{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:29:59Z","timestamp":1760059799604,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2025,7,16]],"date-time":"2025-07-16T00:00:00Z","timestamp":1752624000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation program","award":["766118"],"award-info":[{"award-number":["766118"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Platelets play critical roles in haemostasis and thrombosis. The platelet activation process is driven by agonist-induced rises in cytosolic [Ca2+]i, where the patterns of Ca2+ responses are still incompletely understood. In this study, we developed a number of techniques to model the [Ca2+]i curves of platelets from a single blood donor. Fura-2-loaded platelets were quasi-simultaneously stimulated with various agonists, i.e., thrombin, collagen, or CRP, in the presence or absence of extracellular Ca2+ entry, secondary mediator effects, or Ca2+ reuptake into intracellular stores. To understand the calibrated time curves of [Ca2+]i rises, we developed two non-linear models, a multilayer perceptron (MLP) network and an autoregressive network with exogenous inputs (NARX). The trained networks accurately predicted the [Ca2+]i curves for combinations of agonists and inhibitors, with the NARX model achieving an R2 of 0.64 for the trend prediction of unforeseen data. In addition, we used the same dataset for the construction of a partial least square (PLS) linear regression model, which estimated the explained variance of each input. The NARX model demonstrated that good fits could be obtained for the nanomolar [Ca2+]i curves modelled, whereas the PLS model gave useful interpretable information on the importance of each variable. These modelling results can be used for the development of novel platelet [Ca2+]i-inhibiting drugs, such as the drug 2-aminomethyl diphenylborinate, blocking Ca2+ entry in platelets, or for the evaluation of general platelet signalling defects in patients with a bleeding disorder.<\/jats:p>","DOI":"10.3390\/ijms26146820","type":"journal-article","created":{"date-parts":[[2025,7,16]],"date-time":"2025-07-16T15:48:22Z","timestamp":1752680902000},"page":"6820","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Extended Modelling of Molecular Calcium Signalling in Platelets by Combined Recurrent Neural Network and Partial Least Squares Analyses"],"prefix":"10.3390","volume":"26","author":[{"given":"Chukiat","family":"Tantiwong","sequence":"first","affiliation":[{"name":"Institute for Cardiovascular and Metabolic Research (ICMR), School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK"},{"name":"Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hilaire Yam Fung","family":"Cheung","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands"},{"name":"Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanne L.","family":"Dunster","sequence":"additional","affiliation":[{"name":"Institute for Cardiovascular and Metabolic Research (ICMR), School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0372-5352","authenticated-orcid":false,"given":"Jonathan M.","family":"Gibbins","sequence":"additional","affiliation":[{"name":"Institute for Cardiovascular and Metabolic Research (ICMR), School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2848-5121","authenticated-orcid":false,"given":"Johan W. M.","family":"Heemskerk","sequence":"additional","affiliation":[{"name":"Institute for Cardiovascular and Metabolic Research (ICMR), School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK"},{"name":"Synapse Research Institute Maastricht, Kon. Emmaplein 7, 6217 KD Maastricht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3796-1687","authenticated-orcid":false,"given":"Rachel","family":"Cavill","sequence":"additional","affiliation":[{"name":"Department of Data Science and Knowledge Engineering, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1172\/JCI26891","article-title":"The biogenesis of platelets from megakaryocyte proplatelets","volume":"115","author":"Patel","year":"2005","journal-title":"J. Clin. Investig."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.1182\/blood.V67.6.1744.1744","article-title":"Substrate for endothelial prostacyclin production in the presence of platelets exposed to collagen is derived from the platelets rather than the endothelium","volume":"67","author":"Chesterman","year":"1986","journal-title":"Blood"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1161\/01.RES.0000191547.64391.e3","article-title":"Endothelial extracellular matrix: Biosynthesis, remodelling, and functions during vascular morphogenesis and neovessel stabilisation","volume":"97","author":"Davis","year":"2005","journal-title":"Circ. Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/s41569-018-0110-0","article-title":"Platelet biology and functions: New concepts and clinical perspectives","volume":"16","author":"Heemskerk","year":"2019","journal-title":"Nat. Rev. Cardiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/eurheartj\/ehi041","article-title":"Venous and arterial thrombosis: A continuous spectrum of the same disease?","volume":"26","year":"2005","journal-title":"Eur. Heart J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1038\/nm.2515","article-title":"Arterial thrombosis-insidious, unpredictable and deadly","volume":"17","author":"Jackson","year":"2011","journal-title":"Nat. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ceca.2018.11.005","article-title":"Store-operated calcium entry in blood cells in thrombo-inflammation","volume":"77","author":"Nagy","year":"2019","journal-title":"Cell Calcium"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1152\/physrev.00016.2011","article-title":"New fundamentals in hemostasis","volume":"93","author":"Versteeg","year":"2013","journal-title":"Physiol. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"13199","DOI":"10.1016\/S0021-9258(18)90677-0","article-title":"The rapid formation of inositol phosphates in human platelets by thrombin is inhibited by prostacyclin","volume":"259","author":"Watson","year":"1984","journal-title":"J. Biol. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/0014-5793(86)81000-6","article-title":"ADP stimulates IP3 formation in human platelets","volume":"206","author":"Daniel","year":"1986","journal-title":"FEBS Lett."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1111\/jth.12472","article-title":"Impact of vascular thromboxane prostanoid receptor activation on hemostasis, thrombosis, oxidative stress, and inflammation","volume":"12","author":"Capra","year":"2014","journal-title":"J. Thromb. Haemost."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1055\/s-0037-1616060","article-title":"The ATP-gated P2X1 ion channel acts as a positive regulator of platelet responses to collagen","volume":"86","author":"Oury","year":"2001","journal-title":"Thromb. Haemost."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2049","DOI":"10.1016\/j.bpj.2014.03.028","article-title":"Systems modelling of Ca2+ homeostasis and mobilisation in platelets mediated by IP3 and store-operated Ca2+ entry","volume":"106","author":"Dolan","year":"2014","journal-title":"Biophys. J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/nbt.1642","article-title":"Pairwise agonist scanning predicts cellular signalling responses to combinatorial stimuli","volume":"28","author":"Chatterjee","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"102738","DOI":"10.1016\/j.ceca.2023.102738","article-title":"High-throughput assessment identifying major platelet Ca2+ entry pathway via tyrosine kinase-linked and G protein-coupled receptors","volume":"112","author":"Cheung","year":"2023","journal-title":"Cell Calcium"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1613\/jair.953","article-title":"SMOTE: Synthetic minority over-sampling technique","volume":"16","author":"Chawla","year":"2002","journal-title":"J. Artific. Intell. Res."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Shawer, H., Norman, K., Cheng, C.W., Foster, R., Beech, D.J., and Bailey, M.A. (2021). ORAI1 Ca2+ channel as a therapeutic target in pathological vascular remodelling. Front. Cell Dev. Biol., 9.","DOI":"10.3389\/fcell.2021.653812"},{"key":"ref_18","unstructured":"Neyshabur, B., Sedghi, H., and Zhang, C. (2020, January 6\u201312). What is being transferred in transfer learning?. Proceedings of the 34th International Conference on Neural Information Processing Systems, Vancouver BC, Canada."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Dana, D., Gadhiya, S.V., Surin, L.G., Li, D., Naaz, F., Ali, Q., Paka, L., Yamin, M.A., Narayan, M., and Goldberg, I.D. (2018). Deep learning in drug discovery and medicine; scratching the surface. Molecules, 23.","DOI":"10.3390\/molecules23092384"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1007\/s11302-022-09880-4","article-title":"The P2X1 receptor as a therapeutic target","volume":"18","author":"Bennetts","year":"2022","journal-title":"Purinergic Signal."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"33750","DOI":"10.1074\/jbc.M109.048439","article-title":"Non-redundant roles of phosphoinositide 3-kinase isoforms \u03b1 and \u03b2 in glycoprotein VI-induced platelet signalling and thrombus formation","volume":"284","author":"Gilio","year":"2009","journal-title":"J. Biol. Chem."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Jooss, N.J., De Simone, I., Provenzale, I., Fern\u00e1ndez, D.I., Brouns, S.L., Farndale, R.W., Henskens, Y.M., Kuijpers, M.J., ten Cate, H., and van der Meijden, P.E. (2019). Role of platelet glycoprotein VI and tyrosine kinase Syk in thrombus formation on collagen-like surfaces. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20112788"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Zou, J., Zhang, P., Solari, F.A., Sch\u00f6nichen, C., Provenzale, I., Mattheij, N.J., Kuijpers, M.J., Rauch, J.S., Swieringa, F., and Sickmann, A. (2024). Suppressed ORAI1-STIM1-dependent Ca2+ entry by protein kinase C isoforms regulating platelet procoagulant activity. J. Biol. Chem., 300.","DOI":"10.1016\/j.jbc.2024.107899"},{"key":"ref_24","unstructured":"Xie, H., Tang, H., and Liao, Y. (2009, January 12\u201315). Time series prediction based on NARX neural networks: An advanced approach. Proceedings of the 2009 International Conference on Machine Learning and Cybernetics, Hebei, China."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.ijforecast.2020.06.008","article-title":"Recurrent neural networks for time series forecasting: Current status and future directions","volume":"37","author":"Hewamalage","year":"2021","journal-title":"Int. J. Forecast."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3070","DOI":"10.1002\/2014WR016527","article-title":"What do we mean by sensitivity analysis? The need for comprehensive characterisation of global sensitivity in earth and environmental systems models","volume":"51","author":"Razavi","year":"2015","journal-title":"Water Resourc. Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0169-7439(01)00155-1","article-title":"PLS-regression: A basic tool of chemometrics","volume":"58","author":"Wold","year":"2001","journal-title":"Chemom. Intell. Lab. Syst."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1002\/wics.51","article-title":"Partial least squares regression and projection on latent structure regression (PLS regression)","volume":"2","author":"Abdi","year":"2010","journal-title":"Wiley Interdiscip. Rev. Comput. Stat."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/14\/6820\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:10:48Z","timestamp":1760033448000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/14\/6820"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,16]]},"references-count":28,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["ijms26146820"],"URL":"https:\/\/doi.org\/10.3390\/ijms26146820","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2025,7,16]]}}}