Welcome to the quarterly round up of news from the Physical Sciences for Health Centre for Doctoral Training. This newsletter will outline goings-on in the centre, from general news; publications and awards; to events and opportunities to get involved.

The opportunities section of this newsletter may be of particular interest to our industrial partners as we present an opportunity to sponsor the upcoming TransMed 2017 CDT Conference.

The annual Birmingham University Awards for tremendous Achievement recognise professional services staff who have gone above and beyond in their roles and we are thrilled that Ann’s work has been recognised in this way. This text explaining the reasons for her nomination and shortlisting reflects the pivotal role she plays in ensuring the centre is a well-run and pleasant place to work: 


“Ann is the backbone of two Doctoral Training Centres and handles the administration single-handedly. She is incredibly helpful and ensures students have properly coordinated modules and progress smoothly through each stage of their PhD. Known for her calm and friendly manner, Ann has great interaction with the 50 PhD students and knows them all by first name. She is an absolute star who deserves this recognition”.

We have recently updated our website, and now all students have individual pages. For those already in the PhD part of the course the page contains a summary of their research, while for our first years the pages serve as an introduction to the community – each containing a biography detailing the students’ academic experience and interests. Get to know our newest students by following the links from the Students page on the website. Year 1 Sci-Phy students will be presenting their mini project 1 work on Friday 26th May 2017. All are welcome to attend the oral presentation, details of which are to follow.

We were pleased to welcome Ruchi Gupta as a new senior lecturer to the centre at the beginning of the year. Ruchi is a Birmingham Fellow in Healthcare Technologies and brings with her expertise in chemistry and optics. Her research is largely focused on developing high performance optical sensors made of soft materials for applications in healthcare and life sciences. She is a recipient of the 2016 Royal Society of Chemistry Tom West Fellowship, Royal Academy of Engineering Enterprise fellowship and Brian L. Barge first runner-up award for excellence in microsystems integration.


 Artist Anna Dumitriu is undertaking a Leverhulme Artist in Residence project with the School of Chemistry, collaborating with Physical Sciences for Health Centre member Rob Neely and colleagues to explore the impact of new developments in chemistry on biotechnology. Anna’s distinctive style often involves physically incorporating biological material into her artwork. Over the next several months Anna and Rob will be working together to develop artwork and workshops employing different craft techniques, sculpture and digital technology, along with the tools of chemistry and biotechnology; and exploring new ways of communicating Rob’s group’s work on optical DNA mapping.
Read the full article here.


Second year student Emma Metcalfe-Smith responded to a call from the EPSRC for guest bloggers to write for the official EPSRC blog, and produced a fantastic article reflecting on her experience moving
from a physics degree into interdisciplinary research.
Read the blog post here.

Second year student Chris O’Shea, with Davor Pavlovic, Kashif Rajpoot and Rob Neely together with Cairn Research are in the final round of the Enterprising Birmingham Innovation Competition with their entry ‘High throughput, automated software for studying electrophysiology’. To get to this point in the competition they have demonstrated innovative collaborative work through an application and interview stage, and will soon be pitching to the judging panel at the final showcase on 29th March 2017. Further details on the showcase can be found in the events section of this newsletter.

 During February half-term students from the Physical Sciences for Health (Sci-Phy) CDT at the University of Birmingham made their annual visit to the Thinktank Science Museum Birmingham for the ‘Meet The Expert’ event. This year 25 PhD students from the centre attended over two days to run a variety of activities for enquiring young minds. To read more about the activities they put on read the full article here.

all students

Emily J Guggenheim, Iseult Lynch, Joshua Z. Rappoport

Abstract: Reflectance imaging is a broad term that describes the formation of images by the detection of illumination light that is back-scattered from reflective features within a sample. Reflectance imaging can be performed in a variety of different configurations, such as confocal, oblique angle illumination, structured illumination, interferometry and total internal reflectance, permitting a plethora of biomedical applications. Reflectance imaging has proven indispensable for critical investigations into the safety and understanding of biomedically and environmentally relevant nano-materials, an area of high priority and investment. The non-destructive in vivo imaging ability of reflectance techniques permits alternative diagnostic strategies that may eventually facilitate the eradication of some invasive biopsy procedures. Reflectance can also provide additional structural information and clarity necessary in fluorescent based in vivo studies. Near-coverslip interrogation techniques, such as reflectance interferometry and total internal reflection, have provided a label free means to investigate cell-surface contacts, cell motility and vesicle trafficking in vivo and in vitro. Other key advances include the ability to acquire superresolution reflectance images providing increased spatial resolution.
Read the article in full.

Samuel R. Moxon, Megan E. Cooke, Sophie C. Cox, Martyn Snow, Lee Jeys, Simon W. Jones, Alan M. Smith, Liam M. Grover

Abstract: A method for the production of complex cell-laden structures is reported, which allows high-levels of spatial control over mechanical and chemical properties. The potential of this method for producing complicated tissues is demonstrated by manufacturing a complex hard/soft tissue interface and demonstrating that cell phenotype can be maintained over four weeks of culture.
Read the article in full.

N. Vyas, R.L. Sammons, Z. Pikramenou, W.M. Palin, H. Dehghani, A.D. Walmsley

Abstract: Objectives - Functionalised silica sub-micron particles are being investigated as a method of delivering antimicrobials and remineralisation agents into dentinal tubules. However, their methods of application are not optimised, resulting in shallow penetration and aggregation. The aim of this study is to investigate the impact of cavitation occurring around ultrasonic scalers for enhancing particle penetration into dentinal tubules.
Results - Qualitative observations of SEM images showed some tubule occlusion. The particles could penetrate inside the tubules up to 60 μm when there was no cavitation and up to ∼180 μm when there was cavitation.
Read the article in full.

Jeremy A. Pike, Iain B. Styles, Joshua Z. Rappoport, John K. Heath

Abstract: Confocal microscopy is a powerful tool for the study of cellular receptor trafficking and endocytosis. Unbiased and robust image analysis workflows are required for the identification, and study, of aberrant trafficking. After a brief review of related strategies, identifying both good and bad practice, custom workflows for the analysis of live cell 3D time-lapse data are presented. Strategies for data pre-processing, including denoising and background subtraction are considered. We use a 3D level set protocol to accurately segment cells using only the signal from fluorescently labelled receptor. A protocol for the quantification of changes to subcellular receptor distribution over time is then presented. As an example, ligand stimulated trafficking of epidermal growth factor receptor (EGFR) is shown to be significantly reduced in both AG1478 and Dynasore treated cells. Protocols for the quantitative analysis of colocalization between receptor and endosomes are also introduced, including strategies for signal isolation and statistical testing. By calculating the Manders and Pearson coefficients, both co-occurrence and correlation can be assessed. A statistically significant decrease in the level of ligand induced co-occurrence between EGFR and rab5 positive endosomes is demonstrated for both the AG1478 and Dynasore treated cells relative to a control. Finally, a strategy for the visualisation of co-occurrence is presented, which provides an unbiased alternative to colour overlays.
Read the article in full.

Hao Yang Wu, Andrew Filer, Iain Styles, and Hamid Dehghani

Abstract: A multi-wavelength diffuse optical tomography (DOT) system has been developed to directly extract physiological information, such as total haemoglobin concentration, from tissue in human hand joints. Novel methods for 3D surface imaging and spectrally constrained image reconstruction are introduced and their potential application to imaging of rheumatoid arthritis is discussed. Results are presented from simulation studies as well as experiments using phantoms and data from imaging of three healthy volunteers. The image features are recovered partially for phantom data using transmission measurements only. Images that reveal joint regions and surrounding features within the hand are shown to co-register with co–acquired ultrasound images which are shown to be related to total haemoglobin concentration. Read the article in full.

David James Davies, Michael Clancy, Daniel Lighter, George M. Balanos, Samuel John Edwin Lucas, Hamid Dehghani, Zhangjie Su, Mario Forcione, Antonio Belli

Abstract: The Near-infrared spectroscopy (NIRS) has not been adopted as a mainstream monitoring modality in acute neurosurgical care due to concerns about its reliability and consistency. However, improvements in NIRS parameter recovery techniques are now available that may improve the quantitative accuracy of NIRS for this clinical context. Therefore, the aim of this study was to compare the abilities of a continuous-wave (CW) NIRS device with a similarly clinically viable NIRS device utilising a frequency-domain (FD) parameter recovery technique in detecting changes in cerebral tissue saturation during stepwise increases of experimentally induced hypoxia. Nine healthy individuals (6M/3F) underwent a dynamic end-tidal forced manipulation of their expiratory gases to induce a stepwise induced hypoxia. The minimum end-tidal oxygen partial pressure (EtO2) achieved was 40 mm Hg. Simultaneous neurological and extra-cranial tissue NIRS reading were obtained during this protocol by both tested devices. Both devices detected significant changes in cerebral tissue saturation during the induction of hypoxia (CW 9.8 ± 2.3 %; FD 7.0 ± 3.4 %; Wilcoxon signed rank test P < 0.01 for both devices). No significant difference was observed between the saturation changes observed by either device (P = 0.625). An observably greater degree of noise was noticed in parameters recovered by the FD device, and both demonstrated equally variable baseline readings (Coefficient of variance 8.4 and 9.7 % for the CW and FD devices, respectively) between individuals tested. No advantageous difference was observed in parameters recovered from the FD device compared with those detected by CW.
Read the article in full.

Designing biomaterials to mimic the function of antifreeze proteins for cell cryopreservation
Professor Matthew Gibson, University of Warwick
Thursday 9th March 2017 - 1.00pm, Mech Eng G29

Unlocking gene expression and repair by tracking single molecules in vivo
Professor Achillefs Kapanidis, University of Oxford
Thursday 27th April 2017 - 1.00pm, Bio-E102

Using physics to understand cancer
Dr Daniel Frankel, Newcastle University 
Thursday 11th May 2017 - 1.00pm, Bio-E102

Using the power of light to provide a rapid near patient molecular diagnosis
Professor Nicholas Stone, University of Exeter
Thursday 25th May 2017 - 1.00pm, Bio-E102

See seminars page for details of further upcoming talks.

Transmed Conference 2017
20-21 June 2017, Birmingham, UK
Students from Sci-Phy CDT are organising the TransMed 2017 Conference. TransMed is a two-day student led conference which showcases the work of postgraduate students within translational medicine and physical science UK-wide. The conference will focus on the use of physical sciences to solve key healthcare challenges. The meeting facilitates an interdisciplinary, inter-university discussion of a diverse range of biomedical research. The conference will feature presentations by PhD students, keynote presentations from leading academics in the translational medical field, and workshops on communication and paper writing. Alongside presentations, poster sessions will be display the work of attendees. To find out more and register attendance click here.

Arts and Science Festival
13-19 March 2017

The University of Birmingham’s Art & Science Festival returns from 13-19 March, bringing talks, exhibitions, performances, workshops and screenings that showcase collaboration, research and ideas from the University of Birmingham to an ever-growing public audience. Details and a programme of events can be found here.

Enterprising Birmingham Innovation Competition
Wednesday 29th March 2017

Discover how University of Birmingham research is solving real world problems at the Final Showcase of the Enterprising Birmingham Innovation Competition. The University’s brightest commercial innovators will pitch their ideas to a Dragon’s Den style judging panel at the Bramall Music Building on Wednesday 29th March, 12.30 – 5.00pm. The event will include a buffet lunch, pitching event, awards ceremony and drinks reception presenting the opportunity to network with researchers, alumni, public and private sector partners, funders and investors. Register for free tickets here.

TransMed 2016 was held in Edinburgh and attended by 60+ students from over 10 different CDTs and we expect comparable attendance here in Birmingham, thus this is an excellent opportunity to publicise your brand to a significant number of high-calibre, early career researchers. Different levels of sponsorship are welcome - please contact transmed2017@contacts.bham.ac.uk for further information.

We are currently taking proposals for mini-project 2, deadline Friday 17th March 2017. Projects are approximately 12 weeks full-time including 1 reading week and 1 write-up week and must involve the development of physical and computational sciences applied to one of the three healthcare challenges:

  • Rebuilding the ageing and diseased body
  • Understanding cardiovascular disease
  • Improving trauma and emergency medicine

For full details of the call see the website.

  • The Big Bang Fair
    Volunteer at the Big Bang Fair – the largest celebration of science, technology, engineering and maths (STEM) for young people in the UK - at Birmingham NEC any day from 15th-18th March 2017. Roles available include judging, ‘Meet the Future You’, careers advising and general assisting. Find details on how to apply here.
  • PubhD – Can you explain your PhD in the pub?
    PubhD is a public speaking event in the pub. At each event (roughly every 2 months) 3 speakers talk about their research at “pub-level” (an intelligent but non-specialist audience) for 10 minutes, and earn themselves a free drink in the process. Speakers are only allowed a whiteboard and whatever props they can gather to present their work, and there’s an informal Q&A after each presentation. If you are interested in volunteering to be a speaker or finding out more about attending see their website and Facebook pages.
  • Three Minute Thesis (3MT)
    Could you present your thesis in three minutes using a maximum of one PowerPoint slide and no additional props? Key dates have not yet been released for 3MT 2017 but last year the deadline for entries was early May, so they will likely come out soon. Click here for details of last years’ competition and keep an eye out for updates on this years details.