Insigneo Newsletter - March 2024

Welcome to our monthly Insigneo newsletter!  

Our monthly e-newsletter keeps you up to date with events, funding, success stories and information. We hope you will find it useful! 

Insigneo Showcase 2024: plenary speaker confirmed

Exciting fundamental science and beyond: from innovative research to translation and commercialisation.

This full day event is an opportunity for our members, funding agencies, regulatory agencies, industrial colleagues, and other academic groups in the UK to meet and see first-hand the innovative research produced by our Institute.

The day will feature:

• A plenary talk from Prof Peter Coveney from the Centre for Computational Medicine at UCL;
• Sessions from our five research themes:  Biomaterials / Biomechanics / Cell engineering; Computational modelling in medicine; Imaging life; Smart devices and sensors; and Healthcare data / AI;
• Early Career Researcher presentations – hear about emerging research with perspectives from the next generation of researchers;
• Poster exhibition - We are pleased to offer a prize for the best poster for each research theme and a best student poster prize sponsored by the Society of Chemical Industry. 
• Networking opportunities with industry, funders, academics and clinicians.

Abstract submission:
The deadline for abstract submissions for the poster display is 8 April 2024. To submit an abstract you will need to register for the Insigneo Showcase. You will be asked if you wish to submit an abstract as part of this process.

New paper reveals dramatic implications with using the tibia loading model to treat osteoporosis

Osteoporosis is a health condition that weakens bones. Research by Insigneo member Saira Farage-O'Reilly highlights how the direction of applying external force to the bone dramatically affects the strength of mouse tibia.

Meet Jude Stone – the new Programme Director for the National Centre for Child Health Technology

Sheffield Children’s has appointed the Programme Director for the National Centre for Child Health Technology (NCCHT). Insigneo member Jude Stone will be leading the team of people who are bringing the National Centre to life.

New guidance approves AI-derived software for stroke assessments

Insigneo members Professors Li Su and Nigel Hoggard from the Neuroscience Institute and other Specialist committee members in NICE have endorsed two AI tools for aiding stroke diagnosis.

Insigneo and Sano continue to strengthen their collaborations

Insigneo member Dr Ivan Benemerito visited the Sano Centre for Computational Medicine in Krakow, Poland as part of the University of Sheffield's activities on the EU-funded Sano project. During the week he spent there, Ivan collaborated with Dr Sousa's team to help develop their data analysis and visualisation tools, and apply them to the prediction of aneurysm rupture risk.

Ivan also worked with Sano Office Specialist Ms Maria Sendecka to plan the next Insigneo-Sano PhD training event which will take place in Sheffield from 16 September. The event will see ten researchers from Sano come to Sheffield for a week of seminars and workshops on computational medicine. These activities will be open to Insigneo members to join.

South Yorkshire Digital Health Hub: first innovation pipeline sandpit event

On Monday 4 March 2024, our South Yorkshire Digital Health Hub held their first innovation pipeline sandpit at the Advance Wellbeing Research Centre in Sheffield, bringing together multidisciplinary teams from industry, healthcare, academia & the public to creatively solve problems using digital health data.

South Yorkshire Digital Health Hub: BBC Politics North and Look North programme

Insigneo Research Theme Director for Healthcare data/AI Prof Tim Chico and Prof Steve Haake from our South Yorkshire Digital Health Hub spoke to the BBC about how the hub is working to narrow health inequalities in South Yorkshire (from 23:40). 

METASTRA project leaflet

Our METASTRA project has shared a new leaflet to summarise the details of the project and explore what lies ahead.

The project aims to revolutionise cancer patient care by addressing the complexities of vertebral metastases, providing innovative solutions for fracture risk assessment, and delivering personalised surgical interventions.

VPH Institute: code & cure video series

Code & Cure is a series of divulgation videos from the VPH Institute to spread the knowledge of in silico medicine towards a larger public with accessible animated videos spanning from models to real-world applications.

Improving South Yorkshire childrens’ health outcomes

A significant milestone in the shared mission to improve health outcomes for children across the region has been established through the South Yorkshire Children and Young People's Health Research network (SYCPHeR).

This new network, which includes partnerships between the University of Sheffield, Sheffield Hallam University, and Sheffield Children's NHS Foundation Trust, aims to lead cutting-edge therapies and treatments while establishing a direct link between research conducted at both institutions and the everyday experiences of patients.

BORS 2024: save the date!

We are delighted to announce that we are hosting the 2024 British Orthopaedic Research Society (BORS) Annual Meeting at the University of Sheffield's The Edge venue on 9 - 10 September 2024.

Insigneo Early Career Researcher (ECR) Group

The Insigneo Institute’s ECR group aims to help ECRs across our interdisciplinary membership connect and enrich their research, with a focus on networking and career development opportunities.

This group is inclusive of PhD students, postdocs, fellows and those who self-define as an ECR at the University of Sheffield.  

Coming soon:

Our ECR Committee will be organising a number of activities related to the following themes:

• Grant writing and specific calls dedicated to ECR
• Data sharing
• Publications and journal clubs
• Conferences and networking

If you are interested in taking part please make sure you are signed up to our ECR group. If you are not already an Insigneo member, apply for membership and join here.

UKRI Shaping the Future of UK large-scale compute survey - deadline: 29 March

UKRI are working closely with DSIT to deliver the recommendations of the Future of Compute review and are continuing to develop their Digital Research Infrastructure (DRI) programme. They are looking to further improve large-scale compute capacities to supercharge research and innovation across the country. 

They have launched a survey to capture the needs and priorities of potential users where insights gained from the survey will guide the design and capabilities of this world-class large-scale compute resource, ensuring it meets the diverse demands of UK research and industry. 

The survey is for researchers from any field. It will take only 10 minutes to fill in and by contributing your thoughts hopefully your future compute needs are met. 

https://engagementhub.ukri.org/ukri-infrastructure/shaping-the-future-of-uk-large-scale-compute/

 7^th IEEE UK and Ireland Robotics and Autonomous Systems Chapter Conference

Insigneo members, Sanja Dogramadzi, Dana Damian, Shuhei Miyashita and Lin Cao were involved in the organisation of the 7^th IEEE UK and Ireland Robotics and Autonomous Systems Chapter Conference, which took place on February 21-22 in Sheffield. The conference was a great success with speakers from industry, government and academia. The event entertained valuable discussions on medical devices and enabling technologies.

Soft Robotics for Healthcare Conference keynote

Insigneo member Dana Damian was a keynote speaker at the Soft Robotics for Healthcare Conference, which took place in London on 26-27 February 2024, entitled "Mapping the Future of Soft Robotics for Healthcare", on the theme "Developing and translating technologies in soft robotics from concept to clinic". Dana discussed her research group's latest work on soft sensors for tissue regenerative technologies and capsule robots.

We would like to introduce some of our new members who have joined the Insigneo Institute recently.

Find out more about Insigneo membership and our members here: https://www.sheffield.ac.uk/insigneo/membership 

My work is in the field of Computational Pathology, which seeks to utilise modern hardware advancements, developments in algorithms, and connect between different disciplines, to forward healthcare. I am specifically examining detections of head and neck cancers, with the aim of improving the detection and prognosis.

I have previously completed a PhD in computer science, with the thesis title “Constraint-Based Simulation of Virtual Crowds”, which started in 2016.

I have been a Research Associate for a number of years. My earlier projects explored accurately simulating people at train station platforms, and modelling the process of boarding and alighting.

Full profile

Prior to this, I undertook a BEng in Mechanical Engineering and MSc in Bioengineering at the University of Nottingham.

I am interested in the musculoskeletal system and orthopaedic research.

My research project is focused on developing an osteochondral tissue engineering scaffold fabricated from polyhydroxyalkanoates using 3D printing and electrospinning aiming to treat early stages of osteoarthritis.

In particular, I am interested in how vascular endothelial cells lining blood vessels sense and respond to mechanical signals associated with blood flow, which plays a crucial role in development and progression of atherosclerotic plaques in arteries.

It is known that disturbed flow conditions lead to endothelial injury and dysfunction, contributing to the development of cardiovascular disease, a leading cause of death globally – however, the underlying mechanisms are still not fully understood.

My lab integrates in vivo (mouse, zebrafish) and in vitro (primary human cells) models of studying cellular responses to flow with –omics approaches to identify and characterise endothelial mechanoreceptors and link them to the downstream signaling pathways.

I received my PhD as a Marie Curie Fellow from the University of Cambridge in 2013 and subsequently took up the position of John Stokes Postdoctoral Fellow at the University of Sheffield.  In the lab of Professor Paul Evans in Sheffield, I developed a platform for functional screening of flow-responsive regulators of endothelial cell survival in zebrafish. I used this model for a functional screening of known and putative endothelial mechanoreceptors, which was the basis for my British Heart Foundation Intermediate Fellowship, awarded in 2018.

Full profile

He was awarded a PhD from a joint program between Eindhoven University of Technology in the Netherlands and Philips Research, focused on physiological monitoring. He earned his BEng and MEng in Electrical Engineering from Harbin Institute of Technology and Dalian University of Technology, China, respectively.
 
Dr Sun has over 30 peer-reviewed publications and 2 patents granted through the PCT system. He served on the technical program committees for IEEE CHASE 2022 and IEEE BSN 2023. He is also a guest editor for Frontiers in Signal Processing, Frontiers in Digital Health, and Algorithms.
 
Dr Sun's research interests primarily revolve around physiological and behavioural monitoring, leveraging advanced signal processing and machine learning methodologies. In the realm of physiological monitoring, he focuses on estimating vital parameters such as blood pressure, heart rate, and respiration rate through the analysis of biomedical signals, such as photoplethysmography (PPG). In behavioural monitoring, his work centres on assessing mobility and social interaction patterns using wearable devices and smartphones. Dr Sun has developed innovative technologies aimed at assisting individuals with a range of medical conditions, including depression, multiple sclerosis, epilepsy, ADHD, and COVID-19.

Full profile
Research group webpage

For four years, I have worked as part of the mathematical modelling in medicine group, focusing on computational modelling of the cardiovascular system. This work originally started when I completed an MRes in cardiovascular science, and has continued in my role as an early career clinical academic.

My main research interests focus on development and validation of 3D computational fluid dynamics tools for simulating blood flow in the coronary arteries. From August 2024, when I will complete my clinical foundation training, I will undertake a BRC clinical research fellowship for a 12 month period.

His current work blends mechanistic biophysical modelling with machine learning approaches.  In particular, he is using multi-fidelity fusion to efficiently infer epithelial cell mechanics.

His previous postdoctoral research focused on developing advanced digital tools for enhancing the development and operation of RNA vaccine and therapeutics production processes. He got his PhD degree from The University of Manchester, with the research topic on intelligent methodologies of large-scale distributed parameter systems.

He started his career as a Research Technician in the virology lab of Professor Wendy Barclay, who inspired him to pursue a career in science. After a year working in a molecular biology consultancy, he studied for his PhD by researching the membrane protein CD63 using zebrafish models, in the Department of Molecular Biology and Biotechnology. After a postdoctoral research position researching drug-kinase interactions in the Oncology department of the University of Sheffield Medical School, he transitioned to teaching focussed work, set up the Diamond Bioengineering labs and managed a technical team.

He is now a University Teacher in the Materials Science and Engineering department, with research interests in brain tissue modelling and collagen biology.

One of his current interests is managing the Practical Engineering Education blog: https://practicalengineeringeducation.blogspot.com/

My research interests are still focused around developing and advancing clinically relevant methods of patient stratification to oncology therapeutics.

I have led the Ex vivo drug screening group at the University of Sheffield since 2019. I am currently the scientific lead of the Ex VIvo DEtermined caNcer Therapy (EVIDENT) trial alongside clinical lead Prof Sarah Danson. My group undertakes image-based drug screens directly on patient tumour tissue, measuring drug efficacy at single-cell resolution. This is achieved using high-throughput and high-content microscopy alongside supervised AI image analysis to segment the various cell populations, measuring viability, morphology and changes in cell-on-cell interactions.

EVIDENT has two major aims, the first is designed to address cancer patient stratification to provide cancer patients with pharmacological profile/signature of their actual tumour, which could be used in the future to direct therapy. The second is to develop this methodology as preclinical drug development tool, screening preclinical compounds directly on samples which reflect the genetic diversity observed in the cancer patient population.

Twitter
LinkedIn
Full profile

My overarching research interests involve harnessing sophisticated mathematical and machine learning approaches to enrich the information that we can extract from microscopy images and developing automated tools that support the scientific community in addressing fundamental questions in biology and biophysics. 

I am a post-doctoral research associate within the Pyne lab, where our team has pioneered the development of TopoStats, a leading Python-based software designed for automated processing and analysis of atomic force microscopy images. As well as taking a lead role in designing and implementing novel features and machine learning capabilities in TopoStats to meet the specific needs of the scientific community, I collaborate closely with experimentalists to develop analysis workflows to quantitatively characterise DNA dynamics and explore the intricate relationship between DNA conformation and its functional implications. 

Prior to this role I completed a PhD in Biology at the University of York where my work involved the development of CellPhe, an open-source toolkit for automated cell phenotyping from microscopy time-lapse videos. CellPhe has enhanced the amount of phenotypic information that can be extracted from cell time-lapses, facilitating detailed characterisation of single-cells and identification of heterogeneous subtypes within samples.

Check out Laura's recent Euro-BioImaging Virtual Pub talk on Gaining more from time-lapse microscopy through automated single-cell phenomics.

Do you have news to share with us?

If you would like us to include information and/or events to this newsletter please email: info@insigneo.org (the newsletter will be issued during the 2nd week of the month, excluding January and August). 

Insigneo members - please let us know when your students are graduating so that we can celebrate their success!

Please ensure that you submit items for inclusion with a minimum of one week's notice.

Guest Lectures, Conferences & Seminars

We will share a link to our Online Training Opportunities document here each month.

Insigneo events

19 March
Insigneo healthcare data - HPC roadmap workshop

25 March
CompBioMedX: Using in silico medicine to improve management of stroke and intracranial aneurysms

8 April
Insigneo medical device research roadmap workshop

19 April
Joint Insigneo Biomaterials, Biomechanics and Cell Engineering theme/Mechanobiology seminar: Studying cancer cell metastases in the era of deep learning for microscopy

14 June
Insigneo Showcase 2024 - abstract subission is open

1 July
Joint Insigneo Biomaterials, Biomechanics and Cell Engineering theme Mechanobiology Summer event - Save the date!
Speaker: Guillaume Charras, UCL
Further details to follow

A selection of Insigneo seminar recordings are available to view on our YouTube channel.

Other events

18 - 22 March
N8 CIR: Digital Research Infrastructure (DRI) Retreat 2024, Manchester

22 March
PubHD March 2024, Sheffield
Speakers:
Bhoomika Ghandi - Motion capture pillow for tracking head and neck motion during radiotherapy,
Rui Zhang - Visual simulataneous localislation and mapping for sewer pipe networks

19 March
Sheffield Cancer Research Away Day 2024 (open to University of Sheffield staff, honorory members of staff, or PhD students with an interest in cancer research at the university)

20 March
Sano Workshop: Code verification using Method of Manufactured Solutions – an example from contact of deformable bodies
Presenter: Pinaki Bhattacharya 
Time: 10:00-11:30 GMT
Target Audience: PhD Students and Early Career Researchers

Insigneo Members please check your calendar invitations for joining details, otherwise please contact Norman Powell: n.j.powell@sheffield.ac.uk for meeting link.

Abstract:
Numerical codes written by research groups are usually quite complex. This makes it challenging to judge whether a piece of code is written correctly, which is the objective of code verification. The Method of Manufactured Solutions (MMS) is a robust approach to verification but appears to have been used sparingly outside the computational fluid dynamics community. MMS allows one to test a piece of code aiming to solve a partial differential equation problem against any number of solutions, each of any order of differentiability. Compare this situation, for instance, against only six (6) NAFEMS benchmark problems – based on simple geometries and involving symmetry conditions – that are available to verify whether a candidate code correctly solves problems involving contact between two deformable bodies. The first part of the talk will introduce the concept of code verification, provide examples of current practice (and gaps) and outline the general MMS approach. The second part will delve into the details of a process to manufacture solutions for contact between deformable bodies, highlighting how some challenging aspects such as geometric nonlinearity and disjoint volumes can be accounted for within the MMS approach.

22 March
NIHR ARC Yorkshire & Humber Lunch & Learn: What is an ICS?

25 March
NorthernBUG 11, Sheffield

9 April
 ResearchComputing@Sheffield

ResearchComputing@Sheffield is the annually hosted research computing event at The University of Sheffield showcasing projects using research computing facilities ('on premises' HPC, and Tier 2 Bede & Jade2 GPU clusters).

ResearchComputing@Sheffield comprises a series of presentations, which will address how researchers access and utilise the facilities available for research computing. This in-person event will be hosted in Firth Hall on the 9 April 2024 (09.30-16.45).

November 2023 saw the decommission of ShARC HPC, leaving Bessemer and the newest HPC Stanage (launched in April 2023) to serve our researchers. Stanage has over 11200 compute cores, and 72 graphical processing units (A100 & H100 GPUs).

This year the event, Data and Compute enabled Research at the University of Sheffield, will consist of four sessions each with three speakers and will align closely with the Special Interest Groups (SIGs) of Data Analytics, AI/ML, RSE & HPC. 

You can see the current confirmed speakers and register by entering your University of Sheffield email & clicking submit: https://forms.gle/Dn5MeWNkTusZDH9dA 
NHS colleagues Please request an invitation via Dr Des Ryan: des.ryan@sheffield.ac.uk

22 April
BIOREME network webinar: Democratising mathematical modelling with Prof Peter Hunter and Prof Liesbet Geris

10 May
NIHR Sheffield Biomedical Research Centre (BRC) Showcase

1 July
NIHR ARC Yorkshire & Humber Lunch & Learn: Practicalities of research with NHS data

10 -12 July
BRS Annual Meeting 2024, Sheffield

16 July
NIHR ARC Yorkshire & Humber Lunch & Learn: Using routine data for decision making

4 - 9 September
VPH2024 - abstract deadline extended until 22 March.

9 - 10 September
BORS Conference 2024, Sheffield - save the date!

For a full list of upcoming events visit: https://www.sheffield.ac.uk/insigneo/overview/events

Vacancies

Research Associate in Sleep-Disordered Breathing (closing date 22/03/24)

Research Associate in EIS data Analysis for Oral Cancer Diagnosis (closing date 21/03/24)

Publications

DXA-based statistical models of shape and intensity outperform aBMD hip fracture prediction: A retrospective study (Bone) A. Aldieri M. Paggiosi, R. Eastell, C. Bignardi, A. L. Audenino, P. Bhattacharya, M. Terzini

Bone remodelling prediction using mechanical stimulus with bone connectivity theory in porous implants (Journal of the Mechanical Behavior of Biomedical Materials) Z. Zou, V. S. Cheong, P. Fromme

Explainable deep learning-based survival prediction for non-small cell lung cancer patients undergoing radical radiotherapy (Radiotherapy and Oncology) J. R. Astley, J. M. Reilly, S. Robinson, J. M. Wild, M. Q. Hatton, B. A. Tahir

DCP: A pipeline toolbox for diffusion connectome (Human Brain Mapping) W. Huang, X. Dong, T. Zhao, L. Kucikova, A. Fu, N. Shu

The Effects of Fucoidan Derived from Sargassum filipendula and Fucus vesiculosus on the Survival and Mineralisation of Osteogenic Progenitor (International Journal of Molecular Sciences) D. Gupta, D. C. Martinez, M. A. Puertas-Mejía, V. L. Hearnden, G. C. Reilly

Cortical bone adaptation response is region specific, but not peak load dependent: insights from μ CT image analysis and mechanostat simulations of the mouse tibia loading model (Biomechanics and Modeling in Mechanobiology) C. J. Miller, E. Pickering, S.Martelli, E. Dall’Ara, P. Delisser, P. Pivonka

The loading direction dramatically affects the mechanical properties of the mouse tibia (Frontiers in Bioengineering and Biotechnology) S. M. Farage-O'Reilly,  V. S. Cheong, E. Pickering, P. Pivonka, I. Bellantuono, V. Kadirkamanathan, E. Dall'Ara

Modeling the selective growth advantage of genetically variant human pluripotent stem cells to identify opportunities for manufacturing process control (Cytotherapy) C. Beltran-Rendon, C. J. Price, K. Glen, A. Stacey, I. Barbaric, R. J. Thomas

Advancements in cardiac structures segmentation: a comprehensive systematic review of deep learning in CT imaging (Frontiers in Cardiovascular Medicine) T. N. Alnasser, L. Abdulaal, A. Maiter, M. Sharkey, K. Dwivedi, M. Salehi, P. Garg,  A. J. Swift, S. Alabed