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Literature mining for the discovery of hidden connections between drugs, genes and diseases

The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence. Apart from its use in knowledge retrieval, the co-occurrence method is also wellsuited to discover new, hidden relationships between biomedical concepts following a simple ABC-principle, in which A and C have no direct relationship, but are connected via shared B-intermediates. In this paper we describe CoPub Discovery, a tool that mines the literature for new relationships between biomedical concepts. Statistical analysis using ROC curves showed that CoPub Discovery performed well over a wide range of settings and keyword thesauri. We subsequently used CoPub Discovery to search for new relationships between genes, drugs, pathways and diseases. Several of the newly found relationships were validated using independent literature sources. In addition, new predicted relationships between compounds and cell proliferation were validated and confirmed experimentally in an in vitro cell proliferation assay. The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid. This makes CoPub Discovery a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to find novel applications for existing drugs. © 2010 Frijters et al.

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Nanomaterials and the Serosal Immune System in the Thoracic and Peritoneal Cavities

The thoracic and peritoneal cavities are lined by serous membranes and are home of the serosal immune system. This immune system fuses innate and adaptive immunity, to maintain local homeostasis and repair local tissue damage, and to cooperate closely with the mucosal immune system. Innate lymphoid cells (ILCs) are found abundantly in the thoracic and peritoneal cavities, and they are crucial in first defense against pathogenic viruses and bacteria. Nanomaterials (NMs) can enter the cavities intentionally for medical purposes, or unintentionally following environmental exposure; subsequent serosal inflammation and cancer (mesothelioma) has gained significant interest. However, reports on adverse effects of NMon ILCs and other components of the serosal immune systemare scarce or even lacking. As ILCs are crucial in the first defense against pathogenic viruses and bacteria, it is possible that serosal exposure to NMmay lead to a reduced resistance against pathogens. Additionally, affected serosal lymphoid tissues and cells may disturb adipose tissue homeostasis. This review aims to provide insight into key effects of NMon the serosal immune system.

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Nanomaterials and the Serosal Immune System in the Thoracic and Peritoneal Cavities

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Why do volunteers participate in phase I clinical trials? An exploratory study

Study goal: This study was carried out to answer the following research question: which motivation do healthy volunteers have to participate in phase I clinical trials? - Methods: A literature search was done through Google Scholar and Academic Search Premier, followed by three interviews with volunteers who had recently concluded their participation in a (non-commercial) phase I trial. - Results: Our literature search revealed mainly commercial motives for volunteers to participate in phase I clinical trials. The interviews (with volunteers in a non-commercial trial) showed that other factors may also play a decisive role, such as: (1) wish to support the investigator (2) wish to contribute to science, (3) access to more/better health care (4) sociability: possibility to relax and to communicate with other participants (5) general curiosity. Precondition is that risks and burden are deemed acceptable. - Conclusions: financial remuneration appears to be the predominant motive to participate voluntarily in a clinical trial. Other reasons were also mentioned however, such as general curiosity, the drive to contribute to science and the willingness to help the investigator. In addition, social reasons were given such as possibility to relax and to meet other people. Potential subjects state that they adequately assess the (safety) risks of participating in a trial as part of their decision process.

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Why do volunteers participate in phase I clinical trials? An exploratory study

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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).

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

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Molecular insights into human taste perception and umami tastants: A review

Understanding taste is key for optimizing the palatability of seaweeds and other non-animal-based foods rich in protein. The lingual papillae in the mouth hold taste buds with taste receptors for the five gustatory taste qualities. Each taste bud contains three distinct cell types, of which Type II cells carry various G protein-coupled receptors that can detect sweet, bitter, or umami tastants, while type III cells detect sour, and likely salty stimuli. Upon ligand binding, receptor-linked intracellular heterotrimeric G proteins initiate a cascade of downstream events which activate the afferent nerve fibers for taste perception in the brain. The taste of amino acids depends on the hydrophobicity, size, charge, isoelectric point, chirality of the alpha carbon, and the functional groups on their side chains. The principal umami ingredient monosodium l-glutamate, broadly known as MSG, loses umami taste upon acetylation, esterification, or methylation, but is able to form flat configurations that bind well to the umami taste receptor. Ribonucleotides such as guanosine monophosphate and inosine monophosphate strongly enhance umami taste when l-glutamate is present. Ribonucleotides bind to the outer section of the venus flytrap domain of the receptor dimer and stabilize the closed conformation. Concentrations of glutamate, aspartate, arginate, and other compounds in food products may enhance saltiness and overall flavor. Umami ingredients may help to reduce the consumption of salts and fats in the general population and increase food consumption in the elderly.

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Molecular insights into human taste perception and umami tastants: A review

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In search of balance

Healthy gestational weight gain (GWG) is associated with better pregnancy outcomes and with improved health in the later lives of women and babies. In this thesis the author describes the process of developing an intervention to help pregnant women reach a healthy GWG. The need for this intervention was derived from discussions with midwives, working in primary care in the Netherlands. In this introduction, the author describes the background of the larger project “Promoting Health Pregnancy”, of which this study is a part (1.2), the problem of unhealthy GWG (1.3-1.6) and offers a brief introduction to the theoretical framework of the study and to the subsequent chapters (1.7-1.9).

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The probable future of toxicology - probabilistic risk assessment

Both because of the shortcomings of existing risk assessment methodologies, as well as newly available tools to predict hazard and risk with machine learning approaches, there has been an emerging emphasis on probabilistic risk assessment. Increasingly sophisticated AI models can be applied to a plethora of exposure and hazard data to obtain not only predictions for particular endpoints but also to estimate the uncertainty of the risk assessment outcome. This provides the basis for a shift from deterministic to more probabilistic approaches but comes at the cost of an increased complexity of the process as it requires more resources and human expertise. There are still challenges to overcome before a probabilistic paradigm is fully embraced by regulators. Based on an earlier white paper (Maertens et al., 2022), a workshop discussed the prospects, challenges and path forward for implementing such AI-based probabilistic hazard assessment. Moving forward, we will see the transition from categorized into probabilistic and dose-dependent hazard outcomes, the application of internal thresholds of toxicological concern for data-poor substances, the acknowledgement of user-friendly open-source software, a rise in the expertise of toxicologists required to understand and interpret artificial intelligence models, and the honest communication of uncertainty in risk assessment to the public.

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Literature mining for the discovery of hidden connections between drugs, genes and diseases

Nanomaterials and the Serosal Immune System in the Thoracic and Peritoneal Cavities

Why do volunteers participate in phase I clinical trials? An exploratory study

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

Molecular insights into human taste perception and umami tastants: A review

In search of balance

The probable future of toxicology - probabilistic risk assessment

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Literature mining for the discovery of hidden connections between drugs, genes and diseases

Nanomaterials and the Serosal Immune System in the Thoracic and Peritoneal Cavities

Why do volunteers participate in phase I clinical trials? An exploratory study

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

Molecular insights into human taste perception and umami tastants: A review

In search of balance

The probable future of toxicology - probabilistic risk assessment