Mining Early Life Risk and Resiliency Factors and Their Influences in Human Populations from PubMed: A Machine Learning Approach to Discover DOHaD Evidence

Abstract

The Developmental Origins of Health and Disease (DOHaD) framework aims to understand how early life exposures shape lifecycle health. To date, no comprehensive list of these exposures and their interactions has been developed, which limits our ability to predict trajectories of risk and resiliency in humans. To address this gap, we developed a model that uses text-mining, machine learning, and natural language processing approaches to automate search, data extraction, and content analysis from DOHaD-related research articles available in PubMed. Our first model captured 2469 articles, which were subsequently categorised into topics based on word frequencies within the titles and abstracts. A manual screening validated 848 of these as relevant, which were used to develop a revised model that finally captured 2098 articles that largely fell under the most prominently researched domains related to our specific DOHaD focus. The articles were clustered according to latent topic extraction, and 23 experts in the field independently labelled the perceived topics. Consensus analysis on this labelling yielded mostly from fair to substantial agreement, which demonstrates that automated models can be developed to successfully retrieve and classify research literature, as a first step to gather evidence related to DOHaD risk and resilience factors that influence later life human health.

A Narrative Literature Review of Natural Language Processing Applied to the Occupational Exposome

“…Next, topic modelling is used to analyse and visualise the content of the literature. The authors of [ 15 ] propose to use scientific literature on PubMed to assess the impact of environmental exposures from early life using different unsupervised learning methods (e.g., LDA (Latent Dirichlet Allocation)) to gain insight into the different topics. The work by [ 29 ] models the impact of COPD (chronic obstructive pulmonary) from smoking using Adverse Outcome Pathways generated from the scientific literature.…”

“…Tool used NLTK [9][10][11][12][13], [14] Other [9,[15][16][17][18], [19][20][21], [13,[22][23][24], [25][26][27] Not declared [15,[28][29][30][31][32], [33][34][35][36][37], [38][39][40] Resources Scientific literature [12,15,28,29,41,42], [14,22,23,31], [24,43,44], [19][20][21]33,…”

Using Microbiome-Based Approaches to Deprogram Chronic Disorders and Extend the Healthspan following Adverse Childhood Experiences

“…In effect, human systems are readily programmed for later life dysfunction and chronic disease when the fetus, newborn, infant, and adolescent are inadequately protected during critical windows of developmental vulnerability. This special vulnerability in early life and the need for special protections of the young have been described in a series of papers and reports [1][2][3][4][5] that contributed to what became known as the scientific field of Developmental Origins of Health and Disease (DOHaD).…”

Using Microbiome-Based Approaches to Deprogram Chronic Disorders and Extend the Healthspan Following Adverse Childhood Experiences

“…In effect human systems are readily programmed for later life dysfunction and chronic disease when the fetus, newborn, infant, and adolescent are inadequately protected during critical windows of developmental vulnerability. This special vulnerability in early life and the need for special protections of the young have been described in a series of papers and reports [1][2][3][4][5] that contributed to what became known as the scientific field of Developmental Origins of Health and Disease (DOHaD).…”