@phdthesis{6825, abstract = {The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions. With tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay. We found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by maze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between cell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC trajectory-replay at the goal positively correlated with rule-switching performance. Finally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. }, author = {Käfer, Karola}, issn = {2663-337X}, pages = {89}, publisher = {Institute of Science and Technology Austria}, title = {{The hippocampus and medial prefrontal cortex during flexible behavior}}, doi = {10.15479/AT:ISTA:6825}, year = {2019}, } @article{5949, abstract = {Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.}, author = {Käfer, Karola and Malagon-Vina, Hugo and Dickerson, Desiree and O'Neill, Joseph and Trossbach, Svenja V. and Korth, Carsten and Csicsvari, Jozsef L}, journal = {Hippocampus}, number = {9}, pages = {802--816}, publisher = {Wiley}, title = {{Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization}}, doi = {10.1002/hipo.23076}, volume = {29}, year = {2019}, } @article{6328, abstract = {During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.}, author = {Renkawitz, Jörg and Kopf, Aglaja and Stopp, Julian A and de Vries, Ingrid and Driscoll, Meghan K. and Merrin, Jack and Hauschild, Robert and Welf, Erik S. and Danuser, Gaudenz and Fiolka, Reto and Sixt, Michael K}, journal = {Nature}, pages = {546--550}, publisher = {Springer Nature}, title = {{Nuclear positioning facilitates amoeboid migration along the path of least resistance}}, doi = {10.1038/s41586-019-1087-5}, volume = {568}, year = {2019}, } @phdthesis{6947, abstract = {Lymph nodes are es s ential organs of the immune s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells and form a sponge-like extracellular matrix network, called conduits , which they thems elves enwrap and contract. Lymph, containing s oluble antigens , arrive in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps ular s inus and conduit network. According to the current paradigm, the conduit network dis tributes afferent lymph through lymph nodes and thus provides acces s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s ize remains remarkedly s table under homeostatic conditions. It is only partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is able to swell in inflammation. The role of the FRC network in lymph node s welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal metastases.We examined the role of a mechanical feedback in regulation of lymph node swelling. Using parallel plate compression and UV-las er cutting experiments we dis s ected the mechanical force dynamics of the whole lymph node, and individually for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells ∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps ule, and how are lymphocytes able to enter in conditions that resist swelling remain open ques tions . We s how that tens ion on the FRC network is important to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates and a dis organized FRC network in the inflamed lymph node. Growth of the FRC network in turn is expected to releas e tens ion on thes e s tructures and lowers the res is tance to swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of swelling coincides with a thickening of the caps ule, which forms a thick res is tant band around the organ and lowers tens ion on the FRC network to form a new force equilibrium.The FRC and conduit network are further believed to be a privileged s ite of s oluble information within the lymph node, although many details remain uns olved. We s how by 3D ultra-recons truction that FRCs and antigen pres enting cells cover the s urface of conduit s ys tem for more than 99% and we dis cus s the implications for s oluble information exchangeat the conduit level.Finally, there is an ongoing debate in the cancer field whether and how cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels. Once in the blood circulation, these cells are able to form metastases in distal tissues.}, author = {Assen, Frank P}, issn = {2663-337X}, pages = {142}, publisher = {Institute of Science and Technology Austria}, title = {{Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking}}, doi = {10.15479/AT:ISTA:6947}, year = {2019}, } @article{6351, abstract = {A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. Patterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.}, author = {Marhavá, Petra and Hörmayer, Lukas and Yoshida, Saiko and Marhavy, Peter and Benková, Eva and Friml, Jiří}, issn = {1097-4172}, journal = {Cell}, number = {4}, pages = {957--969.e13}, publisher = {Elsevier}, title = {{Re-activation of stem cell pathways for pattern restoration in plant wound healing}}, doi = {10.1016/j.cell.2019.04.015}, volume = {177}, year = {2019}, } @article{6943, abstract = {Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration.}, author = {Hörmayer, Lukas and Friml, Jiří}, issn = {1369-5266}, journal = {Current Opinion in Plant Biology}, pages = {124--130}, publisher = {Elsevier}, title = {{Targeted cell ablation-based insights into wound healing and restorative patterning}}, doi = {10.1016/j.pbi.2019.08.006}, volume = {52}, year = {2019}, } @article{6486, abstract = {Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.}, author = {Kühnen, Jakob and Scarselli, Davide and Hof, Björn}, issn = {1528-901X}, journal = {Journal of Fluids Engineering}, number = {11}, publisher = {ASME}, title = {{Relaminarization of pipe flow by means of 3D-printed shaped honeycombs}}, doi = {10.1115/1.4043494}, volume = {141}, year = {2019}, } @article{6228, abstract = {Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.}, author = {Scarselli, Davide and Kühnen, Jakob and Hof, Björn}, issn = {1469-7645}, journal = {Journal of Fluid Mechanics}, pages = {934--948}, publisher = {Cambridge University Press}, title = {{Relaminarising pipe flow by wall movement}}, doi = {10.1017/jfm.2019.191}, volume = {867}, year = {2019}, } @inbook{10864, abstract = {We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.}, author = {Kazda, Alexandr and Kozik, Marcin and McKenzie, Ralph and Moore, Matthew}, booktitle = {Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science}, editor = {Czelakowski, J}, isbn = {9783319747712}, issn = {2211-2766}, pages = {203--220}, publisher = {Springer Nature}, title = {{Absorption and directed Jónsson terms}}, doi = {10.1007/978-3-319-74772-9_7}, volume = {16}, year = {2018}, } @article{10880, abstract = {Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation.}, author = {Yuuta, Moriyama and Koshiba-Takeuchi, Kazuko}, issn = {2041-2657}, journal = {Briefings in Functional Genomics}, keywords = {Genetics, Molecular Biology, Biochemistry, General Medicine}, number = {5}, pages = {329--338}, publisher = {Oxford University Press}, title = {{Significance of whole-genome duplications on the emergence of evolutionary novelties}}, doi = {10.1093/bfgp/ely007}, volume = {17}, year = {2018}, } @inproceedings{10882, abstract = {We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger.}, author = {Uijlings, Jasper and Konyushkova, Ksenia and Lampert, Christoph and Ferrari, Vittorio}, booktitle = {2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition}, isbn = {9781538664209}, issn = {2575-7075}, location = {Salt Lake City, UT, United States}, pages = {9175--9184}, publisher = {IEEE}, title = {{Learning intelligent dialogs for bounding box annotation}}, doi = {10.1109/cvpr.2018.00956}, year = {2018}, } @inproceedings{10883, abstract = {Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.}, author = {Chatterjee, Krishnendu and Dvořák, Wolfgang and Henzinger, Monika H and Svozil, Alexander}, booktitle = {22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning}, issn = {2398-7340}, location = {Awassa, Ethiopia}, pages = {233--253}, publisher = {EasyChair}, title = {{Quasipolynomial set-based symbolic algorithms for parity games}}, doi = {10.29007/5z5k}, volume = {57}, year = {2018}, } @article{1092, abstract = {A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. }, author = {Mohammadi, Fatemeh and Uhler, Caroline and Wang, Charles and Yu, Josephine}, journal = {SIAM Journal on Discrete Mathematics}, number = {1}, pages = {64--93}, publisher = {SIAM}, title = {{Generalized permutohedra from probabilistic graphical models}}, doi = {10.1137/16M107894X}, volume = {32}, year = {2018}, } @inproceedings{11, abstract = {We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm.}, author = {Leopold, Nikolai K and Pickl, Peter}, location = {Munich, Germany}, pages = {185 -- 214}, publisher = {Springer}, title = {{Mean-field limits of particles in interaction with quantised radiation fields}}, doi = {10.1007/978-3-030-01602-9_9}, volume = {270}, year = {2018}, } @article{11063, abstract = {The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus.}, author = {McCloskey, Asako and Ibarra, Arkaitz and HETZER, Martin W}, issn = {0890-9369}, journal = {Genes & Development}, keywords = {Developmental Biology, Genetics}, number = {19-20}, pages = {1321--1331}, publisher = {Cold Spring Harbor Laboratory}, title = {{Tpr regulates the total number of nuclear pore complexes per cell nucleus}}, doi = {10.1101/gad.315523.118}, volume = {32}, year = {2018}, } @article{11064, abstract = {Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients.}, author = {Fleischer, Jason G. and Schulte, Roberta and Tsai, Hsiao H. and Tyagi, Swati and Ibarra, Arkaitz and Shokhirev, Maxim N. and Huang, Ling and HETZER, Martin W and Navlakha, Saket}, issn = {1474-760X}, journal = {Genome Biology}, publisher = {BioMed Central}, title = {{Predicting age from the transcriptome of human dermal fibroblasts}}, doi = {10.1186/s13059-018-1599-6}, volume = {19}, year = {2018}, } @article{11508, abstract = {Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution (R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i) the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03) and ii) an unphysical [OII]/Hα ratio ([OII]/Hα >  22). We show that COLA1’s observed B-band flux is explained by a faint extended foreground LAE, for which we detect Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked LAE at z = 6.593, the first discovered at z >  6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3), has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission (r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission from Spitzer/IRAC indicates an extremely low metallicity of Z <  1/20 Z⊙ or reduced strength of nebular lines due to high escape of ionising photons. The small Lyα peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising photon escape fraction of ≈15 − 30%, providing the first direct evidence that such galaxies contribute actively to the reionisation of the Universe at z >  6. Based on simple estimates, we find that COLA1 could have provided just enough photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα line to be observed. However, we also discuss alternative scenarios explaining the detected double peaked nature of COLA1. Our results show that future high-resolution observations of statistical samples of double peaked LAEs at z >  5 are a promising probe of the occurrence of ionised regions around galaxies in the EoR.}, author = {Matthee, Jorryt J and Sobral, David and Gronke, Max and Paulino-Afonso, Ana and Stefanon, Mauro and Röttgering, Huub}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium}, publisher = {EDP Sciences}, title = {{Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe}}, doi = {10.1051/0004-6361/201833528}, volume = {619}, year = {2018}, } @article{11555, abstract = {We investigate the morphology of the [C II] emission in a sample of ‘normal’ star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart. We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In total 29 galaxies were analysed, 21 of which are detected in [C II]. For several of the latter the [C II] emission breaks into multiple components. Only a fraction of these [C II] components, if any, is associated with the primary UV systems, while the bulk of the [C II] emission is associated either with fainter UV components, or not associated with any UV counterpart at the current limits. By taking into account the presence of all these components, we find that the L[CII]–SFR (star formation rate) relation at early epochs is fully consistent with the local relation, but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than observed locally. We also find that the deviation from the local L[CII]–SFR relation has a weak anticorrelation with the EW(Ly α). The morphological analysis also reveals that [C II] emission is generally much more extended than the UV emission. As a consequence, these primordial galaxies are characterized by a [C II] surface brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation. These properties are likely a consequence of a combination of different effects, namely gas metallicity, [C II] emission from obscured star-forming regions, strong variations of the ionization parameter, and circumgalactic gas in accretion or ejected by these primeval galaxies.}, author = {Carniani, S and Maiolino, R and Amorin, R and Pentericci, L and Pallottini, A and Ferrara, A and Willott, C J and Smit, R and Matthee, Jorryt J and Sobral, D and Santini, P and Castellano, M and De Barros, S and Fontana, A and Grazian, A and Guaita, L}, 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, galaxies: formation}, number = {1}, pages = {1170--1184}, publisher = {Oxford University Press}, title = {{Kiloparsec-scale gaseous clumps and star formation at z = 5–7}}, doi = {10.1093/mnras/sty1088}, volume = {478}, year = {2018}, } @article{11557, abstract = {Deep narrow-band surveys have revealed a large population of faint Ly α emitters (LAEs) in the distant Universe, but relatively little is known about the most luminous sources (⁠LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα⁠). Here we present the spectroscopic follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2 and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (⁠β=−2.0+0.3−0.1⁠) and high Ly α escape fractions (⁠50+20−15 per cent) and span five orders of magnitude in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a wide variety of shapes, including significant blue-shifted components and widths from 200 to 4000 km s−1. Overall, 60 ± 11  per cent appear to be active galactic nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11  per cent) have lower ionization parameters (⁠logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2) and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’ starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from star formation dominated to AGN dominated.}, author = {Sobral, David and Matthee, Jorryt J and Darvish, Behnam and Smail, Ian and Best, Philip N and Alegre, Lara and Röttgering, Huub and Mobasher, Bahram and Paulino-Afonso, Ana and Stroe, Andra and Oteo, Iván}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: active, galaxies: evolution, galaxies: high-redshift, galaxies: ISM, galaxies: starburst, cosmology: observations}, number = {2}, pages = {2817--2840}, publisher = {Oxford University Press}, title = {{The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN}}, doi = {10.1093/mnras/sty782}, volume = {477}, year = {2018}, } @article{11558, abstract = {We present and explore deep narrow- and medium-band data obtained with the Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters (LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12⁠, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3, and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6. The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1 at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component vanishes and/or is below our detection limits above z > 3.5, likely linked with the evolution of the AGN population. The Ly α luminosity density rises by a factor ∼2 from z ∼ 2 to 3 but is then found to be roughly constant (⁠1.1+0.2−0.2×1040 erg s−1 Mpc−3) to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to 6, hinting for evolution in both the typical burstiness/stellar populations and even more so in the typical interstellar medium conditions allowing Ly α photons to escape.}, author = {Sobral, David and Santos, Sérgio and Matthee, Jorryt J and Paulino-Afonso, Ana and Ribeiro, Bruno and Calhau, João and Khostovan, Ali A}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution, galaxies: formation, galaxies: high-redshift, galaxies: luminosity function, mass function, galaxies: statistics}, number = {4}, pages = {4725--4752}, publisher = {Oxford University Press}, title = {{Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6}}, doi = {10.1093/mnras/sty378}, volume = {476}, year = {2018}, }