Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

Authors: Yun Zhang, Jeremy A. Miller, Jeongbin Park, Boudewijn P. Lelieveldt, Brian Long, Tamim Abdelaal, Brian D. Aevermann, Tommaso Biancalani, Charles Comiter, Oleh Dzyubachyk, Jeroen Eggermont, Christoffer Mattsson Langseth, Viktor Petukhov, Gabriele Scalia, Eeshit Dhaval Vaishnav, Yilin Zhao, Ed S. Lein, Richard H. Scheuermann

Source: Scientific Reports, Vol 13, Iss 1, Pp 1-17 (2023)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/e59c6e5249474f85a08d3e6a7931d55b

Antisense oligonucleotide-mediated disruption of HTT caspase-6 cleavage site ameliorates the phenotype of YAC128 Huntington disease mice

Authors: Elsa C. Kuijper, Maurice Overzier, Ernst Suidgeest, Oleh Dzyubachyk, Cécile Maguin, Jean-Baptiste Pérot, Julien Flament, Yavuz Ariyurek, Hailiang Mei, Ronald A.M. Buijsen, Louise van der Weerd, Willeke van Roon-Mom

Source: Neurobiology of Disease, Vol 190, Iss , Pp 106368- (2024)

Subject Terms: Huntington disease, YAC128 mice, Antisense oligonucleotides, Caspase-6, RNA splicing, RNA sequence analysis, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S0969996123003844; https://doaj.org/toc/1095-953X

Access URL: https://doaj.org/article/0b4874be3df4497fb539494749184266

Reducing Manual Annotation Costs for Cell Segmentation by Upgrading Low-Quality Annotations

Authors: Serban Vădineanu, Daniël M. Pelt, Oleh Dzyubachyk, Kees Joost Batenburg

Source: Journal of Imaging, Vol 10, Iss 7, p 172 (2024)

Subject Terms: annotation enhancement, annotation errors, cell segmentation, deep learning, Photography, TR1-1050, Computer applications to medicine. Medical informatics, R858-859.7, Electronic computers. Computer science, QA75.5-76.95

File Description: electronic resource

Relation: https://www.mdpi.com/2313-433X/10/7/172; https://doaj.org/toc/2313-433X

Access URL: https://doaj.org/article/54909f79d8f54aa1987cc979550a3b43

Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation

Authors: Philippe C. Habets, Konstantinos Kalafatakis, Oleh Dzyubachyk, Steven J.A. van der Werff, Arlin Keo, Jamini Thakrar, Ahmed Mahfouz, Alberto M. Pereira, Georgina M. Russell, Stafford L. Lightman, Onno C. Meijer

Source: Neurobiology of Stress, Vol 22, Iss , Pp 100514- (2023)

Subject Terms: fMRI, Transcriptomics, Brain, Allen human brain atlas, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429, Neurophysiology and neuropsychology, QP351-495

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352289523000024; https://doaj.org/toc/2352-2895

Access URL: https://doaj.org/article/9eed16f9152f48aa90b190994bf42f39

Biosensor Cell-Fit-HD4D for correlation of single-cell fate and microscale energy deposition in complex ion beams

Authors: Julian Schlegel, Hans Liew, Katrin Rein, Oleh Dzyubachyk, Jürgen Debus, Amir Abdollahi, Martin Niklas

Source: STAR Protocols, Vol 3, Iss 4, Pp 101798- (2022)

Subject Terms: Biophysics, Biotechnology and bioengineering, Cancer, Microscopy, Molecular biology, Molecular/Chemical probes, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166722006785; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/08a3a08b0c7743dfbf15198c38af86c6

Iron loading is a prominent feature of activated microglia in Alzheimer’s disease patients

Authors: Boyd Kenkhuis, Antonios Somarakis, Lorraine de Haan, Oleh Dzyubachyk, Marieke E. IJsselsteijn, Noel F. C. C. de Miranda, Boudewijn P. F. Lelieveldt, Jouke Dijkstra, Willeke M. C. van Roon-Mom, Thomas Höllt, Louise van der Weerd

Source: Acta Neuropathologica Communications, Vol 9, Iss 1, Pp 1-15 (2021)

Subject Terms: Alzheimer, Microglia, Iron, Ferritin, Human, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://doaj.org/toc/2051-5960

Access URL: https://doaj.org/article/3f4646cb0a074c658337fbd49da6c5aa

Transcriptomic Signatures Associated With Regional Cortical Thickness Changes in Parkinson’s Disease

Authors: Arlin Keo, Oleh Dzyubachyk, Jeroen van der Grond, Jacobus J. van Hilten, Marcel J. T. Reinders, Ahmed Mahfouz

Source: Frontiers in Neuroscience, Vol 15 (2021)

Subject Terms: cortical thickness, neurodegenerative diseases, neuroimaging data, imaging-genetics, gene expression analysis, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnins.2021.733501/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/d5a7af1035c84dc9bf48d196aaec0dc7

Molecular characterization of the stress network in individuals at risk for schizophrenia

Authors: Mandy Meijer, Arlin Keo, Judith M.C. van Leeuwen, Oleh Dzyubachyk, Onno C. Meijer, Christiaan H. Vinkers, Ahmed Mahfouz

Source: Neurobiology of Stress, Vol 14, Iss , Pp 100307- (2021)

Subject Terms: Stress reactivity, Stress network, Stress-related diseases, Stress sensitivity, Molecular correlates, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429, Neurophysiology and neuropsychology, QP351-495

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352289521000151; https://doaj.org/toc/2352-2895

Access URL: https://doaj.org/article/c6ba5c1e0e724568860d687c04ec0407

Computer-aided evaluation of inflammatory changes over time on MRI of the spine in patients with suspected axial spondyloarthritis: a feasibility study

Authors: Evgeni Aizenberg, Rosaline van den Berg, Zineb Ez-Zaitouni, Désirée van der Heijde, Monique Reijnierse, Oleh Dzyubachyk, Boudewijn P.F. Lelieveldt

Source: BMC Medical Imaging, Vol 17, Iss 1, Pp 1-9 (2017)

Subject Terms: Axial Spondyloarthritis, Magnetic resonance imaging, Inflammation, Comparative visualization, Image registration, Medical technology, R855-855.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12880-017-0226-4; https://doaj.org/toc/1471-2342

Access URL: https://doaj.org/article/c8259d57eb2a4f68b84cc0beb38293ba

Human Brown Adipose Tissue Estimated With Magnetic Resonance Imaging Undergoes Changes in Composition After Cold Exposure: An in vivo MRI Study in Healthy Volunteers

Authors: Gustavo Abreu-Vieira, Aashley S. D. Sardjoe Mishre, Jedrzej Burakiewicz, Laura G. M. Janssen, Kimberly J. Nahon, Jari A. van der Eijk, Titia T. Riem, Mariëtte R. Boon, Oleh Dzyubachyk, Andrew G. Webb, Patrick C. N. Rensen, Hermien E. Kan

Source: Frontiers in Endocrinology, Vol 10 (2020)

Subject Terms: brown adipose tissue, lipid metabolism, cold exposure, thermogenesis, magnetic resonance imaging, fat fraction, Diseases of the endocrine glands. Clinical endocrinology, RC648-665

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fendo.2019.00898/full; https://doaj.org/toc/1664-2392

Access URL: https://doaj.org/article/15a274d6c28646b1a78bc2da2a5f2bba

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington’s Disease

Authors: Arlin Keo, N. Ahmad Aziz, Oleh Dzyubachyk, Jeroen van der Grond, Willeke M. C. van Roon-Mom, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders, Ahmed Mahfouz

Source: Frontiers in Molecular Neuroscience, Vol 10 (2017)

Subject Terms: gene co-expression, polyglutamine diseases, human brain, Huntington’s disease, neurodegeneration, MRI, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: http://journal.frontiersin.org/article/10.3389/fnmol.2017.00399/full; https://doaj.org/toc/1662-5099

Access URL: https://doaj.org/article/82a38fdd6d4e4c7fa181c03435522c84

MRI Mouse Brain Data of Ischemic Lesion after Transient Middle Cerebral Artery Occlusion

Authors: Inge A. Mulder, Artem Khmelinskii, Oleh Dzyubachyk, Sebastiaan de Jong, Marieke J. H. Wermer, Mathias Hoehn, Boudewijn P. F. Lelieveldt, Arn M. J. M. van den Maagdenberg

Source: Frontiers in Neuroinformatics, Vol 11 (2017)

Subject Terms: ischemic stroke, MRI, mouse, data collection, brain, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: http://journal.frontiersin.org/article/10.3389/fninf.2017.00051/full; https://doaj.org/toc/1662-5196

Access URL: https://doaj.org/article/c91eee59c96349f1b3d01270fed5a9df

Extracellular matrix defects in aneurysmal Fibulin-4 mice predispose to lung emphysema.

Authors: Natasja W M Ramnath, Koen M van de Luijtgaarden, Ingrid van der Pluijm, Menno van Nimwegen, Paula M van Heijningen, Sigrid M A Swagemakers, Bibi S van Thiel, Ruziedi Y Ridwan, Nicole van Vliet, Marcel Vermeij, Luuk J A C Hawinkels, Anne de Munck, Oleh Dzyubachyk, Erik Meijering, Peter van der Spek, Robbert Rottier, Hiromi Yanagisawa, Rudi W Hendriks, Roland Kanaar, Ellen V Rouwet, Alex Kleinjan, Jeroen Essers

Source: PLoS ONE, Vol 9, Iss 9, p e106054 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/54e4a897fc8f4940a384b4aa95d8a42b

Interactive local super-resolution reconstruction of whole-body MRI mouse data: a pilot study with applications to bone and kidney metastases.

Authors: Oleh Dzyubachyk, Artem Khmelinskii, Esben Plenge, Peter Kok, Thomas J A Snoeks, Dirk H J Poot, Clemens W G M Löwik, Charl P Botha, Wiro J Niessen, Louise van der Weerd, Erik Meijering, Boudewijn P F Lelieveldt

Source: PLoS ONE, Vol 9, Iss 9, p e108730 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4181866?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/8ce9aaf6782144f3b9daba23161a20c9

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