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Biomedical Engineering and Medical Physics

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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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