TY - JOUR A1 - Čuklina, Jelena A1 - Hahn, Julia A1 - Imakaev, Maxim A1 - Omasits, Ulrich A1 - Förstner, Konrad U. A1 - Ljubimov, Nikolay A1 - Goebel, Melanie A1 - Pessi, Gabriella A1 - Fischer, Hans-Martin A1 - Ahrens, Christian H. A1 - Gelfand, Mikhail S. A1 - Evguenieva-Hackenberg, Elena T1 - Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation JF - BMC Genomics N2 - Background Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. Results A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. Conclusions The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes. KW - Bradyrhizobium KW - RNA-seq KW - Promoter prediction KW - Genome re-annotation KW - Internal transcription start site KW - Nodule KW - Transcription start site KW - Proteogenomics KW - Antisense RNA Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-164565 VL - 17 ER - TY - JOUR A1 - Straub, Anton A1 - Stapf, Maximilian A1 - Fischer, Markus A1 - Vollmer, Andreas A1 - Linz, Christian A1 - Lâm, Thiên-Trí A1 - Kübler, Alexander A1 - Brands, Roman C. A1 - Scherf-Clavel, Oliver A1 - Hartmann, Stefan T1 - Bone concentration of ampicillin/sulbactam: a pilot study in patients with osteonecrosis of the jaw JF - International Journal of Environmental Research and Public Health N2 - Osteonecrosis of the jaw (ONJ) occurs typically after irradiation of the head and neck area or after the intake of antiresorptive agents. Both interventions can lead to compromised bone perfusion and can ultimately result in infection and necrosis. Treatment usually consists of surgical necrosectomy and prolonged antibiotic therapy, usually through beta-lactams such as ampicillin/sulbactam. The poor blood supply in particular raises the question as to whether this form of antibiosis can achieve sufficient concentrations in the bone. Therefore, we investigated the antibiotic concentration in plasma and bone samples in a prospective study. Bone samples were collected from the necrosis core and in the vital surrounding bone. The measured concentrations in plasma for ampicillin and sulbactam were 126.3 ± 77.6 and 60.2 ± 35.0 µg/mL, respectively. In vital bone and necrotic bone samples, the ampicillin/sulbactam concentrations were 6.3 ± 7.8/1.8 ± 2.0 µg/g and 4.9 ± 7.0/1.7 ± 1.7 µg/g, respectively. These concentrations are substantially lower than described in the literature. However, the concentration seems sufficient to kill most bacteria, such as Streptococci and Staphylococci, which are mostly present in the biofilm of ONJ. We, therefore, conclude that intravenous administration of ampicillin/sulbactam remains a valuable treatment in the therapy of ONJ. Nevertheless, increasing resistance of Escherichia coli towards beta-lactam antibiotics have been reported and should be considered. KW - osteonecrosis of the jaw KW - ARONJ KW - MRONJ KW - ONJ KW - osteoradionecrosis KW - antibiotic bone concentration KW - jaw bone KW - beta-lactam KW - ampicillin Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-297413 SN - 1660-4601 VL - 19 IS - 22 ER - TY - JOUR A1 - Jordan, Martin C. A1 - Bröer, David A1 - Fischer, Christian A1 - Heilig, Philipp A1 - Gilbert, Fabian A1 - Hölscher-Doht, Stefanie A1 - Kalogirou, Charis A1 - Popp, Kevin A1 - Grunz, Jan-Peter A1 - Huflage, Henner A1 - Jakubietz, Rafael G. A1 - Ergün, Süleyman A1 - Meffert, Rainer H. T1 - Development and preclinical evaluation of a cable-clamp fixation device for a disrupted pubic symphysis JF - Communications Medicine N2 - Background Traumatic separation of the pubic symphysis can destabilize the pelvis and require surgical fixation to reduce symphyseal gapping. The traditional approach involves open reduction and the implantation of a steel symphyseal plate (SP) on the pubic bone to hold the reposition. Despite its widespread use, SP-fixation is often associated with implant failure caused by screw loosening or breakage. Methods To address the need for a more reliable surgical intervention, we developed and tested two titanium cable-clamp implants. The cable served as tensioning device while the clamp secured the cable to the bone. The first implant design included a steel cable anterior to the pubic symphysis to simplify its placement outside the pelvis, and the second design included a cable encircling the pubic symphysis to stabilize the anterior pelvic ring. Using highly reproducible synthetic bone models and a limited number of cadaver specimens, we performed a comprehensive biomechanical study of implant stability and evaluated surgical feasibility. Results We were able to demonstrate that the cable-clamp implants provide stability equivalent to that of a traditional SP-fixation but without the same risks of implant failure. We also provide detailed ex vivo evaluations of the safety and feasibility of a trans-obturator surgical approach required for those kind of fixation. Conclusion We propose that the developed cable-clamp fixation devices may be of clinical value in treating pubic symphysis separation. KW - pubic symphysis KW - cable-clamp implants KW - SP-fixation Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-299800 VL - 2 IS - 1 ER - TY - JOUR A1 - Farmer, Adam D. A1 - Strzelczyk, Adam A1 - Finisguerra, Alessandra A1 - Gourine, Alexander V. A1 - Gharabaghi, Alireza A1 - Hasan, Alkomiet A1 - Burger, Andreas M. A1 - Jaramillo, Andrés M. A1 - Mertens, Ann A1 - Majid, Arshad A1 - Verkuil, Bart A1 - Badran, Bashar W. A1 - Ventura-Bort, Carlos A1 - Gaul, Charly A1 - Beste, Christian A1 - Warren, Christopher M. A1 - Quintana, Daniel S. A1 - Hämmerer, Dorothea A1 - Freri, Elena A1 - Frangos, Eleni A1 - Tobaldini, Eleonora A1 - Kaniusas, Eugenijus A1 - Rosenow, Felix A1 - Capone, Fioravante A1 - Panetsos, Fivos A1 - Ackland, Gareth L. A1 - Kaithwas, Gaurav A1 - O'Leary, Georgia H. A1 - Genheimer, Hannah A1 - Jacobs, Heidi I. L. A1 - Van Diest, Ilse A1 - Schoenen, Jean A1 - Redgrave, Jessica A1 - Fang, Jiliang A1 - Deuchars, Jim A1 - Széles, Jozsef C. A1 - Thayer, Julian F. A1 - More, Kaushik A1 - Vonck, Kristl A1 - Steenbergen, Laura A1 - Vianna, Lauro C. A1 - McTeague, Lisa M. A1 - Ludwig, Mareike A1 - Veldhuizen, Maria G. A1 - De Couck, Marijke A1 - Casazza, Marina A1 - Keute, Marius A1 - Bikson, Marom A1 - Andreatta, Marta A1 - D'Agostini, Martina A1 - Weymar, Mathias A1 - Betts, Matthew A1 - Prigge, Matthias A1 - Kaess, Michael A1 - Roden, Michael A1 - Thai, Michelle A1 - Schuster, Nathaniel M. A1 - Montano, Nicola A1 - Hansen, Niels A1 - Kroemer, Nils B. A1 - Rong, Peijing A1 - Fischer, Rico A1 - Howland, Robert H. A1 - Sclocco, Roberta A1 - Sellaro, Roberta A1 - Garcia, Ronald G. A1 - Bauer, Sebastian A1 - Gancheva, Sofiya A1 - Stavrakis, Stavros A1 - Kampusch, Stefan A1 - Deuchars, Susan A. A1 - Wehner, Sven A1 - Laborde, Sylvain A1 - Usichenko, Taras A1 - Polak, Thomas A1 - Zaehle, Tino A1 - Borges, Uirassu A1 - Teckentrup, Vanessa A1 - Jandackova, Vera K. A1 - Napadow, Vitaly A1 - Koenig, Julian T1 - International Consensus Based Review and Recommendations for Minimum Reporting Standards in Research on Transcutaneous Vagus Nerve Stimulation (Version 2020) JF - Frontiers in Human Neuroscience N2 - Given its non-invasive nature, there is increasing interest in the use of transcutaneous vagus nerve stimulation (tVNS) across basic, translational and clinical research. Contemporaneously, tVNS can be achieved by stimulating either the auricular branch or the cervical bundle of the vagus nerve, referred to as transcutaneous auricular vagus nerve stimulation(VNS) and transcutaneous cervical VNS, respectively. In order to advance the field in a systematic manner, studies using these technologies need to adequately report sufficient methodological detail to enable comparison of results between studies, replication of studies, as well as enhancing study participant safety. We systematically reviewed the existing tVNS literature to evaluate current reporting practices. Based on this review, and consensus among participating authors, we propose a set of minimal reporting items to guide future tVNS studies. The suggested items address specific technical aspects of the device and stimulation parameters. We also cover general recommendations including inclusion and exclusion criteria for participants, outcome parameters and the detailed reporting of side effects. Furthermore, we review strategies used to identify the optimal stimulation parameters for a given research setting and summarize ongoing developments in animal research with potential implications for the application of tVNS in humans. Finally, we discuss the potential of tVNS in future research as well as the associated challenges across several disciplines in research and clinical practice. KW - transcutaneous vagus nerve stimulation KW - minimum reporting standards KW - guidelines & recommendations KW - transcutaneous auricular vagus nerve stimulation KW - transcutaneous cervical vagus nerve stimulation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-234346 SN - 1662-5161 VL - 14 ER - TY - RPRT A1 - Imgrund, Florian A1 - Janiesch, Christian A1 - Fischer, Marcus A1 - Winkelmann, Axel T1 - Success Factors for Process Modeling Projects: An Empirical Analysis N2 - Business process modeling is one of the most crucial activities of BPM and enables companies to realize various benefits in terms of communication, coordination, and distribution of organizational knowledge. While numerous techniques support process modeling, companies frequently face challenges when adopting BPM to their organization. Existing techniques are often modified or replaced by self-developed approaches so that companies cannot fully exploit the benefits of standardization. To explore the current state of the art in process modeling as well as emerging challenges and potential success factors, we conducted a large-scale quantitative study. We received feedback from 314 respondents who completed the survey between July 2 and September 6, 2017. Thus, our study provides in-depth insights into the status quo of process modeling and allows us to provide three major contributions. Our study suggests that the success of process modeling projects depends on four major factors, which we extracted using exploratory factor analysis. We found employee education, management involvement, usability of project results, and the companies’ degree of process orientation to be decisive for the success of a process modeling project. We conclude this report with a summary of results and present potential avenues for future research. We thereby emphasize the need of quantitative and qualitative insights to process modeling in practice is needed to strengthen the quality of process modeling in practice and to be able to react quickly to changing conditions, attitudes, and possible constraints that practitioners face. T3 - Working Paper Series of the Institute of Business Management - 6 KW - Business Process Modeling KW - Business Process Management KW - Success Factors KW - Empirical Analysis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-179246 ER - TY - JOUR A1 - Seibold, Sebastian A1 - Hothorn, Torsten A1 - Gossner, Martin M. A1 - Simons, Nadja K. A1 - Blüthgen, Nico A1 - Müller, Jörg A1 - Ambarlı, Didem A1 - Ammer, Christian A1 - Bauhus, Jürgen A1 - Fischer, Markus A1 - Habel, Jan C. A1 - Penone, Caterina A1 - Schall, Peter A1 - Schulze, Ernst‐Detlef A1 - Weisser, Wolfgang W. T1 - Insights from regional and short‐term biodiversity monitoring datasets are valuable: a reply to Daskalova et al. 2021 JF - Insect Conservation and Diversity N2 - Reports of major losses in insect biodiversity have stimulated an increasing interest in temporal population changes. Existing datasets are often limited to a small number of study sites, few points in time, a narrow range of land‐use intensities and only some taxonomic groups, or they lack standardised sampling. While new monitoring programs have been initiated, they still cover rather short time periods. Daskalova et al. 2021 (Insect Conservation and Diversity, 14, 1‐18) argue that temporal trends of insect populations derived from short time series are biased towards extreme trends, while their own analysis of an assembly of shorter‐ and longer‐term time series does not support an overall insect decline. With respect to the results of Seibold et al. 2019 (Nature, 574, 671–674) based on a 10‐year multi‐site time series, they claim that the analysis suffers from not accounting for temporal pseudoreplication. Here, we explain why the criticism of missing statistical rigour in the analysis of Seibold et al. (2019) is not warranted. Models that include ‘year’ as random effect, as suggested by Daskalova et al. (2021), fail to detect non‐linear trends and assume that consecutive years are independent samples which is questionable for insect time‐series data. We agree with Daskalova et al. (2021) that the assembly and analysis of larger datasets is urgently needed, but it will take time until such datasets are available. Thus, short‐term datasets are highly valuable, should be extended and analysed continually to provide a more detailed understanding of insect population changes under the influence of global change, and to trigger immediate conservation actions. KW - Arthropod KW - biodiversity KW - insect decline KW - land use KW - time series Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-228309 VL - 14 IS - 1 SP - 144 EP - 148 ER -