53 research outputs found

    Nanoinformatics: developing new computing applications for nanomedicine

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    Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

    Nanoinformatics: a new area of research in nanomedicine

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    Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and ?omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

    Bionanomedicine: A “Panacea” In Medicine?

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    Recent advances in nanotechnology, biotechnology, bioinformatics, and materials science have prompted novel developments in the field of nanomedicine. Enhancements in the theranostics, computational information, and management of diseases/disorders are desperately required. It may now be conceivable to accomplish checked improvements in both of these areas utilising nanomedicine. This scientific and concise review concentrates on the fundamentals and potential of nanomedicine, particularly nanoparticles and their advantages, nanoparticles for siRNA conveyance, nanopores, nanodots, nanotheragnostics, nanodrugs and targeting mechanisms, and aptamer nanomedicine. The combination of various scientific fields is quickening these improvements, and these interdisciplinary endeavours to have significant progressively outstretching influences on different fields of research. The capacities of nanomedicine are immense, and nanotechnology could give medicine a completely new standpoint

    Nanoinformatics: a new area of research in nanomedicine

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    pre-printAbstract: Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and -omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings

    Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

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    Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts

    D10.6 - Final Version of NanoCommons Sustainability Plan

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    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

    Nanoinformática: retos e iniciativas para la gestión de la información generada en la investigación nanomédica

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    Durante la última década la investigación en nanomedicina ha generado gran cantidad de datos, heterogéneos, distribuidos en múltiples fuentes de información. El uso de las Tecnologías de la Información y la Comunicación (TIC) puede facilitar la investigación médica a escala nanométrica, proporcionando mecanismos y herramientas que permitan gestionar todos esos datos de una manera inteligente. Mientras que la informática biomédica comprende el procesamiento y gestión de la información generada desde el nivel de salud pública y aplicación clínica hasta el nivel molecular, la nanoinformática extiende este ámbito para incluir el “nivel nano”, ocupándose de gestionar y analizar los resultados generados durante la investigación en nanomedicina y desarrollar nuevas líneas de trabajo en este espacio interdisciplinar. En esta nueva área científica, la nanoinformática (que podría consolidarse como una auténtica disciplina en los próximos años), elGrupo de Informática Biomédica (GIB) de la Universidad Politécnica de Madrid (UPM) participa en numerosas iniciativas, que se detallan a continuación

    Doctor of Philosophy

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    dissertationNanoinformatics is a relatively young field of study that is important due to its implications in the field of nanomedicine, specifically toward the development of nanoparticle drug delivery systems. As more structural, biochemical, and physiochemical data become available regarding nanoparticles, the greater the knowledge-gain from using nanoinformatics methods will become. While there are challenges that exist with nanoparticle data, including heterogeneity of data and complexity of the particles, nanoinformatics will be at the forefront of processing these data and aid in the design of nanoparticles for biomedical applications. In this dissertation, a review of data mining and machine learning studies performed in the field of nanomedicine is presented. Next, the use of natural language processing methods to extract numeric values of biomedical property terms of poly(amido amine) (PAMAM) dendrimers from nanomedicine literature is demonstrated, along with successful extraction results. Following this is an implementation and its results of data mining techniques used for the development of predictive models of cytotoxicity of PAMAM dendrimers using their chemical and structural properties. Finally, a method and its results for using molecular dynamics simulations to test the ability of EDTA, as a gold standard, and generation 3.5 (G3.5) PAMAM dendrimers to chelate calcium

    A nanoinformatics decision support tool for the virtual screening of gold nanoparticle cellular association using protein corona fingerprints

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    The increasing use of nanoparticles (NPs) in a wide range of consumer and industrial applications has necessitated significant effort to address the challenge of characterizing and quantifying the underlying nanostructure – biological response relationships to ensure that these novel materials can be exploited responsibly and safely. Such efforts demand reliable experimental data not only in terms of the biological dose-response, but also regarding the physicochemical properties of the NPs and their interaction with the biological environment. The latter has not been extensively studied, as a large surface to bind biological macromolecules is a unique feature of NPs that is not relevant for chemicals or pharmaceuticals, and thus only limited data have been reported in the literature quantifying the protein corona formed when NPs interact with a biological medium and linking this with NP cellular association/uptake. In this work we report the development of a predictive model for the assessment of the biological response (cellular association, which can include both internalized NPs and those attached to the cell surface) of surface-modified gold NPs, based on their physicochemical properties and protein corona fingerprints, utilizing a dataset of 105 unique NPs. Cellular association was chosen as the end-point for the original experimental study due to its relevance to inflammatory responses, biodistribution, and toxicity in vivo. The validated predictive model is freely available online through the Enalos Cloud Platform (http://enalos.insilicotox.com/NanoProteinCorona/) to be used as part of a regulatory or NP safe-by-design decision support system. This online tool will allow the virtual screening of NPs, based on a list of the significant NP descriptors, identifying those NPs that would warrant further toxicity testing on the basis of predicted NP cellular association.</p
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