Dr Isaac Afara
Honorary Associate Professor
School of Electrical Engineering and Computer Science
Journal Articles
Fan, Xiwei, Donose, Bogdan, Jones, Michael W M, Howard, Daryl, Torniainen, Jari, Bertling, Karl, Guo, Xiao, Kewish, Cameron M, Lee, Kah Meng, Sun, Antonia Rujia, Rakic, Aleksandar, Crawford, Ross, Afara, Isaac O. and Prasadam, Indira (2024). A novel tape-free sample preparation method for human osteochondral cryosections for high throughput hyperspectral imaging. Histochemistry and Cell Biology, 163 (1) 16. doi: 10.1007/s00418-024-02338-1
Ristaniemi, Aapo, Tuppurainen, Juuso, Jäntti, Jiri, Nippolainen, Ervin, Afara, Isaac O., Mononen, Mika E., Korhonen, Rami K. and Mäkelä, Janne T.A. (2024). Comparison of site-specific tensile, compressive, and friction properties of human tibiofemoral joint cartilage and their relationship to degeneration. Journal of Biomechanics, 177 112386, 112386-177. doi: 10.1016/j.jbiomech.2024.112386
Kositsky, Adam, Stenroth, Lauri, Nippolainen, Ervin, Torniainen, Jari, Mäkelä, Janne T.A., Paakkari, Petri, Paakkonen, Tommi, Kröger, Heikki, Töyräs, Juha, Afara, Isaac O. and Korhonen, Rami K. (2024). The human patellar tendon is mechanically homogenous at its mid-substance. Journal of the Mechanical Behavior of Biomedical Materials, 163 106875, 106875. doi: 10.1016/j.jmbbm.2024.106875
Khan, Bilour, Nippolainen, Ervin, Shahini, Fatemeh, Nonappa, , Popov, Alexey, Töyräs, Juha and Afara, Isaac O. (2024). Relationship between depth-wise refractive index and biomechanical properties of human articular cartilage. Journal of biomedical optics, 29 (9) 095003, 095003-095003. doi: 10.1117/1.JBO.29.9.095003
Krebs, P., Nägele, M., Fomina, P., Virtanen, V., Nippolainen, E., Shaikh, R., Afara, I. O., Töyräs, J., Usenov, I., Sakharova, T., Artyushenko, V., Tafintseva, V., Solheim, J.H., Zimmermann, B., Kohler, A., König, O., Saarakkala, S. and Mizaikoff, B. (2024). Laser-irradiating infrared attenuated total reflection spectroscopy of articular cartilage: potential and challenges for diagnosing osteoarthritis. Osteoarthritis and Cartilage Open, 6 (2) 100466. doi: 10.1016/j.ocarto.2024.100466
Linus, Awuniji, Tanska, Petri, Nippolainen, Ervin, Tiitu, Virpi, Töyras, Juha, Korhonen, Rami K., Afara, Isaac O. and Mononen, Mika E. (2024). Site-specific elastic and viscoelastic biomechanical properties of healthy and osteoarthritic human knee joint articular cartilage. Journal of Biomechanics, 169 112135. doi: 10.1016/j.jbiomech.2024.112135
Fan, Xiwei, Sun, Antonia Rujia, Young, Reuben S. E., Afara, Isaac O., Hamilton, Brett R., Ong, Louis Jun Ye, Crawford, Ross and Prasadam, Indira (2024). Spatial analysis of the osteoarthritis microenvironment: techniques, insights, and applications. Bone Research, 12 (1) 7, 7. doi: 10.1038/s41413-023-00304-6
Elkadi, Omar Anwar, Abinzano, Florencia, Nippolainen, Ervin, González, Ona Bach, Levato, Riccardo, Malda, Jos and Afara, Isaac O. (2024). Non-neotissue constituents as underestimated confounders in the assessment of tissue engineered constructs by near-infrared spectroscopy. Materials Today Bio, 24 100879. doi: 10.1016/j.mtbio.2023.100879
Kafian-Attari, I., Nippolainen, E., Bergmann, F., George, A., Paakkari, P., Mirhashemi, A., Foschum, F., Kienle, A., Toyras, J. and Afara, I. O. (2024). Estimation of Photon Path Length and Penetration Depth in Articular Cartilage Zonal Architecture over the Therapeutic Window. IEEE Transactions on Biomedical Engineering, PP (99), 1-11. doi: 10.1109/TBME.2024.3368012
Shahini, Fatemeh, Oskouei, Soroush, Nippolainen, Ervin, Mohammadi, Ali, Sarin, Jaakko K., Moller, Nikae C. R. te, Brommer, Harold, Shaikh, Rubina, Korhonen, Rami K., van Weeren, P. René, Töyräs, Juha and Afara, Isaac O. (2024). Infrared Spectroscopy Can Differentiate Between Cartilage Injury Models: Implication for Assessment of Cartilage Integrity. Annals of Biomedical Engineering, 52 (9), 2521-2533. doi: 10.1007/s10439-024-03540-x
Pala, S., Paajanen, A., Ristaniemi, A., Nippolainen, E., Afara, I. O., Nykänen, O. and Nissi, M. J. (2024). Measurement of T1ρ dispersion with compressed sensing and magnetization prepared radial balanced steady-state free precession in spontaneous human osteoarthritis. Magnetic Resonance in Medicine, 92 (5), 2127-2139. doi: 10.1002/mrm.30206
Tafintseva, Valeria, Nippolainen, Ervin, Virtanen, Vesa, Solheim, Johanne Heitmann, Zimmermann, Boris, Saarakkala, Simo, Kröger, Heikki, Kohler, Achim, Töyräs, Juha, Afara, Isaac O and Shaikh, Rubina (2024). Machine Learning Approaches for the Fusion of Near-Infrared, Mid-Infrared, and Raman Data to Identify Cartilage Degradation in Human Osteochondral Plugs. Applied Spectroscopy. doi: 10.1177/00037028241285583
Kafian-Attari, Iman, Nippolainen, Ervin, Bergmann, Florian, George, Akuroma, Paakkari, Petri, Mirhashemi, Arash, Foschum, Florian, Kienle, Alwin, Töyräs, Juha and Afara, Isaac O. (2023). Broadband scattering properties of articular cartilage zones and their relationship with the heterogenous structure of articular cartilage extracellular matrix. Journal of biomedical optics, 28 (12) 125003, 1-16. doi: 10.1117/1.JBO.28.12.125003
Pala, Swetha, Hänninen, Nina E., Mohammadi, Ali, Ebrahimi, Mohammadhossein, te Moller, Nikae C. R., Brommer, Harold, René van Weeren, P., Mäkelä, Janne T. A., Korhonen, Rami K., Afara, Isaac O., Töyräs, Juha, Mikkonen, Santtu, Nissi, Mikko J. and Nykänen, Olli (2023). 3D T1 relaxation time measurements in an equine model of subtle post‐traumatic osteoarthritis using MB‐SWIFT. Journal of Orthopaedic Research, 41 (12), 2657-2666. doi: 10.1002/jor.25629
Sharma, Varun J., Green, Alexander, McLean, Aaron, Adegoke, John, Gordon, Claire L., Starkey, Graham, D’Costa, Rohit, James, Fiona, Afara, Isaac, Lal, Sean, Wood, Bayden and Raman, Jaishankar (2023). Towards a point-of-care multimodal spectroscopy instrument for the evaluation of human cardiac tissue. Heart and Vessels, 38 (12), 1476-1485. doi: 10.1007/s00380-023-02292-3
Sharma, Varun J., Adegoke, John A., Fasulakis, Michael, Green, Alexander, Goh, Su K., Peng, Xiuwen, Liu, Yifan, Jackett, Louise, Vago, Angela, Poon, Eric K. W., Starkey, Graham, Moshfegh, Sarina, Muthya, Ankita, D'Costa, Rohit, James, Fiona, Gordon, Claire L., Jones, Robert, Afara, Isaac O., Wood, Bayden R. and Raman, Jaishankar (2023). Point-of-care detection of fibrosis in liver transplant surgery using near-infrared spectroscopy and machine learning. Health Science Reports, 6 (11) e1652. doi: 10.1002/hsr2.1652
Khan, Bilour, Nippolainen, Ervin, Shahini, Fatemeh, Torniainen, Jari, Mikkonen, Santtu, Nonappa, Popov, Alexey, Töyräs, Juha and Afara, Isaac (2023). Refractive index of human articular cartilage varies with tissue structure and composition. Journal of the Optical Society of America A, 40 (12), 2205-2214. doi: 10.1364/josaa.498722
Kafian-Attari, Iman, Nippolainen, Ervin, Bergmann, Florian, Mirhashemi, Arash, Pakkari, Petri, Foschum, Florian, Kienle, Alwin, Töyräs, Juha and Afara, Isaac (2023). Impact of experimental setup parameters on measurement of articular cartilage optical properties in the visible and short near-infrared spectral bands. Biomedical Optics Express, 14 (7), 3397-3412. doi: 10.1364/boe.488801
Shaikh, Rubina, Tafintseva, Valeria, Nippolainen, Ervin, Virtanen, Vesa, Solheim, Johanne, Zimmermann, Boris, Saarakkala, Simo, Töyräs, Juha, Kohler, Achim and Afara, Isaac O. (2023). Characterisation of cartilage damage via fusing mid-infrared, near-infrared, and Raman spectroscopic data. Journal of Personalized Medicine, 13 (7) 1036, 1036. doi: 10.3390/jpm13071036
Linus, Awuniji, Tanska, Petri, Sarin, Jaakko K., Nippolainen, Ervin, Tiitu, Virpi, Mäkelä, Janne. T. A., Töyräs, Juha, Korhonen, Rami K., Mononen, Mika E. and Afara, Isaac O. (2023). Visible and near-infrared spectroscopy enables differentiation of normal and early osteoarthritic human knee joint articular cartilage. Annals of Biomedical Engineering, 51 (10), 2245-2257. doi: 10.1007/s10439-023-03261-7
Shehata, Eslam, Nippolainen, Ervin, Shaikh, Rubina, Ronkainen, Ari-Petteri, Töyräs, Juha, Sarin, Jaakko K. and Afara, Isaac O. (2023). Raman spectroscopy and machine learning enables estimation of articular cartilage structural, compositional, and functional properties. Annals of Biomedical Engineering, 51 (10), 2301-2312. doi: 10.1007/s10439-023-03271-5
Sharma, Varun J., Adegoke, John A., Afara, Isaac O., Stok, Kathryn, Poon, Eric, Gordon, Claire L., Wood, Bayden R. and Raman, Jaishankar (2023). Near-infrared spectroscopy for structural bone assessment: a potential point-of-care tool. Bone and Joint Open, 4 (4), 250-261. doi: 10.1302/2633-1462.44.bjo-2023-0014.r1
Adegoke, John A., Gassner, Callum, Sharma, Varun J., Patel, Sheila K., Jackett, Louise, Afara, Isaac O., Raman, Jaishankar, Burrell, Louise M. and Wood, Bayden R. (2023). Near‐infrared spectroscopic characterization of cardiac and renal fibrosis in fixed and fresh rat tissue. Analysis and Sensing, 3 (1) e202200030, 1-11. doi: 10.1002/anse.202200030
Adegoke, John A., Gassner, Callum, Sharma, Varun J., Patel, Sheila K., Jackett, Louise, Afara, Isaac O., Raman, Jaishankar, Burrell, Louise M. and Wood, Bayden R. (2022). Near‐infrared spectroscopic characterization of cardiac and renal fibrosis in fixed and fresh rat tissue. Analysis and Sensing, 3 (1). doi: 10.1002/anse.202200106
Adegoke, John A., Gassner, Callum, Sharma, Varun J., Patel, Sheila K., Jackett, Louise, Afara, Isaac O., Raman, Jaishankar, Burrell, Louise M. and Wood, Bayden R. (2022). Front Cover: Near‐Infrared Spectroscopic Characterization of Cardiac and Renal Fibrosis in Fixed and Fresh Rat Tissue (Anal. Sens. 1/2023). Analysis & Sensing, 3 (1). doi: 10.1002/anse.202200105
Cui, Andy, Nippolainen, Ervin, Shaikh, Rubina, Torniainen, Jari, Ristaniemi, Aapo, Finnilä, Mikko, Korhonen, Rami K., Saarakkala, Simo, Herzog, Walter, Töyräs, Juha and Afara, Isaac O. (2022). Assessment of Ligament Viscoelastic Properties Using Raman Spectroscopy. Annals of Biomedical Engineering, 50 (9), 1134-1142. doi: 10.1007/s10439-022-02988-z
Virtanen, V., Tafintseva, V., Shaikh, R., Nippolainen, E., Haas, J., Afara, I. O., Töyräs, J., Kröger, H., Solheim, J., Zimmermann, B., Kohler, A., Mizaikoff, B., Finnilä, M., Rieppo, L. and Saarakkala, S. (2022). Infrared spectroscopy is suitable for objective assessment of articular cartilage health. Osteoarthritis and Cartilage Open, 4 (2) 100250, 1-7. doi: 10.1016/j.ocarto.2022.100250
Rehman, Hafeez Ur, Tafintseva, Valeria, Zimmermann, Boris, Solheim, Johanne Heitmann, Virtanen, Vesa, Shaikh, Rubina, Nippolainen, Ervin, Afara, Isaac, Saarakkala, Simo, Rieppo, Lassi, Krebs, Patrick, Fomina, Polina, Mizaikoff, Boris and Kohler, Achim (2022). Preclassification of broadband and sparse infrared data by multiplicative signal correction approach. Molecules, 27 (7) 2298, 2298. doi: 10.3390/molecules27072298
Torniainen, Jari, Ristaniemi, Aapo, Sarin, Jaakko K., Prakash, Mithilesh, Afara, Isaac O., Finnilä, Mikko A.J., Stenroth, Lauri, Korhonen, Rami K. and Töyräs, Juha (2022). Near infrared spectroscopic evaluation of biochemical and crimp properties of knee joint ligaments and patellar tendon. PLoS ONE, 17 (2) e0263280, e0263280. doi: 10.1371/journal.pone.0263280
Tafintseva, Valeria, Lintvedt, Tiril Aurora, Solheim, Johanne Heitmann, Zimmermann, Boris, Rehman, Hafeez Ur, Virtanen, Vesa, Shaikh, Rubina, Nippolainen, Ervin, Afara, Isaac, Saarakkala, Simo, Rieppo, Lassi, Krebs, Patrick, Fomina, Polina, Mizaikoff, Boris and Kohler, Achim (2022). Preprocessing strategies for sparse infrared spectroscopy: a case study on cartilage diagnostics. Molecules, 27 (3) 873, 873. doi: 10.3390/molecules27030873
Sarin, Jaakko K., Prakash, Mithilesh, Shaikh, Rubina, Torniainen, Jari, Joukainen, Antti, Kröger, Heikki, Afara, Isaac O. and Töyräs, Juha (2022). Near-Infrared Spectroscopy Enables Arthroscopic Histologic Grading of Human Knee Articular Cartilage. Arthroscopy, Sports Medicine, and Rehabilitation, 4 (5), e1767-e1775. doi: 10.1016/j.asmr.2022.07.002
Afara, Isaac O. and Oloyede, Adekunle (2021). Resolving the near-infrared spectrum of articular cartilage. Cartilage, 13 (1_suppl), 194760352110354-737S. doi: 10.1177/19476035211035417
Adegoke, John A., De Paoli, Amanda, Afara, Isaac O., Kochan, Kamila, Creek, Darren J., Heraud, Philip and Wood, Bayden R. (2021). Ultraviolet/visible and near-infrared dual spectroscopic method for detection and quantification of low-level malaria Parasitemia in whole blood. Analytical Chemistry, 93 (39), 13302-13310. doi: 10.1021/acs.analchem.1c02948
Linus, Awuniji, Ebrahimi, Mohammadhossein, Turunen, Mikael J., Saarakkala, Simo, Joukainen, Antti, Kröger, Heikki, Koistinen, Arto, Finnilä, Mikko A.J., Afara, Isaac O., Mononen, Mika E., Tanska, Petri and Korhonen, Rami K. (2021). High-resolution infrared microspectroscopic characterization of cartilage cell microenvironment. Acta Biomaterialia, 134, 252-260. doi: 10.1016/j.actbio.2021.08.001
Khan, Bilour, Kafian-Attari, Iman, Nippolainen, Ervin, Shaikh, Rubina, Semenov, Dmitry, Hauta-Kasari, Markku, Töyräs, Juha and Afara, Isaac O. (2021). Articular cartilage optical properties in the near-infrared (NIR) spectral range vary with depth and tissue integrity. Biomedical Optics Express, 12 (10), 6066-6080. doi: 10.1364/boe.430053
Shaikh, Rubina, Nippolainen, Ervin, Virtanen, Vesa, Torniainen, Jari, Rieppo, Lassi, Saarakkala, Simo, Afara, Isaac O. and Töyräs, Juha (2021). Raman spectroscopy is sensitive to biochemical changes related to various cartilage injuries. Journal of Raman Spectroscopy, 52 (4) jrs.6062, 796-804. doi: 10.1002/jrs.6062
Virtanen, Vesa, Nippolainen, Ervin, Shaikh, Rubina, Afara, Isaac O., Töyräs, Juha, Solheim, Johanne, Tafintseva, Valeria, Zimmermann, Boris, Kohler, Achim, Saarakkala, Simo and Rieppo, Lassi (2021). Infrared fiber-optic spectroscopy detects bovine articular cartilage degeneration. Cartilage, 13 (2_suppl), 1-10. doi: 10.1177/1947603521993221
Kainulainen, Samu, Töyräs, Juha, Oksenberg, Arie, Korkalainen, Henri, Afara, Isaac O, Leino, Akseli, Kalevo, Laura, Nikkonen, Sami, Gadoth, Natan, Kulkas, Antti, Myllymaa, Sami and Leppänen, Timo (2021). Corrigendum to "Power spectral densities of nocturnal pulse oximetry signals differ in OSA patients with and without daytime sleepiness" [Sleep Med 73 (2020) 231-237]. Sleep medicine, 78, 202. doi: 10.1016/j.sleep.2020.11.006
Afara, Isaac O., Shaikh, Rubina, Nippolainen, Ervin, Querido, William, Torniainen, Jari, Sarin, Jaakko K., Kandel, Shital, Pleshko, Nancy and Töyräs, Juha (2021). Characterization of connective tissues using near-infrared spectroscopy and imaging. Nature Protocols, 16 (2), 1297-1329. doi: 10.1038/s41596-020-00468-z
Te Moller, Nikae C R, Mohammadi, Ali, Plomp, Saskia, Serra Bragança, Filipe M, Beukers, Martijn, Pouran, Behdad, Afara, Isaac O, Nippolainen, Ervin, Mäkelä, Janne T A, Korhonen, Rami K, Töyräs, Juha, Brommer, Harold and van Weeren, P René (2021). Structural, compositional, and functional effects of blunt and sharp cartilage damage on the joint: A 9-month equine groove model study. Journal of Orthopaedic Research, 39 (11) jor.24971, 1-13. doi: 10.1002/jor.24971
Sarin, J. K., Te Moller, N. C. R., Mohammadi, A., Prakash, M., Torniainen, J., Brommer, H., Nippolainen, E., Shaikh, R., Mäkelä, J. T. A., Korhonen, R. K., van Weeren, P. R., Afara, I. O. and Töyräs, J. (2020). Machine learning augmented near-infrared spectroscopy: in vivo follow-up of cartilage defects. Osteoarthritis and Cartilage, 29 (3), 423-432. doi: 10.1016/j.joca.2020.12.007
Korkalainen, Henri, Leppanen, Timo, Duce, Brett, Kainulainen, Samu, Aakko, Juhani, Leino, Akseli, Kalevo, Laura, Afara, Isaac O, Myllymaa, Sami and Toyras, Juha (2020). Detailed assessment of sleep architecture with deep learning and shorter epoch-to-epoch duration reveals sleep fragmentation of patients with obstructive sleep apnea. IEEE Journal of Biomedical and Health Informatics, PP (7) 9288902, 1-8. doi: 10.1109/JBHI.2020.3043507
Kafian-Attari, Iman, Nippolainen, Ervin, Semenov, Dmitry, Hauta-Kasari, Markku, Töyräs, Juha and Afara, Isaac O. (2020). Tissue optical properties combined with machine learning enables estimation of articular cartilage composition and functional integrity. Biomedical Optics Express, 11 (11), 6480-6494. doi: 10.1364/BOE.402929
Kainulainen, Samu, Töyräs, Juha, Oksenberg, Arie, Korkalainen, Henri, Afara, Isaac O., Leino, Akseli, Kalevo, Laura, Nikkonen, Sami, Gadoth, Natan, Kulkas, Antti, Myllymaa, Sami and Leppänen, Timo (2020). Power spectral densities of nocturnal pulse oximetry signals differ in OSA patients with and without daytime sleepiness. Sleep Medicine, 73, 231-237. doi: 10.1016/j.sleep.2020.07.015
Husso, Minna, Afara, Isaac O., Nissi, Mikko J., Kuivanen, Antti, Halonen, Paavo, Tarkia, Miikka, Teuho, Jarmo, Saunavaara, Virva, Vainio, Pauli, Sipola, Petri, Manninen, Hannu, Ylä-Herttuala, Seppo, Knuuti, Juhani and Töyräs, Juha (2020). Quantification of myocardial blood flow by machine learning analysis of modified dual bolus MRI examination. Annals of Biomedical Engineering, 49 (2), 653-662. doi: 10.1007/s10439-020-02591-0
Ala-Myllymäki, Juho, Paakkonen, Tommi, Joukainen, Antti, Kröger, Heikki, Lehenkari, Petri, Töyräs, Juha and Afara, Isaac O. (2020). Near-infrared spectroscopy for mapping of human meniscus biochemical constituents. Annals of Biomedical Engineering, 49 (1), 469-476. doi: 10.1007/s10439-020-02578-x
Korkalainen, Henri, Leppanen, Timo, Aakko, Juhani, Nikkonen, Sami, Kainulainen, Samu, Leino, Akseli, Duce, Brett, Afara, Isaac Oluwaseun, Myllymaa, Sami and Toyras, Juha (2020). Accurate deep learning-based sleep staging in a clinical population with suspected obstructive sleep apnea. IEEE Journal of Biomedical and Health Informatics, 24 (7) 8936942, 2073-2081. doi: 10.1109/JBHI.2019.2951346
Korkalainen, Henri, Aakko, Juhani, Duce, Brett, Kainulainen, Samu, Leino, Akseli, Nikkonen, Sami, Afara, Isaac O., Myllymaa, Sami, Töyräs, Juha and Leppänen, Timo (2020). Deep learning enables sleep staging from photoplethysmogram for patients with suspected sleep apnea. Sleep, 43 (11) zsaa098. doi: 10.1093/sleep/zsaa098
Torniainen, Jari, Afara, Isaac O., Prakash, Mithilesh, Sarin, Jaakko K., Stenroth, Lauri and Töyräs, Juha (2020). Open-source python module for automated preprocessing of near infrared spectroscopic data. Analytica Chimica Acta, 1108, 1-9. doi: 10.1016/j.aca.2020.02.030
Nikkonen, Sami, Afara, Isaac O., Leppänen, Timo and Töyräs, Juha (2020). Author Correction: Artificial neural network analysis of the oxygen saturation signal enables accurate diagnostics of sleep apnea (Scientific Reports, (2019), 9, 1, (13200), 10.1038/s41598-019-49330-7). Scientific Reports, 10 (1) 4977, 4977. doi: 10.1038/s41598-020-62003-0
Afara, Isaac O., Sarin, Jaakko K., Ojanen, Simo, Finnilä, Mikko A. J., Herzog, Walter, Saarakkala, Simo, Korhonen, Rami K. and Töyräs, Juha (2020). Machine learning classification of articular cartilage integrity using near infrared spectroscopy. Cellular and Molecular Bioengineering, 13 (3), 219-228. doi: 10.1007/s12195-020-00612-5
Nippolainen, Ervin, Shaikh, Rubina, Virtanen, Vesa, Rieppo, Lassi, Saarakkala, Simo, Töyräs, Juha and Afara, Isaac O. (2020). Near infrared spectroscopy enables differentiation of mechanically and enzymatically induced cartilage injuries. Annals of Biomedical Engineering, 48 (9), 2343-2353. doi: 10.1007/s10439-020-02506-z
Rasel, Md Alim Iftekhar, Singh, Sanjleena, Nguyen, Trung Dung, Afara, Isaac O. and Gu, Yuantong (2019). Impact of nanoparticle uptake on the biophysical properties of cell for biomedical engineering applications. Scientific Reports, 9 (1) 5859, 1-13. doi: 10.1038/s41598-019-42225-7
Mancini, I. A.D., Rieppo, L., Pouran, B., Afara, I. O., Braganca, F.M. Serra, van Rijen, M. H.P., Kik, M., Weinans, H., Toyras, J., van Weeren, P. R. and Malda, J. (2019). Effects of body mass on microstructural features of the osteochondral unit: A comparative analysis of 37 mammalian species. Bone, 127, 664-673. doi: 10.1016/j.bone.2019.07.001
Nikkonen, Sami, Afara, Isaac O., Leppänen, Timo and Töyräs, Juha (2019). Artificial neural network analysis of the oxygen saturation signal enables accurate diagnostics of sleep apnea. Scientific Reports, 9 (1) 13200, 13200. doi: 10.1038/s41598-019-49330-7
Sarin, Jaakko K., Torniainen, Jari, Prakash, Mithilesh, Rieppo, Lassi, Afara, Isaac O. and Toyras, Juha (2019). Dataset on equine cartilage near infrared spectra, composition, and functional properties. Scientific Data, 6 (1) 164, 164. doi: 10.1038/s41597-019-0170y
Prakash, M., Joukainen, A., Torniainen, J., Honkanen, M. K.M., Rieppo, L., Afara, I. O., Kröger, H., Töyräs, J. and Sarin, J. K. (2019). Near-infrared spectroscopy enables quantitative evaluation of human cartilage biomechanical properties during arthroscopy. Osteoarthritis and Cartilage, 27 (8), 1235-1243. doi: 10.1016/j.joca.2019.04.008
Sarin, Jaakko K., Nykänen, Olli, Tiitu, Virpi, Mancini, Irina A. D., Brommer, Harold, Visser, Jetze, Malda, Jos, van Weeren, P. René, Afara, Isaac O. and Töyräs, Juha (2019). Arthroscopic determination of cartilage proteoglycan content and collagen network structure with near-infrared spectroscopy. Annals of Biomedical Engineering, 47 (8), 1815-1826. doi: 10.1007/s10439-019-02280-7
Torniainen, Jari, Ristaniemi, Aapo, Sarin, Jaakko K., Mikkonen, Santtu, Afara, Isaac O., Stenroth, Lauri, Korhonen, Rami K. and Töyräs, Juha (2019). Near infrared spectroscopic evaluation of ligament and tendon biomechanical properties. Annals of Biomedical Engineering, 47 (1), 213-222. doi: 10.1007/s10439-018-02125-9
Prakash, M., Sarin, J. K., Rieppo, L., Afara, I. O. and Töyräs, J. (2018). Accounting for spatial dependency in multivariate spectroscopic data. Chemometrics and Intelligent Laboratory Systems, 182, 166-171. doi: 10.1016/j.chemolab.2018.09.010
Sarin, Jaakko K., te Moller, Nikae C. R., Mancini, Irina A. D., Brommer, Harold, Visser, Jetze, Malda, Jos, van Weeren, P. René, Afara, Isaac O. and Töyräs, Juha (2018). Arthroscopic near infrared spectroscopy enables simultaneous quantitative evaluation of articular cartilage and subchondral bone in vivo. Scientific Reports, 8 (1) 13409, 13409. doi: 10.1038/s41598-018-31670-5
Afara, Isaac O., Florea, Cristina, Olumegbon, Ismail A., Eneh, Chibuzor T., Malo, Markus K. H., Korhonen, Rami K. and Töyräs, Juha (2018). Characterizing human subchondral bone properties using near-infrared (NIR) spectroscopy. Scientific Reports, 8 (1) 9733, 9733. doi: 10.1038/s41598-018-27786-3
Moody, Hayley R., Afara, Isaac O., Singh, Sanjleena and Oloyede, Adekunle (2018). Potential enhancement of articular cartilage histological grading with collagen integrity. Clinical Biomechanics, 56, 1-10. doi: 10.1016/j.clinbiomech.2018.04.016
Arabshahi, Zohreh, Afara, Isaac Oluwaseun, Moody, Hayley Ruscoe, Schrobback, Karsten, Kashani, Jamal, Fischer, Nadine, Oloyede, Adekunle and Klein, Travis Jacob (2018). A new mechanical indentation framework for functional assessment of articular cartilage. Journal of the Mechanical Behavior of Biomedical Materials, 81, 83-94. doi: 10.1016/j.jmbbm.2018.02.028
Ala-Myllymäki, Juho, Danso, Elvis K., Honkanen, Juuso T. J., Korhonen, Rami K., Toÿräs, Juha and Afara, Isaac O. (2017). Optical spectroscopic characterization of human meniscus biomechanical properties. Journal of Biomedical Optics, 22 (12) 125008, 1. doi: 10.1117/1.JBO.22.12.125008
Afara, Isaac O., Prasadam, Indira, Arabshahi, Zohreh, Xiao, Yin and Oloyede, Adekunle (2017). Monitoring osteoarthritis progression using near infrared (NIR) spectroscopy. Scientific Reports, 7 (1) 11463, 1-9. doi: 10.1038/s41598-017-11844-3
Prakash, Mithilesh, Sarin, Jaakko K., Rieppo, Lassi, Afara, Isaac O. and Töyräs, Juha (2017). Optimal regression method for near-infrared spectroscopic evaluation of articular cartilage. Applied Spectroscopy, 71 (10), 2253-2262. doi: 10.1177/0003702817726766
Sarin, Jaakko K., Rieppo, Lassi, Brommer, Harold, Afara, Isaac O., Saarakkala, Simo and Töyräs, Juha (2017). Combination of optical coherence tomography and near infrared spectroscopy enhances determination of articular cartilage composition and structure. Scientific Reports, 7 (1) 10586, 10586. doi: 10.1038/s41598-017-10973-z
Sarin, J. K., Brommer, H., Argüelles, D., Puhakka, P. H., Inkinen, S. I., Afara, I. O., Saarakkala, S. and Töyräs, J. (2017). Corrigendum to “Multimodality scoring of chondral injuries in the equine fetlock joint ex vivo” [Osteoarthritis Cartilage 25 (5) (2017 May) 790–798] (S1063458416304666), (10.1016/j.joca.2016.12.007)). Osteoarthritis and Cartilage, 25 (8), 1377-1378. doi: 10.1016/j.joca.2017.05.010
Olumegbon, Ismail Adewale, Oloyede, Adekunle and Afara, Isaac Oluwaseun (2017). Near-infrared (NIR) spectroscopic evaluation of articular cartilage: A review of current and future trends. Applied Spectroscopy Reviews, 52 (6), 541-559. doi: 10.1080/05704928.2016.1250010
te Moller, N. C.R., Pitkänen, M., Sarin, J. K., Väänänen, S., Liukkonen, J., Afara, I. O., Puhakka, P. H., Brommer, H., Niemelä, T., Tulamo, R. M., Argüelles Capilla, D. and Töyräs, J. (2017). Semi-automated International Cartilage Repair Society scoring of equine articular cartilage lesions in optical coherence tomography images. Equine Veterinary Journal, 49 (4), 552-558. doi: 10.1111/evj.12637
Afara, Isaac Oluwaseun, Singh, Sanjleena, Moody, Hayley, Zhang, Lihai and Oloyede, Adekunle (2017). Characterization of articular cartilage recovery and its correlation with optical response in the near-infrared spectral range. Cartilage, 8 (3), 307-316. doi: 10.1177/1947603516662502
Sarin, J. K., Brommer, H., Argüelles, D., Puhakka, P. H., Inkinen, S. I., Afara, I. O., Saarakkala, S. and Töyräs, J. (2017). Multimodality scoring of chondral injuries in the equine fetlock joint ex vivo. Osteoarthritis and Cartilage, 25 (5), 790-798. doi: 10.1016/j.joca.2016.12.007
Bandara, Chaturanga D., Singh, Sanjleena, Afara, Isaac O., Wolff, Annalena, Tesfamichael, Tuquabo, Ostrikov, Kostya and Oloyede, Adekunle (2017). Bactericidal effects of natural nanotopography of dragonfly wing on Escherichia coli. ACS Applied Materials and Interfaces, 9 (8), 6746-6760. doi: 10.1021/acsami.6b13666
Eneh, Chibuzor T. M., Afara, Isaac O., Malo, Markus K. H., Jurvelin, Jukka S. and Töyräs, Juha (2017). Porosity predicted from ultrasound backscatter using multivariate analysis can improve accuracy of cortical bone thickness assessment. Journal of the Acoustical Society of America, 141 (1), 575-585. doi: 10.1121/1.4973572
Sarin, Jaakko K., Amissah, Michael, Brommer, Harold, Argüelles, David, Töyräs, Juha and Afara, Isaac O. (2016). Near infrared spectroscopic mapping of functional properties of equine articular cartilage. Annals of Biomedical Engineering, 44 (11), 3335-3345. doi: 10.1007/s10439-016-1659-6
Puhakka, Jani, Afara, Isaac O., Paatela, Teemu, Sormaala, Markus J., Timonen, Matti A., Virén, Tuomas, Jurvelin, Jukka S., Töyräs, Juha and Kiviranta, Ilkka (2016). In vivo evaluation of the potential of high-frequency ultrasound for arthroscopic examination of the shoulder joint. Cartilage, 7 (3), 248-255. doi: 10.1177/1947603515617280
Ala-Myllymäki, Juho, Honkanen, Juuso T.J., Töyräs, Juha and Afara, Isaac O. (2016). Optical spectroscopic determination of human meniscus composition. Journal of Orthopaedic Research, 34 (2), 270-278. doi: 10.1002/jor.23025
Pawlak, Zenon, Urbaniak, Wieslaw, Afara, Isaac O., Yusuf, Kehinde Q., Banaszak-Piechowska, Agnieszka and Oloyede, Adekunle (2016). Tribological efficacy and stability of phospholipid-based membrane lubricants in varying ph chemical conditions. Biointerphases, 11 (1) 019002, 1-5. doi: 10.1116/1.4939246
Puhakka, P. H., te Moller, N. C.R., Afara, I. O., Mäkelä, J. T.A., Tiitu, V., Korhonen, R. K., Brommer, H., Virén, T., Jurvelin, J. S. and Töyräs, J. (2015). Estimation of articular cartilage properties using multivariate analysis of optical coherence tomography signal. Osteoarthritis and Cartilage, 23 (12), 2206-2213. doi: 10.1016/j.joca.2015.05.034
Singh, Sanjleena, Afara, Isaac O., Tehrani, Ashkan H. and Oloyede, Adekunle (2015). Effect of decellularization on the load-bearing characteristics of articular cartilage matrix. Tissue Engineering and Regenerative Medicine, 12 (5), 294-305. doi: 10.1007/s13770-014-0083-y
Afara, Isaac O., Hauta-Kasari, Markku, Jurvelin, Jukka S., Oloyede, Adekunle and Töyräs, Juha (2015). Optical absorption spectra of human articular cartilage correlate with biomechanical properties, histological score and biochemical composition. Physiological Measurement, 36 (9) 1913, 1913-1928. doi: 10.1088/0967-3334/36/9/1913
Afara, Isaac O., Moody, Hayley, Singh, Sanjleena, Prasadam, Indira and Oloyede, Adekunle (2015). Spatial mapping of proteoglycan content in articular cartilage using near-infrared (NIR) spectroscopy. Biomedical Optics Express, 6 (1), 144-154. doi: 10.1364/BOE.6.000144
Afara, Isaac Oluwaseun, Prasadam, Indira, Moody, Hayley, Crawford, Ross, Xiao, Yin and Oloyede, Adekunle (2014). Near infrared spectroscopy for rapid determination of Mankin score components: a potential tool for quantitative characterization of articular cartilage at surgery. Arthroscopy: The Journal of Arthroscopy and Related Surgery, 30 (9), 1146-1155. doi: 10.1016/j.arthro.2014.04.097
Fan, Wei, Wu, Chengtie, Miao, Xigeng, Liu, Gang, Saifzadeh, Siamak, Sugiyama, Sadahiro, Afara, Isaac, Crawford, Ross and Xiao, Yin (2013). Biomaterial scaffolds in cartilage-subchondral bone defects influencing the repair of autologous articular cartilage transplants. Journal of Biomaterials Applications, 27 (8), 979-989. doi: 10.1177/0885328211431310
Afara, I. O., Singh, S. and Oloyede, A. (2013). Load-unloading response of intact and artificially degraded articular cartilage correlated with near infrared (NIR) absorption spectra. Journal of the Mechanical Behavior of Biomedical Materials, 20, 249-258. doi: 10.1016/j.jmbbm.2012.11.022
Afara, Isaac Oluwaseun, Prasadam, Indira, Crawford, Ross, Xiao, Yin and Oloyede, Adekunle (2013). Near infrared (NIR) absorption spectra correlates with subchondral bone micro-CT parameters in osteoarthritic rat models. Bone, 53 (2), 350-357. doi: 10.1016/j.bone.2012.12.042
Afara, I., Singh, S. and Oloyede, A. (2013). Application of near infrared (NIR) spectroscopy for determining the thickness of articular cartilage. Medical Engineering and Physics, 35 (1), 88-95. doi: 10.1016/j.medengphy.2012.04.003
Afara, I., Wallace, S., Singh, S. and Oloyede, A. (2012). Can proteoglycan change in articular cartilage be detected by ultrasound evaluation?. RILEM Bookseries, 6, 393-398. doi: 10.1007/978-94-007-0723-8_57
Afara, I., Sahama, T. and Oloyede, A. (2012). Near infrared for non-destructive testing of articular cartilage. RILEM Bookseries, 6, 399-404. doi: 10.1007/978-94-007-0723-8_58
Pawlak, Zenon, Urbaniak, W., Gadomski, Adam, Yusuf, Kehinde Q., Afara, Isaac O. and Oloyede, Adekunle (2012). The role of lamellate phospholipid bilayers in lubrication of joints. Acta of Bioengineering and Biomechanics, 14 (4), 101-106. doi: 10.5277/abb120411
Afara, I., Prasadam, I., Crawford, R., Xiao, Y. and Oloyede, A. (2012). Non-destructive evaluation of articular cartilage defects using near-infrared (NIR) spectroscopy in osteoarthritic rat models and its direct relation to Mankin score. Osteoarthritis and Cartilage, 20 (11), 1367-1373. doi: 10.1016/j.joca.2012.07.007
Conference Papers
Sharma, V., Green, A., Mclean, A., Adegoke, J., Gordon, C., Starkey, G., D'Costa, R., James, F., Afara, I., Lal, S., Wood, B. and Raman, J. (2024). Towards a point-of-care multimodal spectroscopy instrument for the evaluation of human cardiac tissue. ANZSCTS Annual Scientific Meeting, Wellington, New Zealand, 9–11 November 2023. Amsterdam, Netherlands: Elsevier. doi: 10.1016/j.hlc.2024.04.015
Pala, Swetha, Paajanen, Antti, Ristaniemi, Aapo, Nippolainen, Ervin, Afara, Isaac, Nykänen, Olli and Nissi, Mikko (2024). Validating accelerated T1rho dispersion measurement with samples from spontaneous human osteoarthritis. 2024 ISMRM & ISMRT Annual Meeting, Singapore, 4-9 May 2024. Concord, CA United States: ISMRM. doi: 10.58530/2024/2287
Kainulainen, S., Toyras, J., Oksenberg, A., Korkalainen, H., Afara, I., Leino, A., Kalevo, L., Nikkonen, S., Gadoth, N., Kulkas, A., Myllymaa, S. and Leppanen, T. (2019). Differentiating Sleepy and non-sleepy obstructive sleep apnea patients using nocturnal pulse oximetry and deep learning. World Sleep Congress, Vancouver, Canada, 20-25 September 2019. Amsterdam, Netherlands: Elsevier . doi: 10.1016/j.sleep.2019.11.508
Nikkonen, S., Afara, I., Myllymaa, S., Toyras, J. and Leppanen, T. (2019). Artificial neural network analysis of blood oxygen saturation signal enables accurate automatic screening of sleep apnea. World Sleep Congress, Vancouver, Canada, 20-25 September 2019. Amsterdam, Netherlands: Elsevier . doi: 10.1016/j.sleep.2019.11.624
Korkalainen, H., Aakko, J., Nikkonen, S., Kainulainen, S., Leino, A., Duce, B., Afara, I. O., Myllymaa, S., Toyras, J. and Leppanen, T. (2019). Deep learning enables accurate sleep staging based on a single frontal EEG channel. 15th World Sleep Congress, World Sleep 2019, Vancouver, Canada, 20-25 September, 2019 . Amsterdam, Netherlands: Elsevier BV.
Ala-Myllymäki, Juho, Paakkonen, Tommi, Töyräsa, Juha and Afara, Isaac O. (2019). Arthroscopic near-infrared spectroscopic prediction of human meniscus properties. Bio-Optics: Design and Application 2019, Tucson, AZ, United States, 14–17 April 2019. Washington, D.C.: Optical Society of America (OSA). doi: 10.1364/BODA.2019.JT4A.35
Virtanen, V. K., Nippolainen, E., Shaikh, R., Afara, I., Toyras, J., Saarakkala, S. and Rieppo, L. (2019). Detection of enzymatically and mechanically induced degradation of bovine articular cartilage tissue with mid-infrared spectroscopy. OARSI World Congress on Osteoarthritis - Promoting Clinical and Basic Research in Osteoarthritis, Toronto, Canada, 2-5 May 2019. Oxford, United Kingdom: Elsevier . doi: 10.1016/j.joca.2019.02.035
Bibikova, Olga, Nippolainen, Ervin, Afara, Isaac, Haas, Julian, Virtanen, Vesa, Rieppo, Lasi, Adomaviciute, Sonata, Brommer, Harold, van Weeren, René, Melenteva, Anastasija, Belikova, Valeria, Zabarylo, Urszula, Minet, Olaf, Töyräs, Juha, Sablinskas, Valdas, Mizaikoff, Boris and Artyushenko, Viacheslav (2019). Multi-spectral fiber spectroscopy methods as solutions for label-free medical diagnostics. SPIE BiOS, 2019, San Francisco, CA, United States, 4 March 2019. Bellingham, WA, United States: SPIE. doi: 10.1117/12.2509174
Shaikh, Rubina, Nippolainen, Ervin, Virtanen, Vesa, Rieppo, Lassi, Haas, Julian, Mizaikoff, Boris, Artyushenko, Viacheslav, Bibikova, Olga, Afara, Isaac, Saarakkala, Simo and Töyräs, Juha (2019). Mid-infrared spectroscopic assessment of cartilage degeneration. Biophotonics Congress, Tucson, AZ, United States, 14–17 April 2019. Washington, D.C.: Optical Society of America (OSA). doi: 10.1364/BODA.2019.DS1A.3
Nippolainen, Ervin, Shaikh, Rubina, Virtanen, Vesa, Rieppo, Lassi, Afara, Isaac, Saarakkala, Simo and Töyräs, Juha (2019). Mid-infrared and near infrared spectroscopic analysis of mechanically and enzymatically damaged cartilage. Biophotonics Congress: Optics in the Life Sciences Congress 2019 (BODA,BRAIN,NTM,OMA,OMP), Tucson, AZ USA, 14-17 April 2019. Washington, DC USA: Optical Society of America. doi: 10.1364/BODA.2019.JT4A.37
Torniainen, Jari, Afara, Isaac O., Prakash, Mithilesh, Sarin, Jaakko K., Stenroth, Lauri and Töyräs, Juha (2019). Automated preprocessing of near infrared spectroscopic data. Biophotonics Congress: Optics in the Life Sciences Congress 2019 (BODA,BRAIN,NTM,OMA,OMP), Tucson, AZ, United States, 14-17 April 2019. Washington, DC, United States: Optical Society of America. doi: 10.1364/BODA.2019.DS2A.6
Afara, Isaac O., Sarin, Jaakko K., Ojanen, Simo, Finnila, Mikko, Herzog, Walter, Saarakkala, Simo, Korhonen, Rami K. and To¨yräs, Juha (2018). Deep learning classification of cartilage integrity using near infrared spectroscopy. Clinical and Translational Biophotonics, TRANSLATIONAL 2018, Hollywood, FL United States, 3-6 April 2018. Washington, DC United States: The Optical Society. doi: 10.1364/TRANSLATIONAL.2018.JTu3A.27
Ala-Myllymäki, Juho, To¨yräs, Juha and Afara, Isaac O. (2018). Near-infrared spectroscopy: A potential tool for mapping meniscus properties. Clinical and Translational Biophotonics, TRANSLATIONAL 2018, Hollywood, FL United States, 3-6 April 2018. Washington, DC United States: The Optical Society. doi: 10.1364/TRANSLATIONAL.2018.JW3A.38
Sarin, Jaakko K., te Moller, Nikae, Brommer, Harold, van Weeren, Rene´, Mancini, Irina, Malda, Jos, Afara, Isaac O. and Töyräs, Juha (2018). Spectroscopic evaluation of post-traumatic osteoarthritis in Shetland ponies. Optical Tomography and Spectroscopy (OTS 2018), Hollywood, FL, United States, 3-6 April 2018. Washington, D.C.: OSA - The Optical Society. doi: 10.1364/OTS.2018.OTu4D.5
Prakash, Mithilesh, Joukainen, Antti, Sarin, Jaakko, Rieppo, Lassi, Afara, Isaac and Töyräs, Juha (2018). Near-infrared spectroscopy based arthroscopic evaluation of human knee joint cartilage, through automated selection of an anatomically specific regression model. Optical Tomography and Spectroscopy (OTS 2018), Hollywood, FL, United States, 3-6 April 2018. Washington, D.C.: OSA - The Optical Society. doi: 10.1364/OTS.2018.OF4D.3
Pawlak, Z., Urbaniak, W., Yusuf, K. Q., Afara, I. O. and Oloyede, A. (2013). Lamellar-roller-bearing lubrication model on the cartilage surface. Politecnico di Torino (DIMEAS).