---
_id: '11478'
abstract:
- lang: eng
  text: Cerebral organoids differentiated from human-induced pluripotent stem cells
    (hiPSC) provide a unique opportunity to investigate brain development. However,
    organoids usually lack microglia, brain-resident immune cells, which are present
    in the early embryonic brain and participate in neuronal circuit development.
    Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3
    and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol.
    Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented,
    3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When
    we guide the retinal organoid differentiation with low-dosed BMP4, we prevent
    cup development and enhance microglia and 3D-cysts formation. Mass spectrometry
    identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed
    this microglia-preferred environment also within the unguided protocol, providing
    insight into microglial behavior and migration and offer a model to study how
    they enter and distribute within the human brain.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank the scientific service units at ISTA, specifically the lab
  support facility and imaging & optics facility for their support; Nicolas Armel
  for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner
  for their help in human brain tissue collection, Rouven Schulz for his insights
  into the functional assays We thank all members of the Siegert group for constant
  feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for
  feedback on the manuscript. This project has received funding from the European
  Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
  program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung
  Niederösterreich (grant No. Sc19-017 to V.H.).
article_number: '104580'
article_processing_charge: Yes
article_type: original
author:
- first_name: Katarina
  full_name: Bartalska, Katarina
  id: 4D883232-F248-11E8-B48F-1D18A9856A87
  last_name: Bartalska
- first_name: Verena
  full_name: Hübschmann, Verena
  id: 32B7C918-F248-11E8-B48F-1D18A9856A87
  last_name: Hübschmann
- first_name: Medina
  full_name: Korkut, Medina
  id: 4B51CE74-F248-11E8-B48F-1D18A9856A87
  last_name: Korkut
  orcid: 0000-0003-4309-2251
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Alessandro
  full_name: Venturino, Alessandro
  id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
  last_name: Venturino
  orcid: 0000-0003-2356-9403
- first_name: Karl
  full_name: Rössler, Karl
  last_name: Rössler
- first_name: Thomas
  full_name: Czech, Thomas
  last_name: Czech
- first_name: Sandra
  full_name: Siegert, Sandra
  id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
  last_name: Siegert
  orcid: 0000-0001-8635-0877
citation:
  ama: Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of
    microglia-like cell occurrence during retinal organoid differentiation. <i>iScience</i>.
    2022;25(7). doi:<a href="https://doi.org/10.1016/j.isci.2022.104580">10.1016/j.isci.2022.104580</a>
  apa: Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler,
    K., … Siegert, S. (2022). A systematic characterization of microglia-like cell
    occurrence during retinal organoid differentiation. <i>IScience</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.isci.2022.104580">https://doi.org/10.1016/j.isci.2022.104580</a>
  chicago: Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro
    Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization
    of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>.
    Elsevier, 2022. <a href="https://doi.org/10.1016/j.isci.2022.104580">https://doi.org/10.1016/j.isci.2022.104580</a>.
  ieee: K. Bartalska <i>et al.</i>, “A systematic characterization of microglia-like
    cell occurrence during retinal organoid differentiation,” <i>iScience</i>, vol.
    25, no. 7. Elsevier, 2022.
  ista: Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech
    T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence
    during retinal organoid differentiation. iScience. 25(7), 104580.
  mla: Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like
    Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>, vol.
    25, no. 7, 104580, Elsevier, 2022, doi:<a href="https://doi.org/10.1016/j.isci.2022.104580">10.1016/j.isci.2022.104580</a>.
  short: K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler,
    T. Czech, S. Siegert, IScience 25 (2022).
date_created: 2022-07-03T22:01:33Z
date_published: 2022-07-15T00:00:00Z
date_updated: 2023-11-02T12:21:33Z
day: '15'
ddc:
- '610'
department:
- _id: SaSi
doi: 10.1016/j.isci.2022.104580
ec_funded: 1
external_id:
  isi:
  - '000830428500005'
file:
- access_level: open_access
  checksum: a470b74e1b3796c710189c81a4cd4329
  content_type: application/pdf
  creator: cchlebak
  date_created: 2022-07-04T08:19:25Z
  date_updated: 2022-07-04T08:19:25Z
  file_id: '11480'
  file_name: 2022_iScience_Bartalska.pdf
  file_size: 19400048
  relation: main_file
  success: 1
file_date_updated: 2022-07-04T08:19:25Z
has_accepted_license: '1'
intvolume: '        25'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715571'
  name: Microglia action towards neuronal circuit formation and function in health
    and disease
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
  name: IST Austria Open Access Fund
- _id: 9B99D380-BA93-11EA-9121-9846C619BF3A
  grant_number: SC19-017
  name: How human microglia shape developing neurons during health and inflammation
publication: iScience
publication_identifier:
  eissn:
  - 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '12117'
    relation: other
    status: public
scopus_import: '1'
status: public
title: A systematic characterization of microglia-like cell occurrence during retinal
  organoid differentiation
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2022'
...
---
_id: '12244'
abstract:
- lang: eng
  text: Environmental cues influence the highly dynamic morphology of microglia. Strategies
    to characterize these changes usually involve user-selected morphometric features,
    which preclude the identification of a spectrum of context-dependent morphological
    phenotypes. Here we develop MorphOMICs, a topological data analysis approach,
    which enables semiautomatic mapping of microglial morphology into an atlas of
    cue-dependent phenotypes and overcomes feature-selection biases and biological
    variability. We extract spatially heterogeneous and sexually dimorphic morphological
    phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines
    with maturation but increases over the disease trajectories in two neurodegeneration
    mouse models, with females showing a faster morphological shift in affected brain
    regions. Remarkably, microglia morphologies reflect an adaptation upon repeated
    exposure to ketamine anesthesia and do not recover to control morphologies. Finally,
    we demonstrate that both long primary processes and short terminal processes provide
    distinct insights to morphological phenotypes. MorphOMICs opens a new perspective
    to characterize microglial morphology.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: ScienComp
acknowledgement: We thank the scientific service units at ISTA, in particular M. Schunn’s
  team at the preclinical facility, and especially our colony manager S. Haslinger,
  for excellent support. We are also grateful to the ISTA Imaging & Optics Facility,
  and in particular C. Sommer for helping with the data file conversions. We thank
  R. Erhart from the ISTA Scientific Computing Unit for improving the script performance.
  We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert
  group for constant feedback on the project and on the manuscript. This research
  was supported by the European Union Horizon 2020 research and innovation program
  under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the
  European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding
  to the Blue Brain Project, a research center of the École polytechnique fédérale
  de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes
  of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB
  Foundation. The funders had no role in study design, data collection and analysis,
  decision to publish or preparation of the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Gloria
  full_name: Colombo, Gloria
  id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
  last_name: Colombo
  orcid: 0000-0001-9434-8902
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Lida
  full_name: Kanari, Lida
  last_name: Kanari
- first_name: Alessandro
  full_name: Venturino, Alessandro
  id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
  last_name: Venturino
  orcid: 0000-0003-2356-9403
- first_name: Rouven
  full_name: Schulz, Rouven
  id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
  last_name: Schulz
  orcid: 0000-0001-5297-733X
- first_name: Martina
  full_name: Scolamiero, Martina
  last_name: Scolamiero
- first_name: Jens
  full_name: Agerberg, Jens
  last_name: Agerberg
- first_name: Hansruedi
  full_name: Mathys, Hansruedi
  last_name: Mathys
- first_name: Li-Huei
  full_name: Tsai, Li-Huei
  last_name: Tsai
- first_name: Wojciech
  full_name: Chachólski, Wojciech
  last_name: Chachólski
- first_name: Kathryn
  full_name: Hess, Kathryn
  last_name: Hess
- first_name: Sandra
  full_name: Siegert, Sandra
  id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
  last_name: Siegert
  orcid: 0000-0001-8635-0877
citation:
  ama: Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology,
    morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>.
    2022;25(10):1379-1393. doi:<a href="https://doi.org/10.1038/s41593-022-01167-6">10.1038/s41593-022-01167-6</a>
  apa: Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero,
    M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs,
    reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41593-022-01167-6">https://doi.org/10.1038/s41593-022-01167-6</a>
  chicago: Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven
    Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial
    Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature
    Neuroscience</i>. Springer Nature, 2022. <a href="https://doi.org/10.1038/s41593-022-01167-6">https://doi.org/10.1038/s41593-022-01167-6</a>.
  ieee: G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs,
    reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>,
    vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.
  ista: Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg
    J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping
    microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes.
    Nature Neuroscience. 25(10), 1379–1393.
  mla: Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs,
    Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>,
    vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href="https://doi.org/10.1038/s41593-022-01167-6">10.1038/s41593-022-01167-6</a>.
  short: G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero,
    J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature
    Neuroscience 25 (2022) 1379–1393.
date_created: 2023-01-16T09:53:07Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2024-03-25T23:30:10Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41593-022-01167-6
ec_funded: 1
external_id:
  isi:
  - '000862214700001'
  pmid:
  - '36180790'
file:
- access_level: open_access
  checksum: 28431146873096f52e0107b534f178c9
  content_type: application/pdf
  creator: dernst
  date_created: 2023-01-30T08:06:56Z
  date_updated: 2023-01-30T08:06:56Z
  file_id: '12437'
  file_name: 2022_NatureNeuroscience_Colombo.pdf
  file_size: 23789835
  relation: main_file
  success: 1
file_date_updated: 2023-01-30T08:06:56Z
has_accepted_license: '1'
intvolume: '        25'
isi: 1
issue: '10'
keyword:
- General Neuroscience
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1379-1393
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715571'
  name: Microglia action towards neuronal circuit formation and function in health
    and disease
publication: Nature Neuroscience
publication_identifier:
  eissn:
  - 1546-1726
  issn:
  - 1097-6256
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - description: News on ISTA website
    relation: press_release
    url: https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/
  record:
  - id: '12378'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: A tool for mapping microglial morphology, morphOMICs, reveals brain-region
  and sex-dependent phenotypes
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 25
year: '2022'
...
---
_id: '9642'
abstract:
- lang: eng
  text: Perineuronal nets (PNNs), components of the extracellular matrix, preferentially
    coat parvalbumin-positive interneurons and constrain critical-period plasticity
    in the adult cerebral cortex. Current strategies to remove PNN are long-lasting,
    invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic
    ketamine as a method with minimal behavioral effect. We find that this paradigm
    strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like
    plasticity. Microglia are critically involved in PNN loss because they engage
    with parvalbumin-positive neurons in their defined cortical layer. We identify
    external 60-Hz light-flickering entrainment to recapitulate microglia-mediated
    PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques,
    does not induce PNN loss, suggesting microglia might functionally tune to distinct
    brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative
    form of PNN intervention in the healthy adult brain.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: We thank the scientific service units at IST Austria, especially
  the IST bioimaging facility, the preclinical facility, and, specifically, Michael
  Schunn and Sonja Haslinger for excellent support; Plexxikon for the PLX food; the
  Csicsvari group for advice and equipment for in vivo recording; Jürgen Siegert for
  the light-entrainment design; Marco Benevento, Soledad Gonzalo Cogno, Pat King,
  and all Siegert group members for constant feedback on the project and manuscript;
  Lorena Pantano (PILM Bioinformatics Core) for assisting with sample-size determination
  for OD plasticity experiments; and Ana Morello from MIT for technical assistance
  with VEPs recordings. This research was supported by a DOC Fellowship from the Austrian
  Academy of Sciences at the Institute of Science and Technology Austria to R.S.,
  from the European Union Horizon 2020 research and innovation program under the Marie
  Skłodowska-Curie Actions program (grants 665385 to G.C.; 754411 to R.J.A.C.), the
  European Research Council (grant 715571 to S.S.), and the National Eye Institute
  of the National Institutes of Health under award numbers R01EY029245 (to M.F.B.)
  and R01EY023037 (diversity supplement to H.D.J-C.).
article_number: '109313'
article_processing_charge: No
article_type: original
author:
- first_name: Alessandro
  full_name: Venturino, Alessandro
  id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
  last_name: Venturino
  orcid: 0000-0003-2356-9403
- first_name: Rouven
  full_name: Schulz, Rouven
  id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87
  last_name: Schulz
  orcid: 0000-0001-5297-733X
- first_name: Héctor
  full_name: De Jesús-Cortés, Héctor
  last_name: De Jesús-Cortés
- first_name: Margaret E
  full_name: Maes, Margaret E
  id: 3838F452-F248-11E8-B48F-1D18A9856A87
  last_name: Maes
  orcid: 0000-0001-9642-1085
- first_name: Balint
  full_name: Nagy, Balint
  id: 93C65ECC-A6F2-11E9-8DF9-9712E6697425
  last_name: Nagy
- first_name: Francis
  full_name: Reilly-Andújar, Francis
  last_name: Reilly-Andújar
- first_name: Gloria
  full_name: Colombo, Gloria
  id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
  last_name: Colombo
  orcid: 0000-0001-9434-8902
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Florianne E
  full_name: Schoot Uiterkamp, Florianne E
  id: 3526230C-F248-11E8-B48F-1D18A9856A87
  last_name: Schoot Uiterkamp
- first_name: Mark F.
  full_name: Bear, Mark F.
  last_name: Bear
- first_name: Sandra
  full_name: Siegert, Sandra
  id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
  last_name: Siegert
  orcid: 0000-0001-8635-0877
citation:
  ama: Venturino A, Schulz R, De Jesús-Cortés H, et al. Microglia enable mature perineuronal
    nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment
    in the healthy brain. <i>Cell Reports</i>. 2021;36(1). doi:<a href="https://doi.org/10.1016/j.celrep.2021.109313">10.1016/j.celrep.2021.109313</a>
  apa: Venturino, A., Schulz, R., De Jesús-Cortés, H., Maes, M. E., Nagy, B., Reilly-Andújar,
    F., … Siegert, S. (2021). Microglia enable mature perineuronal nets disassembly
    upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain.
    <i>Cell Reports</i>. Elsevier. <a href="https://doi.org/10.1016/j.celrep.2021.109313">https://doi.org/10.1016/j.celrep.2021.109313</a>
  chicago: Venturino, Alessandro, Rouven Schulz, Héctor De Jesús-Cortés, Margaret
    E Maes, Balint Nagy, Francis Reilly-Andújar, Gloria Colombo, et al. “Microglia
    Enable Mature Perineuronal Nets Disassembly upon Anesthetic Ketamine Exposure
    or 60-Hz Light Entrainment in the Healthy Brain.” <i>Cell Reports</i>. Elsevier,
    2021. <a href="https://doi.org/10.1016/j.celrep.2021.109313">https://doi.org/10.1016/j.celrep.2021.109313</a>.
  ieee: A. Venturino <i>et al.</i>, “Microglia enable mature perineuronal nets disassembly
    upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain,”
    <i>Cell Reports</i>, vol. 36, no. 1. Elsevier, 2021.
  ista: Venturino A, Schulz R, De Jesús-Cortés H, Maes ME, Nagy B, Reilly-Andújar
    F, Colombo G, Cubero RJ, Schoot Uiterkamp FE, Bear MF, Siegert S. 2021. Microglia
    enable mature perineuronal nets disassembly upon anesthetic ketamine exposure
    or 60-Hz light entrainment in the healthy brain. Cell Reports. 36(1), 109313.
  mla: Venturino, Alessandro, et al. “Microglia Enable Mature Perineuronal Nets Disassembly
    upon Anesthetic Ketamine Exposure or 60-Hz Light Entrainment in the Healthy Brain.”
    <i>Cell Reports</i>, vol. 36, no. 1, 109313, Elsevier, 2021, doi:<a href="https://doi.org/10.1016/j.celrep.2021.109313">10.1016/j.celrep.2021.109313</a>.
  short: A. Venturino, R. Schulz, H. De Jesús-Cortés, M.E. Maes, B. Nagy, F. Reilly-Andújar,
    G. Colombo, R.J. Cubero, F.E. Schoot Uiterkamp, M.F. Bear, S. Siegert, Cell Reports
    36 (2021).
date_created: 2021-07-11T22:01:16Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2023-08-10T14:09:39Z
day: '06'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1016/j.celrep.2021.109313
ec_funded: 1
external_id:
  isi:
  - '000670188500004'
  pmid:
  - '34233180'
file:
- access_level: open_access
  checksum: f056255f6d01fd9a86b5387635928173
  content_type: application/pdf
  creator: cziletti
  date_created: 2021-07-19T13:32:17Z
  date_updated: 2021-07-19T13:32:17Z
  file_id: '9693'
  file_name: 2021_CellReports_Venturino.pdf
  file_size: 56388540
  relation: main_file
  success: 1
file_date_updated: 2021-07-19T13:32:17Z
has_accepted_license: '1'
intvolume: '        36'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '715571'
  name: Microglia action towards neuronal circuit formation and function in health
    and disease
publication: Cell Reports
publication_identifier:
  eissn:
  - '22111247'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  link:
  - description: News on IST Homepage
    relation: press_release
    url: https://ist.ac.at/en/news/the-twinkle-and-the-brain/
scopus_import: '1'
status: public
title: Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine
  exposure or 60-Hz light entrainment in the healthy brain
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2021'
...
---
_id: '9874'
abstract:
- lang: eng
  text: Myocardial regeneration is restricted to early postnatal life, when mammalian
    cardiomyocytes still retain the ability to proliferate. The molecular cues that
    induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated
    adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster
    is higher expressed in the early postnatal myocardium and decreases in expression
    towards adulthood, especially under conditions of overload, and orchestrates the
    transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy
    by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse
    heart provokes cardiomyocyte proliferation by targeting a network of negative
    cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted
    miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated
    remodeling to overload by derepression of the prohypertrophic transcription factors
    Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on
    cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25
    provokes nearly complete regeneration of the adult myocardium after ischemic injury.
    Our data demonstrate that exploitation of conserved molecular programs can enhance
    the regenerative capacity of the injured heart.
acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands
  Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship
  (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number
  627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência,
  Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator
  of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular
  Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European
  Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council
  and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).
article_number: '4808'
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
  full_name: Raso, Andrea
  last_name: Raso
- first_name: Ellen
  full_name: Dirkx, Ellen
  last_name: Dirkx
- first_name: Vasco
  full_name: Sampaio-Pinto, Vasco
  last_name: Sampaio-Pinto
- first_name: Hamid
  full_name: el Azzouzi, Hamid
  last_name: el Azzouzi
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Daniel W.
  full_name: Sorensen, Daniel W.
  last_name: Sorensen
- first_name: Lara
  full_name: Ottaviani, Lara
  last_name: Ottaviani
- first_name: Servé
  full_name: Olieslagers, Servé
  last_name: Olieslagers
- first_name: Manon M.
  full_name: Huibers, Manon M.
  last_name: Huibers
- first_name: Roel
  full_name: de Weger, Roel
  last_name: de Weger
- first_name: Sailay
  full_name: Siddiqi, Sailay
  last_name: Siddiqi
- first_name: Silvia
  full_name: Moimas, Silvia
  last_name: Moimas
- first_name: Consuelo
  full_name: Torrini, Consuelo
  last_name: Torrini
- first_name: Lorena
  full_name: Zentillin, Lorena
  last_name: Zentillin
- first_name: Luca
  full_name: Braga, Luca
  last_name: Braga
- first_name: Diana S.
  full_name: Nascimento, Diana S.
  last_name: Nascimento
- first_name: Paula A.
  full_name: da Costa Martins, Paula A.
  last_name: da Costa Martins
- first_name: Jop H.
  full_name: van Berlo, Jop H.
  last_name: van Berlo
- first_name: Serena
  full_name: Zacchigna, Serena
  last_name: Zacchigna
- first_name: Mauro
  full_name: Giacca, Mauro
  last_name: Giacca
- first_name: Leon J.
  full_name: De Windt, Leon J.
  last_name: De Windt
citation:
  ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance
    between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
    <i>Nature Communications</i>. 2021;12. doi:<a href="https://doi.org/10.1038/s41467-021-25211-4">10.1038/s41467-021-25211-4</a>
  apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen,
    D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between
    cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration.
    <i>Nature Communications</i>. Springer Nature. <a href="https://doi.org/10.1038/s41467-021-25211-4">https://doi.org/10.1038/s41467-021-25211-4</a>
  chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan
    J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates
    the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac
    Regeneration.” <i>Nature Communications</i>. Springer Nature, 2021. <a href="https://doi.org/10.1038/s41467-021-25211-4">https://doi.org/10.1038/s41467-021-25211-4</a>.
  ieee: A. Raso <i>et al.</i>, “A microRNA program regulates the balance between cardiomyocyte
    hyperplasia and hypertrophy and stimulates cardiac regeneration,” <i>Nature Communications</i>,
    vol. 12. Springer Nature, 2021.
  ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani
    L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin
    L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca
    M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte
    hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications.
    12, 4808.
  mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte
    Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>,
    vol. 12, 4808, Springer Nature, 2021, doi:<a href="https://doi.org/10.1038/s41467-021-25211-4">10.1038/s41467-021-25211-4</a>.
  short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen,
    L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas,
    C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H.
    van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).
date_created: 2021-08-10T11:49:20Z
date_published: 2021-08-10T00:00:00Z
date_updated: 2023-08-11T10:27:03Z
day: '10'
ddc:
- '610'
- '570'
department:
- _id: SaSi
doi: 10.1038/s41467-021-25211-4
external_id:
  isi:
  - '000683910200042'
  pmid:
  - '34376683'
file:
- access_level: open_access
  checksum: 48d8562e8229e4282f3f354b329722c5
  content_type: application/pdf
  creator: asandaue
  date_created: 2021-08-10T12:29:59Z
  date_updated: 2021-08-10T12:29:59Z
  file_id: '9876'
  file_name: 2021_NatureCommunications_Raso.pdf
  file_size: 4364333
  relation: main_file
  success: 1
file_date_updated: 2021-08-10T12:29:59Z
genbank:
- GSE178867
has_accepted_license: '1'
intvolume: '        12'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
  eissn:
  - 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1038/s41467-022-32785-0
scopus_import: '1'
status: public
title: A microRNA program regulates the balance between cardiomyocyte hyperplasia
  and hypertrophy and stimulates cardiac regeneration
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '7369'
abstract:
- lang: eng
  text: Neuronal responses to complex stimuli and tasks can encompass a wide range
    of time scales. Understanding these responses requires measures that characterize
    how the information on these response patterns are represented across multiple
    temporal resolutions. In this paper we propose a metric – which we call multiscale
    relevance (MSR) – to capture the dynamical variability of the activity of single
    neurons across different time scales. The MSR is a non-parametric, fully featureless
    indicator in that it uses only the time stamps of the firing activity without
    resorting to any a priori covariate or invoking any specific structure in the
    tuning curve for neural activity. When applied to neural data from the mEC and
    from the ADn and PoS regions of freely-behaving rodents, we found that neurons
    having low MSR tend to have low mutual information and low firing sparsity across
    the correlates that are believed to be encoded by the region of the brain where
    the recordings were made. In addition, neurons with high MSR contain significant
    information on spatial navigation and allow to decode spatial position or head
    direction as efficiently as those neurons whose firing activity has high mutual
    information with the covariate to be decoded and significantly better than the
    set of neurons with high local variations in their interspike intervals. Given
    these results, we propose that the MSR can be used as a measure to rank and select
    neurons for their information content without the need to appeal to any a priori
    covariate.
acknowledgement: This research was supported by the Kavli Foundation and the Centre
  of Excellence scheme of the Research Council of Norway (Centre for Neural Computation).
  RJC is currently receiving funding from the European Union’s Horizon 2020 research
  and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Matteo
  full_name: Marsili, Matteo
  last_name: Marsili
- first_name: Yasser
  full_name: Roudi, Yasser
  last_name: Roudi
citation:
  ama: Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding
    in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. 2020;48:85-102.
    doi:<a href="https://doi.org/10.1007/s10827-020-00740-x">10.1007/s10827-020-00740-x</a>
  apa: Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2020). Multiscale relevance and
    informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>.
    Springer Nature. <a href="https://doi.org/10.1007/s10827-020-00740-x">https://doi.org/10.1007/s10827-020-00740-x</a>
  chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance
    and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational
    Neuroscience</i>. Springer Nature, 2020. <a href="https://doi.org/10.1007/s10827-020-00740-x">https://doi.org/10.1007/s10827-020-00740-x</a>.
  ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative
    encoding in neuronal spike trains,” <i>Journal of Computational Neuroscience</i>,
    vol. 48. Springer Nature, pp. 85–102, 2020.
  ista: Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative
    encoding in neuronal spike trains. Journal of Computational Neuroscience. 48,
    85–102.
  mla: Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal
    Spike Trains.” <i>Journal of Computational Neuroscience</i>, vol. 48, Springer
    Nature, 2020, pp. 85–102, doi:<a href="https://doi.org/10.1007/s10827-020-00740-x">10.1007/s10827-020-00740-x</a>.
  short: R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience
    48 (2020) 85–102.
date_created: 2020-01-28T10:34:00Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2023-08-17T14:35:22Z
day: '01'
ddc:
- '004'
- '519'
- '570'
department:
- _id: SaSi
doi: 10.1007/s10827-020-00740-x
ec_funded: 1
external_id:
  isi:
  - '000515321800006'
file:
- access_level: open_access
  checksum: 036e9451d6cd0c190ad25791bf82393b
  content_type: application/pdf
  creator: rcubero
  date_created: 2020-01-28T09:31:09Z
  date_updated: 2020-07-14T12:47:56Z
  file_id: '7380'
  file_name: 10827_2020_740_MOESM1_ESM.pdf
  file_size: 1941355
  relation: supplementary_material
- access_level: open_access
  checksum: 4dd8b1fd4b54486f79d82ac7b2a412b2
  content_type: application/pdf
  creator: rcubero
  date_created: 2020-01-28T09:31:09Z
  date_updated: 2020-07-14T12:47:56Z
  file_id: '7381'
  file_name: Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf
  file_size: 3257880
  relation: main_file
file_date_updated: 2020-07-14T12:47:56Z
has_accepted_license: '1'
intvolume: '        48'
isi: 1
keyword:
- Time series analysis
- Multiple time scale analysis
- Spike train data
- Information theory
- Bayesian decoding
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 85-102
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Journal of Computational Neuroscience
publication_identifier:
  eissn:
  - 1573-6873
  issn:
  - 0929-5313
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multiscale relevance and informative encoding in neuronal spike trains
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 48
year: '2020'
...
---
_id: '7632'
abstract:
- lang: eng
  text: The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical
    network supporting goal-directed behaviour, with functions including sensorimotor
    transformations and decision making. In primates, this network links performed
    and observed actions via mirror neurons, which fire both when individuals perform
    an action and when they observe the same action performed by a conspecific. Mirror
    neurons are believed to be important for social learning, but it is not known
    whether mirror-like neurons occur in similar networks in other social species,
    such as rodents, or if they can be measured in such models using paradigms where
    observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in
    PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching
    and wheel-running tasks, and found that cell populations in both areas robustly
    encoded several naturalistic behaviours. However, neural responses to the same
    set of observed actions were absent, although we verified that observer mice were
    attentive to performers and that PPC neurons responded reliably to visual cues.
    Statistical modelling also indicated that executed actions outperformed observed
    actions in predicting neural responses. These results raise the possibility that
    sensorimotor action recognition in rodents could take place outside of the parieto-frontal
    circuit, and underscore that detecting socially-driven neural coding depends critically
    on the species and behavioural paradigm used.
article_number: '5559'
article_processing_charge: No
article_type: original
author:
- first_name: Tuce
  full_name: Tombaz, Tuce
  last_name: Tombaz
- first_name: Benjamin A.
  full_name: Dunn, Benjamin A.
  last_name: Dunn
- first_name: Karoline
  full_name: Hovde, Karoline
  last_name: Hovde
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Bartul
  full_name: Mimica, Bartul
  last_name: Mimica
- first_name: Pranav
  full_name: Mamidanna, Pranav
  last_name: Mamidanna
- first_name: Yasser
  full_name: Roudi, Yasser
  last_name: Roudi
- first_name: Jonathan R.
  full_name: Whitlock, Jonathan R.
  last_name: Whitlock
citation:
  ama: Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal
    network. <i>Scientific reports</i>. 2020;10(1). doi:<a href="https://doi.org/10.1038/s41598-020-62089-6">10.1038/s41598-020-62089-6</a>
  apa: Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P.,
    … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network.
    <i>Scientific Reports</i>. Springer Nature. <a href="https://doi.org/10.1038/s41598-020-62089-6">https://doi.org/10.1038/s41598-020-62089-6</a>
  chicago: Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica,
    Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation
    in the Mouse Parieto-Frontal Network.” <i>Scientific Reports</i>. Springer Nature,
    2020. <a href="https://doi.org/10.1038/s41598-020-62089-6">https://doi.org/10.1038/s41598-020-62089-6</a>.
  ieee: T. Tombaz <i>et al.</i>, “Action representation in the mouse parieto-frontal
    network,” <i>Scientific reports</i>, vol. 10, no. 1. Springer Nature, 2020.
  ista: Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock
    JR. 2020. Action representation in the mouse parieto-frontal network. Scientific
    reports. 10(1), 5559.
  mla: Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.”
    <i>Scientific Reports</i>, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:<a
    href="https://doi.org/10.1038/s41598-020-62089-6">10.1038/s41598-020-62089-6</a>.
  short: T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y.
    Roudi, J.R. Whitlock, Scientific Reports 10 (2020).
date_created: 2020-04-05T22:00:47Z
date_published: 2020-03-27T00:00:00Z
date_updated: 2023-08-18T10:25:13Z
day: '27'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41598-020-62089-6
external_id:
  isi:
  - '000560406800007'
file:
- access_level: open_access
  checksum: e6cfaaaf7986532132934400038b824a
  content_type: application/pdf
  creator: dernst
  date_created: 2020-04-06T10:44:23Z
  date_updated: 2020-07-14T12:48:01Z
  file_id: '7644'
  file_name: 2020_ScientificReports_Tombaz.pdf
  file_size: 2621249
  relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: '        10'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific reports
publication_identifier:
  eissn:
  - '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Action representation in the mouse parieto-frontal network
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '7128'
abstract:
- lang: eng
  text: Loss of functional cardiomyocytes is a major determinant of heart failure
    after myocardial infarction. Previous high throughput screening studies have identified
    a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate
    cardiac regeneration in mice. Here, we show that all of the most effective of
    these miRNAs activate nuclear localization of the master transcriptional cofactor
    Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In
    particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging
    on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin
    ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative
    miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization
    by targeting Cofilin2, a process that by itself activates YAP nuclear translocation.
    Thus, activation of YAP and modulation of the actin cytoskeleton are major components
    of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte
    proliferation.
article_processing_charge: Yes
article_type: original
author:
- first_name: Consuelo
  full_name: Torrini, Consuelo
  last_name: Torrini
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Ellen
  full_name: Dirkx, Ellen
  last_name: Dirkx
- first_name: Luca
  full_name: Braga, Luca
  last_name: Braga
- first_name: Hashim
  full_name: Ali, Hashim
  last_name: Ali
- first_name: Giulia
  full_name: Prosdocimo, Giulia
  last_name: Prosdocimo
- first_name: Maria Ines
  full_name: Gutierrez, Maria Ines
  last_name: Gutierrez
- first_name: Chiara
  full_name: Collesi, Chiara
  last_name: Collesi
- first_name: Danilo
  full_name: Licastro, Danilo
  last_name: Licastro
- first_name: Lorena
  full_name: Zentilin, Lorena
  last_name: Zentilin
- first_name: Miguel
  full_name: Mano, Miguel
  last_name: Mano
- first_name: Serena
  full_name: Zacchigna, Serena
  last_name: Zacchigna
- first_name: Michele
  full_name: Vendruscolo, Michele
  last_name: Vendruscolo
- first_name: Matteo
  full_name: Marsili, Matteo
  last_name: Marsili
- first_name: Areejit
  full_name: Samal, Areejit
  last_name: Samal
- first_name: Mauro
  full_name: Giacca, Mauro
  last_name: Giacca
citation:
  ama: Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity
    of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. 2019;27(9):2759-2771.e5.
    doi:<a href="https://doi.org/10.1016/j.celrep.2019.05.005">10.1016/j.celrep.2019.05.005</a>
  apa: Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G.,
    … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs
    inducing cardiomyocyte proliferation. <i>Cell Reports</i>. Elsevier. <a href="https://doi.org/10.1016/j.celrep.2019.05.005">https://doi.org/10.1016/j.celrep.2019.05.005</a>
  chicago: Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali,
    Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate
    Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>.
    Elsevier, 2019. <a href="https://doi.org/10.1016/j.celrep.2019.05.005">https://doi.org/10.1016/j.celrep.2019.05.005</a>.
  ieee: C. Torrini <i>et al.</i>, “Common regulatory pathways mediate activity of
    microRNAs inducing cardiomyocyte proliferation,” <i>Cell Reports</i>, vol. 27,
    no. 9. Elsevier, p. 2759–2771.e5, 2019.
  ista: Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI,
    Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili
    M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs
    inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.
  mla: Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs
    Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>, vol. 27, no. 9, Elsevier,
    2019, p. 2759–2771.e5, doi:<a href="https://doi.org/10.1016/j.celrep.2019.05.005">10.1016/j.celrep.2019.05.005</a>.
  short: C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I.
    Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo,
    M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.
date_created: 2019-11-26T22:30:07Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2021-01-12T08:11:56Z
day: '28'
ddc:
- '576'
doi: 10.1016/j.celrep.2019.05.005
extern: '1'
external_id:
  pmid:
  - '31141697'
file:
- access_level: open_access
  checksum: c5d855d07263bfec718673385d0ea2d7
  content_type: application/pdf
  creator: rcubero
  date_created: 2019-11-26T22:30:43Z
  date_updated: 2020-07-14T12:47:50Z
  file_id: '7129'
  file_name: torrini_cellreports_2019.pdf
  file_size: 4650750
  relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: '        27'
issue: '9'
keyword:
- cardiomyocyte
- cell cycle
- Cofilin2
- cytoskeleton
- Hippo
- microRNA
- regeneration
- YAP
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 2759-2771.e5
pmid: 1
publication: Cell Reports
publication_identifier:
  issn:
  - 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte
  proliferation
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2019'
...
---
_id: '7130'
abstract:
- lang: eng
  text: "We show that statistical criticality, i.e. the occurrence of power law frequency
    distributions, arises in samples that are maximally informative about the underlying
    generating process. In order to reach this conclusion, we first identify the frequency
    with which different outcomes occur in a sample, as the variable carrying useful
    information on the generative process. The entropy of the frequency, that we call
    relevance, provides an upper bound to the number of informative bits. This differs
    from the entropy of the data, that we take as a measure of resolution. Samples
    that maximise relevance at a given resolution—that we call maximally informative
    samples—exhibit statistical criticality. In particular, Zipf's law arises at the
    optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct,
    we derive a bound of the maximal number of parameters that can be estimated from
    a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore,
    we relate criticality to the statistical properties of the representation of the
    data generating process. We show that, as a consequence of the concentration property
    of the asymptotic equipartition property, representations that are maximally informative
    about the data generating process are characterised by an exponential distribution
    of energy levels. This arises from a principle of minimal entropy, that is conjugate
    of the maximum entropy principle in statistical mechanics. This explains why statistical
    criticality requires no parameter fine tuning in maximally informative samples."
acknowledgement: We acknowledge interesting discussions with M Abbott, E Aurell, J
  Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research
  was supported by the Kavli Foundation and the Centre of Excellence scheme of the
  Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the
  Basic Science Research Program through the National Research Foundation of Korea
  (NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part,
  by the ICTP through the OEA-AC-98 (JS).
article_number: '063402'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Junghyo
  full_name: Jo, Junghyo
  last_name: Jo
- first_name: Matteo
  full_name: Marsili, Matteo
  last_name: Marsili
- first_name: Yasser
  full_name: Roudi, Yasser
  last_name: Roudi
- first_name: Juyong
  full_name: Song, Juyong
  last_name: Song
citation:
  ama: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises
    in most informative representations. <i>Journal of Statistical Mechanics: Theory
    and Experiment</i>. 2019;2019(6). doi:<a href="https://doi.org/10.1088/1742-5468/ab16c8">10.1088/1742-5468/ab16c8</a>'
  apa: 'Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., &#38; Song, J. (2019). Statistical
    criticality arises in most informative representations. <i>Journal of Statistical
    Mechanics: Theory and Experiment</i>. IOP Publishing. <a href="https://doi.org/10.1088/1742-5468/ab16c8">https://doi.org/10.1088/1742-5468/ab16c8</a>'
  chicago: 'Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song.
    “Statistical Criticality Arises in Most Informative Representations.” <i>Journal
    of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2019. <a
    href="https://doi.org/10.1088/1742-5468/ab16c8">https://doi.org/10.1088/1742-5468/ab16c8</a>.'
  ieee: 'R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality
    arises in most informative representations,” <i>Journal of Statistical Mechanics:
    Theory and Experiment</i>, vol. 2019, no. 6. IOP Publishing, 2019.'
  ista: 'Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality
    arises in most informative representations. Journal of Statistical Mechanics:
    Theory and Experiment. 2019(6), 063402.'
  mla: 'Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative
    Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>,
    vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:<a href="https://doi.org/10.1088/1742-5468/ab16c8">10.1088/1742-5468/ab16c8</a>.'
  short: 'R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical
    Mechanics: Theory and Experiment 2019 (2019).'
date_created: 2019-11-26T22:36:09Z
date_published: 2019-06-17T00:00:00Z
date_updated: 2021-01-12T08:11:57Z
day: '17'
doi: 10.1088/1742-5468/ab16c8
extern: '1'
external_id:
  arxiv:
  - '1808.00249'
intvolume: '      2019'
issue: '6'
keyword:
- optimization under uncertainty
- source coding
- large deviation
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1808.00249
month: '06'
oa: 1
oa_version: Preprint
publication: 'Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
  issn:
  - 1742-5468
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: Statistical criticality arises in most informative representations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2019
year: '2019'
...
---
_id: '7126'
abstract:
- lang: eng
  text: In the Minimum Description Length (MDL) principle, learning from the data
    is equivalent to an optimal coding problem. We show that the codes that achieve
    optimal compression in MDL are critical in a very precise sense. First, when they
    are taken as generative models of samples, they generate samples with broad empirical
    distributions and with a high value of the relevance, defined as the entropy of
    the empirical frequencies. These results are derived for different statistical
    models (Dirichlet model, independent and pairwise dependent spin models, and restricted
    Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition
    point where the symmetry between the sampled outcomes is spontaneously broken.
    The order parameter controlling the phase transition is the coding cost of the
    samples. The phase transition is a manifestation of the optimality of MDL codes,
    and it arises because codes that achieve a higher compression do not exist. These
    results suggest a clear interpretation of the widespread occurrence of statistical
    criticality as a characterization of samples which are maximally informative on
    the underlying generative process.
article_number: '755'
article_processing_charge: No
article_type: original
author:
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Matteo
  full_name: Marsili, Matteo
  last_name: Marsili
- first_name: Yasser
  full_name: Roudi, Yasser
  last_name: Roudi
citation:
  ama: Cubero RJ, Marsili M, Roudi Y. Minimum description length codes are critical.
    <i>Entropy</i>. 2018;20(10). doi:<a href="https://doi.org/10.3390/e20100755">10.3390/e20100755</a>
  apa: Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2018). Minimum description length
    codes are critical. <i>Entropy</i>. MDPI. <a href="https://doi.org/10.3390/e20100755">https://doi.org/10.3390/e20100755</a>
  chicago: Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Minimum Description
    Length Codes Are Critical.” <i>Entropy</i>. MDPI, 2018. <a href="https://doi.org/10.3390/e20100755">https://doi.org/10.3390/e20100755</a>.
  ieee: R. J. Cubero, M. Marsili, and Y. Roudi, “Minimum description length codes
    are critical,” <i>Entropy</i>, vol. 20, no. 10. MDPI, 2018.
  ista: Cubero RJ, Marsili M, Roudi Y. 2018. Minimum description length codes are
    critical. Entropy. 20(10), 755.
  mla: Cubero, Ryan J., et al. “Minimum Description Length Codes Are Critical.” <i>Entropy</i>,
    vol. 20, no. 10, 755, MDPI, 2018, doi:<a href="https://doi.org/10.3390/e20100755">10.3390/e20100755</a>.
  short: R.J. Cubero, M. Marsili, Y. Roudi, Entropy 20 (2018).
date_created: 2019-11-26T22:18:05Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2021-01-12T08:11:56Z
day: '01'
ddc:
- '519'
doi: 10.3390/e20100755
extern: '1'
file:
- access_level: open_access
  checksum: d642b7b661e1d5066b62e6ea9986b917
  content_type: application/pdf
  creator: rcubero
  date_created: 2019-11-26T22:23:08Z
  date_updated: 2020-07-14T12:47:50Z
  file_id: '7127'
  file_name: entropy-20-00755-v2.pdf
  file_size: 1366813
  relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: '        20'
issue: '10'
keyword:
- Minimum Description Length
- normalized maximum likelihood
- statistical criticality
- phase transitions
- large deviations
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Entropy
publication_identifier:
  issn:
  - 1099-4300
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Minimum description length codes are critical
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2018'
...