Multiomics, artificial intelligence, and precision medicine in perinatology

Artificial Intelligence and cancer: Profile of registered clinical trials

Artificial Intelligence (AI) has made significant strides due to advancements in processing algorithms and data availability. Recent years have shown a resurgence in AI, driven by breakthroughs in deep machine learning. AI has attracted particular interest in the medical sector, especially in the field of personalized medicine, which for example uses large-scale genomic and molecular data to predict individual patient treatment responses. The applications of AI in disease diagnosis, monitoring, and treatment are expanding rapidly, leading to a growing number of registered trials. Therefore, this study aimed to identify and evaluate clinical trials registered between January 1st 2016, and September 30th 2023 that connect AI and cancer. Our findings show that the number of clinical trials linking AI with cancer research has grown significantly compared to other diseases, with colorectal and breast tumour types showing the highest number of registered trials. The most frequent intervention was disease diagnosis and monitoring. Regarding countries, China and the United States hold the highest numbers of registered trials. In conclusion, oncology is a field with a great interest in AI, where the developed countries are leading the studies in this field. Unfortunately, developing countries are still crawling in this aspect and government policies should be made to improve that area.

Explainable Artificial Intelligence in Paediatric: Challenges for the Future

Background

Explainable artificial intelligence (XAI) emerged to improve the transparency of machine learning models and increase understanding of how models make actions and decisions. It helps to present complex models in a more digestible form from a human perspective. However, XAI is still in the development stage and must be used carefully in sensitive domains including paediatrics, where misuse might have adverse consequences.

Objective

This commentary paper discusses concerns and challenges related to implementation and interpretation of XAI methods, with the aim of rising awareness of the main concerns regarding their adoption in paediatrics.

Methods

A comprehensive literature review was undertaken to explore the challenges of adopting XAI in paediatrics.

Results

Although XAI has several favorable outcomes, its implementation in paediatrics is prone to challenges including generalizability, trustworthiness, causality and intervention, and XAI evaluation.

Conclusion

Paediatrics is a very sensitive domain where consequences of misinterpreting AI outcomes might be very significant. XAI should be adopted carefully with focus on evaluating the outcomes primarily by including paediatricians in the loop, enriching the pipeline by injecting domain knowledge promoting a cross-fertilization perspective aiming at filling the gaps still preventing its adoption.

Therapeutic peptide development revolutionized: Harnessing the power of artificial intelligence for drug discovery

Due to the spread of antibiotic resistance, global attention is focused on its inhibition and the expansion of effective medicinal compounds. The novel functional properties of peptides have opened up new horizons in personalized medicine. With artificial intelligence methods combined with therapeutic peptide products, pharmaceuticals and biotechnology advance drug development rapidly and reduce costs. Short-chain peptides inhibit a wide range of pathogens and have great potential for targeting diseases. To address the challenges of synthesis and sustainability, artificial intelligence methods, namely machine learning, must be integrated into their production. Learning methods can use complicated computations to select the active and toxic compounds of the drug and its metabolic activity. Through this comprehensive review, we investigated the artificial intelligence method as a potential tool for finding peptide-based drugs and providing a more accurate analysis of peptides through the introduction of predictable databases for effective selection and development.

Predictive analytics in bronchopulmonary dysplasia: past, present, and future

Bronchopulmonary dysplasia (BPD) remains a significant complication of prematurity, impacting approximately 18,000 infants annually in the United States. Advances in neonatal care have not reduced BPD, and its management is challenged by the rising survival of extremely premature infants and the variability in clinical practices. Leveraging statistical and machine learning techniques, predictive analytics can enhance BPD management by utilizing large clinical datasets to predict individual patient outcomes. This review explores the foundations and applications of predictive analytics in the context of BPD, examining commonly used data sources, modeling techniques, and metrics for model evaluation. We also highlight bioinformatics' potential role in understanding BPD's molecular basis and discuss case studies demonstrating the use of machine learning models for risk prediction and prognosis in neonates. Challenges such as data bias, model complexity, and ethical considerations are outlined, along with strategies to address these issues. Future directions for advancing the integration of predictive analytics into clinical practice include improving model interpretability, expanding data sharing and interoperability, and aligning predictive models with precision medicine goals. By overcoming current challenges, predictive analytics holds promise for transforming neonatal care and providing personalized interventions for infants at risk of BPD.

Paediatric systemic inflammatory response syndrome (SIRS) and the development of patient-specific therapy: ethical perspectives through experts' opinions

Background

Research for personalised therapies concerning the Systemic Inflammatory Response Syndrome (SIRS) in children involves the utilisation of OMICS technologies and Artificial Intelligence (AI).

Methods

To identify specific ethical challenges through the perspective of healthcare professionals, we conducted 10 semi-structured interviews. The development of interview questions for the interviews was preceded by a systematic review of the scientific literature. To address the complexities of paediatric emergency research, informed consent, and data processing, experts with expertise in paediatric intensive care, computer science, and medical law were sought. After the transcription and anonymisation, the analysis followed established guidelines for qualitative content and thematic analysis.

Results

Interviewees highlighted the intricacies of managing consent in personalised SIRS research due to the large amount and complexity of information necessary for autonomous decision-making. Thus, instruments aimed at enhancing the understanding of legal guardians and to empowering the child were appreciated and the need for specific guidelines and establishing standards was expressed. Medical risks were estimated to be low, but the challenges of securing anonymisation and data protection were expected. It was emphasised that risks and benefits cannot be anticipated at this stage. Social justice issues were identified because of possible biases within the research population. Our findings were analysed using current ethical and legal frameworks for research with a focus on the particularities of the patient group and the emergency background. In this particular context, experts advocated for an enabling approach pertaining to AI in combination with OMICS technologies.

Conclusion

As with every new technological development, ethical and legal challenges cannot be foreseen for SIRS-personalised treatment. Given this circumstance, experts emphasised the importance of extending the ethics-legal discourse beyond mere restrictions. The organisation of supervision should be reconsidered and not limited only to the precautionary principle, which per se was seen as impeding both the medical progress and clinical flexibility. It was noted that the establishment and monitoring of guidelines were emergent and should evolve through an interdisciplinary discourse. Therefore, it was recommended to enhance the qualifications of physicians in the field of computer science, impart ethics training to AI developers, and involve experts with expertise in medical law and data protection.

WIMOAD: Weighted Integration of Multi-Omics data for Alzheimer's Disease (AD) Diagnosis

As the most common subtype of dementia, Alzheimer's disease (AD) is characterized by a progressive decline in cognitive functions, especially in memory, thinking, and reasoning ability. Early diagnosis and interventions enable the implementation of measures to reduce or slow further regression of the disease, preventing individuals from severe brain function decline. The current framework of AD diagnosis depends on A/T/(N) biomarkers detection from cerebrospinal fluid or brain imaging data, which is invasive and expensive during the data acquisition process. Moreover, the pathophysiological changes of AD accumulate in amino acids, metabolism, neuroinflammation, etc., resulting in heterogeneity in newly registered patients. Recently, next generation sequencing (NGS) technologies have found to be a non-invasive, efficient and less-costly alternative on AD screening. However, most of existing studies rely on single omics only. To address these concerns, we introduce WIMOAD, a weighted integration of multi-omics data for AD diagnosis. WIMOAD synergistically leverages specialized classifiers for patients' paired gene expression and methylation data for multi-stage classification. The resulting scores were then stacked with MLP-based meta-models for performance improvement. The prediction results of two distinct meta-models were integrated with optimized weights for the final decision-making of the model, providing higher performance than using single omics only. Remarkably, WIMOAD achieves significantly higher performance than using single omics alone in the classification tasks. The model's overall performance also outperformed most existing approaches, highlighting its ability to effectively discern intricate patterns in multi-omics data and their correlations with clinical diagnosis results. In addition, WIMOAD also stands out as a biologically interpretable model by leveraging the SHapley Additive exPlanations (SHAP) to elucidate the contributions of each gene from each omics to the model output. We believe WIMOAD is a very promising tool for accurate AD diagnosis and effective biomarker discovery across different progression stages, which eventually will have consequential impacts on early treatment intervention and personalized therapy design on AD.

Struggling to Understand the NEC Spectrum-Could the Integration of Metabolomics, Clinical-Laboratory Data, and Other Emerging Technologies Help Diagnosis?

Necrotizing enterocolitis (NEC) is the most prevalent and potentially fatal intestinal injury mainly affecting premature infants, with significant long-term consequences for those who survive. This review explores the scale of the problem, highlighting advancements in epidemiology, the understanding of pathophysiology, and improvements in the prediction and diagnosis of this complex, multifactorial, and multifaced disease. Additionally, we focus on the potential role of metabolomics in distinguishing NEC from other conditions, which could allow for an earlier and more accurate classification of intestinal injuries in infants. By integrating metabolomic data with other diagnostic approaches, it is hoped to enhance our ability to predict outcomes and tailor treatments, ultimately improving care for affected infants.

Reassessing acquired neonatal intestinal diseases using unsupervised machine learning

BACKGROUND

Acquired neonatal intestinal diseases have an array of overlapping presentations and are often labeled under the dichotomous classification of necrotizing enterocolitis (which is poorly defined) or spontaneous intestinal perforation, hindering more precise diagnosis and research. The objective of this study was to take a fresh look at neonatal intestinal disease classification using unsupervised machine learning.

METHODS

Patients admitted to the University of Florida Shands Neonatal Intensive Care Unit January 2013-September 2019 diagnosed with an intestinal injury, or had imaging findings of portal venous gas, pneumatosis, abdominal free air, or had an abdominal drain placed or exploratory laparotomy during admission were included. Congenital gastroschisis, omphalocele, intestinal atresia, malrotation were excluded. Data was collected via retrospective chart review with subsequent hierarchal, unsupervised clustering analysis.

RESULTS

Five clusters of intestinal injury were identified: Cluster 1 deemed the "Low Mortality" cluster, Cluster 2 deemed the "Mature with Inflammation" cluster, Cluster 3 deemed the "Immature with High Mortality" cluster, Cluster 4 deemed the "Late Injury at Full Feeds" cluster, and Cluster 5 deemed the "Late Injury with High Rate of Intestinal Necrosis" cluster.

CONCLUSION

Unsupervised machine learning can be used to cluster acquired neonatal intestinal injuries. Future study with larger multicenter datasets is needed to further refine and classify types of intestinal diseases.

IMPACT

Unsupervised machine learning can be used to cluster types of acquired neonatal intestinal injury. Five major clusters of acquired neonatal intestinal injury are described, each with unique features. The clusters herein described deserve future, multicenter study to determine more specific early biomarkers and tailored therapeutic interventions to improve outcomes of often devastating neonatal acquired intestinal injuries.

Computational Approaches for Predicting Preterm Birth and Newborn Outcomes

Preterm birth (PTB) and its associated morbidities are a leading cause of infant mortality and morbidity. Accurate predictive models and a better biological understanding of PTB-associated morbidities are critical in reducing their adverse effects. Increasing availability of multimodal high-dimensional data sets with concurrent advances in artificial intelligence (AI) have created a rich opportunity to gain novel insights into PTB, a clinically complex and multifactorial disease. Here, the authors review the use of AI to analyze 3 modes of data: electronic health records, biological omics, and social determinants of health metrics.

A Theoretical Exploration of Artificial Intelligence's Impact on Feto-Maternal Health from Conception to Delivery

The implementation of Artificial Intelligence (AI) in healthcare is enhancing diagnostic accuracy in clinical setups. The use of AI in healthcare is steadily increasing with advancing technology, extending beyond disease diagnosis to encompass roles in feto-maternal health. AI harnesses Machine Learning (ML), Natural Language Processing (NLP), Artificial Neural Networks (ANN), and computer vision to analyze data and draw conclusions. Considering maternal health, ML analyzes vast datasets to predict maternal and fetal health outcomes, while NLP interprets medical texts and patient records to assist in diagnosis and treatment decisions. ANN models identify patterns in complex feto-maternal medical data, aiding in risk assessment and intervention planning whereas, computer vision enables the analysis of medical images for early detection of feto-maternal complications. AI facilitates early pregnancy detection, genetic screening, and continuous monitoring of maternal health parameters, providing real-time alerts for deviations, while also playing a crucial role in the early detection of fetal abnormalities through enhanced ultrasound imaging, contributing to informed decision-making. This review investigates into the application of AI, particularly through predictive models, in addressing the monitoring of feto-maternal health. Additionally, it examines potential future directions and challenges associated with these applications.

Comprehensive overview of the anesthesiology research landscape: A machine Learning Analysis of 737 NIH-funded anesthesiology primary Investigator's publication trends

Background

Anesthesiology plays a crucial role in perioperative care, critical care, and pain management, impacting patient experiences and clinical outcomes. However, our understanding of the anesthesiology research landscape is limited. Accordingly, we initiated a data-driven analysis through topic modeling to uncover research trends, enabling informed decision-making and fostering progress within the field.

Methods

The easyPubMed R package was used to collect 32,300 PubMed abstracts spanning from 2000 to 2022. These abstracts were authored by 737 Anesthesiology Principal Investigators (PIs) who were recipients of National Institute of Health (NIH) funding from 2010 to 2022. Abstracts were preprocessed, vectorized, and analyzed with the state-of-the-art BERTopic algorithm to identify pillar topics and trending subtopics within anesthesiology research. Temporal trends were assessed using the Mann-Kendall test.

Results

The publishing journals with most abstracts in this dataset were Anesthesia & Analgesia 1133, Anesthesiology 992, and Pain 671. Eight pillar topics were identified and categorized as basic or clinical sciences based on a hierarchical clustering analysis. Amongst the pillar topics, "Cells & Proteomics" had both the highest annual and total number of abstracts. Interestingly, there was an overall upward trend for all topics spanning the years 2000-2022. However, when focusing on the period from 2015 to 2022, topics "Cells & Proteomics" and "Pulmonology" exhibit a downward trajectory. Additionally, various subtopics were identified, with notable increasing trends in "Aneurysms", "Covid 19 Pandemic", and "Artificial intelligence & Machine Learning".

Conclusion

Our work offers a comprehensive analysis of the anesthesiology research landscape by providing insights into pillar topics, and trending subtopics. These findings contribute to a better understanding of anesthesiology research and can guide future directions.

A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions

Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of implementation of Machine Learning (ML) in metadata retrieval, offering promising avenues for a deeper understanding of microbial communities and their ecological roles. Leveraging these tools will enhance our insights into microbial functional capabilities and ecological dynamics in diverse ecosystems. Finally, we emphasize the crucial metadata role in ML models development.

Multimodal machine learning for modeling infant head circumference, mothers' milk composition, and their shared environment

Links between human milk (HM) and infant development are poorly understood and often focus on individual HM components. Here we apply multi-modal predictive machine learning to study HM and head circumference (a proxy for brain development) among 1022 mother-infant dyads of the CHILD Cohort. We integrated HM data (19 oligosaccharides, 28 fatty acids, 3 hormones, 28 chemokines) with maternal and infant demographic, health, dietary and home environment data. Head circumference was significantly predictable at 3 and 12 months. Two of the most associated features were HM n3-polyunsaturated fatty acid C22:6n3 (docosahexaenoic acid, DHA; p = 9.6e-05) and maternal intake of fish (p = 4.1e-03), a key dietary source of DHA with established relationships to brain function. Thus, using a systems biology approach, we identified meaningful relationships between HM and brain development, which validates our statistical approach, gives credence to the novel associations we observed, and sets the foundation for further research with additional cohorts and HM analytes.

Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence

With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.

Medical Data Analysis Meets Artificial Intelligence (AI) and Internet of Medical Things (IoMT)

AI is a contemporary methodology rooted in the field of computer science [...].

Metabolomic signatures distinguish extracellular vesicles from osteoclasts and odontoclasts

AIMS

Pathological dental root resorption and alveolar bone loss are often detected only after irreversible damage. Biomarkers in the gingival crevicular fluid or saliva could provide a means for early detection; however, such biomarkers have proven elusive. We hypothesize that a multiomic approach might yield reliable diagnostic signatures for root resorption and alveolar bone loss. Previously, we showed that extracellular vesicles (EVs) from osteoclasts and odontoclasts differ in their protein composition. In this study, we investigated the metabolome of EVs from osteoclasts, odontoclasts and clasts (non-resorbing clastic cells).

MATERIALS AND METHODS

Mouse haematopoietic precursors were cultured on dentine, bone or plastic, in the presence of recombinant RANKL and CSF-1 to trigger differentiation along the clastic line. On Day 7, the cells were fixed and the differentiation state and resorptive status of the clastic cells were confirmed. EVs were isolated from the conditioned media on Day 7 and characterized by nanoparticle tracking and electron microscopy to ensure quality. Global metabolomic profiling was performed using a Thermo Q-Exactive Orbitrap mass spectrometer with a Dionex UHPLC and autosampler.

RESULTS

We identified 978 metabolites in clastic EVs. Of those, 79 are potential biomarkers with Variable Interdependent Parameters scores of 2 or greater. Known metabolites cytidine, isocytosine, thymine, succinate and citrulline were found at statistically higher levels in EVs from odontoclasts compared with osteoclasts.

CONCLUSION

We conclude that numerous metabolites found in odontoclast EVs differ from those in osteoclast EVs, and thus represent potential biomarkers for root resorption and periodontal tissue destruction.

Multiomic Investigations into Lung Health and Disease

Diseases of the lung account for more than 5 million deaths worldwide and are a healthcare burden. Improving clinical outcomes, including mortality and quality of life, involves a holistic understanding of the disease, which can be provided by the integration of lung multi-omics data. An enhanced understanding of comprehensive multiomic datasets provides opportunities to leverage those datasets to inform the treatment and prevention of lung diseases by classifying severity, prognostication, and discovery of biomarkers. The main objective of this review is to summarize the use of multiomics investigations in lung disease, including multiomics integration and the use of machine learning computational methods. This review also discusses lung disease models, including animal models, organoids, and single-cell lines, to study multiomics in lung health and disease. We provide examples of lung diseases where multi-omics investigations have provided deeper insight into etiopathogenesis and have resulted in improved preventative and therapeutic interventions.

Endophytes in Agriculture: Potential to Improve Yields and Tolerances of Agricultural Crops

Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting in improved crop yields. Evidence shows that endophytes can provide improved tolerances to salinity, moisture, and drought conditions, highlighting the capacity to farm them in marginal land with the use of endophyte-based strategies. Furthermore, endophytes offer a sustainable alternative to traditional agricultural practices, reducing the need for synthetic fertilizers and pesticides, and in turn reducing the risks associated with chemical treatments. In this review, we summarise the current knowledge on endophytes in agriculture, highlighting their potential as a sustainable solution for improving crop productivity and general plant health. This review outlines key nutrient, environmental, and biotic stressors, providing examples of endophytes mitigating the effects of stress. We also discuss the challenges associated with the use of endophytes in agriculture and the need for further research to fully realise their potential.

Development of a peripheral blood transcriptomic gene signature to predict bronchopulmonary dysplasia

Bronchopulmonary dysplasia (BPD) is the most common lung disease of extreme prematurity, yet mechanisms that associate with or identify neonates with increased susceptibility for BPD are largely unknown. Combining artificial intelligence with gene expression data is a novel approach that may assist in better understanding mechanisms underpinning chronic lung disease and in stratifying patients at greater risk for BPD. The objective of this study is to develop an early peripheral blood transcriptomic signature that can predict preterm neonates at risk for developing BPD. Secondary analysis of whole blood microarray data from 97 very low birth weight neonates on day of life 5 was performed. BPD was defined as positive pressure ventilation or oxygen requirement at 28 days of age. Participants were randomly assigned to a training (70%) and testing cohort (30%). Four gene-centric machine learning models were built, and their discriminatory abilities were compared with gestational age or birth weight. This study adheres to the transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD) statement. Neonates with BPD (n = 62 subjects) exhibited a lower median gestational age (26.0 wk vs. 30.0 wk, P < 0.01) and birth weight (800 g vs. 1,280 g, P < 0.01) compared with non-BPD neonates. From an initial pool (33,252 genes/patient), 4,523 genes exhibited a false discovery rate (FDR) <1%. The area under the receiver operating characteristic curve (AUC) for predicting BPD utilizing gestational age or birth weight was 87.8% and 87.2%, respectively. The machine learning models, using a combination of five genes, revealed AUCs ranging between 85.8% and 96.1%. Pathways integral to T cell development and differentiation were associated with BPD. A derived five-gene whole blood signature can accurately predict BPD in the first week of life.