functions T2 - Computational Optimization and Applications N2 - No abstract available. KW - correction Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-348858 VL - 80 IS - 2 ER - TY - JOUR A1 - Kanzow, Christian A1 - Lechner, Theresa T1 - Globalized inexact proximal Newton-type methods for nonconvex composite functions JF - Computational Optimization and Applications N2 - 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. KW - globalized proximal Newton-type method KW - nonconvex smooth term Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-283715 VL - 78 IS - 2 ER - TY - JOUR A1 - Loos, Jacqueline A1 - Krauss, Jochen A1 - Lyons, Ashley A1 - Föst, Stephanie A1 - Ohlendorf, Constanze A1 - Racky, Severin A1 - Röder, Marina A1 - Hudel, Lennart A1 - Herfert, Volker A1 - Tscharntke, Teja T1 - Local and landscape responses of biodiversity in calcareous grasslands JF - Biodiversity and Conservation N2 - 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 Göttingen, 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. KW - abandonment KW - birds KW - butterflies KW - land use intensification KW - nature conservation KW - vascular plants Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-308595 SN - 0960-3115 SN - 1572-9710 VL - 30 IS - 8-9 ER - TY - GEN A1 - Hauf, Juliane E. K. A1 - Nieding, Gerhild A1 - Seger, Benedikt T. T1 - Correction to: The development of dynamic perceptual simulations during sentence comprehension T2 - Cognitive Processing N2 - No abstract available. KW - Erratum Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-352611 N1 - The original article can be found online at https://doi.org/10.1007/s10339-020-00959-7 VL - 22 IS - 4 ER - TY - JOUR A1 - Righesso, L. A. R. A1 - Terekhov, M. A1 - Götz, H. A1 - Ackermann, M. A1 - Emrich, T. A1 - Schreiber, L. M. A1 - Müller, W. E. G. A1 - Jung, J. A1 - Rojas, J. P. A1 - Al-Nawas, B. T1 - Dynamic contrast-enhanced magnetic resonance imaging for monitoring neovascularization during bone regeneration — a randomized in vivo study in rabbits JF - Clinical Oral Investigations N2 - 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. KW - animal experimentation KW - bone regeneration KW - multiparametric magnetic resonance imaging KW - neovascularization, physiologic KW - tissue engineering KW - translational medical research Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-307614 SN - 1432-6981 SN - 1436-3771 VL - 25 IS - 10 ER -