Scientific publications

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Thanks to compatibility with a rich tradition of algorithms written in Pascal, generation of fast native code, and extensive cross-platform availability Free Pascal is an ideal basis for scientific applications. This may be the main reason why a plethora of research projects uses Lazarus and FPC.

This is a (probably always incomplete) list of research papers, abstracts, reports and other scientific publications about projects that employed Lazarus, Free Pascal or Pascal Script for computational science.

The collection presented here is restricted to publications in English. Versions of this article in other languages are primarily intended for publications in the respective locale.

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Papers and book sections

Mathematics and Statistics

  1. Aleksander Mendyk, Renata Jachowicz, Kamil Fijorek, Przemysław Dorożyński, Piotr Kulinowski, and Sebastian Polak. KinetDS: An Open Source Software for Dissolution Test Data Analysis. Dissolution Technologies. 2012. doi https://doi.org/10.14227/dt190112p6.
  2. Roberto D. Pascual-Marqui, Dietrich Lehmann, Kieko Kochi, Toshihiko Kinoshita, Naoto Yamada. A measure of association between vectors based on "similarity covariance". 2013. arXiv:1301.4291.
  3. Spekken M., Anselmi A.A., Molin J.P. (2013) A simple method for filtering spatial data. In: Stafford J.V. (eds) Precision agriculture ’13. Wageningen Academic Publishers, Wageningen. doi 10.3920/978-90-8686-778-3_30.
  4. C. P. E. Agbachi "Optimisation of Least Squares Algorithm: A Study of Frame Based Programming Techniques in Horizontal Networks", International Journal of Mathematics Trends and Technology (IJMTT). V37(3):190-198 September 2016. ISSN:2231-5373. doi 10.14445/22315373/IJMTT-V37P526
  5. Knežo D., Zajac J., Michalik P. (2019) Critical Values of Some Probability Distributions and Standard Numerical Methods. In: Cagáňová D., Balog M., Knapčíková L., Soviar J., Mezarcıöz S. (eds) Smart Technology Trends in Industrial and Business Management. EAI/Springer Innovations in Communication and Computing. Springer, Cham. doi 10.1007/978-3-319-76998-1_5.
  6. Jäntschi, L. Detecting Extreme Values with Order Statistics in Samples from Continuous Distributions. Mathematics 2020, 8, 216. doi 10.3390/math8020216.

Physics

  1. Ovidio Peña-Rodríguez, Pedro Pablo González Pérez, Umapada Pal, "MieLab: A Software Tool to Perform Calculations on the Scattering of Electromagnetic Waves by Multilayered Spheres", International Journal of Spectroscopy, vol. 2011, Article ID 583743, 10 pages, 2011. doi 10.1155/2011/583743
  2. Daniluk, A. (2011). Cooperative and competitive concurrency in scientific computing. A full open-source upgrade of the program for dynamical calculations of RHEED intensity oscillations. Computer Physics Communications, 182(6), 1389–1390. doi 10.1016/j.cpc.2011.02.014
  3. Janik M, Łoskiewicz J, Tokonami S, Kozak K, Mazur J, Ishikawa T. Determination of the minimum measurement time for estimating long-term mean radon concentration. Radiat Prot Dosimetry. 2012 Nov;152(1-3):168-73. doi: 10.1093/rpd/ncs217. Epub 2012 Aug 23. doi 10.1093/rpd/ncs217. PMID 22923240.
  4. Gurgel, W.P., Gomes, L.M., Ferreira, F.C.L., & Gester, R.M.. (2015). Cálculo de velocidades em acidentes de trânsito: Um software para investigação em física forense. Revista Brasileira de Ensino de Física, 37(4), 4305-1-4305-10. doi 10.1590/S1806-11173741966.
  5. Tanaka, J. S.; O., Paiva-Santos. C.; Antonio, S. G.; "JST-DRX: A SOFTWARE TO GENERATE X-RAY POWDER DIFFRACTOGRAMS FROM PATENTS DATA", p. 42 . In: Proceedings of the International Symposium on Crystallography [Blucher Physics Proceedings, v.1, n.3]. São Paulo: Blucher, 2015. doi 10.5151/phypro-sic100-042.
  6. Sergey Prostov, Evgeniy Shabanov. Diagnostics of Oil Pollution Zones by Electro-Physical Method. E3S Web of Conferences 21, 02007 (2017) doi 10.1051/e3sconf/20172102007.
  7. Venkat Chandrasekhara. A microchip microcontroller-based transducer controller for non-contact scanning probe microscopy with phase-locked loop, amplitude, and Q control. Rev. Sci. Instrum. 2020 91, 023705; doi 10.1063/1.5131657.
  8. Šmit, Z. (2023). XANTHO – A simple basic program for fitting X-ray spectra. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms. 540. 19-23 doi 10.1016/j.nimb.2023.04.006

Chemistry and Chemoinformatics

  1. Ruggiu, F., Marcou, G., Varnek, A. and Horvath, D. (2010), ISIDA Property‐Labelled Fragment Descriptors. Mol. Inf., 29: 855-868. doi 10.1002/minf.201000099
  2. Saeb MR, Rezaee B, Shadman A, Formela K, Ahmadi Z, Hemmati F, Kermaniyan TS, Mohammadi Y. Controlled grafting of vinylic monomers on polyolefins: a robust mathematical modeling approach. Des Monomers Polym. 2016 Oct 25;20(1):250-268. doi 10.1080/15685551.2016.1239166. PMID 29491797; PMCID PMC5812188.
  3. Kostanyan AE, Shishilov ON. An easy-to-use calculating machine to simulate steady state and non-steady-state preparative separations by multiple dual mode counter-current chromatography with semi-continuous loading of feed mixtures. J Chromatogr A. 2018 Jun 1;1552:92-98. doi 10.1016/j.chroma.2018.04.010. Epub 2018 Apr 10. PMID 29673766.
  4. Kune C, Haler JRN, Far J, De Pauw E. Effectiveness and Limitations of Computational Chemistry and Mass Spectrometry in the Rational Design of Target-specific Shift Reagents for Ion Mobility Spectrometry. Chemphyschem. 2018 Nov 5;19(21):2921-2930. doi 10.1002/cphc.201800555. Epub 2018 Aug 21. PMID 30071143.
  5. Nagy, L.; Kuki, Á.; Nagy, T.; Vadkerti, B.; Erdélyi, Z.; Kárpáti, L.; Zsuga, M.; Kéki, S. Encoding Information into Polyethylene Glycol Using an Alcohol-Isocyanate “Click” Reaction. Int. J. Mol. Sci. 2020, 21, 1318. doi 10.3390/ijms21041318
  6. Li, R.I., Rizaeva, Y.N., Psarev, D.N. et al. Calculation of Structural and Operational Parameters of a Facility for Infrared Heating of Base Parts during Restoration with a Polymer Material. Polym. Sci. Ser. D 13, 387–390 (2020). doi 10.1134/S1995421220040139.
  7. Guillén, E., Ferrer-Roselló, M., Agrisuelas, J., García-Jareño, J. J., & Vicente, F. (2021). Digital video-electrochemistry (DVEC) to assess electrochromic materials in the frequency domain: RGB colorimetry impedance spectroscopy. Electrochimica Acta, 366, 137340. doi 10.1016/j.electacta.2020.137340.

Astronomy

  1. Zack M., Gannon A., McRoberts J. (2018) Software and Apps to Help the Suburban Astronomer. In: Stargazing Under Suburban Skies. The Patrick Moore Practical Astronomy Series. Springer, Cham. doi 10.1007/978-3-319-90116-9_7.

Meteorology and Athmospheric Sciences

  1. Bezanilla, A., Krüger, A., Stremme, W., & Grutter, M. (2014). Solar absorption infrared spectroscopic measurements over Mexico City: Methane enhancements. Atmósfera, 27(2), 173–183. doi 10.1016/S0187-6236(14)71108-7.
  2. V. M. Vashchenko, I. B. Korduba, Ye. A. Loza, Zh. I. Patlashenko, O. O. Bannikov, Yu. M. Kryzska. Tornado statistics in Ukraine based on new data. Geofizicheskiy Zhurnal. 2018 40{3): 199-213. doi 10.24028/gzh.0203-3100.v40i3.2018.137206.
  3. V. Vashchenko, Ye. Loza, Zh. Patlashenko, O. Bannikov. Reliability of Tornado Ecological Hazard Estimate in Ukraine and Europe. EKB jurnal 2019. doi 10.30929/2073-5057.2019.1.19-22.

Geography and Geoinformatics

  1. Straka M. Design of a Computer-Aided Location Expert System Based on a Mathematical Approach. Mathematics. 2021; 9(9):1052. doi 10.3390/math9091052

Geology

  1. Fiener P, Dlugoß V, van Ooost K (2015). Erosion-induced carbon redistribution, burial and mineralisation — Is the episodic nature of erosion processes important? CATENA, 133, 282–292. doi 10.1016/j.catena.2015.05.027
  2. Sergey Kotov and Heiko Paelike. MyDTW – Dynamic Time Warping program for stratigraphical time series. Geophysical Research Abstracts. 19, EGU2017-2157, 2017.
  3. Sergey Prostov and Evgeniy Shabanov. Geological-and-Geophysical Monitoring of Electrochemical Cleaning of Soil from Petroleum Pollution. E3S Web Conf., 41 (2018) 02002 doi 10.1051/e3sconf/20184102002.
  4. Sergey Prostov and Evgeniy Shabanov. Substantiation of the Method of Operational Monitoring of Soil Contamination and Oil Decontamination Processes. E3S Web Conf. 105 02013 (2019) doi 10.1051/e3sconf/201910502013

General Cybernetics

  1. Andres B., Poler R., Rosas J., Camarinha-Matos L. (2016) A Decision-Support Tool to Deal with the Strategies Alignment Process in Collaborative Networks. In: Camarinha-Matos L.M., Falcão A.J., Vafaei N., Najdi S. (eds) Technological Innovation for Cyber-Physical Systems. DoCEIS 2016. IFIP Advances in Information and Communication Technology, vol 470. Springer, Cham. doi 10.1007/978-3-319-31165-4_1.
  2. Andres B, Poler R. A decision support system for the collaborative selection of strategies in enterprise networks. Decision Support Systems 2016 91: 113-23. doi 10.1016/j.dss.2016.08.005
  3. Sun, H.-M., & Sheu, R.-L. (2019). Minimum variance allocation among constrained intervals. Journal of Global Optimization, 74(1), 21–44. doi 10.1007/s10898-019-00748-3.

Computer Science / Informatics

  1. Daniluk, A. (2011). Cooperative and competitive concurrency in scientific computing. A full open-source upgrade of the program for dynamical calculations of RHEED intensity oscillations. Computer Physics Communications, 182(6), 1389–1390. doi 10.1016/j.cpc.2011.02.014 (Accompanying source code available via doi 10.17632/tdxt7djz4w.1).
  2. S. Ribić and M. Beganović, "Cross compilation under Lazarus IDE," 2013 21st Telecommunications Forum Telfor (TELFOR), Belgrade, 2013, pp. 1007-1010, doi 10.1109/TELFOR.2013.6716402.
  3. C. P. E. Agbachi "Design and Application of Concurrent Double Key Survey Data Structures". International Journal of Computer Trends and Technology (IJCTT) V36(3):119-126, June 2016. ISSN:2231-2803. www.ijcttjournal.org. Seventh Sense Research Group. doi 10.14445/22312803/IJCTT-V36P121.
  4. Rui Pereira, Marco Couto, Francisco Ribeiro, Rui Rua, Jácome Cunha, João Paulo Fernandes, and João Saraiva. 2017. Energy efficiency across programming languages: how do energy, time, and memory relate? In Proceedings of the 10th ACM SIGPLAN International Conference on Software Language Engineering (SLE 2017). Association for Computing Machinery, New York, NY, USA, 256–267. doi 10.1145/3136014.3136031.
  5. Lvov M., Shishko L., Chernenko I., & Kozlovsky E. (2020). VISUAL SUPPORT OF THE TOPIC "ALGORITHMS FOR SORTING AND SEARCHING" COURSE OF BASIC PROGRAMMING . Journal of Information Technologies in Education (ITE), (44), 7-17. doi 10.14308/ite000721

Life Sciences

Biochemical Methods

  1. Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL. PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinformatics. 2009 Aug 15;25(16):2085-7. doi 10.1093/bioinformatics/btp345. Epub 2009 Jun 3. PMID 19497931; PMCID PMC2723000.
  2. Guan DG, Liao JY, Qu ZH, Zhang Y, Qu LH. mirExplorer: detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features. RNA Biol. 2011 Sep-Oct;8(5):922-34. doi 10.4161/rna.8.5.16026. Epub 2011 Sep 1. PMID 21881406.

Bioinformatics

  1. Duplij V, Duplij S. Triander: A new program for visual analysis of nucleotide sequences. 2015. doi 10.13140/RG.2.1.2256.3360. arXiv:1504.04866
  2. Guillermin Agüero-Chapin, Reinaldo Molina-Ruiz, Gisselle Pérez- Machado, Vitor Vasconcelos, Zenaida Rodríguez-Negrin and Agostinho Antunes (March 9th 2016). TI2BioP — Topological Indices to BioPolymers. A Graphical-Numerical Approach for Bioinformatics, Recent Advances in Biopolymers, Farzana Khan Perveen, IntechOpen, doi 10.5772/61887.
  3. Tinker NA, Bekele WA, Hattori J. Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis. G3 (Bethesda). 2016 Apr 7;6(4):857-63. doi 10.1534/g3.115.024596. PMID 26818073; PMCID PMC4825656.
  4. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018 Jun 1;35(6):1547-1549. doi 10.1093/molbev/msy096. PMID 29722887; PMCID PMC5967553.
  5. Ihsan Fazal M, Kacprzyk R, Timson DJ. In silico analysis of the effects of disease-associated mutations of β-hexosaminidase A in Tay-Sachs disease. J Genet. 2020;99:42. doi https://doi.org/10.1007/s12041-020-01208-8. PMID 32529985.

Biophysics

  1. Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL. Integrative NMR for biomolecular research. J Biomol NMR. 2016 Apr;64(4):307-32. doi 10.1007/s10858-016-0029-x. Epub 2016 Mar 29. PMID 27023095; PMCID PMC4861749.

Ecology

  1. Sergio Canovas, Carlos E. Cugnasca. Applying Model Driven Engineering to Develop a Bee Information System. 2015.
  2. Milica Lakovic, Oliver Mitesser, Thomas Hovestadt. Mating timing, dispersal and local adaptation in patchy environments. OIKOS 2017. doi 10.1111/oik.04369.
  3. Adams ES, Plowes NJR. Self-organizing conflicts: Group assessment and the spatio-temporal dynamics of ant territory battles. Behav Processes. 2019 May;162:119-129. doi 10.1016/j.beproc.2019.01.009. Epub 2019 Feb 10. PMID 30753885.
  4. Edinaldo Nelson dos Santos-Silva, Raize Castro Mendes, Mauro José Cavalcanti. BioCalc: A software tool for the calculation of biovolume of phytoplankton samples. Tropical Diversity 2019; 1(1): 26-31.
  5. Edward B. Rastetter and Bonnie L. Kwiatkowski. An approach to modeling resource optimization for substitutable and interdependent resources. Ecological Modelling 2020 425: 109033. doi 10.1016/j.ecolmodel.2020.109033.
  6. Rastetter, E.B., Kling, G.W., Shaver, G.R. et al. Ecosystem Recovery from Disturbance is Constrained by N Cycle Openness, Vegetation-Soil N Distribution, Form of N Losses, and the Balance Between Vegetation and Soil-Microbial Processes. Ecosystems (2020). doi 10.1007/s10021-020-00542-3.
  7. Pold, G., Kwiatkowski, B. L., Rastetter, E. B., & Sistla, S. A. (2022). Sporadic P limitation constrains microbial growth and facilitates SOM accumulation in the stoichiometrically coupled, acclimating microbe–plant–soil model. Soil Biology and Biochemistry, 165, 108489. doi 10.1016/j.soilbio.2021.108489
  8. Rastetter EB, Kwiatkowski BL, Kicklighter DW, Barker Plotkin A, Genet H, Nippert JB, O'Keefe K, Perakis SS, Porder S, Roley SS, Ruess RW, Thompson JR, Wieder WR, Wilcox K, Yanai RD. N and P constrain C in ecosystems under climate change: Role of nutrient redistribution, accumulation, and stoichiometry. Ecol Appl. 2022 Dec;32(8):e2684. doi 10.1002/eap.2684. Epub 2022 Jul 25. PMID 35633204.
Source code available from doi 10.5281/zenodo.6502582

Electrophysiology

  1. Sawahata, H., Toda, H., Suzuki, T., & Hasegawa, I. (2011). Time-frequency domain analyses of the multi-channel electrocorticogram in the primary visual cortex of the hooded rat. Acta Medica et Biologica, 58(2). Archived PDF version available.

Genetics and Genetic Engineering

  1. Sun D, Ostermaier MK, Heydenreich FM, Mayer D, Jaussi R, Standfuss J, Veprintsev DB. AAscan, PCRdesign and MutantChecker: a suite of programs for primer design and sequence analysis for high-throughput scanning mutagenesis. PLoS One. 2013 Oct 30;8(10):e78878. doi 10.1371/journal.pone.0078878. PMID 24205336; PMCID PMC3813622.
  2. Heydenreich FM, Miljuš T, Jaussi R, Benoit R, Milić D, Veprintsev DB. High-throughput mutagenesis using a two-fragment PCR approach. Sci Rep. 2017 Jul 28;7(1):6787. doi 10.1038/s41598-017-07010-4. PMID 28754896; PMCID PMC5533798.
  3. Yarus M. Evolution of the Standard Genetic Code. J Mol Evol. 2021 Jan 24. doi 10.1007/s00239-020-09983-9. PMID 33486549.
  4. Tinker NA, Wight CP, Bekele WA, Yan W, Jellen EN, Renhuldt NT, Sirijovski N, Lux T, Spannagl M, Mascher M. Genome analysis in Avena sativa reveals hidden breeding barriers and opportunities for oat improvement. Commun Biol. 2022 May 18;5(1):474. doi 10.1038/s42003-022-03256-5. PMID 35585176.
  5. Yarus M. Ordering events in a developing genetic code. RNA Biol. 2024 Jan;21(1):1-8. doi: 10.1080/15476286.2023.2299615. Epub 2024 Jan 3. PMID: 38169326; PMCID: PMC10766418.

Microbiology

  1. Šimkus R, Meškienė R, Aučynaitė A, Ledas Ž, Baronas R, Meškys R. Phoretic interactions and oscillations in active suspensions of growing Escherichia coli. R Soc Open Sci. 2018 May 30;5(5):180008. doi 10.1098/rsos.180008. PMID 29892439; PMCID PMC5990789.
  2. Pold, G., Kwiatkowski, B. L., Rastetter, E. B., & Sistla, S. A. (2022). Sporadic P limitation constrains microbial growth and facilitates SOM accumulation in the stoichiometrically coupled, acclimating microbe–plant–soil model. Soil Biology and Biochemistry, 165, 108489. doi 10.1016/j.soilbio.2021.108489
  3. Nilsson AS. Cocktail, a Computer Program for Modelling Bacteriophage Infection Kinetics. Viruses. 2022 Nov 9;14(11):2483. doi 10.3390/v14112483. PMID 36366581; PMCID PMC9695944.

Neurosciences

  1. Toda H, Suzuki T, Sawahata H, Majima K, Kamitani Y, Hasegawa I. Simultaneous recording of ECoG and intracortical neuronal activity using a flexible multichannel electrode-mesh in visual cortex. Neuroimage. 2011 Jan 1;54(1):203-12. doi 10.1016/j.neuroimage.2010.08.003. Epub 2010 Aug 7. PMID 20696254.
  2. Pascual-Marqui RD, Biscay RJ, Bosch-Bayard J, Lehmann D, Kochi K, Kinoshita T, Yamada N, Sadato N. Assessing direct paths of intracortical causal information flow of oscillatory activity with the isolated effective coherence (iCoh). Front Hum Neurosci. 2014 Jun 20;8:448. doi 10.3389/fnhum.2014.00448. PMID 24999323; PMCID PMC4064566.
  3. Evans L, Champion RA, Rushton SK, Montaldi D, Warren PA. Detection of scene-relative object movement and optic flow parsing across the adult lifespan. J Vis. 2020 Sep 2;20(9):12. doi 10.1167/jov.20.9.12. PMID 32945848; PMCID PMC7509779.

Systems and Theoretical Biology

  1. Michael Yarus. Evolution of the standard genetic code. bioRxiv 2020. doi 10.1101/2020.02.20.958546.
  2. Rubtsov, A.S. Computer Simulation Model of a Hybrid Zone: Assortative Mating in the Role of Selection against Hybrids. Biol Bull Rev 10, 186–192 (2020). doi 10.1134/S2079086420030068
  3. Yarus M. Crick Wobble and Superwobble in Standard Genetic Code Evolution. J Mol Evol. 2021 Feb;89(1-2):50-61. doi 10.1007/s00239-020-09985-7. PMID 33409542; PMCID PMC7884361.
  4. Dietrich JW. A Methodology for Vertical Translation Between Molecular and Organismal Level in Biological Feedback Loops. bioRxiv 2021.09.20.461028; doi https://doi.org/10.1101/2021.09.20.461028.
  5. Yarus M. A crescendo of competent coding (c3) contains the Standard Genetic Code. RNA. 2022 Oct;28(10):1337-1347. doi 10.1261/rna.079275.122. PMID 35868841; PMCID PMC9479743.
  6. Dietrich JW, Siegmar N, Hojjati JR, Gardt O, Boehm BO. CyberUnits Bricks: An Implementation Study of a Class Library for Simulating Nonlinear Biological Feedback Loops. ADCAIJ: Advances in Distributed Computing and Artificial Intelligence Journal, 2024 Aug 27;13(1):e31762.doi 10.14201/adcaij.31762

Zoology

  1. Walter, T., Degen, J., Pfeiffer, K. et al. A new innovative real-time tracking method for flying insects applicable under natural conditions. BMC Zool 6, 35 (2021). doi 10.1186/s40850-021-00097-3

Medicine

Endocrinology

  1. Dietrich JW, Landgrafe G, Fotiadou EH. TSH and Thyrotropic Agonists: Key Actors in Thyroid Homeostasis. J Thyroid Res. 2012;2012:351864. doi 10.1155/2012/351864. Epub 2012 Dec 30. PMID 23365787; PMCID PMC3544290.
  2. Dietrich JW, Landgrafe-Mende G, Wiora E, Chatzitomaris A, Klein HH, Midgley JE, Hoermann R. Calculated Parameters of Thyroid Homeostasis: Emerging Tools for Differential Diagnosis and Clinical Research. Front Endocrinol (Lausanne). 2016 Jun 9;7:57. doi 10.3389/fendo.2016.00057. PMID 27375554; PMCID PMC4899439.
  3. Chatzitomaris A, Hoermann R, Midgley JE, Hering S, Urban A, Dietrich B, Abood A, Klein HH, Dietrich JW. Thyroid Allostasis-Adaptive Responses of Thyrotropic Feedback Control to Conditions of Strain, Stress, and Developmental Programming. Front Endocrinol (Lausanne). 2017 Jul 20;8:163. doi 10.3389/fendo.2017.00163. PMID 28775711; PMCID PMC5517413.
  4. Dietrich JW, Dasgupta R, Anoop S, Jebasingh F, Kurian ME, Inbakumari M, Boehm BO, Thomas N. SPINA Carb: a simple mathematical model supporting fast in-vivo estimation of insulin sensitivity and beta cell function. Sci Rep. 2022 Oct 21;12(1):17659. doi: 10.1038/s41598-022-22531-3. PMID 36271244; PMCID PMC9587026.
  5. Dietrich JW, Abood A, Dasgupta R, Anoop S, Jebasingh FK, Spurgeon R, Thomas N, Boehm BO. A novel simple disposition index (SPINA-DI) from fasting insulin and glucose concentration as a robust measure of carbohydrate homeostasis. J Diabetes. 2024 Jan 2. doi 10.1111/1753-0407.13525. PMID 38169110.

Infectious Diseases

  1. Fuentes-Pananá EM, Larios-Serrato V, Méndez-Tenorio A, Morales-Sánchez A, Arias CF, Torres J. Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples. Mem Inst Oswaldo Cruz. 2016 Mar;111(3):200-8. doi 10.1590/0074-02760150405. Epub 2016 Feb 19. PMID 26910355; PMCID PMC4804503.

Neurology

  1. Warren PA, Rushton SK, Foulkes AJ. Does optic flow parsing depend on prior estimation of heading? J Vis. 2012 Oct 11;12(11):8. doi: 10.1167/12.11.8. PMID 23064244; PMCID PMC3826327.
  2. Sato JR, Basilio R, Paiva FF, Garrido GJ, Bramati IE, Bado P, Tovar-Moll F, Zahn R, Moll J. Real-time fMRI pattern decoding and neurofeedback using FRIEND: an FSL-integrated BCI toolbox. PLoS One. 2013 Dec 2;8(12):e81658. doi 10.1371/journal.pone.0081658. PMID 24312569; PMCID PMC3847114.
  3. Foulkes AJ, Rushton SK, Warren PA. Heading recovery from optic flow: comparing performance of humans and computational models. Front Behav Neurosci. 2013 Jun 21;7:53. doi 10.3389/fnbeh.2013.00053. PMID 23801946; PMCID PMC3689323.
  4. Foulkes AJ, Rushton SK, Warren PA. Flow parsing and heading perception show similar dependence on quality and quantity of optic flow. Front Behav Neurosci. 2013 Jun 19;7:49. doi 10.3389/fnbeh.2013.00049. PMID 23801945; PMCID PMC3685810.
  5. Pascual-Marqui RD, Biscay RJ, Bosch-Bayard J, Lehmann D, Kochi K, Kinoshita T, Yamada N, Sadato N. Assessing direct paths of intracortical causal information flow of oscillatory activity with the isolated effective coherence (iCoh). Front Hum Neurosci. 2014 Jun 20;8:448. doi 10.3389/fnhum.2014.00448. PMID 24999323; PMCID PMC4064566.

Ophthalmology

  1. Warren PA, Rushton SK, Foulkes AJ. Does optic flow parsing depend on prior estimation of heading? J Vis. 2012 Oct 11;12(11):8. doi: 10.1167/12.11.8. PMID 23064244; PMCID PMC3826327.

Pharmacology

  1. Aleksander Mendyk, Renata Jachowicz, Kamil Fijorek, Przemysław Dorożyński, Piotr Kulinowski, and Sebastian Polak. KinetDS: An Open Source Software for Dissolution Test Data Analysis. Dissolution Technologies. 2012. doi https://doi.org/10.14227/dt190112p6.
  2. Mendyk, A., Pacławski, A., Szlek, J., & Jachowicz, R. (2013). PhEq_bootstrap: open-source software for the simulation of f2 distribution in cases of large variability in dissolution profiles. Dissolution Technology, 20(1), 13-17. doi 10.14227/DT200113P13.
  3. Nevozhay D. Cheburator software for automatically calculating drug inhibitory concentrations from in vitro screening assays. PLoS One. 2014 Sep 3;9(9):e106186. doi 10.1371/journal.pone.0106186. PMID 25184280; PMCID PMC4153570.
  4. Mendyk A, Güres S, Jachowicz R, Szlęk J, Polak S, Wiśniowska B, Kleinebudde P. From Heuristic to Mathematical Modeling of Drugs Dissolution Profiles: Application of Artificial Neural Networks and Genetic Programming. Comput Math Methods Med. 2015;2015:863874. doi 10.1155/2015/863874. Epub 2015 May 26. PMID 26101544; PMCID PMC4460208.
  5. Arampatzis AS, Giannakoula K, Kontogiannopoulos KN, Theodoridis K, Aggelidou E, Rat A, Kampasakali E, Willems A, Christofilos D, Kritis A, Papageorgiou VP, Tsivintzelis I, Assimopoulou AN. Novel electrospun poly-hydroxybutyrate scaffolds as carriers for the wound healing agents alkannins and shikonins. Regen Biomater. 2021 Jun 10;8(3):rbab011. doi 10.1093/rb/rbab011. PMID: 34211727; PMCID PMC8240617.

Radiology

  1. Sato JR, Basilio R, Paiva FF, Garrido GJ, Bramati IE, Bado P, Tovar-Moll F, Zahn R, Moll J. Real-time fMRI pattern decoding and neurofeedback using FRIEND: an FSL-integrated BCI toolbox. PLoS One. 2013 Dec 2;8(12):e81658. doi 10.1371/journal.pone.0081658. PMID 24312569; PMCID PMC3847114.
  2. Tol JP, Dahele M, Peltola J, Nord J, Slotman BJ, Verbakel WF. Automatic interactive optimization for volumetric modulated arc therapy planning. Radiat Oncol. 2015 Apr 1;10:75. doi 10.1186/s13014-015-0388-6. PMID 25885689; PMCID PMC4394415.

Psychology

  1. Hoppe K, Küper K, Wascher E. Sequential Modulations in a Combined Horizontal and Vertical Simon Task: Is There ERP Evidence for Feature Integration Effects? Front Psychol. 2017 Jun 30;8:1094. doi 10.3389/fpsyg.2017.01094. PMID 28713305; PMCID PMC5492773.
  2. Zhao, F., Gaschler, R., Schneider, L., Thomaschke, R., Röttger, E., & Haider, H. (2019). Sequence Knowledge on When and What Supports Dual-Tasking. Journal of Cognition, 2(1), 18. doi 10.5334/joc.76.
  3. Alexandrowicz RW. The diffusion model visualizer: an interactive tool to understand the diffusion model parameters. Psychol Res. 2020 Jun;84(4):1157-1165. doi 10.1007/s00426-018-1112-6. Epub 2018 Oct 25. PMID 30361811; PMCID PMC7239816.
  4. Picanço CR, Tonneau F. A low-cost platform for eye-tracking research: Using Pupil© in behavior analysis. J Exp Anal Behav. 2018 Sep;110(2):157-170. doi 10.1002/jeab.448. Epub 2018 Jun 21. PMID 29926919.
  5. Zickerick B, Thönes S, Kobald SO, Wascher E, Schneider D, Küper K. Differential Effects of Interruptions and Distractions on Working Memory Processes in an ERP Study. Front Hum Neurosci. 2020 Mar 16;14:84. doi 10.3389/fnhum.2020.00084. PMID 32231527; PMCID PMC7088125.
  6. Zhao F, Gaschler R, Kneschke A, Radler S, Gausmann M, Duttine C, Haider H. Origami folding: Taxing resources necessary for the acquisition of sequential skills. PLoS One. 2020 Oct 5;15(10):e0240226. doi 10.1371/journal.pone.0240226. PMID 33017450; PMCID PMC7535859.
  7. Röttger E, Zhao F, Gaschler R, Haider H. Why Does Dual-Tasking Hamper Implicit Sequence Learning? J Cogn. 2021 Jan 7;4(1):1. doi 10.5334/joc.136. PMID 33506167; PMCID PMC7792471.
  8. Zickerick, B, Kobald, SO, Thönes, S, Küper, K, Wascher, E, Schneider, D. Don't stop me now: Hampered retrieval of action plans following interruptions. Psychophysiology. 2021; 58:e13725. doi 10.1111/psyp.13725.
  9. Pelzer L, Naefgen C, Gaschler R, Haider H. Learning of across- and within-task contingencies modulates partial-repetition costs in dual-tasking. Psychol Res. 2021 Apr 22. doi 10.1007/s00426-021-01518-1. PMID 33885955.
  10. Ülkü S, Getzmann S, Wascher E, Schneider D. Be prepared for interruptions: EEG correlates of anticipation when dealing with task interruptions and the role of aging. Sci Rep. 2024 Mar 7;14(1):5679. doi: 10.1038/s41598-024-56400-y. PMID: 38454047; PMCID: PMC10920752.

Agriculture

  1. Sergio Canovas, Carlos E. Cugnasca. Applying Model Driven Engineering to Develop a Bee Information System. 2015.
  2. Mark Spekken, Sytze de Bruin, José Paulo Molin, Gerd Sparovek. Planning machine paths and row crop patterns on steep surfaces to minimize soil erosion. Computers and Electronics in Agriculture 2016. 124: 194-210. doi: 10.1016/j.compag.2016.03.013
  3. Belov MI. Forage harvester chopper units and the method of cut length evaluation. CIGR Journal 2019; 21(4)
  4. Calisti, R., Regni, L., & Proietti, P. (2020). Compost-recipe: A new calculation model and a novel software tool to make the composting mixture. Journal of Cleaner Production, 270, 122427. doi 10.1016/j.jclepro.2020.122427.
  5. Nikolaos Malamos & Demetris Koutsoyiannis (2018) Field survey and modelling of irrigation water quality indices in a Mediterranean island catchment: a comparison between spatial interpolation methods, Hydrological Sciences Journal, 63:10, 1447-1467, doi 10.1080/02626667.2018.1508874.
  6. Alexander Zhuk, Alexander Stolyanov, Alexander Kaychenov, Lyudmila Kuranova and Vladimir Grokhovsky (2021) Software for calculating the actual lethality of canned food heat treatment processes: development and application. E3S Web Conf., 273 (2021) 13002 doi 10.1051/e3sconf/202127313002.
  7. Tinker NA, Wight CP, Bekele WA, Yan W, Jellen EN, Renhuldt NT, Sirijovski N, Lux T, Spannagl M, Mascher M. Genome analysis in Avena sativa reveals hidden breeding barriers and opportunities for oat improvement. Commun Biol. 2022 May 18;5(1):474. doi 10.1038/s42003-022-03256-5. PMID 35585176.

Archaeology

  1. Shishov, V.V., Tychkov, I. I., Popkova, M.I., Ilyin, V.A., Bryukhanova, M.V., Kirdyanov, A.V., 2015. VS-oscilloscope: a new tool to parameterize tree radial growth based on climate conditions. Dendrochronologia. doi 10.1016/j.dendro.2015.10.001

Architecture and Construction

  1. Snigireva V. (2016). Program for calculation snow and wind loads design individual house in the Perm Region. Bulletin of Science and Practice, 456(11 (12)), 166–169. doi 10.5281/zenodo.166802.

Technology and Engineering

Computer-aided Design

  1. S Ilchev, R Andreev, Z Ilcheva, E Otsetova-Dudin (2021) Software for laser projection of CAD files for the clothing industry. IOP Conf. Ser.: Mater. Sci. Eng. 1031 012040 doi 10.1088/1757-899X/1031/1/012040
  2. Cepowski, T. (2020). The prediction of ship added resistance at the preliminary design stage by the use of an artificial neural network. Ocean Engineering, 195, 106657. doi 10.1016/j.oceaneng.2019.106657. Supplementary data with software

Electronics and Electricity

  1. Grebenchikov, N.P., Varlamov, D.O., Zuev, S.M. et al. Study of Solar Panel Charge Controllers. J. Commun. Technol. Electron. 65, 1053–1061 (2020). doi 10.1134/S1064226920080057.

Energy Technology

  1. Grebenchikov, N.P., Varlamov, D.O., Zuev, S.M. et al. Study of Solar Panel Charge Controllers. J. Commun. Technol. Electron. 65, 1053–1061 (2020). doi 10.1134/S1064226920080057.

Imaging

  1. Sebők, D., Vásárhelyi, L., Szenti, I., Vajtai, R., Kónya, Z., & Kukovecz, Á. (2021). Fast and accurate lacunarity calculation for large 3D micro-CT datasets. Acta Materialia, 214, 116970. doi 10.1016/j.actamat.2021.116970

Process Control

  1. Krivtcova, N. I., Tataurshikov, A. A., Ivanchina, I. D., Krivtsov, E. B., & Golovko, A. K. (2015). Calculation of the Kinetic Parameters of the Hydrofining Process of Diesel Fraction Using Mathematical Modeling. Procedia Engineering, 113, 73–78. doi 10.1016/j.proeng.2015.07.294
  2. Alisa Kosach, Evgeny Kovshov. Development of a Computer Based Problem-Oriented Automated Remote Leakage Detection Control System. ITM Web Conf. 10 01005 (2017). doi 10.1051/itmconf/20171001005.
  3. Costa, José Nilton de Abreu, Castro, Marco Aurélio Holanda de, Costa, Luís Henrique Magalhães, & Barbosa, João Marcelo Costa. (2018). New formula proposal for the determination of variable speed pumps efficiency. RBRH, 23, e44. Epub October 11, 2018. doi 10.1590/2318-0331.231820180003.
  4. Li, R.I., Rizaeva, Y.N., Psarev, D.N. et al. A Method for Calculating the Parameters of a Unit for Thermoradiation Treatment of Polymer Coatings in the Restoration of Car Body Parts. Polym. Sci. Ser. D 14, 517–521 (2021). doi 10.1134/S1995421221040110
  5. Alexandr Kaychenov, Aleksandr Vlasov, Alexey Maslov, Ilia Selyakov, Yana Glukhikh. Development of an Autoclave Thermal Processes Model for the Simulator of Canned Food Sterilization Process. KnE Life Sciences 2020: 437–49. doi 10.18502/kls.v5i1.6103
  6. Simonelli, G., Silva, L.S. e, Vilares Filho, R.S. e Lins, P.G.C. 2019. ESTUDO NUMÉRICO E ANALÍTICO DE UM ENSAIO DE FRATURAMENTO HIDRÁULICO. The Journal of Engineering and Exact Sciences. 5, 2 (abr. 2019), 0189-0194. doi 10.18540/jcecvl5iss2pp0189-0194.
  7. Belov MI. Kinematics of twin rotary tiller. CIGR Journal 2018; 20(4).
  8. V S Tynchenko, V V Kukartsev, V V Tynchenko, E A Chzhan and L N Korpacheva. Automation of monitoring and management of conveyor shop oil-pumping station of coal industry enterprise. IOP Conf. Ser.: Earth Environ. Sci. 194 022044. 2018. doi 10.1088/1755-1315/194/2/022044.
  9. Alvarez, M., Brancalião, L., Carneiro, J., Costa, P., Coelho, J.P., Gonçalves, J. (2023). Automated Ceramics Tableware Finishing: A Laboratory Prototype for Concept Validation. In: García-Peñalvo, F.J., García-Holgado, A. (eds) Proceedings TEEM 2022: Tenth International Conference on Technological Ecosystems for Enhancing Multiculturality. TEEM 2022. Lecture Notes in Educational Technology. Springer, Singapore. doi 10.1007/978-981-99-0942-1_122

Robotics

  1. António Paulo Moreira, Paulo Gomes da Costa, Fernando Veloso Gomes, Francisco Taveira Pinto, Paulo Lima Malheiros, Paulo Jorge Rosa Santos (2009). Robust and real-time motion capture of rigid bodies based on stereoscopic vision. Paper Ref: S0215_P0429. 3rd International Conference on Integrity, Reliability and Failure, Porto/Portugal, 20-24 July 2009. handle 10216/73129
  2. Moreira J, Pinto VH, Gonçalves J, Costa P. State Estimation of Over-Sensored Systems Applied to a Low-Cost Robotic Manipulator. Applied Sciences. 2021; 11(6):2519. doi 10.3390/app11062519
  3. Ferreira, T., Braun, J., Lima, J., Pinto, V.H., Santos, M., Costa, P. (2023). Robot at Factory 4.0: An Auto-Referee Proposal Based on Artificial Vision. In: Tardioli, D., Matellán, V., Heredia, G., Silva, M.F., Marques, L. (eds) ROBOT2022: Fifth Iberian Robotics Conference. ROBOT 2022. Lecture Notes in Networks and Systems, vol 589. Springer, Cham. doi 10.1007/978-3-031-21065-5_39
  4. Brancalião, L., Alvarez, M., Conde, M.Á., Costa, P., Gonçalves, J. (2023). Towards a More Accurate Time of Flight Distance Sensor to Be Applied in a Mobile Robotics Application. In: García-Peñalvo, F.J., García-Holgado, A. (eds) Proceedings TEEM 2022: Tenth International Conference on Technological Ecosystems for Enhancing Multiculturality. TEEM 2022. Lecture Notes in Educational Technology. Springer, Singapore. doi 10.1007/978-981-99-0942-1_121

Quality Control

  1. Zhukov, D. V, & Konovalov, S. V. (2020). Express quality analysis of metal structure based on thickness data. AIP Conference Proceedings, 2315(1), 40051. doi 10.1063/5.0036787

Other Applications

  1. Gabriel J, Restivo MT. Hands-on using on-line engineering: The trend to better solutions. 2009 3rd IEEE International Conference on E-Learning in Industrial Electronics (ICELIE), Porto, 2009, pp. 64-68, doi 10.1109/ICELIE.2009.5413210.
  2. Matheus Henrique de Castro, José Aurélio Medeiros da Luz, Felipe de Orquiza Milhomem, Cellular automaton-based simulation of bulk stacking and recovery, Journal of Materials Research and Technology 2022. 16, 263-275. doi 10.1016/j.jmrt.2021.11.127.
  3. Nakoneczny DJDS, Kaviski E. Computational model for continuous flow of autonomous vehicles at road intersections. PLoS One. 2023 May 4;18(5):e0285291. doi 10.1371/journal.pone.0285291. PMID 37141186; PMCID: PMC10159187.

Nutritional Science

  1. Alexandr Kaychenov, Aleksandr Vlasov, Alexey Maslov, Ilia Selyakov, Yana Glukhikh. Development of an Autoclave Thermal Processes Model for the Simulator of Canned Food Sterilization Process. KnE Life Sciences 2020: 437–49. doi 10.18502/kls.v5i1.6103
  2. Alexander Zhuk, Alexander Stolyanov, Alexander Kaychenov, Lyudmila Kuranova and Vladimir Grokhovsky (2021) Software for calculating the actual lethality of canned food heat treatment processes: development and application. E3S Web Conf., 273 (2021) 13002 doi 10.1051/e3sconf/202127313002.

Sports

  1. Kashiwagura DB, Kashiwagura FB, Agostinho MF, de Moraes ALG, Franchini E. Objectivity and reliability of the Judo Attack System Software. Proceedings of the Institution of Mechanical Engineers, Part P: Journal of Sports Engineering and Technology. April 2022. doi 10.1177/17543371221088191.

Education

  1. Laucius R. (2006) Issues of Selecting a Programming Environment for a Programming Curriculum in General Education. In: Mittermeir R.T. (eds) Informatics Education – The Bridge between Using and Understanding Computers. ISSEP 2006. Lecture Notes in Computer Science, vol 4226. Springer, Berlin, Heidelberg. doi 10.1007/11915355_16.
  2. Lin YW, Zini E. Free/libre open source software implementation in schools: Evidence from the field and implications for the future. Computers & Education. 2008;50(3):1092-1102. doi 10.1016/j.compedu.2006.11.001.
  3. Adorni, G., Coccoli, M., Stanganelli, L. & Maresca, P. (2009). EifFE-L meets ECLIPSE: an integrated open source e-learning environment. Journal of e-Learning and Knowledge Society, 5(3), 123-131. Italian e-Learning Association.
  4. Haruo Toda, Saki Tokai, Emi Nishimura, Takuto Komatsu, Hokuto Ubukata. Application of omni-purpose electric devices to electrophysiological student practices at the Department of Orthoptics and Visual Sciences, Niigata University of Health and Welfare. Niigata Journal of Health and Welfare. 2017

General Methodology and Instrumentation

  1. Chandrasekhar, V., & Mehta, M. M. (2013). RTSPM: Real-time Linux control software for scanning probe microscopy. Review of Scientific Instruments, 84(1), 13705. doi 10.1063/1.4775717
  2. Venkat Chandrasekhara. (2020) A microchip microcontroller-based transducer controller for non-contact scanning probe microscopy with phase-locked loop, amplitude, and Q control. Rev. Sci. Instrum. 2020 91, 023705; doi 10.1063/1.5131657.
  3. Hinge, M., Johnson, J. A., & Henriksen, M. L. L. (2021). A low-cost tabletop tensile tester with optical extensometer. Materials Advances. DOI https://doi.org/10.1039/D1MA00598G.

Books

  1. Jamie Carter (2015) A Stargazing Program for Beginners – A Pocket Field Guide. Springer International Publishing. ISBN 978-3-319-22071-0 and 978-3-319-22072-7. doi 10.1007/978-3-319-22072-7
  2. Malcolm Zack, Andrew Gannon, John McRoberts (2018) Stargazing Under Suburban Skies – A Star-Hopper's Guide. Springer, Cham. ISBN 978-3-319-90115-2 and 978-3-319-90116-9. doi 10.1007/978-3-319-90116-9

Theses

  1. Gregorovič, T. (2007) Carbon port of the Lazarus Component Library (Port Lazarus Component Library pro Carbon). (Bachelor's thesis. Masaryk University, Faculty of Informatics. Thesis supervisor Vlastimil Holer). Brno, 2007 [cit. 2020-12-31].
  2. Joaquín, E., & Pegoraro, M. (2009). Neuro-Fuzzy Software for Intelligent Control and Education. (Master thesis, Universidade do Porto, Portugal) PDF version; Archived version
  3. Mariotti, S. (2011). Development and validation of a pre-post processor for a rotorcraft simulation code. (Dissertation, University of Pisa, Italy, and Pisa University Press) URN etd-09142011-214059.
  4. Hjern, G. (2019). The modernization of a DOS-based time critical solar cell LBIC measurement system (Moderniseringen av ett DOS-baserat tidskritiskt LBIC mätsystem för solceller). (Dissertation, Karlstad University, Sweden). URN urn:nbn:se:kau:diva-74322.
  5. Gustavo Soares de Moura (2020) Development and Simulation of a Low-Cost Ground-Truth Localization System for Mobile Robots. (Master thesis, School of Technology and Management of Bragança, Portugal).
  6. Sílvia Dolores Nogueira Faria (2021) Sensor Fusion for Mobile Robot Localization using UWB and ArUco Markers. (Dissertation, Engineering department, University of Porto, Portugal). Handle 10216/135227.

Academic reports

  1. Marcou, Gilles & Engler, Etienne & Varnek, Alexandre. (2021). How to use C code in Free Pascal projects. Université de Strasbourg, France.
  2. DeDeo, M.R. and Thomas M. (2021). In Search of Odd Perfect Numbers: A Computational Sandbox. University of North Florida, Jacksonville, FL, USA. Archived version

See also

External Links

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