MRC Transition Support Award CSF Tomoki Arichi

Lead Research Organisation: King's College London
Department Name: Imaging & Biomedical Engineering

Abstract

The goal of the research is to understand how injury to the brain during the crucial stages of early life in the womb and around the time of birth can lead to life-long difficulties with brain function. Damage at this time to the specific areas of the brain which control how the body moves in particular, can result in cerebral palsy, leading to life-long difficulties such as limb paralysis or painful uncontrolled movements. There is currently no cure for cerebral palsy, perhaps due to a basic lack of knowledge about how the brain and its activity actually develop the ability to control how the body moves in the earliest stages of life. Importantly, although current medical tests (such as brain scans) can identify brain injuries in babies, they cannot accurately identify which of these babies will develop cerebral palsy later in childhood. This means that treatments cannot be started as soon as an injury is seen and that families are often left with several months of stressful uncertainty.

We know that the earliest stages of human life are important for the development of the brain and body systems that control movement as even during the earliest stages of pregnancy, babies can be seen and felt to be moving inside the womb. After birth, they continue to move in a seemingly random way until 6 months of age when they begin to make clearer controlled and purposeful movements. In addition, our research suggests that even at this early stage, the brain can alter how it controls movement through simple learning. This is all important as in this crucial early period of life, the human brain is undergoing more dramatic changes in size, shape, and structure than at any other time, and therefore there must also be enormous changes in how its activity evolves to allow these new patterns of movement.

The research therefore plans to use specialist techniques such as robotic devices and highly accurate sensors to precisely measure how babies move (both inside and outside the womb) and then identify and locate the accompanying brain activity using brain scanning. I will study how this changes as a baby grows during their first 6 months, and explore how the relationship is affected by early brain injury. I have also carried out studies to understand how brain activity and movements are altered through learning by gently stimulating the babies.

Together, the results of the studies will provide new and important insights about how the brain matures through and then controls movements in the first year. This fundamental knowledge will help doctors and scientists understand how to try and ensure healthy brain development and movements in early life. It will also help them to diagnose, potentially prevent and treat conditions like cerebral palsy which affect the control of movement in children.

Technical Summary

The research of the fellowship and transition award uses non-invasive neuroimaging techniques to study the maturation of human brain activity related to early spontaneous motor behaviour. This is being carried out through inter-institutional (KCL, Imperial College London, UCL, INSERM, Oxford University) and multi-disciplinary collaboration (Neonatal medicine, Imaging Sciences, Bioengineering, Neuroscience). This unique comprehensive approach ensures that state-of-the-art techniques are used to answer important questions grounded in fundamental neuroscience, all being carried out within a research environment with colleagues at the forefront of their respective fields.

This will include using foetal fMRI to study the brain activity associated with emerging patterns of motor behaviour. Although challenging, across the 4 years of the fellowship, we have built a comprehensive pipeline of acquisition and processing methods (multi-slice and multi-shot acquisition sequence, dynamic B0 field correction, motion-tolerant reconstruction) and an analysis pipeline (denoising of physiological noise and motion correction). The TSA will provide entirely novel world-first insights into the earliest stages of in-utero human brain activity by systematically apply this methodology. I am also studying the neural correlates of emerging motor behaviour in early human infancy using novel sensor technology and fMRI compatible robotics. The associated brain activity is characterised with simultaneous EEG-fMRI, which provides complimentary information about both temporal (EEG) and spatial (fMRI) features. I have already performed the first-ever infant studies using this method (Arichi et al. eLife 2017) and have optimised the methods further over the fellowship.

In the TSA, I will build on this with multi-contrast tissue information and normative growth curves (developed using Gaussian Process Regression) and make the data open for dissemination to academic and clinical colleagues.

Publications

10 25 50
 
Description Royal College of Obstetrics and Gynaecology: Fetal Awareness: Review of Research and Recommendations for Practice
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
URL https://www.rcog.org.uk/en/guidelines-research-services/guidelines/fetal-awareness---review-of-resea...
 
Description Developing responsible neurotechnology for infants and children with neurodevelopmental conditions
Amount £1,048,588 (GBP)
Funding ID EP/W035154/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 05/2022 
End 05/2025
 
Description Developing responsible neurotechnology for infants and children with neurodevelopmental conditions
Amount £1,065,728 (GBP)
Funding ID EP/W035154/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2022 
End 08/2025
 
Description Mind & Skin: Understanding the neurocutaneous axis in atopic eczema
Amount £515,168 (GBP)
Funding ID MRF-176-0002-RG-FLOH-C0929 
Organisation Medical Research Council (MRC) 
Department Medical Research Foundation
Sector Charity/Non Profit
Country United Kingdom
Start 06/2022 
End 05/2027
 
Title Simultaneous EEG data with passive motor stimulus from preterm infants 
Description Preprocessed EEG data - infants were fitted with neonatal 25-electrode EEG caps (29 - 32 cm head circumference) and connected to an MR-compatible system (EASYCAP and Brain Products GmbH). EEG data preprocessing was performed using Analyzer 2 software (Brain Products GmbH), with an initial 0.2 Hz high-pass filter used to remove slow frequency drift in the EEG data. After exclusion of TRs with visible motion on the raw EEG, MR gradient artifact was cleaned using a 25 TR sliding window template subtraction. A 40 Hz lowpass and 50 Hz notch filter were applied. Electrodes with poor signal or bridged to the reference (FCz) were removed. MRI data were acquired with a 3 Tesla Philips Achieva scanner (Best, Netherlands) and a 32 channel adult head coil. Infants were scanned following feeding, during natural sleep and were fitted with ear protection (molded dental putty and adhesive earmuffs: Minimuffs, Natus Medical Inc, San Carlos CA, USA) and immobilized in a vacuum cushion (Med-Vac, CFI Medical Solutions, Fenton, MI, USA). fMRI data were acquired using T2*-weighted single-shot gradient echo echo-planar imaging (GRE-EPI) sequence (resolution: 2.5*2.5*3.25mm; 21 slices; TE: 30ms; TR: 1500ms, flip angle: 90°, lasting up to 13.5 minutes). A custom-built MR compatible robotic device (Dall'Orso et al., 2018) was fitted to the right wrist to deliver blocks of 1Hz passive right wrist flexion-extension for 7.5 to 10.5 seconds (5 to 7 TRs, up to 24 epochs of stimulation), with a variable inter-stimulus interval (21 to 24 seconds) to minimize anticipatory responses. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Manuscript has been submitted to eLife 
URL https://figshare.com/articles/dataset/Simultaneous_EEG_data_with_passive_motor_stimulus_from_preterm...
 
Title developing Human Connectome Project data 
Description The Developing Human Connectome Project has created a large open science resource which provides researchers with data for investigating normal and abnormal brain development across the perinatal period. It has collected 1228 multimodal magnetic resonance images of fetal and/or neonatal brain from 1173 participants, together with collateral demographic, clinical, family, neurocognitive and genomic data. All subjects were studied in utero and/or soon after birth on a single MRI scanner using specially developed scanning sequences which included novel motion-tolerant imaging methods. Imaging data are complemented by rich demographic, clinical, neurodevelopmental, clinical, and genomic information. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data has been downloaded and used widely by peers 
URL http://www.developingconnectome.org/data-release/third-data-release/
 
Description Collaboration for general movements in infants 
Organisation Norwegian University of Science and Technology (NTNU)
Country Norway 
Sector Academic/University 
PI Contribution Research collaboration to use automated methods (using computer vision and deep learning) for studying and classifying infant general movements.
Collaborator Contribution Partners are providing large amount of data and access to their methods for comparision with those developed as part of our EPSRC project.
Impact none as yet
Start Year 2021
 
Description Collaboration with Harvard University for ultra-high field fMRI 
Organisation Harvard University
Country United States 
Sector Academic/University 
PI Contribution New collaboration with Professor Jonathan Polimeni who has expertise in ultra-high field fMRI but has not worked with infants. We are therefore working together on developing the methods for infant 7T fMRI.
Collaborator Contribution Professor Polimeni is a world leader on ultra-high field fMRI so has advised on the acquisition and analysis methods.
Impact OHBM 2023 annual meeting abstract: Exploration of cortical depth analysis of 7T fMRI in the neonatal brain Tomoki Arichi 1,2,3, Jonathan R Polimeni 4, Philippa Bridgen 3,5, Raphael Tomi-Tricot 1,5,6, Jucha Willers Moore 1,2, Daniel Cromb 1, Paul Cawley 1,3, Megan Quirke 1,3, Anthony N Price 1,3, Alena Uus 1, E De Vita 1, Maria Deprez 1, Sharon L Giles 1,5, J O'Muircheartaigh 1,2, Serena J Counsell 1, A David Edwards 1,2,3, Jo V Hajnal 1, Shaihan Malik 1,5
Start Year 2022
 
Description MRC Centre for Neurodevelopmental Disorders 
Organisation King's College London
Department MRC Centre for Developmental Neurobiology
Country United Kingdom 
Sector Academic/University 
PI Contribution I am a group leader in the MRC Centre for Neurodevelopmental disorders at King's College London. I have been invited to provide insight about the clinical aspects of these disorders and research expertise about studying brain development with neuroimaging
Collaborator Contribution This provides routes for collaboration within the centre and a route for PhD students to access scholarships and to access our work.
Impact 2 PhD students currently enrolled through the scheme. These students have co-authored two publications: 1. Poppe T, Moore JW, Arichi T. Individual focused studies of functional brain development in early infancy. Current Opinion in Behavioural Sciences 2021; 40: 137-43. https://doi.org/10.1016/j.cobeha.2021.04.017 citations: 1 2. Wilson S, Pietsch M, Cordero-Grande L, Price AN, Hutter J, Xiao J, McCabe L, Rutherford MA, Hughes EJ, Counsell SJ, Tournier JD, Arichi T, Hajnal JV, Edwards AD, Christiaens D, O'Muircheartaigh J. Development of human white matter pathways in utero over the second and third trimester. Proceedings of the National Academy of Sciences 2021; 118(20). https://doi.org/10.1073/pnas.2023598118 citations: 9
Start Year 2021
 
Title Software for 'Unsupervised Human Pose Estimation through Transforming Shape Templates" 
Description Human pose estimation is a major computer vision problem with applications ranging from augmented reality and video capture to surveillance and movement tracking. In the medical context, the latter may be an important biomarker for neurological impairments in infants. Whilst many methods exist, their application has been limited by the need for well annotated large datasets and the inability to generalize to humans of different shapes and body compositions, e.g. children and infants. In this paper we present a novel method for learning pose estimators for human adults and infants in an unsupervised fashion. We approach this as a learnable template matching problem facilitated by deep feature extractors. Human-interpretable landmarks are estimated by transforming a template consisting of predefined body parts that are characterized by 2D Gaussian distributions. Enforcing a connectivity prior guides our model to meaningful human shape representations. We demonstrate the effectiveness of our approach on two different datasets including adults and infants. 
Type Of Technology Software 
Year Produced 2021 
Open Source License? Yes  
Impact Software was presented at the prestigious CVPR conference 2021 and has initiated a collboration with researchers at the Norwegian Technical University. 
URL https://github.com/lschmidtke/shape_templates
 
Description Corpal - Agensis of the Corpus Callosum family event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Invited presentation to the Corpal charity for Agenesis of the Corpus Callosuum awareness day. Gave an online lecture to members of the public and patient families.
Year(s) Of Engagement Activity 2021
 
Description DevNeuro Academy 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact I have also recently joined the public engagement committee for the MRC Centre for Neurodevelopmental Disorders (CNDD), which includes the organisation of the DevNeuro Academy. The DevNeuro academy which is a widening participation project to improve progression and success of school students from under-represented backgrounds, who have a particular interest in understanding Neuroscience. It includes specific events across the year and a week long programme of activities in the Summer which provides exposure and teaching about different aspects of Neuroscience and research.
Year(s) Of Engagement Activity 2021,2022
URL https://devneuro.org/cdn/public-engagement-dna.ph
 
Description In2science UK programme 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact In2science is a programme designed to boost diversity and inclusion in STEM for school children from disadvantaged backgrounds. I acted as mentor for 3 school children interested in a career in medicine and science, and hosted two mentorship sessions and a visit to my department to give them exposure to a science/hospital environment.
Year(s) Of Engagement Activity 2021
URL https://in2scienceuk.org/
 
Description Paper accepted for CVPR (Computer Vision and Pattern Recognition) 2021 conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact "Unsupervised Human Pose Estimation through Transforming Shape Templates; Luca Schmidtke, Simon Ellershaw, Athanasios Vlontzos, Bernhard Kainz, Anna Lukens, Tomoki Arichi" accepted for the prestigious 2021 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). The paper presents a novel method for learning pose estimators for human adults and infants in an unsupervised fashion.
This will be presented later in the year at the meeting. This meeting reaches a wide audience including academic, industrial, and media outlets as it is the most important meeting in the field annually.
Year(s) Of Engagement Activity 2021
URL http://cvpr2021.thecvf.com/
 
Description Parent Power family engagement event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact I took part in a "Parent Power" event for families from Lambeth and Southwark organised by King's College London. This event was designed to provide a forum for families from the local community to hear about research and to be able to engage with researchers to ask questions. I spoke about my own work using MRI to study brain development and autism, and then had an open discussion and question/answer session with these families.
Year(s) Of Engagement Activity 2021
 
Description William Little Foundation - evaluation of need for early intervention and recognition in cerebral palsy 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Supporters
Results and Impact Inivited to participate in the working group and to review the draft document of an assessment and statement from the Willam Little Foundation about early recognition and intervention in cerebral palsy.
Year(s) Of Engagement Activity 2021