Publications

Publication: Authorea

Nick K Jones, Lucy Rivett, Chris Workman, Mark Ferris, Ashley Shaw, Paul J LehnerRob HowesGiles WrightNicholas J Matheson, Michael P Weekes

24 February 2020


Summary:

New data from Addenbrooke’s hospital in Cambridge suggests a significant drop in the spread of Covid-19 amongst staff following vaccination. It’s one of the first indications from UK scientists that the Pfizer vaccine reduces the transmission of SARS-CoV-2, the virus that causes Covid-19, as well as protecting people from getting ill. Read the full story.

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Publication: MedRxiV

Martin Wiegand, Sarah L. Cowan, Claire S. Waddington, David J. Halsall,  Victoria L. Keevil,  Brian D. M. Tom, Vince Taylor,  Effrossyni Gkrania-Klotsas, Jacobus Preller,  Robert J. B. Goudie

18 February 2021


Summary

Researchers propose a prognostic dynamic risk stratification for 48-hour in-hospital mortality in patients with COVID-19, using demographics and routinely-collected observations and laboratory tests: age, Clinical Frailty Scale score, heart rate, respiratory rate,

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Publication: ELife

William L Hamilton, Dinesh Aggarwal, Charlotte Houldcroft, Ben Warne, Luke Meredith, Myra Hosmillo, Aminu Jahun,  Laura Caller, Sarah Caddy, Fahad Khokhar, Anna Yakovleva, Grant Hall, Theresa Feltwell, Malte Pinckert, Iliana Georgana, Yasmin Chaudhry, Nicholas Brown, Ewan Harrison,  Gordon Dougan, Sharon Peacock,   Ian Goodfellow,  M. Estee Torok

16 February 2021


Summary:

Approximately 70% of residents in the genomic analysis were admitted to hospital during the study period, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission between care home residents should be a key target for infection control to reduce COVID-19 mortality in this population

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Publication: OSF Preprints

Christopher J. R. Illingworth,  William L. Hamilton,  Ben Warne, Matthew Routledge, Ashley Popay, Chris Jackson, Tom Fieldman, Luke Meredith, Charlotte J. Houldcroft, Myra Hosmillo, Aminu Jahun, Laura Caller, Sarah Caddy, Anna Yakovleva, Grant Hall, Fahad A. Khokhar, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Dominic Sparkes, Lucy Rivett, Nick K. Jones, Sushmita Sridhar, Sally Forrest, Tom Dymond, Kayleigh Grainger, Chris Workman, Effrossyni Gkrania-Klotsas, Nicholas M. Brown, Michael P. Weekes, Stephen Baker, Sharon J. Peacock, Ian Goodfellow, Theodore Gouliouris, Daniela De Angelis, M. Estée Török

15 February 2021


Summary

The SARS-CoV-2 virus has been noted both for its rapid spread, but also for the heterogeneity of transmission, with incidences noted of superspreading behaviour.

Researchers applied a novel network reconstruction algorithm to find patterns of viral transmission occurring between patients and health care workers.

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Publication: Medrxiv

Laura BergamaschiFederica MesciaLorinda TurnerAimee HansonPrasanti KotagiriBenjamin J. DunmoreHelene RuffieuxAloka De SaOisin HuhnMark R. WillsStephen BakerRainer DoffingerGordon DouganAnne ElmerIan G Goodfellow, Ravindra K. GuptaMyra HosmilloKelvin HunterNathalie KingstonPaul J. LehnerNicholas J. MathesonJeremy K. NicholsonAnna M. PetrunkinaSylvia RichardsonCaroline Saunders, James E.D. ThaventhiranErik J. M. ToonenMichael P. WeekesMark ToshnerChristoph HessJohn R. BradleyPaul A. LyonsKenneth G.C. Smith

15 January 2021


Summary

It may be possible to predict which patients will go on to develop severe or long-term COVID symptoms (sometimes known as ‘long COVID’).

Cambridge researchers looked at blood samples taken regularly over three months from more than 200 people, ranging from COVID-19 patients who were severely ill and needed ventilation to asymptomatic NHS staff who had tested positive for the virus but showed no symptoms.

The immune systems in patients who were the sickest showed early evidence of an abnormal inflammatory response, leading to a flood of immune cells which damaged healthy cells as well as the virus. Finding inflammation early in the blood samples and at the point of diagnosis could help doctors to identify and predict patients who will develop severe COVID-19.

The results have been released as a pre-print, read the full news story.

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Publication: MedRxiV

Christopher J. R. Illingworth, ProfileWilliam L. Hamilton,  ProfileChris Jackson, Ashley Popay, Luke Meredith, Charlotte J. Houldcroft, Myra Hosmillo, Aminu Jahun, Matthew Routledge, Ben Warne, Laura Caller, Sarah Caddy, Anna Yakovleva, Grant Hall, Fahad A. Khokhar, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Martin Curran, Surendra Parmar, Dominic Sparkes, Lucy Rivett, Nick K. Jones, Sushmita Sridhar, Sally Forrest, Tom Dymond, Kayleigh Grainger, Chris Workman, Effrossyni Gkrania-Klotsas, Nicholas M. Brown, Michael P. Weekes, Stephen Baker, Sharon J. Peacock, Theodore Gouliouris, Ian Goodfellow, Daniela de Angelis, M. Estée Török

27 October 2020


Summary:

A new software tool will help doctors identify where cases of COVID-19 were caused by transmission within a hospital, helping them to prevent further spread of the disease.

The new software package, A2B-Covid, combines knowledge about infection dynamics, data describing the movements of individuals, and genome sequence data to assess whether or not coronavirus has been transmitted between people in the hospital environment.

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Publication: Cell Reports Medicine

Petra Mlcochova, Dami Collier, Allyson Ritchie, Sonny M. Assennato, Myra Hosmillo, Neha Goel, Bo Meng, Krishna Chatterjee, Vivien Mendoza, Nigel Temperton, Leo Kiss, Leo C. James, Katarzyna A. Ciazynska, Xiaoli Xiong, John AG. Briggs, James A. Nathan, Federica Mescia, Laura Bergamaschi, Hongyi Zhang, Petros Barmpounakis, Nikos Demeris, Richard Skells, Paul A. Lyons, John Bradley, Steven Baker, Jean Pierre Allain, Kenneth GC. Smith, Rachel Bousfield, Michael Wilson, Dominic Sparkes, Glenn Amoroso, Effrosyni Gkrania-Klotsas, Susie Hardwick, Adrian Boyle, Ian Goodfellow, Ravindra K. Gupta 

1 September 2020


Summary

Testing patients for COVID-19 as soon as they arrive at hospital is essential to obtain a diagnosis and to make sure they receive the correct treatment as soon as possible.

In a recent Cambridge study, the use of the SAMBA II test reduced the amount of time patients spent on holding wards. Now Cambridge researchers wanted to go further to create a ‘gold-standard’ method of testing.

The most common form of testing is taking a swab of the nose and throat (known as PCR) to see if the virus is present. However, it can take as long as 14 days for an individual to show symptoms of COVID-19, by which time the virus may have moved from the nose and throat and into the lungs and other tissues and organs, making it harder to detect via a swab test. Another way to detect the virus is looking for antibodies (from blood samples) in individuals.

Cambridge researchers combined the two tests – PCR and the antibody test – to help identify who may have the virus. They found combining both tests was more effective to identify patients who had Covid than those who had just one of the tests. Read the full news story.

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Publication: medRxiv

Dami A Collier, Sonny M Assennato, Nyarie Sithole, Katherine Sharrocks, Allyson Ritchie, Pooja Ravji, Matt Routledge, Dominic Sparkes, Jordan Skittrall, Ben Warne, Anna Smielewska, Isobel Ramsey, Neha Goel, Martin Curran, David Enoch, Rhys Tassell, Michelle Lineham, Devan Vaghela, Clare Leong, Hoi Ping Mok, John Bradley, Kenneth Gc Smith, Vivien Mendoza, Nikos Demiris, Martin Besser, Gordon Dougan, Paul J Lehner, Hongyi Zhang, Claire Waddington, Helen Lee,  Ravindra K Gupta

03 June 2020


Summary:

SAMBA II machines were deployed in the ED and holding wards at Addenbrooke’s hospital to help detect COVID-19 in patients as part of a research trial called COVIDx.

Researchers investigated whether using the new machines could accurately provide a faster diagnosis than standard testing practices and review how it would affect patient waiting times.

After collecting nose and throat swabs from over 140 patients, the samples were processed using the SAMBA II machine. Researchers found they were able to provide an accurate diagnostic result within 90 minutes, compared to the standard 24-48-hour lab waiting time. Read the full story.

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Publication: Nature

James E. D. Thaventhiran, Hana Lango Allen, Kenneth G. C. Smith 

06 May 2020


Summary:

Cambridge researchers sequenced the entire genetic code of 974 people with PID. The team were able to identify variations in genes already known to cause PID. To help identify genetic causes for the remaining participants and other patients with PID, the team used a statistical program known as BeviMed. BeviMed can be used to predict genes that may cause PID, by comparing the genomes of cases and controls. Using this technique, the team were able to identify new genes that cause PID. Full press release here

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Publication: Science

Jong-Eun Park, Rachel A. Botting, Cecilia Domínguez Conde, Dorin-Mirel Popescu, Marieke Lavaert, Daniel J. Kunz, Issac Goh, Emily Stephenson, Roberta Ragazzini, Elizabeth Tuck, Anna Wilbrey-Clark, Kenny Roberts, Veronika R. Kedlian, John R. Ferdinand, Xiaoling He, Simone Webb, Daniel Maunder, Niels Vandamme, Krishnaa T. Mahbubani, Krzysztof Polanski, Lira Mamanova, Liam Bolt, David Crossland, Fabrizio de Rita, Andrew Fuller, Andrew Filby, Gary Reynolds, David Dixon, Kourosh Saeb-Parsy, Steven Lisgo, Deborah Henderson, Roser Vento-Tormo, Omer A. Bayraktar, Roger A. Barker, Kerstin B. Meyer, Yvan Saeys, Paola Bonfanti, Sam Behjati, Menna R. Clatworthy, Tom Taghon, Muzlifah Haniffa, Sarah A. Teichmann

21 February 2020


Summary:

Human thymus tissue makes T-cells for adaptive immunity and this research made a comprehensive cell atlas of thymus tissue over the course of human life, from embryo to adult thus gaining new insights into human T-cell development.

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Publication: Genome Biology

E. Madissoon, A. Wilbrey-Clark, R. J. Miragaia, K. Saeb-Parsy, K. T. Mahbubani, N. Georgakopoulos, P. Harding, K. Polanski, N. Huang, K. Nowicki-Osuch, R. C. Fitzgerald, K. W. Loudon, J. R. Ferdinand, M. R. Clatworthy, A. Tsingene, S. van Dongen, M. Dabrowska, M. Patel, M. J. T. Stubbington, S. A. Teichmann, O. Stegle & K. B. Meyer

31 December 2019


Summary: 

The Human Cell Atlas, which is an international collaboration to map all the cell types in the human body.

However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design.

This study looked at the effect of cold storage on fresh healthy spleen, esophagus, and lung from donors and concluded that cold storage of tissue works well and increases the time frame for processing samples; however robust protocols are needed for tissue preservation that can be used by all the research teams involved.

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Publication: Immunity

Tomas Castro-Dopico, Thomas W. Dennison, John R. Ferdinand, Simon Clare, Miles Parkes, Menna R. Clatworthy et al

12 March 2019


Summary: 

Inflammatory bowel disease (IBD) is due to aberrant responses of the gut mucosa to the resident microbiome.

This research looked at Crohn’s and Ulcerative Colitis (both types of IBD) to identify which immune cells are involved in IBD, and to help identify novel therapeutic targets.

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Publication: Nature Immunology

Kylie R. James, Tomas Gomes, Rasa Elmentaite, Nitin Kumar, Emily L. Gulliver, Hamish W. King, Mark D. Stares, Bethany R. Bareham, John R. Ferdinand, Velislava N. Petrova, Krzysztof Polański, Samuel C. Forster, Lorna B. Jarvis, Ondrej Suchanek, Sarah Howlett, Louisa K. James, Joanne L. Jones, Kerstin B. Meyer, Menna R. Clatworthy, Kourosh Saeb-Parsy, Trevor D. Lawley, Sarah A. Teichmann

17 February 2020

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Summary:

This research surveyed the microbiome in different regions along the length of a healthy human colon, and in parallel surveyed the populations of immune cells.The map of the bacterial composition in the human colon showed that specific genera had preferences for colonising certain regions of the colon. B and T cells also changed along the length of the colon. This is the first survey to find out what constitutes a healthy homeostatic relationship between the microbiome in the human colon and host immune cells.

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Publication: Nature

Duuamene Nyimanu, Richard G. Kay, Petra Sulentic, Rhoda E. Kuc, Philip Ambery, Lutz Jermutus, Frank Reimann, Fiona M. Gribble, Joseph Cheriyan, Janet J. Maguire, Anthony P. Davenport

27 December 2019

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Summary:

An LC-MS method was developed to measure Apelin in human plasma, and demonstrate apelin dosing achieved the correct concentration in volunteers. The extracts were also analysed on an LC-MS system to identify break-down products of the peptide that were produced in the body. The researchers found out that apelin is broken down from both ends of the peptide, but more so from the C-terminal. This information can be used to develop a better peptide that is stabilised against degradation, therefore improving its characteristics as a drug; and apelin-derived peptides may be potential new drugs for cardiovascular disease.

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Publication: QJM: An International Journal of Medicine

R El-Damanawi, M Lee, T Harris, L B Cowley, S Bond, H Pavey, R N Sandford, I B Wilkinson, F E Karet Frankl, T F Hiemstra

30 October 2019
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Summary:

Vasopressin is a hormone that is made by the body to conserve water in states of dehydration. In Polycystic Kidney disease (PKD) this hormone accelerates cyst growth and kidney damage, making it the fourth leading global cause of kidney failure.  High water intake reduces blood levels of vasopressin, and may slow cyst growth and disease progression similarly to currently available vasopressin blockers.  However, the feasibility, safety and sustaintability of this therapeutic strategy remains unknown.

In this randomised controlled trial, patients with PKD were randomised to either high water intake (HW) or Ad libitum water intake (AW) over an 8-week period.  The primary outcome was to determine if the HW group could maintain dilute urine, and the AW group could keep their urine more concentrated over an 8-week follow up period.  We used a self-management strategy and smartphone applications to promote compliance.

Researchers found that high water intake is feasible, sustainable and safe, and can be started early in the disease course prior to the onset of irreversible kidney damage; while the use of smartphone applications to record home-monitoring of urine dipstick tests promoted adherence, driving a difference in urine results between the groups. A definitive global randomised controlled trial of high versus normal water intake is possible and will be the next stage of this work.

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Publication: Nature

Henry Lee-Six, Sigurgeir Olafsson, Peter Ellis, Robert J. Osborne, Mathijs A. Sanders, Luiza Moore, Nikitas Georgakopoulos, Franco Torrente, Ayesha Noorani, Martin Goddard, Philip Robinson, Tim H. H. Coorens, Laura O’Neill, Christopher Alder, Jingwei Wang, Rebecca C. Fitzgerald, Matthias Zilbauer, Nicholas Coleman, Kourosh Saeb-Parsy, Inigo Martincorena, Peter J. Campbell & Michael R. Stratton

23 October 2019

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This was a study of early changes in human colorectal tissue that could lead to adenomas/carconomas. These are rare outcomes even after a substantially increased mutational burden has been placed on the tissue, but it is important to study the earliest stages of colorectal carcinogenesis.

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Publication: Nature

Bashford-Rogers, R.J.M., Bergamaschi, L., McKinney, E.F., Pombal, D.C., Mescia, F., Lee, J.C., Thomas, D.C., Flint, S.M., Kellam, P., Jayne, D.R.W., Lyons P.A. and Smith, K.G.C.

25 September 2019

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Publication: Pediatric Nephrology

Jack L. Martin, Anja V. Gruszczyk, Timothy E. Beach, Michael P. Murphy, Kourosh Saeb-Parsy 

2 June 2018

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Acute kidney injury (AKI) is a major problem in critically unwell children, including ischaemic reperfusion (IR) injury involving mitochondria. This research proposes a variety of novel therapeutic targets as potential treaments of AKI.

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Publication: Immunity

Tomas Castro-Dopico, Thomas W. Dennison, John R. Ferdinand, Rebeccah J. Mathews, Aaron Fleming, Dean Clift, Benjamin J. Stewart, Chenzhi Jing, Konstantina Strongili, Larisa I. Labzin, Edward J.M. Monk, Kourosh Saeb-Parsy, Clare E. Bryant, Simon Clare, Miles Parkes, Menna R. Clatworthy

12 March 2019

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Summary:

Inflammatory bowel disease (IBD) is due to aberrant responses of the gut mucosa to the resident microbiome. The identification of which immune cells are involved in IBD will lead to identification of novel therapeutic targets.

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Publication: Cell

Berry MR, Mathews RJ, Ferdinand JR, Jing C, Loudon KW, Wlodek E, Dennison TW, Kuper C, Neuhofer W, Clatworthy MR.

10 August 2017

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Publication: Journal of Experimental Medicine

Spencer S, Köstel Bal S, Egner W, Lango Allen H, Raza SI, Ma CA, Gürel M, Zhang Y, Sun G, Sabroe RA, Greene D, Rae W, Shahin T, Kania K, Ardy RC, Thian M, Staples E, Pecchia-Bekkum A, Worrall WPM, Stephens J, Brown M, Tuna S, York M, Shackley F, Kerrin D, Sargur R, Condliffe A, Tipu HN, Kuehn HS, Rosenzweig SD, Turro E, Tavaré S, Thrasher AJ, Jodrell DI, Smith KGC, Boztug K, Milner JD, Thaventhiran JED.

24 June 2019

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Publication: Journal of Experimental Medicine

Zhang Z, Gothe F, Pennamen P, James JR, McDonald D, Mata CP, Modis Y, Alazami AM, Acres M, Haller W, Bowen C, Döffinger R, Sinclair J, Brothers S, Zhang Y, Matthews HF, Naudion S, Pelluard F, Alajlan H, Yamazaki Y, Notarangelo LD, Thaventhiran JE, Engelhardt KR, Al-Mousa H, Hambleton S†, Rooryck C†, Smith KGC†, Lenardo MJ†.

30 April 2019

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Publication: Nature

Gupta RK, Abdul-Jawad S, McCoy LE, Mok HP, Salgado DPM, Martinez-Picado J, Nijhuis M, Wensing AMJ, Lee H, Grant P, Nastouli E, Lambert J, Pace M, Salasc F, Monit C, Innes, Mui L, Waters L, Frater J, Lever AML, Edwards SG, Gabriel IH, Olavarria E.

5 March 2019

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Publication: Science

Cuchet-Lourenço D, Eletto D, Wu C, Plagnol V, Papapietro O, Curtis J, Ceron-Gutierrez L, Bacon CM, Hackett S, Alsaleem B, Maes M, Gaspar M, Alisaac A, Goss E, AlIdrissi E, Siegmund D, Wajant H, Kumararatne D, Al Zahrani MS, Arkwright PD, Abinun M, Doffinger R, Nejentsev S.

24 August 2018

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Publication: Nature

Mills EL, Ryan DG, Prag HA, Dikovskaya D, Menon D, Zaslona Z, Jedrychowski MP, Costa ASH, Higgins M, Hams E, Szpyt J, Runtsch MC, King MS, McGouran JF, Fischer R, Kessler BM, McGettrick AF, Hughes MM, Carroll RG, Booty LM, Knatko EV, Meakin PJ, Ashford MLJ, Modis LK, Brunori G, Sévin DC, Fallon PG, Caldwell ST, Kunji ERS, Chouchani ET, Frezza C, Dinkova-Kostova AT, Hartley RC, Murphy MP, O’Neill LA.

28 March 2018

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Publication: Nature

Burr ML, Sparbier CE, Chan-YC, Williamson JC, Woods K, Beavis P,Lam EYN, Henderson MA, Bell CC, Stolzenburg S, Gilan O, Noori T, Morgens D, Bassik MC, Neeson PJ, Behren A, Darcy PK, Dawson S-J, Voskoboinik I, Trapani JA, Cebon J, Lehner PJ, Dawson MA.

16 August 2017

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Publication: Nature Genetics

Lee, J.C., Biasci, D., Roberts, R., Gearry, R.B., Mansfield, J.C., Ahmad, T., Prescott, N.J., Satsangi, J., Wilson, D.C., Jostins, L., Anderson, C.A., Consortium, U.I.G., Traherne, J.A., Lyons, P.A., Parkes, M. and Smith, K.G.C.,

9 January 2017

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Publication: Cell

C.A. Madigan, C.J. Cambier, K.M. Kelly-Scumpia, P.O. Scumpia, T.Y. Cheng, J. Zailaa, B.R. Bloom, D.B. Moody, S.T. Smale, A. Sagasti, R.L. Modlin, L. Ramakrishnan.

24 August 2017

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Publication: Nature Genetics

Tchasovnikarova IA, Timms RT, Douse DH, Roberts RC, Dougan G, Kingston RE Modis Y, Lehner PJ .

5 June 2017

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Publication: Arthritis Res Ther

Vanderleyden, I., Linterman, M.A. and Smith, K.G.C.

30 October 2014

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