TY - JOUR A1 - Omranian, Sara A1 - Nikoloski, Zoran A1 - Grimm, Dominik G. T1 - Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward BT - present state, challenges, and the way forward JF - Computational and structural biotechnology journal N2 - Physically interacting proteins form macromolecule complexes that drive diverse cellular processes. Advances in experimental techniques that capture interactions between proteins provide us with protein-protein interaction (PPI) networks from several model organisms. These datasets have enabled the prediction and other computational analyses of protein complexes. Here we provide a systematic review of the state-of-the-art algorithms for protein complex prediction from PPI networks proposed in the past two decades. The existing approaches that solve this problem are categorized into three groups, including: cluster-quality-based, node affinity-based, and network embedding-based approaches, and we compare and contrast the advantages and disadvantages. We further include a comparative analysis by computing the performance of eighteen methods based on twelve well-established performance measures on four widely used benchmark protein-protein interaction networks. Finally, the limitations and drawbacks of both, current data and approaches, along with the potential solutions in this field are discussed, with emphasis on the points that pave the way for future research efforts in this field. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/). KW - Protein Complex Prediction KW - Protein-Protein interaction network KW - Network KW - Clustering Algorithms KW - Network embedding Y1 - 2022 U6 - https://doi.org/10.1016/j.csbj.2022.05.049 SN - 2001-0370 VL - 20 SP - 2699 EP - 2712 PB - Research Network of Computational and Structural Biotechnology (RNCSB) CY - Gotenburg ER - TY - JOUR A1 - Heyde, Jürgen T1 - Daniel B. Schwartz, Ghetto: The History of a Word (Cambridge, MA: Harvard University Press, 2019), 288 p. JF - PaRDeS : Journal of the Association for Jewish Studies in Germany JF - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-537530 SN - 978-3-86956-520-0 SN - 1614-6492 SN - 1862-7684 IS - 27 SP - 151 EP - 154 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Talabardon, Susanne T1 - David Biale, David Assaf, Benjamin Brown, Uriel Gellman, Samuel Heilman, Moshe Rosman, Gadi Sagiv, Marcin Wodziński, Hasidism: A New History. With an Afterword by Arthur Green (Princeton: Princeton University Press, 2018), 875 p., $ 45. JF - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien = Transformative Translations in Jewish History and Culture Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-486164 SN - 978-3-86956-493-7 SN - 1614-6492 SN - 1862-7684 VL - 2020 IS - 26 SP - 149 EP - 152 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Schulz, Michael Karl T1 - David Sorkin, Jewish Emancipation: A History across Five Centuries (Princeton/Oxford: Princeton University Press, 2019), 528 p. JF - PaRDeS : Journal of the Association for Jewish Studies in Germany JF - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-538040 SN - 978-3-86956-520-0 SN - 1614-6492 SN - 1862-7684 IS - 27 SP - 170 EP - 173 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Ries, Rotraud T1 - Debra Kaplan, The Patrons and Their Poor: Jewish Community and Public Charity in Early Modern Germany (= Jewish Culture and Contexts), (Philadelphia: University of Pennsylvania Press, 2020), 239 p. JF - PaRDeS : Journal of the Association for Jewish Studies in Germany JF - PaRDeS : Zeitschrift der Vereinigung für Jüdische Studien Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-538012 SN - 978-3-86956-520-0 SN - 1614-6492 SN - 1862-7684 IS - 27 SP - 159 EP - 162 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Wong, Kevin A1 - Mason, Emily A1 - Brune, Sascha A1 - East, Madison A1 - Edmonds, Marie A1 - Zahirovic, Sabin T1 - Deep Carbon Cycling Over the Past 200 Million Years: A Review of Fluxes in Different Tectonic Settings JF - Frontiers in Earth Science KW - deep carbon cycle KW - carbonate assimilation KW - solid Earth degassing KW - plate reconstructions KW - carbon dioxide KW - subduction zone Y1 - 2019 U6 - https://doi.org/10.3389/feart.2019.00263 SN - 2296-6463 VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Petersen, Jens T1 - Die Klassiker lesen – vier Buchbesprechungen JF - Studien zur juristischen Ideengeschichte Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-604318 SN - 978-3-86956-543-9 SP - 161 EP - 176 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - JOUR A1 - Kleuser, Burkhard T1 - Divergent role of sphingosine 1-phosphate in liver health and disease JF - International journal of molecular sciences N2 - Two decades ago, sphingosine 1-phosphate (S1P) was discovered as a novel bioactive molecule that regulates a variety of cellular functions. The plethora of S1P-mediated effects is due to the fact that the sphingolipid not only modulates intracellular functions but also acts as a ligand of G protein-coupled receptors after secretion into the extracellular environment. In the plasma, S1P is found in high concentrations, modulating immune cell trafficking and vascular endothelial integrity. The liver is engaged in modulating the plasma S1P content, as it produces apolipoprotein M, which is a chaperone for the S1P transport. Moreover, the liver plays a substantial role in glucose and lipid homeostasis. A dysfunction of glucose and lipid metabolism is connected with the development of liver diseases such as hepatic insulin resistance, non-alcoholic fatty liver disease, or liver fibrosis. Recent studies indicate that S1P is involved in liver pathophysiology and contributes to the development of liver diseases. In this review, the current state of knowledge about S1P and its signaling in the liver is summarized with a specific focus on the dysregulation of S1P signaling in obesity-mediated liver diseases. Thus, the modulation of S1P signaling can be considered as a potential therapeutic target for the treatment of hepatic diseases. KW - sphingolipids KW - sphingosine kinase KW - fibrosis KW - non-alcoholic fatty liver disease KW - insulin resistance KW - liver fibrosis Y1 - 2018 U6 - https://doi.org/10.3390/ijms19030722 SN - 1422-0067 VL - 19 IS - 3 PB - MDPI CY - Basel ER - TY - JOUR A1 - Yarman, Aysu A1 - Jetzschmann, Katharina J. A1 - Neumann, Bettina A1 - Zhang, Xiaorong A1 - Wollenberger, Ulla A1 - Cordin, Aude A1 - Haupt, Karsten A1 - Scheller, Frieder W. T1 - Enzymes as Tools in MIP-Sensors JF - Chemosensors N2 - Molecularly imprinted polymers (MIPs) have the potential to complement antibodies in bioanalysis, are more stable under harsh conditions, and are potentially cheaper to produce. However, the affinity and especially the selectivity of MIPs are in general lower than those of their biological pendants. Enzymes are useful tools for the preparation of MIPs for both low and high-molecular weight targets: As a green alternative to the well-established methods of chemical polymerization, enzyme-initiated polymerization has been introduced and the removal of protein templates by proteases has been successfully applied. Furthermore, MIPs have been coupled with enzymes in order to enhance the analytical performance of biomimetic sensors: Enzymes have been used in MIP-sensors as tracers for the generation and amplification of the measuring signal. In addition, enzymatic pretreatment of an analyte can extend the analyte spectrum and eliminate interferences. KW - enzymatic MIP synthesis KW - template digestion KW - enzyme tracer KW - enzymatic analyte conversion KW - molecularly imprinted polymers Y1 - 2017 U6 - https://doi.org/10.3390/chemosensors5020011 SN - 2227-9040 VL - 5 PB - MDPI CY - Basel ER - TY - JOUR A1 - Lawrence, Mark A1 - Schäfer, Stefan A1 - Muri, Helene A1 - Scott, Vivian A1 - Oschlies, Andreas A1 - Vaughan, Naomi E. A1 - Boucher, Olivier A1 - Schmidt, Hauke A1 - Haywood, Jim A1 - Scheffran, Jürgen T1 - Evaluating climate geoengineering proposals in the context of the Paris Agreement temperature goals JF - Nature Communications N2 - Current mitigation efforts and existing future commitments are inadequate to accomplish the Paris Agreement temperature goals. In light of this, research and debate are intensifying on the possibilities of additionally employing proposed climate geoengineering technologies, either through atmospheric carbon dioxide removal or farther-reaching interventions altering the Earth’s radiative energy budget. Although research indicates that several techniques may eventually have the physical potential to contribute to limiting climate change, all are in early stages of development, involve substantial uncertainties and risks, and raise ethical and governance dilemmas. Based on present knowledge, climate geoengineering techniques cannot be relied on to significantly contribute to meeting the Paris Agreement temperature goals. KW - Atmospheric chemistry KW - Atmospheric dynamics KW - Atmospheric science KW - Climate change KW - Environmental impact Y1 - 2018 U6 - https://doi.org/10.1038/s41467-018-05938-3 SN - 2041-1723 VL - 9 PB - Nature Publ. Group CY - London ER -