Publishing Data [Workshop]

Context: This short workshop was held on September 05 2023 in the context of the 115th Annual meeting of the German Zoological Society (DZG) in Kassel as part of the satellite workshop "Unlocking the rhythms of life with multiscale clocks", organized by the research training group "multiscale clocks" (https://www.uni-kassel.de/forschung/multiscale-clocks/welcome). Description: This short workshop specifically considers three questions that were raised in the preceding workshop part. During the working time with data and data visualizations, the participants were asked to reflect on the following: „Would you know how to obtain the underlying data?“, „Are you allowed to do with the data what you want?“, „What data/info would you require to check your hypothesis?“. The workshop consequently revolves around data publication. Designed to give a general overview, it covers access, locations and usage rights of published data from a user perspective; as a last part, the generation of reusable data is highlighted from the creator's perspective. Covered topics are open access requirements and colors; publication as supplement, in data journals, or in repositories; copyright and creative commons; research data management, life cycle, and the FAIR principles. The meaning of the FAIR principles was explored with the help of the FAIR Card Deck (unpubl.). Learning Goals: Be aware of research data management topics around data publication Understand the importance of labelling and documentation Know the FAIR principles Duration: 60 min Target Audience: Researchers (Students, PhD candidates, PostDocs) Anyone interested Prerequisites: none (participation in the preceding workshop was expected, but not absolutely necessary) Tools: For the presenter: FAIR Card Deck Mentimeter set up as "Open ended" statement collection for the take home messages from participants Upload Content: Itemized Upload Content File Description 2023-08-30_DZG-Clocks-DataPublication.key Slide deck in editable .key format 2023-08-30_DZG-Clocks-DataPublication.pptx Slide deck in editable .pptx format 2023-08-30_DZG-Clocks-DataPublication.pdf Slide deck as .pdf 2023-08-30_DataPubl_Script.xlsx Presenter's script in editable .xlsx format 2023-08-30_DataPubl_Script.pdf Presenter's script as .pdf Notes: Three FAIR Card Decks were used, with only the cards 9-5 from each deck

Sądowa kontrola zintegrowanych złożonych postępowań administracyjnych – monizm czy dualizm ochrony praw jednostki?

The article analyses and evaluates legal standards concerning administrative legal remedies in administrative matters dealt with in composite proceedings, i.e. proceedings in which Member State administrative bodies and the EU administration cooperate. The issue of judicial control in such procedures is particularly important from the point of view of the implementation of the principle of effective judicial protection expressed in Article 47 of the Charter of Fundamental Rights. The issue of an adequate system of legal remedies – monistic (based solely on national or EU remedies) or dualistic (assuming coexistence of national and EU remedies in cases of a given type) one – raises particular concerns. Considerations in this respect are based on the doctrinal concept of composite proceedings as a specific group of proceedings integrated into the EU law, as well as the current case law of the Court of Justice of the European Union. The conclusion presents de lege lata and de lege ferenda postulates to ensure effective judicial protection in this type of proceedings.Przedmiotem artykułu jest analiza i ocena standardów prawnych dotyczących środków zaskarżenia w sprawach administracyjnych rozpatrywanych w postępowaniach złożonych, tj. w postępowaniach, w których organy administracji państw członkowskich i administracja unijna współpracują ze sobą. Problematyka kontroli sądowej w tego typu procedurach jest szczególnie istotna z punktu widzenia realizacji wyrażonej w art. 47 Karty Praw Podstawowych zasady efektywnej ochrony sądowej. Wątpliwości budzi zwłaszcza kwestia adekwatnego systemu środków zaskarżenia: monistycznego (opartego wyłącznie na krajowych lub unijnych środkach zaskarżenia) bądź dualistycznego (zakładającego współistnienie w sprawach danego rodzaju środków krajowych i unijnych). Rozważania w tym przedmiocie oparto na doktrynalnej koncepcji postępowań złożonych jako specyficznej grupy postępowań zintegrowanych z prawem unijnym, a także na aktualnym orzecznictwie Trybunału Sprawiedliwości Unii Europejskiej. W zakończeniu przedstawiono postulaty de lege lata i de lege ferenda służące zapewnieniu efektywnej ochrony sądowej w tego typu postępowaniach

Protein-Coding Gene Repertoires : Annotation, Characterization, and Variability in Holometabola

Three previously unavailable prerequisites for gene repertoire analyses are established and used within this thesis: (1) a new tool (COGNATE, written in Perl) was developed and used that records all gene structure parameters instead of relying on summary metrics; (2) it was ensured that automatically generated gene models are suitable for gene structure analyses; and (3) a unique species sample was employed, which representatively covers a younger radiation and allows the comparison of holometabolous and hemimetabolous. Goal of this thesis was to describe and analyze the variation of gene structures within and between repertoires of the species-rich and diverse insects as a step towards understanding and explaining the mechanisms and driving factors of insect genome evolution. COGNATE was employed to evaluate the magnitude of changes in predicted structural properties of protein-coding genes due to manual curation by comparing annotated gene sets from seven insect species sequenced by the i5k initiative. The properties of automatically generated gene models and their manually curated replacements do not differ extensively, and major correlative trends regarding gene structures can be recovered from both sets. From these results I conclude that gene models yielded from unsupervised annotation procedures are a suitable data basis to characterize structural gene features of a whole repertoire. The gene repertoires of twelve Hymenoptera were structurally characterized using COGNATE. The two focal species, non-apocritan "symphytans", possess small genomes and gene repertoires, but a strikingly high GC content of more than 41 %. Striking features are highlighted and lead to the conclusion that structural analyses of gene structure parameters can be used to direct efforts of detailed investigations, for example focused on here discovered miniature introns of ants. The established analysis approach was used to assess the variability in protein-coding gene repertoires in a characterization of the repertoires of a large, unique species sample. Previous research suggested universal patterns of conservation within a gene repertoire in relation to others by which it could be partitioned: highly conserved genes, genes moderately conserved and unevenly distributed across taxa, and lineage- or species-specific genes. My results show that considerable differences exist in gene structural parameters between and within these gene sets beyond previously described patterns. This work provides a solid baseline of expectations on insect gene structure variation as well as manifold investigative leads prompting further research

UPHILL TRANSPORT INDUCED BY COUNTERFLOW

1. In a membrane transport system containing a mobile carrier with affinities for two substrates a concentration gradient with respect to one of the substrates under certain conditions is able to induce an "uphill" transport (against the concentration gradient) of the other. 2. In a kinetic treatment quantitative conditions for such a "flow-induced uphill transport" and some of its characteristics are derived. 3. Experimentally the uphill transport of labelled glucose induced by a concentration gradient for mannose or unlabelled glucose is demonstrated in the human red cell. 4. It is shown that the flow-induced uphill transport is a feature characteristic for mobile carrier systems only and is not to be expected in systems in which the substrate is bound to a fixed membrane component ("adsorption membrane"), although such a system may yield identical transport kinetics. Also with respect to Ussing's flux ratio the two systems are different, the adsorption membrane meeting Ussing's criterion, the carrier membrane not. 5. It is concluded that the transport system in the human red cells must contain a mobile carrier, identical for glucose and mannose

Optimal control of a buoyancy-driven liquid steel stirring modeled with single-phase Navier--Stokes equations

Gas stirring is an important process used in secondary metallurgy. It allows to homogenize the temperature and the chemical composition of the liquid steel and to remove inclusions which can be detrimental for the end-product quality. In this process, argon gas is injected from two nozzles at the bottom of the vessel and rises by buoyancy through the liquid steel thereby causing stirring, i.e., a mixing of the bath. The gas flow rates and the positions of the nozzles are two important control parameters in practice. A continuous optimization approach is pursued to find optimal values for these control variables. The effect of the gas appears as a volume force in the single-phase incompressible NavierStokes equations. Turbulence is modeled with the Smagorinsky Large Eddy Simulation (LES) model. An objective functional based on the vorticity is used to describe the mixing in the liquid bath. Optimized configurations are compared with a default one whose design is based on a setup from industrial practice

Optimal control of a buoyancy-driven liquid steel stirring modeled with single-phase Navier--Stokes equations

Gas stirring is an important process used in secondary metallurgy. It allows to homogenize the temperature and the chemical composition of the liquid steel and to remove inclusions which can be detrimental for the end-product quality. In this process, argon gas is injected from two nozzles at the bottom of the vessel and rises by buoyancy through the liquid steel thereby causing stirring, i.e., a mixing of the bath. The gas flow rates and the positions of the nozzles are two important control parameters in practice. A continuous optimization approach is pursued to find optimal values for these control variables. The effect of the gas appears as a volume force in the single-phase incompressible NavierStokes equations. Turbulence is modeled with the Smagorinsky Large Eddy Simulation (LES) model. An objective functional based on the vorticity is used to describe the mixing in the liquid bath. Optimized configurations are compared with a default one whose design is based on a setup from industrial practice

On iterative subdomain methods for the Stokes--Darcy problem

Iterative subdomain methods for the Stokes--Darcy problem that use Robin boundary conditions on the interface are reviewed. Their common underlying structure and their main differences are identified. In particular, it is clarified that there are different updating strategies for the interface conditions. For small values of fluid viscosity and hydraulic permeability, which are relevant in applications from geosciences, it is shown in numerical studies that only one of these updating strategies leads to an efficient numerical method, if this strategy is used in combination with appropriate parameters in the Robin boundary conditions. In particular, it is observed that the values of appropriate parameters are larger than those proposed so far. Not only the size but also the ratio of appropriate Robin parameters depends on the coefficients of the problem

Linear and nonlinear absorption of titanium dioxide films produced by plasma ion-assisted electron beam evaporation: Modeling and experiments

Titanium dioxide films were prepared by plasma ion-assisted electron beam evaporation. Linear optical properties were investigated in terms of spectrophotometry using the beta-distributed oscillator (ss_do) model as a parametrized dispersion law. The nonlinear two-photon absorption coecient of titanium dioxide was determined by means of the laser-induced deflection technique at a wavelength of 800 nm. The obtained values of (2-5) x 10-11 cm/W were consistent with published experimental values for rutile as well as for simulations performed in the frames of the ss_do and Sheik-Bahae models. © 2020 by the authors