Imperial College London

Dr Alex Thompson

Faculty of MedicineDepartment of Surgery & Cancer

Lecturer in Sensing in Cancer



alex.thompson08 Website




B411Bessemer BuildingSouth Kensington Campus





Publication Type

51 results found

Monfort Sanchez E, Avery J, Wei J, Qian J, Mandal N, Agarwal A, Mwiinga M, Banda R, Darzi A, Kelly P, Thompson Aet al., 2024, Transcutaneous fluorescence spectroscopy: development and characterization of a compact, portable, fiber-optic sensor, Journal of Biomedical Optics, ISSN: 1083-3668

Journal article

Ennis A, Nicdao D, Kolagatla S, Dowling L, Tskhe Y, Thompson AJ, Trimble D, Delaney C, Florea Let al., 2023, Two‐photon polymerization of sugar responsive 4D microstructures, Advanced Functional Materials, Vol: 33, ISSN: 1616-301X

Stimuli-responsive hydrogels have attracted much attention owing to the versatility of their programmed response in offering intelligent solutions for biomimicry applications, such as soft robotics, tissue engineering, and drug delivery. To achieve the complexity of biomimetic structures, two photon polymerization (2PP) has provided a means of fabricating intricate 3D structures from stimuli-responsive hydrogels. Rapid swelling hydrogel microstructures are advantageous for osmotically driven stimuli-response, where actuation speed, that is reliant on the diffusion of analytes or bioanalytes, can be optimized. Herein, the flexibility of 2PP is exploited to showcase a novel sugar-responsive, phenylboronic acid-based photoresist. This offers a remarkable solution for achieving fast response hydrogel systems that have been often hindered by the volume-dependent diffusion times of analytes to receptor sites. A phenylboronic acid-based photoresist compatible with 2PP is presented to fabricate stimuli-responsive microstructures with accelerated response times. Moreover, microstructures with programmable actuation (i.e., bending and opening) are fabricated using the same photoresist within a one-step fabrication process. By combining the flexibility of 2PP with an easily adaptable photoresist, an accessible fabrication method is showcased for sophisticated and chemo-responsive 3D hydrogel actuators.

Journal article

Kim JA, Hou Y, Keshavarz M, Yeatman E, Thompson Aet al., 2023, Characterization of bacteria swarming effect under plasmonic optical fiber illumination, Journal of Biomedical Optics, Vol: 28, Pages: 1-15, ISSN: 1083-3668

SignificancePlasmo-thermo-electrophoresis (PTEP) involves using plasmonic microstructures to generate both a large-scale convection current and a near-field attraction force (thermo-electrophoresis). These effects facilitate the collective locomotion (i.e., swarming) of microscale particles in suspension, which can be utilized for numerous applications, such as particle/cell manipulation and targeted drug delivery. However, to date, PTEP for ensemble manipulation has not been well characterized, meaning its potential is yet to be realized.AimOur study aims to provide a characterization of PTEP on the motion and swarming effect of various particles and bacterial cells to allow rational design for bacteria-based microrobots and drug delivery applications.ApproachPlasmonic optical fibers (POFs) were fabricated using two-photon polymerization. The particle motion and swarming behavior near the tips of optical fibers were characterized by image-based particle tracking and analyzing the spatiotemporal concentration variation. These results were further correlated with the shape and surface charge of the particles defined by the zeta potential.ResultsThe PTEP demonstrated a drag force ranging from a few hundred fN to a few tens of pN using the POFs. Furthermore, bacteria with the greater (negative) zeta potential ( | ζ | > 10 mV) and smoother shape (e.g., Klebsiella pneumoniae and Escherichia coli) exhibited the greatest swarming behavior.ConclusionsThe characterization of PTEP-based bacteria swarming behavior investigated in our study can help predict the expected swarming behavior of given particles/bacterial cells. As such, this may aid in realizing the potential of PTEP in the wide-ranging applications highlighted above.

Journal article

Fletcher T, Monfort-Sanchez E, Keshavarz M, Avery J, Ashrafian H, Darzi AW, Thompson AJet al., 2023, Quantifying hypoxia with diffuse reflectance spectroscopy for advanced prognostication and real-time response monitoring in rectal cancer: an in vivo feasibility study, Optical Fibers and Sensors for Medical Diagnostics, Treatment and Environmental Applications XXIII, Publisher: SPIE, Pages: 1-6, ISSN: 1605-7422

Tumour hypoxia is a critical factor in treatment failure and resistance, and its accurate measurement with diffuse reflectance spectroscopy (DRS) could be used for prognostic and response monitoring purposes. In this in vivo characterisation study, we sequentially measured oxygenation trends over the entire course of tumour growth in mice using a multi-depth, fibre-optic DRS probe. Results demonstrated a clear downtrend in oxygenation over time. This progression was not always linear, with significant heterogeneity over time and between mice. Our findings will be further validated against gold standards prior to investigating whether hypoxia can be used to predict radiotherapy responses.

Conference paper

Li X, Keshavarz M, Kassanos P, Kidy Z, Roddan A, Yeatman E, Thompson Aet al., 2023, SERS detection of breast cancer-derived exosomes using a nanostructured Pt-black template, Advanced Sensor Research, Vol: 4, Pages: 1-12, ISSN: 2751-1219

At present, there are no cancer treatments that are both non-invasive and highly accurate. New tests that can diagnose cancer at an early stage would help to facilitate such improved therapies, and many recent studies have focused on the development of liquid biopsy tests for this purpose. Exosomes are extracellular vesicles secreted by cells as a means of communication that can be simply collected from blood samples. Current studies have shown the potential of surface-enhanced Raman spectroscopy (SERS) in differentiating cancerous cells from healthy cells. Herein, a bespoke platinum-black (Pt-black) SERS template is developed—via a cost-effective fabrication method of electroplating—to detect malfunctioned (cancerous) exosomes. The results demonstrate that the Pt-black SERS substrate exhibits stable and consistent spectra, which produces the high reproducibility required for a reliable diagnostic template. More importantly, using the Pt-black SERS template allows for the differentiation of cancer-derived exosomes (extracted from 4T1 cells—a triple-negative breast cancer cell line) and exosomes from healthy fibroblast cells with an 83.3% sensitivity and a 95.8% specificity. This study establishes the potential of the Pt-black template in detecting cancerous exosomes and lays a solid foundation for future studies in the clinical application of SERS in cancer diagnosis.

Journal article

Monfort Sánchez E, Avery J, Gan J, Qian J, Mwiinga M, Banda R, Hoare J, Ashranfian H, Darzi A, Kelly P, Thompson AJet al., 2023, A compact fluorescence sensor for low-cost non-invasive monitoring of gut permeability in undernutrition, Optics and Biophotonics in Low-Resource Settings IX, Publisher: SPIE, Pages: 1-7, ISSN: 1605-7422

Undernutrition is associated with approximately 45% of deaths among children under the age of 5. Furthermore, in 2020, around 149 million children suffered impaired physical/cognitive development due to lack of adequate nutrition. Environmental enteropathy (EE) is associated with undernutrition and is characterized by a multifaceted breakdown in gut function, including an increase in intestinal permeability that can lead to inflammatory responses. However, the role and mechanisms associated with EE (particularly gut permeability) are not well understood. This is partly because current techniques to assess changes in gut permeability, such as endoscopic biopsies, histopathology and chemical tests such as Lactulose:Mannitol assays, are either highly invasive, unreliable or difficult to perform on specific groups of patients (such as infants and patients with urine retention problems). Therefore, low-cost, non-invasive and reliable diagnostic tools are urgently needed for better evaluation of intestinal permeability. Here, we present a compact transcutaneous fluorescence spectroscopy sensor for non-invasive evaluation of gut permeability and report the first in vivo data collected from volunteers in an undernutrition trial. Using this technique and device, fluorescence signals are detected transcutaneously after oral ingestion of a fluorescent solution. Preliminary results demonstrate the potential use of the presented sensor for clinical assessment of gut permeability in low-income settings.

Conference paper

Maleki AN, Thompson A, Runciman MS, Murray J, Mylonas GPet al., 2023, A soft hydraulic endorectal actuator for prostate radiotherapy

Despite advances in radiotherapy, motion error remains a challenge in prostate radiotherapy. Rectal obturators and endorectal balloons may reduce motion error and improve outcomes but have limitations. We aimed to create a deployable rectal obturator with precise angle control to personalise to a patient's rectal anatomy, by using an antagonistic pair of "muscle"actuators to flex and extend the device. Results on deployability, angle control, and radial stiffness are presented here. The device can be compressed down to 16 x 3 x 91 mm, and be deployed to maximum dimensions of 24 x 25.5 x 77 mm. The device provides radial stiffness that may be sufficient to stabilise the rectum during radiotherapy. Angle control can be achieved with an average change of 7.5°/ml inflation in the extensor actuator.

Conference paper

Wei J, Monfort Sanchez E, Avery J, Barbouti O, Hoare J, Ashrafian H, Darzi A, Thompson Aet al., 2022, Non-invasive assessment of intestinal permeability in healthy volunteers using transcutaneous fluorescence spectroscopy, Methods and Applications in Fluorescence, Vol: 10, Pages: 1-9, ISSN: 2050-6120

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.

Journal article

DeLorey C, Davids JD, Cartucho J, Xu C, Roddan A, Nimer A, Ashrafian H, Darzi A, Thompson AJ, Akhond S, Runciman M, Mylonas G, Giannarou S, Avery Jet al., 2022, A cable‐driven soft robotic end‐effector actuator for probe‐based confocal laser endomicroscopy: Development and preclinical validation, Translational Biophotonics, ISSN: 2627-1850

Journal article

Fletcher E, Thompson A, Ashrafian H, Darzi Aet al., 2022, The measurement and modification of hypoxia in colorectal cancer: overlooked but not forgotten, Gastroenterology Report, Vol: 10, Pages: 1-13, ISSN: 2052-0034

Tumour hypoxia is the inevitable consequence of a tumour’s rapid growth and disorganised, inefficient vasculature. The compensatory mechanisms employed by tumours, and indeed the absence of oxygen itself, hinder the ability of all treatment modalities. The clinical consequence is poorer overall survival, disease-free survival, and locoregional control. Recognising this, clinicians have been attenuating the effect of hypoxia, primarily with hypoxic modification or with hypoxia activated pro-drugs, and notable success has been demonstrated. However, in the case of colorectal cancer (CRC), there is a general paucity of knowledge and evidence surrounding the measurement and modification of hypoxia, and this is possibly due to the comparative inaccessibility of such tumours. We specifically review the role of hypoxia in CRC, and focus on: the current evidence for the existence of hypoxia in CRC, the majority of which originates from indirect positron emission topography (PET) imaging with hypoxia selective radiotracers; the evidence correlating CRC hypoxia with poorer oncological outcome, which is largely based on the measurement of Hypoxia Inducible Factor (HIF) in correlation with clinical outcome; the evidence of hypoxic modification in CRC, of which no direct evidence exists, but is reflected in a number of indirect markers; the prognostic and monitoring implications of accurate CRC hypoxia quantification and its potential in the field of precision oncology; and the present and future imaging tools and technologies being developed for the measurement of CRC hypoxia, including the use of blood oxygen level dependent (BOLD) MRI imaging and diffuse reflectance spectroscopy.

Journal article

S√°nchez EM, Avery J, Darzi A, Thompson AJet al., 2022, Development of a wearable fluorescence sensor for non-invasive monitoring of gut permeability, The Hamlyn Symposium on Medical Robotics: "MedTech Reimagined", Publisher: The Hamlyn Centre, Imperial College London London, UK

<jats:p>Inflammatory bowel disease, coeliac disease, and malnutrition have all been linked to changes in intestinal function, particularly gut permeability [1]. Endoscopic biopsies and histopathology, together with chemical tests such as Lactulose:Mannitol assays, are the techniques currently used to assess permeability in the clinic. However, those methods are either invasive, unable to offer comprehensive diagnoses, or challenging to perform in infants [2]. Further, the mechanisms and in interactions behind function the the gut’s aforementioned (and additional) disorders are currently not well understood. As a result, novel diagnostic technologies that provide non-invasive and accurate measurements of intestinal permeability (and other aspects of gut function) could have major therapeutic implications [3]. Recent studies in both humans and animals have shown the potential of transcutaneous fluorescence spectroscopy to provide information relevant to gastrointestinal (GI) function – including gut permeability – in a non-invasive manner (e.g. [4-7]). This method entails oral administration of a fluorescent contrast agent combined with the use of a wearable probe to non-invasively measure the permeation of the contrast agent from the gut into the blood stream, thereby facilitating measurements of gut leakiness/permeability and other clinically relevant GI functions [4-7]. However, the devices that have been used for this purpose are laser-based, large and expensive, which make them unsuitable for large scale clinical deployment [4-7].To address the above limitations, here we report preliminary results from a compact fluorescence spectroscopy sensor for transcutaneous monitoring of gut function. The primary functionality of the device is to detect fluorescence signals at the skin

Conference paper

Monfort Sanchez E, Avery J, Darzi A, Thompson Aet al., 2022, Development of a compact fluorescence spectroscopy sensor for non-invasive monitoring gut function, Optica Biophotonics Congress: Biomedical Optics 2022, Publisher: Optica Publishing Group

Monitoring gut permeability is currently either invasive, inaccurate or difficult to perform in infants. We present a compact fluorescence sensor that overcomes some of these limitations, paving the way for non-invasive gut permeability monitoring.

Conference paper

Wei J, Nazarian S, Teare J, Darzi A, Ashrafian H, Thompson Aet al., 2022, A case for improved assessment of gut permeability: a meta-analysis quantifying the lactulose:mannitol ratio in coeliac and Crohn’s disease, BMC Gastroenterology, Vol: 22, ISSN: 1471-230X

Background:A widely used method in assessing small bowel permeability is the lactulose:mannitol test, where the lactulose:mannitol ratio (LMR) is measured. However, there is discrepancy in how the test is conducted and in the values of LMR obtained across studies. This meta-analysis aims to determine LMR in healthy subjects, coeliac and Crohn’s disease.Methods:A literature search was performed using PRISMA guidance to identify studies assessing LMR in coeliac or Crohn’s disease. 19 studies included in the meta-analysis measured gut permeability in coeliac disease, 17 studies in Crohn’s disease. Outcomes of interest were LMR values and comparisons of standard mean difference (SMD) and weighted mean difference (WMD) in healthy controls, inactive Crohn’s, active Crohn’s, treated coeliac and untreated coeliac. Pooled estimates of differences in LMR were calculated using the random effects model.Results:Pooled LMR in healthy controls was 0.014 (95% CI: 0.006–0.022) while pooled LMRs in untreated and treated coeliac were 0.133 (95% CI: 0.089–0.178) and 0.037 (95% CI: 0.019–0.055). In active and inactive Crohn’s disease, pooled LMRs were 0.093 (95% CI: 0.031–0.156) and 0.028 (95% CI: 0.015–0.041). Significant differences were observed in LMR between: (1) healthy controls and treated coeliacs (SMD = 0.409 95% CI 0.034 to 0.783, p = 0.032), (2) healthy controls and untreated coeliacs (SMD = 1.362 95% CI: 0.740 to 1.984, p < 0.001), (3) treated coeliacs and untreated coeliacs (SMD = 0.722 95% CI: 0.286 to 1.157, p = 0.001), (4) healthy controls and inactive Crohn’s (SMD = 1.265 95% CI: 0.845 to 1.686, p < 0.001), (5) healthy controls and active Crohn’s (SMD = 2.868 95% CI: 2.112 to 3.623, p < 0.001), and (6) active Crohn’s and inactive Crohn&rsquo

Journal article

Mbuki R, Chileya S, Thompson AJ, Kelly P, Kayamba Vet al., 2021, Rapid testing of gut permeability using oral fluorescein and confocal laser endomicroscopy in Zambian adults, TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE, Vol: 115, Pages: 1226-1228, ISSN: 0035-9203

Journal article

Thompson A, Bourke C, Robertson R, Shivakumar N, Edwards C, Preston T, Holmes E, Paul K, Gary F, Douglas Met al., 2021, Understanding the role of the gut in undernutrition: what can technology tell us?, Gut, Vol: 70, Pages: 1580-1594, ISSN: 0017-5749

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.

Journal article

Lett A, Lim A, Skinner C, Maurice J, Vergis N, Darzi A, Goldin R, Thursz M, Thompson Aet al., 2021, Rapid, non-invasive measurement of gastric emptying rate using transcutaneous fluorescence spectroscopy, Biomedical Optics Express, Vol: 12, Pages: 4249-4264, ISSN: 2156-7085

Gastric emptying rate (GER) signifies the rate at which the stomach empties following ingestion of a meal and is relevant to a wide range of clinical conditions. GER also represents a rate limiting step in small intestinal absorption and so is widely assessed for research purposes. Despite the clinical and physiological importance of gastric emptying, methods used to measure GER possess a series of limitations (including being invasive, slow or unsuitable for certain patient populations). Here, we present a new technique based on transcutaneous (through-the-skin) fluorescence spectroscopy that is fast, non-invasive, and does not require the collection of samples or laboratory-based analysis. Thus, this approach has the potential to allow immediate reporting of clinical results. Using this new method, participants receive an oral dose of a fluorescent contrast agent and a wearable probe detects the uptake of the agent from the gut into the blood stream. Analysis of the resulting data then permits the calculation of GER. We compared our spectroscopic technique to the paracetamol absorption test (a clinically approved GER test) in a clinical study of 20 participants. Results demonstrated good agreement between the two approaches and, hence, the clear potential of transcutaneous fluorescence spectroscopy for clinical assessment of GER.

Journal article

Kim J, Yeatman E, Thompson A, 2021, Plasmonic optical fiber for bacteria manipulation—characterization and visualization of accumulation behavior under plasmo-thermal trapping, Biomedical Optics Express, Vol: 12, Pages: 3917-3933, ISSN: 2156-7085

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

Journal article

Dryden SD, Anastasova S, Satta G, Thompson AJ, Leff DR, Darzi Aet al., 2021, Rapid uropathogen identification using surface enhanced Raman spectroscopy active filters., Scientific Reports, Vol: 11, Pages: 1-10, ISSN: 2045-2322

Urinary tract infection is one of the most common bacterial infections leading to increased morbidity, mortality and societal costs. Current diagnostics exacerbate this problem due to an inability to provide timely pathogen identification. Surface enhanced Raman spectroscopy (SERS) has the potential to overcome these issues by providing immediate bacterial classification. To date, achieving accurate classification has required technically complicated processes to capture pathogens, which has precluded the integration of SERS into rapid diagnostics. This work demonstrates that gold-coated membrane filters capture and aggregate bacteria, separating them from urine, while also providing Raman signal enhancement. An optimal gold coating thickness of 50 nm was demonstrated, and the diagnostic performance of the SERS-active filters was assessed using phantom urine infection samples at clinically relevant concentrations (105 CFU/ml). Infected and uninfected (control) samples were identified with an accuracy of 91.1%. Amongst infected samples only, classification of three bacteria (Escherichia coli, Enterococcus faecalis, Klebsiella pneumoniae) was achieved at a rate of 91.6%.

Journal article

Skinner C, Thompson AJ, Thursz MR, Marchesi JR, Vergis Net al., 2020, Intestinal permeability and bacterial translocation in patients with liver disease, focusing on alcoholic aetiology: methods of assessment and therapeutic intervention, Therapeutic Advances in Gastroenterology, Vol: 13, Pages: 1-16, ISSN: 1756-2848

Increased bacterial translocation (BT) across the gut barrier due to greater intestinal permeability (IP) is seen across a range of conditions, including alcohol-related liver disease (ArLD). The phenomenon of BT may contribute to both the pathogenesis and the development of complications in ArLD. There are a number of methods available to assess IP and in this review we look at their various advantages and limitations. The knowledge around BT and IP in ArLD is also reviewed, as well as the therapeutic strategies currently in use and in development.

Journal article

Maurice J, Lett A, Skinner C, Lim A, Richardson M, Painadath Thomas A, Summers P, Vyas K, Tadbier A, Vilar R, Kuimova M, Miodragovic S, Vergis N, Kelly P, Cordeiro M, Hoare J, Darzi A, Goldin R, Thursz M, Thompson Aet al., 2020, Transcutaneous fluorescence spectroscopy as a tool for non-invasive monitoring of gut function: first clinical experiences, Scientific Reports, Vol: 10, ISSN: 2045-2322

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.

Journal article

Kim JA, Wales D, Thompson A, Yang G-Zet al., 2020, Fiber-optic SERS probes fabricated using two-photon polymerization for rapid detection of bacteria, Advanced Optical Materials, Vol: 8, Pages: 1-12, ISSN: 2195-1071

This study presents a novel fiber-optic surface-enhanced Raman spectroscopy (SERS) probe (SERS-on-a-tip) fabricated using a simple, two-step protocol based on off-the-shelf components and materials, with a high degree of controllability and repeatability. Two-photon polymerization and subsequent metallization was adopted to fabricate a range of SERS arrays on both planar substrates and end-facets of optical fibers. For the SERS-on-a-tip probes, a limit of detection of 10-7 M (Rhodamine 6G) and analytical enhancement factors of up to 1300 were obtained by optimizing the design, geometry and alignment of the SERS arrays on the tip of the optical fiber. Furthermore, strong repeatability and consistency were achieved for the fabricated SERS arrays, demonstrating that the technique may be suitable for large-scale fabrication procedures in the future. Finally, rapid SERS detection of live Escherichia coli cells was demonstrated using integration times in the milliseconds to seconds range. This result indicates strong potential for in vivo diagnostic use, particularly for detection of infections. Moreover, to the best of our knowledge, this represents the first report of detection of live, unlabeled bacteria using a fiber-optic SERS probe.

Journal article

Dryden S, Anastasova S, Satta G, Thompson AJ, Leff DR, Darzi AWet al., 2020, Toward point-of-care uropathogen detection using SERS active filters, Optical Diagnostics and Sensing XX: Toward Point-of-Care Diagnostics, Publisher: SPIE, Pages: 1124705-1-1124705-7

150 million people worldwide suffer one or more urinary tract infections (UTIs) annually. UTIs are a significant health burden: societal costs of UTI exceed $3.5 billion in the U.S. alone; 5% of sepsis cases arise from a urinary source; and UTIs are a prominent contributor toward antimicrobial resistance (AMR). Current diagnostic frameworks exacerbate this burden by providing inaccurate and delayed diagnosis. Rapid point-of-care bacterial identification will allow for early precision treatment, fundamentally altering the UTI paradigm. Raman spectroscopy has a proven ability to provide rapid bacterial identification but is limited by weak bacterial signal and a susceptibility to background fluorescence. These limitations may be overcome using surface enhanced Raman spectroscopy (SERS), provided close and consistent application of bacteria to the SERS-active surface can be achieved. Physical filtration provides a means of capturing uropathogens, separating them from the background solution and acting as SERS-active surface. This work demonstrates that filters can provide a means of aggregating bacteria, thereby allowing subsequent enhancement of the acquired Raman signal using metallic nanoparticles. 60 bacterial suspensions of common uropathogens were vacuum filtered onto commercial polyvinylidene fluoride membrane filters and Raman signals were enhanced by the addition of silver nanoparticles directly onto the filter surface. SERS spectra were acquired using a commercial Raman spectrometer (Ocean Optics, Inc.). Principal Component – Linear Discriminant Analysis provided discrimination of infected from control samples (accuracy: 88.75%, 95% CI: 79.22-94.59%, p-value <0.05). Amongst infected samples uropathogens were classified with 80% accuracy. This study has demonstrated that combining Raman spectroscopy with membrane filtration and SERS can provide identification of infected samples and rapid bacterial classification.

Conference paper

Kim JA, Wales DJ, Thompson AJ, Yang G-Zet al., 2019, Towards development of fibre-optic surface enhanced Raman spectroscopy probes using 2-photon polymerisation for rapid detection of bacteria, Plasmonics in Biology and Medicine XVI, Publisher: SPIE, ISSN: 0277-786X

In this study, a variety of direct laser written surface-enhanced Raman spectroscopy (SERS) micro-structures, designed for bacteria detection, are presented. Various SERS micro-structures were designed to achieve both a high density of plasmonic hot spots and a strong probability of interaction between the hot spots and the target bacterial cells. Twophoton polymerization was used for initial fabrication of the polymeric skeletons of the SERS micro-structures, which were then coated with a 50 nm-thick gold layer via e-beam evaporation. The micro-structures were fabricated on glass coverslips and were assessed using a confocal Raman microscope. To this end, Rhodamine 6G was used as an analyte under 785 nm laser illumination. The optimal SERS micro-structures showed approximately 7×103 enhancement in Raman signal (analytical enhancement factor, AEF) at a wavenumber of 600 cm-1. Real-time detection of E. coli in solution was demonstrated using the fabricated SERS platform with low laser powers and a short acquisition time (785 nm, 5 mW, 50 ms).

Conference paper

Consortium H, Drake L, Frost G, Holmes E, Lett A, Maitland K, Marchesi J, Swann J, thompson, Thompson A, Walsh Ket al., 2019, Health outcomes in Undernutrition: the role of Nutrients, Gut dysfunction and the gut microbiome (HUNGer), Health outcomes in Undernutrition: the role of Nutrients, Gut dysfunction and the gut microbiome (HUNGer), Publisher: Imperial College London

The HUNGer consortium is comprised of a multi-disciplinary, multi-national consortium of world leading researchers, with expertise in physiology and nutrition, through to clinical research, public health and agriculture in LMIC settings. The HUNGer consortium was awarded the MRC Confidence in Global Nutrition and Health award in 2018.The HUNGer consortium is developing a programme of work that will directly address United Nations Sustainable Development Goal 2 (SDG-2): End hunger, achieve food security and improve nutrition, and promote sustainable agriculture. We believe there are a number of critical unanswered questions regarding the role of the gut in undernutrition, which if answered could significantly improve the effective management and prevention of undernutrition.The following document represents the consensus opinion of the HUNGer consortium concerning the key challenges that currently limit the effective management and prevention of undernutrition and the most promising potential solutions.


Tudor A, Delaney C, Zhang H, Thompson AJ, Curto VF, Yang GZ, Higgins MJ, Diamond D, Florea Let al., 2018, Fabrication of soft, stimulus-responsive structures with sub-micron resolution via two-photon polymerization of poly(ionic liquid)s, Materials Today, Vol: 21, Pages: 807-816, ISSN: 1369-7021

Soft, stimulus-responsive 3D structures created from crosslinked poly(ionic liquid)s (PILs) have been fabricated at unprecedented sub-micron resolution by direct laser writing (DLW). These structures absorb considerable quantities of solvent (e.g., water, alcohol, and acetone) to produce PIL hydrogels that exhibit stimulus-responsive behavior. Due to their flexibility and soft, responsive nature, these structures are much more akin to biological systems than the conventional, highly crosslinked, rigid structures typically produced using 2-photon polymerization (2-PP). These PIL gels expand/contract due to solvent uptake/release, and, by exploiting inherited properties of the ionic liquid monomer (ILM), thermo-responsive gels that exhibit reversible area change (30 ± 3%, n = 40) when the temperature is raised from 20 °C to 70 °C can be created. The effect is very rapid, with the response indistinguishable from the microcontroller heating rate of 7.4 °C s−1. The presence of an endoskeleton-like framework within these structures influences movement arising from expansion/contraction and assists the retention of structural integrity during actuation cycling.

Journal article

Thompson AJ, Power M, Yang G-Z, 2018, A micro-scale fiber-optic force sensor fabricated using direct laser writing and calibrated using machine learning, Optics Express, Vol: 26, Pages: 14186-14200, ISSN: 1094-4087

Fiber-optic sensors have numerous existing and emerging applications spanning areas from industrial process monitoring to medical diagnosis. Two of the most common fiber sensors are based on the fabrication of Bragg gratings or Fabry-Perot etalons. While these techniques offer a large array of sensing targets, their utility can be limited by the difficulties involved in fabricating forward viewing probes (Bragg gratings) and in obtaining sufficient signal-to-noise ratios (Fabry-Perot systems). In this article we present a microscale fiber-optic force sensor produced using direct laser writing (DLW). The fabrication entails a single-step process that can be undertaken in a reliable and repeatable manner using a commercial DLW system. The sensor is made of a series of thin plates (i.e. Fabry-Perot etalons), which are supported by springs that compress under an applied force. At the proximal end of the fiber, the interferometric changes that are induced as the sensor is compressed are read out using reflectance spectroscopy, and the resulting spectral changes are calibrated with respect to applied force. This calibration is performed using either singular value decomposition (SVD) followed by linear regression or artificial neural networks. We describe the design and optimization of this device, with a particular focus on the data analysis required for calibration. Finally, we demonstrate proof-of-concept force sensing over the range 0-50 μN, with a measurement error of approximately 1.5 μN.

Journal article

Vysniauskas A, Lopez Duarte I, Thompson AJ, Bull JA, Kuimova MKet al., 2018, Surface functionalisation with viscosity-sensitive BODIPY molecular rotor, Methods and Applications in Fluorescence, Vol: 6, ISSN: 2050-6120

Surface functionalisation with viscosity sensitive dyes termed ‘molecular rotors’ can potentially open up new opportunities in sensing, for example for non-invasive biological viscosity imaging, in studying the effect of shear stress on lipid membranes and in cells, and in imaging contacts between surfaces upon applied pressure. We have functionalised microscope slides with BODIPY-based molecular rotor capable of viscosity sensing via its fluorescence lifetime. We have optimised functionalisation conditions and prepared the slides with the BODIPY rotor attached directly to the surface of glass slides and through polymer linkers of 5 kDa and 40 kDa in mass. The slides were characterised for their sensitivity to viscosity, and used to measure viscosity of supported lipid bilayers during photooxidation, and of giant unilamellar vesicles lying on the surface of the slide. We conclude that our functionalised slides show promise for a variety of viscosity sensing applications.

Journal article

Thompson AJ, Yang G-Z, 2018, Tethered and Implantable Optical Sensors, Implantable Sensors and Systems, Editors: Yang, Publisher: Springer, Pages: 439-505, ISBN: 978-3-319-69747-5

Optical imaging and sensing modalities have been used in medical diagnosis for many years. An obvious example is endoscopy, which allows remote wide-field imaging of internal tissues using optical fibers and/or miniature charge-coupled device (CCD) cameras. While techniques such as endoscopy provide useful tools for clinicians, they do not typically allow a complete diagnosis to be made. Instead, physical biopsies may be required to confirm or refute the presence of disease. Furthermore, endoscopic procedures are both invasive and time-consuming. As such, much research is currently directed toward the development of devices that can provide a complete in vivo diagnosis without the requirement for a physical biopsy. Ideally, such devices should also be minimally or non-invasive, and they should provide immediate identification of disease at the point of care. Additionally, there is significant interest in the development of implantable diagnostic devices that can be left within patients’ bodies for extended periods of time (for several days or longer). Such systems could be used for automated disease diagnosis, and example applications include the detection of post-surgical infections as well as monitoring of the health status of patients undergoing chemotherapy. This chapter focuses on the development of optical instruments that can provide in situ diagnosis at the point of care, with an emphasis on progress towards miniature devices that may function as implants in the future.

Book chapter

Power MC, Thompson A, Anastasova-Ivanova S, Yang G, Power M, Thompson AJ, Anastasova S, Yang G-Zet al., 2018, A monolithic force-sensitive 3D microgripper fabricated on the tip of an optical fiber using 2-photon polymerization, Small, Vol: 14, Pages: 1703964-1-1703964-10, ISSN: 1613-6810

Microscale robotic devices have myriad potential applications including drug delivery, biosensing, cell manipulation, and microsurgery. In this work, a tethered, 3D, compliant grasper with an integrated force sensor is presented, the entirety of which is fabricated on the tip of an optical fiber in a single-step process using 2-photon polymerization. This gripper can prove useful for the interrogation of biological microstructures such as alveoli, villi, or even individual cells. The position of the passively actuated grasper is controlled via micromanipulation of the optical fiber, and the microrobotic device measures approximately 100 µm in length and breadth. The force estimation is achieved using optical interferometry: high-dimensional spectral readings are used to train artificial neural networks to predict the axial force exerted on/by the gripper. The design, characterization, and testing of the grasper are described and its real-time force-sensing capability with an accuracy below 2.7% of the maximum calibrated force is demonstrated.

Journal article

Schmitz A, Thompson AJ, Berthet-Rayne P, Seneci CA, Wisanuvej P, Yang GZet al., 2017, Shape sensing of miniature snake-like robots using optical fibers, IEEE International Conference on Intelligent Robots and Systems (IROS), Publisher: IEEE, Pages: 947-952, ISSN: 2153-0858

Snake like continuum robots are increasingly used for minimally invasive surgery. Most robotic devices of this sort that have been reported to date are controlled in an open loop manner. Using shape sensing to provide closed loop feedback would allow for more accurate control of the robot's position and, hence, more precise surgery. Fiber Bragg Gratings, magnetic sensors and optical reflectance sensors have all been reported for this purpose but are often limited by their cost, size, stiffness or complexity of fabrication. To address this issue, we designed, manufactured and tested a prototype two-link robot with a built-in fiber-optic shape sensor that can deliver and control the position of a CO 2 -laser fiber for soft tissue ablation. The shape sensing is based on optical reflectance, and the device (which has a 4 mm outer diameter) is fabricated using 3D printing. Here we present proof-of-concept results demonstrating successful shape sensing - i.e. measurement of the angular displacement of the upper link of the robot relative to the lower link - in real time with a mean measurement error of only 0.7°.

Conference paper

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