@phdthesis{8620, abstract = {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. De 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. In 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.}, author = {Morandell, Jasmin}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Illuminating the role of Cul3 in autism spectrum disorder pathogenesis}}, doi = {10.15479/AT:ISTA:8620}, year = {2020}, } @unpublished{7800, abstract = {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.}, author = {Morandell, Jasmin and Schwarz, Lena A and Basilico, Bernadette and Tasciyan, Saren and Nicolas, Armel and Sommer, Christoph M and Kreuzinger, Caroline and Knaus, Lisa and Dobler, Zoe and Cacci, Emanuele and Danzl, Johann G and Novarino, Gaia}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development}}, doi = {10.1101/2020.01.10.902064 }, year = {2020}, } @article{7885, abstract = {Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.}, author = {Reversat, Anne and Gärtner, Florian R and Merrin, Jack and Stopp, Julian A and Tasciyan, Saren and Aguilera Servin, Juan L and De Vries, Ingrid and Hauschild, Robert and Hons, Miroslav and Piel, Matthieu and Callan-Jones, Andrew and Voituriez, Raphael and Sixt, Michael K}, issn = {1476-4687}, journal = {Nature}, pages = {582–585}, publisher = {Springer Nature}, title = {{Cellular locomotion using environmental topography}}, doi = {10.1038/s41586-020-2283-z}, volume = {582}, year = {2020}, } @article{8131, abstract = {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.}, author = {Basilico, Bernadette and Morandell, Jasmin and Novarino, Gaia}, issn = {1879-0380}, journal = {Current Opinion in Genetics and Development}, number = {12}, pages = {126--137}, publisher = {Elsevier}, title = {{Molecular mechanisms for targeted ASD treatments}}, doi = {10.1016/j.gde.2020.06.004}, volume = {65}, year = {2020}, } @article{7815, abstract = {Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.}, author = {Beattie, Robert J and Streicher, Carmen and Amberg, Nicole and Cheung, Giselle T and Contreras, Ximena and Hansen, Andi H and Hippenmeyer, Simon}, issn = {1940-087X}, journal = {Journal of Visual Experiments}, number = {159}, publisher = {MyJove Corporation}, title = {{Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)}}, doi = {10.3791/61147}, year = {2020}, } @phdthesis{7902, abstract = {Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments. In summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression. This work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation.}, author = {Contreras, Ximena}, issn = {2663-337X}, pages = {214}, publisher = {Institute of Science and Technology Austria}, title = {{Genetic dissection of neural development in health and disease at single cell resolution}}, doi = {10.15479/AT:ISTA:7902}, year = {2020}, } @inproceedings{7810, abstract = {Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries. In this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques.}, author = {Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas}, booktitle = {European Symposium on Programming}, isbn = {9783030449131}, issn = {1611-3349}, location = {Dublin, Ireland}, pages = {112--140}, publisher = {Springer Nature}, title = {{Optimal and perfectly parallel algorithms for on-demand data-flow analysis}}, doi = {10.1007/978-3-030-44914-8_5}, volume = {12075}, year = {2020}, } @inproceedings{8728, abstract = {Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are two standard formalisms in system analysis. Their main associated quantitative objectives are hitting probabilities, discounted sum, and mean payoff. Although there are many techniques for computing these objectives in general MCs/MDPs, they have not been thoroughly studied in terms of parameterized algorithms, particularly when treewidth is used as the parameter. This is in sharp contrast to qualitative objectives for MCs, MDPs and graph games, for which treewidth-based algorithms yield significant complexity improvements. In this work, we show that treewidth can also be used to obtain faster algorithms for the quantitative problems. For an MC with n states and m transitions, we show that each of the classical quantitative objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for each objective on MDPs, where κ is the number of strategy-iteration refinements required for the given input and objective. Finally, we make an experimental evaluation of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms outperform existing well-established methods by one or more orders of magnitude.}, author = {Asadi, Ali and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Mohammadi, Kiarash and Pavlogiannis, Andreas}, booktitle = {Automated Technology for Verification and Analysis}, isbn = {9783030591519}, issn = {1611-3349}, location = {Hanoi, Vietnam}, pages = {253--270}, publisher = {Springer Nature}, title = {{Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth}}, doi = {10.1007/978-3-030-59152-6_14}, volume = {12302}, year = {2020}, } @inproceedings{8089, abstract = {We consider the classical problem of invariant generation for programs with polynomial assignments and focus on synthesizing invariants that are a conjunction of strict polynomial inequalities. We present a sound and semi-complete method based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize positive polynomials over a semi-algebraic set. On the theoretical side, the worst-case complexity of our approach is subexponential, whereas the worst-case complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential. Even when restricted to linear invariants, the best previous complexity for complete invariant generation is exponential (Colon et al, CAV 2003). On the practical side, we reduce the invariant generation problem to quadratic programming (QCLP), which is a classical optimization problem with many industrial solvers. We demonstrate the applicability of our approach by providing experimental results on several academic benchmarks. To the best of our knowledge, the only previous invariant generation method that provides completeness guarantees for invariants consisting of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination and cannot even handle toy programs such as our running example.}, author = {Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir Kafshdar and Goharshady, Ehsan Kafshdar}, booktitle = {Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation}, isbn = {9781450376136}, location = {London, United Kingdom}, pages = {672--687}, publisher = {Association for Computing Machinery}, title = {{Polynomial invariant generation for non-deterministic recursive programs}}, doi = {10.1145/3385412.3385969}, year = {2020}, } @article{6918, abstract = {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. We 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.}, author = {Goharshady, Amir Kafshdar and Mohammadi, Fatemeh}, issn = {0951-8320}, journal = {Reliability Engineering and System Safety}, publisher = {Elsevier}, title = {{An efficient algorithm for computing network reliability in small treewidth}}, doi = {10.1016/j.ress.2019.106665}, volume = {193}, year = {2020}, } @article{8986, abstract = {Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.}, author = {Zhang, Yuzhou and Rodriguez Solovey, Lesia and Li, Lanxin and Zhang, Xixi and Friml, Jiří}, issn = {2375-2548}, journal = {Science Advances}, number = {50}, publisher = {AAAS}, title = {{Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants}}, doi = {10.1126/sciadv.abc8895}, volume = {6}, year = {2020}, } @article{8283, abstract = {Drought and salt stress are the main environmental cues affecting the survival, development, distribution, and yield of crops worldwide. MYB transcription factors play a crucial role in plants’ biological processes, but the function of pineapple MYB genes is still obscure. In this study, one of the pineapple MYB transcription factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4 is localized in the cell nucleus, and its expression is induced by low temperature, drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA). Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to osmotic stress; it led to an increase in the number stomata on leaf surfaces and lower germination rate under salt and drought stress. Furthermore, in AcoMYB4 OE lines, the membrane oxidation index, free proline, and soluble sugar contents were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content increased significantly due to membrane injury, indicating higher sensitivity to drought and salinity stresses. Besides the above, both the expression level and activities of several antioxidant enzymes were decreased, indicating lower antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress, overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates osmotic stress by attenuating cellular ABA biosynthesis and signal transduction pathways. }, author = {Chen, Huihuang and Lai, Linyi and Li, Lanxin and Liu, Liping and Jakada, Bello Hassan and Huang, Youmei and He, Qing and Chai, Mengnan and Niu, Xiaoping and Qin, Yuan}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, number = {16}, publisher = {MDPI}, title = {{AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress through negative regulation of ABA signaling}}, doi = {10.3390/ijms21165727}, volume = {21}, year = {2020}, } @article{8529, abstract = {Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.}, author = {Arnold, Georg M and Wulf, Matthias and Barzanjeh, Shabir and Redchenko, Elena and Rueda Sanchez, Alfredo R and Hease, William J and Hassani, Farid and Fink, Johannes M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Converting microwave and telecom photons with a silicon photonic nanomechanical interface}}, doi = {10.1038/s41467-020-18269-z}, volume = {11}, year = {2020}, } @article{9114, abstract = {Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion efficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication.}, author = {Hease, William J and Rueda Sanchez, Alfredo R and Sahu, Rishabh and Wulf, Matthias and Arnold, Georg M and Schwefel, Harald G.L. and Fink, Johannes M}, issn = {2691-3399}, journal = {PRX Quantum}, number = {2}, publisher = {American Physical Society}, title = {{Bidirectional electro-optic wavelength conversion in the quantum ground state}}, doi = {10.1103/prxquantum.1.020315}, volume = {1}, year = {2020}, } @article{11499, abstract = {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.}, author = {Nanayakkara, Themiya and Brinchmann, Jarle and Boogaard, Leindert and Bouwens, Rychard and Cantalupo, Sebastiano and Feltre, Anna and Kollatschny, Wolfram and Marino, Raffaella Anna and Maseda, Michael and Matthee, Jorryt J and Paalvast, Mieke and Richard, Johan and Verhamme, Anne}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: ISM / galaxies: star formation / galaxies: evolution / galaxies: high-redshift}, publisher = {EDP Sciences}, title = {{Exploring He II λ1640 emission line properties at z ∼2−4}}, doi = {10.1051/0004-6361/201834565}, volume = {648}, year = {2019}, } @article{11505, abstract = {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. Aims. 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. Methods. 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. Results. 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. Conclusions. 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.}, author = {de La Vieuville, G. and Bina, D. and Pello, R. and Mahler, G. and Richard, J. and Drake, A. B. and Herenz, E. C. and Bauer, F. E. and Clément, B. and Lagattuta, D. and Laporte, N. and Martinez, J. and Patrício, V. and Wisotzki, L. and Zabl, J. and Bouwens, R. J. and Contini, T. and Garel, T. and Guiderdoni, B. and Marino, R. A. and Maseda, M. V. and Matthee, Jorryt J and Schaye, J. and Soucail, G.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {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}, publisher = {EDP Sciences}, title = {{Faint end of the z ∼ 3–7 luminosity function of Lyman-alpha emitters behind lensing clusters observed with MUSE}}, doi = {10.1051/0004-6361/201834471}, volume = {628}, year = {2019}, } @article{11507, abstract = {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.}, author = {Sobral, David and Matthee, Jorryt J}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: star formation / galaxies: statistics / galaxies: evolution / galaxies: formation / galaxies: ISM}, publisher = {EDP Sciences}, title = {{Predicting Lyα escape fractions with a simple observable: Lyα in emission as an empirically calibrated star formation rate indicator}}, doi = {10.1051/0004-6361/201833075}, volume = {623}, year = {2019}, } @article{11514, abstract = {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.}, author = {Boogaard, Leindert A. and Decarli, Roberto and González-López, Jorge and van der Werf, Paul and Walter, Fabian and Bouwens, Rychard and Aravena, Manuel and Carilli, Chris and Bauer, Franz Erik and Brinchmann, Jarle and Contini, Thierry and Cox, Pierre and da Cunha, Elisabete and Daddi, Emanuele and Díaz-Santos, Tanio and Hodge, Jacqueline and Inami, Hanae and Ivison, Rob and Maseda, Michael and Matthee, Jorryt J and Oesch, Pascal and Popping, Gergö and Riechers, Dominik and Schaye, Joop and Schouws, Sander and Smail, Ian and Weiss, Axel and Wisotzki, Lutz and Bacon, Roland and Cortes, Paulo C. and Rix, Hans-Walter and Somerville, Rachel S. and Swinbank, Mark and Wagg, Jeff}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {IOP Publishing}, title = {{The ALMA spectroscopic survey in the HUDF: Nature and physical properties of gas-mass selected galaxies using MUSE spectroscopy}}, doi = {10.3847/1538-4357/ab3102}, volume = {882}, year = {2019}, } @article{11515, abstract = {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.}, author = {Matthee, Jorryt J and Sobral, D. and Boogaard, L. A. and Röttgering, H. and Vallini, L. and Ferrara, A. and Paulino-Afonso, A. and Boone, F. and Schaerer, D. and Mobasher, B.}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {IOP Publishing}, title = {{Resolved UV and [C ii] structures of luminous galaxies within the epoch of reionization}}, doi = {10.3847/1538-4357/ab2f81}, volume = {881}, year = {2019}, } @article{11516, abstract = {The well-known quasar SDSS J095253.83+011421.9 (J0952+0114) at z = 3.02 has one of the most peculiar spectra discovered so far, showing the presence of narrow Lyα and broad metal emission lines. Although recent studies have suggested that a proximate damped Lyα absorption (PDLA) system causes this peculiar spectrum, the origin of the gas associated with the PDLA is unknown. Here we report the results of observations with the Multi Unit Spectroscopic Explorer (MUSE) that reveal a new giant (≈100 physical kpc) Lyα nebula. The detailed analysis of the Lyα velocity, velocity dispersion, and surface brightness profiles suggests that the J0952+0114 Lyα nebula shares similar properties with other QSO nebulae previously detected with MUSE, implying that the PDLA in J0952+0144 is covering only a small fraction of the solid angle of the QSO emission. We also detected bright and spectrally narrow C iv λ1550 and He ii λ1640 extended emission around J0952+0114 with velocity centroids similar to the peak of the extended and central narrow Lyα emission. The presence of a peculiarly bright, unresolved, and relatively broad He ii λ1640 emission in the central region at exactly the same PDLA redshift hints at the possibility that the PDLA originates in a clumpy outflow with a bulk velocity of about 500 km s−1. The smaller velocity dispersion of the large-scale Lyα emission suggests that the high-speed outflow is confined to the central region. Lastly, the derived spatially resolved He ii/Lyα and C iv/Lyα maps show a positive gradient with the distance to the QSO, hinting at a non-homogeneous distribution of the ionization parameter.}, author = {Marino, Raffaella Anna and Cantalupo, Sebastiano and Pezzulli, Gabriele and Lilly, Simon J. and Gallego, Sofia and Mackenzie, Ruari and Matthee, Jorryt J and Brinchmann, Jarle and Bouché, Nicolas and Feltre, Anna and Muzahid, Sowgat and Schroetter, Ilane and Johnson, Sean D. and Nanayakkara, Themiya}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {1}, publisher = {IOP Publishing}, title = {{A giant Lyα nebula and a small-scale clumpy outflow in the system of the exotic quasar J0952+0114 unveiled by MUSE}}, doi = {10.3847/1538-4357/ab2881}, volume = {880}, year = {2019}, }