Position paper: The potential role of optical biopsy in the study and diagnosis of environmental enteric dysfunction

Self-Supervised Joint Learning for pCLE Image Denoising

Probe-based confocal laser endoscopy (pCLE) has emerged as a powerful tool for disease diagnosis, yet it faces challenges such as the formation of hexagonal patterns in images due to the inherent characteristics of fiber bundles. Recent advancements in deep learning offer promise in image denoising, but the acquisition of clean-noisy image pairs for training networks across all potential scenarios can be prohibitively costly. Few studies have explored training denoising networks on such pairs. Here, we propose an innovative self-supervised denoising method. Our approach integrates noise prediction networks, image quality assessment networks, and denoising networks in a collaborative, jointly trained manner. Compared to prior self-supervised denoising methods, our approach yields superior results on pCLE images and fluorescence microscopy images. In summary, our novel self-supervised denoising technique enhances image quality in pCLE diagnosis by leveraging the synergy of noise prediction, image quality assessment, and denoising networks, surpassing previous methods on both pCLE and fluorescence microscopy images.

Transcutaneous fluorescence spectroscopy: development and characterization of a compact, portable, and fiber-optic sensor

Significance

The integrity of the intestinal barrier is gaining recognition as a significant contributor to various pathophysiological conditions, including inflammatory bowel disease, celiac disease, environmental enteric dysfunction (EED), and malnutrition. EED, for example, manifests as complex structural and functional changes in the small intestine leading to increased intestinal permeability, inflammation, and reduced absorption of nutrients. Despite the importance of gut function, current techniques to assess intestinal permeability (such as endoscopic biopsies or dual sugar assays) are either highly invasive, unreliable, and/or difficult to perform in certain patient populations (e.g., infants).

Aim

We present a portable, optical sensor based on transcutaneous fluorescence spectroscopy to assess gut function (in particular, intestinal permeability) in a fast and noninvasive manner.

Approach

Participants receive an oral dose of a fluorescent contrast agent, and a wearable fiber-optic probe detects the permeation of the contrast agent from the gut into the blood stream by measuring the fluorescence intensity noninvasively at the fingertip. We characterized the performance of our compact optical sensor by comparing it against an existing benchtop spectroscopic system. In addition, we report results from a human study in healthy volunteers investigating the impact of skin tone and contrast agent dose on transcutaneous fluorescence signals.

Results

The first study with eight healthy participants showed good correlation between our compact sensor and the existing benchtop spectroscopic system [correlation coefficient ( r ) > 0.919 , p < 0.001 ]. Further experiments in 14 healthy participants revealed an approximately linear relationship between the ingested contrast agent dose and the collected signal intensity. Finally, a parallel study on the impact of different skin tones showed no significant differences in signal levels between participants with different skin tones (p > 0.05 ).

Conclusions

In this paper, we demonstrate the potential of our compact transcutaneous fluorescence sensor for noninvasive monitoring of intestinal health.

Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy

Environmental enteric dysfunction (EED) is a subclinical syndrome of intestinal inflammation, malabsorption and barrier disruption that is highly prevalent in low- and middle-income countries in which poverty, food insecurity and frequent exposure to enteric pathogens impair growth, immunity and neurodevelopment in children. In this Review, we discuss advances in our understanding of EED, intestinal adaptation and the gut microbiome over the 'first 1,000 days' of life, spanning pregnancy and early childhood. Data on maternal EED are emerging, and they mirror earlier findings of increased risks for preterm birth and fetal growth restriction in mothers with either active inflammatory bowel disease or coeliac disease. The intense metabolic demands of pregnancy and lactation drive gut adaptation, including dramatic changes in the composition, function and mother-to-child transmission of the gut microbiota. We urgently need to elucidate the mechanisms by which EED undermines these critical processes so that we can improve global strategies to prevent and reverse intergenerational cycles of undernutrition.

Non-invasive assessment of intestinal permeability in healthy volunteers using transcutaneous fluorescence spectroscopy

The permeability of the intestinal barrier is altered in a multitude of gastrointestinal conditions such as Crohn's and coeliac disease. However, the clinical utility of gut permeability is currently limited due to a lack of reliable diagnostic tests. To address this issue, we report a novel technique for rapid, non-invasive measurement of gut permeability based on transcutaneous ('through-the-skin') fluorescence spectroscopy. In this approach, participants drink an oral dose of a fluorescent dye (fluorescein) and a fibre-optic fluorescence spectrometer is attached to the finger to detect permeation of the dye from the gut into the blood stream in a non-invasive manner. To validate this technique, clinical trial measurements were performed in 11 healthy participants. First, after 6 h of fasting, participants ingested 500 mg of fluorescein dissolved in 100 ml of water and fluorescence measurements were recorded at the fingertip over the following 3 h. All participants were invited back for a repeat study, this time ingesting the same solution but with 60 g of sugar added (known to transiently increase intestinal permeability). Results from the two study datasets (without and with sugar respectively) were analysed and compared using a number of analysis procedures. This included both manual and automated calculation of a series of parameters designed for assessment of gut permeability. Calculated values were compared using Student's T-tests, which demonstrated significant differences between the two datasets. Thus, transcutaneous fluorescence spectroscopy shows promise in non-invasively discriminating between two differing states of gut permeability, demonstrating potential for future clinical use.

13C-sucrose breath test for the non-invasive assessment of environmental enteropathy in Zambian adults

Objectives

Environmental enteropathy (EE) is a subclinical disorder highly prevalent in tropical and disadvantaged populations and is thought to play a role in growth faltering in children, poor responses to oral vaccines, and micronutrient deficiencies. This study aims to evaluate the potential of a non-invasive breath test based on stable isotopes for evaluation of impaired digestion and absorption of sucrose in EE.

Methods

We optimized a ¹³C-sucrose breath test (¹³C-SBT) in 19 young adults in Glasgow, United Kingdom. In a further experiment (in 18 adults) we validated the ¹³C-SBT using Reducose, an intestinal glucosidase inhibitor. We then compared the ¹³C-SBT to intestinal mucosal morphometry, immunostaining for sucrose-isomaltase (SI) expression, and SI activity in 24 Zambian adults with EE.

Results

Fully labeled sucrose (0.3 mg/kg) provided clear breath enrichment signals over 2–3 h in both British and Zambian adults, more than fivefold higher than naturally enriched sucrose. Reducose dramatically impaired ¹³C-sucrose digestion, reducing 4 h ¹³CO₂ breath recovery by > 50%. Duodenal biopsies in Zambian adults confirmed the presence of EE, and SI immunostaining was present in 16/24 adults. The kinetics of ¹³CO₂ evolution were consistently faster in participants with detectable SI immunostaining. Although sucrase activity was strongly correlated with villus height (r = 0.72; P < 0.05) after adjustment for age, sex and body mass index, there were no correlations between ¹³C-SBT and villus height or measured sucrase activity in pinch biopsies.

Conclusion

A ¹³C-SBT was developed which was easy to perform, generated clear enrichment of ¹³CO₂ in breath samples, and clearly reports sucrase activity. Further work is needed to validate it and understand its applications in evaluating EE.

Gut microbiome development and childhood undernutrition

Forty-five percent of deaths among children under 5 years of age are associated with undernutrition. Globally, almost 200 million children exhibit the two major forms of undernutrition-wasting (low weight-for-height) or stunting (low height-for-age), with many affected by both. Undernutrition is not due to food insecurity alone. Growing evidence indicates that perturbed postnatal gut microbiome development contributes to its pathogenesis. This perspective focuses on defining and repairing these defects in gut microbiome development. We describe an approach that involves the analysis of well-phenotyped human cohorts, followed by preclinical studies using gnotobiotic animals colonized with microbiota from these cohorts. Additionally, these models can be used to identify therapeutic targets and candidates that can then be tested clinically. Furthermore, introducing pretreatment microbiota from trial participants into gnotobiotic animals and re-enacting trial conditions allow mechanisms to be dissected. We highlight these recent advances as well as gaps in existing knowledge that present opportunities for future research.

Serum Biomarkers of Environmental Enteric Dysfunction and Growth Perspective in Egyptian Children

BACKGROUND: Environmental enteric dysfunction (EED) is a chronic subclinical condition, contributed to limited sources and poor countries. EED pathology is concerned with small intestine structure and function, which affect the macronutrients and micronutrients absorption with consequent growth faltering. AIM: This study aimed to evaluate some serum biomarkers involved in EED and determine their association with stunting and faltering growth in children; zonulin, endotoxin core antibody (EndoCAb), high-sensitive C-reactive protein (hsCRP), alpha-1-acid glycoprotein (AGP), and tumor necrosis factor (TNF), serum iron, and Vitamins A and D. PATIENTS AND METHODS: This case–control study enrolled 105 children aged from 1 to 10 years old, having weight-for-age z-scores and height-for-age z-scores (WAZ or HAZ) ranging from −1.5 to −2. They were compared with control group consisted of 100 children having WAZ or HAZ > −1 of matched age and sex. Assessment of serum markers levels of enteric dysfunction (zonulin and EndoCAb), markers of systemic inflammation (Hs CRP and AGP), along with serum micronutrients (vitamin A, vitamin D and iron) in children with malnutrition in comparison to controls. RESULTS: There was a highly significant decrease as regarding the anthropometric measurements; weight, height, BMI, and arm circumference. Moreover, significant increase in serum zonulin, EndoCAb, HsCRP, and AGP and highly significant decrease of serum Vitamin D and iron in cases group as compared to control group. Height Z score showed negative correlation with zonulin, HsCRP, and AGP and positive correlation with Vitamin D. Weight Z score showed negative correlation with zonulin, HsCRP, and AGP and positive correlation with Vitamin D and Vitamin A. Regression analysis noted increase of zonulin and α1AGP as high associative markers with height Z score affection, however, increase of zonulin was high associative markers with weight Z score affection. CONCLUSION: Faltering growth is associated with elevated serum systemic markers of intestinal inflammation (HsCRP and α1AGP). EED may be a cause of faltering growth.

Towards Intraoperative Quantification of Atrial Fibrosis Using Light-Scattering Spectroscopy and Convolutional Neural Networks

Light-scattering spectroscopy (LSS) is an established optical approach for characterization of biological tissues. Here, we investigated the capabilities of LSS and convolutional neural networks (CNNs) to quantitatively characterize the composition and arrangement of cardiac tissues. We assembled tissue constructs from fixed myocardium and the aortic wall with a thickness similar to that of the atrial free wall. The aortic sections represented fibrotic tissue. Depth, volume fraction, and arrangement of these fibrotic insets were varied. We gathered spectra with wavelengths from 500–1100 nm from the constructs at multiple locations relative to a light source. We used single and combinations of two spectra for training of CNNs. With independently measured spectra, we assessed the accuracy of the CNNs for the classification of tissue constructs from single spectra and combined spectra. Combined spectra, including the spectra from fibers distal from the illumination fiber, typically yielded the highest accuracy. The maximal classification accuracy of the depth detection, volume fraction, and permutated arrangements was (mean ± standard deviation (stddev)) 88.97 ± 2.49%, 76.33 ± 1.51%, and 84.25 ± 1.88%, respectively. Our studies demonstrate the reliability of quantitative characterization of tissue composition and arrangements using a combination of LSS and CNNs. The potential clinical applications of the developed approach include intraoperative quantification and mapping of atrial fibrosis, as well as the assessment of ablation lesions.

Plasmonic optical fiber for bacteria manipulation-characterization and visualization of accumulation behavior under plasmo-thermal trapping

In this article, we demonstrate a plasmo-thermal bacterial accumulation effect using a miniature plasmonic optical fiber. The combined action of far-field convection and a near-field trapping force (referred to as thermophoresis)-induced by highly localized plasmonic heating-enabled the large-area accumulation of Escherichia coli. The estimated thermophoretic trapping force agreed with previous reports, and we applied speckle imaging analysis to map the in-plane bacterial velocities over large areas. This is the first time that spatial mapping of bacterial velocities has been achieved in this setting. Thus, this analysis technique provides opportunities to better understand this phenomenon and to drive it towards in vivo applications.

Understanding the role of the gut in undernutrition: what can technology tell us?

Gut function remains largely underinvestigated in undernutrition, despite its critical role in essential nutrient digestion, absorption and assimilation. In areas of high enteropathogen burden, alterations in gut barrier function and subsequent inflammatory effects are observable but remain poorly characterised. Environmental enteropathy (EE)-a condition that affects both gut morphology and function and is characterised by blunted villi, inflammation and increased permeability-is thought to play a role in impaired linear growth (stunting) and severe acute malnutrition. However, the lack of tools to quantitatively characterise gut functional capacity has hampered both our understanding of gut pathogenesis in undernutrition and evaluation of gut-targeted therapies to accelerate nutritional recovery. Here we survey the technology landscape for potential solutions to improve assessment of gut function, focussing on devices that could be deployed at point-of-care in low-income and middle-income countries (LMICs). We assess the potential for technological innovation to assess gut morphology, function, barrier integrity and immune response in undernutrition, and highlight the approaches that are currently most suitable for deployment and development. This article focuses on EE and undernutrition in LMICs, but many of these technologies may also become useful in monitoring of other gut pathologies.

Serum Biomarkers of Environmental Enteric Dysfunction and Growth Perspective in Egyptian Children

BACKGROUND: Environmental enteric dysfunction (EED) is a chronic subclinical condition, contributed to limited sources and poor countries. EED pathology is concerned with small intestine structure and function, which affect the macronutrients and micronutrients absorption with consequent growth faltering. AIM: This study aimed to evaluate some serum biomarkers involved in EED and determine their association with stunting and faltering growth in children; zonulin, endotoxin core antibody (EndoCAb), high-sensitive C-reactive protein (hsCRP), alpha-1-acid glycoprotein (AGP), and tumor necrosis factor (TNF), serum iron, and Vitamins A and D. PATIENTS AND METHODS: This case–control study enrolled 105 children aged from 1 to 10 years old, having weight-for-age z-scores and height-for-age z-scores (WAZ or HAZ) ranging from −1.5 to −2. They were compared with control group consisted of 100 children having WAZ or HAZ > −1 of matched age and sex. Assessment of serum markers levels of enteric dysfunction (zonulin and EndoCAb), markers of systemic inflammation (Hs CRP and AGP), along with serum micronutrients (vitamin A, vitamin D and iron) in children with malnutrition in comparison to controls. RESULTS: There was a highly significant decrease as regarding the anthropometric measurements; weight, height, BMI, and arm circumference. Moreover, significant increase in serum zonulin, EndoCAb, HsCRP, and AGP and highly significant decrease of serum Vitamin D and iron in cases group as compared to control group. Height Z score showed negative correlation with zonulin, HsCRP, and AGP and positive correlation with Vitamin D. Weight Z score showed negative correlation with zonulin, HsCRP, and AGP and positive correlation with Vitamin D and Vitamin A. Regression analysis noted increase of zonulin and α1AGP as high associative markers with height Z score affection, however, increase of zonulin was high associative markers with weight Z score affection. CONCLUSION: Faltering growth is associated with elevated serum systemic markers of intestinal inflammation (HsCRP and α1AGP). EED may be a cause of faltering growth.

Transcutaneous fluorescence spectroscopy as a tool for non-invasive monitoring of gut function: first clinical experiences

Gastro-intestinal function plays a vital role in conditions ranging from inflammatory bowel disease and HIV through to sepsis and malnutrition. However, the techniques that are currently used to assess gut function are either highly invasive or unreliable. Here we present an alternative, non-invasive sensing modality for assessment of gut function based on fluorescence spectroscopy. In this approach, patients receive an oral dose of a fluorescent contrast agent and a fibre-optic probe is used to make fluorescence measurements through the skin. This provides a readout of the degree to which fluorescent dyes have permeated from the gut into the blood stream. We present preliminary results from our first measurements in human volunteers demonstrating the potential of the technique for non-invasive monitoring of multiple aspects of gastro-intestinal health.

Aptamers in Diagnostic and Molecular Imaging Applications

The origin of the term diagnostic comes from the Greek word gnosis, meaning "to know." In medicine, a diagnostic can predict the pathology risk, disease status, treatment, and prognosis, even following therapy. An early and correct diagnosis is necessary for an efficient treatment. Moreover, it is possible to predict if and why a therapy will be successful or fail, enabling the timely application of alternative therapeutic strategies. Available diagnostics are due to the advances in biotechnology; however, more sensitive, low-cost, and noninvasive methodologies are still a challenge. Knowledge about molecular characteristics provide personalized information, which is the goal of future medicine. Today, multiple diagnostic techniques have emerged, with which it is possible to distinguish molecular patterns.In this way, aptamers are the perfect tools to recognize molecular targets and can be easily modified to confer additional functions. Their versatile characteristics and low cost make aptamers ideal for diagnostic applications.This chapter is a review of aptamer-based diagnostics in biomedicine, with a special focus on probe design and molecular imaging. Graphical Abstract.

Environmental enteric dysfunction: a review of potential mechanisms, consequences and management strategies

BACKGROUND

Environmental enteric dysfunction (EED) is an acquired enteropathy of the small intestine, characterized by enteric inflammation, villus blunting and decreased crypt-to-villus ratio. EED has been associated with poor outcomes, including chronic malnutrition (stunting), wasting and reduced vaccine efficacy among children living in low-resource settings. As a result, EED may be a valuable interventional target for programs aiming to reduce childhood morbidity in low and middle-income countries.

MAIN TEXT

Several highly plausible mechanisms link the proposed pathophysiology underlying EED to adverse outcomes, but causal attribution of these pathways has proved challenging. We provide an overview of recent studies evaluating the causes and consequences of EED. These include studies of the role of subclinical enteric infection as a primary cause of EED, and efforts to understand how EED-associated systemic inflammation and malabsorption may result in long-term morbidity. Finally, we outline recently completed and upcoming clinical trials that test novel interventions to prevent or treat this highly prevalent condition.

CONCLUSIONS

Significant strides have been made in linking environmental exposure to enteric pathogens and toxins with EED, and in understanding the multifactorial mechanisms underlying this complex condition. Further insights may come from several ongoing and upcoming interventional studies trialing a variety of novel management strategies.

Gastrointestinal diagnosis using non-white light imaging capsule endoscopy

Capsule endoscopy (CE) has proved to be a powerful tool in the diagnosis and management of small bowel disorders since its introduction in 2001. However, white light imaging (WLI) is the principal technology used in clinical CE at present, and therefore, CE is limited to mucosal inspection, with diagnosis remaining reliant on visible manifestations of disease. The introduction of WLI CE has motivated a wide range of research to improve its diagnostic capabilities through integration with other sensing modalities. These developments have the potential to overcome the limitations of WLI through enhanced detection of subtle mucosal microlesions and submucosal and/or transmural pathology, providing novel diagnostic avenues. Other research aims to utilize a range of sensors to measure physiological parameters or to discover new biomarkers to improve the sensitivity, specificity and thus the clinical utility of CE. This multidisciplinary Review summarizes research into non-WLI CE devices by organizing them into a taxonomic structure on the basis of their sensing modality. The potential of these capsules to realize clinically useful virtual biopsy and computer-aided diagnosis (CADx) is also reported.

Modular Robotic Scanning Device for Real-Time Gastric Endomicroscopy

Optical biopsy methods, such as probe-based endomicroscopy, can be used for the identification of early mucosal dysplasia in various gastrointestinal conditions and have potential applications in the screening of early-stage gastric cancer in vivo. However, it is difficult to scan a large area of the gastric mucosa for mosaicing during standard endoscopy. This paper proposes a novel 'snap-on' robotic scanning device that can integrate distally with a commercial endoscope. A customized low-cost endomicroscopy system is used for obtaining micro imaging. The developed device could scan a large area of gastric tissue during standard endoscopy. The device achieves positioning accuracy that is less than 0.23 mm. Experimental results showed that the device could achieve large area mosaicing (15.8-18.6 mm²) and demonstrated the potential clinical value of the device for real-time gastric tissue identification and margin assessment. This approach presents an important alternative to current histology techniques for gastrointestinal tract diagnosis.

EB 2017 Article: Interpretation of the lactulose:mannitol test in rural Malawian children at risk for perturbations in intestinal permeability

The dual sugar absorption test, specifically the lactulose:mannitol test, is used to assess gut health. Lactulose absorption is said to represent gut damage and mannitol absorption is used as a measure of normal small bowel function and serves as normalizing factor for lactulose. A underappreciated limitation of this common understanding of the lactulose:mannitol test is that mannitol is not absorbed to any substantial extent by a transcellular process. Additionally, this interpretation of lactulose:mannitol is not consistent with current understanding of paracellular pathways, where three pathway types exist: pore, leak, and unrestricted. Pore and leak pathways are regulated biological constructions of the small bowel barrier, and unrestricted pathways represent micropathological damage. We analyzed 2334 lactulose:mannitol measurements rigorously collected from 622 young rural Malawian children at high risk for poor gut health in light of the pathway model. An alternative method of normalizing for gut length utilizing autopsy data is described. In our population, absorbed lactulose and mannitol are strongly correlated, r = 0.68 P <0.0001, suggesting lactulose and mannitol are traversing the gut barrier via the same pathways. Considering measurements where pore pathways predominate, mannitol flux is about 14 times that of lactulose. As more leak pathways are present, this differential flux mannitol:lactulose falls to 8:1 and when increased numbers of unrestricted pathways are present, the differential flux of mannitol:lactulose is 6:1. There was no substantial correlation between the lactulose:mannitol and linear growth. Given that mannitol will always pass through a given pathway at a rate at least equal to that of lactulose, and lactulose absorption is a composite measure of flux through both physiologic and pathologic pathways, we question the utility of the lactulose:mannitol test. We suggest using lactulose alone is as informative as lactulose:mannitol in a sugar absorption testing in subclinical gut inflammation. Impact statement Our work integrates the standard interpretation of the lactulose:mannitol test (L:M), with mechanistic insight of intestinal permeability. There are three paracellular pathways in the gut epithelium; pore, leak, and unrestricted. Using thousands of L:M measurements from rural Malawian children at risk for increased intestinal permeability, we predict the differential flux of L and M through the pathways. Our findings challenge the traditional notions that little L is absorbed through a normal epithelial barrier and that M is a normalizing factor for L. Our observations are consistent with pore pathways allowing only M to pass. And that substantial amounts of L and M pass through leak pathways which are normal, regulated, cell-junctional adaptations. So M is a composite measure of all pathways, and L is not a measure solely of pathologic gut damage. Using L alone as a probe will yield more information about gut health than L:M.