TY - JOUR A1 - Bulla, Mattia A1 - Coughlin, Michael W. A1 - Dhawan, Suhail A1 - Dietrich, Tim T1 - Multi-messenger constraints on the Hubble constant through combination of gravitational waves, gamma-ray bursts and kilonovae from neutron star mergers JF - Universe : open access journal N2 - The simultaneous detection of gravitational waves and light from the binary neutron star merger GW170817 led to independent measurements of distance and redshift, providing a direct estimate of the Hubble constant H-0 that does not rely on a cosmic distance ladder, nor assumes a specific cosmological model. By using gravitational waves as "standard sirens", this approach holds promise to arbitrate the existing tension between the H-0 value inferred from the cosmic microwave background and those obtained from local measurements. However, the known degeneracy in the gravitational-wave analysis between distance and inclination of the source led to a H-0 value from GW170817 that was not precise enough to resolve the existing tension. In this review, we summarize recent works exploiting the viewing-angle dependence of the electromagnetic signal, namely the associated short gamma-ray burst and kilonova, to constrain the system inclination and improve on H-0. We outline the key ingredients of the different methods, summarize the results obtained in the aftermath of GW170817 and discuss the possible systematics introduced by each of these methods. KW - gravitational waves KW - stars: neutron KW - stars: binaries KW - cosmology: cosmological parameters KW - cosmology: distance scale KW - cosmology: cosmic background radiation Y1 - 2022 U6 - https://doi.org/10.3390/universe8050289 SN - 2218-1997 VL - 8 IS - 5 PB - MDPI CY - Basel ER - 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 - Kühne, Katharina A1 - Gianelli, Claudia T1 - Is Embodied Cognition Bilingual? BT - current evidence and perspectives of the embodied cognition approach to bilingual language processing JF - Frontiers in psychology N2 - Accumulating behavioral and neurophysiological evidence supports the idea of language being grounded in sensorimotor processes, with indications of a functional role of motor, sensory and emotional systems in processing both concrete and abstract linguistic concepts. However, most of the available studies focused on native language speakers (L1), with only a limited number of investigations testing embodied language processing in the case of a second language (L2). In this paper we review the available evidence on embodied effects in L2 and discuss their possible integration into existing models of linguistic processing in L1 and L2. Finally, we discuss possible avenues for future research towards an integrated model of L1 and L2 sensorimotor and emotional grounding. KW - embodied language KW - grounding KW - sensorimotor KW - native language KW - second language Y1 - 2019 U6 - https://doi.org/10.3389/fpsyg.2019.00108 SN - 1664-1078 VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Basler, Georg A1 - Fernie, Alisdair R. A1 - Nikoloski, Zoran T1 - Advances in metabolic flux analysis toward genome-scale profiling of higher organisms JF - Bioscience reports : communications and reviews in molecular and cellular biology N2 - Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies. Y1 - 2018 U6 - https://doi.org/10.1042/BSR20170224 SN - 0144-8463 SN - 1573-4935 VL - 38 PB - Portland Press (London) CY - London ER - TY - JOUR A1 - Miklashevsky, Alex A1 - Kulkova, Elena A1 - Michirev, Alexej A1 - Jeglinski-Mende, Melinda A. A1 - Bertonatti, Matias T1 - Book review on: Raab, Markus: Judgment, decision-making, and embodied choices. - London ; San Diego ; Cambridge, MA ; Oxford: Academic Press, 2020. - xv, 155 pages. - ISBN: 978-0-12-823523-2 JF - Frontiers in psychology KW - embodied cognition KW - decision making KW - embodied choice KW - book review KW - mind-body Y1 - 2021 U6 - https://doi.org/10.3389/fpsyg.2021.665728 SN - 1664-1078 VL - 12 PB - Frontiers Research Foundation CY - Lausanne ER -