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The application of natural language processing for the extraction of mechanistic information in toxicology

To study the ways in which compounds can induce adverse effects, toxicologists have been constructing Adverse Outcome Pathways (AOPs). An AOP can be considered as a pragmatic tool to capture and visualize mechanisms underlying different types of toxicity inflicted by any kind of stressor, and describes the interactions between key entities that lead to the adverse outcome on multiple biological levels of organization. The construction or optimization of an AOP is a labor intensive process, which currently depends on the manual search, collection, reviewing and synthesis of available scientific literature. This process could however be largely facilitated using Natural Language Processing (NLP) to extract information contained in scientific literature in a systematic, objective, and rapid manner that would lead to greater accuracy and reproducibility. This would support researchers to invest their expertise in the substantive assessment of the AOPs by replacing the time spent on evidence gathering by a critical review of the data extracted by NLP. As case examples, we selected two frequent adversities observed in the liver: namely, cholestasis and steatosis denoting accumulation of bile and lipid, respectively. We used deep learning language models to recognize entities of interest in text and establish causal relationships between them. We demonstrate how an NLP pipeline combining Named Entity Recognition and a simple rules-based relationship extraction model helps screen compounds related to liver adversities in the literature, but also extract mechanistic information for how such adversities develop, from the molecular to the organismal level. Finally, we provide some perspectives opened by the recent progress in Large Language Models and how these could be used in the future. We propose this work brings two main contributions: 1) a proof-of-concept that NLP can support the extraction of information from text for modern toxicology and 2) a template open-source model for recognition of toxicological entities and extraction of their relationships. All resources are openly accessible via GitHub (https://github.com/ontox-project/en-tox).

Towards a Natural Social Contract

This open access book states that the endemic societal faultlines of our times are deeply intertwined and that they confront us with challenges affecting the security and sustainability of our societies. It states that new ways of inhabiting and cultivating our planet are needed to keep it healthy for future generations. This requires a fundamental shift from the current anthropocentric and economic growth-oriented social contract to a more ecocentric and regenerative natural social contract. The author posits that in a natural social contract, society cannot rely on the market or state alone for solutions to grand societal challenges, nor leave them to individual responsibility. Rather, these problems need to be solved through transformative social-ecological innovation (TSEI), which involves systemic changes that affect sustainability, health and justice. The TSEI framework presented in this book helps to diagnose and advance innovation and change across sectors and disciplines, and at different levels of governance. It identifies intervention points and helps formulate sustainable solutions for policymakers, administrators, concerned citizens and professionals in moving towards a more just and equitable society.

The waterharmonica

Environmental identity and natural resources: a dialogical learning process

In this article, we elaborate on the role of dialogical learning in identity formation in the context of environmental education. First, we distinguish this kind of learning from conditioning and reproductive learning. We also show that identity learning is not self-evident and we point out the role of emotions. Using Dialogical Self Theory, we then suggest that individuals do not have an “identity hierarchy” but a dialogical self that attaches meaning to experiences in both conscious and unconscious ways. We describe the learning process that enables the dialogical self to develop itself, and we elaborate on the characteristics of a good dialogue. We conclude with some remarks expanding room for a dialogue that would foster identity learning. https://doi.org/10.3390/resources5010011 https://www.linkedin.com/in/helenkopnina/

Nature, natural resources and valuation in the Anthropocene

Biodiversity, including entire habitats and ecosystems, is recognized to be of great social and economic value. Conserving biodiversity has therefore become a task of international NGO’s as well as grass-roots organisations. The ‘classical’ model of conservation has been characterised by creation of designated nature areas to allow biodiversity to recover from the effects of human activities. Typically, such areas prohibit entry other than through commercial ecotourism or necessary monitoring activities, but also often involve commodification nature. This classical conservation model has been criticized for limiting valuation of nature to its commercial worth and for being insensitive to local communities. Simultaneously, ‘new conservation’ approaches have emerged. Propagating openness of conservation approaches, ‘new conservation’ has counteracted the calls for strict measures of biodiversity protection as the only means of protecting biodiversity. In turn, the ’new conservation’ was criticised for being inadequate in protecting those species that are not instrumental for human welfare. The aim of this article is to inquire whether sustainable future for non-humans can be achieved based on commodification of nature and/or upon open approaches to conservation. It is argued that while economic development does not necessarily lead to greater environmental protection, strict regulation combined with economic interests can be effective. Thus, economic approaches by mainstream conservation institutions cannot be easily dismissed. However, ‘new conservation’ can also be useful in opening up alternatives, such as care-based and spiritual approaches to valuation of nature. Complementary to market-based approaches to conservation, alternative ontologies of the human development as empathic beings embedded in intimate ethical relations with non-humans are proposed. https://www.linkedin.com/in/helenkopnina/

Improving the Performance of Periodic Real-time Processes: a Graph Theoretical Approach

In this paper, the performance gain obtained by combining parallel peri- odic real-time processes is elaborated. In certain single-core mono-processor configurations, for example, embedded control systems in robotics comprising many short processes, process context switches may consume a considerable amount of the available processing power. For this reason, it can be advantageous to combine processes, to reduce the number of context switches and thereby increase the performance of the application. As we consider robotic applications only, often consisting of processes with identical periods, release times and deadlines, we restrict these configurations to periodic real-time processes executing on a single-core mono-processor. By graph-theoretical concepts and means, we provide necessary and sufficient conditions so that the number of context switches can be reduced by combining synchronising processes.