{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T01:39:22Z","timestamp":1760233162775,"version":"build-2065373602"},"reference-count":56,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2022,12,23]],"date-time":"2022-12-23T00:00:00Z","timestamp":1671753600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"National Funds through FCT\u2014Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia, I.P.","doi-asserted-by":"publisher","award":["UIDB\/04279\/2020"],"award-info":[{"award-number":["UIDB\/04279\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BIAL Foundation","award":["UIDB\/04279\/2020"],"award-info":[{"award-number":["UIDB\/04279\/2020"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Symmetry"],"abstract":"<jats:p>Many scientific publications that affect machine learning have set the basis for pattern recognition and symmetry. In this paper, we revisit the concept of \u201cMind-life continuity\u201d published by the authors, testing the symmetry between cognitive and electrophoretic strata. We opted for machine learning to analyze and understand the total protein profile of neurotypical subjects acquired by capillary electrophoresis. Capillary electrophoresis permits a cost-wise solution but lacks modern proteomic techniques\u2019 discriminative and quantification power. To compensate for this problem, we developed tools for better data visualization and exploration in this work. These tools permitted us to examine better the total protein profile of 92 young adults, from 19 to 25 years old, healthy university students at the University of Lisbon, with no serious, uncontrolled, or chronic diseases affecting the nervous system. As a result, we created a graphical user interface toolbox named MODeLING.Vis, which showed specific expected protein profiles present in saliva in our neurotypical sample. The developed toolbox permitted data exploration and hypothesis testing of the biomolecular data. In conclusion, this analysis offered the data mining of the acquired neuroproteomics data in the molecular weight range from 9.1 to 30 kDa. This molecular weight range, obtained by pattern recognition of our dataset, is characteristic of the small neuroimmune molecules and neuropeptides. Consequently, MODeLING.Vis offers a machine-learning solution for probing into the neurocognitive response.<\/jats:p>","DOI":"10.3390\/sym15010042","type":"journal-article","created":{"date-parts":[[2022,12,27]],"date-time":"2022-12-27T04:45:54Z","timestamp":1672116354000},"page":"42","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MODeLING.Vis: A Graphical User Interface Toolbox Developed for Machine Learning and Pattern Recognition of Biomolecular Data"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5465-470X","authenticated-orcid":false,"given":"Jorge Emanuel","family":"Martins","sequence":"first","affiliation":[{"name":"Laboratory of Mind-Matter Interaction with Therapeutic Intention (LIMMIT), Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal"},{"name":"Universidade Cat\u00f3lica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal"},{"name":"Division of Psychiatric Specialties, Department of Mental Health and Psychiatry, University of Geneva School of Medicine, 1226 Geneva, Switzerland"}]},{"given":"Davide","family":"D\u2019Alimonte","sequence":"additional","affiliation":[{"name":"Aequora, 1600-774 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3180-164X","authenticated-orcid":false,"given":"Joana","family":"Sim\u00f5es","sequence":"additional","affiliation":[{"name":"Laboratory of Mind-Matter Interaction with Therapeutic Intention (LIMMIT), Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal"}]},{"given":"Sara","family":"Sousa","sequence":"additional","affiliation":[{"name":"Universidade Cat\u00f3lica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5458-4978","authenticated-orcid":false,"given":"Eduardo","family":"Esteves","sequence":"additional","affiliation":[{"name":"Universidade Cat\u00f3lica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4604-0780","authenticated-orcid":false,"given":"Nuno","family":"Rosa","sequence":"additional","affiliation":[{"name":"Universidade Cat\u00f3lica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6141-9089","authenticated-orcid":false,"given":"Maria Jos\u00e9","family":"Correia","sequence":"additional","affiliation":[{"name":"Universidade Cat\u00f3lica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal"}]},{"given":"M\u00e1rio","family":"Sim\u00f5es","sequence":"additional","affiliation":[{"name":"Laboratory of Mind-Matter Interaction with Therapeutic Intention (LIMMIT), Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal"}]},{"given":"Marlene","family":"Barros","sequence":"additional","affiliation":[{"name":"Universidade Cat\u00f3lica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,12,23]]},"reference":[{"key":"ref_1","first-page":"74","article-title":"Saliva Print: Sheep saliva electrophoretic protein profile in a bioinformatics approach","volume":"2017","author":"Esteves","year":"2017","journal-title":"Cut. Edge Pathol."},{"key":"ref_2","unstructured":"Saavedra Silva, M., Sousa, S., Silva, A., Martins, J.E., Esteves, E., Fernandes, M., Rosa, N., Correia, M.J., and Barros, M. (2017). Salivary Protein Profile as a Tool for Patient Stratification in Peri-Implantitis, ITI World Symposium."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Henson, R., and Cetto, L. (2005). The MATLAB bioinformatics toolbox. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley.","DOI":"10.1002\/047001153X.g409308"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.3892\/ijo.2013.1803","article-title":"Identification of candidate biomarkers using the Experion\u2122 automated electrophoresis system in serum samples from ovarian cancer patients","volume":"42","author":"Kim","year":"2013","journal-title":"Int. J. Oncol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Thakur, N., and Han, C.Y. (2021). A study of fall detection in assisted living: Identifying and improving the optimal machine learning method. J. Sens. Actuator Netw., 10.","DOI":"10.3390\/jsan10030039"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Pande, S., Kamparia, A., and Gupta, D. (2022). Recommendations for DDOS Threats Using Tableau. Proceedings of Data Analytics and Management, Springer.","DOI":"10.1007\/978-981-16-6285-0_7"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bishop, C.M. (1995). Neural Networks for Pattern Recognition, Oxford University Press.","DOI":"10.1093\/oso\/9780198538493.001.0001"},{"key":"ref_8","unstructured":"Nabney, I. (2002). NETLAB: Algorithms for Pattern Recognition, Springer Science & Business Media."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Kumar, R., Singh, S., and Dubey, V.K. (2015). Bioinformatics Tools to Analyze Proteome and Genome Data. Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches, Springer.","DOI":"10.1007\/978-3-319-17157-9_11"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e01014-17","DOI":"10.1128\/AEM.01014-17","article-title":"Genome-scale model and omics analysis of metabolic capacities of Akkermansia muciniphila reveal a preferential mucin-degrading lifestyle","volume":"83","author":"Ottman","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s12953-018-0134-8","article-title":"Profiling the interactome of protein kinase C \u03b6 by proteomics and bioinformatics","volume":"16","author":"Hou","year":"2018","journal-title":"Proteome Sci."},{"key":"ref_12","unstructured":"Cruz, I., Esteves, E., Fernandes, M., Martins, J.E., Silva, M., Sousa, S., Rosa, N., Correia, M.J., Arrais, J.P., and Barros, M. (2017). Bringing Saliva into Research\u2014SalivaPrint, Algorithms and Personalized Medicine, Science and Technology Foundation. Science 2017."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.jprot.2017.08.011","article-title":"Saliva PRINT Toolkit\u2013Protein profile evaluation and phenotype stratification","volume":"171","author":"Cruz","year":"2018","journal-title":"J. Proteom."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1089\/ars.2009.2810","article-title":"Redox proteomic analysis of carbonylated brain proteins in mild cognitive impairment and early Alzheimer\u2019s disease","volume":"12","author":"Sultana","year":"2010","journal-title":"Antioxid. Redox Signal."},{"key":"ref_15","first-page":"253","article-title":"Symmetry","volume":"28","author":"Weyl","year":"1938","journal-title":"J. Wash. Acad. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100864","DOI":"10.1016\/j.dark.2021.100864","article-title":"Unifying an asymmetric bounce to the dark energy in Chern\u2013Simons F (R) gravity","volume":"33","author":"Odintsov","year":"2021","journal-title":"Phys. Dark Universe"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.pbiomolbio.2017.09.004","article-title":"Mind-life continuity: A qualitative study of conscious experience","volume":"131","author":"Martins","year":"2017","journal-title":"Prog. Biophys. Mol. Biol."},{"key":"ref_18","first-page":"51","article-title":"Happiness as a self state and trait of consciousness: Saliva molecular biomarkers\u2014A brief revision","volume":"8","author":"Martins","year":"2016","journal-title":"Exp. Pathol. Health Sci. Res. Clin. Teach. Soc."},{"key":"ref_19","first-page":"55","article-title":"Self-reflexive consciousness: A model for the experimental use of neurofeedback in sensorial immersion in a center for consciousness knowledge","volume":"8","author":"Martins","year":"2016","journal-title":"Exp. Pathol. Health Sci. Res. Clin. Teach. Soc."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Newell, D.B., and Tiesinga, E. (2019). The International System of Units (SI), NIST Special Publication.","DOI":"10.6028\/NIST.SP.330-2019"},{"key":"ref_21","unstructured":"Helmenstine, A.M. (2014). Molecular Weight Definition, Tennessee at Knoxville."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4918","DOI":"10.1158\/0008-5472.CAN-08-4806","article-title":"Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry","volume":"69","author":"Hirayama","year":"2009","journal-title":"Cancer Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"9890","DOI":"10.1073\/pnas.0900617106","article-title":"Measurement of internal body time by blood metabolomics","volume":"106","author":"Minami","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"16442","DOI":"10.1074\/jbc.M109.002089","article-title":"Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli","volume":"284","author":"Saito","year":"2009","journal-title":"J. Biol. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1021\/ac051437y","article-title":"XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification","volume":"78","author":"Smith","year":"2006","journal-title":"Anal. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Baran, R., Kochi, H., Saito, N., Suematsu, M., Soga, T., Nishioka, T., and Tomita, M. (2006). Math DAMP: A package for differential analysis of metabolite profiles. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-530"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"16768","DOI":"10.1074\/jbc.M601876200","article-title":"Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption","volume":"281","author":"Soga","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2446","DOI":"10.1021\/ac0354701","article-title":"An operator-independent approach to mass spectral peak identification and integration","volume":"76","author":"Wallace","year":"2004","journal-title":"Anal. Chem."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/S0378-4347(01)00527-8","article-title":"Pherogram normalization in capillary electrophoresis and micellar electrokinetic chromatography analysis in cases of sample matrix-induced migration time shifts","volume":"770","author":"Reijenga","year":"2002","journal-title":"J. Chromatogr. B"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.7717\/peerj-cs.1","article-title":"Achieving human and machine accessibility of cited data in scholarly publications","volume":"1","author":"Starr","year":"2015","journal-title":"PeerJ Comput. Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1038\/nbt1406","article-title":"What is the expectation-maximization algorithm?","volume":"26","author":"Do","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1186\/1471-2377-9-S1-S3","article-title":"Characteristics of compounds that cross the blood-brain barrier","volume":"Volume 9","author":"Banks","year":"2009","journal-title":"BMC Neurology"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/j.drudis.2006.10.013","article-title":"Blood-brain barrier delivery","volume":"12","author":"Pardridge","year":"2007","journal-title":"Drug Discov. Today"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/bs.apha.2014.06.004","article-title":"Delivery of therapeutic peptides and proteins to the CNS","volume":"Volume 71","author":"Salameh","year":"2014","journal-title":"Advances in Pharmacology"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.peptides.2015.03.010","article-title":"Peptides and the blood-brain barrier","volume":"72","author":"Banks","year":"2015","journal-title":"Peptides"},{"key":"ref_37","first-page":"143","article-title":"The blood-brain barrier in neuroinflammatory diseases","volume":"49","author":"Kuiper","year":"1997","journal-title":"Pharmacol. Rev."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1124\/pr.117.014647","article-title":"Neuroimmune Axes of the Blood-Brain Barriers and Blood-Brain Interfaces: Bases for Physiological Regulation, Disease States, and Pharmacological Interventions","volume":"70","author":"Erickson","year":"2018","journal-title":"Pharmacol. Rev."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1750-1172-3-16","article-title":"Hereditary alpha-1-antitrypsin deficiency and its clinical consequences","volume":"3","author":"Fregonese","year":"2008","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"8202","DOI":"10.18632\/oncotarget.1159","article-title":"Tissue-specific isoform switch and DNA hypomethylation of the pyruvate kinase PKM gene in human cancers","volume":"5","author":"Desai","year":"2014","journal-title":"Oncotarget"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1163","DOI":"10.2215\/CJN.10441015","article-title":"Biomarkers of cardiovascular disease and mortality risk in patients with advanced CKD","volume":"11","author":"Sun","year":"2016","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.archoralbio.2011.12.010","article-title":"From the salivary proteome to the OralOme: Comprehensive molecular oral biology","volume":"57","author":"Rosa","year":"2012","journal-title":"Arch. Oral Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1016\/j.archoralbio.2012.12.012","article-title":"OralCard: A bioinformatics tool for the study of oral proteome","volume":"58","author":"Arrais","year":"2013","journal-title":"Arch. Oral Biol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/2045-8118-10-15","article-title":"Measurement of cystatin C functional activity in the cerebrospinal fluid of amyotrophic lateral sclerosis and control subjects","volume":"10","author":"Wilson","year":"2013","journal-title":"Fluids Barriers CNS"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.imlet.2014.08.003","article-title":"Involvement of IL-6 and IL-1 receptor antagonist on intellectual disability","volume":"162","author":"Aureli","year":"2014","journal-title":"Immunol. Lett."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Suzumura, A., and Ikenaka, K. (2013). Neuron-Glia Interaction in Neuroinflammation, Springer Science & Business Media.","DOI":"10.1007\/978-1-4614-8313-7"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"bav038","DOI":"10.1093\/database\/bav038","article-title":"NeuroPep: A comprehensive resource of neuropeptides","volume":"2015","author":"Wang","year":"2015","journal-title":"Database"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s13229-016-0068-x","article-title":"From molecules to neural morphology: Understanding neuroinflammation in autism spectrum condition","volume":"7","author":"Young","year":"2016","journal-title":"Mol. Autism"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.ijdevneu.2004.05.006","article-title":"Neuropeptides and the social brain: Potential rodent models of autism","volume":"23","author":"Lim","year":"2005","journal-title":"Int. J. Dev. Neurosci."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Hip\u00f3lito, I., Gon\u00e7alves, J., and Pereira, J. (2018). A \u201cSecond-Person\u201d Model to Anomalous Social Cognition. Schizophrenia and Common Sense, Studies in Brain and Mind; Springer.","DOI":"10.1007\/978-3-319-73993-9"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"4192","DOI":"10.1093\/bioinformatics\/bti676","article-title":"MILVA: An interactive tool for the exploration of multidimensional microarray data","volume":"21","author":"Lowe","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_52","first-page":"1","article-title":"Research objects: Towards exchange and reuse of digital knowledge","volume":"1","author":"Bechhofer","year":"2010","journal-title":"Nat. Preced."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: A hub for protein information","volume":"43","author":"Consortium","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"D41","DOI":"10.1093\/nar\/gkx1094","article-title":"GenBank","volume":"46","author":"Benson","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1038\/nsb1203-980","article-title":"Announcing the worldwide protein data bank","volume":"10","author":"Berman","year":"2003","journal-title":"Nat. Struct. Mol. Biol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Martins, J.E., Sim\u00f5es, J., Barros, M., and Sim\u00f5es, M. (2022). Pre-Molecular Assessment of Self-Processes in Neurotypical Subjects Using a Single Cognitive Behavioral Intervention Evoking Autobiographical Memory. Behav. Sci., 12.","DOI":"10.3390\/bs12100381"}],"container-title":["Symmetry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-8994\/15\/1\/42\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:49:21Z","timestamp":1760147361000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-8994\/15\/1\/42"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,23]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1]]}},"alternative-id":["sym15010042"],"URL":"https:\/\/doi.org\/10.3390\/sym15010042","relation":{},"ISSN":["2073-8994"],"issn-type":[{"type":"electronic","value":"2073-8994"}],"subject":[],"published":{"date-parts":[[2022,12,23]]}}}