Clinical Infrared and Raman Spectroscopy Network (CLIRSPEC)
Lead Research Organisation:
University of Manchester
Department Name: Chem Eng and Analytical Science
Abstract
A major part of the diagnosis of any disease but particularly various forms of cancer, is obtained though a biopsy. This involves removing a small sample of tissue, or a few cells, from the patient. These samples, either tissue or cells are then examined by a pathologist looking down an optical microscope. In most cases the sample is stained with a combination of dyes to help gain some contrast. In most cases, based upon visual inspection of the sample a diagnosis is made. This process if far from ideal since it relies on the expertise of the clinician concerned as is subject to intra in inter observer error. Recently a number of proof of concept studies have shown that molecular spectroscopic techniques such as infrared and Raman are capable of distinguishing diseased from non diseased cells and tissue based upon the inherent chemistry contained within the cells. The UK is at the forefront of these developments but there are many hurdles that need to be overcome if this technology is to move from the proof of concept stage through the translational stage and into the clinical setting. It is the belief of the academic community that we are much more likely to overcome these hurdles if we pool our resources, bring in both industrial and clinical partners and work on these generic problems together. This application is for funding to support such a network of partners for the next three years.
Planned Impact
One of the key aims of this project is to maximise the impact of current disjointed research in the field of spectral diagnostics and related technologies. The CLIRSPEC network is designed to deliver a step change in the awareness of spectral diagnosis by fellow academics, clinicians, patients industrialists, venture capitalists and policy makers.
At present, the field of spectral diagnosis is still in a dynamic phase with a number of key problems still to be solved, very little in the way of standardisation in either measurement or reporting and with very few clinical trials. Though a concerted approach the CLIRSPEC Network will bring these disparate strands together to bring stability to the field thus creating a more suitable and attractive environment for investment. This will be achieved through the CLIRSPEC network activities. These impact events will enable the academic leaders in the field to engage with instrument manufacturers, medical diagnostic companies and potential investors in order to discuss, not only the current state of the art, but also the potential barriers to market. It is anticipated that the CLIRSPEC network will lead to accelerated development and eventual acceptance of new technology. In the longer term it is expected that spectral diagnostic companies will contribute significantly to wealth creation and increased employment in the sector. Having a supply of well-trained PhD and early career researches in this interdisciplinary field will help facilitate this in the UK and increase the UK competitiveness in this area. In the case of curable diseases where early diagnosis is essential there will be significant long term economic benefits to the development of these rapid, accurate and relatively inexpensive alternatives to current diagnostic methods.
A wide range of people will benefit from the formation and working of the CLIRSPEC network. PhD students will benefit significantly. This is a very multidisciplinary and interdisciplinary research field and very few spectroscopy laboratories have good access to clinicians, statisticians or links to instrument manufacturers. The CLIRSPEC summer school in years two and three of the grant and rolled out as an international summer school at the end of the grant will enable PhD students to get specialist training in the field early in their career. In this way, the new generation of interdisciplinary scientists essential for the development of this field will be produced. The members of the network will benefit from greater sharing of ideas and having access to a wider range of samples and data as well as pooling data. The instrument manufacturers will benefit from having access to the latest research and being able to work with clinicians for an early stage of product development. Ultimately, it is envisaged that patients will benefit once the new technology is introduced to the clinic. In particular, cancer patient and sufferers of other diseases will benefit from reduction stress anxiety through faster testing and reduced waiting times for results.
It is still the case that most clinicians and pathologists are unaware of the research in this field and how both spectral pathology and cytology have the potential to revolutionise the way in which disease is diagnosed. This network grant is intended to help realise this potential by bringing the scientists, engineers and industrialists together. A major vehicle for enhancing our collaboration is the data sharing / data analysis portal. This will enable the net work members to have access to the data analysis tool box that contains the latest algorithms from various groups that represent current best practice or can be used for multi site testing. This type of multicentre activity currently does not exist in this field in the UK. A major part of our exit strategy is that this facility would be rolled out as part of the new society that would eventually give access to all members working in the field.
At present, the field of spectral diagnosis is still in a dynamic phase with a number of key problems still to be solved, very little in the way of standardisation in either measurement or reporting and with very few clinical trials. Though a concerted approach the CLIRSPEC Network will bring these disparate strands together to bring stability to the field thus creating a more suitable and attractive environment for investment. This will be achieved through the CLIRSPEC network activities. These impact events will enable the academic leaders in the field to engage with instrument manufacturers, medical diagnostic companies and potential investors in order to discuss, not only the current state of the art, but also the potential barriers to market. It is anticipated that the CLIRSPEC network will lead to accelerated development and eventual acceptance of new technology. In the longer term it is expected that spectral diagnostic companies will contribute significantly to wealth creation and increased employment in the sector. Having a supply of well-trained PhD and early career researches in this interdisciplinary field will help facilitate this in the UK and increase the UK competitiveness in this area. In the case of curable diseases where early diagnosis is essential there will be significant long term economic benefits to the development of these rapid, accurate and relatively inexpensive alternatives to current diagnostic methods.
A wide range of people will benefit from the formation and working of the CLIRSPEC network. PhD students will benefit significantly. This is a very multidisciplinary and interdisciplinary research field and very few spectroscopy laboratories have good access to clinicians, statisticians or links to instrument manufacturers. The CLIRSPEC summer school in years two and three of the grant and rolled out as an international summer school at the end of the grant will enable PhD students to get specialist training in the field early in their career. In this way, the new generation of interdisciplinary scientists essential for the development of this field will be produced. The members of the network will benefit from greater sharing of ideas and having access to a wider range of samples and data as well as pooling data. The instrument manufacturers will benefit from having access to the latest research and being able to work with clinicians for an early stage of product development. Ultimately, it is envisaged that patients will benefit once the new technology is introduced to the clinic. In particular, cancer patient and sufferers of other diseases will benefit from reduction stress anxiety through faster testing and reduced waiting times for results.
It is still the case that most clinicians and pathologists are unaware of the research in this field and how both spectral pathology and cytology have the potential to revolutionise the way in which disease is diagnosed. This network grant is intended to help realise this potential by bringing the scientists, engineers and industrialists together. A major vehicle for enhancing our collaboration is the data sharing / data analysis portal. This will enable the net work members to have access to the data analysis tool box that contains the latest algorithms from various groups that represent current best practice or can be used for multi site testing. This type of multicentre activity currently does not exist in this field in the UK. A major part of our exit strategy is that this facility would be rolled out as part of the new society that would eventually give access to all members working in the field.
Organisations
- University of Manchester (Lead Research Organisation)
- Jagiellonian University (Collaboration)
- AGH University of Science and Technology (Collaboration)
- Dublin Institute of Technology (Collaboration)
- Daresbury Laboratory (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- THE CHRISTIE NHS FOUNDATION TRUST (Collaboration)
- Agilent Technologies (Austria) (Collaboration)
- UNIVERSITY OF STRATHCLYDE (Collaboration)
- UNIVERSITY OF EXETER (Collaboration)
Publications
Casabella S
(2016)
Automated analysis of single cells using Laser Tweezers Raman Spectroscopy.
in The Analyst
Jimenez-Hernandez M
(2015)
Characterising cytotoxic agent action as a function of the cell cycle using Fourier transform infrared microspectroscopy.
in The Analyst
Baker MJ
(2018)
Clinical applications of infrared and Raman spectroscopy: state of play and future challenges.
in The Analyst
Pilling MJ
(2015)
Comparison of transmission and transflectance mode FTIR imaging of biological tissue.
in The Analyst
Hughes C
(2015)
Enhanced FTIR bench-top imaging of single biological cells.
in The Analyst
Pilling M
(2016)
Fundamental developments in infrared spectroscopic imaging for biomedical applications.
in Chemical Society reviews
Pilling MJ
(2016)
High-throughput quantum cascade laser (QCL) spectral histopathology: a practical approach towards clinical translation.
in Faraday discussions
Hughes C
(2016)
Introducing Discrete Frequency Infrared Technology for High-Throughput Biofluid Screening.
in Scientific reports
Pilling MJ
(2017)
Quantum Cascade Laser Spectral Histopathology: Breast Cancer Diagnostics Using High Throughput Chemical Imaging.
in Analytical chemistry
Description | This Network grant has carried out some key projects involving round robin studies that show how robust infrared diagnosis can be across a number of different platforms in a number of different hospital and university lab based environments. We have engaged with industry and have held a translation day that was highly successful. We have established robust data sharing tools. We have developed IR spectroscopy using glass substrates that offers an alternative solution to the substrate problem We have increased significantly our interaction with pathologists as evidence by an invited presentation at Digital Pathology Asia |
Exploitation Route | The setting up of the society means that we can disseminate best practice and other key findings to key stakeholders. Matt Baker, the CoI on this award has set up a company in 2016 to diagnose brain cancer using infrared spectroscopy. The system is now undergoing major clinical trials and has attracted large investment. http://ow.ly/oxs250yGBLL See also https://theanalyticalscientist.com/fields-applications/the-infrared-invasion-in-our-hospitals In addition our external partner Prof Bayden Wood in Australia had also set up a company to use infrared spectroscopy for infrared diagnosis of Malaria which has also attracted investment and wide interest. See below It is clear that the EPSRC funding has had a major impact on moving this field forward "Australians trial 'game changing' technology with capacity to eradicate malaria in Papua New Guinea" https://www.abc.net.au/news/2017-03-25/malaria-testing-new-technology-to-battle-endemic-in-png/8385504 |
Sectors | Healthcare |
URL | https://www.clinspecdx.com/clinspec-dx |
Description | The International Society for Clinical Spectroscopy (CLIRSPEC) is a non-profit organisation, constituted in 2015. The Society exists to act as a platform for those individuals, teams and organisations wishing to promote the translation of spectroscopy into the clinical environment, for the general benefit of patients; for example, to improve patient diagnosis and prognosis.The setting up of an international Society has brought the field together and we have a single forum for discussion how the field can move forward. Since being formed the International society has gone from strength to strength and is now a member of Federation of Analytical Chemistry and Spectroscopy Societies (FACSS) . We have run an international summer school every year for postgraduate students to learn more about clinical spectroscopy and this year (2019) we are running our first Asian summer school in Japan. The finding have led directly to two companies being formed and infrared spectroscopy is now undergoing major clinical trials. The company DXcover has been spun out by Prof Matt Baker who was a CoI on this grant. The company has been granted numerous patents for infrared spectroscopic analysis of liquid biopsy (see Matt Baker Researchfish) |
Sector | Healthcare |
Impact Types | Societal |
Description | Establishment of the International Society for Clinical Spectroscopy |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
URL | https://clirspec.org/ |
Description | Integrating Clinical Infrared and Raman Spectroscopy with digital pathology and AI: CLIRPath-AI |
Amount | £799,226 (GBP) |
Funding ID | EP/W00058X/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2021 |
End | 08/2025 |
Description | MRC Confidence in Concept |
Amount | £79,611 (GBP) |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2016 |
End | 05/2017 |
Title | Community data sharing |
Description | • Created a Community on the Zenodo repository platform for data in this field. This promotes data sharing. https://zenodo.org/communities/clirspec/ |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | Community starting to use this facility |
URL | https://zenodo.org/communities/ |
Title | File software |
Description | • Released software to allow users to read proprietary file formats from infrared instruments and perform statistical analyses in a common methodology: https://doi.org/10.5281/zenodo.57398 and https://doi.org/10.5281/zenodo.399238 |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | Several other groups are now using this software |
URL | https://doi.org/10.5281/zenodo.57398 |
Title | The use of Glass substrates |
Description | Have shown that FTIR analysis of human biopsy samples can be performed on glass substrates, thus greatly reducing the cost of analysis and opening up the ability to screen samples in the clinic. |
Type Of Material | Biological samples |
Provided To Others? | No |
Impact | M. J Pilling, A. Henderson, J. H. Shanks, M. D. Brown, N. W. Clarke and P. Gardner, Infrared Spectral Histopathology Using Haematoxylin and Eosin (H&E) Stained Glass Slides: A major step forward towards clinical translation. Analyst on line Comment on above paper " It might be a bold statement, but this could one of those defining studies that changes the course of FTIR imaging in biomed" Agilent Technologies. |
Title | Quantum Cascade Laser Spectral Histopathology: Breast Cancer Diagnostics Using High Throughput Chemical Imaging |
Description | Fourier transform infrared (FT-IR) microscopy, coupled with machine learning approaches, has been demonstrated to be a powerful technique for identifying abnormalities in human tissue. The ability to objectively identify the prediseased state, and diagnose cancer with high levels of accuracy, has the potential to revolutionise current histopathological practice. Despite recent technological advances in FT-IR microscopy, sample throughput and speed of acquisition are key barriers to clinical translation. Wide-field quantum cascade laser (QCL) infrared imaging systems with large focal plane array detectors utilising discrete frequency imaging, have demonstrated that large tissue microarrays (TMA) can be imaged in a matter of minutes. However this ground breaking technology is still in its infancy and its applicability for routine disease diagnosis is, as yet, unproven. In light of this we report on a large study utilising a breast cancer TMA comprised of 207 different patients. We show that by using QCL imaging with continuous spectra acquired between 912 and 1800 cm -1, we can accurately differentiate between 4 different histological classes. We demonstrate that we can discriminate between malignant and non-malignant stroma spectra with high sensitivity (93.56%) and specificity (85.64%) for an independent test set. Finally, we classify each core in the TMA and achieve high diagnostic accuracy on a patient basis with 100% sensitivity and 86.67% specificity. The absence of false negatives reported here opens up the possibility of utilising high throughput chemical imaging for cancer screening, thereby reducing pathologist workload and improving patient care. |
Type Of Material | Database/Collection of data |
Year Produced | 2017 |
Provided To Others? | Yes |
Description | Agilent |
Organisation | Agilent Technologies |
Country | United States |
Sector | Private |
PI Contribution | We have been working with Agilent on a number of projects to speed up data collection. We have provided know-how in data analysis |
Collaborator Contribution | Agilent have provided many hours of consultation regarding the software. |
Impact | This paper was ca direct result of our EPSRC Impact Acceleration award. P. Bassan, A. Sachdeva, J. H. Shanks, M. D. Brown, N. W. Clarke, P. Gardner, Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging, Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410D We have also presented at numerous conferences and workshops. High-throughput assessment of biopsy tissue using infrared spectroscopic chemical imaging, Agilent FTIR imaging workshop, Montreal, Canada, 26 June 2016 Rapid assessment of breast and prostate biopsy tissue using infrared spectroscopic chemical imaging. Agilent FTIR imaging workshop, Krakow, Poland 17th August 2014 The use of infrared imaging in urological pathology. Agilent International Imaging Workshop 2012, 11th November, Chiang Mai, Thailand |
Start Year | 2010 |
Description | Hugh Byrne Dublin Institute of Technology |
Organisation | Dublin Institute of Technology |
Country | Ireland |
Sector | Academic/University |
PI Contribution | We have developed a strong collaboration involving exchange of students and joint publications. We focus mainly on infrared imaging |
Collaborator Contribution | The Dublin group are experts in Raman imaging and provide access to state of the art Raman systems. Most importantly both groups have a keen interest in Data analysis. |
Impact | P. Bassan, H. J. Byrne, F. Bonnier, J. Lee, P. Dumas, P. Gardner, Resonant Mie scattering in Infrared spectroscopy of biological materials - understanding the "dispersion artefact" Analyst, 134 (2009), 1586-1593 P. Bassan, H. J. Byrne, J. Lee, F. Bonnier, C. Clarke, P. Dumas, E. Gazi, M. D. Brown, N. W. Clarke, P. Gardner., Reflection contributions to dispersion artefact in FTIR spectra of cellular samples, Analyst, 134, (2009), 1171-1175 P. Bassan, A. Kohler, H. Martens, J. Lee, H. J. Byrne, P. Dumas, E. Gazi, M. Brown, N. Clarke, P. Gardner, Resonant Mie Scattering (RMieS) Correction of Infrared Spectra from Highly Scattering Biological Samples, Analyst, 135 (2010) 268-277 Multi disciplinary, Physics, Chemistry, chemical Engineering, Medical. |
Start Year | 2008 |
Description | Magdalena Szczerbowska-Boruchowska |
Organisation | AGH University of Science and Technology |
Department | Faculty of Physics and Applied Computer Science |
Country | Poland |
Sector | Academic/University |
PI Contribution | We have had an exchange PhD student working in our lab for 6 months |
Collaborator Contribution | They have sent an exchange student, Artur Surowka, to our lab |
Impact | Joint Publication A. D. Surowka, M. Pilling, Alex Henderson, H. Boutin, L. Christie, M. Szczerbowska-Boruchowska, P. Gardner, FTIR imaging of the molecular burden around Aß deposits in an early-stage 3-Tg-APP-PSP1-TAU mouse model of Alzheimer's, Analyst, 2017, 142, 156 - 168 Plus several posters presented at international conferences |
Start Year | 2014 |
Description | Matt Baker Strathclyde |
Organisation | University of Strathclyde |
Department | Department of Pure and Applied Chemistry |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Exchange visits. We have hosted Matt Baker and his students. This has resulted in joint publications. |
Collaborator Contribution | We have had many meeting is Strathclyde and have exchanged ideas. |
Impact | M. J Baker, J. Trevisan, P. Bassan, R. Bhargava, H. Butler, K. M. Dorling, P. R Fielden, S.W. Fogarty, N.J. Fullwood, K. Heys, C. Hughes, P. Lasch, P. L. Martin-Hirsch, B. Obinaju, G. D Sockalingum, J. Sulé-Suso, R. Strong, M. J Walsh, B. R Wood, P. Gardner & F. L Martin, Using Fourier transform IR spectroscopy to analyze biological materials, Nature Protocols, 2014, 9, 1771-1791 |
Start Year | 2013 |
Description | Nick Stone Exeter |
Organisation | University of Exeter |
Department | Department of Economics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Exchange visits, round robin experiments |
Collaborator Contribution | Exchange visits etc |
Impact | Caryn Hughes, Hugh Byrne, Roy Goodacre, Alex Henderson, Martin Isabelle, Nallala Jayakrupakar, Catherine Kendall, Gavin Lloyd, David Perez-Guaita, Michael Pilling, Nick Stone, Bayden Wood, Matt Baker, Peter Gardner The University of Manchester Multicentre Infrared Round Robin: Same Samples, Same Diagnostic Outcome? Poster presented at SPEC2016 Montreal June 2016 |
Start Year | 2013 |
Description | Noel Clarke |
Organisation | The Christie NHS Foundation Trust |
Country | United Kingdom |
Sector | Public |
PI Contribution | We have had a number of joint projects and joint studentship over the last 18 years. We have provided access to state of the art infrared imaging systems. |
Collaborator Contribution | Noel's group have provided access to tissue samples, and numerous consultations regarding our work. We have regular project meeting at the Christie. |
Impact | This has been a very successful collaboration resulting in 34 peer reviewed publications and numerous presentations at international conferences. Publications 1. M. J Pilling, A. Henderson, J. H. Shanks, M. D. Brown, N. W. Clarke and P. Gardner, Infrared Spectral Histopathology Using Haematoxylin and Eosin (H&E) Stained Glass Slides: A major step forward towards clinical translation. Analyst on line 2. M. Jimenez-Hernandez, M. D. Brown , C. Hughes, N. W. Clarke, P. Gardner, Characterising cytotoxic agent action as a function of the cell cycle using Fourier Transform Infrared Mircospectroscopy, Analyst, 2015, 140, 4453 - 4464 3. C. Hughes, A. Henderson, M. Kansiz, K. M. Dorling, M. Jimenez-Hernandez, M. D. Brown, N. W. Clarkeb, and P. Gardner, Enhanced FTIR benchtop imaging of single biological cells, Analyst, 2015, 140, 2080 - 2085. DOI: 10.1039/C4AN02053G 4. P. Bassan, A. Sachdeva, J. H. Shanks, M. D. Brown, N. W. Clarke, P. Gardner, Automated high-throughput assessment of prostate biopsy tissue using infrared spectroscopic chemical imaging, Proc. SPIE 9041, Medical Imaging 2014: Digital Pathology, 90410D 5. C. Hughes, M. Brown, G. Clemens, A. Henderson, G. Monjardez, N.W. Clarke, P. Gardner, Assessing the challenges of Fourier transform infrared spectroscopic analysis of blood serum, J Biophotonics 2014 7(3-4) 180-188 6. C. Hughes, L. Gaunt, M. Brown, N.W. Clarke, P. Gardner, Assessment of Paraffin Removal from prostate FFPE Sections using transmission mode FTIR-FPA Imaging, Analytical Methods. 2014, 6 (4), 1028 - 1035 7. P. Bassan, A. Sachdeva, J. Shanks, Mick D. Brown, N.W. Clarke, P.Gardner, Whole organ cross-section chemical imaging using label-free mega-mosaic FTIR microscopy, Analyst 2013, 138(23), 7066-7069 8. M. Jimenez-Hernandez, C. Hughes, P. Bassan, F. Ball, M.D. Brown, N.W Clarke, P. Gardner. Exploring the spectroscopic differences of Caki-2 cells progressing through the cell cycle while proliferating in-vitro. Analyst 2013, 138(14), 3957-3966 9. C. Hughes, M. Brown, J. H Shanks J. Iqbal-Wahid, A. Eustac, H. Denley, P. J Hoskin, C. West, N. W Clarke, P. Gardner, FTIR microspectroscopy of diverse sub-variants of carcinoma of the urinary bladder: a pilot study. J Biophotonics, 6(1) (2013) 73-87 10. C. Hughes , M. D. Brown , F. Ball , G. Monjardez, P. Dumas, N. W. Clarke, K. R. Flower and P Gardner, Highlighting a Need to Distinguish Cell Cycle Signatures from Cellular Responses to Chemotherapeutics in SR-FTIR Spectroscopy, Analyst 137 (24),(2012), 5736 - 5742 11. C. Hughes , M. D. Brown , P. Dumas, N. W. Clarke, K. R. Flower and P Gardner, Tracking Cellular Responses to Chemotherapeutics in Renal Cell Carcinoma using Synchrotron and Benchtop FTIR Spectroscopy, Analyst, 137 (20), (2012), 4720 - 4726 12. P. Bassan, A. Sachdeva, A. Kohler, C. Hughes, A. Henderson, J. Boyle, J. H. Shanks, M. Brown, N. W. Clarke P.Gardner, FTIR Microscopy of biological cells and tissue: data analysis using resonant Mie scattering (RMieS) EMSC algorithm, Analyst 137, (2012) 1370-1377 13. C. Hughes, M. Liew, M. D. Brown, A. Sachdeva, P. Bassan, P. Dumas, C.Hart, N. W. Clarke, P.Gardner, SR-FTIR Spectroscopy of Renal Epithelial Carcinoma Cells Displaying Stem Cell Characteristics, Analyst, 135, (2010) 3133-3141 14. P. Bassan, A. Kohler, H. Martens, J. Lee, E. Jackson, N. Lockyer, P. Dumas, M. Brown, N. Clarke, P. Gardner RMieS-EMSC correction for infrared spectra of biological cells: Extension using full Mie theory and GPU computing, J. Biophotonics, 3 (2010) 609-620 15. M.J. Baker, C. Clarke, D. Démoulin, J. Nicholson, F. Lyng, H.J. Byrne, C.A. Hart, M.D. Brown, N.W. Clarke, P. Gardner, An Investigation of the RWPE Prostate Derived Family of Cell Lines Using FTIR Spectroscopy, Analyst, 135, (2010) 887- 894 16. P. Bassan, A. Kohler, H. Martens, J. Lee, H. J. Byrne, P. Dumas, E. Gazi, M. Brown, N. Clarke, P. Gardner, Resonant Mie Scattering (RMieS) Correction of Infrared Spectra from Highly Scattering Biological Samples, Analyst, 135 (2010) 268-277 (Front Cover) 17. M. Brown, C. Hart, E. Gazi, P. Gardner, N. Lockyer, N. Clarke, The influence of the omega 6 PUFA arachidonic acid and bone marrow adipocytes on the metastatic spread of prostate cancer, British Journal of Cancer, 102 (2010) 403-413 18. P. Bassan, H. J. Byrne, J. Lee, F. Bonnier, C. Clarke, P. Dumas, E. Gazi, M. D. Brown, N. W. Clarke, P. Gardner., Reflection contributions to dispersion artefact in FTIR spectra of cellular samples, Analyst, 134, (2009), 1171-1175 19. T. J. Harvey, E. Gazi, A. Henderson, R. D Snook, N. W. Clarke, M. Brown, P Gardner. Factors Influencing the Discrimination and Classification of Prostate Cancer Cells Lines by FTIR Microspectroscopy, Analyst 134, (2009) 1083-1091 20. M.J. Baker, E.Gazi, M.D. Brown, J.H. Shanks, N.W. Clarke, P. Gardner, Investigating FTIR Based Histopathology for the Diagnosis of Prostate Cancer, J. Biophotonics, 2 (2009) 104-113 21. T J Harvey, C Hughes, A D Ward, E Correia Faria, A Henderson, N W Clarke, M D Brown, R D Snook P. Gardner, Classification of Fixed Urological Cells using Raman Tweezers, J. Biophotonics, 2 (2009) 47-69 22. E. Gazi, T.J. Harvey, M.D.Brown, N.W. Clarke, N.P. Lockyer, P. Gardner, A FTIR Microspectroscopic Study of the Uptake and Metabolism of Isotopically Labelled Fatty Acids by Metastatic Prostate Cancer, Vibrational Spectroscopy, 50 (2009) 99-105 23. T. J. Harvey, E Correia Faria, E Gazi, A D Ward, N W Clarke, M D Brown, R.D. Snook, P Gardner, The Spectral Discrimination of Live Prostate and Bladder Cancer Cell Lines Using Raman Optical Tweezers, Journal of Biomedical Optics, 13 (2008) 064004 24. 76. M.J. Baker, E.Gazi, M.D. Brown, J.H. Shanks, P. Gardner, N.W. Clarke, FTIR Based Spectroscopic Analysis in the Identification of Clinically Aggressive Prostate Cancer, British Journal of Cancer, 99 (2008) 1859-1866 25. 74. E. Gazi, P. Gardner, N.P Lockyer, C.A Hart, N.W. Clarke, M.D Brown, Probing Lipid Translocation Between Adipocytes and Prostate Cancer Cells with Imaging FTIR Microspectroscopy, J. Lipid Research 48 (2007) 1846 26. 73. J. Lee, E Gazi, J Dwyer, M. D. Brown, N. W. Clarke, P. Gardner, Optical artefacts in transflection mode FTIR microspectroscopic images of single cells on a biological support: the effect of back-scattering into collection optics. Analyst 132 (2007) 750-755 27. T. J. Harvey, A. Henderson, E. Gazi, N. W. Clarke, M. Brown, E Correia Faria, R. D. Snook P. Gardner, Discrimination of prostate cancer cells by reflection mode FTIR photo-acoustic spectroscopy, Analyst 132 (2007) 292-295 28. E. Gazi, J. Dwyer, N.P Lockyer, P. Gardner, J.H Shanks, Jo-An Roulson, C.A Hart, N.W Clarke, M.D Brown, Biomolecular Profiling of Metastatic Prostate Cancer Cells in Bone Marrow Tissue Using FTIR Microspectroscopy: A Pilot Study, Analytical and Bioanalytical Chemistry, 387 (2007) 1621-1631. 29. E. Gazi, M. Baker, J. Dwyer, N. P. Lockyer, P. Gardner, J.H. Shanks, R. S. Reeve, C. Hart, N.W. Clarke M. Brown, A Correlation of FTIR Spectra Derived from Prostate Cancer Tissue with Gleason Grade, and Tumour Stage, 30. E. Gazi, J. Dwyer, N. P. Lockyer. J. Miyan, P. Gardner, C.A Hart, M.D Brown, N.W. Clarke, A Study of Cytokinetic and Motile Prostate Cancer Cells Using Synchrotron Based FTIR - Microspectroscopic Imaging, Vibrational Spectroscopy 38 (2005) 193 - 201 31. E. Gazi, J. Dwyer, J. Miyan, P. Gardner, C. Hart, M. Brown, N.W. Clarke, Fixation Protocols for Sub-cellular Imaging by Synchrotron Based FTIR Microspectroscopy, Biopolymers 77 (2005) 18-30 32. E. Gazi, N. P. Lockyer, J. C. Vickerman, P. Gardner, J. Dwyer, C. A. Hart, M. B. Brown, N. W. Clarke J. Miyan, Imaging ToF-SIMS and synchrotron based FTIR-microspectroscopic studies of prostate cancer cell lines, Applied Surface Science 231 - 232 (2004) 452 - 456 33. E. Gazi, J. Dwyer, N. Lockyer, P. Gardner, J.C. Vickerman, J. Miyan, C. Hart, M. Brown and N. Clarke, Application of FTIR Microspectroscopy and ToF-SIMS Imaging in the Study of Prostate Cancer, Faraday Discussions 126 (2004) 41 - 59 34. E. Gazi, J. Dwyer, P. Gardner, A. Ghanbari-Siakhali, A. P. Wade. J. Myan. N.P.Lockyer, J. C. Vickerman, N. W. Clarke, J. H. Shanks, C. Hart, M.Brown, Applications of Fourier Transform Infrared Microspectroscopy in Studies of Benign Prostate & Prostate Cancer. A pilot Study, J. Pathology 201 (2003) 99-108 |
Description | Peter Weightman |
Organisation | University of Liverpool |
Department | Institute of Translational Medicine |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have worked closely with Prof Weightman on imaging tissue samples. We have provided Access to state of the art IR imaging equipment available in our lab |
Collaborator Contribution | They have contributed personel to the project and data analysis experties. |
Impact | Joint publications in preparation. |
Start Year | 2015 |
Description | Prof. Malgorzata Baranska |
Organisation | Jagiellonian University |
Department | Faculty of Chemistry |
Country | India |
Sector | Academic/University |
PI Contribution | We have had a collaboration resulting in a number of exchange visits of students. I have hosted two PhD student from this group in my laboratory. |
Collaborator Contribution | They have provided excellent PhD students for exchange visits. I have also been to the university on Krakow for an exchange visit and to work with their PhD students. |
Impact | Joint papers in preparation. We are both on the Management committee of the EU Raman4Clinics network. |
Start Year | 2012 |
Description | STFC Daresbury Laboratory |
Organisation | Daresbury Laboratory |
Country | United Kingdom |
Sector | Private |
PI Contribution | We are heavy users of the IR beamline and have had two jointly funded studentships. I have also been chair of the IR user group and have sat on the Diamond Light Source Scientific Advisory Board 2012-2016 and have conducedted a number of beamline reviews. I have several joint publications. |
Collaborator Contribution | Diamond have jointly funded two PhD studentships and we have several joint publications. |
Impact | We have had several joint publications in which Gianfelice Cinque is a coauthor. G. Clemens, F. J. Ball, A. Henderson, S. Mohr, P. R Fielden, N. J Goddard, A. Whiting, S. A. Przyborski, G. Cinque, P. Gardner, A Microfluidic Device for the Infrared Study of Single Cells in Aqueous Media: An Evaluation Using Differentiating Stem Cells, Analyst submitted J. Doherty, G. Cinque and P. Gardner, Single Cell Analysis Using Fourier Transform Infrared Microspectroscopy, Applied Spectroscopy Reviews, 2016, 1252014 A. L. M. Batista de Carvalho, M. Pilling, P. Gardner, J. Doherty, G. Cinque, K. Wehbe, C. Kelley, L. A. E. Batista de Carvalho and M. P. M. Marquesa, Chemotherapeutic Response to Cisplatin-like Drugs in Human Breast Cancer Cells Probed by Vibrational Microspectroscopy. Faraday Discussion, 2016, 187, 273-298 DOI: 10.1039/c5fd00148j G. Clemens, K. R. Flower, A. P. Henderson, A. Whiting, S. A. Przyborski, M. Jimenez-Hernandez, F. Ball, P. Bassan, G. Cinque, P. Gardner. The action of all-trans-retinoic acid (ATRA) and synthetic retinoid analogues (EC19 and EC23) on human pluripotent stem cells differentiation investigated using single cell infrared microspectroscopy. Molecular BioSystems, 2013, 9 (4), 677 - 692 |
Start Year | 2006 |
Title | Created Zenodo |
Description | • Created a Community on the Zenodo repository platform for data in this field. This promotes data sharing. https://zenodo.org/communities/clirspec/ |
Type Of Technology | Webtool/Application |
Year Produced | 2016 |
Impact | Groups are starting to use this. |
URL | https://zenodo.org/communities/clirspec/ |
Title | software to allow users to read proprietary file formats from infrared instruments |
Description | Released software to allow users to read proprietary file formats from infrared instruments and perform statistical analyses in a common methodology: https://doi.org/10.5281/zenodo.57398 and https://doi.org/10.5281/zenodo.399238 |
Type Of Technology | Software |
Year Produced | 2016 |
Impact | Several groups are now using this software. |
URL | https://doi.org/10.5281/zenodo.57398 |
Description | CLIRCON 15 The UK CLIRSPEC Network conference EXETER |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | This was an international conference run by the CLIRSPEC network that brought together Industry, clinicians and academics working in the field of biomedical and clinical spectroscopy. This was a three day meeting that incorporated workshops and breakout sessions specifically design to facilitate interaction and collaboration between these groupings. |
Year(s) Of Engagement Activity | 2015 |
URL | https://clirspec.org/uk-network/groups/exeter-conference/ |
Description | CLIRCON 17 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | CLIRCON 17 was a follow up to CLIRCON 15 which brought together industry academia and clinicians working in the field of clinical spectroscopy. We also added speakers involved in policy making. |
Year(s) Of Engagement Activity | 2017 |
Description | CLIRSPEC summer school 2016 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This was an international summer school. |
Year(s) Of Engagement Activity | 2016 |
Description | CLIRSPEC summer school 2017 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This was an international summer school. |
Year(s) Of Engagement Activity | 2017 |
Description | CLIRSPEC/CLIRPath-AI Summer school 2022 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | The International Society for Clinical Spectroscopy (CLIRSPEC) would like to invite all students, industrialists and postdoctoral researchers in the multidisciplinary area of clinical infrared and Raman spectroscopy to attend the 6th CLIRSPEC Summer School. This year we will be co-hosting the Summer School with CLIRPath-AI, a UK funded network connecting clinical spectroscopy, digital pathology and artificial intelligence. Building upon previous successful summer schools the 2022 Summer School will provide an excellent grounding in spectroscopic fundamentals through to current cutting edge clinical applications and discuss the future of vibrational spectroscopy in the clinical environment including interactive and exciting group problem-based learning sessions. This Summer School will have more of a data analysis focus than in previous years. |
Year(s) Of Engagement Activity | 2022 |
URL | https://clirspec.org/summer-school/ |
Description | International Summer School 2015 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This was an international summer school aimed mainly at postgraduate students and early career researchers working in the field of biomedical and clinical spectroscopy. We had 38 participants who were there to learn off experts in the field. |
Year(s) Of Engagement Activity | 2015 |
Description | International Summer School 2018 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | The CLIRSPEC Summer School is designed to teach mainly postgraduate students the fundamental of spectroscopy for the clinical environment. |
Year(s) Of Engagement Activity | 2018 |
URL | https://clirspec.org/summer-school/ |