AIMS: An Automatic Semantic Machine Learning Microservice Framework to Support Biomedical and Bioengineering Research

The fusion of machine learning and biomedical research offers novel ways to understand, diagnose, and treat various health conditions. However, the complexities of biomedical data, coupled with the intricate process of developing and deploying machine learning solutions, often pose significant challenges to researchers in these fields. Our pivotal achievement in this research is the introduction of the Automatic Semantic Machine Learning Microservice Framework (AIMS). AIMS addresses these challenges by automating various stages of the machine learning pipeline, with a particular emphasis on the ontology of machine learning services tailored for the biomedical domain. This ontology encompasses everything from task representation, service modeling, and knowledge acquisition to knowledge reasoning and the establishment of a self-supervised learning policy. Our framework has been crafted to prioritize model interpretability, integrate domain knowledge effortlessly, and handle biomedical data with efficiency. Additionally, AIMS boasts a distinctive feature: it leverages self-supervised knowledge learning through reinforcement learning techniques, paired with an ontology-based policy recording schema. This enables it to autonomously generate, fine-tune, and continually adapt to machine learning models, especially when faced with new tasks and data. Our work has two standout contributions of demonstrating that machine learning processes in the biomedical domain can be automated, while integrating a rich domain knowledge base and providing a way for machines to have a self-learning ability, ensuring they handle new tasks effectively. To showcase AIMS in action, we've highlighted its prowess in three case studies from biomedical tasks. These examples emphasize how our framework can simplify research routines, uplift the caliber of scientific exploration, and set the stage for notable advances

Nanotoxicology

As the production and use of nanomaterials (NMs) in medicine and many other applications develops, so the need to understand the potential risks posed by NMs to human health (and the environment) increases (Aitken et al. 2006). At the nanoscale (1-100 nm), materials exhibit properties that are different to larger or bulk materials. These new properties are exploited by researchers and industry to generate new products; however, the same properties can also inuence how the NM behaves in biological systems, including affecting toxicity. Nanotoxicology is a relatively new eld of research that aims to assess the human and environmental hazard of nanomaterials. In recent years, this new discipline has seen a rapid expansion in the number of studies concerned with assessing the safety of engineered NMs (Figure 20.1)

The intestinal expulsion of the roundworm Ascaris suum is associated with eosinophils, intra-epithelial T cells and decreased intestinal transit time

Ascaris lumbricoides remains the most common endoparasite in humans, yet there is still very little information available about the immunological principles of protection, especially those directed against larval stages. Due to the natural host-parasite relationship, pigs infected with A. suum make an excellent model to study the mechanisms of protection against this nematode. In pigs, a self-cure reaction eliminates most larvae from the small intestine between 14 and 21 days post infection. In this study, we investigated the mucosal immune response leading to the expulsion of A. suum and the contribution of the hepato-tracheal migration. Self-cure was independent of previous passage through the liver or lungs, as infection with lung stage larvae did not impair self-cure. When animals were infected with 14-day-old intestinal larvae, the larvae were being driven distally in the small intestine around 7 days post infection but by 18 days post infection they re-inhabited the proximal part of the small intestine, indicating that more developed larvae can counter the expulsion mechanism. Self-cure was consistently associated with eosinophilia and intra-epithelial T cells in the jejunum. Furthermore, we identified increased gut movement as a possible mechanism of self-cure as the small intestinal transit time was markedly decreased at the time of expulsion of the worms. Taken together, these results shed new light on the mechanisms of self-cure that occur during A. suum infections

Polylactic is a Sustainable, Low Absorption, Low Autofluorescence Alternative to Other Plastics for Microfluidic and Organ-on-Chip Applications

Organ-on-chip (OOC) devices are miniaturized devices replacing animal models in drug discovery and toxicology studies. The majority of OOC devices are made from polydimethylsiloxane (PDMS), an elastomer widely used in microfluidic prototyping, but posing a number of challenges to experimentalists, including leaching of uncured oligomers and uncontrolled absorption of small compounds. Here we assess the suitability of polylactic acid (PLA) as a replacement material to PDMS for microfluidic cell culture and OOC applications. We changed the wettability of PLA substrates and demonstrated the functionalization method to be stable over a time period of at least 9 months. We successfully cultured human cells on PLA substrates and devices, without coating. We demonstrated that PLA does not absorb small molecules, is transparent (92% transparency), and has low autofluorescence. As a proof of concept of its manufacturability, biocompatibility, and transparency, we performed a cell tracking experiment of prostate cancer cells in a PLA device for advanced cell culture

Assessing the transferability and reproducibility of 3D in vitro liver models from primary human multi-cellular microtissues to cell-line based HepG2 spheroids

To reduce, replace, and refine in vivo testing, there is increasing emphasis on the development of more physiologically relevant in vitro test systems to improve the reliability of non-animal-based methods for hazard assessment. When developing new approach methodologies, it is important to standardize the protocols and demonstrate the methods can be reproduced by multiple laboratories. The aim of this study was to assess the transferability and reproducibility of two advanced in vitro liver models, the Primary Human multicellular microtissue liver model (PHH) and the 3D HepG2 Spheroid Model, for nanomaterial (NM) and chemical hazard assessment purposes. The PHH model inter-laboratory trial showed strong consistency across the testing sites. All laboratories evaluated cytokine release and cytotoxicity following exposure to titanium dioxide (TiO2) and zinc oxide (ZnO) nanoparticles. No significant difference was observed in cytotoxicity or IL-8 release for the test materials. The data were reproducible with all three laboratories with control readouts within a similar range. The PHH model ZnO induced the greatest cytotoxicity response at 50.0 μg/mL and a dose-dependent increase in IL-8 release. For the 3D HepG2 spheroid model, all test sites were able to construct the model and demonstrated good concordance in IL-8 cytokine release and genotoxicity data. This trial demonstrates the successful transfer of new approach methodologies across multiple laboratories, with good reproducibility for several hazard endpoints.Toxicolog

The application of existing genotoxicity methodologies for grouping of nanomaterials: Towards an integrated approach to testing and assessment.

The incorporation of nanomaterials (NMs) in consumer products has proven to be highly valuable in many sectors. Unfortunately, however, the same nano specific physicochemical properties, which make these material attractive, might also contribute to hazards for people exposed to these materials. The physicochemical properties of NMs will impact their interaction with biological surroundings and influence their fate and their potential adverse effects such as genotoxicity. Due to the large and expanding number of NMs produced, their availability in different nanoforms (NFs) and their utilization in various formats, it is impossible for risk assessment to be conducted on an individual NF basis. Alternative methods, such as grouping are needed for streamlining hazard assessment. The GRACIOUS Framework provides a logical and science evidenced approach to group similar NFs, allowing read-across of hazard information from source NFs (or non-NFs) with adequate hazard data to target NFs that lack such data. Here, we propose a simple three-tiered testing strategy to gather evidence to determine whether different NFs are sufficiently similar with respect to their potential to induce genotoxicity, in order to be grouped. The tiered testing strategy includes simple in vitro models as well as a number of alternative more complex multi-cellular in vitro models to allow for a better understanding of secondary NM-induced DNA damage, something that has been more appropriate in vivo until recently

Next generation in vitro primary hepatic cell test systems—their suitability as an alternative to in vivo testing?

To date traditional toxicity testing has relied heavily on in-life animal studies that are expensive and restrictive with regards to very important ethical implications. In addition, these studies often yield data that are not relevant to human exposures or biological responses due to intra-species variations, necessitating the requirement for further testing or candidate (drug) abandonment in late development stages. There is increasing global pressure from regulatory agencies, the general public, and the scientific community to develop in vitro alternatives for toxicity testing that can be utilized for mechanistic dose response hazard identification prior to embarking on small well designed and absolutely necessary in vivo studies

Nanomaterial-Induced Extra-Pulmonary Health Effects – the Importance of Next Generation Physiologically Relevant In Vitro Test Systems for the Future of Nanotoxicology

Manufactured nanomaterials (NMs) offer incredible scientific and societal benefits but their potential hazard to human health is not yet fully comprehended. In the last decade, a significant body of evidence indicates that certain NMs are capable of translocating from the primary exposure site (skin, lungs and gastrointestinal tract) to a number of secondary organs which includes the liver. Moreover, recent advances in the field of nanomedicine has resulted in increasing direct intravenous injection of NMs with the liver being a particularly important organ with regards to potential toxic effects and accumulation of said materials. It is generally acknowledged that it is not always possible to make direct or meaningful comparisons between in vitro and in vivo xenobiotic-induced toxicological responses. One of the main reasons for the lack of comparability between the testing strategies is that biological responses are not often alike which can in part be attributed to the numerous limitations of traditional mono-cellular in vitro test systems which are acting as a surrogate for a whole organ. In an attempt to address and highlight this important issue, this chapter will discuss the progress made in the production and validation oof next generation more physiologically relevant multi-cellular in vitro models of skin, GIT and the liver utilised for the assessment of the NM-induced toxicological effects

Effect of Arbuscular Mycorrhizal Fungi and Organic Fertilizers Application on Yield Components of Two Wheat Cultivars

This investigation was conducted in order to evaluate the direct effects of organic and bio - fertilizers on yield components of two native wheat cultivars, Bolani and cross - Bolani. The experiment conducted as a factorial in a completely randomized design with three replications. Treatment includes fertilizer factor: vermicompost (F1), vermicompost + compost (F2), vermicompost + mycorrhiza (F3), compost + vermicompost + mycorrhiza (F4), compost (F5), mycorrhiza + compost (F6), mycorrhiza (F7) and control (no fertilizer application F8) and cultivar factor includes two cultivar Bolani (C1) and cross - Bolani (C2). The results showed that the interaction effect of combined treatments (F7C2) of high yield (1.13 g.pot-1) obtained. The treatment combination (F7C2) of (0.355) was highest harvest index. The high correlation between weight per plant with plant height, spike length, grain yield and harvest index were observed. Generally the combined application of vermicompost and mycorrhiza cultivar cross - Bolani is more suitable for grain production