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	<title> &#187; Science</title>
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		<title>Scientific Publications</title>
		<link>http://www.rogertatoud.com/2008/02/28/scientific-publications/</link>
		<comments>http://www.rogertatoud.com/2008/02/28/scientific-publications/#comments</comments>
		<pubDate>Thu, 28 Feb 2008 11:00:46 +0000</pubDate>
		<dc:creator>Roger</dc:creator>
				<category><![CDATA[Scientific publications]]></category>
		<category><![CDATA[Publication]]></category>
		<category><![CDATA[Science]]></category>

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		<description><![CDATA[Fearnside JF, Dumas ME, Rothwell AR, Wilder SP, Cloarec O, Toye A, Blancher C, Holmes E, Tatoud R, Barton RH, Scott J, Nicholson JK, Gauguier D. Phylometabonomic patterns of adaptation to high fat diet feeding in inbred mice. PLoS ONE 3, e1668 (2008). Toye AA, Dumas ME, Blancher C, Rothwell AR, Fearnside JF, Wilder SP, [...]]]></description>
			<content:encoded><![CDATA[<ul>
<li>Fearnside JF, Dumas ME, Rothwell AR, Wilder SP, Cloarec O, Toye A, Blancher C, Holmes E, Tatoud R, Barton RH, Scott J, Nicholson JK, Gauguier D. Phylometabonomic patterns of adaptation to high fat diet feeding in inbred mice. PLoS ONE 3, e1668 (2008).</li>
<li>Toye AA, Dumas ME, Blancher C, Rothwell AR, Fearnside JF, Wilder SP, Bihoreau MT, Cloarec O, Azzouzi I, Young S, Barton RH, Holmes E, McCarthy MI, Tatoud R, Nicholson JK, Scott J, Gauguier D.  Subtle metabolic and liver gene transcriptional changes underlie diet-induced fatty liver susceptibility in insulin-resistant mice. Diabetologia 50, 1867-79 (2007).</li>
<li>Daly-Burns B, Alam TN, Mackay A. Clark J, Shepherd CJ, Rizzo S, Tatoud R. O’Hare MJ, Masters JR, Hudson DL. A conditionally immortalized cell line model for the study of human prostatic epithelial cell differentiation. Differentiation 75:35–48, (2007).</li>
<li>Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside A, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier J, Nicholson JK. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. P.N.A.S. 103:12511–12516, (2006).</li>
<li>Arya M, Patel HR, McGurk C, Tatoud R, Klocker H, Masters J, Williamson M. The importance of the CXCL12-CXCR4 chemokine ligand-receptor interaction in prostate cancer metastasis. J Exp Ther Oncol. 4, 291-303 (2004).</li>
<li>Stephen RL, Gustafsson MC, Jarvis M, Tatoud R, Marshall BR, Knight D, Ehrenborg E, Harris AL, Wolf CR, Palmer CN. Activation of peroxisome proliferator-activated receptor delta stimulates the proliferation of human breast and prostate cancer cell lines. Cancer Res. 64, 3162-70 (2004)</li>
<li>Adamson DJA, Frew D, Tatoud R, Wolf CR &amp; Palmer CNA. Diclofenac antagonizes peroxisome proliferator-activated receptor-? signalling. Mol Pharmacol. 61, 7-12 (2002).</li>
<li>Maillard M, Cadot B, Ball RY, Sethia K, Perbal B, Edwards D &amp; Tatoud R. Differential expression of novH proto-oncogene in human prostate cell lines and tissues. Mol Pathol. 54, 275-280 (2001).</li>
<li>Tatoud R. Insulin-like growth factor (IGF) network in prostate pathologies. Pr Cancer Pr Dis 2,66-69 (1999).</li>
<li>Sangrajrang S, Denoulet P, Millot G, Tatoud R, Podgorniak MP, Tew KD, Calvo F, &amp; Fellous A. Estramustine resistance correlates with tau over-expression in human prostatic carcinoma cells. Int J Cancer 77,626-631 (1998).</li>
<li>Sangrajrang S, Denoulet P, Laing NM, Tatoud R, Millot G, Calvo F, Tew KD &amp; Fellous A. Association of estramustine resistance in human prostatic carcinoma cells with modified patterns of tubulin expression. Biochem Pharmacol 55, 325-331 (1998).</li>
<li>Le Moyec L, Millot G, Tatoud R, Calvo F &amp; Eugene M. Lipid signals detected by NMR proton spectroscopy of whole cells are not correlated to lipid droplets evidenced by the Nile red staining. Cell Molec Biol 43, 703-709, (1997).</li>
<li>deCremoux P, Ravery V, Podgorniak MP, Chevillard S, Toublanc M, Thiounn N, Tatoud R, Delmas V, Calvo F &amp; Boccon-Gibod L. Value of the preoperative detection of prostate-specific-antigen-positive circulating cells by nested RT-PCR in patients submitted to radical prostatectomy. Eur Urol 32, 69-74 (1997).</li>
<li>Prévost G, Benamouzig R, Veber N, Fajac A, Tatoud R, Degeorges A. &amp; Eden P. The somatostatin receptor subtype 2 is expressed in normal and tumoral human tissues. Cancer Detection &amp; Prevention 21, 62-70 (1997)</li>
<li>Lebbe C, Pellet C, Tatoud R, Agbalika F, Dosquet P, Desgrez JP, Morel P &amp; Calvo F. Absence of human herpesvirus 8 sequences in prostate specimens. AIDS 11, 270 (1997).</li>
<li>Lebbé C, Tatoud R, Morel P, Calvo F, Euvrard S, Kanitakis J, Faure M, &amp; Claudy A. Human herpesvirus 8 sequences are not detected in epithelial tumors from patients receiving transplant. Arch Dermatol 133, 111 (1997).</li>
<li>Degeorges A, Tatoud R, Fauvel-Lafève F, Podgorniak MP, Millot G, de Cremoux P. &amp; Calvo F. Stromal cells from human benign prostate hyperplasia produce a growth inhibitory factor for LNCaP prostate cancer cells. Int. J. Cancer 68, 207-214 (1996).</li>
<li>Le Moyec L, Tatoud R, Degeorges A, Calabresse C, Bauza G, Eugène M. &amp; Calvo F. Multidrug resistance and cellular lipids detected by proton nuclear magnetic resonance spectroscopy in K562 leukemia cell line. Cancer Res 56, 3461-3467 (1996).</li>
<li>Tatoud R, Degeorges A, Prévost G, Hoepffner JL, Gauvillé C, Millot G, Thomas F. &amp; Calvo F. Somatostatin receptors in prostate tissues and derived cell cultures, and the in vitro growth inhibitory effect of BIM-23014 analog. Mol Cell Endocrinol 113, 195-204, (1995).</li>
<li>Tatoud R, Desgranchamps F, Degeorges A, &amp; Thomas, F. Les facteurs de croissances peptidiques de la prostate. Pathol Biol 41, 731-740, (1993).</li>
<li>Le Moyec L, Tatoud R, Eugène M, Gauvillé C, Primot I, Charlemagne D, &amp; Calvo F. Cell and lipid membrane lipid analysis by proton magnetic resonance spectroscopy in five breast cancer cell lines. Br J Cancer 66, 623-628, (1992).</li>
<li>Desgranchamps F, Tatoud R, Cussenot O, Teillac P, &amp; Leduc A. Facteurs de croissance prostatiques et hypertrophie bénigne de la prostate. Etat des connaissances actuelles et perspectives. Progres Urol 2, 1031-1044 (1992).</li>
<li>Le Moyec L, Eugène M, Gauvillé C, Tatoud R, Ouvrard BN, &amp; Calvo F. Profils lipidiques de lignées de cancer du sein: spectrométrie par résonance magnétique nucléaire du proton. C R Acad Sci Paris, 312(III), 25-30, (1991).</li>
</ul>
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		<title>Challenges facing the UK Research Base</title>
		<link>http://www.rogertatoud.com/2007/09/13/32/</link>
		<comments>http://www.rogertatoud.com/2007/09/13/32/#comments</comments>
		<pubDate>Wed, 12 Sep 2007 23:00:01 +0000</pubDate>
		<dc:creator>Roger</dc:creator>
				<category><![CDATA[Selected writings]]></category>
		<category><![CDATA[Education]]></category>
		<category><![CDATA[Science]]></category>

		<guid isPermaLink="false">http://www.rogertatoud.com/?p=32</guid>
		<description><![CDATA[The academic year 2007 started with a “Time Bomb” uncovered by the Higher Education Policy Institute (HEPI): student in England are having it the easy way with an average of 26 hours a week spent studying compared to 30 in Ireland, 35 in France and 41 in Portugal. Variations are wide depending on the subject [...]]]></description>
			<content:encoded><![CDATA[<p>The academic year 2007 started with a “Time Bomb” uncovered by the Higher Education Policy Institute (<a title="HEPI" href="http://www.hepi.ac.uk" target="_blank">HEPI</a>): student in England are having it the easy way with an average of 26 hours a week spent studying compared to 30 in Ireland, 35 in France and 41 in Portugal. Variations are wide depending on the subject but with less than 15 hours of tuition a week, fears and concerns are raised that Higher Education is going down the drain and will have serious academic consequences for the future of Science in the UK.<span id="more-32"></span></p>
<p>Some object that quantity does not equate quality; however, content is not the only challenge the UK science base is facing. Science faces a continuum of challenges from school to university, from university to the public world. It is a challenge to teach and train people in science but also to publicise and exploit, commercially or not, the results of scientific research. In this article, I will introduce 5 major challenges that should inform education and science policies.</p>
<p>The first challenge: changing the image of science in the public and the scientific community.</p>
<p>Science does not have a good public image, particularly in the media. When it is not “mad” scientists developing Frankenfood or carelessly releasing food and mouth virus into the English countryside, we are inflicted with TV-boffins trivialising science.</p>
<p>It results that the public lack confidence in science (MMR) or engineering (nanotechnologies), does not understand what science is about or what scientists do and can’t judge if science is good or bad. Often in this situation, bad prevails. We know the problem stems from <a title="Royal Society" href="http://www.royalsoc.ac.uk/page.asp?id=3180" target="_blank">scientists being bad communicators</a> but also that the public has received little science education. It is right to complain of the lack of science teachers or of the declining number of students taking science A-level, but let it be clear, for many young people a career in science does not sound a good career move. Studies are long, difficult, career prospects are uncertain and wages are not very good.</p>
<p>But science image-problem goes beyond the public and is manifest within the scientific community, where it originates as revealed by a report from the Council for Science and Technology <a title="CST" href="http://www2.cst.gov.uk/cst/reports/files/science-government/cst_pathways.pdf" target="_blank">in a recent report</a>. Forsaken PhD students, badly managed Post-docs and scientists fed up that science is not at the heart of what they are doing, contribute to the feeling that the pain is not worth the game.</p>
<p>The situation could be improved by tackling the second major challenged faced by science, that of improving science administration and management.</p>
<p>Scientists are professional people trained in science, but they are often unaware of basic administration and management skills that they will need in their career. This is a problem because grants need to be administered, projects need to be managed, and crucially people need to be managed and mentored. Too often Ph.D. students are left on their own, post doctoral fellows do not get the professional support they need, and researchers spend more time doing paperwork and politics than research. The result is a waste of time and resources.</p>
<p>Resources and in particular funding could be a challenge in itself, but because it is a pervasive issue, I’ll only underline the commercialisation of science and the funding priorities. It is nowadays common for senior scientists to be involved in a biotech company. Public/Private partnerships are becoming a necessity because research is costly and also because there is a political will to develop these collaborations. Such ventures influence the direction scientific research is taking as well as how it is administered and managed. It is important to ensure that the private sector does not dictate what science should be about as it is also important for research councils not to constrain research to what they are willing to fund.</p>
<p>If administration and management are new essential skills needed by scientists, they also need more scientific skills. Science has benefited for fast engineering development leading to the next challenge which, to borrow from Thomas Homer Dixon who wrote extensively about it, is the Ingenuity Gap challenge.</p>
<p>Dixon describes a world where complexity increases very quickly but where our ability to manage and comprehend it does not follow as quickly, hence an “ingenuity gap”. During the last 30 years, science had made tremendous technical progresses allowing us to do research at a very different scale. There are two major problems with the speed and breadth of these developments.</p>
<p>First the data collected can be so vast or so new (such as generated by genomic or metabonomic study) that scientists don’t always know how to handle them. Often people do not have the skills needed, in particular statistical skills, to analyse the data and new mathematical model need to be developed before sense can be make out of numbers. More often, the problem is that of 21st century science analysed with a 20th century mindset and of the nature and immensity of data confronting our inability to fathom it.</p>
<p>Second, these methodologies and equipment require specialist technicians to handle them, but technicians are not common in science; university does not produce them. Post doctoral fellow can be reluctant to accept a position where they will have limited input in the scientific work and little prospect for first author publication that they would need to progress in their career.</p>
<p>But the problem of analytical skills goes far beyond analysing complex data. There is a general problem of numeracy and literacy amongst the population that also affect science students and that seriously challenge their future ability to do research.</p>
<p>Unfortunately, this increased complexity is not happening in isolation but in a wider context leading to the next challenge, that of the globalisation of science.</p>
<p>5% of the world research is done in the UK. Students come from all over the world to study here, the UK counts four universities in the top 25 world universities.</p>
<p>But this should not hide the fact that less than 30% of the post graduates comes from the UK, that China is producing 2 millions graduates a year, that South Korea’s R&amp;D public budget will match that of the UK this year and that the situation worldwide is changing. The report from the HEPI indicates that some foreign students are not satisfied with the value they get for their money and that they now prefer to go to the US where there are more facilities and more scholarships.</p>
<p>Foreign students do not only contribute financially to UK science by paying heavy university fees, but they also sustain UK science. The truth is not that the UK cannot deliver good science but that other countries are able to do so and not only the US.</p>
<p>The challenge of globalisation also impacts on the scientist ability to conduct their work. The recent outburst from Lord Winston who was denied the possibility to carry on with a research work on humanised pig and decided to move this research to the US is an example of how red tape and policy can be an obstacle to research in the UK. Withholding judgement, this highlights a need to review processes and policies.</p>
<p>Falling standard, inadequate training, worldwide competition, and a bad press, is UK public science doomed? That would be painting too much a dark picture of a still thriving sector. The last challenge may give a new direction and provide innovative and relevant answers.</p>
<h3>Mainstreaming science and empowering scientists</h3>
<p>Although students and scientists organisations and Trade Unions have made <a href="http://www.officeronline.co.uk/about/274470.aspx" target="_blank">impressive achievements</a>, the policy-making process seems often in the hand of distant policy makers and the scientific establishment. It is fundamental to engage more students and scientists into the governance and political process and to value their day-to-day experience of science when drawing new policies. It is also important for these organisations to be representative of their base. And move the process “closer to the bench”.</p>
<p>Moreover, because so many aspects of our life today are connected to scientific or engineering issues, from health to personal freedom, mainstreaming science is a necessity. Science can not anymore be considered the exclusive domain of the white-coat-clad scientist who knows better. The challenge is to bring scientists and their science out into the public domain and into the political process and to make scientists the agents of science policy.</p>
<p>There is a long journey ahead to make science more relevant for public policies, less nebulous in the public eye and more considerate for science students and academics. But scientists are overall passionate people and it is possible to channel some of this passion into the social and political process.</p>
<p><em>© Roger TATOUD.</em></p>
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		<title>The Reactome</title>
		<link>http://www.rogertatoud.com/2005/07/01/the-reactome/</link>
		<comments>http://www.rogertatoud.com/2005/07/01/the-reactome/#comments</comments>
		<pubDate>Fri, 01 Jul 2005 11:00:21 +0000</pubDate>
		<dc:creator>Roger</dc:creator>
				<category><![CDATA[Projects]]></category>
		<category><![CDATA[Resource]]></category>
		<category><![CDATA[Science]]></category>

		<guid isPermaLink="false">http://www.rogertatoud.com/?p=13</guid>
		<description><![CDATA[The Reactome project is a collaboration between Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. Project Summary: curation of the IRS/PKB cascade of events (6 months). Role: Supervision and contribution to the work. The information in the [...]]]></description>
			<content:encoded><![CDATA[<p><a title="The Reactome" href="http://www.reactome.org" target="_blank">The Reactome</a> project is a collaboration between Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.</p>
<p><strong><em>Project Summary:</em></strong> curation of the IRS/PKB cascade of events (6 months).</p>
<p><em><strong>Role:</strong></em> Supervision and contribution to the work.</p>
<p>The information in the Reactome database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with PubMed, GO, and the sequence databases at NCBI, Ensembl and UniProt. In addition to curated human events, inferred orthologous events in 21 non-human species including mouse, rat, chicken, fugu fish, worms, fly, yeast and E.coli are also available.</p>
<p>This work involved:</p>
<ul>
<li>researching the literature</li>
<li>summarising the published knowledge in a synthetic format</li>
<li>training and directing the work of a student</li>
</ul>
<p>The results of this project is now available online to the scientific community.</p>
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