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757 results on '"Sims, S."'

2. Control software drives sustainable performance and production

Author

Sims, S.

Subjects
Petroleum industry -- Equipment and supplies -- Production processes -- Environmental aspects, Process control software, Business, Petroleum, energy and mining industries
Abstract

In the face of changing dynamics around the world, hydrocarbon manufacturers are finding the need to not only change strategies, but also to continually adapt those strategies to meet new [...]

Published
2021

4. An analysis-ready and quality controlled resource for pediatric brain white-matter research

Author

Richie-Halford, A., Cieslak, M., Ai, L., Caffarra, S., Covitz, S., Franco, A., Karipidis, I., Kruper, J., Milham, M., Avelar-Pereira, B., Roy, E., Sydnor, V., Yeatman, J., Abbott, N., Anderson, J., Gagana, B., Bleile, M., Bloomfield, P., Bottom, V., Bourque, J., Boyle, R., Brynildsen, J., Calarco, N., Castrellon, J., Chaku, N., Chen, B., Chopra, S., Coffey, E., Colenbier, N., Cox, D., Crippen, J., Crouse, J., David, S., Leener, B., Delap, G., Deng, Z., Dugre, J., Eklund, A., Ellis, K., Ered, A., Farmer, H., Faskowitz, J., Finch, J., Flandin, G., Flounders, M., Fonville, L., Frandsen, S., Garic, D., Garrido-Vásquez, P., Gonzalez-Escamilla, G., Grogans, S., Grotheer, M., Gruskin, D., Guberman, G., Haggerty, E., Hahn, Y., Hall, E., Hanson, J., Harel, Y., Vieira, B., Hettwer, M., Hobday, H., Horien, C., Huang, F., Huque, Z., James, A., Kahhale, I., Kamhout, S., Keller, A., Khera, H., Kiar, G., Kirk, P., Kohl, S., Korenic, S., Korponay, C., Kozlowski, A., Kraljevic, N., Lazari, A., Leavitt, M., Li, Z., Liberati, G., Lorenc, E., Lossin, A., Lotter, L., Lydon-Staley, D., Madan, C., Magielse, N., Marusak, H., Mayor, J., McGowan, A., Mehta, K., Meisler, S., Michael, C., Mitchell, M., Morand-Beaulieu, S., Newman, B., Nielsen, J., O’Mara, S., Ojha, A., Omary, A., Özarslan, E., Parkes, L., Peterson, M., Pines, A., Pisanu, C., Rich, R., Sahoo, A., Samara, A., Sayed, F., Schneider, J., Shaffer, L., Shatalina, E., Sims, S., Sinclair, S., Song, J., Hogrogian, G., Tooley, U., Tripathi, V., Turker, H., Valk, S., https://orcid.org/0000-0003-2998-6849, Wall, M., Walther, C., Wang, Y., Wegmann, B., Welton, T., Wiesman, A., Wiesman, M., Winters, D., Yuan, R., Zacharek, S., Zajner, C., Zakharov, I., Zammarchi, G., Zhou, D., Zimmerman, B., Zoner, K., Satterthwaite, T., Rokem, A., and Fibr Community Science Consortium

Subjects
Statistics and Probability, Brain, Neuroimaging, Library and Information Sciences, White Matter, Computer Science Applications, Education, Diffusion Magnetic Resonance Imaging, Image Processing, Computer-Assisted, Humans, Radiologi och bildbehandling, Statistics, Probability and Uncertainty, Child, Information Systems, Radiology, Nuclear Medicine and Medical Imaging
Abstract

We created a set of resources to enable research based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N = 2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Preprocessed, analysis-ready data was made openly available. Data quality plays a key role in the analysis of dMRI. To optimize QC and scale it to this large dataset, we trained a neural network through the combination of a small data subset scored by experts and a larger set scored by community scientists. The network performs QC highly concordant with that of experts on a held out set (ROC-AUC = 0.947). A further analysis of the neural network demonstrates that it relies on image features with relevance to QC. Altogether, this work both delivers resources to advance transdiagnostic research in brain connectivity and pediatric mental health, and establishes a novel paradigm for automated QC of large datasets., Scientific Data, 9 (1), ISSN:2052-4463

Published
2022

9. Inaugural Huntington Disease Clinical Research Symposium Organized by the Huntington Study Group

Author

Moser, Katharine, Biglan, K. M., Ross, C. A., Langbehn, D. R., Aylward, E., Stout, J. C., Queller, S., Carlozzi, N., Duff, K., Beglinger, L. J., Paulsen, J. S., Tomusk, A., Lifer, S., Hastings, S., Dawson, J., Walker, B., Whitlock, K., Johnson, S., Pacifici, Robert, Hersch, S., Dorsey, E. R., Katz, Russell, Tempkin, T., Wheelock, V., Schwartz, G., Corey-Bloom, J., Mattis, P., Feigin, A., Young, P., McArthur, D. L., Perlman, S., Higginson, C., Carr, L., Sigvardt, K., Chirieac, M. C., Shinaman, A., Shoulson, I., Kane, A. E., Peavy, G. M., Goldstein, J. L., Jacobson, M. W., Lessig, S., Wasserman, L., Kayson, E. P., Tang, C., Zgaljardic, D., Ma, Y., Dhawan, V., Guttman, M., Eidelberg, D., Peng, S., Kingsley, P., Rosas, H. D., Gevorkian, S., Oakes, D., Matson, W., Massood, T., Latourelle, J., Mysore, J. Srinidhi, Fossale, E., Gillis, T., Gusella, J. F., MacDonald, M. E., Myers, R. H., Yastrubetskaya, O., Preston, J., Chiu, E., Goh, A., Oster, E., Bausch, J., Kayson, E., Quaid, K., Sims, S., Swenson, M., Harrison, J., Moskowitz, C., Stepanov, N., Suter, G., Westphal, B., Johnson, S. A., Langbehn, D., Paulsen, J., Nopoulos, P., Beglinger, L., Johnson, H., Magnotta, V., Pierson, R., Lipe, H., Bird, T. D., McCusker, E. A., Lownie, A., Lechich, A. J., Montas, S., Duckett, A., Klager, J., Sandler, S., Pae, A., Apostol, B. L., Simmons, D. A., Zuccato, C., Illes, K., Pallos, J., Casale, M., Kathuria, S., Cattaneo, E., Marsh, J. L., Thompson, L. Michels, Patzke, H., Chesworth, R., Li, Z., Rahil, G., Wang, J., Smith, J., Huet, F. L., Shapiro, G., Leit, S., Beaulieu, P., Raeppel, F., Fournel, M., Sainte-Croix, H., Nolan, S. J., Albayya, F. P., Barbier, A., Besterman, J., Ahlijanian, M. K., Deziel, R., Aubeeluck, A., Buchanan, H., Ross, C., Biglan, K., Landwehrmeyer, B., Whitlock, K. B., Carlozzi, N. E., Mickes, L., Lee, J., Kim, R. Y., Di Toro, B., Fine, E., Cahill, T., Johnson, D., Goldstein, J., Peavy, G., Jacobson, M., Goodman, L. Veatch, Como, P. G., Cha, J. H., Beck, C., Adams, M., Chadwick, G., de Blieck, E. A., McCallum, C., Deuel, L., Clarke, A., Stewart, R., Adams, W. H., Paulson, H., Fiedorowicz, J. G., Hanson, J. M., Ramza, N., Priller, J., Ecker, D., PREDICT-HD Investigators of the Huntington Study Group, Huntington Study Group CoHort Investigators, Huntington Study Group PHAROS Investigators, PREDICT-HD Investigators and Coordinators of the Huntington Study Group, Huntington Study Group TREND-HD Investigators, and EHDN Working Group ‘Symptomatic Treatment.’

Published
2008
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10. Flattening the curve before it flattens us: hospital critical care capacity limits and mortality from novel coronavirus (SARS-CoV2) cases in US counties

Author

Andrew Rundle, James W. Quinn, Sen Pei, Brendan G. Carr, Zebrowski A, Jeffrey Shaman, Wan Yang, Neil W. Schluger, Ronan Doorley, Sims S, and Charles C. Branas

Subjects
Care capacity, education.field_of_study, Geography, Contact precautions, Surge Capacity, Environmental health, Social distance, Pandemic, Population, Psychological intervention, Severe acute respiratory syndrome coronavirus, education
Abstract

BackgroundAs of March 26, 2020, the United States had the highest number of confirmed cases of Novel Coronavirus (COVID-19) of any country in the world. Hospital critical care is perhaps the most important medical system choke point in terms of preventing deaths in a disaster scenario such as the current COVID-19 pandemic. We therefore brought together previously established disease modeling estimates of the growth of the COVID-19 epidemic in the US under various social distancing contact reduction assumptions, with local estimates of the potential critical care surge response across all US counties.MethodsEstimates of spatio-temporal COVID-19 demand and medical system critical care supply were calculated for all continental US counties. These estimates were statistically summarized and mapped for US counties, regions and urban versus non-urban areas. Estimates of COVID-19 infections and patients needing critical care were calculated from March 24, 2020 to April 24, 2020 for three different estimated population levels – 0%, 25%, and 50% – of contact reduction (through actions such as social distancing). Multiple national public and private datasets were linked and harmonized in order to calculate county-level critical care bed counts that included currently available beds and those that could be made available under four surge response scenarios – very low, low, medium, and high – as well as excess deaths stemming from inaccessible critical care.ResultsSurge response scenarios ranged from a very low total supply 77,588 critical care beds to a high total of 278,850 critical care beds. Over the four week study period, excess deaths from inaccessible critical care ranged from 24,688 in the very low response scenario to 13,268 in the high response scenario. Northeastern and urban counties were projected to be most affected by excess deaths due to critical care shortages, and counties in New York, Colorado, and Virginia were projected to exceed their critical care bed limits despite high levels of COVID-19 contact reduction. Over the four week study period, an estimated 12,203-19,594 excess deaths stemming from inaccessible critical care could be averted through greater preventive actions such as travel restrictions, publicly imposed contact precautions, greater availability of rapid testing for COVID-19, social distancing, self-isolation when sick, and similar interventions. An estimated 4,029-11,420 excess deaths stemming from inaccessible critical care could be averted through aggressive critical care surge response and preparations, including high clearance of ICU and non-ICU critical care beds and extraordinary measures like using a single ventilator for multiple patients.ConclusionsUnless the epidemic curve of COVID-19 cases is flattened over an extended period of time, the US COVID-19 epidemic will cause a shortage of critical care beds and drive up otherwise preventable deaths. The findings here support value of preventive actions to flatten the epidemic curve, as well as the value of exercising extraordinary surge capacity measures to increase access to hospital critical care for severely ill COVID-19 patients.

Published
2020
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11. The DNA sequence and biological annotation of human chromosome 1

Author

Gregory, S. G., Barlow, K. F., McLay, K. E., Kaul, R., Swarbreck, D., Dunham, A., Scott, C. E., Howe, K. L., Woodfine, K., Spencer, C. C. A., Jones, M. C., Gillson, C., Searle, S., Zhou, Y., Kokocinski, F., McDonald, L., Evans, R., Phillips, K., Atkinson, A., Cooper, R., Jones, C., Hall, R. E., Andrews, T. D., Lloyd, C., Ainscough, R., Almeida, J. P., Ambrose, K. D., Anderson, F., Andrew, R. W., Ashwell, R. I. S., Aubin, K., Babbage, A. K., Bagguley, C. L., Bailey, J., Beasley, H., Bethel, G., Bird, C. P., Bray-Allen, S., Brown, J. Y., Brown, A. J., Buckley, D., Burton, J., Bye, J., Carder, C., Chapman, J. C., Clark, S. Y., Clarke, G., Clee, C., Cobley, V., Collier, R. E., Corby, N., Coville, G. J., Davies, J., Deadman, R., Dunn, M., Earthrowl, M., Ellington, A. G., Errington, H., Frankish, A., Frankland, J., French, L., Garner, P., Garnett, J., Gay, L., Ghori, M. R. J., Gibson, R., Gilby, L. M., Gillett, W., Glithero, R. J., Grafham, D. V., Griffiths, C., Griffiths-Jones, S., Grocock, R., Hammond, S., Harrison, E. S. I., Hart, E., Haugen, E., Heath, P. D., Holmes, S., Holt, K., Howden, P. J., Hunt, A. R., Hunt, S. E., Hunter, G., Isherwood, J., James, R., Johnson, C., Johnson, D., Joy, A., Kay, M., Kershaw, J. K., Kibukawa, M., Kimberley, A. M., King, A., Knights, A. J., Lad, H., Laird, G., Lawlor, S., Leongamornlert, D. A., Lloyd, D. M., Loveland, J., Lovell, J., Lush, M. J., Lyne, R., Martin, S., Mashreghi-Mohammadi, M., Matthews, L., Matthews, N. S. W., McLaren, S., Milne, S., Mistry, S., Nickerson, T., O'Dell, C. N., Oliver, K., Palmeiri, A., Palmer, S. A., Parker, A., Patel, D., Pearce, A. V., Peck, A. I., Pelan, S., Phelps, K., Phillimore, B. J., Plumb, R., Rajan, J., Raymond, C., Rouse, G., Saenphimmachak, C., Sehra, H. K., Sheridan, E., Shownkeen, R., Sims, S., Skuce, C. D., Smith, M., Steward, C., Subramanian, S., Sycamore, N., Tracey, A., Tromans, A., Van Helmond, Z., Wall, M., Wallis, J. M., White, S., Whitehead, S. L., Wilkinson, J. E., Willey, D. L., Williams, H., Wilming, L., Wray, P. W., Wu, Z., Coulson, A., Vaudin, M., Sulston, J. E., Durbin, R., Hubbard, T., Wooster, R., Dunham, I., Carter, N. P., McVean, G., Ross, M. T., Harrow, J., Olson, M. V., Beck, S., Rogers, J., and Bentley, D. R.

Abstract

Author(s): S. G. Gregory (corresponding author) [1, 2]; K. F. Barlow [1]; K. E. McLay [1]; R. Kaul [3]; D. Swarbreck [1]; A. Dunham [1]; C. E. Scott [1]; K. [...]

Published
2006
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14. DNA sequence and analysis of human chromosome 9

Author

Humphray, S. J., Oliver, K., Hunt, A. R., Plumb, R. W., Loveland, J. E., Howe, K. L., Andrews, T. D., Searle, S., Hunt, S. E., Scott, C. E., Jones, M. C., Ainscough, R., Almeida, J. P., Ambrose, K. D., Ashwell, R. I. S., Babbage, A. K., Babbage, S., Bagguley, C. L., Bailey, J., Banerjee, R., Barker, D. J., Barlow, K. F., Bates, K., Beasley, H., Beasley, O., Bird, C. P., Bray-Allen, S., Brown, A. J., Brown, J. Y., Burford, D., Burrill, W., Burton, J., Carder, C., Carter, N. P., Chapman, J. C., Chen, Y., Clarke, G., Clark, S. Y., Clee, C. M., Clegg, S., Collier, R. E., Corby, N., Crosier, M., Cummings, A. T., Davies, J., Dhami, P., Dunn, M., Dutta, I., Dyer, L. W., Earthrowl, M. E., Faulkner, L., Fleming, C. J., Frankish, A., Frankland, J. A., French, L., Fricker, D. G., Garner, P., Garnett, J., Ghori, J., Gilbert, J. G. R., Glison, C., Grafham, D. V., Gribble, S., Griffiths, C., Griffiths-Jones, S., Grocock, R., Guy, J., Hall, R. E., Hammond, S., Harley, J. L., Harrison, E. S. I., Hart, E. A., Heath, P. D., Henderson, C. D., Hopkins, B. L., Howard, P. J., Howden, P. J., Huckle, E., Johnson, C., Johnson, D., Joy, A. A., Kay, M., Keenan, S., Kershaw, J. K., Kimberley, A. M., King, A., Knights, A., Laird, G. K., Langford, C., Lawlor, S., Leongamornlert, D. A., Leversha, M., Lloyd, C., Lloyd, D. M., Lovell, J., Martin, S., Mashreghi-Mohammadi, M., Matthews, L., McLaren, S., McLay, K. E., McMurray, A., Milne, S., Nickerson, T., Nisbett, J., Nordsiek, G., Pearce, A. V., Peck, A. I., Porter, K. M., Pandian, R., Pelan, S., Phillimore, B., Povey, S., Ramsey, Y., Rand, V., Scharfe, M., Sehra, H. K., Shownkeen, R., Sims, S. K., Skuce, C. D., Smith, M., Steward, C. A., Swarbreck, D., Sycamore, N., Tester, J., Thorpe, A., Tracey, A., Tromans, A., Thomas, D. W., Wall, M., Wallis, J. M., West, A. P., Whitehead, S. L., Willey, D. L., Williams, S. A., Wilming, L., Wray, P. W., Young, L., Ashurst, J. L., Coulson, A., Blocker, H., Durbin, R., Sulston, J. E., Hubbard, T., Jackson, M. J., Bentley, D. R., Beck, S., Rogers, J., and Dunham, I.

Abstract

Author(s): S. J. Humphray (corresponding author) [1]; K. Oliver [1]; A. R. Hunt [1]; R. W. Plumb [1]; J. E. Loveland [1]; K. L. Howe [1]; T. D. Andrews [1]; [...]

Published
2004
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15. The DNA sequence and comparative analysis of human chromosome 10

Author

Deloukas, P., Earthrowl, M. E., Grafham, D. V., Rubenfield, M., French, L., Steward, C. A., Sims, S. K., Jones, M. C., Searle, S., Scott, C., Howe, K., Hunt, S. E., Andrews, T. D., Gilbert, J. G. R., Swarbreck, D., Ashurst, J. L., Taylor, A., Battles, J., Bird, C. P., Ainscough, R., Almeida, J. P., Ashwell, R. I. S., Ambrose, K. D., Babbage, A. K., Bagguley, C. L., Bailey, J., Banerjee, R., Bates, K., Beasley, H., Bray-Allen, S., Brown, A. J., Brown, J. Y., Burford, D. C., Burrill, W., Burton, J., Cahill, P., Camire, D., Carter, N. P., Chapman, J. C., Clark, S. Y., Clarke, G., Clee, C. M., Clegg, S., Corby, N., Coulson, A., Dhami, P., Dutta, I., Dunn, M., Faulkner, L., Frankish, A., Frankland, J. A., Garner, P., Garnett, J., Gribble, S., Griffiths, C., Grocock, R., Gustafson, E., Hammond, S., Harley, J. L., Hart, E., Heath, P. D., Ho, T. P., Hopkins, B., Horne, J., Howden, P. J., Huckle, E., Hynds, C., Johnson, C., Johnson, D., Kana, A., Kay, M., Kimberley, A. M., Kershaw, J. K., Kokkinaki, M., Laird, G. K., Lawlor, S., Lee, H. M., Leongamornlert, D. A., Laird, G., Lloyd, C., Lloyd, D. M., Loveland, J., Lovell, J., McLaren, S., McLay, K. E., McMurray, A., Mashreghi-Mohammadi, M., Matthews, L., Milne, S., Nickerson, T., Nguyen, M., Overton-Larty, E., Palmer, S. A., Pearce, A. V., Peck, A. I., Pelan, S., Phillimore, B., Porter, K., Rice, C. M., Rogosin, A., Ross, M. T., Sarafidou, T., Sehra, H. K., Shownkeen, R., Skuce, C. D., Smith, M., Standring, L., Sycamore, N., Tester, J., Thorpe, A., Torcasso, W., Tracey, A., Tromans, A., Tsolas, J., Wall, M., Walsh, J., Wang, H., Weinstock, K., West, A. P., Willey, D. L., Whitehead, S. L., Wilming, L., Wray, P. W., Young, L., Chen, Y., Lovering, R. C., Moschonas, N. K., Siebert, R., Fechtel, K., Bentley, D., Durbin, R., Hubbard, T., Doucette-Stamm, L., Beck, S., Smith, D. R., and Rogers, J.

Abstract

Author(s): P. Deloukas (corresponding author) [1]; M. E. Earthrowl [1]; D. V. Grafham [1]; M. Rubenfield [2, 3]; L. French [1]; C. A. Steward [1]; S. K. Sims [1]; M. [...]

Published
2004
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17. The DNA sequence and analysis of human chromosome 6

Author

Mungall, A. J., Palmer, S. A., Sims, S. K., Edwards, C. A., Ashurst, J. L., Wilming, L., Jones, M. C., Horton, R., Hunt, S. E., Scott, C. E., Gilbert, J. G. R., Clamp, M. E., Bethel, G., Milne, S., Ainscough, R., Almeida, J. P., Ambrose, K. D., Andrews, T. D., Ashwell, R. I. S., Babbage, A. K., Bagguley, C. L., Bailey, J., Banerjee, R., Barker, D. J., Barlow, K. F., Bates, K., Beare, D. M., Beasley, H., Beasley, O., Bird, C. P., Blakey, S., Bray-Allen, S., Brook, J., Brown, A. J., Brown, J. Y., Burford, D. C., Burrill, W., Burton, J., Carder, C., Carter, N. P., Chapman, J. C., Clark, S. Y., Clark, G., Clee, C. M., Clegg, S., Cobley, V., Collier, R. E., Collins, J. E., Colman, L. K., Corby, N. R., Coville, G. J., Culley, K. M., Dhami, P., Davies, J., Dunn, M., Earthrowl, M. E., Ellington, A. E., Evans, K. A., Faulkner, L., Francis, M. D., Frankish, A., Frankland, J., French, L., Garner, P., Garnett, J., Ghori, M. J. R., Gilby, L. M., Gillson, C. J., Glithero, R. J., Grafham, D. V., Grant, M., Gribble, S., Griffiths, C., Griffiths, M., Hall, R., Halls, K. S., Hammond, S., Harley, J. L., Hart, E. A., Heath, P. D., Heathcott, R., Holmes, S. J., Howden, P. J., Howe, K. L., Howell, G. R., Huckle, E., Humphray, S. J., Humphries, M. D., Hunt, A. R., Johnson, C. M., Joy, A. A., Kay, M., Keenan, S. J., Kimberley, A. M., King, A., Laird, G. K., Langford, C., Lawlor, S., Leongamornlert, D. A., Leversha, M., Lloyd, C. R., Lloyd, D. M., Loveland, J. E., Lovell, J., Martin, S., Mashreghi-Mohammadi, M., Maslen, G. L., Matthews, L., McCann, O. T., McLaren, S. J., McLay, K., McMurray, A., Moore, M. J. F., Mullikin, J. C., Niblett, D., Nickerson, T., Novik, K. L., Oliver, K., Overton-Larty, E. K., Parker, A., Patel, R., Pearce, A. V., Peck, A. I., Phillimore, B., Phillips, S., Plumb, R. W., Porter, K. M., Ramsey, Y., Ranby, S. A., Rice, C. M., Ross, M. T., Searle, S. M., Sehra, H. K., Sheridan, E., Skuce, C. D., Smith, S., Smith, M., Spraggon, L., Squares, S. L., Steward, C. A., Sycamore, N., Tamlyn-Hall, G., Tester, J., Theaker, A. J., Thomas, D. W., Thorpe, A., Tracey, A., Tromans, A., Tubby, B., Wall, M., Wallis, J. M., West, A. P., White, S. S., Whitehead, S. L., Whittaker, H., Wild, A., Willey, D. J., Wilmer, T. E., Wood, J. M., Wray, P. W., Wyatt, J. C., Young, L., Younger, R. M., Bentley, D. R., Coulson, A., Durbin, R., Hubbard, T., Sulston, J. E., Dunham, I., Rogers, J., and Beck, S.

Abstract

Author(s): A. J. Mungall (corresponding author) [1, 2]; S. A. Palmer [1]; S. K. Sims [1]; C. A. Edwards [1]; J. L. Ashurst [1]; L. Wilming [1]; M. C. Jones [...]

Published
2003
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24. The DNA sequence and comparative analysis of human chromosome 20

Author

Deloukas, P., Matthews, L. H., Ashurst, J., Burton, J., Gilbert, J. G. R., Jones, M., Stavrides, G., Almeida, J. P., Babbage, A. K., Bagguley, C. L., Bailey, J., Barlow, K. F., Bates, K. N., Beard, L. M., Beare, D. M., Beasley, O. P., Bird, C. P., Blakey, S. E., Bridgeman, A. M., Brown, A. J., Buck, D., Burrill, W., Butler, A. P., Carder, C., Carter, N. P., Chapman, J. C., Clamp, M., Clark, G., Clark, L. N., Clark, S. Y., Clee, C. M., Clegg, S., Cobley, V. E., Collier, R. E., Connor, R., Corby, N. R., Coulson, A., Coville, G. J., Deadman, R., Dhami, P., Dunn, M., Ellington, A. G., Frankland, J. A., Fraser, A., French, L., Garner, P., Grafham, D. V., Griffiths, C., Griffiths, M. N. D., Gwilliam, R., Hall, R. E., Hammond, S., Harley, J. L., Heath, P. D., Ho, S., Holden, J. L., Howden, P. J., Huckle, E., Hunt, A. R., Hunt, S. E., Jekosch, K., Johnson, C. M., Johnson, D., Kay, M. P., Kimberley, A. M., King, A., Knights, A., Laird, G. K., Lawlor, S., Lehvaslaiho, M. H., Leversha, M., Lloyd, C., Lloyd, D. M., Lovell, J. D., Marsh, V. L., Martin, S. L., McConnachie, L. J., McLay, K., McMurray, A. A., Milne, S., Mistry, D., Moore, M. J. F., Mullikin, J. C., Nickerson, T., Oliver, K., Parker, A., Patel, R., Pearce, T. A. V., Peck, A. I., Phillimore, B. J. C. T., Prathalingam, S. R., Plumb, R. W., Ramsay, H., Rice, C. M., Ross, M. T., Scott, C. E., Sehra, H. K., Shownkeen, R., Sims, S., Skuce, C. D., Smith, M. L., Soderlund, C., Steward, C. A., Sulston, J. E., Swann, M., Sycamore, N., Taylor, R., Tee, L., Thomas, D. W., Thorpe, A., Tracey, A., Tromans, A. C., Vaudin, M., Wall, M., Wallis, J. M., Whitehead, S. L., Whittaker, P., Willey, D. L., Williams, L., Williams, S. A., Wilming, L., Wray, P. W., Hubbard, T., Durbin, R. M., Bentley, D. R., Beck, S., and Rogers, J.

Abstract

Author(s): The Wellcome Trust Sanger Institute ; P. Deloukas (corresponding author); L. H. Matthews; J. Ashurst; J. Burton; J. G. R. Gilbert; M. Jones; G. Stavrides; J. P. Almeida; A. [...]

Published
2001
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26. An SNP map of human chromosome 22

Author

Mullikin, J. C., Hunt, S. E., Cole, C. G., Mortimore, B. J., Rice, C. M., Burton, J., Matthews, L. H., Pavitt, R., Plumb, R. W., Sims, S. K., Ainscough, R. M. R., Attwood, J., Bailey, J. M., Barlow, K., Bruskiewich, R. M. M., Butcher, P. N., Carter, N. P., Chen, Y., Clee, C. M., Coggill, P. C., Davies, J., Davies, R. M., Dawson, E., Francis, M. D., Joy, A. A., Lamble, R. G., Langford, C. F., Macarthy, J., Mall, V., Moreland, A., Overton-Larty, E. K., Ross, M. T., Smith, L. C., Steward, C. A., Sulston, J. E., Tinsley, E. J., Turney, K. J., Willey, D. L., Wilson, G. D., McMurray, A. A., Dunham, I., Rogers, J., and Bentley, D. R.

Abstract

Author(s): J. C. Mullikin; S. E. Hunt; C. G. Cole; B. J. Mortimore; C. M. Rice; J. Burton; L. H. Matthews; R. Pavitt; R. W. Plumb; S. K. Sims; R. [...]

Published
2000
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33. Texture, color and sensory characteristics of ground beef patties containing bovine blood proteins

Author

Guzman, J.C., Mcmillin, K.W., Dugas-Sims S., and Godber, J.S.

Subjects
Beef -- Research, Blood proteins -- Research, Business, Food/cooking/nutrition
Abstract

Inclusion of blood proteins as a substitute for lean in ground beef patties does not cause significant taste or texture changes or harm oxidative stability. Cooking loss and oxidative steadiness undergo minimal change in ground beef with 0.5% RC, 0.75% DC, or 3.5% BP. Every kind of blood protein provides distinct flavor notes to ground beef, even at minimum levels.

Published
1995

39. New Polymer Coatings for Chemically Selective Mass Sensors

Author

Sims, S. C, Wright, Cassandra, Cobb, J, McCalla, T, Revelle, R, Morris, V. R, and Pollack, S. K

Subjects
Nonmetallic Materials
Abstract

There is a current need to develop sensitive and chemically specific sensors for the detection of nitric acid for in-situ measurements in the atmosphere. Polymer coatings have been synthesized and tested for their sensitivity and selectivity to nitric acid. A primary requirement for these polymers is detectability down to the parts per trillion range. The results of studies using these polymers as coatings for quartz crystal microbalances (QCM) and surface acoustic wave (SAW) devices will be presented.

Published
1997

40. Calibration of the QCM/SAW Cascade Impactor for Measurement of Ozone in the Stratosphere

Author

Wright, Cassandra K, Sims, S. C, Peterson, C. B, and Morris, V. R

Subjects
Geophysics
Abstract

The Quartz Crystal Microbalance Surface Acoustic Wave (QCM/SAW) cascade impactor collects size-fractionated distributions of aerosols on a series of 10 MHz quartz crystals and employs SAW devices coated with chemical sensors for gas detection. Presently, we are calibrating the ER-2 certified QCM/SAW cascade impactor in the laboratory for the detection of ozone. Experiments have been performed to characterize the QCM and SAW mass loading, saturation limits, mass frequency relationships, and sensitivity. We are also characterizing sampling efficiency by measuring the loss of ozone on different materials. There are parallel experiments underway to measure the variations in the sensitivity and response of the QCM/SAW crystals as a function of temperature and pressure. Results of the work to date will be shown.

Published
1997

41. Characteristic of Nitron for Use as a Chemical Sensor in Studies of the Upper Atmosphere

Author

Meadows, Kapres, Wright, Cassandra K, Sims, S. C, and Morris, V. R

Subjects
Geophysics
Abstract

We are investigating the use of nitron as a potential chemical sensor for nitric acid and other electron deficient nitrogen oxides. Solutions of nitron in 1-propanol, toluene, and chloroform have been tested for use on a piezoelectric quartz crystal microbalance. We are testing various solvents and metal cations which can maximize the lifetime and reaction specificity of nitron so that they may be used as chemical coatings for stratospheric measurement of trace gases. Results of the work to date will be shown, and future direction discussed.

Published
1997

42. Molecular profiling CD8+ T-cell memory inflation

Author

Sims, S, sims, stuart, and Klenerman, P

Subjects
Viruses, Immunology, Biology
Abstract

Infection with murine cytomegalovirus (MCMV) induces a large population of virus-specific CD8+ T-cells that is maintained at a high frequency in the peripheral organs for the lifetime of the host. This striking response to MCMV is termed "memory inflation". It has also been shown that a similar response occurs after immunization with a non-replicating adenovirus expressing a transgene. The key features which distinguish "inflating" CD8+ T-cell memory responses from classical "non-inflating" CD8+ T-cell memory responses have not been fully defined. To determine the molecular signature of memory inflation I sorted antigen-specific cells ex vivo and compared the gene expression profiles of inflationary CD8+ T-cells to those of central memory and effector CD8+ T-cells. This data showed that memory inflation has a distinct expression profile, with high expression of KLR receptors, specific chemokine receptors such as CX3CR1, transcription factors such as T-bet and Foxk1, and survival factors, such as Bcl-XL and down regulation of inhibitory molecules such as BTLA. These inflationary cells are functional - expressing an array of cytokines, granzymes, IFN&gama;, and TNFα, and lack transcriptional features of T-cell exhaustion. Similar features were identified in CD8+ T-cells undergoing memory inflation using both the MCMV and adenovirus models. To address the turnover of these "inflationary" CD8+ T cells and their role in vivo, I created tetramers bound to the toxin saporin to specifically knock out inflationary cells. I found that they contribute to the control of viral replication, since depletion was followed by a rise in viral load and a subsequent rebound increase in the tetramer+ population. In the final chapter I addressed the role of one specific cell surface molecule, CD73, during CD8+ T-cell memory. I found that although CD73 is thought to play a role in immune regulation, CD73-/- mice showed normal memory inflation and classical non-inflationary memory development. Overall the data in this thesis define for the first time the transcriptional profile associated with CD8+ T-cell memory and show the distinct nature of this T-cell programme in vivo. Future work using further genetically modified mouse strains should allow definition of the critical molecules and pathways involved in the development of these important memory pools.

Published
2017

44. Abstracts of Selected Posters

Author

Albanese, R., Antoine, J. L., Dutrillaux, B., Ashley, T., Avivi, L., Kariv, I., Barigozzi, C., Baratelli, L., Profeta, S., Bartram, C. R., de Klein, A., Hagemeijer, A., Grosveld, G., Bootsma, D., Bennett, Michael D., Smith, J. B., Ward, J. P., Heslop-Harrison, J. S., Blin, N., Kopun, M., Buys, C. H. C. M., Koerts, T., van der Veen, A. Y., de Leij, L., Civitelli, M. V., Capanna, E., Couturier, J., Arnason, U., Mandahl, N., Créau-Goldberg, N., Turleau, C., Cochet, C., de Grouchy, J., Dietrich, A. J. J., Delhanty, J. D. A., Mazzullo, H. A., Cooke, H. M. G., Dotan, A., Dresser, M. E., Moses, M. J., Evans, E. P., Burgoyne, P. B., Ferraro, M., Lavia, P., Fonatsch, C., Kirchner, H. H., Pajunk, A., Schaadt, M., Burrichter, H., Diehl, V., Ford, J. H., Roberts, C. G., Friebe, B., Vogel, R., Friedländer, M., Gamperl, R., Amtmann, E., Pfister, H., Gebhart, E., Wagner, H., Goetz, P., Chandley, A. C., Speed, R. M., Goyanes, V. J., Schvartzman, J. B., Graeven, U., Weh, H. J., Hossfeld, D. K., Greenblatt, I. M., Gripenberg, U., Söderlund, V., Wahlberg, C., Blomqvist, L., Guichaoua, M. R., Delafontaine, D., Taillemite, J. L., Luciani, J. M., Naaf, T., Grunert, D., Schmid, M., Hameister, H., Sperling, K., Hamers, A., Jongbloet, P., Peeters, G., Geraedts, J., Hartley-Asp, B., Heneen, W. K., Hens, L., Kirsch-Volders, M., Susanne, C., Herbst, E. W., Winking, H., Claussen, C. P., Putz, B., Sellin, D., Kolbus, U., Gropp, A., Bennett, M. D., Heyting, C., Koperdraad, F., Redeker, E. J. W., Holmquist, G., Goldman, M., Jaworska, Halina, Johannisson, R., Kerem, B., Goitein, R., Richier, C., Marcus, M., Cedar, H., Koch, H., Hoehn, H., Kubbies, Manfred, Rabinovitch, Peter S., Kunz, W., Franz, G., Lacadena, J. R., Cermeno, M. C., Orellana, J., Santos, J. L., Lemeunier, F., Derbin, C., Lin, C. C., Hoar, D. I., Hoo, J. J., Macgregor, H. C., Sims, S., Horner, H. A., Pellatt, P., Mackay, J. M., Fox, D. P., Brunt, P. W., Johnston, A. W., Magenis, R. E., Chamberlin, J., Allen, L., Tomar, D., Olson, S., Donlon, T., Marlekaj, P., Balcini, A., Fantoni, A., de Capoa, A., Martinsson, T., Dahllöf, B., Levan, G., Matsukuma, S., Utakoji, T., del Mazo, J., Avila, J., Miller, D. A., Feinstein, S. I., Miller, O. J., Morita, T., Delarbre, C., Gachelin, G., Kourilsky, P., Moritz, K., Moriwaki, K., Miyashita, N., Imai, H. T., Wang, C. H., Bonhomme, F., Murer-Orlando, M., Peterson, A. C., Neitzel, H., Bogenberger, J., Fittler, F., Gaenge, M., Schulze, C., Nietzel, H., Nürnberger, F., Höhn, H., van Ommen, G. J. B., Baas, F., Arnberg, A. C., Pearson, P. L., De Vijilder, J. J. M., Bakker, E., Hofker, M., Wapenaar, M. C., Parrington, J. M., West, L. F., Povey, S., Pasquali, F., Casalone, R., Bernasconi, P., Paul, J., Froster-Iskenius, U., Schwinger, E., Moje, W., Pearson, P. O., Beverstock, G. C., Veenema, H., v.d Kamp, J. J., Petitpierre, E., Philip, J., Lundsteen, C., van der Ploeg, M., van Prooijen-Knegt, A. C., Bauman, J. G. J., van Duijn, P., Puertas, M. J., de la Pena, A., Estades, B., Merino, F., Rao, S. R. V., Vasantha, K., Thelma, B. K., Juyal, R. C., Jhanwar, S. C., Ratomponirina, Ch, Hamilton, A., Rumpler, Y., Moses, M., Raveh, D., Ben-Zeoev, A., Redi, C. A., Garagna, S., Italy, C. N. R., Robert-Nicoud, M., Streichhan, I., Möhr, E., Westermann, R., Grossbach, U., Sandberg, P., Levan, A., Schäfer, Mireille, Schempp, W., Scheres, J. M. J. C., Hustinx, T. W. J., Holdrinet, R. S. G., Tice, R. R., Schwarzacher, T., Finch, R. A., Searle, J. B., Sharma, T., Sen, S., Cheong, N., Siebert, E., Loidl, J., Slater, R. M., de Kraker, J., Voute, P. A., Delemarre, J. F. M., Smeets, D. F. C. M., Smits, A. P. T., Solleder, E., Inglin, B., Geile, B., Somssich, I., Schwarz, E., Speit, G., Mehnert, K., Vogel, W., Stahl, A., Hartung, M., Devictor, M., Guichaoua, M., Stoll, C., Roth, M.-P., Dott, B., Tabor, A., Madsen, M., Tommerup, N., Traut, W., Chavin-Colin, F., Junien, C., Vekemans, M., Esseltine, D., Venegas, W., Lasne, Cl, Chouroulinkov, I., Vidal, F., Navarro, J., Templado, C., Egozcue, J., Viegas-Péquignot, E., Malfoy, B., Taillandier, E., Leng, M., Viinikka, Y., Spielmann, H., Boldin, S., Volobouev, V. T., Webb, G. C., Krumins, E., Wegner, R.-D., Lüdtke, E.-L., Weith, A., Westerman, M., Thomson, R., Sinclair, A., Yacobi, Y. Z., Feldman, M., Yoon, J. S., Bennett, M. D., editor, Gropp, A., editor, and Wolf, U., editor

Published
1984
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45. Effects of Changing Environments on Survival of a Widely Distributed Ungulate

Author

Sims, S Andrew

Subjects
cox regression, NDVI, Ecology and Evolutionary Biology, mule deer, odocolieus hemionus, survival
Abstract

Widely distributed species are experiencing a continual pattern of range shifts due to anthropogenic expansion and climate change, forcing these species into novel environments and out of critical habitat. The ability to estimate current and forecasted states of demographic parameters of species distributed along a gradient of environments is becoming increasingly important in a time of large-scale environmental change. Consulting models that provide temporally relevant estimates of population dynamics based on the latest realizations of environmental conditions can allow for informed, quick and decisive conservation and management actions. Modelling the drivers of demography across a wide range of environmental conditions will provide a more comprehensive understanding of how species will respond to novel environments. In this study we provide an example of relating seasonal-environmental variables to survival in a widely distributed ungulate species. We used a mule deer (Odocoileus hemionus) survival dataset collected in Utah with seven sites distributed across the multiple ecoregions of the state, allowing for the elucidation of relationships across a variety of environmental conditions. Multivariate analyses predicting survival of young and adult females were performed using geographic location, elevation, and seasonal satellite-derived primary productivity data and weather variables. We developed frameworks for estimating past and current states of survival and predicting short-term (sub-year) forecasts of survival. Furthermore, we investigated adaptive modelling techniques for increasing the certainty of the forecasted predictions of survival. We found that increased winter precipitation had a negative effect on survival across the state. Survival was lower in the northern region of the state and in higher elevations. Furthermore, measures of summer primary productivity had a positive relationship with survival. Lastly, our adaptive modelling demonstration shows that uncertainty of forecasted survival predictions can be reduced with the addition of data. This study provides a framework for developing models that will provide invaluable information to managers in a time of large-scale environmental change.

Published
2017
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47. Correction

Author

Sims, S, Bolinger, B, and Klenerman, P

Abstract

Murine CMV (MCMV) infection induces effector CD8(+) T cells that continue to increase in frequency after acute infection ("inflation") and are stably maintained at a high frequency, with up to 20% of the CD8(+) T-cell compartment being specific for one epitope, although the flexibility and turnover of these populations is not fully defined. Here we report that effector/memory CD8(+) T cells induced by MCMV can be paradoxically boosted following transient depletion of epitope specific CD8(+) T cells. Treatment of MCMV-infected mice with MHC-Class I-saporin tetramers led to partial (80-90%) depletion of epitope-specific CD8(+) T cells-rapidly followed by a rebound, leading to expansion and maintenance of up to 40% of total CD8(+) T cells, with minimal changes in response to a control epitope (M45). These data indicate the tight balance between host and virus during persistent infection and the functional flexibility of the "inflated" CD8(+) T cell responses during persistent infection.

Published
2016

49. Initial sequencing and analysis of the human genome

Author

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M, FitzHugh, W, Funke, R, Gage, D, Harris, K, Heaford, A, Howland, J, Kann, L, Lehoczky, J, LeVine, R, McEwan, P, McKernan, K, Meldrim, J, Mesirov, JP, Miranda, C, Morris, W, Naylor, J, Raymond, C, Rosetti, M, Santos, R, Sheridan, A, Sougnez, C, Stange-Thomann, N, Stojanovic, N, Subramanian, A, Wyman, D, Rogers, J, Sulston, J, Ainscough, R, Beck, S, Bentley, D, Burton, J, Clee, C, Carter, N, Coulson, A, Deadman, R, Deloukas, P, Dunham, A, Dunham, I, Durbin, R, French, L, Grafham, D, Gregory, S, Hubbard, T, Humphray, S, Hunt, A, Jones, M, Lloyd, C, McMurray, A, Matthews, L, Mercer, S, Milne, S, Mullikin, JC, Mungall, A, Plumb, R, Ross, M, Shownkeen, R, Sims, S, Waterston, RH, Wilson, RK, Hillier, LW, McPherson, JD, Marra, MA, Mardis, ER, Fulton, LA, Chinwalla, AT, Pepin, KH, Gish, WR, Chissoe, SL, Wendl, MC, Delehaunty, KD, Miner, TL, Delehaunty, A, Kramer, JB, Cook, LL, Fulton, RS, Johnson, DL, Minx, PJ, Clifton, SW, Hawkins, T, Branscomb, E, Predki, P, Richardson, P, Wenning, S, Slezak, T, Doggett, N, Cheng, JF, Olsen, A, Lucas, S, Elkin, C, Uberbacher, E, Frazier, M, Gibbs, RA, Muzny, DM, Scherer, SE, Bouck, JB, Sodergren, EJ, Worley, KC, Rives, CM, Gorrell, JH, Metzker, ML, Naylor, SL, Kucherlapati, RS, Nelson, DL, Weinstock, GM, Sakaki, Y, Fujiyama, A, Hattori, M, Yada, T, Toyoda, A, Itoh, T, Kawagoe, C, Watanabe, H, Totoki, Y, Taylor, T, Weissenbach, J, Heilig, R, Saurin, W, Artiguenave, F, Brottier, P, Bruls, T, Pelletier, E, Robert, C, Wincker, P, Smith, DR, Doucette-Stamm, L, Rubenfield, M, Weinstock, K, Lee, HM, Dubois, J, Rosenthal, A, Platzer, M, Nyakatura, G, Taudien, S, Rump, A, Yang, H, Yu, J, Wang, J, Huang, G, Gu, J, Hood, L, Rowen, L, Madan, A, Qin, S, Davis, RW, Federspiel, NA, Abola, AP, Proctor, MJ, Myers, RM, Schmutz, J, Dickson, M, Grimwood, J, Cox, DR, Olson, MV, Kaul, R, Shimizu, N, Kawasaki, K, Minoshima, S, Evans, GA, Athanasiou, M, Schultz, R, Roe, BA, Chen, F, Pan, H, Ramser, J, Lehrach, H, Reinhardt, R, McCombie, WR, de la Bastide, M, Dedhia, N, Blöcker, H, Hornischer, K, Nordsiek, G, Agarwala, R, Aravind, L, Bailey, JA, Bateman, A, Batzoglou, S, Birney, E, Bork, P, Brown, DG, Burge, CB, Cerutti, L, Chen, HC, Church, D, Clamp, M, Copley, RR, Doerks, T, Eddy, SR, Eichler, EE, Furey, TS, Galagan, J, Gilbert, JG, Harmon, C, Hayashizaki, Y, Haussler, D, Hermjakob, H, Hokamp, K, Jang, W, Johnson, LS, Jones, TA, Kasif, S, Kaspryzk, A, Kennedy, S, Kent, WJ, Kitts, P, Koonin, EV, Korf, I, Kulp, D, Lancet, D, Lowe, TM, McLysaght, A, Mikkelsen, T, Moran, JV, Mulder, N, Pollara, VJ, Ponting, CP, Schuler, G, Schultz, J, Slater, G, Smit, AF, Stupka, E, Szustakowski, J, Thierry-Mieg, D, Thierry-Mieg, J, Wagner, L, Wallis, J, Wheeler, R, Williams, A, Wolf, YI, Wolfe, KH, Yang, SP, Yeh, RF, Collins, F, Guyer, MS, Peterson, J, Felsenfeld, A, Wetterstrand, KA, Patrinos, A, Morgan, MJ, de Jong, P, Catanese, JJ, Osoegawa, K, Shizuya, H, Choi, S, Chen, YJ, and Szustakowki, J

Subjects
Genetics, Cancer genome sequencing, Chimpanzee genome project, Multidisciplinary, Cancer Genome Project, Gene density, DNA sequencing theory, Hybrid genome assembly, Computational biology, Biology, Genome, Personal genomics
Abstract

The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Published
2016
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50. CD73 is dispensable for the regulation of inflationary CD8+ T-cells after murine cytomegalovirus infection and adenovirus immunisation

Author

Sims, S, Colston, J, Emery, V, and Klenerman, P

Subjects
Cell biology, Blood cells, Biology and life sciences, Animal cells, Immune Cells, Cellular types, Immunology, T cells, White blood cells, Clinical Immunology, Infectious Disease Immunology, Memory T cells, Research Article
Abstract

The ecto-5'-nucleotidase (CD73) is expressed by T-cell subsets, myeloid derived suppressive cells and endothelial cells. It works in conjunction with CD39 to regulate the formation and degradation of adenosine in vivo. Adenosine has previously been shown to suppress the proliferation and cytokine secretion of T-cells and recent evidence suggests that inhibition of CD73 has the potential to enhance T-cell directed therapies. Here we utilised a CD73 knockout mouse model to assess the suppressive ability of CD73 on CD8+ T-cell classical memory and memory “inflation”, induced by murine cytomegalovirus (MCMV) infection and adenovirus immunisation. We show that CD73 is dispensable for normal CD8+ T-cell differentiation and function in both models. Thus CD73 as a suppressor of CD8+ T-cells is unlikely to play a deterministic role in the generation and functional characteristics of antiviral memory in these settings.

Published
2016
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