Biomedical Engineering and Medical Physics

Deliverables

Inform for each call the Project Officer by sending the link to the Euraxess website where the Call has been published

Publications

Paradoxical Rules of Spike Train Decoding Revealed at the Sensitivity Limit of Vision

Author(s): Smeds, Lina; Takeshita, Daisuke; Turunen, Tuomas; Tiihonen, Jussi; Westö, Johan; Martyniuk, Nataliia; Seppänen, Aarni; Ala-Laurila, Petri
Published in: Neuron, Issue 104, 2019, Page(s) 576-587, ISSN 0896-6273
Publisher: Cell Press
DOI: 10.1016/j.neuron.2019.08.005

Mineralization of dental tissues and caries lesions detailed with Raman microspectroscopic imaging

Author(s): Shuvashis Das Gupta; Markus Killenberger; Tarja Tanner; Tarja Tanner; Lassi Rieppo; Simo Saarakkala; Simo Saarakkala; Jarkko Heikkilä; Vuokko Anttonen; Vuokko Anttonen; Mikko A. J. Finnilä
Published in: Analyst, Issue 146, 2021, Page(s) 1705-1713, ISSN 0003-2654
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0an01938k

EMG-Assisted Muscle Force Driven Finite Element Model of the Knee Joint with Fibril-Reinforced Poroelastic Cartilages and Menisci

Author(s): Esrafilian, A.; Stenroth, L.; Mononen, M. E.; Tanska, P.; Avela, J.; Korhonen, R. K.
Published in: Scientific Reports, Vol 10, Iss 1, Pp 1-16 (2020), Issue 10, 2020, Page(s) 1-16, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-59602-2

Experimental mechanical strain measurement of tissues

Author(s): Lingwei Huang; Rami K. Korhonen; Mikael J. Turunen; Mikko A. J. Finnilä; Mikko A. J. Finnilä; Mikko A. J. Finnilä
Published in: PeerJ, Vol 7, p e6545 (2019), Issue 7, 2019, Page(s) e6545, ISSN 2167-8359
Publisher: PeerJ
DOI: 10.7717/peerj.6545

Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies

Author(s): Huang Y., Nguyen M., Nguyen H., Loo J., Lehtonen A., Kuzyk A
Published in: Langmuir, Issue 38, 2022, Page(s) 2954-2960, ISSN 0743-7463
Publisher: American Chemical Society
DOI: 10.1021/acs.langmuir.1c03434

Calibration and validation of accelerometer-based activity monitors: A systematic review of machine-learning approaches

Author(s): Farrahi V., Niemelä M., Kangas M., Korpelainen R., Jämsä T.
Published in: Gait and Posture, Issue 68, 2019, Page(s) 285-299, ISSN 0966-6362
Publisher: Elsevier BV
DOI: 10.1016/j.gaitpost.2018.12.003

Compositional associations of sleep and activities within the 24-h cycle with cardiometabolic health markers in adults

Author(s): Farrahi V., Kangas M., Walmsley R., Niemelä M., Kiviniemi A., Puukka K., Collings P.J., Korpelainen R., Jämsä T.
Published in: Medicine & Science in Sports & Exercise, Issue 53, 2021, Page(s) 324-332, ISSN 0195-9131
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1249/mss.0000000000002481

Intensity and temporal patterns of physical activity and cardiovascular disease risk in midlife

Author(s): Niemelä, Maisa; Kangas, Maarit; Farrahi, Vahid; Kiviniemi, Antti; Leinonen, Anna-Maiju; Ahola, Riikka; Puukka, Katri; Auvinen, Juha; Korpelainen, Raija; Jämsä, Timo
Published in: Preventive Medicine, Issue 124, 2019, Page(s) 33-41, ISSN 0091-7435
Publisher: Academic Press
DOI: 10.1016/j.ypmed.2019.04.023

Accumulation patterns of sedentary time and breaks and their association with cardiometabolic health markers in adults

Author(s): Farrahi, V. (Vahid); Kangas, M. (Maarit); Kiviniemi, A. (Antti); Puukka, K. (Katri); Korpelainen, R. (Raija); Jämsä, T. (Timo)
Published in: The Scandinavian Journal of Medicine & Science in Sports, Issue 31, 2021, Page(s) 1489–1507, ISSN 0905-7188
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/sms.13958

Fracture strength of the proximal femur injected with a calcium sulfate/hydroxyapatite bone substitute.

Author(s): Kok J., Širka A., Grassi L., Raina D.B., Tarasevičius Š., Tägil M., Lidgren L., Isaksson H.
Published in: Clinical Biomechanics, Issue 63, 2019, Page(s) 172-178, ISSN 0268-0033
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.clinbiomech.2019.03.008

Augmenting a dynamic hip screw with a calcium sulfate/hydroxyapatite biomaterial.

Author(s): Kok J., Širka A., Liu Y., Tarasevičius, Belickas J., Tägil M., Lidgren L., Isaksson H., Raina D.B.
Published in: Medical Engineering & Physics, Issue 92, 2021, Page(s) 102-109, ISSN 1350-4533
Publisher: Elsevier BV
DOI: 10.1016/j.medengphy.2021.05.006

Assembly of Gold Nanorods into Chiral Plasmonic Metamolecules Using DNA Origami Templates

Author(s): Huang, Yike; Nguyen; Kha; Kuzyk, Anton
Published in: Journal of visualized experiments, Issue 145, 2019, Page(s) 1-8, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/59280

Hyaluronan derived nanoparticle for simvastatin delivery: evaluation of simvastatin induced myotoxicity in tissue engineered skeletal muscle.

Author(s): Jones, Julia M.; Player, Darren J.; Samanta, Sumanta; Rangasami, Vignesh K.; Hilborn, Jöns; Lewis, Mark P.; Oommen, Oommen P.; Mudera, Vivek
Published in: Biomaterials Science, Issue 8, 2020, Page(s) 302-331, ISSN 2047-4830
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9bm00986h

Predicting overall survival time in glioblastoma patients using gradient boosting machines algorithm and recursive feature elimination technique

Author(s): Karami G., Orlando M.G., Pizzi A.D., Caulo M., Gratta C.D.
Published in: Cancers, Issue 13, 2021, Page(s) 4976, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers13194976

Pluronic Micelle-Mediated Tissue Factor Silencing Enhances Hemocompatibility, Stemness, Differentiation Potential, and Paracrine Signaling of Mesenchymal Stem Cells.

Author(s): Vignesh K. Rangasami; Ganesh N. Nawale; Kenta Asawa; Sandeep Kadekar; Sumanta Samanta; Bo Nilsson; Kristina Nilsson Ekdahl; Kristina Nilsson Ekdahl; Susanna Miettinen; Jöns Hilborn; Yuji Teramura; Yuji Teramura; Oommen P. Varghese; Oommen P. Oommen
Published in: Biomacromolecules, Issue 22/5, 2021, Page(s) 1980-1989, ISSN 1525-7797
Publisher: American Chemical Society
DOI: 10.1021/acs.biomac.1c00070

Astrocytes exhibit a protective role on neuronal firing patterns under chemically-induced seizures in neuron-astrocyte co-cultures

Author(s): Ahtiainen A., Genocchi B., Tanskanen J.M.A., Barros M.T., Hyttinen J.A.K., Lenk K.
Published in: International Journal of Molecular Sciences, Issue 22, 2021, Page(s) 12770, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222312770

Mechanobiological model for simulation of injured cartilage degradation via pro-inflammatory cytokines and mechanical stimulus

Author(s): Eskelinen A.S.A., Tanska P., Florea C., Orozco G.A., Julkunen P., Grodzinsky A.J., Korhonen R.K.
Published in: PLoS computational biology, Issue 6, 2020, Page(s) 1007998, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1007998

Toward Tailored Rehabilitation by Implementation of a Novel Musculoskeletal Finite Element Analysis Pipeline.

Author(s): Esrafilian A, Stenroth L, Mononen ME, Vartiainen P, Tanska P, Karjalainen PA, Suomalainen JS, Arokoski JPA, Saxby DJ, Lloyd DG, Korhonen RK
Published in: IEEE Transactions on Neural Systems and Rehabilitation Engineering, Issue 30, 2022, Page(s) 789-802, ISSN 1534-4320
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tnsre.2022.3159685

A DNA Origami-Based Chiral Plasmonic Sensing Device

Author(s): Huang, Y., Nguyen, M.-K., Natarajan, A.K., Nguyen, V.H., Kuzyk, A.
Published in: ACS Applied Materials and Interfaces, Issue 10, 2018, Page(s) 44221-44225, ISSN 1944-8244
Publisher: American Chemical Society
DOI: 10.1021/acsami.8b19153

An unexpected role of an extra phenolic hydroxyl on the chemical reactivity and bioactivity of catechol or gallol modified hyaluronic acid hydrogels

Author(s): Sumanta Samanta; Vignesh K. Rangasami; N. Arul Murugan; Vijay Singh Parihar; Oommen P. Varghese; Oommen P. Oommen
Published in: Polymer Chemistry, Issue 12, 2021, Page(s) 2987-2991, ISSN 1759-9954
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1py00013f

Subchondral bone plate thickness is associated with micromechanical and microstructural changes in the bovine patella osteochondral junction with different levels of cartilage degeneration.

Author(s): Das Gupta S., Workman J., Finnilä M.A.J., Saarakkala S., Thambyah A.
Published in: Journal of the Mechanical Behavior of Biomedical Materials, Issue 129, 2022, Page(s) 105158, ISSN 1751-6161
Publisher: Elsevier BV
DOI: 10.1016/j.jmbbm.2022.105158

Evaluating and Enhancing the Generalization Performance of Machine Learning Models for Physical Activity Intensity Prediction From Raw Acceleration Data

Author(s): Farrahi, Vahid; Niemela, Maisa; Tjurin, Petra; Kangas, Maarit; Korpelainen, Raija; Jamsa, Timo
Published in: IEEE Journal of Biomedical and Health Informatics, Issue 24, 2020, Page(s) 27-38, ISSN 2168-2194
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/jbhi.2019.2917565

Harnessing hyaluronic acid-based nanoparticles for combination therapy: A novel approach for suppressing systemic inflammation and to promote antitumor macrophage polarization.

Author(s): Vignesh K. Rangasami; Sumanta Samanta; Vijay Singh Parihar; Kenta Asawa; Keying Zhu; Oommen P. Varghese; Yuji Teramura; Yuji Teramura; Bo Nilsson; Jöns Hilborn; Robert A. Harris; Oommen P. Oommen
Published in: Carbohydrate Polymers, Issue 254, 2020, Page(s) 117291, ISSN 0144-8617
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.carbpol.2020.117291

Femoral strength and strains in sideways fall: Validation of finite element models against bilateral strain measurements

Author(s): Kok J., Grassi L., Gustafsson A., Isaksson H.
Published in: Journal of Biomechanics, Issue 122, 2021, Page(s) 110445, ISSN 0021-9290
Publisher: Elsevier BV
DOI: 10.1016/j.jbiomech.2021.110445

Decoding working memory task condition using magnetoencephalography source level long-range phase coupling patterns.

Author(s): Jaakko Johannes Syrjälä; Alessio Basti; Roberto Guidotti; Laura Marzetti; Vittorio Pizzella
Published in: Journal of Neural Engineering, Issue 18, 2021, Page(s) 016027, ISSN 1741-2560
Publisher: Institute of Physics Publishing
DOI: 10.1088/1741-2552/abcefe

Prediction of local fixed charge density loss in cartilage following ACL injury and reconstruction: A computational proof-of-concept study with MRI follow-up

Author(s): Orozco G.A., Bolcos P., Mohammadi A., Tanaka M.S., Yang M., Link T.M., Ma B., Li X., Tanska P., Korhonen R.K.
Published in: Journal of Orthopaedic Research, Issue 39, 2020, Page(s) 1064-1081, ISSN 0736-0266
Publisher: Elsevier BV
DOI: 10.1002/jor.24797

A numerical framework for mechano-regulated tendon healing-Simulation of early regeneration of the Achilles tendon

Author(s): Notermans T., Tanska P., Korhonen R.K., Khayyeri H., Isaksson H.
Published in: Plos Computational Biology, Issue 17, 2021, Page(s) e1008636, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1008636

Raman microspectroscopic analysis of the tissue-specific composition of the human osteochondral junction in osteoarthritis:a pilot study

Author(s): Das Gupta, S. (Shuvashis); Finnilä, M. A. (Mikko A.J.); Karhula, S. S. (Sakari S.); Kauppinen, S. (Sami); Joukainen, A. (Antti); Kröger, H. (Heikki); Korhonen, R. K. (Rami K.); Thambyah, A. (Ashvin); Rieppo, L. (Lassi); Saarakkala, S. (Simo)
Published in: Acta Biomaterialia, Issue 106, 2020, Page(s) 145-155, ISSN 1742-7061
Publisher: Elsevier BV

Larger Connection Radius Increases Hub Astrocyte Number in a 3-D Neuron–Astrocyte Network Model

Author(s): Kerstin Lenk; Barbara Genocchi; Michael Taynnan Barros; Jari Hyttinen
Published in: IEEE Transactions on Molecular, Biological and Multi-Scale Communications, Issue 7, 2021, Page(s) 83-88, ISSN 2332-7804
Publisher: Institute of Electrical and Electronics Engineers Inc.
DOI: 10.1109/tmbmc.2021.3054890

Correlates of physical activity behavior in adults : a data mining approach

Author(s): Farrahi V., Niemelä M., Kärmeniemi M., Puhakka S., Kangas M., Korpelainen R., Jämsä T.
Published in: International journal of behavioral nutrition and physical activity, Issue 17, 2020, Page(s) 94, ISSN 1479-5868
Publisher: BioMed Central
DOI: 10.1186/s12966-020-00996-7

Automated analysis of rabbit knee calcified cartilage morphology using micro-computed tomography and deep learning.

Author(s): Santeri J. O. Rytky; Lingwei Huang; Petri Tanska; Aleksei Tiulpin; Aleksei Tiulpin; Egor Panfilov; Walter Herzog; Rami K. Korhonen; Simo Saarakkala; Simo Saarakkala; Mikko A. J. Finnilä; Mikko A. J. Finnilä; Mikko A. J. Finnilä
Published in: Journal of Anatomy, Issue 239/2, 2021, Page(s) 251-263, ISSN 0021-8782
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/joa.13435

An EMG-assisted muscle-force driven finite element analysis pipeline to investigate joint- and tissue-level mechanical responses in functional activities: towards a rapid assessment toolbox

Author(s): Esrafilian A, Stenroth L, Mononen ME, Vartiainen PEJ, Tanska P, Karjalainen PA, Suomalainen JS, Arokoski JPA, Saxby D, Lloyd DG, Korhonen RK
Published in: IEEE Transactions on Bio-medical Engineering, 2022, ISSN 0018-9294
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tbme.2022.3156018

Prolonged bouts of sedentary time and cardiac autonomic function in midlife

Author(s): Niemelä M., Kiviniemi A., Kangas M., Farrahi V., Leinonen A., Ahola R., Tammelin T., Auvinen J., Korpelainen R., Jämsä T.
Published in: Translational Sports Medicine, Issue 2, 2019, Page(s) 341-350, ISSN 2573-8488
Publisher: John Wiley & Sons
DOI: 10.1002/tsm2.100

http://urn.fi/urn:nbn:fi-fe202201031034

Author(s): Huang L., Riihioja I., Tanska P., Ojanen S., Palosaari S., Kröger H., Saarakkala S.J., Herzog W., Korhonen R.K., Finnilä M.A.J.
Published in: Journal of orthopaedic research, Issue 39, 2022, Page(s) 2556 - 2567, ISSN 0736-0266
Publisher: Elsevier BV
DOI: 10.1002/jor.25009

The effect of constitutive representations and structural constituents of ligaments on knee joint mechanics

Author(s): Gustavo A. Orozco, Petri Tanska, Mika E. Mononen, Kimmo S. Halonen, Rami K. Korhonen
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-20739-w

A novel mechanobiological model can predict how physiologically relevant dynamic loading causes proteoglycan loss in mechanically injured articular cartilage.

Author(s): Orozco, Gustavo A.; Tanska, Petri; Florea, Cristina; Grodzinsky, Alan J.; Korhonen, Rami K.
Published in: Scientific Reports, Issue 8, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-33759-3

Shear strain and inflammation-induced fixed charge density loss in the knee joint cartilage following ACL injury and reconstruction: A computational study

Author(s): Orozco G.A., Eskelinen A.S.A., Kosonen J.P., Tanaka M.S., Yang M., Link T.M., Ma B., Li X., Grodzinsky A.J., Korhonen R.K., Tanska P.
Published in: Journal of orthopaedic research, 2021, ISSN 0736-0266
Publisher: Elsevier BV
DOI: 10.1002/jor.25177

Machine-learning models for activity class prediction : a comparative study of feature selection and classification algorithms

Author(s): Chong J, Tjurin P, Niemelä M, Jämsä T, Farrahi V.
Published in: Gait & posture, Issue 89, 2021, Page(s) 45-53, ISSN 0966-6362
Publisher: Elsevier BV
DOI: 10.1016/j.gaitpost.2021.06.017

Brain Functional Connectivity Through Phase Coupling of Neuronal Oscillations: A Perspective From Magnetoencephalography.

Author(s): Laura Marzetti; Laura Marzetti; Alessio Basti; Alessio Basti; Federico Chella; Federico Chella; Antea D'Andrea; Antea D'Andrea; Jaakko Syrjälä; Jaakko Syrjälä; Vittorio Pizzella; Vittorio Pizzella
Published in: Frontiers in Neuroscience, Vol 13 (2019), Issue 13, 2019, Page(s) 964, ISSN 1662-4548
Publisher: Frontiers Research Foundation
DOI: 10.3389/fnins.2019.00964

12 Degrees of Freedom Muscle Force Driven Fibril-Reinforced Poroviscoelastic Finite Element Model of the Knee Joint

Author(s): Esrafilian A., Stenroth L., Mononen M.E., Tanska P., Van Rossom S., Lloyd D.G., Jonkers I., Korhonen R.K.
Published in: IEEE Transactions on Neural Systems and Rehabilitation Engineering, Issue 29, 2020, Page(s) 123-133, ISSN 1534-4320
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tnsre.2020.3037411

Bidirectional cell-matrix interaction dictates neuronal network formation in a brain-mimetic 3D scaffold.

Author(s): Samanta S., Ylä-Outinen L., Rangasami V.K., Narkilahti S., Oommen O.P.
Published in: Acta Biomaterialia, Issue 140, 2021, Page(s) 314-323, ISSN 1742-7061
Publisher: Elsevier BV
DOI: 10.1016/j.actbio.2021.12.010

Fracture behavior of a composite of bone and calcium sulfate/hydroxyapatite.

Author(s): Kok J., Törnquist E., Raina D.B., Le Cann S., Novak V., Sirka A., Lidgren L., Grassi L., Isaksson H.
Published in: Journal of the Mechanical Behavior of Biomedical Materials, Issue 130, 2022, Page(s) 105201, ISSN 1751-6161
Publisher: Elsevier BV
DOI: 10.1016/j.jmbbm.2022.105201

Interpenetrating gallol functionalized tissue adhesive hyaluronic acid hydrogel polarizes macrophages to an immunosuppressive phenotype.

Author(s): Samanta S., Rangasami V.K., Sarlus H., Samal J.R.K., Evans A.D., Parihar V.S., Varghese O.P., Harris R.A., Oommen O.P.
Published in: Acta Biomaterialia, Issue 142, 2022, Page(s) 36-48, ISSN 1742-7061
Publisher: Elsevier BV
DOI: 10.1016/j.actbio.2022.01.048

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