Toward Semantic Interoperability of Public Available Data Sources

Nowadays combining data from different sources is a time-consuming endeavor. First, the data must be searched using multiple interfaces, downloaded in the format provided by the database and then curated and harmonized to identify corresponding entries like compound name, concentration and finally biological effect. We will present a new concept of application programming interfaces (APIs) for data sources that can be added to already existing data warehouses or to wrap simple files and hold the data in tabular formats that are more accessible to both humans and computers. Using examples of reference sources like ToxRefDB, ToxCast and TG-GATES, we will demonstrate how these APIs can be used to generate tools for searching and browsing across all sources and how the selected data can then directly be integrated in analysis and modelling services using scripting languages like Python and R or workflow managers like KNIME. We will also show the first approaches to make these API semantically rich. Data schemas, i.e. descriptions of the data format easily understandable to humans and computers will be used to annotate important features of the datasets like compounds under investigation, concentrations and exposure times

Influence of Oxygen Partial Pressure during Processing on the Thermoelectric Properties of Aerosol-Deposited CuFeO2

In the field of thermoelectric energy conversion, oxide materials show promising potential due to their good stability in oxidizing environments. Hence, the influence of oxygen partial pressure during synthesis on the thermoelectric properties of Cu-Delafossites at high temperatures was investigated in this study. For these purposes, CuFeO2 powders were synthetized using a conventional mixed-oxide technique. X-ray diffraction (XRD) studies were conducted to determine the crystal structures of the delafossites associated with the oxygen content during the synthesis. Out of these powders, films with a thickness of about 25 µm were prepared by the relatively new aerosol-deposition (AD) coating technique. It is based on a room temperature impact consolidation process (RTIC) to deposit dense solid films of ceramic materials on various substrates without using a high-temperature step during the coating process. On these dense CuFeO2 films deposited on alumina substrates with electrode structures, the Seebeck coefficient and the electrical conductivity were measured as a function of temperature and oxygen partial pressure. We compared the thermoelectric properties of both standard processed and aerosol deposited CuFeO2 up to 900 °C and investigated the influence of oxygen partial pressure on the electrical conductivity, on the Seebeck coefficient and on the high temperature stability of CuFeO2. These studies may not only help to improve the thermoelectric material in the high-temperature case, but may also serve as an initial basis to establish a defect chemical model

Magnetic transport in a straight parabolic channel

We study a charged two-dimensional particle confined to a straight parabolic-potential channel and exposed to a homogeneous magnetic field under influence of a potential perturbation $W$. If $W$ is bounded and periodic along the channel, a perturbative argument yields the absolute continuity of the bottom of the spectrum. We show it can have any finite number of open gaps provided the confining potential is sufficiently strong. However, if $W$ depends on the periodic variable only, we prove by Thomas argument that the whole spectrum is absolutely continuous, irrespectively of the size of the perturbation. On the other hand, if $W$ is small and satisfies a weak localization condition in the the longitudinal direction, we prove by Mourre method that a part of the absolutely continuous spectrum persists

D10.6 - Final Version of NanoCommons Sustainability Plan

NanoCommons was funded as an infrastructure project for a starting community. This means that it was supposed to build the concepts and foundation on which the community can continue to build solutions and services; in the case of NanoCommons, the infrastructure goal was to address the starting community’s data and nanoinformatics needs. NanoCommons did not start entirely from scratch, as it was building on efforts of the Nanosafety Cluster’s Working Group F on data management, and benefited from a general appreciation of the value of data reuse and computational predictions in the community. The push towards increasing use of chemoinformatics and nanoinformatics approaches was also endorsed by the public, regulatory and funding agencies, including being accelerated by the European ban on animal testing in the cosmetics industry and the European Green Deal. Similarly, industry is increasingly acting as a driver: fostering implementation and adoption of data harmonisation, FAIRness (Findability, Accessibility, Interoperability and Reusability of data) and openness and recognising that these activities require targeted and centralised efforts, which were provided by NanoCommons. However, a starting community is just that: a start upon which the community can build, a coalescence point around which collective efforts can nucleate. Our journey is still at the earliest stages, and much is needed in terms of automation, tooling, and continued training and education to drive the mindset changes within the community to fully embed data management at the start of the data lifecycle. Sustained and continuous support will be needed to achieve sufficient levels of digitalisation, global adoption of reporting standards both in scientific and regulatory settings, and machine-readability and machine-actionable data, all of which will lead to better quality and reproducible research, and more trust in the data and understanding of its applicability and suitability for reuse thus enhancing the value of the data and knowledge generated. This starts with sustaining what we already have, which in our case is the NanoCommons Knowledge Infrastructure, the implemented services from NanoCommons, as well as other associated partners and projects, and the collaboration with other projects established beyond the borders of nanosafety research. The term sustainability can be described as “the ability to be maintained at a certain rate or level”. Applied to NanoCommons, this means that the services/tools/materials that were designed and developed during the project and are already being offered to support the nanosafety community will continue to be maintained and ideally further developed, beyond the end of the funded period of the project, ensuring future accessibility for users and potential customers. Since there will be no direct public funding for these services anymore (pending further applications via Horizon Europe for example), planning for sustainability and creation of a (not necessarily commercial) business model were started very early in the project as a central task of WP10 and possible options were continuously evaluated and adapted based on stakeholder feedback coming from surveys and, more importantly, from users of the starting infrastructure services and expertise who received support in the form of Transnational Access (TA) projects or as part of the Demonstration Cases (see deliverable reports D9.3 and D9.4 for details of the first and second round Demonstration Cases, respectively). Deliverable D10.6 presented here builds on the previous deliverables D10.4 “First Testing and Evaluation Results of NanoCommons Sustainability Plan” and D10.5 “Second Testing and Evaluation Results on the NanoCommons Sustainability Plan”, proposing the first version of the business model and analysing all project activities related to sustainability during the last period, respectively. Together, these three reports outline the considerations and activities undertaken with the aim of ensuring the sustained existence and utilisation of the NanoCommons project outcomes beyond the project lifetime. A major NanoCommons objective has been to achieve a sustainable and open knowledge infrastructure for the whole nanosafety community, and thus a considerable effort was invested in exploring the options and approaches, focussing on those business models consistent with the ethos of openness and accessibility, given the public funding used to develop the services, and the critical importance of access to Environmental Health and Safety (EHS) data globally. In this final deliverable, evaluation of the TAs and Demonstration Cases with respect to their (potential) contributions to the UN Sustainable Development Goals (SDGs) is completed by looking at the results from the third funding period. Additionally, the targeted activities with the strategic partners most of whom were previously identified as significant routes via which to sustain and further develop the NanoCommons tools and services, are summarised. The NanoCommons focus areas for short/long term sustainability are presented, along with the justifications of these choices. All of this information is then condensed into the final NanoCommons sustainability plan

Exploiting transient protein states for the design of small-molecule stabilizers of mutant p53

The destabilizing p53 cancer mutation Y220C creates an extended crevice on the surface of the protein that can be targeted by small-molecule stabilizers. Here, we identify different classes of small molecules that bind to this crevice and determine their binding modes by X-ray crystallography. These structures reveal two major conformational states of the pocket and a cryptic, transiently open hydrophobic subpocket that is modulated by Cys220. In one instance, specifically targeting this transient protein state by a pyrrole moiety resulted in a 40-fold increase in binding affinity. Molecular dynamics simulations showed that both open and closed states of this subsite were populated at comparable frequencies along the trajectories. Our data extend the framework for the design of high-affinity Y220C mutant binders for use in personalized anticancer therapy and, more generally, highlight the importance of implementing protein dynamics and hydration patterns in the drug-discovery process

On the structure of eigenfunctions corresponding to embedded eigenvalues of locally perturbed periodic graph operators

The article is devoted to the following question. Consider a periodic self-adjoint difference (differential) operator on a graph (quantum graph) G with a co-compact free action of the integer lattice Z^n. It is known that a local perturbation of the operator might embed an eigenvalue into the continuous spectrum (a feature uncommon for periodic elliptic operators of second order). In all known constructions of such examples, the corresponding eigenfunction is compactly supported. One wonders whether this must always be the case. The paper answers this question affirmatively. What is more surprising, one can estimate that the eigenmode must be localized not far away from the perturbation (in a neighborhood of the perturbation's support, the width of the neighborhood determined by the unperturbed operator only). The validity of this result requires the condition of irreducibility of the Fermi (Floquet) surface of the periodic operator, which is expected to be satisfied for instance for periodic Schroedinger operators.Comment: Submitted for publicatio