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Article

Conn, Jonathan G. M. and Ahmad, Abdullah and Palmer, David S. (2024) A machine learning free energy functional for the 1D reference interaction site model : towards prediction of solvation free energy for all solvent systems. Liquids, 4 (4). pp. 710-731. ISSN 2673-8015

Rianjongdee, Francesco and Palmer, David and Pickett, Stephen D. and Pogány, Peter and Tomkinson, Nicholas C.O. and Green, Darren V.S. (2024) bbSelect : an open-source tool for performing a 3D pharmacophore-driven diverse selection of R-groups. Journal of Chemical Information and Modeling, 64 (12). pp. 4687-4699. ISSN 1549-9596

Christie, Loren and Rutherford, Samantha and Palmer, David S. and Baker, Matthew J. and Butler, Holly J. (2024) Bioprocess monitoring applications of an innovative ATR-FTIR spectroscopy platform. Frontiers in Bioengineering and Biotechnology, 12. 1349473. ISSN 2296-4185

Christie, Loren and Sala, Alexandra and Cameron, James M. and Conn, Justin J.A. and Palmer, David S. and McGeown, William J. and Cannon, Jane A. and Sharp, John and Baker, Matthew J. (2023) Rapid detection of heart failure using a spectroscopic liquid biopsy. Clinical Spectroscopy, 5. 100029. ISSN 2666-0547

Bradley, Erin and Fusani, Lucia and Chung, Chun-wa and Craggs, Peter D. and Demont, Emmanuel H. and Humphreys, Philip G. and Mitchell, Darren J. and Phillipou, Alexander and Rioja, Inmaculada and Shah, Rishi R. and Wellaway, Christopher R. and Prinjha, Rab K. and Palmer, David S. and Kerr, William J. and Reid, Marc and Wall, Ian D. and Cookson, Rosa (2023) Structure-guided design of a domain-selective bromodomain and extra terminal N-terminal bromodomain chemical probe. Journal of Medicinal Chemistry, 66 (23). pp. 15728-15749. ISSN 0022-2623

Sala, Alexandra and Cameron, James M. and Brennan, Paul M. and Crosbie, Emma J. and Curran, Tom and Gray, Ewan and Martin-Hirsch, Pierre and Palmer, David S. and Rehman, Ihtesham U. and Rattray, Nicholas J. W. and Baker, Matthew J. (2023) Global serum profiling an opportunity for earlier cancer detection. Journal of Experimental & Clinical Cancer Research, 42 (1). 207. ISSN 1756-9966

McHardy, Rose G. and Antoniou, Georgios and Conn, Justin J. A. and Baker, Matthew J. and Palmer, David S. (2023) Augmentation of FTIR spectral datasets using Wasserstein generative adversarial networks for cancer liquid biopsies. Analyst, 148 (16). pp. 3860-3869. ISSN 0003-2654

Antoniou, Georgios and Conn, Justin J. A. and Smith, Benjamin R. and Brennan, Paul M. and Baker, Matthew J. and Palmer, David S. (2023) Recurrent neural networks for time domain modelling of FTIR spectra : application to brain tumour detection. Analyst, 148 (8). pp. 1770-1776. ISSN 0003-2654

Fowles, Daniel J. and Palmer, David S. (2023) Solvation entropy, enthalpy and free energy prediction using a multi-task deep learning functional in 1D-RISM. Physical Chemistry Chemical Physics, 25 (9). pp. 6944-6954. ISSN 1463-9084

Conn, Jonathan G. M. and Carter, James W. and Conn, Justin J. A. and Subramanian, Vigneshwari and Baxter, Andrew and Engkvist, Ola and Llinas, Antonio and Ratkova, Ekaterina L. and Pickett, Stephen D. and McDonagh, James L and Palmer, David S. (2023) Blinded predictions and post-hoc analysis of the second solubility challenge data : exploring training data and feature set selection for machine and deep learning models. Journal of Chemical Information and Modeling, 63 (4). pp. 1099-1113. ISSN 1549-9596

Connal, Siobhan and Cameron, James M. and Sala, Alexandra and Brennan, Paul M. and Palmer, David S. and Palmer, Joshua D. and Perlow, Haley and Baker, Matthew J. (2023) Liquid biopsies : the future of cancer early detection. Journal of Translational Medicine, 21 (1). 118. ISSN 1479-5876

Fowles, Daniel J. and McHardy, Rose G. and Ahmad, Abdullah and Palmer, David S. (2023) Accurately predicting solvation free energy in aqueous and organic solvents beyond 298 K by combining deep learning and the 1D reference interaction site model. Digital Discovery, 2 (1). pp. 177-188. ISSN 2635-098X

Rashed, Hamad S. and Parrott, Andrew J. and Nordon, Alison and Baker, Matthew J. and Palmer, David S. (2022) Pocket-size near-IR spectrometers for rapid examination of contaminated textile fibres at the crime-scene. Vibrational Spectroscopy, 123. 103464. ISSN 0924-2031

Sala, Alexandra and Cameron, James M. and Jenkins, Cerys A. and Barr, Hugh and Christie, Loren and Conn, Justin J. A. and Evans, Thomas R. Jeffry and Harris, Dean A. and Palmer, David S. and Rinaldi, Christopher and Theakstone, Ashton G. and Baker, Matthew J. (2022) Liquid biopsy for pancreatic cancer detection using infrared spectroscopy. Cancers, 14 (13). 3048. ISSN 2072-6694

Cameron, James M. and Brennan, Paul M. and Antoniou, Georgios and Butler, Holly J. and Christie, Loren and Conn, Justin J.A. and Curran, Tom and Gray, Ewan and Hegarty, Mark G. and Jenkinson, Michael D. and Orringer, Daniel and Palmer, David S. and Sala, Alexandra and Smith, Benjamin R. (2022) Clinical validation of a spectroscopic liquid biopsy for earlier detection of brain cancer. Neuro-Oncology Advances, 4 (1). vdac024. ISSN 2632-2498

Theakstone, Ashton G. and Brennan, Paul M. and Jenkinson, Michael D. and Mills, Samantha J. and Syed, Khaja and Rinaldi, Christopher and Xu, Yun and Goodacre, Royston and Butler, Holly J. and Palmer, David S. and Smith, Benjamin R. and Baker, Matthew J. (2021) Rapid spectroscopic liquid biopsy for the universal detection of brain tumours. Cancers, 13 (15). 3851. ISSN 2072-6694

Fowles, Daniel J. and Palmer, David S. and Guo, Rui and Price, Sarah L. and Mitchell, John B. O. (2021) Towards physics-based solubility computation for pharmaceuticals to rival informatics. Journal of Chemical Theory and Computation, 17 (6). pp. 3700-3709. ISSN 1549-9618

Brennan, Paul M. and Butler, Holly J. and Christie, Loren and Hegarty, Mark G. and Jenkinson, Michael D. and Keerie, Catriona and Norrie, John and O'Brien, Rachel and Palmer, David S. and Smith, Benjamin R. and Baker, Matthew J. (2021) Early diagnosis of brain tumours using a novel spectroscopic liquid biopsy. Brain Communications, 3 (2). fcab056.

Rashed, Hamad S. and Mishra, Puneet and Nordon, Alison and Palmer, David S. and Baker, Matthew J. (2021) A comparative investigation of two handheld near-IR spectrometers for direct forensic examination of fibres in-situ. Vibrational Spectroscopy, 113. 103205. ISSN 0924-2031

Gray, Ewan and Cameron, James M. and Butler, Holly J. and Jenkinson, Michael D. and Hegarty, Mark G. and Palmer, David S. and Brennan, Paul M. and Baker, Matthew J. (2021) Early economic evaluation to guide the development of a spectroscopic liquid biopsy for the detection of brain cancer. International Journal of Technology Assessment in Health Care, 37 (1). e41. ISSN 1471-6348

Cameron, James M. and Conn, Justin J. A. and Rinaldi, Christopher and Sala, Alexandra and Brennan, Paul M. and Jenkinson, Michael D. and Caldwell, Helen and Cinque, Gianfelice and Syed, Khaja and Butler, Holly J. and Hegarty, Mark G. and Palmer, David S. and Baker, Matthew J. (2020) Interrogation of IDH1 status in gliomas by Fourier transform infrared spectroscopy. Cancers, 12 (12). 3682. ISSN 2072-6694

Sala, Alexandra and Spalding, Katie E. and Ashton, Katharine M. and Board, Ruth and Butler, Holly J. and Dawson, Timothy P. and Harris, Dean A. and Hughes, Caryn S. and Jenkins, Cerys A. and Jenkinson, Michael D. and Palmer, David S. and Smith, Benjamin R. and Thornton, Catherine A. and Baker, Matthew J. (2020) Rapid analysis of disease state in liquid human serum combining infrared spectroscopy and "digital drying". Journal of Biophotonics, 13 (9). e202000118. ISSN 1864-0648

Cameron, James M. and Rinaldi, Christopher and Butler, Holly J. and Hegarty, Mark G and Brennan, Paul M. and Jenkinson, Michael D. and Syed, Khaja and Ashton, Katherine M. and Dawson, Timothy P. and Palmer, David S. and Baker, Matthew J. (2020) Stratifying brain tumour histological sub-types : the application of ATR-FTIR serum spectroscopy in secondary care. Cancers, 12 (7). 1710. ISSN 2072-6694

Subramanian, Vigneshwari and Ratkova, Ekaterina and Palmer, David S. and Engkvist, Ola and Fedorov, Maxim V. and Llinas, Antonio (2020) Multi-solvent models for solvation free energy predictions using 3D-RISM hydration thermodynamic descriptors. Journal of Chemical Information and Modeling, 60 (6). pp. 2977-2988. ISSN 1549-9596

Fusani, Lucia and Palmer, David S. and Somers, Donald O. and Wall, Ian D. (2020) Exploring ligand stability in protein crystal structures using binding pose metadynamics. Journal of Chemical Information and Modeling, 60 (3). pp. 1528-1539. ISSN 1549-9596

Cameron, James M. and Butler, Holly J. and Smith, Benjamin R. and Hegarty, Mark G. and Jenkinson, Michael D. and Syed, Khaja and Brennan, Paul M. and Ashton, Katherine and Dawson, Timothy and Palmer, David S. and Baker, Matthew J. (2019) Developing infrared spectroscopic detection for stratifying brain tumour patients : glioblastoma multiforme vs. lymphoma. Analyst, 144 (22). pp. 6736-6750. ISSN 0003-2654

Butler, Holly J. and Brennan, Paul M. and Cameron, James M. and Finlayson, Duncan and Hegarty, Mark G. and Jenkinson, Michael D. and Palmer, David S. and Smith, Benjamin R. and Baker, Matthew J. (2019) Development of high-throughput ATR-FTIR technology for rapid triage of brain cancer. Nature Communications, 10. 4501. ISSN 2041-1723

Butler, Holly J. and Smith, Benjamin R. and Fritzsch, Robby and Radhakrishnan, Pretheepan and Palmer, David S. and Baker, Matthew J. (2018) Optimised spectral pre-processing for discrimination of biofluids via ATR-FTIR spectroscopy. Analyst. ISSN 0003-2654

Sosnin, Sergey and Misin, Maksim and Palmer, David S. and Fedorov, Maxim V. (2018) 3D matters! 3D-RISM and 3D convolutional neural network for accurate bioaccumulation prediction. Journal of Physics: Condensed Matter, 30. 32LT03. ISSN 0953-8984

Gray, Ewan and Butler, Holly J and Board, Ruth and Brennan, Paul M and Chalmers, Anthony J and Dawson, Timothy and Goodden, John and Hamilton, Willie and Hegarty, Mark G and James, Allan and Jenkinson, Michael D and Kernick, David and Lekka, Elvira and Livermore, Laurent J and Mills, Samantha J and O'Neill, Kevin and Palmer, David S and Vaqas, Babar and Baker, Matthew J (2018) Health economic evaluation of a serum based blood test for brain tumour diagnosis : exploration of two clinical scenarios. BMJ Open, 8 (5). e017593. ISSN 2044-6055

Cameron, James M. and Butler, Holly J. and Palmer, David S. and Baker, Matthew J. (2018) Biofluid spectroscopic disease diagnostics : a review on the processes and spectral impact of drying. Journal of Biophotonics, 11 (4). e201700299. ISSN 1864-0648

Ansari, Samiul M. and Palmer, David S. (2018) Comparative molecular field analysis using molecular integral equation theory. Journal of Chemical Information and Modeling. ISSN 1549-9596

Fusani, Lucia and Wall, Ian and Palmer, David and Cortes, Alvaro (2018) Optimal water networks in protein cavities with GAsol and 3D-RISM. Bioinformatics. ISSN 1367-4811

Smith, Benjamin R. and Baker, Matthew J. and Palmer, David S. (2018) PRFFECT : a versatile tool for spectroscopists. Chemometrics and Intelligent Laboratory Systems. ISSN 0169-7439

Ansari, Samiul M. and Sørensen, Jesper and Schiøtt, Birgit and Palmer, David S. (2017) On the effect of mutations in bovine or camel chymosin on the thermodynamics of binding κ-caseins. Proteins: Structure, Function, and Bioinformatics. pp. 1-36. ISSN 0887-3585

Misin, Maksim and Vainikka, Petteri A. and Fedorov, Maxim V. and Palmer, David S. (2016) Salting-out effects by pressure-corrected 3D-RISM. Journal of Chemical Physics. ISSN 0021-9606 (In Press)

McDonagh, James and Palmer, David S. and van Mourik, Tanja and Mitchell, John B.O. (2016) Are the sublimation thermodynamics of organic molecules predictable? Journal of Chemical Information and Modeling. ISSN 1549-9596

Ansari, Samiul M. and Coletta, Andrea and Kirkeby Skeby, Katrine and Sørensen, Jesper and Schiøtt, Birgit and Palmer, David S. (2016) Allosteric activation mechanism of bovine chymosin revealed by bias-exchange metadynamics and molecular dynamics simulations. Journal of Physical Chemistry B, 120 (40). pp. 10453-10462. ISSN 1520-6106

Smith, Benjamin Richard and Ashton, Katherine M. and Brodbelt, Andrew and Dawson, Timothy and Jenkinson, Michael D. and Hunt, Neil T. and Palmer, David S. and Baker, Matthew J. (2016) Combining random forest and 2D correlation analysis to identify serum spectral signatures for neuro-oncology. Analyst, 141. pp. 3668-3678. ISSN 0003-2654

Misin, Maksim and Palmer, David S. and Fedorov, Maxim V. (2016) Predicting solvation free energies using parameter-free solvent models. Journal of Physical Chemistry B. ISSN 1520-6106

Misin, Maksim and Fedorov, Maxim V. and Palmer, David S. (2016) Hydration free energies of molecular ions from theory and simulation. Journal of Physical Chemistry B, 120 (5). pp. 975-983. ISSN 1520-6106

Palmer, David S. and Misin, Maksim and Fedorov, Maxim V. and Llinas, Antonio (2015) Fast and general method to predict the physicochemical properties of druglike molecules using the integral equation theory of molecular liquids. Molecular Pharmaceutics, 12 (9). 3420–3432. ISSN 1543-8384

Misin, Maksim and Fedorov, Maxim V. and Palmer, David S. (2015) Accurate hydration free energies at a wide range of temperatures from 3D-RISM. Journal of Chemical Physics, 142 (9). 091105. ISSN 0021-9606

Ratkova, Ekaterina L. and Palmer, David S. and Fedorov, Maxim V. (2015) Solvation thermodynamics of organic molecules by the molecular integral equation theory : approaching chemical accuracy. Chemical Reviews, 115 (13). 6312–6356. ISSN 0009-2665

Palmer, David S. and Mitchell, John B. O. (2014) Is experimental data quality the limiting factor in predicting the aqueous solubility of druglike molecules? Molecular Pharmaceutics, 11 (8). 2962–2972. ISSN 1543-8384

Somavarapu, Arun Kumar and Balakrishnan, Satish and Gautam, Amit Kumar Singh and Palmer, David and Venkatraman, Prasanna (2014) Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation. BMC Structural Biology, 14 (9).

Palmer, David and Sørensen, Jesper Givskov J.G. and Schiøtt, Birgit B. and Fedorov, Maxim V. M.V. (2013) Solvent binding analysis and computational alanine scanning of the bovine chymosin-bovine κ-casein complex using molecular integral equation theory. Journal of Chemical Theory and Computation, 9 (12). pp. 5706-5717. ISSN 1549-9618

Sørensen, Jesper and Palmer, David and Schiøtt, Birgit (2013) Hot-spot mapping of the interactions between chymosin and bovine κ-casein. Journal of Agricultural and Food Chemistry, 61 (33). pp. 7949-7959. ISSN 0021-8561

Palmer, David and McDonagh, James L and Mitchell, John B.O. and van Mourik, Tanja and Fedorov, Maxim (2012) First principles calculation of the intrinsic aqueous solubility of crystalline druglike molecules. Journal of Chemical Theory and Computation, 8 (9). 3322–3337. ISSN 1549-9618

Palmer, D. S. and Jensen, F. (2011) Predicting large-scale conformational changes in proteins using energy-weighted normal modes. Proteins: Structure, Function, and Bioinformatics, 79 (10). pp. 2778-2793.

Fedorov, Maxim V. and Frolov, Andrey I. and Ratkova, Ekaterina L. and Palmer, David S. and Sergiievskyi, Volodymyr P. (2011) Efficient predictions of physchem properties of biomolecules in aqueous solutions using the Reference Interaction Site Model. Abstracts of papers - American Chemical Society, 242. ISSN 0065-7727

Palmer, David S. and Chuev, Gennady N. and Ratkova, Ekaterina L. and Fedorov, Maxim V. (2011) In silico screening of bioactive and biomimetic solutes using Integral Equation Theory. Current Pharmaceutical Design, 17 (17). pp. 1695-1708. ISSN 1381-6128

Frolov, Andrey I. and Ratkova, Ekaterina L. and Palmer, David and Fedorov, Maxim V. (2011) Hydration thermodynamics using the reference interaction site model : speed or accuracy? Journal of Physical Chemistry B, 115 (19). pp. 6011-6022. ISSN 1520-6106

Sørensen, J. and Palmer, D. S. and Qvist, K. B. and Schiøtt, B. (2011) Initial stage of cheese production: a molecular modeling study of bovine and camel chymosin complexed with peptides from the chymosin-sensitive region of kappa-casein. Journal of Agricultural and Food Chemistry, 59 (10). pp. 5636-5647.

Palmer, David and Ratkova, Ekaterina L. and Frolov, Andrey I. and Sergiievskyi, Volodymyr P. and Fedorov, Maxim V. (2011) Accurate calculation of the hydration free energies of biologically active molecules using the reference interaction site model. Abstracts of papers - American Chemical Society, 241. -. ISSN 0065-7727

Palmer, David S. and Jensen, Frank (2011) Predicting large-scale conformational changes in proteins using harmonic vibrational analyses. Abstracts of papers - American Chemical Society, 241. ISSN 0065-7727

Jensen, Frank and Palmer, David S. (2011) Harmonic vibrational analysis in delocalized internal coordinates. Journal of Chemical Theory and Computation, 7 (1). pp. 223-230.

Palmer, David and Frolov, Andrey I. and Ratkova, Ekaterina L. and Fedorov, Maxim V. (2011) Toward a universal model to calculate the solvation thermodynamics of druglike molecules : the importance of new experimental databases. Molecular Pharmaceutics, 8 (4). pp. 1423-1429.

Palmer, David and Frolov, Andrey I. and Ratkova, Ekaterina L. and Fedorov, Maxim V. (2010) Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction. Journal of Physics: Condensed Matter, 22 (49). -. 492101. ISSN 0953-8984

Palmer, David and Fedorov, Maxim (2010) Computational drug discovery : hydration behavior of de novo designed pharmaceuticals. G.I.T. Laboratory Journal Europe. pp. 2-4.

Palmer, David and Sergiievskyi, Volodymyr P. and Jensen, Frank and Fedorov, Maxim V. (2010) Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model. Journal of Chemical Physics, 133 (4). 044104. ISSN 0021-9606

Palmer, D. S. and Christensen, A. U. and Sørensen, J. and Celik, L. and Qvist, K. B. and Schiøtt, B. (2010) Bovine chymosin: a computational study of recognition and binding of bovine kappa-casein. Biochemistry, 49 (11). pp. 2563-2573.

Hughes, L. D. and Palmer, D. S. and Nigsch, F. and Mitchell, J. B. (2008) Why are some properties more difficult to predict than others? A study of QSPR models of solubility, melting point, and Log P. Journal of Chemical Information and Modeling, 48 (1). pp. 220-232.

Palmer, D. S. and Llinas, A. and Morao, I. and Day, G. M. and Goodman, J. M. and Glen, R. C. and Mitchell, J. B. (2008) Predicting intrinsic aqueous solubility by a thermodynamic cycle. Molecular Pharmacology, 5 (2). pp. 266-279.

O'Boyle, Noel M and Palmer, David S and Nigsch, Florian and Mitchell, John BO (2008) Simultaneous feature selection and parameter optimisation using an artificial ant colony : case study of melting point prediction. Chemistry Central Journal, 2. p. 21.

Palmer, D. S. and O'Boyle, N. M. and Glen, R. C. and Mitchell, J. B. (2007) Random forest models to predict aqueous solubility. Journal of Chemical Information and Modeling, 47 (1). pp. 150-158.

Cannon, E. O. and Bender, A. and Palmer, D. S. and Mitchell, J. B. (2006) Chemoinformatics-based classification of prohibited substances employed for doping in sport. Journal of Chemical Information and Modeling, 46 (6). pp. 2369-2380.

Gardiner, E. J. and Hunter, C. A. and Packer, M. J. and Palmer, D. S. and Willett, P. (2003) Sequence-dependent DNA structure: a database of octamer structural parameters. Journal of Molecular Biology, 332 (5). pp. 1025-1035.

Book Section

Palmer, D. S. and Fedorov, M.V.; Abramov, Yuriy A., ed. (2016) Molecular simulation methods to compute intrinsic aqueous solubility of crystalline drug-like molecules. In: Computational Pharmaceutical Solid State Chemistry. John Wiley & Sons Inc., Hoboken, NJ.. ISBN 9781118700747

Conference or Workshop Item

Palmer, David (2015) Computational biomolecular design using the integral equation theory of molecular liquids : from drug discovery to bionanotechnology. In: Thomas Graham Symposium, 2015-03-04 - 2015-03-04, University of Strathclyde.

Palmer, David and Misin, Maksim and Fedorov, Maxim (2014) Solvation thermodynamics of biomolecules from the integral equation theory of molecular liquids. In: Modelling Molecules and Materials – M3 MGMS Meeting, 2014-08-20 - 2014-08-22, University of Strathclyde. (Unpublished)

Palmer, David and Fedorov, Maxim (2014) Is there a role for the integral equation theory of molecular liquids in chemical informatics? In: 248th ACS National Meeting & Exposition, 2014-08-10 - 2014-08-14, California.

Palmer, David (2013) Protein modelling using molecular integral equation theory : applications to chymosin—κ-casein complexes. In: Tools and Strategies to Find Chemical Probes for Your Protein - The Role of Computer-Aided Drug Discovery, 2013-11-15 - 2013-11-15. (Unpublished)

Palmer, David and Fedorov, Maxim (2013) Computing intrinsic aqueous solubility of crystalline organic molecules. In: International Conference on the Properties of Water and Steam (ICPWS16), 2013-09-01 - 2013-09-05.

Palmer, David (2013) Computing intrinsic aqueous solubility of crystalline organic molecules. In: Molecular Modeling and Simulation: Natural Science meets Engineering, 2013-03-11 - 2013-03-12. (Unpublished)

Palmer, David (2013) Computational biomolecular design : from drug discovery to bionanotechnology. In: SUPA Physics and Life Sciences Workshop, 2013-02-27.

Palmer, David and Fedorov, Maxim (2012) Molecular Theories of Solvation: Applications to Biomolecular Thermodynamics. In: Biomolecular Thermodynamics Conference - Institute of Physicists, 2012-11-26 - 2012-11-27. (Unpublished)

Palmer, David (2012) In silico screening of bioactive solutes using molecular integral equation theory. In: ScotChem: Computational Chemistry Symposium 2012, 2012-06-14 - 2012-06-14.

Palmer, David (2012) Computational biomolecular design: predicting the solvation behaviour of De Novo designed molecules. In: University of Strathclyde Research Day 2012, 2012-06-07 - 2012-06-07.

Palmer, David (2012) In silico screening of bioactive solutes using molecular integral equation theory. In: American Chemical Society Spring National Meeting 2012, 2012-03-25 - 2012-03-29.