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ProtSTonKGs: A Sophisticated Transformer Trained on Protein Sequences, Text, and Knowledge Graphs
(2022)
While most approaches individually exploit unstructured data from the biomedical literature or structured data from biomedical knowledge graphs, their union can better exploit the advantages of such approaches, ultimately improving representations of biology. Using multimodal transformers for such purposes can improve performance on context dependent classication tasks, as demonstrated by our previous model, the Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs (STonKGs). In this work, we introduce ProtSTonKGs, a transformer aimed at learning all-encompassing representations of protein-protein interactions. ProtSTonKGs presents an extension to our previous work by adding textual protein descriptions and amino acid sequences (i.e., structural information) to the text- and knowledge graph-based input sequence used in STonKGs. We benchmark ProtSTonKGs against STonKGs, resulting in improved F1 scores by up to 0.066 (i.e., from 0.204 to 0.270) in several tasks such as predicting protein interactions in several contexts. Our work demonstrates how multimodal transformers can be used to integrate heterogeneous sources of information, paving the foundation for future approaches that use multiple modalities for biomedical applications.
In this paper, modeling of piston and generic type gas compressors for a globally convergent algorithm for solving stationary gas transport problems is carried out. A theoretical analysis of the simulation stability, its practical implementation and verification of convergence on a realistic gas network have been carried out. The relevance of the paper for the topics of the conference is defined by a significance of gas transport networks as an advanced application of simulation and modeling, including the development of novel mathematical and numerical algorithms and methods.
In this paper, an analysis of the error ellipsoid in the space of solutions of stationary gas transport problems is carried out. For this purpose, a Principal Component Analysis of the solution set has been performed. The presence of unstable directions is shown associated with the marginal fulfillment of the resistivity conditions for the equations of compressors and other control elements in gas networks. Practically, the instabilities occur when multiple compressors or regulators try to control pressures or flows in the same part of the network. Such problems can occur, in particular, when the compressors or regulators reach their working limits. Possible ways of resolving instabilities are considered.
The electricity grid of the future will be built on renewable energy sources, which are highly variable and dependent on atmospheric conditions. In power grids with an increasingly high penetration of solar photovoltaics (PV), an accurate knowledge of the incoming solar irradiance is indispensable for grid operation and planning, and reliable irradiance forecasts are thus invaluable for energy system operators. In order to better characterise shortwave solar radiation in time and space, data from PV systems themselves can be used, since the measured power provides information about both irradiance and the optical properties of the atmosphere, in particular the cloud optical depth (COD). Indeed, in the European context with highly variable cloud cover, the cloud fraction and COD are important parameters in determining the irradiance, whereas aerosol effects are only of secondary importance.
Thermo-chemical conversion of cucumber peel waste for biobased energy and chemical production
(2022)
Im Zuge der Migrationsbewegung in den Jahren 2015 und 2016 hat die menschenwürdige Unterbringung von geflüchteten Menschen in Kommunen in Deutschland an Aufmerksamkeit gewonnen. Der Anstieg der Asylbewerber:innen in den Kommunen sowie die Bundesinitiative „Schutz von geflüchteten Menschen in Flüchtlingsunterkünften“ haben Veränderungen im Hinblick auf Schutzstandards in der kommunalen Unterbringung geflüchteter Menschen hervorgerufen. Der Artikel erklärt diese Veränderungen mittels einer akteurszentrierten organisationssoziologischen Herangehensweise. Grundlage sind empirische Forschungsergebnisse des Projektes „Organisational Perspectives on Human Security Standards for Refugees in Germany“ aus zwei deutschen Kommunen.
The cooperation between researchers and practitioners during the different stages of the research process is promoted as it can be of benefit to both society and research supporting processes of ‘transformation’. While acknowledging the important potential of research–practice–collaborations (RPCs), this paper reflects on RPCs from a political-economic perspective to also address potential unintended adverse effects on knowledge generation due to divergent interests, incomplete information or the unequal distribution of resources. Asymmetries between actors may induce distorted and biased knowledge and even help produce or exacerbate existing inequalities. Potential merits and limitations of RPCs, therefore, need to be gauged. Taking RPCs seriously requires paying attention to these possible tensions—both in general and with respect to international development research, in particular: On the one hand, there are attempts to contribute to societal change and ethical concerns of equity at the heart of international development research, and on the other hand, there is the relative risk of encountering asymmetries more likely.
Cathepsin K (CatK) is a target for the treatment of osteoporosis, arthritis, and bone metastasis. Peptidomimetics with a cyanohydrazide warhead represent a new class of highly potent CatK inhibitors; however, their binding mechanism is unknown. We investigated two model cyanohydrazide inhibitors with differently positioned warheads: an azadipeptide nitrile Gü1303 and a 3-cyano-3-aza-β-amino acid Gü2602. Crystal structures of their covalent complexes were determined with mature CatK as well as a zymogen-like activation intermediate of CatK. Binding mode analysis, together with quantum chemical calculations, revealed that the extraordinary picomolar potency of Gü2602 is entropically favoured by its conformational flexibility at the nonprimed-primed subsites boundary. Furthermore, we demonstrated by live cell imaging that cyanohydrazides effectively target mature CatK in osteosarcoma cells. Cyanohydrazides also suppressed the maturation of CatK by inhibiting the autoactivation of the CatK zymogen. Our results provide structural insights for the rational design of cyanohydrazide inhibitors of CatK as potential drugs.
Cathepsin K (CatK) is a target for the treatment of osteoporosis, arthritis, and bone metastasis. Peptidomimetics with a cyanohydrazide warhead represent a new class of highly potent CatK inhibitors; however, their binding mechanism is unknown. We investigated two model cyanohydrazide inhibitors with differently positioned warheads: an azadipeptide nitrile Gü1303 and a 3-cyano-3-aza-β-amino acid Gü2602. Crystal structures of their covalent complexes were determined with mature CatK as well as a zymogen-like activation intermediate of CatK. Binding mode analysis, together with quantum chemical calculations, revealed that the extraordinary picomolar potency of Gü2602 is entropically favoured by its conformational flexibility at the nonprimed-primed subsites boundary. Furthermore, we demonstrated by live cell imaging that cyanohydrazides effectively target mature CatK in osteosarcoma cells. Cyanohydrazides also suppressed the maturation of CatK by inhibiting the autoactivation of the CatK zymogen. Our results provide structural insights for the rational design of cyanohydrazide inhibitors of CatK as potential drugs.
Taste is a complex phenomenon that depends on the individual experience and is a matter of collective negotiation and mediation. On the contrary, it is uncommon to include taste and its many facets in everyday design, particularly online shopping for fresh food products. To realize this unused potential, we conducted two Co-Design workshops. Based on the participants’ results in the workshops, we prototyped and evaluated a click-dummy smart-phone app to explore consumers’ needs for digital taste depiction. We found that emphasizing the natural qualities of food products, external reviews, and personalizing features lead to a reflection on the individual taste experience. The self-reflection through our design enables consumers to develop their taste competencies and thus strengthen their autonomy in decision-making. Ultimately, exploring taste as a social experience adds to a broader understanding of taste beyond a sensory phenomenon.
Virtual exchange
(2022)
Hydrophilic surface-enhanced Raman spectroscopy (SERS) substrates were prepared by a combination of TiO2-coatings of aluminium plates through a direct titanium tetraisopropoxide (TTIP) coating and drop coated by synthesised gold nanoparticles (AuNPs). Differences between the wettability of the untreated substrates, the slowly dried Ti(OH)4 substrates and calcinated as well as plasma treated TiO2 substrates were analysed by water contact angle (WCA) measurements. The hydrophilic behaviour of the developed substrates helped to improve the distribution of the AuNPs, which reflects in overall higher lateral SERS enhancement. Surface enhancement of the substrates was tested with target molecule rhodamine 6G (R6G) and a fibre-coupled 638 nm Raman spectrometer. Additionally, the morphology of the substrates was characterised using scanning electron microscopy (SEM) and Raman microscopy. The studies showed a reduced influence of the coffee ring effect on the particle distribution, resulting in a more broadly distributed edge region, which increased the spatial reproducibility of the measured SERS signal in the surface-enhanced Raman mapping measurements on mm scale.
Im Rahmen des 55. Jour Fixe FDM der Landesinitiative fdm.nrw gaben die Mitglieder der Förderlinie FDMScouts.nrw einen Einblick in ihre Zusammenarbeit und stellten die Ergebnisse ihrer bisherigen Arbeit vor. Ziel der Förderlinie ist es, bedarfsgerechte Möglichkeiten zu schaffen, das Thema FDM sowohl strategisch als auch operativ nachhaltig an Hochschulen für angewandte Wissenschaften in NRW zu verankern. 10 Hochschulen in 5 Verbünden arbeiten seit 2020 gemeinsam an Diensten und Angeboten. Koordiniert werden die Aktivitäten von der Landesinitiative fdm.nrw.
Die Originalpräsentation ist über Conceptboard einsehbar: https://app.conceptboard.com/board/c87t-okqh-6utn-74xg-n182
Die Autor*innen sind alphabetisch sortiert und teilen sich die Erstautorschaft.
Forschungsdatenmanagement (FDM) nimmt im Forschungsalltag der Hochschulen für angewandte Wissenschaften (HAW) eine zunehmende größere Rolle ein und stellt an viele Forschende bisher unbekannte Anforderungen. So gilt es ein FAIRes und nachhaltiges Datenmanagement im Sinne des Kodex „Leitlinien zur Sicherung guter wissenschaftlicher Praxis“ der DFG zu betreiben – für sich selbst, für die eigene Forschungsgruppe und für die Forschungsgemeinschaft. In dieser Veranstaltung anlässlich des Tags der Forschungsdaten in NRW am 15.11.2022 wurden die wesentlichen Grundzüge des Forschungsdatenmanagements anhand des Forschungsdatenlebenszyklus nähergebracht und Praxisbeispiele und nützliche Links vorgestellt.
Im Rahmen der Förderlinie „FDMScouts.nrw“ arbeiten zehn Hochschulen kooperativ an Strukturen und Prozessen für einen nachhaltigen Aufbau des Forschungsdatenmanagements an den betreffenden Hochschulen für angewandte Wissenschaften und Fachhochschulen.
Hierbei ist ausschlaggebend, das Forschungsdatenmanagement zielgerichtet und bedarfsorientiert zu konzipieren und sowohl strategisch als auch operativ zu verankern. Ausgangspunkt dieser Bemühungen bildet daher eine Bedarfserhebung, die bestehende Datenworkflows, Vorwissen und Bedarfe der Forschenden zum FDM erfassen soll. In Abstimmung innerhalb der Förderlinie „FDMScouts.nrw“ wurde der vorliegende Umfragebogen erstellt.
Der Erhebungsbogen basiert auf der Vorlage „Fragenkatalog zur Bedarfserhebung zur Archivierung und Bereitstellung von Forschungsdaten an den rheinland-pfälzischen Universitäten und Hochschulen für angewandte Wissenschaften“ (Lemaire et al. 2022). Darüber hinaus wurden Aspekte aus „UNEKE: Forschungsdatenspeicherung - Praxis und Bedarfe: Online-Survey 2019“ (Brenger et al. 2019) und aus „Anforderungserhebung bei den brandenburgischen Hochschulen“ (Radtke et al. 2020) entnommen. Als weitere Quelle diente der „Interviewleitfaden zur Bestands- und Bedarfserhebung im Forschungsdatenmanagement (FDM) - Projekt FDM-TUDO“ der TU Dortmund (Kletke et al. 2022).
P30 - Das Elektrospinnen von halbleitenden Zinndioxidfasern für die Detektion von Wasserstoff
(2022)
Das Ziel dieser Arbeit ist die Entwicklung von dünnen keramischen Fasern als halbleitendes Sensormaterial zum Nachweis von Wasserstoff, möglichst bei Zimmertemperatur. Die elektrische Leitfähigkeit halbleitender Metalloxide ändert sich durch die Einwirkung von oxidierenden und reduzierenden Gasen auf die Oberfläche des Metalloxids. Dieser Effekt kann zur Messung der Gaskonzentration genutzt werden. Die Reaktion von Zinn(IV)-oxid mit Wasserstoff basiert auf der Reduktion des Zinn(IV)-oxids zum Zinn, wobei die Elektronen des Zinn(IV)-oxids im metallischen Zinn verbleiben und dort im nicht gebundenen Zustand zu einer Leitfähigkeitserhöhung beitragen. Die Reaktion des Wasserstoffes kann sowohl mit den Sauerstoffatomen des Oxids als auch mit adsorbierten Sauerstoffatomen an der Oxidoberfläche stattfinden.[ 6] Da die Reaktionen an der Oberfläche des Oxids stattfinden, sollten Sensoren mit einer großen Oberfläche im Vergleich zu metalloxidischen Bulkmaterialien eine höhere Empfindlichkeit aufweisen. [3] Die Verwendung von Fasern anstelle von Dünn- oder Dickschichten führt dabei zu einer besseren Sensitivität gegenüber Gasen.
Vection underwater
(2022)