Notes on the Treatment of Charged Particles for Studying Cyclotide/Membrane Interactions with Dissipative Particle Dynamics

Different charge treatment approaches are examined for cyclotide-induced plasma membrane disruption by lipid extraction studied with dissipative particle dynamics. A pure Coulomb approach with truncated forces tuned to avoid individual strong ion pairing still reveals hidden statistical pairing effects that may lead to artificial membrane stabilization or distortion of cyclotide activity depending on the cyclotide’s charge state. While qualitative behavior is not affected in an apparent manner, more sensitive quantitative evaluations can be systematically biased. The findings suggest a charge smearing of point charges by an adequate charge distribution. For large mesoscopic simulation boxes, approximations for the Ewald sum to account for mirror charges due to periodic boundary conditions are of negligible influence

Digitalizing the Chemical Landscape: A Comprehensive Overview and Progress Report of NFDI4Chem

The Chemistry consortium NFDI4Chem aims to digitalise key steps in chemical research, supporting scientists in managing research data throughout its life cycle. The SmartLab, embedded in a federation of services, integrates various tools such as electronic lab notebooks, data repositories, and search services, to create a smart lab environment for structured data gathering. Utilizing terminology services and adhering to data format standards, NFDI4Chem promotes secure and FAIR data sharing, fostering collaboration and expediting scientific discoveries. This development is supported by community building measures, workshops, and training initiatives, along with collaboration on international minimum information standards

NFDI4Chem - A Research Data Network for International Chemistry

Research data provide evidence for the validation of scientific hypotheses in most areas of science. Open access to them is the basis for true peer review of scientific results and publications. Hence, research data are at the heart of the scientific method as a whole. The value of openly sharing research data has by now been recognized by scientists, funders and politicians. Today, new research results are increasingly obtained by drawing on existing data. Many organisations such as the Research Data Alliance (RDA), the goFAIR initiative, and not least IUPAC are supporting and promoting the collection and curation of research data. One of the remaining challenges is to find matching data sets, to understand them and to reuse them for your own purpose. As a consequence, we urgently need better research data management

Harmonising, Harvesting, and Searching Metadata Across a Repository Federation

The collection of metadata for research data is an important aspect in the FAIR principles. The schema.org and Bioschemas initiatives created a vocabulary to embed markup for many different types, including BioChemEntity, ChemicalSubstance, Gene, MolecularEntity, Protein, and others relevant in the Natural and Life Sciences with immediate benefits for findability of data packages. To bridge the gap between the worlds of semantic-web-driven JSON+LD metadata on the one hand, and established but separately developed interface services in libraries, we have designed an architecture for harmonising, federating and harvesting metadata from several resources. Our approach is to serve JSON+LD embedded in an XML container through a central OAI-Provider. Several resources in NFDI4Chem provide such domain-specific metadata. The CKAN-based NFDI4Chem search service can harvest this metadata using an OAI-PMH harvester extension that can extract the XML-encapsulated JSON+LD metadata, and has search capabilities relevant in the chemistry domain. We invite the community to collaborate and reach a critical mass of providers and consumers in the NFDI

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive reference ligands in terms of structural and pharmacophoric features. We implemented a deterministic compound construction procedure that explicitly considers compound synthesizability, based on a compilation of 25'144 readily available synthetic building blocks and 58 established reaction principles. This enables the software to suggest a synthesis route for each designed compound. Two prospective case studies are presented together with details on the algorithm and its implementation. De novo designed ligand candidates for the human histamine H4 receptor and γ-secretase were synthesized as suggested by the software. The computational approach proved to be suitable for scaffold-hopping from known ligands to novel chemotypes, and for generating bioactive molecules with drug-like properties

Interim Report NFDI4Chem 2023

The progress of the DFG-funded NFDI4Chem consortium (NFDI 4/1 - project number 441958208) in data management in chemistry is outlined in our latest report, highlighting the steps we have taken to integrate a data-centric approach within the chemistry community. This interim report offers a comprehensive overview of our data management activities, covering the reporting period from October 2020 to August 2023.The shift to digital tools in research documentation is driven by our work with Electronic Laboratory Notebooks (ELNs), such as Chemotion ELN, offering systematic data storage for easy retrieval and sharing. Additionally, we focus on developing repositories, such as Chemotion repository and RADAR4Chem, which fulfil the needs for the storage of chemical data. The NFDI4Chem Search Service ensures easy data access from our repositories. Our efforts extend to community engagement through conference visits and online presence, aimed at creating awareness for (digital) research data management and connecting to chemistry students and researchers. Our training programs have reached over 600 participants to date. Initiatives like the FAIR4Chem award and the Chemistry Data Days promote cultural change towards FAIR data. Our Editors4Chem initiative collaborates with publishers for standardised data management and the Ontologies4Chem workshops organised by our consortium promote the ontology development in the field.Apart from the consortium's engagement for chemists, NFDI4Chem members played key roles in the development of the NFDI as a whole. Being actively involved in the sections and task forces, NFDI4Chem promotes collaborative solutions across NFDI consortia

Norma DIN 476, su uso para desarrollar algunos temas de matemática de un programa de segundo año

Se presenta una propuesta de enseñanza, utilizando un material concreto que nos permite desarrollar algunos temas del programa de Matemática correspondiente al 2do año de la Escuela Industrial Superior de la ciudad de Santa Fe. La selección del material tiene que ver con una búsqueda de relaciones con otras asignaturas del mismo nivel (u otros) porque creemos que la enseñanza y aprendizaje de los contenidos de nuestra área tienen mejor recepción en los alumnos cuando se la contextualiza, cuando se evidencia su necesidad, valor o colaboración en otras áreas de estudio. El abordaje transdisciplinario requiere de mentes creativas, abiertas y capaces de resolver situaciones problemáticas específicas desde muchas perspectivas. Esto indica que el docente debe diseñar estrategias de enseñanza basadas en una concepción cognitiva del aprendizaje, favoreciendo el tratamiento de los contenidos disciplinares desde una perspectiva crítica y reflexiva; en la cual el joven pueda poner en juego sus propias capacidades y posibilidades para participar activamente del proceso y construir el conocimiento.Facultad de Humanidades y Ciencias de la Educació

A roadmap to improve the quality of atrial fibrillation management:proceedings from the fifth Atrial Fibrillation Network/European Heart Rhythm Association consensus conference

At least 30 million people worldwide carry a diagnosis of atrial fibrillation (AF), and many more suffer from undiagnosed, subclinical, or 'silent' AF. Atrial fibrillation-related cardiovascular mortality and morbidity, including cardiovascular deaths, heart failure, stroke, and hospitalizations, remain unacceptably high, even when evidence-based therapies such as anticoagulation and rate control are used. Furthermore, it is still necessary to define how best to prevent AF, largely due to a lack of clinical measures that would allow identification of treatable causes of AF in any given patient. Hence, there are important unmet clinical and research needs in the evaluation and management of AF patients. The ensuing needs and opportunities for improving the quality of AF care were discussed during the fifth Atrial Fibrillation Network/European Heart Rhythm Association consensus conference in Nice, France, on 22 and 23 January 2015. Here, we report the outcome of this conference, with a focus on (i) learning from our 'neighbours' to improve AF care, (ii) patient-centred approaches to AF management, (iii) structured care of AF patients, (iv) improving the quality of AF treatment, and (v) personalization of AF management. This report ends with a list of priorities for research in AF patients