@article{HubervanderBurgvanderHooftetal.2021, author = {Huber, Florian and van der Burg, Sven and van der Hooft, Justin J. J. and Ridder, Lars}, title = {MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra}, series = {Journal of Cheminformatics}, volume = {13}, journal = {Journal of Cheminformatics}, number = {1}, publisher = {Cold Spring Harbor Laboratory}, issn = {1758-2946}, doi = {10.1186/s13321-021-00558-4}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34847}, pages = {84}, year = {2021}, abstract = {Mass spectrometry data is one of the key sources of information in many workflows in medicine and across the life sciences. Mass fragmentation spectra are generally considered to be characteristic signatures of the chemical compound they originate from, yet the chemical structure itself usually cannot be easily deduced from the spectrum. Often, spectral similarity measures are used as a proxy for structural similarity but this approach is strongly limited by a generally poor correlation between both metrics. Here, we propose MS2DeepScore: a novel Siamese neural network to predict the structural similarity between two chemical structures solely based on their MS/MS fragmentation spectra. Using a cleaned dataset of > 100,000 mass spectra of about 15,000 unique known compounds, we trained MS2DeepScore to predict structural similarity scores for spectrum pairs with high accuracy. In addition, sampling different model varieties through Monte-Carlo Dropout is used to further improve the predictions and assess the model's prediction uncertainty. On 3600 spectra of 500 unseen compounds, MS2DeepScore is able to identify highly-reliable structural matches and to predict Tanimoto scores for pairs of molecules based on their fragment spectra with a root mean squared error of about 0.15. Furthermore, the prediction uncertainty estimate can be used to select a subset of predictions with a root mean squared error of about 0.1. Furthermore, we demonstrate that MS2DeepScore outperforms classical spectral similarity measures in retrieving chemically related compound pairs from large mass spectral datasets, thereby illustrating its potential for spectral library matching. Finally, MS2DeepScore can also be used to create chemically meaningful mass spectral embeddings that could be used to cluster large numbers of spectra. Added to the recently introduced unsupervised Spec2Vec metric, we believe that machine learning-supported mass spectral similarity measures have great potential for a range of metabolomics data processing pipelines.}, language = {en} } @article{HuberVerhoevenMeijeretal.2020, author = {Huber, Florian and Verhoeven, Stefan and Meijer, Christiaan and Spreeuw, Hanno and Castilla, Efra{\´i}n and Geng, Cunliang and van der Hooft, Justin J. J. and Rogers, Simon and Belloum, Adam and Diblen, Faruk and Spaaks, Jurriaan H.}, title = {matchms - processing and similarity evaluation of mass spectrometry data}, series = {Journal of Open Source Software}, volume = {5}, journal = {Journal of Open Source Software}, number = {52}, publisher = {Cold Spring Harbor Laboratory}, issn = {2475-9066}, doi = {10.21105/joss.02411}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34856}, pages = {2411}, year = {2020}, language = {en} } @article{PreciadoLopezHuberGrigorievetal.2014, author = {Preciado L{\´o}pez, Magdalena and Huber, Florian and Grigoriev, Ilya and Steinmetz, Michel O. and Akhmanova, Anna and Dogterom, Marileen and Koenderink, Gijsje H.}, title = {In vitro reconstitution of dynamic microtubules interacting with actin filament networks}, series = {Methods in Enzymology}, volume = {540}, journal = {Methods in Enzymology}, publisher = {Elsevier}, issn = {1557-7988}, doi = {10.1016/B978-0-12-397924-7.00017-0}, pages = {301 -- 320}, year = {2014}, language = {en} } @article{PreciadoLopezHuberGrigorievetal.2014, author = {Preciado L{\´o}pez, Magdalena and Huber, Florian and Grigoriev, Ilya and Steinmetz, Michel O. and Akhmanova, Anna and Koenderink, Gijsje H. and Dogterom, Marileen}, title = {Actin-microtubule coordination at growing microtubule ends}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, publisher = {Springer Nature}, issn = {2041-1723}, doi = {10.1038/ncomms5778}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34878}, pages = {4778}, year = {2014}, abstract = {To power dynamic processes in cells, the actin and microtubule cytoskeletons organize into complex structures. Although it is known that cytoskeletal coordination is vital for cell function, the mechanisms by which cross-linking proteins coordinate actin and microtubule activities remain poorly understood. In particular, it is unknown how the distinct mechanical properties of different actin architectures modulate the outcome of actin-microtubule interactions. To address this question, we engineered the protein TipAct, which links growing microtubule ends via end-binding proteins to actin filaments. We show that growing microtubules can be captured and guided by stiff actin bundles, leading to global actin-microtubule alignment. Conversely, growing microtubule ends can transport, stretch and bundle individual actin filaments, thereby globally defining actin filament organization. Our results provide a physical basis to understand actin-microtubule cross-talk, and reveal that a simple cross-linker can enable a mechanical feedback between actin and microtubule organization that is relevant to diverse biological contexts.}, language = {en} } @article{SiccardiAdamatzkyTuszyńskietal.2020, author = {Siccardi, Stefano and Adamatzky, Andrew and Tuszyński, Jack and Huber, Florian and Schnauß, J{\"o}rg}, title = {Actin networks voltage circuits}, series = {Physical Review E}, volume = {101}, journal = {Physical Review E}, number = {5-1}, publisher = {American Physical Society (APS)}, issn = {2470-0053}, doi = {10.1103/PhysRevE.101.052314}, year = {2020}, language = {en} } @article{SmithGentryStuhrmannetal.2009, author = {Smith, David and Gentry, Brian and Stuhrmann, Bj{\"o}rn and Huber, Florian and Strehle, D. A.N. and Brunner, Claudia and Koch, Daniel and Steinbeck, Matthias and Betz, Timo and K{\"a}s, Josef A.}, title = {The cytoskeleton: An active polymer-based scaffold}, series = {Biophysical Reviews and Letters}, volume = {04}, journal = {Biophysical Reviews and Letters}, issn = {1793-7035}, doi = {10.1142/S1793048009000983}, pages = {179 -- 208}, year = {2009}, language = {en} } @article{StuhrmannHuberKaes2011, author = {Stuhrmann, Bj{\"o}rn and Huber, Florian and K{\"a}s, Josef}, title = {Robust organizational principles of protrusive biopolymer networks in migrating living cells}, series = {Plos One}, volume = {6}, journal = {Plos One}, number = {1}, publisher = {Public Library of Science (PLoS)}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014471}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34901}, year = {2011}, abstract = {Cell migration is associated with the dynamic protrusion of a thin actin-based cytoskeletal extension at the cell front, which has been shown to consist of two different substructures, the leading lamellipodium and the subsequent lamellum. While the formation of the lamellipodium is increasingly well understood, organizational principles underlying the emergence of the lamellum are just beginning to be unraveled. We report here on a 1D mathematical model which describes the reaction-diffusion processes of a polarized actin network in steady state, and reproduces essential characteristics of the lamellipodium-lamellum system. We observe a steep gradient in filament lengths at the protruding edge, a local depolymerization maximum a few microns behind the edge, as well as a differential dominance of the network destabilizer ADF/cofilin and the stabilizer tropomyosin. We identify simple and robust organizational principles giving rise to the derived network characteristics, uncoupled from the specifics of any molecular implementation, and thus plausibly valid across cell types. An analysis of network length dependence on physico-chemical system parameters implies that to limit array treadmilling to cellular dimensions, network growth has to be truncated by mechanisms other than aging-induced depolymerization, e.g., by myosin-associated network dissociation at the transition to the cell body. Our work contributes to the analytical understanding of the cytoskeletal extension's bisection into lamellipodium and lamellum and sheds light on how cells organize their molecular machinery to achieve motility.}, language = {en} } @article{vonBergSteffensWeinzierletal.2021, author = {von Berg, Markus and Steffens, Jochen and Weinzierl, Stefan and M{\"u}llensiefen, Daniel}, title = {Assessing room acoustic listening expertise}, series = {Journal of the Acoustical Society of America}, volume = {150}, journal = {Journal of the Acoustical Society of America}, number = {4}, publisher = {Acoustical Society of America}, doi = {10.1121/10.0006574}, pages = {2539 -- 2548}, year = {2021}, abstract = {Musicians and music professionals are often considered to be expert listeners for listening tests on room acoustics. However, these tests often target acoustic parameters other than those typically relevant in music such as pitch, rhythm, amplitude, or timbre. To assess the expertise in perceiving and understanding room acoustical phenomena, a listening test battery was constructed to measure the perceptual sensitivity and cognitive abilities in the identification of rooms with different reverberation times and different spectral envelopes. Performance in these tests was related to data from the Goldsmiths Musical Sophistication Index, self-reported previous experience in music recording and acoustics, and academic knowledge on acoustics. The data from 102 participants show that sensory and cognitive abilities are both correlated significantly with musical training, analytic listening skills, recording experience, and academic knowledge on acoustics, whereas general interest in and engagement with music do not show any significant correlations. The regression models, using only significantly correlated criteria of musicality and professional expertise, explain only small to moderate amounts (11\%-28\%) of the variance in the "room acoustic listening expertise" across the different tasks of the battery. Thus, the results suggest that the traditional criteria for selecting expert listeners in room acoustics are only weak predictors of their actual performances.}, language = {en} } @misc{Lambert2021, author = {Lambert, Jens}, title = {Podcast: Einf{\"u}hrung in Oracle SQL Command Line (SQLcl)}, editor = {Rakow, Thomas C.}, address = {D{\"u}sseldorf}, organization = {Hochschule D{\"u}sseldorf}, doi = {10.20385/opus4-3461}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34619}, year = {2021}, abstract = {Als Einf{\"u}hrung in die Benutzung der Software SQL Developer Command Line (SQLcl) von Oracle werden folgende Aktionen erkl{\"a}rt: Anmelden, Ausgeben von Tabellen und ihren Metadaten, Verwenden der Befehlshistorie, Formatieren der Ausgabe, Speichern, Bearbeiten und Wiederverwenden von Befehlen sowie das Anlegen von Logdateien. Vorausgesetzt werden geringe Vorkenntnisse von relationalen Datenbankmanagementsystemen mit SQL. Das Video wurde im Rahmen des Projektes EILD.nrw entwickelt, gef{\"o}rdert durch das Ministerium f{\"u}r Kultur und Wissenschaft gemeinsam mit der Digitalen Hochschule NRW (DH.NRW) in der F{\"o}rderlinie „OERContent.nrw" (Open Education Resources).}, language = {de} } @misc{OPUS4-3462, title = {801 - Zweite Satzung zur {\"A}nderung der Pr{\"u}fungsordnung f{\"u}r den Bachelorstudiengang Medieninformatik an der Hochschule D{\"u}sseldorf vom 28.10.2021}, address = {D{\"u}sseldorf}, organization = {Hochschule D{\"u}sseldorf}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34624}, pages = {2}, year = {2021}, abstract = {Aufgrund der \S\S 2 Abs. 4, 64 Abs. 1 des Gesetzes {\"u}ber die Hochschulen des Landes Nordrhein-Westfalen (Hochschulgesetz - HG) vom 16.09.2014 (GV. NRW. S. 547) in der aktuell g{\"u}ltigen Fassung hat die Hochschule D{\"u}sseldorf die folgende Ordnung als Satzung erlassen.}, language = {de} }