---
_id: '6918'
abstract:
- lang: eng
  text: "We consider the classic problem of Network Reliability. A network is given
    together with a source vertex, one or more target vertices, and probabilities
    assigned to each of the edges. Each edge of the network is operable with its associated
    probability and the problem is to determine the probability of having at least
    one source-to-target path that is entirely composed of operable edges. This problem
    is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve
    the Network Reliability problem when the treewidth of the underlying network is
    small. We also show our algorithm’s applicability for real-world transit networks
    that have small treewidth, including the metro networks of major cities, such
    as London and Tokyo. Our algorithm leverages tree decompositions to shrink the
    original graph into much smaller graphs, for which reliability can be efficiently
    and exactly computed using a brute force method. To the best of our knowledge,
    this is the first exact algorithm for Network Reliability that can scale to handle
    real-world instances of the problem."
acknowledgement: We are grateful to the anonymous reviewers for their comments, which
  significantly improved the present work. The research was partially supported by
  the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London
  Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian
  Academy of Sciences (ÖAW).
article_number: '106665'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Amir Kafshdar
  full_name: Goharshady, Amir Kafshdar
  id: 391365CE-F248-11E8-B48F-1D18A9856A87
  last_name: Goharshady
  orcid: 0000-0003-1702-6584
- first_name: Fatemeh
  full_name: Mohammadi, Fatemeh
  last_name: Mohammadi
citation:
  ama: Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability
    in small treewidth. <i>Reliability Engineering and System Safety</i>. 2020;193.
    doi:<a href="https://doi.org/10.1016/j.ress.2019.106665">10.1016/j.ress.2019.106665</a>
  apa: Goharshady, A. K., &#38; Mohammadi, F. (2020). An efficient algorithm for computing
    network reliability in small treewidth. <i>Reliability Engineering and System
    Safety</i>. Elsevier. <a href="https://doi.org/10.1016/j.ress.2019.106665">https://doi.org/10.1016/j.ress.2019.106665</a>
  chicago: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm
    for Computing Network Reliability in Small Treewidth.” <i>Reliability Engineering
    and System Safety</i>. Elsevier, 2020. <a href="https://doi.org/10.1016/j.ress.2019.106665">https://doi.org/10.1016/j.ress.2019.106665</a>.
  ieee: A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network
    reliability in small treewidth,” <i>Reliability Engineering and System Safety</i>,
    vol. 193. Elsevier, 2020.
  ista: Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network
    reliability in small treewidth. Reliability Engineering and System Safety. 193,
    106665.
  mla: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for
    Computing Network Reliability in Small Treewidth.” <i>Reliability Engineering
    and System Safety</i>, vol. 193, 106665, Elsevier, 2020, doi:<a href="https://doi.org/10.1016/j.ress.2019.106665">10.1016/j.ress.2019.106665</a>.
  short: A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety
    193 (2020).
date_created: 2019-09-29T22:00:44Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2026-11-06T23:30:48Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ress.2019.106665
external_id:
  arxiv:
  - '1712.09692'
  isi:
  - '000501641400050'
fulldoi: https://doi.org/10.1016/j.ress.2019.106665
intvolume: '       193'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1712.09692
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
  name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
    Contracts
publication: Reliability Engineering and System Safety
publication_identifier:
  issn:
  - 0951-8320
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '8934'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: An efficient algorithm for computing network reliability in small treewidth
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 193
year: '2020'
...
---
_id: '8569'
abstract:
- lang: eng
  text: Concerted radial migration of newly born cortical projection neurons, from
    their birthplace to their final target lamina, is a key step in the assembly of
    the cerebral cortex. The cellular and molecular mechanisms regulating the specific
    sequential steps of radial neuronal migration in vivo are however still unclear,
    let alone the effects and interactions with the extracellular environment. In
    any in vivo context, cells will always be exposed to a complex extracellular environment
    consisting of (1) secreted factors acting as potential signaling cues, (2) the
    extracellular matrix, and (3) other cells providing cell–cell interaction through
    receptors and/or direct physical stimuli. Most studies so far have described and
    focused mainly on intrinsic cell-autonomous gene functions in neuronal migration
    but there is accumulating evidence that non-cell-autonomous-, local-, systemic-,
    and/or whole tissue-wide effects substantially contribute to the regulation of
    radial neuronal migration. These non-cell-autonomous effects may differentially
    affect cortical neuron migration in distinct cellular environments. However, the
    cellular and molecular natures of such non-cell-autonomous mechanisms are mostly
    unknown. Furthermore, physical forces due to collective migration and/or community
    effects (i.e., interactions with surrounding cells) may play important roles in
    neocortical projection neuron migration. In this concise review, we first outline
    distinct models of non-cell-autonomous interactions of cortical projection neurons
    along their radial migration trajectory during development. We then summarize
    experimental assays and platforms that can be utilized to visualize and potentially
    probe non-cell-autonomous mechanisms. Lastly, we define key questions to address
    in the future.
acknowledgement: AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy
  of Sciences. This work also received support from IST Austria institutional funds;
  the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
  Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.
article_number: '574382'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andi H
  full_name: Hansen, Andi H
  id: 38853E16-F248-11E8-B48F-1D18A9856A87
  last_name: Hansen
- first_name: Simon
  full_name: Hippenmeyer, Simon
  id: 37B36620-F248-11E8-B48F-1D18A9856A87
  last_name: Hippenmeyer
  orcid: 0000-0003-2279-1061
citation:
  ama: Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection
    neuron migration in the developing cerebral cortex. <i>Frontiers in Cell and Developmental
    Biology</i>. 2020;8(9). doi:<a href="https://doi.org/10.3389/fcell.2020.574382">10.3389/fcell.2020.574382</a>
  apa: Hansen, A. H., &#38; Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms
    in radial projection neuron migration in the developing cerebral cortex. <i>Frontiers
    in Cell and Developmental Biology</i>. Frontiers. <a href="https://doi.org/10.3389/fcell.2020.574382">https://doi.org/10.3389/fcell.2020.574382</a>
  chicago: Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms
    in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers
    in Cell and Developmental Biology</i>. Frontiers, 2020. <a href="https://doi.org/10.3389/fcell.2020.574382">https://doi.org/10.3389/fcell.2020.574382</a>.
  ieee: A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial
    projection neuron migration in the developing cerebral cortex,” <i>Frontiers in
    Cell and Developmental Biology</i>, vol. 8, no. 9. Frontiers, 2020.
  ista: Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection
    neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
    Biology. 8(9), 574382.
  mla: Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in
    Radial Projection Neuron Migration in the Developing Cerebral Cortex.” <i>Frontiers
    in Cell and Developmental Biology</i>, vol. 8, no. 9, 574382, Frontiers, 2020,
    doi:<a href="https://doi.org/10.3389/fcell.2020.574382">10.3389/fcell.2020.574382</a>.
  short: A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology
    8 (2020).
corr_author: '1'
date_created: 2020-09-26T06:11:07Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2026-11-06T23:30:49Z
day: '25'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3389/fcell.2020.574382
ec_funded: 1
external_id:
  isi:
  - '000577915900001'
  pmid:
  - '33102480'
file:
- access_level: open_access
  checksum: 01f731824194c94c81a5da360d997073
  content_type: application/pdf
  creator: dernst
  date_created: 2020-09-28T13:11:17Z
  date_updated: 2020-09-28T13:11:17Z
  file_id: '8584'
  file_name: 2020_Frontiers_Hansen.pdf
  file_size: 5527139
  relation: main_file
  success: 1
file_date_updated: 2020-09-28T13:11:17Z
fulldoi: https://doi.org/10.3389/fcell.2020.574382
has_accepted_license: '1'
intvolume: '         8'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
  grant_number: '24812'
  name: Molecular mechanisms of radial neuronal migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '618444'
  name: Molecular Mechanisms of Cerebral Cortex Development
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
  issn:
  - 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
  record:
  - id: '9962'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Non-cell-autonomous mechanisms in radial projection neuron migration in the
  developing cerebral cortex
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: 8
year: '2020'
...
---
_id: '7161'
abstract:
- lang: eng
  text: In this paper, we introduce an inertial projection-type method with different
    updating strategies for solving quasi-variational inequalities with strongly monotone
    and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions,
    we establish different strong convergence results for the proposed algorithm.
    Primary numerical experiments demonstrate the potential applicability of our scheme
    compared with some related methods in the literature.
acknowledgement: We are grateful to the anonymous referees and editor whose insightful
  comments helped to considerably improve an earlier version of this paper. The research
  of the first author is supported by an ERC Grant from the Institute of Science and
  Technology (IST).
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
  full_name: Shehu, Yekini
  id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
  last_name: Shehu
  orcid: 0000-0001-9224-7139
- first_name: Aviv
  full_name: Gibali, Aviv
  last_name: Gibali
- first_name: Simone
  full_name: Sagratella, Simone
  last_name: Sagratella
citation:
  ama: Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving
    quasi-variational inequalities in real Hilbert spaces. <i>Journal of Optimization
    Theory and Applications</i>. 2020;184:877–894. doi:<a href="https://doi.org/10.1007/s10957-019-01616-6">10.1007/s10957-019-01616-6</a>
  apa: Shehu, Y., Gibali, A., &#38; Sagratella, S. (2020). Inertial projection-type
    methods for solving quasi-variational inequalities in real Hilbert spaces. <i>Journal
    of Optimization Theory and Applications</i>. Springer Nature. <a href="https://doi.org/10.1007/s10957-019-01616-6">https://doi.org/10.1007/s10957-019-01616-6</a>
  chicago: Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type
    Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” <i>Journal
    of Optimization Theory and Applications</i>. Springer Nature, 2020. <a href="https://doi.org/10.1007/s10957-019-01616-6">https://doi.org/10.1007/s10957-019-01616-6</a>.
  ieee: Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods
    for solving quasi-variational inequalities in real Hilbert spaces,” <i>Journal
    of Optimization Theory and Applications</i>, vol. 184. Springer Nature, pp. 877–894,
    2020.
  ista: Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for
    solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization
    Theory and Applications. 184, 877–894.
  mla: Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational
    Inequalities in Real Hilbert Spaces.” <i>Journal of Optimization Theory and Applications</i>,
    vol. 184, Springer Nature, 2020, pp. 877–894, doi:<a href="https://doi.org/10.1007/s10957-019-01616-6">10.1007/s10957-019-01616-6</a>.
  short: Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications
    184 (2020) 877–894.
date_created: 2019-12-09T21:33:44Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2024-11-04T13:52:44Z
day: '01'
ddc:
- '518'
- '510'
- '515'
department:
- _id: VlKo
doi: 10.1007/s10957-019-01616-6
ec_funded: 1
external_id:
  isi:
  - '000511805200009'
file:
- access_level: open_access
  checksum: 9f6dc6c6bf2b48cb3a2091a9ed5feaf2
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-12T10:40:27Z
  date_updated: 2021-03-16T23:30:04Z
  embargo: 2021-03-15
  file_id: '8647'
  file_name: 2020_JourOptimizationTheoryApplic_Shehu.pdf
  file_size: 332641
  relation: main_file
file_date_updated: 2021-03-16T23:30:04Z
fulldoi: https://doi.org/10.1007/s10957-019-01616-6
has_accepted_license: '1'
intvolume: '       184'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 877–894
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '616160'
  name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Journal of Optimization Theory and Applications
publication_identifier:
  eissn:
  - 1573-2878
  issn:
  - 0022-3239
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inertial projection-type methods for solving quasi-variational inequalities
  in real Hilbert spaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 184
year: '2020'
...
---
_id: '8532'
abstract:
- lang: eng
  text: The molecular anatomy of synapses defines their characteristics in transmission
    and plasticity. Precise measurements of the number and distribution of synaptic
    proteins are important for our understanding of synapse heterogeneity within and
    between brain regions. Freeze–fracture replica immunogold electron microscopy
    enables us to analyze them quantitatively on a two-dimensional membrane surface.
    Here, we introduce Darea software, which utilizes deep learning for analysis of
    replica images and demonstrate its usefulness for quick measurements of the pre-
    and postsynaptic areas, density and distribution of gold particles at synapses
    in a reproducible manner. We used Darea for comparing glutamate receptor and calcium
    channel distributions between hippocampal CA3-CA1 spine synapses on apical and
    basal dendrites, which differ in signaling pathways involved in synaptic plasticity.
    We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
    acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic
    size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA)
    receptors with size. Interestingly, AMPA and NMDA receptors are segregated within
    postsynaptic sites and negatively correlated in density among both apical and
    basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels
    show similar densities in apical and basal synapses with distributions consistent
    with an exclusion zone model of calcium channel-release site topography.
acknowledgement: "This research was funded by Austrian Academy of Sciences, DOC fellowship
  to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human
  Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner
  for technical support."
article_number: '6737'
article_processing_charge: No
article_type: original
author:
- first_name: David
  full_name: Kleindienst, David
  id: 42E121A4-F248-11E8-B48F-1D18A9856A87
  last_name: Kleindienst
- first_name: Jacqueline-Claire
  full_name: Montanaro-Punzengruber, Jacqueline-Claire
  id: 3786AB44-F248-11E8-B48F-1D18A9856A87
  last_name: Montanaro-Punzengruber
- first_name: Pradeep
  full_name: Bhandari, Pradeep
  id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
  last_name: Bhandari
  orcid: 0000-0003-0863-4481
- first_name: Matthew J
  full_name: Case, Matthew J
  id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87
  last_name: Case
- first_name: Yugo
  full_name: Fukazawa, Yugo
  last_name: Fukazawa
- first_name: Ryuichi
  full_name: Shigemoto, Ryuichi
  id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
  last_name: Shigemoto
  orcid: 0000-0001-8761-9444
citation:
  ama: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y,
    Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture
    replica images applied to glutamate receptors and calcium channels at hippocampal
    synapses. <i>International Journal of Molecular Sciences</i>. 2020;21(18). doi:<a
    href="https://doi.org/10.3390/ijms21186737">10.3390/ijms21186737</a>
  apa: Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J.,
    Fukazawa, Y., &#38; Shigemoto, R. (2020). Deep learning-assisted high-throughput
    analysis of freeze-fracture replica images applied to glutamate receptors and
    calcium channels at hippocampal synapses. <i>International Journal of Molecular
    Sciences</i>. MDPI. <a href="https://doi.org/10.3390/ijms21186737">https://doi.org/10.3390/ijms21186737</a>
  chicago: Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari,
    Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted
    High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate
    Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal
    of Molecular Sciences</i>. MDPI, 2020. <a href="https://doi.org/10.3390/ijms21186737">https://doi.org/10.3390/ijms21186737</a>.
  ieee: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y.
    Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of
    freeze-fracture replica images applied to glutamate receptors and calcium channels
    at hippocampal synapses,” <i>International Journal of Molecular Sciences</i>,
    vol. 21, no. 18. MDPI, 2020.
  ista: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y,
    Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture
    replica images applied to glutamate receptors and calcium channels at hippocampal
    synapses. International Journal of Molecular Sciences. 21(18), 6737.
  mla: Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis
    of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels
    at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>,
    vol. 21, no. 18, 6737, MDPI, 2020, doi:<a href="https://doi.org/10.3390/ijms21186737">10.3390/ijms21186737</a>.
  short: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y.
    Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).
corr_author: '1'
date_created: 2020-09-20T22:01:35Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2026-11-06T23:30:52Z
day: '14'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3390/ijms21186737
ec_funded: 1
external_id:
  isi:
  - '000579945300001'
file:
- access_level: open_access
  checksum: 2e4f62f3cfe945b7391fc3070e5a289f
  content_type: application/pdf
  creator: dernst
  date_created: 2020-09-21T14:08:58Z
  date_updated: 2020-09-21T14:08:58Z
  file_id: '8551'
  file_name: 2020_JournMolecSciences_Kleindienst.pdf
  file_size: 5748456
  relation: main_file
  success: 1
file_date_updated: 2020-09-21T14:08:58Z
fulldoi: https://doi.org/10.3390/ijms21186737
has_accepted_license: '1'
intvolume: '        21'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '694539'
  name: 'In situ analysis of single channel subunit composition in neurons: physiological
    implication in synaptic plasticity and behaviour'
- _id: 25D32BC0-B435-11E9-9278-68D0E5697425
  name: Mechanism of formation and maintenance of input side-dependent asymmetry in
    the hippocampus
- _id: 26436750-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '785907'
  name: Human Brain Project Specific Grant Agreement 2
publication: International Journal of Molecular Sciences
publication_identifier:
  eissn:
  - 1422-0067
  issn:
  - 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
  record:
  - id: '9562'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Deep learning-assisted high-throughput analysis of freeze-fracture replica
  images applied to glutamate receptors and calcium channels at hippocampal synapses
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: 21
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '7426'
abstract:
- lang: eng
  text: This paper presents a novel abstraction technique for analyzing Lyapunov and
    asymptotic stability of polyhedral switched systems. A polyhedral switched system
    is a hybrid system in which the continuous dynamics is specified by polyhedral
    differential inclusions, the invariants and guards are specified by polyhedral
    sets and the switching between the modes do not involve reset of variables. A
    finite state weighted graph abstracting the polyhedral switched system is constructed
    from a finite partition of the state–space, such that the satisfaction of certain
    graph conditions, such as the absence of cycles with product of weights on the
    edges greater than (or equal) to 1, implies the stability of the system. However,
    the graph is in general conservative and hence, the violation of the graph conditions
    does not imply instability. If the analysis fails to establish stability due to
    the conservativeness in the approximation, a counterexample (cycle with product
    of edge weights greater than or equal to 1) indicating a potential reason for
    the failure is returned. Further, a more precise approximation of the switched
    system can be constructed by considering a finer partition of the state–space
    in the construction of the finite weighted graph. We present experimental results
    on analyzing stability of switched systems using the above method.
article_number: '100856'
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
  full_name: Garcia Soto, Miriam
  id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
  last_name: Garcia Soto
  orcid: 0000−0003−2936−5719
- first_name: Pavithra
  full_name: Prabhakar, Pavithra
  last_name: Prabhakar
citation:
  ama: 'Garcia Soto M, Prabhakar P. Abstraction based verification of stability of
    polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>. 2020;36(5).
    doi:<a href="https://doi.org/10.1016/j.nahs.2020.100856">10.1016/j.nahs.2020.100856</a>'
  apa: 'Garcia Soto, M., &#38; Prabhakar, P. (2020). Abstraction based verification
    of stability of polyhedral switched systems. <i>Nonlinear Analysis: Hybrid Systems</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.nahs.2020.100856">https://doi.org/10.1016/j.nahs.2020.100856</a>'
  chicago: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification
    of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>.
    Elsevier, 2020. <a href="https://doi.org/10.1016/j.nahs.2020.100856">https://doi.org/10.1016/j.nahs.2020.100856</a>.'
  ieee: 'M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability
    of polyhedral switched systems,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol.
    36, no. 5. Elsevier, 2020.'
  ista: 'Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability
    of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.'
  mla: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification
    of Stability of Polyhedral Switched Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>,
    vol. 36, no. 5, 100856, Elsevier, 2020, doi:<a href="https://doi.org/10.1016/j.nahs.2020.100856">10.1016/j.nahs.2020.100856</a>.'
  short: 'M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).'
corr_author: '1'
date_created: 2020-02-02T23:00:59Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2026-07-28T12:57:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1016/j.nahs.2020.100856
external_id:
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file:
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fulldoi: https://doi.org/10.1016/j.nahs.2020.100856
has_accepted_license: '1'
intvolume: '        36'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: S11407
  name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z211
  name: Formal methods for the design and analysis of complex systems
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_identifier:
  issn:
  - 1751-570X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abstraction based verification of stability of polyhedral switched systems
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: 36
year: '2020'
...
---
_id: '7680'
abstract:
- lang: eng
  text: "Proteins and their complex dynamic interactions regulate cellular mechanisms
    from sensing and transducing extracellular signals, to mediating genetic responses,
    and sustaining or changing cell morphology. To manipulate these protein-protein
    interactions (PPIs) that govern the behavior and fate of cells, synthetically
    constructed, genetically encoded tools provide the means to precisely target proteins
    of interest (POIs), and control their subcellular localization and activity in
    vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger
    that does not activate any other endogenous process, thereby allowing manipulation
    of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain
    from plants, algae and bacteria are re-purposed and genetically fused to POIs.
    Illumination with light of a specific wavelength triggers a conformational change
    that can mediate PPIs, such as dimerization or oligomerization. By using light
    as a trigger, these tools can be activated with high spatial and temporal precision,
    on subcellular and millisecond scales. Chemogenetic tools consist of protein domains
    that recognize and bind small molecules. By genetic fusion to POIs, these domains
    can mediate PPIs upon addition of their specific ligands, which are often synthetically
    designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost
    optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding
    to red, blue or near-UV light, leaving a striking gap in the green band of the
    visible light spectrum. Among both optogenetic and chemogenetic tools, there is
    an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination,
    rely on covalent linkage and subsequent enzymatic cleavage or initially result
    in protein clustering of unknown stoichiometry.\r\nThis work describes how the
    recently structurally and photochemically characterized green-light responsive
    cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed
    to function as a green-light responsive optogenetic tool. In contrast to previously
    engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI
    already upon expression, which can be rapidly disrupted by illumination. This
    was employed to mimic inhibition of constitutive activity of a growth factor receptor,
    and successfully implement for cell signalling in mammalian cells and in vivo
    to rescue development in zebrafish. This work further describes the development
    and application of a chemically induced de-dimerizer (CDD) based on a recently
    identified and structurally described bacterial oxyreductase. CDD forms a dimer
    upon expression in absence of its cofactor, the flavin derivative F420. Safety
    and of domain expression and ligand exposure are demonstrated in vitro and in
    vivo in zebrafish. The system is further applied to inhibit cell signalling output
    from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire
    of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing
    previously not utilized cues. In the future, they can readily be combined with
    existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
  full_name: Kainrath, Stephanie
  id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
  last_name: Kainrath
  orcid: 0000-0002-6709-2195
citation:
  ama: Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of
    cellular signals. 2020. doi:<a href="https://doi.org/10.15479/AT:ISTA:7680">10.15479/AT:ISTA:7680</a>
  apa: Kainrath, S. (2020). <i>Synthetic tools for optogenetic and chemogenetic inhibition
    of cellular signals</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:7680">https://doi.org/10.15479/AT:ISTA:7680</a>
  chicago: Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic
    Inhibition of Cellular Signals.” Institute of Science and Technology Austria,
    2020. <a href="https://doi.org/10.15479/AT:ISTA:7680">https://doi.org/10.15479/AT:ISTA:7680</a>.
  ieee: S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition
    of cellular signals,” Institute of Science and Technology Austria, 2020.
  ista: Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition
    of cellular signals. Institute of Science and Technology Austria.
  mla: Kainrath, Stephanie. <i>Synthetic Tools for Optogenetic and Chemogenetic Inhibition
    of Cellular Signals</i>. Institute of Science and Technology Austria, 2020, doi:<a
    href="https://doi.org/10.15479/AT:ISTA:7680">10.15479/AT:ISTA:7680</a>.
  short: S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition
    of Cellular Signals, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-04-24T16:00:51Z
date_published: 2020-04-24T00:00:00Z
date_updated: 2026-08-12T09:19:22Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7680
file:
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language:
- iso: eng
month: '04'
oa: 1
oa_version: None
page: '98'
publication_identifier:
  eissn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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  - id: '1028'
    relation: dissertation_contains
    status: public
status: public
supervisor:
- first_name: Harald L
  full_name: Janovjak, Harald L
  id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
  last_name: Janovjak
  orcid: 0000-0002-8023-9315
title: Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: publisher
_id: '8620'
abstract:
- lang: eng
  text: "The development of the human brain occurs through a tightly regulated series
    of dynamic and adaptive processes during prenatal and postnatal life. A disruption
    of this strictly orchestrated series of events can lead to a number of neurodevelopmental
    conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common,
    etiologically and phenotypically heterogeneous group of disorders sharing the
    core symptoms of social interaction and communication deficits and restrictive
    and repetitive interests and behaviors. They are estimated to affect one in 59
    individuals in the U.S. and, over the last three decades, mutations in more than
    a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet,
    for the vast majority of these ASD-risk genes their role during brain development
    and precise molecular function still remain elusive.\r\nDe novo loss of function
    mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In
    the study described here, we used Cul3 mouse models to evaluate the consequences
    of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice
    exhibit deficits in motor coordination as well as ASD-relevant social and cognitive
    impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display
    cortical lamination abnormalities due to defective migration of post-mitotic excitatory
    neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line
    with the observed abnormal cortical organization, Cul3 heterozygous deletion is
    associated with decreased spontaneous excitatory and inhibitory activity in the
    cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion
    protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal
    proteins in Cul3 mutant neural cells results in atypical organization of the actin
    mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult
    mice does not induce the majority of the behavioral defects observed in constitutive
    Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn
    conclusion, our data indicate that Cul3 plays a critical role in the regulation
    of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral
    abnormalities are primarily due to dosage sensitive Cul3 functions at early brain
    developmental stages."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: I would like to especially thank Armel Nicolas from the Proteomics
  and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to
  thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka,
  Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line
  maintenance and their great support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jasmin
  full_name: Morandell, Jasmin
  id: 4739D480-F248-11E8-B48F-1D18A9856A87
  last_name: Morandell
citation:
  ama: Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis.
    2020. doi:<a href="https://doi.org/10.15479/AT:ISTA:8620">10.15479/AT:ISTA:8620</a>
  apa: Morandell, J. (2020). <i>Illuminating the role of Cul3 in autism spectrum disorder
    pathogenesis</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:8620">https://doi.org/10.15479/AT:ISTA:8620</a>
  chicago: Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder
    Pathogenesis.” Institute of Science and Technology Austria, 2020. <a href="https://doi.org/10.15479/AT:ISTA:8620">https://doi.org/10.15479/AT:ISTA:8620</a>.
  ieee: J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,”
    Institute of Science and Technology Austria, 2020.
  ista: Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder
    pathogenesis. Institute of Science and Technology Austria.
  mla: Morandell, Jasmin. <i>Illuminating the Role of Cul3 in Autism Spectrum Disorder
    Pathogenesis</i>. Institute of Science and Technology Austria, 2020, doi:<a href="https://doi.org/10.15479/AT:ISTA:8620">10.15479/AT:ISTA:8620</a>.
  short: J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis,
    Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-10-07T14:53:13Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2026-08-12T09:55:08Z
day: '12'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:8620
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has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
project:
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
  grant_number: F7807
  name: Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem
    cells in autism and epilepsy
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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    relation: part_of_dissertation
    status: public
  - id: '8131'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
title: Illuminating the role of Cul3 in autism spectrum disorder pathogenesis
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '7800'
abstract:
- lang: eng
  text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3
    (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models
    to evaluate the consequences of Cul3 mutations in vivo. Our results show that
    Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as
    ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical
    lamination abnormalities due to defective neuronal migration and reduced numbers
    of excitatory and inhibitory neurons. In line with the observed abnormal columnar
    organization, Cul3 haploinsufficiency is associated with decreased spontaneous
    excitatory and inhibitory activity in the cortex. At the molecular level, employing
    a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and
    adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal
    proteins in Cul3 mutant neuronal cells results in atypical organization of the
    actin mesh at the cell leading edge, likely causing the observed migration deficits.
    In contrast to these important functions early in development, Cul3 deficiency
    appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency
    in adult mice does not result in the behavioral defects observed in constitutive
    Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has
    a critical role in the regulation of cytoskeletal proteins and neuronal migration
    and that ASD-associated defects and behavioral abnormalities are primarily due
    to Cul3 functions at early developmental stages.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Jasmin
  full_name: Morandell, Jasmin
  id: 4739D480-F248-11E8-B48F-1D18A9856A87
  last_name: Morandell
- first_name: Lena A
  full_name: Schwarz, Lena A
  id: 29A8453C-F248-11E8-B48F-1D18A9856A87
  last_name: Schwarz
- first_name: Bernadette
  full_name: Basilico, Bernadette
  id: 36035796-5ACA-11E9-A75E-7AF2E5697425
  last_name: Basilico
  orcid: 0000-0003-1843-3173
- first_name: Saren
  full_name: Tasciyan, Saren
  id: 4323B49C-F248-11E8-B48F-1D18A9856A87
  last_name: Tasciyan
  orcid: 0000-0003-1671-393X
- first_name: Armel
  full_name: Nicolas, Armel
  id: 2A103192-F248-11E8-B48F-1D18A9856A87
  last_name: Nicolas
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Lisa
  full_name: Knaus, Lisa
  id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
  last_name: Knaus
- first_name: Zoe
  full_name: Dobler, Zoe
  id: D23090A2-9057-11EA-883A-A8396FC7A38F
  last_name: Dobler
- first_name: Emanuele
  full_name: Cacci, Emanuele
  last_name: Cacci
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
citation:
  ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein
    homeostasis and cell migration during a critical window of brain development.
    <i>bioRxiv</i>. doi:<a href="https://doi.org/10.1101/2020.01.10.902064 ">10.1101/2020.01.10.902064
    </a>
  apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer,
    C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis
    and cell migration during a critical window of brain development. <i>bioRxiv</i>.
    <a href="https://doi.org/10.1101/2020.01.10.902064 ">https://doi.org/10.1101/2020.01.10.902064
    </a>
  chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan,
    Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates
    Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of
    Brain Development.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2020.01.10.902064
    ">https://doi.org/10.1101/2020.01.10.902064 </a>.
  ieee: J. Morandell <i>et al.</i>, “Cul3 regulates cytoskeleton protein homeostasis
    and cell migration during a critical window of brain development,” <i>bioRxiv</i>.
    .
  ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger
    C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton
    protein homeostasis and cell migration during a critical window of brain development.
    bioRxiv, <a href="https://doi.org/10.1101/2020.01.10.902064 ">10.1101/2020.01.10.902064
    </a>.
  mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis
    and Cell Migration during a Critical Window of Brain Development.” <i>BioRxiv</i>,
    doi:<a href="https://doi.org/10.1101/2020.01.10.902064 ">10.1101/2020.01.10.902064
    </a>.
  short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer,
    C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv
    (n.d.).
corr_author: '1'
das_tickbox: '1'
date_created: 2020-05-05T14:31:33Z
date_published: 2020-01-11T00:00:00Z
date_updated: 2026-11-06T23:30:54Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
- _id: LifeSc
doi: '10.1101/2020.01.10.902064 '
file:
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  checksum: c6799ab5daba80efe8e2ed63c15f8c81
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  date_updated: 2020-07-14T12:48:03Z
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  file_size: 2931370
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file_date_updated: 2020-07-14T12:48:03Z
fulldoi: 'https://doi.org/10.1101/2020.01.10.902064 '
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I03600
  name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
publication: bioRxiv
publication_status: draft
related_material:
  record:
  - id: '9429'
    relation: later_version
    status: public
  - id: '8620'
    relation: dissertation_contains
    status: public
status: public
title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a
  critical window of brain development
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8131'
abstract:
- lang: eng
  text: The possibility to generate construct valid animal models enabled the development
    and testing of therapeutic strategies targeting the core features of autism spectrum
    disorders (ASDs). At the same time, these studies highlighted the necessity of
    identifying sensitive developmental time windows for successful therapeutic interventions.
    Animal and human studies also uncovered the possibility to stratify the variety
    of ASDs in molecularly distinct subgroups, potentially facilitating effective
    treatment design. Here, we focus on the molecular pathways emerging as commonly
    affected by mutations in diverse ASD-risk genes, on their role during critical
    windows of brain development and the potential treatments targeting these biological
    processes.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bernadette
  full_name: Basilico, Bernadette
  id: 36035796-5ACA-11E9-A75E-7AF2E5697425
  last_name: Basilico
  orcid: 0000-0003-1843-3173
- first_name: Jasmin
  full_name: Morandell, Jasmin
  id: 4739D480-F248-11E8-B48F-1D18A9856A87
  last_name: Morandell
- first_name: Gaia
  full_name: Novarino, Gaia
  id: 3E57A680-F248-11E8-B48F-1D18A9856A87
  last_name: Novarino
  orcid: 0000-0002-7673-7178
citation:
  ama: Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD
    treatments. <i>Current Opinion in Genetics &#38; Development</i>. 2020;65(12):126-137.
    doi:<a href="https://doi.org/10.1016/j.gde.2020.06.004">10.1016/j.gde.2020.06.004</a>
  apa: Basilico, B., Morandell, J., &#38; Novarino, G. (2020). Molecular mechanisms
    for targeted ASD treatments. <i>Current Opinion in Genetics &#38; Development</i>.
    Elsevier. <a href="https://doi.org/10.1016/j.gde.2020.06.004">https://doi.org/10.1016/j.gde.2020.06.004</a>
  chicago: Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms
    for Targeted ASD Treatments.” <i>Current Opinion in Genetics &#38; Development</i>.
    Elsevier, 2020. <a href="https://doi.org/10.1016/j.gde.2020.06.004">https://doi.org/10.1016/j.gde.2020.06.004</a>.
  ieee: B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted
    ASD treatments,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 65,
    no. 12. Elsevier, pp. 126–137, 2020.
  ista: Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted
    ASD treatments. Current Opinion in Genetics &#38; Development. 65(12), 126–137.
  mla: Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.”
    <i>Current Opinion in Genetics &#38; Development</i>, vol. 65, no. 12, Elsevier,
    2020, pp. 126–37, doi:<a href="https://doi.org/10.1016/j.gde.2020.06.004">10.1016/j.gde.2020.06.004</a>.
  short: B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics &#38;
    Development 65 (2020) 126–137.
corr_author: '1'
date_created: 2020-07-19T22:00:58Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2026-11-06T23:30:54Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.gde.2020.06.004
ec_funded: 1
external_id:
  isi:
  - '000598918900019'
  pmid:
  - '32659636'
file:
- access_level: open_access
  content_type: application/pdf
  creator: dernst
  date_created: 2020-07-22T06:47:45Z
  date_updated: 2020-07-22T06:47:45Z
  file_id: '8146'
  file_name: 2020_CurrentOpGenetics_Basilico.pdf
  file_size: 1381545
  relation: main_file
  success: 1
file_date_updated: 2020-07-22T06:47:45Z
fulldoi: https://doi.org/10.1016/j.gde.2020.06.004
has_accepted_license: '1'
intvolume: '        65'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 126-137
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232
  name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
  grant_number: F7807
  name: Stem Cell Modulation in Neural Development and Regeneration/ P07-Neural stem
    cells in autism and epilepsy
publication: Current Opinion in Genetics & Development
publication_identifier:
  eissn:
  - 1879-0380
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '8620'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Molecular mechanisms for targeted ASD treatments
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: 65
year: '2020'
...
---
_id: '9198'
abstract:
- lang: eng
  text: "The optimization of multilayer neural networks typically leads to a solution\r\nwith
    zero training error, yet the landscape can exhibit spurious local minima\r\nand
    the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon:
    we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization
    makes the landscape of multilayer neural networks\r\napproximately connected and
    thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions
    are connected via a piecewise linear\r\npath, and the increase in loss along this
    path vanishes as the number of\r\nneurons grows large. This result is a consequence
    of the fact that the\r\nparameters found by SGD are increasingly dropout stable
    as the network becomes\r\nwider. We show that, if we remove part of the neurons
    (and suitably rescale the\r\nremaining ones), the change in loss is independent
    of the total number of\r\nneurons, and it depends only on how many neurons are
    left. Our results exhibit\r\na mild dependence on the input dimension: they are
    dimension-free for two-layer\r\nnetworks and depend linearly on the dimension
    for multilayer networks. We\r\nvalidate our theoretical findings with numerical
    experiments for different\r\narchitectures and classification tasks."
acknowledgement: M. Mondelli was partially supported by the 2019 LopezLoreta Prize.
  The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed
  Algorithms and Systems Lab for providing computational resources.
article_processing_charge: No
arxiv: 1
author:
- first_name: Aleksandr
  full_name: Shevchenko, Aleksandr
  id: F2B06EC2-C99E-11E9-89F0-752EE6697425
  last_name: Shevchenko
- first_name: Marco
  full_name: Mondelli, Marco
  id: 27EB676C-8706-11E9-9510-7717E6697425
  last_name: Mondelli
  orcid: 0000-0002-3242-7020
citation:
  ama: 'Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of
    SGD solutions for over-parameterized neural networks. In: <i>Proceedings of the
    37th International Conference on Machine Learning</i>. Vol 119. ML Research Press;
    2020:8773-8784.'
  apa: Shevchenko, A., &#38; Mondelli, M. (2020). Landscape connectivity and dropout
    stability of SGD solutions for over-parameterized neural networks. In <i>Proceedings
    of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 8773–8784).
    ML Research Press.
  chicago: Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and
    Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In
    <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:8773–84.
    ML Research Press, 2020.
  ieee: A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability
    of SGD solutions for over-parameterized neural networks,” in <i>Proceedings of
    the 37th International Conference on Machine Learning</i>, 2020, vol. 119, pp.
    8773–8784.
  ista: Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability
    of SGD solutions for over-parameterized neural networks. Proceedings of the 37th
    International Conference on Machine Learning. vol. 119, 8773–8784.
  mla: Shevchenko, Aleksandr, and Marco Mondelli. “Landscape Connectivity and Dropout
    Stability of SGD Solutions for Over-Parameterized Neural Networks.” <i>Proceedings
    of the 37th International Conference on Machine Learning</i>, vol. 119, ML Research
    Press, 2020, pp. 8773–84.
  short: A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference
    on Machine Learning, ML Research Press, 2020, pp. 8773–8784.
date_created: 2021-02-25T09:36:22Z
date_published: 2020-07-13T00:00:00Z
date_updated: 2026-11-06T23:31:03Z
day: '13'
ddc:
- '000'
department:
- _id: MaMo
- _id: DaAl
external_id:
  arxiv:
  - '1912.10095'
file:
- access_level: open_access
  checksum: f042c8d4316bd87c6361aa76f1fbdbbe
  content_type: application/pdf
  creator: dernst
  date_created: 2021-03-02T15:38:14Z
  date_updated: 2021-03-02T15:38:14Z
  file_id: '9217'
  file_name: 2020_PMLR_Shevchenko.pdf
  file_size: 5336380
  relation: main_file
  success: 1
file_date_updated: 2021-03-02T15:38:14Z
has_accepted_license: '1'
intvolume: '       119'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 8773-8784
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
  name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of the 37th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
  record:
  - id: '17465'
    relation: dissertation_contains
    status: public
status: public
title: Landscape connectivity and dropout stability of SGD solutions for over-parameterized
  neural networks
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 119
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '8707'
abstract:
- lang: eng
  text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
    associated with central biological processes, such as transcription, replication
    and development. Therefore, the comprehensive identification and quantification
    of these changes is fundamental to understanding of evolutionary and regulatory
    mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
    (CHESS), an algorithm for the comparison of chromatin contact maps and automatic
    differential feature extraction. We demonstrate the robustness of CHESS to experimental
    variability and showcase its biological applications on (1) interspecies comparisons
    of syntenic regions in human and mouse models; (2) intraspecies identification
    of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
    aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
    (4) the systematic identification of chromatin contact differences in high-resolution
    Capture-C data. In summary, CHESS is a computationally efficient method for the
    comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
  the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
  Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
  DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
  no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
  programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
  to J.M.V.) and the Medical Research Council in the UK. This research was partially
  funded by the European Union’s H2020 Framework Programme through the European Research
  Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
  de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
  The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
  Innovación y Universidades to the European Molecular Biology Laboratory partnership,
  the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
  the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
  y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
  through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
  by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
  the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
  Operating Program. S.G. thanks the support from the Company of Biologists (grant
  no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
  programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
  full_name: ' Galan, Silvia'
  last_name: ' Galan'
- first_name: Nick N
  full_name: Machnik, Nick N
  id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
  last_name: Machnik
  orcid: 0000-0001-6617-9742
- first_name: Kai
  full_name: Kruse, Kai
  last_name: Kruse
- first_name: Noelia
  full_name: Díaz, Noelia
  last_name: Díaz
- first_name: Marc A
  full_name: Marti-Renom, Marc A
  last_name: Marti-Renom
- first_name: Juan M
  full_name: Vaquerizas, Juan M
  last_name: Vaquerizas
citation:
  ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
    enables quantitative comparison of chromatin contact data and automatic feature
    extraction. <i>Nature Genetics</i>. 2020;52:1247-1255. doi:<a href="https://doi.org/10.1038/s41588-020-00712-y">10.1038/s41588-020-00712-y</a>
  apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &#38; Vaquerizas,
    J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
    and automatic feature extraction. <i>Nature Genetics</i>. Springer Nature. <a
    href="https://doi.org/10.1038/s41588-020-00712-y">https://doi.org/10.1038/s41588-020-00712-y</a>
  chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
    and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
    Data and Automatic Feature Extraction.” <i>Nature Genetics</i>. Springer Nature,
    2020. <a href="https://doi.org/10.1038/s41588-020-00712-y">https://doi.org/10.1038/s41588-020-00712-y</a>.
  ieee: S.  Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
    Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
    automatic feature extraction,” <i>Nature Genetics</i>, vol. 52. Springer Nature,
    pp. 1247–1255, 2020.
  ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
    CHESS enables quantitative comparison of chromatin contact data and automatic
    feature extraction. Nature Genetics. 52, 1247–1255.
  mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
    Data and Automatic Feature Extraction.” <i>Nature Genetics</i>, vol. 52, Springer
    Nature, 2020, pp. 1247–55, doi:<a href="https://doi.org/10.1038/s41588-020-00712-y">10.1038/s41588-020-00712-y</a>.
  short: S.  Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
    Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2026-11-06T23:31:14Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
  isi:
  - '000579693500004'
  pmid:
  - '33077914'
fulldoi: https://doi.org/10.1038/s41588-020-00712-y
intvolume: '        52'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/
month: '10'
oa: 1
oa_version: Submitted Version
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '18642'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
  feature extraction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2020'
...
---
_id: '11059'
abstract:
- lang: eng
  text: The genome is packaged and organized nonrandomly within the 3D space of the
    nucleus to promote efficient gene expression and to faithfully maintain silencing
    of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope
    membrane, which contains a set of proteins that actively participate in chromatin
    organization and gene regulation. Technological advances are providing views of
    genome organization at unprecedented resolution and are beginning to reveal the
    ways that cells co-opt the structures of the nuclear periphery for nuclear organization
    and gene regulation. These genome regulatory roles of proteins of the nuclear
    periphery have important influences on development, disease and ageing.
article_processing_charge: No
article_type: review
author:
- first_name: Abigail
  full_name: Buchwalter, Abigail
  last_name: Buchwalter
- first_name: Jeanae M.
  full_name: Kaneshiro, Jeanae M.
  last_name: Kaneshiro
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: 'Buchwalter A, Kaneshiro JM, Hetzer M. Coaching from the sidelines: The nuclear
    periphery in genome regulation. <i>Nature Reviews Genetics</i>. 2019;20(1):39-50.
    doi:<a href="https://doi.org/10.1038/s41576-018-0063-5">10.1038/s41576-018-0063-5</a>'
  apa: 'Buchwalter, A., Kaneshiro, J. M., &#38; Hetzer, M. (2019). Coaching from the
    sidelines: The nuclear periphery in genome regulation. <i>Nature Reviews Genetics</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41576-018-0063-5">https://doi.org/10.1038/s41576-018-0063-5</a>'
  chicago: 'Buchwalter, Abigail, Jeanae M. Kaneshiro, and Martin Hetzer. “Coaching
    from the Sidelines: The Nuclear Periphery in Genome Regulation.” <i>Nature Reviews
    Genetics</i>. Springer Nature, 2019. <a href="https://doi.org/10.1038/s41576-018-0063-5">https://doi.org/10.1038/s41576-018-0063-5</a>.'
  ieee: 'A. Buchwalter, J. M. Kaneshiro, and M. Hetzer, “Coaching from the sidelines:
    The nuclear periphery in genome regulation,” <i>Nature Reviews Genetics</i>, vol.
    20, no. 1. Springer Nature, pp. 39–50, 2019.'
  ista: 'Buchwalter A, Kaneshiro JM, Hetzer M. 2019. Coaching from the sidelines:
    The nuclear periphery in genome regulation. Nature Reviews Genetics. 20(1), 39–50.'
  mla: 'Buchwalter, Abigail, et al. “Coaching from the Sidelines: The Nuclear Periphery
    in Genome Regulation.” <i>Nature Reviews Genetics</i>, vol. 20, no. 1, Springer
    Nature, 2019, pp. 39–50, doi:<a href="https://doi.org/10.1038/s41576-018-0063-5">10.1038/s41576-018-0063-5</a>.'
  short: A. Buchwalter, J.M. Kaneshiro, M. Hetzer, Nature Reviews Genetics 20 (2019)
    39–50.
date_created: 2022-04-07T07:44:45Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2024-10-14T11:18:54Z
day: '01'
doi: 10.1038/s41576-018-0063-5
extern: '1'
external_id:
  pmid:
  - '30356165'
fulldoi: https://doi.org/10.1038/s41576-018-0063-5
intvolume: '        20'
issue: '1'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
language:
- iso: eng
month: '01'
oa_version: None
page: 39-50
pmid: 1
publication: Nature Reviews Genetics
publication_identifier:
  eissn:
  - 1471-0064
  issn:
  - 1471-0056
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Coaching from the sidelines: The nuclear periphery in genome regulation'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '11060'
abstract:
- lang: eng
  text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum
    (ER) that is gated by the nuclear pore complex. It is unknown whether proteins
    of the INM and ER are degraded through shared or distinct pathways in mammalian
    cells. We applied dynamic proteomics to profile protein half-lives and report
    that INM and ER residents turn over at similar rates, indicating that the INM’s
    unique topology is not a barrier to turnover. Using a microscopy approach, we
    observed that the proteasome can degrade INM proteins in situ. However, we also
    uncovered evidence for selective, vesicular transport-mediated turnover of a single
    INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared
    from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular
    trafficking to lysosomes. This work demonstrates that the INM can be dynamically
    remodeled in response to environmental inputs.
article_number: e49796
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
  full_name: Buchwalter, Abigail
  last_name: Buchwalter
- first_name: Roberta
  full_name: Schulte, Roberta
  last_name: Schulte
- first_name: Hsiao
  full_name: Tsai, Hsiao
  last_name: Tsai
- first_name: Juliana
  full_name: Capitanio, Juliana
  last_name: Capitanio
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance
    of the inner nuclear membrane protein emerin by vesicular transport during ER
    stress. <i>eLife</i>. 2019;8. doi:<a href="https://doi.org/10.7554/elife.49796">10.7554/elife.49796</a>
  apa: Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., &#38; Hetzer, M. (2019).
    Selective clearance of the inner nuclear membrane protein emerin by vesicular
    transport during ER stress. <i>ELife</i>. eLife Sciences Publications. <a href="https://doi.org/10.7554/elife.49796">https://doi.org/10.7554/elife.49796</a>
  chicago: Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and
    Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin
    by Vesicular Transport during ER Stress.” <i>ELife</i>. eLife Sciences Publications,
    2019. <a href="https://doi.org/10.7554/elife.49796">https://doi.org/10.7554/elife.49796</a>.
  ieee: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective
    clearance of the inner nuclear membrane protein emerin by vesicular transport
    during ER stress,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.
  ista: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance
    of the inner nuclear membrane protein emerin by vesicular transport during ER
    stress. eLife. 8, e49796.
  mla: Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane
    Protein Emerin by Vesicular Transport during ER Stress.” <i>ELife</i>, vol. 8,
    e49796, eLife Sciences Publications, 2019, doi:<a href="https://doi.org/10.7554/elife.49796">10.7554/elife.49796</a>.
  short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).
date_created: 2022-04-07T07:45:02Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2024-10-14T12:08:36Z
day: '10'
ddc:
- '570'
doi: 10.7554/elife.49796
extern: '1'
external_id:
  pmid:
  - '31599721'
file:
- access_level: open_access
  checksum: 1e8672a1e9c3dc0a2d3d0dad89673616
  content_type: application/pdf
  creator: dernst
  date_created: 2022-04-08T08:18:01Z
  date_updated: 2022-04-08T08:18:01Z
  file_id: '11138'
  file_name: 2019_eLife_Buchwalter.pdf
  file_size: 6984654
  relation: main_file
  success: 1
file_date_updated: 2022-04-08T08:18:01Z
fulldoi: https://doi.org/10.7554/elife.49796
has_accepted_license: '1'
intvolume: '         8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
  issn:
  - 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
  record:
  - id: '13079'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Selective clearance of the inner nuclear membrane protein emerin by vesicular
  transport during ER stress
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: 8
year: '2019'
...
---
_id: '11061'
abstract:
- lang: eng
  text: Many adult tissues contain postmitotic cells as old as the host organism.
    The only organelle that does not turn over in these cells is the nucleus, and
    its maintenance represents a formidable challenge, as it harbors regulatory proteins
    that persist throughout adulthood. Here we developed strategies to visualize two
    classes of such long-lived proteins, histones and nucleoporins, to understand
    the function of protein longevity in nuclear maintenance. Genome-wide mapping
    of histones revealed specific enrichment of long-lived variants at silent gene
    loci. Interestingly, nuclear pores are maintained by piecemeal replacement of
    subunits, resulting in mosaic complexes composed of polypeptides with vastly different
    ages. In contrast, nondividing quiescent cells remove old nuclear pores in an
    ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear
    maintenance, linking lifelong protein persistence to gene regulation and nuclear
    integrity.
article_processing_charge: No
article_type: original
author:
- first_name: Brandon H.
  full_name: Toyama, Brandon H.
  last_name: Toyama
- first_name: Rafael
  full_name: Arrojo e Drigo, Rafael
  last_name: Arrojo e Drigo
- first_name: Varda
  full_name: Lev-Ram, Varda
  last_name: Lev-Ram
- first_name: Ranjan
  full_name: Ramachandra, Ranjan
  last_name: Ramachandra
- first_name: Thomas J.
  full_name: Deerinck, Thomas J.
  last_name: Deerinck
- first_name: Claude
  full_name: Lechene, Claude
  last_name: Lechene
- first_name: Mark H.
  full_name: Ellisman, Mark H.
  last_name: Ellisman
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Toyama BH, Arrojo e Drigo R, Lev-Ram V, et al. Visualization of long-lived
    proteins reveals age mosaicism within nuclei of postmitotic cells. <i>Journal
    of Cell Biology</i>. 2019;218(2):433-444. doi:<a href="https://doi.org/10.1083/jcb.201809123">10.1083/jcb.201809123</a>
  apa: Toyama, B. H., Arrojo e Drigo, R., Lev-Ram, V., Ramachandra, R., Deerinck,
    T. J., Lechene, C., … Hetzer, M. (2019). Visualization of long-lived proteins
    reveals age mosaicism within nuclei of postmitotic cells. <i>Journal of Cell Biology</i>.
    Rockefeller University Press. <a href="https://doi.org/10.1083/jcb.201809123">https://doi.org/10.1083/jcb.201809123</a>
  chicago: Toyama, Brandon H., Rafael Arrojo e Drigo, Varda Lev-Ram, Ranjan Ramachandra,
    Thomas J. Deerinck, Claude Lechene, Mark H. Ellisman, and Martin Hetzer. “Visualization
    of Long-Lived Proteins Reveals Age Mosaicism within Nuclei of Postmitotic Cells.”
    <i>Journal of Cell Biology</i>. Rockefeller University Press, 2019. <a href="https://doi.org/10.1083/jcb.201809123">https://doi.org/10.1083/jcb.201809123</a>.
  ieee: B. H. Toyama <i>et al.</i>, “Visualization of long-lived proteins reveals
    age mosaicism within nuclei of postmitotic cells,” <i>Journal of Cell Biology</i>,
    vol. 218, no. 2. Rockefeller University Press, pp. 433–444, 2019.
  ista: Toyama BH, Arrojo e Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene
    C, Ellisman MH, Hetzer M. 2019. Visualization of long-lived proteins reveals age
    mosaicism within nuclei of postmitotic cells. Journal of Cell Biology. 218(2),
    433–444.
  mla: Toyama, Brandon H., et al. “Visualization of Long-Lived Proteins Reveals Age
    Mosaicism within Nuclei of Postmitotic Cells.” <i>Journal of Cell Biology</i>,
    vol. 218, no. 2, Rockefeller University Press, 2019, pp. 433–44, doi:<a href="https://doi.org/10.1083/jcb.201809123">10.1083/jcb.201809123</a>.
  short: B.H. Toyama, R. Arrojo e Drigo, V. Lev-Ram, R. Ramachandra, T.J. Deerinck,
    C. Lechene, M.H. Ellisman, M. Hetzer, Journal of Cell Biology 218 (2019) 433–444.
date_created: 2022-04-07T07:45:11Z
date_published: 2019-02-04T00:00:00Z
date_updated: 2024-10-14T11:19:21Z
day: '04'
ddc:
- '570'
doi: 10.1083/jcb.201809123
extern: '1'
external_id:
  pmid:
  - '30552100'
file:
- access_level: open_access
  checksum: 7964ebbf833b0b35f9fba840eea9531d
  content_type: application/pdf
  creator: dernst
  date_created: 2022-04-08T08:26:32Z
  date_updated: 2022-04-08T08:26:32Z
  file_id: '11139'
  file_name: 2019_JCB_Toyama.pdf
  file_size: 2503838
  relation: main_file
  success: 1
file_date_updated: 2022-04-08T08:26:32Z
fulldoi: https://doi.org/10.1083/jcb.201809123
has_accepted_license: '1'
intvolume: '       218'
issue: '2'
keyword:
- Cell Biology
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 433-444
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
  eissn:
  - 1540-8140
  issn:
  - 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visualization of long-lived proteins reveals age mosaicism within nuclei of
  postmitotic cells
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 218
year: '2019'
...
---
_id: '11062'
abstract:
- lang: eng
  text: Most neurons are not replaced during an animal’s lifetime. This nondividing
    state is characterized by extreme longevity and age-dependent decline of key regulatory
    proteins. To study the lifespans of cells and proteins in adult tissues, we combined
    isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping,
    we show that liver and pancreas are composed of cells with vastly different ages,
    many as old as the animal. Strikingly, we also found that a subset of fibroblasts
    and endothelial cells, both known for their replicative potential, are characterized
    by the absence of cell division during adulthood. In addition, we show that the
    primary cilia of beta cells and neurons contains different structural regions
    with vastly different lifespans. Based on these results, we propose that age mosaicism
    across multiple scales is a fundamental principle of adult tissue, cell, and protein
    complex organization.
article_processing_charge: No
article_type: original
author:
- first_name: Rafael
  full_name: Arrojo e Drigo, Rafael
  last_name: Arrojo e Drigo
- first_name: Varda
  full_name: Lev-Ram, Varda
  last_name: Lev-Ram
- first_name: Swati
  full_name: Tyagi, Swati
  last_name: Tyagi
- first_name: Ranjan
  full_name: Ramachandra, Ranjan
  last_name: Ramachandra
- first_name: Thomas
  full_name: Deerinck, Thomas
  last_name: Deerinck
- first_name: Eric
  full_name: Bushong, Eric
  last_name: Bushong
- first_name: Sebastien
  full_name: Phan, Sebastien
  last_name: Phan
- first_name: Victoria
  full_name: Orphan, Victoria
  last_name: Orphan
- first_name: Claude
  full_name: Lechene, Claude
  last_name: Lechene
- first_name: Mark H.
  full_name: Ellisman, Mark H.
  last_name: Ellisman
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
citation:
  ama: Arrojo e Drigo R, Lev-Ram V, Tyagi S, et al. Age mosaicism across multiple
    scales in adult tissues. <i>Cell Metabolism</i>. 2019;30(2):343-351.e3. doi:<a
    href="https://doi.org/10.1016/j.cmet.2019.05.010">10.1016/j.cmet.2019.05.010</a>
  apa: Arrojo e Drigo, R., Lev-Ram, V., Tyagi, S., Ramachandra, R., Deerinck, T.,
    Bushong, E., … Hetzer, M. (2019). Age mosaicism across multiple scales in adult
    tissues. <i>Cell Metabolism</i>. Elsevier. <a href="https://doi.org/10.1016/j.cmet.2019.05.010">https://doi.org/10.1016/j.cmet.2019.05.010</a>
  chicago: Arrojo e Drigo, Rafael, Varda Lev-Ram, Swati Tyagi, Ranjan Ramachandra,
    Thomas Deerinck, Eric Bushong, Sebastien Phan, et al. “Age Mosaicism across Multiple
    Scales in Adult Tissues.” <i>Cell Metabolism</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.cmet.2019.05.010">https://doi.org/10.1016/j.cmet.2019.05.010</a>.
  ieee: R. Arrojo e Drigo <i>et al.</i>, “Age mosaicism across multiple scales in
    adult tissues,” <i>Cell Metabolism</i>, vol. 30, no. 2. Elsevier, p. 343–351.e3,
    2019.
  ista: Arrojo e Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E,
    Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer M. 2019. Age mosaicism across
    multiple scales in adult tissues. Cell Metabolism. 30(2), 343–351.e3.
  mla: Arrojo e Drigo, Rafael, et al. “Age Mosaicism across Multiple Scales in Adult
    Tissues.” <i>Cell Metabolism</i>, vol. 30, no. 2, Elsevier, 2019, p. 343–351.e3,
    doi:<a href="https://doi.org/10.1016/j.cmet.2019.05.010">10.1016/j.cmet.2019.05.010</a>.
  short: R. Arrojo e Drigo, V. Lev-Ram, S. Tyagi, R. Ramachandra, T. Deerinck, E.
    Bushong, S. Phan, V. Orphan, C. Lechene, M.H. Ellisman, M. Hetzer, Cell Metabolism
    30 (2019) 343–351.e3.
date_created: 2022-04-07T07:45:21Z
date_published: 2019-08-06T00:00:00Z
date_updated: 2025-12-15T10:02:11Z
day: '06'
department:
- _id: MaHe
doi: 10.1016/j.cmet.2019.05.010
extern: '1'
external_id:
  pmid:
  - '31178361'
fulldoi: https://doi.org/10.1016/j.cmet.2019.05.010
intvolume: '        30'
issue: '2'
keyword:
- Cell Biology
- Molecular Biology
- Physiology
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cmet.2019.05.010
month: '08'
oa: 1
oa_version: Published Version
page: 343-351.e3
pmid: 1
publication: Cell Metabolism
publication_identifier:
  issn:
  - 1550-4131
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Age mosaicism across multiple scales in adult tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2019'
...
---
_id: '11499'
abstract:
- lang: eng
  text: Deep optical spectroscopic surveys of galaxies provide a unique opportunity
    to investigate rest-frame ultra-violet (UV) emission line properties of galaxies
    at z ∼ 2 − 4.5. Here we combine VLT/MUSE Guaranteed Time Observations of the Hubble
    Deep Field South, Ultra Deep Field, COSMOS, and several quasar fields with other
    publicly available data from VLT/VIMOS and VLT/FORS2 to construct a catalogue
    of He II λ1640 emitters at z ≳ 2. The deepest areas of our MUSE pointings reach
    a 3σ line flux limit of 3.1 × 10−19 erg s−1 cm−2. After discarding broad-line
    active galactic nuclei, we find 13 He II λ1640 detections from MUSE with a median
    MUV = −20.1 and 21 tentative He II λ1640 detections from other public surveys.
    Excluding Lyα, all except two galaxies in our sample show at least one other rest-UV
    emission line, with C III] λ1907, λ1909 being the most prominent. We use multi-wavelength
    data available in the Hubble legacy fields to derive basic galaxy properties of
    our sample through spectral energy distribution fitting techniques. Taking advantage
    of the high-quality spectra obtained by MUSE (∼10 − 30 h of exposure time per
    pointing), we use photo-ionisation models to study the rest-UV emission line diagnostics
    of the He II λ1640 emitters. Line ratios of our sample can be reproduced by moderately
    sub-solar photo-ionisation models, however, we find that including effects of
    binary stars lead to degeneracies in most free parameters. Even after considering
    extra ionising photons produced by extreme sub-solar metallicity binary stellar
    models, photo-ionisation models are unable to reproduce rest-frame He II λ1640
    equivalent widths (∼0.2 − 10 Å), thus additional mechanisms are necessary in models
    to match the observed He II λ1640 properties.
acknowledgement: 'The authors wish to thank the referee for constructive comments
  that improved the paper substantially. We thank the BPASS team for making the stellar
  population models available. We thank Elizabeth Stanway, Claus Leitherer, Daniel
  Schaerer, Jorick Vink, and Nell Byler for insightful discussions. We thank the Lorentz
  Centre and the scientific organizers of the Characterizing galaxies with spectroscopy
  with a view for JWST workshop held at the Lorentz Centre in 2017 October, which
  promoted useful discussions in the wider community. TN, JB, and RB acknowledges
  the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) top grant TOP1.16.057.
  AF acknowledges support from the ERC via an Advanced Grant under grant agreement
  no. 339659-MUSICOS. JB acknowledges support by Fundação para a Ciência e a Tecnologia
  (FCT) through national funds (UID/FIS/04434/2013) and Investigador FCT contract
  IF/01654/2014/CP1215/CT0003, and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672).
  JR acknowledges support from the ERC Starting grant 336736 (CALENDS). This research
  made use of astropy (http://www.astropy.org) a community-developed core Python package
  for Astronomy (Astropy Collaboration 2013, 2018) and pandas (McKinney 2010). Figures
  were generated using matplotlib (Hunter 2007) and seaborn (https://seaborn.pydata.org).
  Facilities: VLT (MUSE).'
article_number: A89
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Themiya
  full_name: Nanayakkara, Themiya
  last_name: Nanayakkara
- first_name: Jarle
  full_name: Brinchmann, Jarle
  last_name: Brinchmann
- first_name: Leindert
  full_name: Boogaard, Leindert
  last_name: Boogaard
- first_name: Rychard
  full_name: Bouwens, Rychard
  last_name: Bouwens
- first_name: Sebastiano
  full_name: Cantalupo, Sebastiano
  last_name: Cantalupo
- first_name: Anna
  full_name: Feltre, Anna
  last_name: Feltre
- first_name: Wolfram
  full_name: Kollatschny, Wolfram
  last_name: Kollatschny
- first_name: Raffaella Anna
  full_name: Marino, Raffaella Anna
  last_name: Marino
- first_name: Michael
  full_name: Maseda, Michael
  last_name: Maseda
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
- first_name: Mieke
  full_name: Paalvast, Mieke
  last_name: Paalvast
- first_name: Johan
  full_name: Richard, Johan
  last_name: Richard
- first_name: Anne
  full_name: Verhamme, Anne
  last_name: Verhamme
citation:
  ama: Nanayakkara T, Brinchmann J, Boogaard L, et al. Exploring He II λ1640 emission
    line properties at z ∼2−4. <i>Astronomy &#38; Astrophysics</i>. 2019;648. doi:<a
    href="https://doi.org/10.1051/0004-6361/201834565">10.1051/0004-6361/201834565</a>
  apa: Nanayakkara, T., Brinchmann, J., Boogaard, L., Bouwens, R., Cantalupo, S.,
    Feltre, A., … Verhamme, A. (2019). Exploring He II λ1640 emission line properties
    at z ∼2−4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href="https://doi.org/10.1051/0004-6361/201834565">https://doi.org/10.1051/0004-6361/201834565</a>
  chicago: Nanayakkara, Themiya, Jarle Brinchmann, Leindert Boogaard, Rychard Bouwens,
    Sebastiano Cantalupo, Anna Feltre, Wolfram Kollatschny, et al. “Exploring He II Λ1640
    Emission Line Properties at z ∼2−4.” <i>Astronomy &#38; Astrophysics</i>. EDP
    Sciences, 2019. <a href="https://doi.org/10.1051/0004-6361/201834565">https://doi.org/10.1051/0004-6361/201834565</a>.
  ieee: T. Nanayakkara <i>et al.</i>, “Exploring He II λ1640 emission line properties
    at z ∼2−4,” <i>Astronomy &#38; Astrophysics</i>, vol. 648. EDP Sciences, 2019.
  ista: Nanayakkara T, Brinchmann J, Boogaard L, Bouwens R, Cantalupo S, Feltre A,
    Kollatschny W, Marino RA, Maseda M, Matthee JJ, Paalvast M, Richard J, Verhamme
    A. 2019. Exploring He II λ1640 emission line properties at z ∼2−4. Astronomy &#38;
    Astrophysics. 648, A89.
  mla: Nanayakkara, Themiya, et al. “Exploring He II Λ1640 Emission Line Properties
    at z ∼2−4.” <i>Astronomy &#38; Astrophysics</i>, vol. 648, A89, EDP Sciences,
    2019, doi:<a href="https://doi.org/10.1051/0004-6361/201834565">10.1051/0004-6361/201834565</a>.
  short: T. Nanayakkara, J. Brinchmann, L. Boogaard, R. Bouwens, S. Cantalupo, A.
    Feltre, W. Kollatschny, R.A. Marino, M. Maseda, J.J. Matthee, M. Paalvast, J.
    Richard, A. Verhamme, Astronomy &#38; Astrophysics 648 (2019).
date_created: 2022-07-06T09:07:06Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2022-07-19T09:36:08Z
day: '16'
doi: 10.1051/0004-6361/201834565
extern: '1'
external_id:
  arxiv:
  - '1902.05960'
fulldoi: https://doi.org/10.1051/0004-6361/201834565
intvolume: '       648'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: ISM / galaxies: star formation / galaxies: evolution / galaxies: high-redshift'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1902.05960
month: '04'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
related_material:
  link:
  - relation: erratum
    url: https://doi.org/10.1051/0004-6361/201834565e
scopus_import: '1'
status: public
title: Exploring He II λ1640 emission line properties at z ∼2−4
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 648
year: '2019'
...
---
_id: '11505'
abstract:
- lang: eng
  text: "Contact. This paper presents the results obtained with the Multi-Unit Spectroscopic
    Explorer (MUSE) at the ESO Very Large Telescope on the faint end of the Lyman-alpha
    luminosity function (LF) based on deep observations of four lensing clusters.
    The goal of our project is to set strong constraints on the relative contribution
    of the Lyman-alpha emitter (LAE) population to cosmic reionization.\r\n\r\nAims.
    The precise aim of the present study is to further constrain the abundance of
    LAEs by taking advantage of the magnification provided by lensing clusters to
    build a blindly selected sample of galaxies which is less biased than current
    blank field samples in redshift and luminosity. By construction, this sample of
    LAEs is complementary to those built from deep blank fields, whether observed
    by MUSE or by other facilities, and makes it possible to determine the shape of
    the LF at fainter levels, as well as its evolution with redshift.\r\n\r\nMethods.
    We selected a sample of 156 LAEs with redshifts between 2.9 ≤ z ≤ 6.7 and magnification-corrected
    luminosities in the range 39 ≲ log LLyα [erg s−1] ≲43. To properly take into account
    the individual differences in detection conditions between the LAEs when computing
    the LF, including lensing configurations, and spatial and spectral morphologies,
    the non-parametric 1/Vmax method was adopted. The price to pay to benefit from
    magnification is a reduction of the effective volume of the survey, together with
    a more complex analysis procedure to properly determine the effective volume Vmax
    for each galaxy. In this paper we present a complete procedure for the determination
    of the LF based on IFU detections in lensing clusters. This procedure, including
    some new methods for masking, effective volume integration and (individual) completeness
    determinations, has been fully automated when possible, and it can be easily generalized
    to the analysis of IFU observations in blank fields.\r\n\r\nResults. As a result
    of this analysis, the Lyman-alpha LF has been obtained in four different redshift
    bins: 2.9 <  z <  6, 7, 2.9 <  z <  4.0, 4.0 <  z <  5.0, and 5.0 <  z <  6.7
    with constraints down to log LLyα = 40.5. From our data only, no significant evolution
    of LF mean slope can be found. When performing a Schechter analysis also including
    data from the literature to complete the present sample towards the brightest
    luminosities, a steep faint end slope was measured varying from α = −1.69−0.08+0.08
    to α = −1.87−0.12+0.12 between the lowest and the highest redshift bins.\r\n\r\nConclusions.
    The contribution of the LAE population to the star formation rate density at z ∼ 6
    is ≲50% depending on the luminosity limit considered, which is of the same order
    as the Lyman-break galaxy (LBG) contribution. The evolution of the LAE contribution
    with redshift depends on the assumed escape fraction of Lyman-alpha photons, and
    appears to slightly increase with increasing redshift when this fraction is conservatively
    set to one. Depending on the intersection between the LAE/LBG populations, the
    contribution of the observed galaxies to the ionizing flux may suffice to keep
    the universe ionized at z ∼ 6."
acknowledgement: We thank the anonymous referee for their critical review and useful
  suggestions. This work has been carried out thanks to the support of the OCEVU Labex
  (ANR-11-LABX-0060) and the A*MIDEX project (ANR-11-IDEX-0001-02) funded by the “Investissements
  d’Avenir” French government programme managed by the ANR. Partially funded by the
  ERC starting grant CALENDS (JR, VP, BC, JM), the Agence Nationale de la recherche
  bearing the reference ANR-13-BS05-0010-02 (FOGHAR), and the “Programme National
  de Cosmologie and Galaxies” (PNCG) of CNRS/INSU, France. GdV, RP, JR, GM, JM, BC,
  and VP also acknowledge support by the Programa de Cooperacion Cientifica – ECOS
  SUD Program C16U02. NL acknowledges funding from the European Research Council (ERC)
  under the European Union’s Horizon 2020 research and innovation programme (grant
  agreement No 669253), ABD acknowledges support from the ERC advanced grant “Cosmic
  Gas”. LW acknowledges support by the Competitive Fund of the Leibniz Association
  through grant SAW-2015-AIP-2, and TG acknowledges support from the European Research
  Council under grant agreement ERC-stg-757258 (TRIPLE).. Based on observations made
  with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 060.A-9345,
  094.A-0115, 095.A-0181, 096.A-0710, 097.A0269, 100.A-0249, and 294.A-5032. Also
  based on observations obtained with the NASA/ESA Hubble Space Telescope, retrieved
  from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science
  Institute (STScI). STScI is operated by the Association of Universities for Research
  in Astronomy, Inc. under NASA contract NAS 5-26555. This research made use of Astropy,
  a community-developed core Python package for Astronomy (Astropy Collaboration 2013).
  All plots in this paper were created using Matplotlib (Hunter 2007).
article_number: A3
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: G.
  full_name: de La Vieuville, G.
  last_name: de La Vieuville
- first_name: D.
  full_name: Bina, D.
  last_name: Bina
- first_name: R.
  full_name: Pello, R.
  last_name: Pello
- first_name: G.
  full_name: Mahler, G.
  last_name: Mahler
- first_name: J.
  full_name: Richard, J.
  last_name: Richard
- first_name: A. B.
  full_name: Drake, A. B.
  last_name: Drake
- first_name: E. C.
  full_name: Herenz, E. C.
  last_name: Herenz
- first_name: F. E.
  full_name: Bauer, F. E.
  last_name: Bauer
- first_name: B.
  full_name: Clément, B.
  last_name: Clément
- first_name: D.
  full_name: Lagattuta, D.
  last_name: Lagattuta
- first_name: N.
  full_name: Laporte, N.
  last_name: Laporte
- first_name: J.
  full_name: Martinez, J.
  last_name: Martinez
- first_name: V.
  full_name: Patrício, V.
  last_name: Patrício
- first_name: L.
  full_name: Wisotzki, L.
  last_name: Wisotzki
- first_name: J.
  full_name: Zabl, J.
  last_name: Zabl
- first_name: R. J.
  full_name: Bouwens, R. J.
  last_name: Bouwens
- first_name: T.
  full_name: Contini, T.
  last_name: Contini
- first_name: T.
  full_name: Garel, T.
  last_name: Garel
- first_name: B.
  full_name: Guiderdoni, B.
  last_name: Guiderdoni
- first_name: R. A.
  full_name: Marino, R. A.
  last_name: Marino
- first_name: M. V.
  full_name: Maseda, M. V.
  last_name: Maseda
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
- first_name: J.
  full_name: Schaye, J.
  last_name: Schaye
- first_name: G.
  full_name: Soucail, G.
  last_name: Soucail
citation:
  ama: de La Vieuville G, Bina D, Pello R, et al. Faint end of the z ∼ 3–7 luminosity
    function of Lyman-alpha emitters behind lensing clusters observed with MUSE. <i>Astronomy
    &#38; Astrophysics</i>. 2019;628. doi:<a href="https://doi.org/10.1051/0004-6361/201834471">10.1051/0004-6361/201834471</a>
  apa: de La Vieuville, G., Bina, D., Pello, R., Mahler, G., Richard, J., Drake, A.
    B., … Soucail, G. (2019). Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha
    emitters behind lensing clusters observed with MUSE. <i>Astronomy &#38; Astrophysics</i>.
    EDP Sciences. <a href="https://doi.org/10.1051/0004-6361/201834471">https://doi.org/10.1051/0004-6361/201834471</a>
  chicago: La Vieuville, G. de, D. Bina, R. Pello, G. Mahler, J. Richard, A. B. Drake,
    E. C. Herenz, et al. “Faint End of the z ∼ 3–7 Luminosity Function of Lyman-Alpha
    Emitters behind Lensing Clusters Observed with MUSE.” <i>Astronomy &#38; Astrophysics</i>.
    EDP Sciences, 2019. <a href="https://doi.org/10.1051/0004-6361/201834471">https://doi.org/10.1051/0004-6361/201834471</a>.
  ieee: G. de La Vieuville <i>et al.</i>, “Faint end of the z ∼ 3–7 luminosity function
    of Lyman-alpha emitters behind lensing clusters observed with MUSE,” <i>Astronomy
    &#38; Astrophysics</i>, vol. 628. EDP Sciences, 2019.
  ista: de La Vieuville G, Bina D, Pello R, Mahler G, Richard J, Drake AB, Herenz
    EC, Bauer FE, Clément B, Lagattuta D, Laporte N, Martinez J, Patrício V, Wisotzki
    L, Zabl J, Bouwens RJ, Contini T, Garel T, Guiderdoni B, Marino RA, Maseda MV,
    Matthee JJ, Schaye J, Soucail G. 2019. Faint end of the z ∼ 3–7 luminosity function
    of Lyman-alpha emitters behind lensing clusters observed with MUSE. Astronomy
    &#38; Astrophysics. 628, A3.
  mla: de La Vieuville, G., et al. “Faint End of the z ∼ 3–7 Luminosity Function of
    Lyman-Alpha Emitters behind Lensing Clusters Observed with MUSE.” <i>Astronomy
    &#38; Astrophysics</i>, vol. 628, A3, EDP Sciences, 2019, doi:<a href="https://doi.org/10.1051/0004-6361/201834471">10.1051/0004-6361/201834471</a>.
  short: G. de La Vieuville, D. Bina, R. Pello, G. Mahler, J. Richard, A.B. Drake,
    E.C. Herenz, F.E. Bauer, B. Clément, D. Lagattuta, N. Laporte, J. Martinez, V.
    Patrício, L. Wisotzki, J. Zabl, R.J. Bouwens, T. Contini, T. Garel, B. Guiderdoni,
    R.A. Marino, M.V. Maseda, J.J. Matthee, J. Schaye, G. Soucail, Astronomy &#38;
    Astrophysics 628 (2019).
date_created: 2022-07-06T10:09:36Z
date_published: 2019-07-25T00:00:00Z
date_updated: 2022-07-19T09:36:31Z
day: '25'
doi: 10.1051/0004-6361/201834471
extern: '1'
external_id:
  arxiv:
  - '1905.13696'
fulldoi: https://doi.org/10.1051/0004-6361/201834471
intvolume: '       628'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'gravitational lensing: strong / galaxies: high-redshift / dark ages'
- reionization
- 'first stars / galaxies: clusters: general / galaxies: luminosity function'
- mass function
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1905.13696
month: '07'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind
  lensing clusters observed with MUSE
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 628
year: '2019'
...
---
_id: '11507'
abstract:
- lang: eng
  text: 'Lyman-α (Lyα) is intrinsically the brightest line emitted from active galaxies.
    While it originates from many physical processes, for star-forming galaxies the
    intrinsic Lyα luminosity is a direct tracer of the Lyman-continuum (LyC) radiation
    produced by the most massive O- and early-type B-stars (M⋆ ≳ 10 M⊙) with lifetimes
    of a few Myrs. As such, Lyα luminosity should be an excellent instantaneous star
    formation rate (SFR) indicator. However, its resonant nature and susceptibility
    to dust as a rest-frame UV photon makes Lyα very hard to interpret due to the
    uncertain Lyα escape fraction, fesc, Lyα. Here we explore results from the CAlibrating
    LYMan-α with Hα (CALYMHA) survey at z = 2.2, follow-up of Lyα emitters (LAEs)
    at z = 2.2 − 2.6 and a z ∼ 0−0.3 compilation of LAEs to directly measure fesc, Lyα
    with Hα. We derive a simple empirical relation that robustly retrieves fesc, Lyα
    as a function of Lyα rest-frame EW (EW0): fesc,Lyα = 0.0048 EW0[Å] ± 0.05 and
    we show that it constrains a well-defined anti-correlation between ionisation
    efficiency (ξion) and dust extinction in LAEs. Observed Lyα luminosities and EW0
    are easy measurable quantities at high redshift, thus making our relation a practical
    tool to estimate intrinsic Lyα and LyC luminosities under well controlled and
    simple assumptions. Our results allow observed Lyα luminosities to be used to
    compute SFRs for LAEs at z ∼ 0−2.6 within ±0.2 dex of the Hα dust corrected SFRs.
    We apply our empirical SFR(Lyα,EW0) calibration to several sources at z ≥ 2.6
    to find that star-forming LAEs have SFRs typically ranging from 0.1 to 20 M⊙ yr−1
    and that our calibration might be even applicable for the most luminous LAEs within
    the epoch of re-ionisation. Our results imply high ionisation efficiencies (log10[ξion/Hz erg−1]
    = 25.4−25.6) and low dust content in LAEs across cosmic time, and will be easily
    tested with future observations with JWST which can obtain Hα and Hβ measurements
    for high-redshift LAEs.'
acknowledgement: We thank the anonymous referees for multiple comments and suggestions
  which have improved the manuscript. JM acknowledges the support of a Huygens PhD
  fellowship from Leiden University. We have benefited greatly from the publicly available
  programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt et al. 2011;
  Jones et al. 2001), MATPLOTLIB (Hunter 2007) and ASTROPY (Astropy Collaboration
  2013) packages, and the TOPCAT analysis program (Taylor 2013). The results and samples
  of LAEs used for this paper are publicly available (see e.g. Sobral et al. 2017,
  2018a) and we also provide the toy model used as a PYTHON script.
article_number: A157
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David
  full_name: Sobral, David
  last_name: Sobral
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
citation:
  ama: 'Sobral D, Matthee JJ. Predicting Lyα escape fractions with a simple observable:
    Lyα in emission as an empirically calibrated star formation rate indicator. <i>Astronomy
    &#38; Astrophysics</i>. 2019;623. doi:<a href="https://doi.org/10.1051/0004-6361/201833075">10.1051/0004-6361/201833075</a>'
  apa: 'Sobral, D., &#38; Matthee, J. J. (2019). Predicting Lyα escape fractions with
    a simple observable: Lyα in emission as an empirically calibrated star formation
    rate indicator. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href="https://doi.org/10.1051/0004-6361/201833075">https://doi.org/10.1051/0004-6361/201833075</a>'
  chicago: 'Sobral, David, and Jorryt J Matthee. “Predicting Lyα Escape Fractions
    with a Simple Observable: Lyα in Emission as an Empirically Calibrated Star Formation
    Rate Indicator.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2019. <a href="https://doi.org/10.1051/0004-6361/201833075">https://doi.org/10.1051/0004-6361/201833075</a>.'
  ieee: 'D. Sobral and J. J. Matthee, “Predicting Lyα escape fractions with a simple
    observable: Lyα in emission as an empirically calibrated star formation rate indicator,”
    <i>Astronomy &#38; Astrophysics</i>, vol. 623. EDP Sciences, 2019.'
  ista: 'Sobral D, Matthee JJ. 2019. Predicting Lyα escape fractions with a simple
    observable: Lyα in emission as an empirically calibrated star formation rate indicator.
    Astronomy &#38; Astrophysics. 623, A157.'
  mla: 'Sobral, David, and Jorryt J. Matthee. “Predicting Lyα Escape Fractions with
    a Simple Observable: Lyα in Emission as an Empirically Calibrated Star Formation
    Rate Indicator.” <i>Astronomy &#38; Astrophysics</i>, vol. 623, A157, EDP Sciences,
    2019, doi:<a href="https://doi.org/10.1051/0004-6361/201833075">10.1051/0004-6361/201833075</a>.'
  short: D. Sobral, J.J. Matthee, Astronomy &#38; Astrophysics 623 (2019).
date_created: 2022-07-06T11:08:16Z
date_published: 2019-03-26T00:00:00Z
date_updated: 2022-07-19T09:37:20Z
day: '26'
doi: 10.1051/0004-6361/201833075
extern: '1'
external_id:
  arxiv:
  - '1803.08923'
fulldoi: https://doi.org/10.1051/0004-6361/201833075
intvolume: '       623'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
- 'galaxies: high-redshift / galaxies: star formation / galaxies: statistics / galaxies:
  evolution / galaxies: formation / galaxies: ISM'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1803.08923
month: '03'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
  eissn:
  - 1432-0746
  issn:
  - 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Predicting Lyα escape fractions with a simple observable: Lyα in emission
  as an empirically calibrated star formation rate indicator'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 623
year: '2019'
...
---
_id: '11514'
abstract:
- lang: eng
  text: We discuss the nature and physical properties of gas-mass selected galaxies
    in the ALMA spectroscopic survey (ASPECS) of the Hubble Ultra Deep Field (HUDF).
    We capitalize on the deep optical integral-field spectroscopy from the Multi Unit
    Spectroscopic Explorer (MUSE) HUDF Survey and multiwavelength data to uniquely
    associate all 16 line emitters, detected in the ALMA data without preselection,
    with rotational transitions of carbon monoxide (CO). We identify 10 as CO(2–1)
    at 1 < z < 2, 5 as CO(3–2) at 2 < z < 3, and 1 as CO(4–3) at z = 3.6. Using the
    MUSE data as a prior, we identify two additional CO(2–1) emitters, increasing
    the total sample size to 18. We infer metallicities consistent with (super-)solar
    for the CO-detected galaxies at z ≤ 1.5, motivating our choice of a Galactic conversion
    factor between CO luminosity and molecular gas mass for these galaxies. Using
    deep Chandra imaging of the HUDF, we determine an X-ray AGN fraction of 20% and
    60% among the CO emitters at z ∼ 1.4 and z ∼ 2.6, respectively. Being a CO-flux-limited
    survey, ASPECS-LP detects molecular gas in galaxies on, above, and below the main
    sequence (MS) at z ∼ 1.4. For stellar masses ≥1010 (1010.5) ${M}_{\odot }$, we
    detect about 40% (50%) of all galaxies in the HUDF at 1 < z < 2 (2 < z < 3). The
    combination of ALMA and MUSE integral-field spectroscopy thus enables an unprecedented
    view of MS galaxies during the peak of galaxy formation.
acknowledgement: "We are grateful to the referee for providing a constructive report.
  L.A.B. wants to thank Madusha L.P. Gunawardhana for her help with platefit. Based
  on observations collected at the European Southern Observatory under ESO programme(s):
  094.A-2089(B), 095.A-0010(A), 096.A-0045(A), and 096.A-0045(B). This paper makes
  use of the following ALMA data: ADS/JAO.ALMA#2016.1.00324.L. ALMA is a partnership
  of ESO (representing its member states), NSF (USA) and NINS (Japan), together with
  NRC (Canada), NSC and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation
  with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO,
  and NAOJ. The National Radio Astronomy Observatory is a facility of the National
  Science Foundation operated under cooperative agreement by Associated Universities,
  Inc.\r\n\r\n\"Este trabajo contó con el apoyo de CONICYT+Programa de Astronomía+
  Fondo CHINA-CONICYT\" J.G-L. acknowledges partial support from ALMA-CONICYT project
  31160033. F.E.B. acknowledges support from CONICYT grant Basal AFB-170002 (FEB),
  and the Ministry of Economy, Development, and Tourism's Millennium Science Initiative
  through grant IC120009, awarded to The Millennium Institute of Astrophysics, MAS
  (FEB). J.B. acknowledges support by Fundação para a Ciência e a Tecnologia (FCT)
  through national funds (UID/FIS/04434/2013) and Investigador FCT contract IF/01654/2014/CP1215/CT0003.,
  and by FEDER through COMPETE2020 (POCI-01-0145-FEDER-007672). T.D-S. acknowledges
  support from ALMA-CONYCIT project 31130005 and FONDECYT project 1151239. J.H. acknowledges
  support of the VIDI research programme with project number 639.042.611, which is
  (partly) financed by the Netherlands Organization for Scientific Research (NWO).
  D.R. acknowledges support from the National Science Foundation under grant No. AST-1614213.
  I.R.S. acknowledges support from the ERC Advanced Grant DUSTYGAL (321334) and STFC
  (ST/P000541/1)\r\n\r\nWork on Gnuastro has been funded by the Japanese MEXT scholarship
  and its Grant-in-Aid for Scientific Research (21244012, 24253003), the ERC advanced
  grant 339659-MUSICOS, European Union's Horizon 2020 research and innovation programme
  under Marie Sklodowska-Curie grant agreement No. 721463 to the SUNDIAL ITN, and
  from the Spanish MINECO under grant No. AYA2016-76219-P."
article_number: '140'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Leindert A.
  full_name: Boogaard, Leindert A.
  last_name: Boogaard
- first_name: Roberto
  full_name: Decarli, Roberto
  last_name: Decarli
- first_name: Jorge
  full_name: González-López, Jorge
  last_name: González-López
- first_name: Paul
  full_name: van der Werf, Paul
  last_name: van der Werf
- first_name: Fabian
  full_name: Walter, Fabian
  last_name: Walter
- first_name: Rychard
  full_name: Bouwens, Rychard
  last_name: Bouwens
- first_name: Manuel
  full_name: Aravena, Manuel
  last_name: Aravena
- first_name: Chris
  full_name: Carilli, Chris
  last_name: Carilli
- first_name: Franz Erik
  full_name: Bauer, Franz Erik
  last_name: Bauer
- first_name: Jarle
  full_name: Brinchmann, Jarle
  last_name: Brinchmann
- first_name: Thierry
  full_name: Contini, Thierry
  last_name: Contini
- first_name: Pierre
  full_name: Cox, Pierre
  last_name: Cox
- first_name: Elisabete
  full_name: da Cunha, Elisabete
  last_name: da Cunha
- first_name: Emanuele
  full_name: Daddi, Emanuele
  last_name: Daddi
- first_name: Tanio
  full_name: Díaz-Santos, Tanio
  last_name: Díaz-Santos
- first_name: Jacqueline
  full_name: Hodge, Jacqueline
  last_name: Hodge
- first_name: Hanae
  full_name: Inami, Hanae
  last_name: Inami
- first_name: Rob
  full_name: Ivison, Rob
  last_name: Ivison
- first_name: Michael
  full_name: Maseda, Michael
  last_name: Maseda
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
- first_name: Pascal
  full_name: Oesch, Pascal
  last_name: Oesch
- first_name: Gergö
  full_name: Popping, Gergö
  last_name: Popping
- first_name: Dominik
  full_name: Riechers, Dominik
  last_name: Riechers
- first_name: Joop
  full_name: Schaye, Joop
  last_name: Schaye
- first_name: Sander
  full_name: Schouws, Sander
  last_name: Schouws
- first_name: Ian
  full_name: Smail, Ian
  last_name: Smail
- first_name: Axel
  full_name: Weiss, Axel
  last_name: Weiss
- first_name: Lutz
  full_name: Wisotzki, Lutz
  last_name: Wisotzki
- first_name: Roland
  full_name: Bacon, Roland
  last_name: Bacon
- first_name: Paulo C.
  full_name: Cortes, Paulo C.
  last_name: Cortes
- first_name: Hans-Walter
  full_name: Rix, Hans-Walter
  last_name: Rix
- first_name: Rachel S.
  full_name: Somerville, Rachel S.
  last_name: Somerville
- first_name: Mark
  full_name: Swinbank, Mark
  last_name: Swinbank
- first_name: Jeff
  full_name: Wagg, Jeff
  last_name: Wagg
citation:
  ama: 'Boogaard LA, Decarli R, González-López J, et al. The ALMA spectroscopic survey
    in the HUDF: Nature and physical properties of gas-mass selected galaxies using
    MUSE spectroscopy. <i>The Astrophysical Journal</i>. 2019;882(2). doi:<a href="https://doi.org/10.3847/1538-4357/ab3102">10.3847/1538-4357/ab3102</a>'
  apa: 'Boogaard, L. A., Decarli, R., González-López, J., van der Werf, P., Walter,
    F., Bouwens, R., … Wagg, J. (2019). The ALMA spectroscopic survey in the HUDF:
    Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy.
    <i>The Astrophysical Journal</i>. IOP Publishing. <a href="https://doi.org/10.3847/1538-4357/ab3102">https://doi.org/10.3847/1538-4357/ab3102</a>'
  chicago: 'Boogaard, Leindert A., Roberto Decarli, Jorge González-López, Paul van
    der Werf, Fabian Walter, Rychard Bouwens, Manuel Aravena, et al. “The ALMA Spectroscopic
    Survey in the HUDF: Nature and Physical Properties of Gas-Mass Selected Galaxies
    Using MUSE Spectroscopy.” <i>The Astrophysical Journal</i>. IOP Publishing, 2019.
    <a href="https://doi.org/10.3847/1538-4357/ab3102">https://doi.org/10.3847/1538-4357/ab3102</a>.'
  ieee: 'L. A. Boogaard <i>et al.</i>, “The ALMA spectroscopic survey in the HUDF:
    Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy,”
    <i>The Astrophysical Journal</i>, vol. 882, no. 2. IOP Publishing, 2019.'
  ista: 'Boogaard LA, Decarli R, González-López J, van der Werf P, Walter F, Bouwens
    R, Aravena M, Carilli C, Bauer FE, Brinchmann J, Contini T, Cox P, da Cunha E,
    Daddi E, Díaz-Santos T, Hodge J, Inami H, Ivison R, Maseda M, Matthee JJ, Oesch
    P, Popping G, Riechers D, Schaye J, Schouws S, Smail I, Weiss A, Wisotzki L, Bacon
    R, Cortes PC, Rix H-W, Somerville RS, Swinbank M, Wagg J. 2019. The ALMA spectroscopic
    survey in the HUDF: Nature and physical properties of gas-mass selected galaxies
    using MUSE spectroscopy. The Astrophysical Journal. 882(2), 140.'
  mla: 'Boogaard, Leindert A., et al. “The ALMA Spectroscopic Survey in the HUDF:
    Nature and Physical Properties of Gas-Mass Selected Galaxies Using MUSE Spectroscopy.”
    <i>The Astrophysical Journal</i>, vol. 882, no. 2, 140, IOP Publishing, 2019,
    doi:<a href="https://doi.org/10.3847/1538-4357/ab3102">10.3847/1538-4357/ab3102</a>.'
  short: L.A. Boogaard, R. Decarli, J. González-López, P. van der Werf, F. Walter,
    R. Bouwens, M. Aravena, C. Carilli, F.E. Bauer, J. Brinchmann, T. Contini, P.
    Cox, E. da Cunha, E. Daddi, T. Díaz-Santos, J. Hodge, H. Inami, R. Ivison, M.
    Maseda, J.J. Matthee, P. Oesch, G. Popping, D. Riechers, J. Schaye, S. Schouws,
    I. Smail, A. Weiss, L. Wisotzki, R. Bacon, P.C. Cortes, H.-W. Rix, R.S. Somerville,
    M. Swinbank, J. Wagg, The Astrophysical Journal 882 (2019).
date_created: 2022-07-06T13:31:35Z
date_published: 2019-09-11T00:00:00Z
date_updated: 2022-07-19T09:50:55Z
day: '11'
doi: 10.3847/1538-4357/ab3102
extern: '1'
external_id:
  arxiv:
  - '1903.09167'
fulldoi: https://doi.org/10.3847/1538-4357/ab3102
intvolume: '       882'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1903.09167
month: '09'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
  eissn:
  - 1538-4357
  issn:
  - 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The ALMA spectroscopic survey in the HUDF: Nature and physical properties
  of gas-mass selected galaxies using MUSE spectroscopy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 882
year: '2019'
...
---
_id: '11515'
abstract:
- lang: eng
  text: We present new deep ALMA and Hubble Space Telescope (HST)/WFC3 observations
    of MASOSA and VR7, two luminous Lyα emitters (LAEs) at z = 6.5, for which the
    UV continuum levels differ by a factor of four. No IR dust continuum emission
    is detected in either, indicating little amounts of obscured star formation and/or
    high dust temperatures. MASOSA, with a UV luminosity M1500 = −20.9, compact size,
    and very high Lyα ${\mathrm{EW}}_{0}\approx 145\,\mathring{\rm A} $, is undetected
    in [C ii] to a limit of L[C ii] < 2.2 × 107 L⊙, implying a metallicity Z ≲ 0.07
    Z⊙. Intriguingly, our HST data indicate a red UV slope β = −1.1 ± 0.7, at odds
    with the low dust content. VR7, which is a bright (M1500 = −22.4) galaxy with
    moderate color (β = −1.4 ± 0.3) and Lyα EW0 = 34 Å, is clearly detected in [C
    ii] emission (S/N = 15). VR7's rest-frame UV morphology can be described by two
    components separated by ≈1.5 kpc and is globally more compact than the [C ii]
    emission. The global [C ii]/UV ratio indicates Z ≈ 0.2 Z⊙, but there are large
    variations in the UV/[C ii] ratio on kiloparsec scales. We also identify diffuse,
    possibly outflowing, [C ii]-emitting gas at ≈100 km s−1 with respect to the peak.
    VR7 appears to be assembling its components at a slightly more evolved stage than
    other luminous LAEs, with outflows already shaping its direct environment at z
    ∼ 7. Our results further indicate that the global [C ii]−UV relation steepens
    at SFR < 30 M⊙ yr−1, naturally explaining why the [C ii]/UV ratio is anticorrelated
    with Lyα EW in many, but not all, observed LAEs.
acknowledgement: 'We thank the anonymous referee for constructive comments and suggestions.
  We thank Max Gronke for comments on an earlier version of this paper. L.V. acknowledges
  funding from the European Union’s Horizon 2020 research and innovation program under
  the Marie Skłodowska-Curie grant agreement No. 746119. This paper makes use of the
  following ALMA data: ADS/JAO.ALMA#2017.1.01451.S. ALMA is a partnership of ESO (representing
  its member states), NSF (USA), and NINS (Japan), together with NRC (Canada), NSC
  and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic
  of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. Based
  on observations obtained with the Very Large Telescope, programs 294.A-5018, 097.A-0943,
  and 99.A-0462. Based on observations made with the NASA/ESA Hubble Space Telescope,
  obtained (from the Data Archive) at the Space Telescope Science Institute, which
  is operated by the Association of Universities for Research in Astronomy, Inc.,
  under NASA contract NAS 5-26555. These observations are associated with program
  No. 14699.'
article_number: '124'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jorryt J
  full_name: Matthee, Jorryt J
  id: 7439a258-f3c0-11ec-9501-9df22fe06720
  last_name: Matthee
  orcid: 0000-0003-2871-127X
- first_name: D.
  full_name: Sobral, D.
  last_name: Sobral
- first_name: L. A.
  full_name: Boogaard, L. A.
  last_name: Boogaard
- first_name: H.
  full_name: Röttgering, H.
  last_name: Röttgering
- first_name: L.
  full_name: Vallini, L.
  last_name: Vallini
- first_name: A.
  full_name: Ferrara, A.
  last_name: Ferrara
- first_name: A.
  full_name: Paulino-Afonso, A.
  last_name: Paulino-Afonso
- first_name: F.
  full_name: Boone, F.
  last_name: Boone
- first_name: D.
  full_name: Schaerer, D.
  last_name: Schaerer
- first_name: B.
  full_name: Mobasher, B.
  last_name: Mobasher
citation:
  ama: Matthee JJ, Sobral D, Boogaard LA, et al. Resolved UV and [C ii] structures
    of luminous galaxies within the epoch of reionization. <i>The Astrophysical Journal</i>.
    2019;881(2). doi:<a href="https://doi.org/10.3847/1538-4357/ab2f81">10.3847/1538-4357/ab2f81</a>
  apa: Matthee, J. J., Sobral, D., Boogaard, L. A., Röttgering, H., Vallini, L., Ferrara,
    A., … Mobasher, B. (2019). Resolved UV and [C ii] structures of luminous galaxies
    within the epoch of reionization. <i>The Astrophysical Journal</i>. IOP Publishing.
    <a href="https://doi.org/10.3847/1538-4357/ab2f81">https://doi.org/10.3847/1538-4357/ab2f81</a>
  chicago: Matthee, Jorryt J, D. Sobral, L. A. Boogaard, H. Röttgering, L. Vallini,
    A. Ferrara, A. Paulino-Afonso, F. Boone, D. Schaerer, and B. Mobasher. “Resolved
    UV and [C Ii] Structures of Luminous Galaxies within the Epoch of Reionization.”
    <i>The Astrophysical Journal</i>. IOP Publishing, 2019. <a href="https://doi.org/10.3847/1538-4357/ab2f81">https://doi.org/10.3847/1538-4357/ab2f81</a>.
  ieee: J. J. Matthee <i>et al.</i>, “Resolved UV and [C ii] structures of luminous
    galaxies within the epoch of reionization,” <i>The Astrophysical Journal</i>,
    vol. 881, no. 2. IOP Publishing, 2019.
  ista: Matthee JJ, Sobral D, Boogaard LA, Röttgering H, Vallini L, Ferrara A, Paulino-Afonso
    A, Boone F, Schaerer D, Mobasher B. 2019. Resolved UV and [C ii] structures of
    luminous galaxies within the epoch of reionization. The Astrophysical Journal.
    881(2), 124.
  mla: Matthee, Jorryt J., et al. “Resolved UV and [C Ii] Structures of Luminous Galaxies
    within the Epoch of Reionization.” <i>The Astrophysical Journal</i>, vol. 881,
    no. 2, 124, IOP Publishing, 2019, doi:<a href="https://doi.org/10.3847/1538-4357/ab2f81">10.3847/1538-4357/ab2f81</a>.
  short: J.J. Matthee, D. Sobral, L.A. Boogaard, H. Röttgering, L. Vallini, A. Ferrara,
    A. Paulino-Afonso, F. Boone, D. Schaerer, B. Mobasher, The Astrophysical Journal
    881 (2019).
date_created: 2022-07-06T13:38:15Z
date_published: 2019-08-21T00:00:00Z
date_updated: 2024-10-14T11:32:02Z
day: '21'
doi: 10.3847/1538-4357/ab2f81
extern: '1'
external_id:
  arxiv:
  - '1903.08171'
fulldoi: https://doi.org/10.3847/1538-4357/ab2f81
intvolume: '       881'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1903.08171
month: '08'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
  eissn:
  - 1538-4357
  issn:
  - 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resolved UV and [C ii] structures of luminous galaxies within the epoch of
  reionization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 881
year: '2019'
...