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  1. Article ; Online: Yale University School of Medicine.

    Belitsky, Richard / Schwartz, Michael L / Larkin, Susan E / Roth, Abigail

    Academic medicine : journal of the Association of American Medical Colleges

    2021  Volume 95, Issue 9S A Snapshot of Medical Student Education in the United States and Canada: Reports From 145 Schools, Page(s) S83–S86

    Language English
    Publishing date 2021-02-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 96192-9
    ISSN 1938-808X ; 1040-2446
    ISSN (online) 1938-808X
    ISSN 1040-2446
    DOI 10.1097/ACM.0000000000003458
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D.

    Bearpark, Michael J / Larkin, Susan M / Vreven, Thom

    The journal of physical chemistry. A

    2008  Volume 112, Issue 31, Page(s) 7286–7295

    Abstract: We demonstrate that the ONIOM method can be used to optimize a conical intersection between the ground and first excited-state potential energy surfaces of previtamin D (precalciferol), with excitation localized in a small part of the molecule: the ... ...

    Abstract We demonstrate that the ONIOM method can be used to optimize a conical intersection between the ground and first excited-state potential energy surfaces of previtamin D (precalciferol), with excitation localized in a small part of the molecule: the hexatriene chromophore. These calculations were up to 100 times faster with little loss of accuracy compared to a full non-ONIOM Target calculation. The most accurate ONIOM method combination was CASSCF/4-31G//ROHF/STO-3G(Triplet): in comparison to the Target (CASSCF/4-31G), bond lengths and angles in the hexatriene model region were calculated to within 0.02 A and 0.7 degrees , respectively, and the energy difference between the conical intersection and nearest associated S 1 minimum to within 0.5 kcal x mol (-1). All of the low-level methods selected produced accurate geometries, including the UFF molecular mechanics and AM1 semiempirical methods, suggesting a cheap and efficient way of initially optimizing conical intersections geometries. Furthermore, ONIOM allows for an assessment of the localization of excited states, providing some fundamental insight into the physical processes involved.
    Language English
    Publishing date 2008-08-07
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/jp802204w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Deconstructing the ONIOM Hessian: Investigating Method Combinations for Transition Structures.

    Vreven, Thom / Thompson, Lee M / Larkin, Susan M / Kirker, Ian / Bearpark, Michael J

    Journal of chemical theory and computation

    2012  Volume 8, Issue 12, Page(s) 4907–4914

    Abstract: Developments in biochemistry and materials sciences have led to increasing interest in the reactivity of large chemical systems, presenting theoretical and computational challenges that can be addressed with hybrid methods such as ONIOM. Here, we show ... ...

    Abstract Developments in biochemistry and materials sciences have led to increasing interest in the reactivity of large chemical systems, presenting theoretical and computational challenges that can be addressed with hybrid methods such as ONIOM. Here, we show that the diagonalized ONIOM Hessian can be partitioned/deconstructed into contributions from the individual subcalculations-indicating the curvature of their potential energy surfaces (PESs)-without increasing the computational cost. The resulting pseudofrequencies have particular application in the study of transition structures and higher-order saddle points with ONIOM, where we find that an imaginary frequency may result from combining subcalculations for which the corresponding vibrational frequencies are all real. Two cycloaddition reactions, including functionalization of a 150 atom (5,5) single-walled carbon nanotube, demonstrate how this analysis of pseudofrequencies allows identification of critical points where further exploratory work should be carried out to ensure that the ONIOM PES correctly approximates the target.
    Language English
    Publishing date 2012-12-11
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9618
    ISSN 1549-9618
    DOI 10.1021/ct300612m
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

    Dejnirattisai, Wanwisa / Huo, Jiandong / Zhou, Daming / Zahradník, Jiří / Supasa, Piyada / Liu, Chang / Duyvesteyn, Helen M.E. / Ginn, Helen M. / Mentzer, Alexander J. / Tuekprakhon, Aekkachai / Nutalai, Rungtiwa / Wang, Beibei / Dijokaite, Aiste / Khan, Suman / Avinoam, Ori / Bahar, Mohammad / Skelly, Donal / Adele, Sandra / Johnson, Sile Ann /
    Amini, Ali / Ritter, Thomas G. / Mason, Chris / Dold, Christina / Pan, Daniel / Assadi, Sara / Bellass, Adam / Omo-Dare, Nicola / Koeckerling, David / Flaxman, Amy / Jenkin, Daniel / Aley, Parvinder K. / Voysey, Merryn / Clemens, Sue Ann Costa / Naveca, Felipe Gomes / Nascimento, Valdinete / Nascimento, Fernanda / Fernandes da Costa, Cristiano / Resende, Paola Cristina / Pauvolid-Correa, Alex / Siqueira, Marilda M. / Baillie, Vicky / Serafin, Natali / Kwatra, Gaurav / Da Silva, Kelly / Madhi, Shabir A. / Nunes, Marta C. / Malik, Tariq / Openshaw, Peter J.M. / Baillie, J. Kenneth / Semple, Malcolm G. / Townsend, Alain R. / Huang, Kuan-Ying A. / Tan, Tiong Kit / Carroll, Miles W. / Klenerman, Paul / Barnes, Eleanor / Dunachie, Susanna J. / Constantinides, Bede / Webster, Hermione / Crook, Derrick / Pollard, Andrew J. / Lambe, Teresa / Paterson, Neil G. / Williams, Mark A. / Hall, David R. / Fry, Elizabeth E. / Mongkolsapaya, Juthathip / Ren, Jingshan / Schreiber, Gideon / Stuart, David I. / Screaton, Gavin R. / Conlon, Christopher / Deeks, Alexandra S. / Frater, John / Frending, Lisa / Gardiner, Siobhan / Jämsén, Anni / Jeffery, Katie / Malone, Tom / Phillips, Eloise / Rothwell, Lucy / Stafford, Lizzie / Baillie, J Kenneth / Openshaw, Peter JM. / Carson, Gail / Alex, Beatrice / Andrikopoulos, Petros / Bach, Benjamin / Barclay, Wendy S. / Bogaert, Debby / Chand, Meera / Chechi, Kanta / Cooke, Graham S. / da Silva Filipe, Ana / de Silva, Thushan / Docherty, Annemarie B. / dos Santos Correia, Gonçalo / Dumas, Marc-Emmanuel / Dunning, Jake / Fletcher, Tom / Green, Christoper A. / Greenhalf, William / Griffin, Julian L. / Gupta, Rishi K. / Harrison, Ewen M. / Hiscox, Julian A. / Wai Ho, Antonia Ying / Horby, Peter W. / Ijaz, Samreen / Khoo, Saye / Law, Andrew / Lewis, Matthew R. / Liggi, Sonia / Lim, Wei Shen / Maslen, Lynn / Merson, Laura / Meynert, Alison M. / Moore, Shona C. / Noursadeghi, Mahdad / Olanipekun, Michael / Osagie, Anthonia / Palmarini, Massimo / Palmieri, Carlo / Paxton, William A. / Pollakis, Georgios / Price, Nicholas / Rambaut, Andrew / Robertson, Dave / Russell, Clark D. / Sancho-Shimizu, Vanessa / Sands, Caroline J. / Scott, Janet T. / Sigfrid, Louise / Solomon, Tom / Sriskandan, Shiranee / Stuart, David / Summers, Charlotte / Swann, Olivia V. / Takats, Zoltan / Takis, Panteleimon / Tedder, Richard S. / Thompson, AA Roger / Thomson, Emma C. / Thwaites, Ryan S. / Turtle, Lance CW. / Zambon, Maria / Hardwick, Hayley / Donohue, Chloe / Griffiths, Fiona / Oosthuyzen, Wilna / Donegan, Cara / Spencer, Rebecca G. / Norman, Lisa / Pius, Riinu / Drake, Thomas M. / Fairfield, Cameron J. / Knight, Stephen R. / Mclean, Kenneth A. / Murphy, Derek / Shaw, Catherine A. / Dalton, Jo / Girvan, Michelle / Saviciute, Egle / Roberts, Stephanie / Harrison, Janet / Marsh, Laura / Connor, Marie / Halpin, Sophie / Jackson, Clare / Gamble, C. / Plotkin, Daniel / Lee, James / Leeming, Gary / Wham, Murray / Clohisey, Sara / Hendry, Ross / Scott-Brown, Jas / Shaw, Victoria / McDonald, Sarah E. / Keating, Seán / Ahmed, Katie A. / Armstrong, Jane A. / Ashworth, Milton / Asiimwe, Innocent G. / Bakshi, Siddharth / Barlow, Samantha L. / Booth, Laura / Brennan, Benjamin / Bullock, Katie / Catterall, Benjamin WA. / Clark, Jordan J. / Clarke, Emily A. / Cole, Sarah / Cooper, Louise / Cox, Helen / Davis, Christopher / Dincarslan, Oslem / Dunn, Chris / Dyer, Philip / Elliott, Angela / Evans, Anthony / Finch, Lorna / Fisher, Lewis WS. / Foster, Terry / Garcia-Dorival, Isabel / Gunning, Philip / Hartley, Catherine / Jensen, Rebecca L. / Jones, Christopher B. / Jones, Trevor R. / Khandaker, Shadia / King So, Katharine / Kiy, Robyn T. / Koukorava, Chrysa / Lake, Annette / Lant, Suzannah / Latawiec, Diane / Lavelle-Langham, Lara / Lefteri, Daniella / Lett, Lauren / Livoti, Lucia A. / Mancini, Maria / McDonald, Sarah / McEvoy, Laurence / McLauchlan, John / Metelmann, Soeren / Miah, Nahida S. / Middleton, Joanna / Mitchell, Joyce / Murphy, Ellen G. / Penrice-Randal, Rebekah / Pilgrim, Jack / Prince, Tessa / Reynolds, Will / Ridley, P. Matthew / Sales, Debby / Shaw, Victoria E. / Shears, Rebecca K. / Small, Benjamin / Subramaniam, Krishanthi S. / Szemiel, Agnieska / Taggart, Aislynn / Tanianis-Hughes, Jolanta / Thomas, Jordan / Trochu, Erwan / van Tonder, Libby / Wilcock, Eve / Zhang, J. Eunice / Flaherty, Lisa / Maziere, Nicole / Cass, Emily / Carracedo, Alejandra Doce / Carlucci, Nicola / Holmes, Anthony / Massey, Hannah / Murphy, Lee / McCafferty, Sarah / Clark, Richard / Fawkes, Angie / Morrice, Kirstie / Maclean, Alan / Wrobel, Nicola / Donnelly, Lorna / Coutts, Audrey / Hafezi, Katarzyna / MacGillivray, Louise / Gilchrist, Tammy / Adeniji, Kayode / Agranoff, Daniel / Agwuh, Ken / Ail, Dhiraj / Aldera, Erin L. / Alegria, Ana / Allen, Sam / Angus, Brian / Ashish, Abdul / Atkinson, Dougal / Bari, Shahedal / Barlow, Gavin / Barnass, Stella / Barrett, Nicholas / Bassford, Christopher / Basude, Sneha / Baxter, David / Beadsworth, Michael / Bernatoniene, Jolanta / Berridge, John / Berry, Colin / Best, Nicola / Bothma, Pieter / Chadwick, David / Brittain-Long, Robin / Bulteel, Naomi / Burden, Tom / Burtenshaw, Andrew / Caruth, Vikki / Chambler, Duncan / Chee, Nigel / Child, Jenny / Chukkambotla, Srikanth / Clark, Tom / Collini, Paul / Cosgrove, Catherine / Cupitt, Jason / Cutino-Moguel, Maria-Teresa / Dark, Paul / Dawson, Chris / Dervisevic, Samir / Donnison, Phil / Douthwaite, Sam / Drummond, Andrew / DuRand, Ingrid / Dushianthan, Ahilanadan / Dyer, Tristan / Evans, Cariad / Eziefula, Chi / Fegan, Chrisopher / Finn, Adam / Fullerton, Duncan / Garg, Sanjeev / Garg, Atul / Gkrania-Klotsas, Effrossyni / Godden, Jo / Goldsmith, Arthur / Graham, Clive / Hardy, Elaine / Hartshorn, Stuart / Harvey, Daniel / Havalda, Peter / Hawcutt, Daniel B. / Hobrok, Maria / Hodgson, Luke / Hormis, Anil / Jacobs, Michael / Jain, Susan / Jennings, Paul / Kaliappan, Agilan / Kasipandian, Vidya / Kegg, Stephen / Kelsey, Michael / Kendall, Jason / Kerrison, Caroline / Kerslake, Ian / Koch, Oliver / Koduri, Gouri / Kōśi, Jōrjj / Laha, Shondipon / Laird, Steven / Larkin, Susan / Leiner, Tamas / Lillie, Patrick / Limb, James / Linnett, Vanessa / Little, Jeff / Lyttle, Mark / MacMahon, Michael / MacNaughton, Emily / Mankregod, Ravish / Masson, Huw / Matovu, Elijah / McCullough, Katherine / McEwen, Ruth / Meda, Manjula / Mills, Gary / Minton, Jane / Mirfenderesky, Mariyam / Mohandas, Kavya / Mok, Quen / Moon, James / Moore, Elinoor / Morgan, Patrick / Morris, Craig / Mortimore, Katherine / Moses, S. / Mpenge, Mbiye / Mulla, Rohinton / Murphy, Michael / Nagel, Megan / Nagarajan, Thapas / Nelson, Mark / Norris, Lillian / O’Shea, Matthew K. / Otahal, Igor / Ostermann, Marlies / Pais, Mark / Panchatsharam, Selva / Papakonstantinou, Danai / Paraiso, Hassan / Patel, Brij / Pattison, Natalie / Pepperell, Justin / Peters, Mark / Phull, Mandeep / Pintus, Stefania / Pooni, Jagtur Singh / Planche, Tim / Post, Frank / Price, David / Prout, Rachel / Rae, Nikolas / Reschreiter, Henrik / Reynolds, Tim / Richardson, Neil / Roberts, Mark / Roberts, Devender / Rose, Alistair / Rousseau, Guy / Ruge, Bobby / Ryan, Brendan / Saluja, Taranprit / Schmid, Matthias L. / Shah, Aarti / Shanmuga, Prad / Sharma, Anil / Shawcross, Anna / Sizer, Jeremy / Shankar-Hari, Manu / Smith, Richard / Snelson, Catherine / Spittle, Nick / Staines, Nikki / Stambach, Tom / Stewart, Richard / Subudhi, Pradeep / Szakmany, Tamas / Tatham, Kate / Thomas, Jo / Thompson, Chris / Thompson, Robert / Tridente, Ascanio / Tupper-Carey, Darell / Twagira, Mary / Vallotton, Nick / Vancheeswaran, Rama / Vincent-Smith, Lisa / Visuvanathan, Shico / Vuylsteke, Alan / Waddy, Sam / Wake, Rachel / Walden, Andrew / Welters, Ingeborg / Whitehouse, Tony / Whittaker, Paul / Whittington, Ashley / Papineni, Padmasayee / Wijesinghe, Meme / Williams, Martin / Wilson, Lawrence / Winchester, Stephen / Wiselka, Martin / Wolverson, Adam / Wootton, Daniel G. / Workman, Andrew / Yates, Bryan / Young, Peter

    Cell. 2022 Feb. 03, v. 185, no. 3 p.467-484.e15

    2022  

    Abstract: On 24ᵗʰ November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent ... ...

    Institution OPTIC Consortium
    ISARIC4C Consortium
    Abstract On 24ᵗʰ November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; evolution ; neutralization ; pandemic ; vaccines ; SARS-CoV-2 ; Omicron ; variants ; immune evasion ; receptor interaction ; Spike ; RBD
    Language English
    Dates of publication 2022-0203
    Size p. 467-484.e15.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.12.046
    Database NAL-Catalogue (AGRICOLA)

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