@article{14753,
  abstract     = {Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (PT), in three different frames, using different combinations of beam particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF 0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-PT
 quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion.},
  author       = {Faccioli, Pietro and Krätschmer, Ilse and Lourenço, Carlos},
  issn         = {1873-2445},
  journal      = {Physics Letters B},
  keywords     = {Nuclear and High Energy Physics},
  publisher    = {Elsevier},
  title        = {{Low-pT quarkonium polarization measurements: Challenges and opportunities}},
  doi          = {10.1016/j.physletb.2023.137871},
  volume       = {840},
  year         = {2023},
}

@article{13277,
  abstract     = {Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.},
  author       = {Tucci, Gennaro and De Nicola, Stefano and Wald, Sascha and Gambassi, Andrea},
  issn         = {2666-9366},
  journal      = {SciPost Physics Core},
  keywords     = {Statistical and Nonlinear Physics, Atomic and Molecular Physics, and Optics, Nuclear and High Energy Physics, Condensed Matter Physics},
  number       = {2},
  publisher    = {SciPost Foundation},
  title        = {{Stochastic representation of the quantum quartic oscillator}},
  doi          = {10.21468/scipostphyscore.6.2.029},
  volume       = {6},
  year         = {2023},
}

@phdthesis{12491,
  abstract     = {The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. 
Despite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. 
In this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). 
To this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. 
In order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. 
High-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. 
In summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.},
  author       = {Zens, Bettina},
  isbn         = {978-3-99078-027-5},
  issn         = {2663-337X},
  keywords     = {cryo-EM, cryo-ET, FIB milling, method development, FIBSEM, extracellular matrix, ECM, cell-derived matrices, CDMs, cell culture, high pressure freezing, HPF, structural biology, tomography, collagen},
  pages        = {187},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography}},
  doi          = {10.15479/at:ista:12491},
  year         = {2023},
}

@article{11488,
  abstract     = {Hydrogen Lyα haloes (LAHs) are commonly used as a tracer of the circumgalactic medium (CGM) at high redshifts. In this work, we aim to explore the existence of Lyα haloes around individual UV-selected galaxies, rather than around Lyα emitters (LAEs), at high redshifts. Our sample was continuum-selected with F775W ≤ 27.5, and spectroscopic redshifts were assigned or constrained for all the sources thanks to the deepest (100- to 140-h) existing Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) data with adaptive optics. The final sample includes 21 galaxies that are purely F775W-magnitude selected within the redshift range z ≈ 2.9 − 4.4 and within a UV magnitude range −20 ≤ M1500 ≤ −18, thus avoiding any bias toward LAEs. We tested whether galaxy’s Lyα emission is significantly more extended than the MUSE PSF-convolved continuum component. We find 17 LAHs and four non-LAHs. We report the first individual detections of extended Lyα emission around non-LAEs. The Lyα halo fraction is thus as high as 81.0−11.2+10.3%, which is close to that for LAEs at z = 3 − 6 in the literature. This implies that UV-selected galaxies generally have a large amount of hydrogen in their CGM. We derived the mean surface brightness (SB) profile for our LAHs with cosmic dimming corrections and find that Lyα emission extends to 5.4 arcsec (≃40 physical kpc at the midpoint redshift z = 3.6) above the typical 1σ SB limit. The incidence rate of surrounding gas detected in Lyα per one-dimensional line of sight per unit redshift, dn/dz, is estimated to be 0.76−0.09+0.09 for galaxies with M1500 ≤ −18 mag at z ≃ 3.7. Assuming that Lyα emission and absorption arise in the same gas, this suggests, based on abundance matching, that LAHs trace the same gas as damped Lyα systems (DLAs) and sub-DLAs.},
  author       = {Kusakabe, Haruka and Verhamme, Anne and Blaizot, Jérémy and Garel, Thibault and Wisotzki, Lutz and Leclercq, Floriane and Bacon, Roland and Schaye, Joop and Gallego, Sofia G. and Kerutt, Josephine and Matthee, Jorryt J and Maseda, Michael and Nanayakkara, Themiya and Pelló, Roser and Richard, Johan and Tresse, Laurence and Urrutia, Tanya and Vitte, Eloïse},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations},
  publisher    = {EDP Sciences},
  title        = {{The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4}},
  doi          = {10.1051/0004-6361/202142302},
  volume       = {660},
  year         = {2022},
}

@article{11490,
  abstract     = {Directly characterising the first generations of stars in distant galaxies is a key quest of observational cosmology. We present a case study of ID53 at z = 4.77, the UV-brightest (but L⋆) star-forming galaxy at z > 3 in the MUSE eXtremely Deep Field with a mass of ≈109 M⊙. In addition to very strong Lyman-α (Lyα) emission, we clearly detect the (stellar) continuum and an N V P Cygni feature, interstellar absorption, fine-structure emission and nebular C IV emission lines in the 140 h spectrum. Continuum emission from two spatially resolved components in Hubble Space Telescope data are blended in the MUSE data, but we show that the nebular C IV emission originates from a subcomponent of the galaxy. The UV spectrum can be fit with recent BPASS stellar population models combined with single-burst or continuous star formation histories (SFHs), a standard initial mass function, and an attenuation law. Models with a young age and low metallicity (log10(age/yr) = 6.5–7.6 and [Z/H] = −2.15 to −1.15) are preferred, but the details depend on the assumed SFH. The intrinsic Hα luminosity of the best-fit models is an order of magnitude higher than the Hα luminosity inferred from Spitzer/IRAC data, which either suggests a high escape fraction of ionising photons, a high relative attenuation of nebular to stellar dust, or a complex SFH. The metallicity appears lower than the metallicity in more massive galaxies at z = 3 − 5, consistent with the scenario according to which younger galaxies have lower metallicities. This chemical immaturity likely facilitates Lyα escape, explaining why the Lyα equivalent width is anti-correlated with stellar metallicity. Finally, we stress that uncertainties in SFHs impose a challenge for future inferences of the stellar metallicity of young galaxies. This highlights the need for joint (spatially resolved) analyses of stellar spectra and photo-ionisation models.},
  author       = {Matthee, Jorryt J and Feltre, Anna and Maseda, Michael and Nanayakkara, Themiya and Boogaard, Leindert and Bacon, Roland and Verhamme, Anne and Leclercq, Floriane and Kusakabe, Haruka and Urrutia, Tanya and Wisotzki, Lutz},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / techniques: spectroscopic / galaxies: stellar content / galaxies: formation},
  publisher    = {EDP Sciences},
  title        = {{Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field}},
  doi          = {10.1051/0004-6361/202142187},
  volume       = {660},
  year         = {2022},
}

@article{11497,
  abstract     = {Context. The hydrogen Lyman α line is often the only measurable feature in optical spectra of high-redshift galaxies. Its shape and strength are influenced by radiative transfer processes and the properties of the underlying stellar population. High equivalent widths of several hundred Å are especially hard to explain by models and could point towards unusual stellar populations, for example with low metallicities, young stellar ages, and a top-heavy initial mass function. Other aspects influencing equivalent widths are the morphology of the galaxy and its gas properties.
Aims. The aim of this study is to better understand the connection between the Lyman α rest-frame equivalent width (EW0) and spectral properties as well as ultraviolet (UV) continuum morphology by obtaining reliable EW0 histograms for a statistical sample of galaxies and by assessing the fraction of objects with large equivalent widths.
Methods. We used integral field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) combined with broad-band data from the Hubble Space Telescope (HST) to measure EW0. We analysed the emission lines of 1920 Lyman α emitters (LAEs) detected in the full MUSE-Wide (one hour exposure time) and MUSE-Deep (ten hour exposure time) surveys and found UV continuum counterparts in archival HST data. We fitted the UV continuum photometric images using the Galfit software to gain morphological information on the rest-UV emission and fitted the spectra obtained from MUSE to determine the double peak fraction, asymmetry, full-width at half maximum, and flux of the Lyman α line.
Results. The two surveys show different histograms of Lyman α EW0. In MUSE-Wide, 20% of objects have EW0 > 240 Å, while this fraction is only 11% in MUSE-Deep and ≈16% for the full sample. This includes objects without HST continuum counterparts (one-third of our sample), for which we give lower limits for EW0. The object with the highest securely measured EW0 has EW0 = 589 ± 193 Å (the highest lower limit being EW0 = 4464 Å). We investigate the connection between EW0 and Lyman α spectral or UV continuum morphological properties.
Conclusions. The survey depth has to be taken into account when studying EW0 distributions. We find that in general, high EW0 objects can have a wide range of spectral and UV morphological properties, which might reflect that the underlying causes for high EW0 values are equally varied.},
  author       = {Kerutt, J. and Wisotzki, L. and Verhamme, A. and Schmidt, K. B. and Leclercq, F. and Herenz, E. C. and Urrutia, T. and Garel, T. and Hashimoto, T. and Maseda, M. and Matthee, Jorryt J and Kusakabe, H. and Schaye, J. and Richard, J. and Guiderdoni, B. and Mauerhofer, V. and Nanayakkara, T. and Vitte, E.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations},
  publisher    = {EDP Sciences},
  title        = {{Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep}},
  doi          = {10.1051/0004-6361/202141900},
  volume       = {659},
  year         = {2022},
}

@article{11521,
  abstract     = {The cosmic ionizing emissivity from star-forming galaxies has long been anchored to UV luminosity functions. Here, we introduce an emissivity framework based on Lyα emitters (LAEs), which naturally hones in on the subset of galaxies responsible for the ionizing background due to the intimate connection between production and escape of Lyα and LyC photons. Using constraints on the escape fractions of bright LAEs (LLyα > 0.2L*) at z ≈ 2 obtained from resolved Lyα profiles, and arguing for their redshift-invariance, we show that: (i) quasars and LAEs together reproduce the relatively flat emissivity at z ≈ 2–6, which is non-trivial given the strong evolution in both the star formation density and quasar number density at these epochs and (ii) LAEs produce late and rapid reionization between z ≈ 6−9 under plausible assumptions. Within this framework, the >10 × rise in the UV population-averaged fesc between z ≈ 3–7 naturally arises due to the same phenomena that drive the growing LAE fraction with redshift. Generally, a LAE dominated emissivity yields a peak in the distribution of the ionizing budget with UV luminosity as reported in latest simulations. Using our adopted parameters (⁠fesc=50 per cent⁠, ξion = 1025.9 Hz erg−1 for half the bright LAEs), a highly ionizing minority of galaxies with MUV < −17 accounts for the entire ionizing budget from star-forming galaxies. Rapid flashes of LyC from such rare galaxies produce a ‘disco’ ionizing background. We conclude proposing tests to further develop our suggested Lyα-anchored formalism.},
  author       = {Matthee, Jorryt J and Naidu, Rohan P. and Pezzulli, Gabriele and Gronke, Max and Sobral, David and Oesch, Pascal A. and Hayes, Matthew and Erb, Dawn and Schaerer, Daniel and Amorín, Ricardo and Tacchella, Sandro and Ana Paulino-Afonso, Ana Paulino-Afonso and Llerena, Mario and Calhau, João and Röttgering, Huub},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {galaxies: high-redshift, intergalactic medium, cosmology: observations, dark ages, reionization, first stars, ultraviolet: galaxies},
  number       = {4},
  pages        = {5960--5977},
  publisher    = {Oxford University Press},
  title        = {{(Re)Solving reionization with Lyα: How bright Lyα emitters account for the z ≈ 2 − 8 cosmic ionizing background}},
  doi          = {10.1093/mnras/stac801},
  volume       = {512},
  year         = {2022},
}

@phdthesis{11879,
  abstract     = {As the overall global mean surface temperature is increasing due to climate change, plant
adaptation to those stressful conditions is of utmost importance for their survival. Plants are
sessile organisms, thus to compensate for their lack of mobility, they evolved a variety of
mechanisms enabling them to flexibly adjust their physiological, growth and developmental
processes to fluctuating temperatures and to survive in harsh environments. While these unique
adaptation abilities provide an important evolutionary advantage, overall modulation of plant
growth and developmental program due to non-optimal temperature negatively affects biomass
production, crop productivity or sensitivity to pathogens. Thus, understanding molecular
processes underlying plant adaptation to increased temperature can provide important
resources for breeding strategies to ensure sufficient agricultural food production.
An increase in ambient temperature by a few degrees leads to profound changes in organ growth
including enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and
cotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,
one of the best-studied growth hormones, plays an essential role in this process by direct
activation of transcriptional and non-transcriptional processes resulting in elongation growth
(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature
(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key
components of the polar auxin transport (PAT) machinery, which controls the amount and
direction of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,
PIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT
through either chemical or genetic means dramatically affecting the adaptive responses to hAT.
Intriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether
and how PINs at the level of expression adapt to fluctuation in temperature is scarcely
understood.
With genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN
auxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via
adjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we
identified three Zinc-Finger (ZF) transcription factors as novel molecular components of the
thermo-regulatory network, which through negative regulation of PIN transcription adjust the
transport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the
negative feedback loop attenuating the activity of the thermo-sensing pathway to restrain
exaggerated growth and developmental responses to hAT.},
  author       = {Artner, Christina},
  isbn         = {978-3-99078-022-0},
  issn         = {2663-337X},
  keywords     = {high ambient temperature, auxin, PINs, Zinc-Finger proteins, thermomorphogenesis, stress},
  pages        = {128},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature}},
  doi          = {10.15479/at:ista:11879},
  year         = {2022},
}

@article{12232,
  abstract     = {We derive a precise asymptotic formula for the density of the small singular values of the real Ginibre matrix ensemble shifted by a complex parameter z as the dimension tends to infinity. For z away from the real axis the formula coincides with that for the complex Ginibre ensemble we derived earlier in Cipolloni et al. (Prob Math Phys 1:101–146, 2020). On the level of the one-point function of the low lying singular values we thus confirm the transition from real to complex Ginibre ensembles as the shift parameter z becomes genuinely complex; the analogous phenomenon has been well known for eigenvalues. We use the superbosonization formula (Littelmann et al. in Comm Math Phys 283:343–395, 2008) in a regime where the main contribution comes from a three dimensional saddle manifold.},
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
  issn         = {1424-0661},
  journal      = {Annales Henri Poincaré},
  keywords     = {Mathematical Physics, Nuclear and High Energy Physics, Statistical and Nonlinear Physics},
  number       = {11},
  pages        = {3981--4002},
  publisher    = {Springer Nature},
  title        = {{Density of small singular values of the shifted real Ginibre ensemble}},
  doi          = {10.1007/s00023-022-01188-8},
  volume       = {23},
  year         = {2022},
}

@article{11498,
  abstract     = {Rest-frame ultraviolet (UV) emission lines probe electron densities, gas-phase abundances, metallicities, and ionization parameters of the emitting star-forming galaxies and their environments. The strongest main UV emission line, Lyα, has been instrumental in advancing the general knowledge of galaxy formation in the early universe. However, observing Lyα emission becomes increasingly challenging at z ≳ 6 when the neutral hydrogen fraction of the circumgalactic and intergalactic media increases. Secondary weaker UV emission lines provide important alternative methods for studying galaxy properties at high redshift. We present a large sample of rest-frame UV emission line sources at intermediate redshift for calibrating and exploring the connection between secondary UV lines and the emitting galaxies’ physical properties and their Lyα emission. The sample of 2052 emission line sources with 1.5 < z < 6.4 was collected from integral field data from the MUSE-Wide and MUSE-Deep surveys taken as part of Guaranteed Time Observations. The objects were selected through untargeted source detection (i.e., no preselection of sources as in dedicated spectroscopic campaigns) in the three-dimensional MUSE data cubes. We searched optimally extracted one-dimensional spectra of the full sample for UV emission features via emission line template matching, resulting in a sample of more than 100 rest-frame UV emission line detections. We show that the detection efficiency of (non-Lyα) UV emission lines increases with survey depth, and that the emission line strength of He IIλ1640 Å, [O III] λ1661 + O III] λ1666, and [Si III] λ1883 + Si III] λ1892 correlate with the strength of [C III] λ1907 + C III] λ1909. The rest-frame equivalent width (EW0) of [C III] λ1907 + C III] λ1909 is found to be roughly 0.22 ± 0.18 of EW0(Lyα). We measured the velocity offsets of resonant emission lines with respect to systemic tracers. For C IVλ1548 + C IVλ1551 we find that ΔvC IV ≲ 250 km s−1, whereas ΔvLyα falls in the range of 250−500 km s−1 which is in agreement with previous results from the literature. The electron density ne measured from [Si III] λ1883 + Si III] λ1892 and [C III] λ1907 + C III] λ1909 line flux ratios is generally < 105 cm−3 and the gas-phase abundance is below solar at 12 + log10(O/H)≈8. Lastly, we used “PhotoIonization Model Probability Density Functions” to infer physical parameters of the full sample and individual systems based on photoionization model parameter grids and observational constraints from our UV emission line searches. This reveals that the UV line emitters generally have ionization parameter log10(U) ≈ −2.5 and metal mass fractions that scatter around Z ≈ 10−2, that is Z ≈ 0.66 Z⊙. Value-added catalogs of the full sample of MUSE objects studied in this work and a collection of UV line emitters from the literature are provided with this paper.},
  author       = {Schmidt, K. B. and Kerutt, J. and Wisotzki, L. and Urrutia, T. and Feltre, A. and Maseda, M. V. and Nanayakkara, T. and Bacon, R. and Boogaard, L. A. and Conseil, S. and Contini, T. and Herenz, E. C. and Kollatschny, W. and Krumpe, M. and Leclercq, F. and Mahler, G. and Matthee, Jorryt J and Mauerhofer, V. and Richard, J. and Schaye, J.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, ultraviolet: galaxies / galaxies: high-redshift / galaxies: ISM / ISM: lines and bands / methods: observational / techniques: imaging spectroscopy},
  publisher    = {EDP Sciences},
  title        = {{Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 < z < 6.4}},
  doi          = {10.1051/0004-6361/202140876},
  volume       = {654},
  year         = {2021},
}

@article{11500,
  abstract     = {We report the discovery of diffuse extended Lyα emission from redshift 3.1 to 4.5, tracing cosmic web filaments on scales of 2.5−4 cMpc. These structures have been observed in overdensities of Lyα emitters in the MUSE Extremely Deep Field, a 140 h deep MUSE observation located in the Hubble Ultra-Deep Field. Among the 22 overdense regions identified, five are likely to harbor very extended Lyα emission at high significance with an average surface brightness of 5 × 10−20 erg s−1 cm−2 arcsec−2. Remarkably, 70% of the total Lyα luminosity from these filaments comes from beyond the circumgalactic medium of any identified Lyα emitter. Fluorescent Lyα emission powered by the cosmic UV background can only account for less than 34% of this emission at z ≈ 3 and for not more than 10% at higher redshift. We find that the bulk of this diffuse emission can be reproduced by the unresolved Lyα emission of a large population of ultra low-luminosity Lyα emitters (< 1040 erg s−1), provided that the faint end of the Lyα luminosity function is steep (α ⪅ −1.8), it extends down to luminosities lower than 1038 − 1037 erg s−1, and the clustering of these Lyα emitters is significant (filling factor < 1/6). If these Lyα emitters are powered by star formation, then this implies their luminosity function needs to extend down to star formation rates < 10−4 M⊙ yr−1. These observations provide the first detection of the cosmic web in Lyα emission in typical filamentary environments and the first observational clue indicating the existence of a large population of ultra low-luminosity Lyα emitters at high redshift.},
  author       = {Bacon, R. and Mary, D. and Garel, T. and Blaizot, J. and Maseda, M. and Schaye, J. and Wisotzki, L. and Conseil, S. and Brinchmann, J. and Leclercq, F. and Abril-Melgarejo, V. and Boogaard, L. and Bouché, N. F. and Contini, T. and Feltre, A. and Guiderdoni, B. and Herenz, C. and Kollatschny, W. and Kusakabe, H. and Matthee, Jorryt J and Michel-Dansac, L. and Nanayakkara, T. and Richard, J. and Roth, M. and Schmidt, K. B. and Steinmetz, M. and Tresse, L. and Urrutia, T. and Verhamme, A. and Weilbacher, P. M. and Zabl, J. and Zoutendijk, S. L.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: groups: general / cosmology: observations},
  publisher    = {EDP Sciences},
  title        = {{The MUSE Extremely Deep Field: The cosmic web in emission at high redshift}},
  doi          = {10.1051/0004-6361/202039887},
  volume       = {647},
  year         = {2021},
}

@article{11524,
  abstract     = {We measure the evolution of the rest-frame UV luminosity function (LF) and the stellar mass function (SMF) of Lyman-α (Ly α) emitters (LAEs) from z ∼ 2 to z ∼ 6 by exploring ∼4000 LAEs from the SC4K sample. We find a correlation between Ly α luminosity (LLy α) and rest-frame UV (MUV), with best fit MUV=−1.6+0.2−0.3log10(LLyα/ergs−1)+47+12−11 and a shallower relation between LLy α and stellar mass (M⋆), with best fit log10(M⋆/M⊙)=0.9+0.1−0.1log10(LLyα/ergs−1)−28+4.0−3.8⁠. An increasing LLy α cut predominantly lowers the number density of faint MUV and low M⋆ LAEs. We estimate a proxy for the full UV LFs and SMFs of LAEs with simple assumptions of the faint end slope. For the UV LF, we find a brightening of the characteristic UV luminosity (M∗UV⁠) with increasing redshift and a decrease of the characteristic number density (Φ*). For the SMF, we measure a characteristic stellar mass (⁠M∗⋆/M⊙⁠) increase with increasing redshift, and a Φ* decline. However, if we apply a uniform luminosity cut of log10(LLyα/ergs−1)≥43.0⁠, we find much milder to no evolution in the UV and SMF of LAEs. The UV luminosity density (ρUV) of the full sample of LAEs shows moderate evolution and the stellar mass density (ρM) decreases, with both being always lower than the total ρUV and ρM of more typical galaxies but slowly approaching them with increasing redshift. Overall, our results indicate that both ρUV and ρM of LAEs slowly approach the measurements of continuum-selected galaxies at z > 6, which suggests a key role of LAEs in the epoch of reionization.},
  author       = {Santos, S and Sobral, D and Butterworth, J and Paulino-Afonso, A and Ribeiro, B and da Cunha, E and Calhau, J and Khostovan, A A and Matthee, Jorryt J and Arrabal Haro, P},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution, galaxies: high-redshift, galaxies: luminosity function, mass function},
  number       = {1},
  pages        = {1117--1134},
  publisher    = {Oxford University Press},
  title        = {{The evolution of the UV luminosity and stellar mass functions of Lyman-α emitters from z ∼ 2 to z ∼ 6}},
  doi          = {10.1093/mnras/stab1218},
  volume       = {505},
  year         = {2021},
}

@article{10406,
  abstract     = {Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future.},
  author       = {Mishra, Nikhil and Heisenberg, Carl-Philipp J},
  issn         = {1545-2948},
  journal      = {Annual Review of Genetics},
  keywords     = {morphogenesis, forward genetics, high-resolution microscopy, biophysics, biochemistry, patterning},
  pages        = {209--233},
  publisher    = {Annual Reviews},
  title        = {{Dissecting organismal morphogenesis by bridging genetics and biophysics}},
  doi          = {10.1146/annurev-genet-071819-103748},
  volume       = {55},
  year         = {2021},
}

@article{11501,
  abstract     = {We investigated the ultraviolet (UV) spectral properties of faint Lyman-α emitters (LAEs) in the redshift range 2.9 ≤ z ≤ 4.6, and we provide material to prepare future observations of the faint Universe. We used data from the MUSE Hubble Ultra Deep Survey to construct mean rest-frame spectra of continuum-faint (median MUV of −18 and down to MUV of −16), low stellar mass (median value of 108.4 M⊙ and down to 107 M⊙) LAEs at redshift z ≳ 3. We computed various averaged spectra of LAEs, subsampled on the basis of their observational (e.g., Lyα strength, UV magnitude and spectral slope) and physical (e.g., stellar mass and star-formation rate) properties. We searched for UV spectral features other than Lyα, such as higher ionization nebular emission lines and absorption features. We successfully observed the O III]λ1666 and [C III]λ1907+C III]λ1909 collisionally excited emission lines and the He IIλ1640 recombination feature, as well as the resonant C IVλλ1548,1551 doublet either in emission or P-Cygni. We compared the observed spectral properties of the different mean spectra and find the emission lines to vary with the observational and physical properties of the LAEs. In particular, the mean spectra of LAEs with larger Lyα equivalent widths, fainter UV magnitudes, bluer UV spectral slopes, and lower stellar masses show the strongest nebular emission. The line ratios of these lines are similar to those measured in the spectra of local metal-poor galaxies, while their equivalent widths are weaker compared to the handful of extreme values detected in individual spectra of z >  2 galaxies. This suggests that weak UV features are likely ubiquitous in high z, low-mass, and faint LAEs. We publicly released the stacked spectra, as they can serve as empirical templates for the design of future observations, such as those with the James Webb Space Telescope and the Extremely Large Telescope.},
  author       = {Feltre, Anna and Maseda, Michael V. and Bacon, Roland and Pradeep, Jayadev and Leclercq, Floriane and Kusakabe, Haruka and Wisotzki, Lutz and Hashimoto, Takuya and Schmidt, Kasper B. and Blaizot, Jeremy and Brinchmann, Jarle and Boogaard, Leindert and Cantalupo, Sebastiano and Carton, David and Inami, Hanae and Kollatschny, Wolfram and Marino, Raffaella A. and Matthee, Jorryt J and Nanayakkara, Themiya and Richard, Johan and Schaye, Joop and Tresse, Laurence and Urrutia, Tanya and Verhamme, Anne and Weilbacher, Peter M.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution / galaxies: high-redshift / ISM: lines and bands / ultraviolet: ISM / ultraviolet: galaxies},
  publisher    = {EDP Sciences},
  title        = {{The MUSE Hubble Ultra Deep Field Survey: XV. The mean rest-UV spectra of Lyα emitters at z > 3}},
  doi          = {10.1051/0004-6361/202038133},
  volume       = {641},
  year         = {2020},
}

@article{11503,
  abstract     = {Context. The Lyα emitter (LAE) fraction, XLAE, is a potentially powerful probe of the evolution of the intergalactic neutral hydrogen gas fraction. However, uncertainties in the measurement of XLAE are still under debate.
Aims. Thanks to deep data obtained with the integral field spectrograph Multi Unit Spectroscopic Explorer (MUSE), we can measure the evolution of the LAE fraction homogeneously over a wide redshift range of z ≈ 3–6 for UV-faint galaxies (down to UV magnitudes of M1500 ≈ −17.75). This is a significantly fainter range than in former studies (M1500 ≤ −18.75) and it allows us to probe the bulk of the population of high-redshift star-forming galaxies.
Methods. We constructed a UV-complete photometric-redshift sample following UV luminosity functions and measured the Lyα emission with MUSE using the latest (second) data release from the MUSE Hubble Ultra Deep Field Survey.
Results. We derived the redshift evolution of XLAE for M1500 ∈ [ − 21.75; −17.75] for the first time with a equivalent width range EW(Lyα) ≥ 65 Å and found low values of XLAE ≲ 30% at z ≲ 6. The best-fit linear relation is XLAE = 0.07+0.06−0.03z − 0.22+0.12−0.24. For M1500 ∈ [ − 20.25; −18.75] and EW(Lyα) ≥ 25 Å, our XLAE values are consistent with those in the literature within 1σ at z ≲ 5, but our median values are systematically lower than reported values over the whole redshift range. In addition, we do not find a significant dependence of XLAE on M1500 for EW(Lyα) ≥ 50 Å at z ≈ 3–4, in contrast with previous work. The differences in XLAE mainly arise from selection biases for Lyman Break Galaxies (LBGs) in the literature: UV-faint LBGs are more easily selected if they have strong Lyα emission, hence XLAE is biased towards higher values when those samples are used.
Conclusions. Our results suggest either a lower increase of XLAE towards z ≈ 6 than previously suggested, or even a turnover of XLAE at z ≈ 5.5, which may be the signature of a late or patchy reionization process. We compared our results with predictions from a cosmological galaxy evolution model. We find that a model with a bursty star formation (SF) can reproduce our observed LAE fractions much better than models where SF is a smooth function of time.},
  author       = {Kusakabe, Haruka and Blaizot, Jérémy and Garel, Thibault and Verhamme, Anne and Bacon, Roland and Richard, Johan and Hashimoto, Takuya and Inami, Hanae and Conseil, Simon and Guiderdoni, Bruno and Drake, Alyssa B. and Christian Herenz, Edmund and Schaye, Joop and Oesch, Pascal and Matthee, Jorryt J and Anna Marino, Raffaella and Borello Schmidt, Kasper and Pelló, Roser and Maseda, Michael and Leclercq, Floriane and Kerutt, Josephine and Mahler, Guillaume},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, dark ages / reionization / first stars / early Universe / cosmology: observations / galaxies: evolution / galaxies: high-redshift / intergalactic medium},
  publisher    = {EDP Sciences},
  title        = {{The MUSE Hubble Ultra Deep Field Survey: XIV. Evolution of the Lyα emitter fraction from z = 3 to z = 6}},
  doi          = {10.1051/0004-6361/201937340},
  volume       = {638},
  year         = {2020},
}

@article{11504,
  abstract     = {We present spatially resolved maps of six individually-detected Lyman α haloes (LAHs) as well as a first statistical analysis of the Lyman α (Lyα) spectral signature in the circum-galactic medium of high-redshift star-forming galaxies (−17.5 >  MUV >  −21.5) using the Multi-Unit Spectroscopic Explorer. Our resolved spectroscopic analysis of the LAHs reveals significant intrahalo variations of the Lyα line profile. Using a three-dimensional two-component model for the Lyα emission, we measured the full width at half maximum (FWHM), the peak velocity shift, and the asymmetry of the Lyα line in the core and in the halo of 19 galaxies. We find that the Lyα line shape is statistically different in the halo compared to the core (in terms of width, peak wavelength, and asymmetry) for ≈40% of our galaxies. Similarly to object-by-object based studies and a recent resolved study using lensing, we find a correlation between the peak velocity shift and the width of the Lyα line both at the interstellar and circum-galactic scales. This trend has been predicted by radiative transfer simulations of galactic winds as a result of resonant scattering in outflows. While there is a lack of correlation between the spectral properties and the spatial scale lengths of our LAHs, we find a correlation between the width of the line in the LAH and the halo flux fraction. Interestingly, UV bright galaxies (MUV <  −20) show broader, more redshifted, and less asymmetric Lyα lines in their haloes. The most significant correlation found is for the FWHM of the line and the UV continuum slope of the galaxy, suggesting that the redder galaxies have broader Lyα lines. The generally broad and red line shapes found in the halo component suggest that the Lyα haloes are powered either by scattering processes through an outflowing medium, fluorescent emission from outflowing cold clumps of gas, or a mix of both. Considering the large diversity of the Lyα line profiles observed in our sample and the lack of strong correlation, the interpretation of our results is still broadly open and underlines the need for realistic spatially resolved models of the LAHs.},
  author       = {Leclercq, Floriane and Bacon, Roland and Verhamme, Anne and Garel, Thibault and Blaizot, Jérémy and Brinchmann, Jarle and Cantalupo, Sebastiano and Claeyssens, Adélaïde and Conseil, Simon and Contini, Thierry and Hashimoto, Takuya and Herenz, Edmund Christian and Kusakabe, Haruka and Marino, Raffaella Anna and Maseda, Michael and Matthee, Jorryt J and Mitchell, Peter and Pezzulli, Gabriele and Richard, Johan and Schmidt, Kasper Borello and Wisotzki, Lutz},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations},
  publisher    = {EDP Sciences},
  title        = {{The MUSE Hubble Ultra Deep field survey: XIII. Spatially resolved spectral properties of Lyman α haloes around star-forming galaxies at z > 3}},
  doi          = {10.1051/0004-6361/201937339},
  volume       = {635},
  year         = {2020},
}

@article{11528,
  abstract     = {Ly α emission lines are typically found to be redshifted with respect to the systemic redshifts of galaxies, likely due to resonant scattering of Ly α photons. Here, we measure the average velocity offset for a sample of 96 z ≈ 3.3 Ly α emitters (LAEs) with a median Ly α flux (luminosity) of ≈10−17 erg cm−2 s−1 (⁠≈1042 erg s−1⁠) and a median star formation rate (SFR) of ≈1.3 M⊙ yr−1 (not corrected for possible dust extinction), detected by the Multi-Unit Spectroscopic Explorer as part of our MUSEQuBES circumgalactic medium (CGM) survey. By postulating that the stacked CGM absorption profiles of these LAEs, probed by eight background quasars, must be centred on the systemic redshift, we measure an average velocity offset, Voffset = 171\pm 8 km s−1, between the Ly α emission peak and the systemic redshift. The observed Voffset is lower by factors of ≈1.4 and ≈2.6 compared to the velocity offsets measured for narrow-band-selected LAEs and Lyman break galaxies, respectively, which probe galaxies with higher masses and SFRs. Consistent with earlier studies based on direct measurements for individual objects, we find that the Voffset is correlated with the full width at half-maximum of the red peak of the Ly α line, and anticorrelated with the rest-frame equivalent width. Moreover, we find that Voffset is correlated with SFR with a sub-linear scaling relation, Voffset∝SFR0.16±0.03⁠. Adopting the mass scaling for main-sequence galaxies, such a relation suggests that Voffset scales with the circular velocity of the dark matter haloes hosting the LAEs.},
  author       = {Muzahid, Sowgat and Schaye, Joop and Marino, Raffaella Anna and Cantalupo, Sebastiano and Brinchmann, Jarle and Contini, Thierry and Wendt, Martin and Wisotzki, Lutz and Zabl, Johannes and Bouché, Nicolas and Akhlaghi, Mohammad and Chen, Hsiao-Wen and Claeyssens, Adélaîde and Johnson, Sean and Leclercq, Floriane and Maseda, Michael and Matthee, Jorryt J and Richard, Johan and Urrutia, Tanya and Verhamme, Anne},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: haloes, galaxies: high-redshift, quasars: absorption lines},
  number       = {2},
  pages        = {1013--1022},
  publisher    = {Oxford University Press},
  title        = {{MUSEQuBES: Calibrating the redshifts of Lyα emitters using stacked circumgalactic medium absorption profiles}},
  doi          = {10.1093/mnras/staa1347},
  volume       = {496},
  year         = {2020},
}

@article{11529,
  abstract     = {CR7 is among the most luminous Ly α emitters (LAEs) known at z = 6.6 and consists of at least three UV components that are surrounded by Ly α emission. Previous studies have suggested that it may host an extreme ionizing source. Here, we present deep integral field spectroscopy of CR7 with VLT/Multi Unit Spectroscopic Explorer (MUSE). We measure extended emission with a similar halo scale length as typical LAEs at z ≈ 5. CR7’s Ly α halo is clearly elongated along the direction connecting the multiple components, likely tracing the underlying gas distribution. The Ly α emission originates almost exclusively from the brightest UV component, but we also identify a faint kinematically distinct Ly α emitting region nearby a fainter component. Combined with new near-infrared data, the MUSE data show that the rest-frame Ly α equivalent width (EW) is ≈100 Å. This is a factor 4 higher than the EW measured in low-redshift analogues with carefully matched Ly α profiles (and thus arguably H I column density), but this EW can plausibly be explained by star formation. Alternative scenarios requiring active galactic nucleus (AGN) powering are also disfavoured by the narrower and steeper Ly α spectrum and much smaller IR to UV ratio compared to obscured AGN in other Ly α blobs. CR7’s Ly α emission, while extremely luminous, resembles the emission in more common LAEs at lower redshifts very well and is likely powered by a young metal-poor starburst.},
  author       = {Matthee, Jorryt J and Pezzulli, Gabriele and Mackenzie, Ruari and Cantalupo, Sebastiano and Kusakabe, Haruka and Leclercq, Floriane and Sobral, David and Richard, Johan and Wisotzki, Lutz and Lilly, Simon and Boogaard, Leindert and Marino, Raffaella and Maseda, Michael and Nanayakkara, Themiya},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution, galaxies: high-redshift, dark ages, reionization, first stars, cosmology: observations},
  number       = {2},
  pages        = {3043--3059},
  publisher    = {Oxford University Press},
  title        = {{The nature of CR7 revealed with MUSE: A young starburst powering extended Ly α emission at z = 6.6}},
  doi          = {10.1093/mnras/staa2550},
  volume       = {498},
  year         = {2020},
}

@article{11530,
  abstract     = {A prediction of the classic active galactic nucleus (AGN) unification model is the presence of ionization cones with different orientations depending on the AGN type. Confirmations of this model exist for present times, but it is less clear in the early Universe. Here, we use the morphology of giant Ly α nebulae around AGNs at redshift z ∼ 3 to probe AGN emission and therefore the validity of the AGN unification model at this redshift. We compare the spatial morphology of 19 nebulae previously found around type I AGNs with a new sample of four Ly α nebulae detected around type II AGNs. Using two independent techniques, we find that nebulae around type II AGNs are more asymmetric than around type I, at least at radial distances r > 30 physical kpc (pkpc) from the ionizing source. We conclude that the type I and type II AGNs in our sample show evidence of different surrounding ionizing geometries. This suggests that the classical AGN unification model is also valid for high-redshift sources. Finally, we discuss how the lack of asymmetry in the inner parts (r ≲ 30 pkpc) and the associated high values of the He II to Ly α ratios in these regions could indicate additional sources of (hard) ionizing radiation originating within or in proximity of the AGN host galaxies. This work demonstrates that the morphologies of giant Ly α nebulae can be used to understand and study the geometry of high-redshift AGNs on circumnuclear scales and it lays the foundation for future studies using much larger statistical samples.},
  author       = {den Brok, J S and Cantalupo, S and Mackenzie, R and Marino, R A and Pezzulli, G and Matthee, Jorryt J and Johnson, S D and Krumpe, M and Urrutia, T and Kollatschny, W},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: active, galaxies: high-redshift, intergalactic medium, quasars: emission lines, quasars: general},
  number       = {2},
  pages        = {1874--1887},
  publisher    = {Oxford University Press},
  title        = {{Probing the AGN unification model at redshift z ∼ 3 with MUSE observations of giant Lyα nebulae}},
  doi          = {10.1093/mnras/staa1269},
  volume       = {495},
  year         = {2020},
}

@article{11531,
  abstract     = {While low-luminosity galaxies dominate number counts at all redshifts, their contribution to cosmic reionization is poorly understood due to a lack of knowledge of their physical properties. We isolate a sample of 35 z ≈ 4–5 continuum-faint Lyman-α emitters from deep VLT/MUSE spectroscopy and directly measure their H α emission using stacked Spitzer/IRAC Ch. 1 photometry. Based on Hubble Space Telescope imaging, we determine that the average UV continuum magnitude is fainter than −16 (≈ 0.01 L⋆), implying a median Lyman-α equivalent width of 259 Å. By combining the H α measurement with the UV magnitude, we determine the ionizing photon production efficiency, ξion, a first for such faint galaxies. The measurement of log10 (ξion [Hz erg−1]) = 26.28 (⁠+0.28−0.40⁠) is in excess of literature measurements of both continuum- and emission line-selected samples, implying a more efficient production of ionizing photons in these lower luminosity, Lyman-α-selected systems. We conclude that this elevated efficiency can be explained by stellar populations with metallicities between 4 × 10−4 and 0.008, with light-weighted ages less than 3 Myr.},
  author       = {Maseda, Michael V and Bacon, Roland and Lam, Daniel and Matthee, Jorryt J and Brinchmann, Jarle and Schaye, Joop and Labbe, Ivo and Schmidt, Kasper B and Boogaard, Leindert and Bouwens, Rychard and Cantalupo, Sebastiano and Franx, Marijn and Hashimoto, Takuya and Inami, Hanae and Kusakabe, Haruka and Mahler, Guillaume and Nanayakkara, Themiya and Richard, Johan and Wisotzki, Lutz},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, Galaxies: evolution, Galaxies: high-redshift, Galaxies: ISM},
  number       = {4},
  pages        = {5120--5130},
  publisher    = {Oxford University Press},
  title        = {{Elevated ionizing photon production efficiency in faint high-equivalent-width Lyman-α emitters}},
  doi          = {10.1093/mnras/staa622},
  volume       = {493},
  year         = {2020},
}