@inproceedings{11185, abstract = {Bundling crossings is a strategy which can enhance the readability of graph drawings. In this paper we consider bundlings for families of pseudosegments, i.e., simple curves such that any two have share at most one point at which they cross. Our main result is that there is a polynomial-time algorithm to compute an 8-approximation of the bundled crossing number of such instances (up to adding a term depending on the facial structure). This 8-approximation also holds for bundlings of good drawings of graphs. In the special case of circular drawings the approximation factor is 8 (no extra term), this improves upon the 10-approximation of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection graph of the pseudosegments is bipartite.}, author = {Arroyo Guevara, Alan M and Felsner, Stefan}, booktitle = {WALCOM 2022: Algorithms and Computation}, isbn = {9783030967307}, issn = {1611-3349}, location = {Jember, Indonesia}, pages = {383--395}, publisher = {Springer Nature}, title = {{Approximating the bundled crossing number}}, doi = {10.1007/978-3-030-96731-4_31}, volume = {13174}, year = {2022}, } @article{11339, abstract = {The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.}, author = {Glover, Georgina and Voliotis, Margaritis and Łapińska, Urszula and Invergo, Brandon M. and Soanes, Darren and O’Neill, Paul and Moore, Karen and Nikolic, Nela and Petrov, Peter and Milner, David S. and Roy, Sumita and Heesom, Kate and Richards, Thomas A. and Tsaneva-Atanasova, Krasimira and Pagliara, Stefano}, issn = {2399-3642}, journal = {Communications Biology}, publisher = {Springer Nature}, title = {{Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells}}, doi = {10.1038/s42003-022-03336-6}, volume = {5}, year = {2022}, } @book{11429, abstract = {This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022. The 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions. The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.}, editor = {Karimipour, Farid and Storandt, Sabine}, isbn = {9783031062445}, issn = {1611-3349}, pages = {153}, publisher = {Springer Nature}, title = {{Web and Wireless Geographical Information Systems}}, doi = {10.1007/978-3-031-06245-2}, volume = {13238}, year = {2022}, } @unpublished{17116, abstract = {CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems are a type of adaptive immune response in bacteria and archaea that utilize crRNA (CRISPR RNA)-guided effector complexes to target complementary RNA or DNA for destruction. The prototypical type III-A and III-B CRISPR-Cas systems utilize multi-subunit effector complexes composed of individual proteins to cleave ssRNA targets at 6-nt intervals, as well as non-specifically degrading ssDNA and activating cyclic oligoadenylate (cOA) synthesis. Recent studies have shown that type III systems can contain subunit fusions yet maintain canonical type III RNA-targeting capabilities. To understand how a multi-subunit fusion effector functions, we determine structures of a variant type III-D effector and biochemically characterize how it cleaves RNA targets. These findings provide insights into how multi-subunit fusion proteins are tethered together and assemble into an active and programmable RNA endonuclease, how the effector utilizes a novel mechanism for target RNA seeding, and the structural basis for the evolution of type III effector complexes. Furthermore, our results provide a blueprint for fusing subunits in class 1 effectors for design of user-defined effector complexes with disparate activities.Important noteWhile this manuscript was in preparation, a manuscript describing the structure of the type III-E effector was published1. We reference these important findings; however, a careful comparison of the structures will follow once the coordinates have been released by the PDB.}, author = {Schwartz, Evan A. and Bravo, Jack Peter Kelly and Macias, Luis A. and McCafferty, Caitlyn L. and Dangerfield, Tyler L. and Walker, Jada N. and Brodbelt, Jennifer S. and Fineran, Peter C. and Fagerlund, Robert D. and Taylor, David W.}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{Assembly of multi-subunit fusion proteins into the RNA-targeting type III-D CRISPR-Cas effector complex}}, doi = {10.1101/2022.06.13.496011}, year = {2022}, } @article{17560, abstract = {Observations of the most luminous quasars at high redshifts (z>6) have revealed that the largest supermassive black holes (SMBHs) at those epochs tend to be substantially overmassive relative to their host galaxies compared to the local relations, suggesting they experienced rapid early growth phases. We propose an assembly model for the SMBHs that end up in rare massive ∼1012 M⊙ host halos at z∼6−7, applying a kinetic feedback prescription for BHs accreting above the Eddington rate, provided by radiation hydrodynamic simulations for the long-term evolution of the accretion-flow structure. The large inflow rates into these halos during their assembly enable the formation of >109 M⊙ SMBHs by z∼6, even starting from stellar-mass seeds at z∼30, and even in the presence of outflows that reduce the BH feeding rate, especially at early times. This mechanism also naturally yields a high BH-to-galaxy mass ratio of >0.01 before the SMBH mass reaches MBH>109 M⊙ by z∼6. These fast-growing SMBH progenitors are bright enough to be detected by upcoming observations with the James Webb Space Telescope over a wide range of redshift (73 we prove that the number of rational points away from any rational line contained in X is bounded by O(|P|3/2+ε). From the result in 6 variables we deduce weak approximation for diagonal cubic hypersurfaces for n≥7 over Fq(t) when char(Fq)>3 and handle Waring's problem for cubes in 7 variables over Fq(t) when char(Fq)≠3. Our results answer a question of Davenport regarding the number of solutions of bounded height to x31+x32+x33=x34+x35+x36 with xi∈Fq[t].}, author = {Glas, Jakob and Hochfilzer, Leonhard}, booktitle = {arXiv}, title = {{On a question of Davenport and diagonal cubic forms over Fq(t)}}, doi = {10.48550/arXiv.2208.05422}, year = {2022}, } @phdthesis{11362, abstract = {Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks. One exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. To deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. This can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks. Our goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications. This thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making. First, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry. We show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization. Furthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable. Our results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice. Finally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic. We introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only. Our method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system. We demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.}, author = {Lechner, Mathias}, isbn = {978-3-99078-017-6}, keywords = {neural networks, verification, machine learning}, pages = {124}, publisher = {Institute of Science and Technology Austria}, title = {{Learning verifiable representations}}, doi = {10.15479/at:ista:11362}, year = {2022}, } @article{12174, abstract = {Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease. Here we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs. Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes. ATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.}, author = {Guerrini, Renzo and Mei, Davide and Szigeti, Margit Katalin and Pepe, Sara and Koenig, Mary Kay and Von Allmen, Gretchen and Cho, Megan T and McDonald, Kimberly and Baker, Janice and Bhambhani, Vikas and Powis, Zöe and Rodan, Lance and Nabbout, Rima and Barcia, Giulia and Rosenfeld, Jill A and Bacino, Carlos A and Mignot, Cyril and Power, Lillian H and Harris, Catharine J and Marjanovic, Dragan and Møller, Rikke S and Hammer, Trine B and Keski Filppula, Riikka and Vieira, Päivi and Hildebrandt, Clara and Sacharow, Stephanie and Maragliano, Luca and Benfenati, Fabio and Lachlan, Katherine and Benneche, Andreas and Petit, Florence and de Sainte Agathe, Jean Madeleine and Hallinan, Barbara and Si, Yue and Wentzensen, Ingrid M and Zou, Fanggeng and Narayanan, Vinodh and Matsumoto, Naomichi and Boncristiano, Alessandra and la Marca, Giancarlo and Kato, Mitsuhiro and Anderson, Kristin and Barba, Carmen and Sturiale, Luisa and Garozzo, Domenico and Bei, Roberto and Masuelli, Laura and Conti, Valerio and Novarino, Gaia and Fassio, Anna}, issn = {1460-2156}, journal = {Brain}, keywords = {Neurology (clinical)}, number = {8}, pages = {2687--2703}, publisher = {Oxford University Press}, title = {{Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis}}, doi = {10.1093/brain/awac145}, volume = {145}, year = {2022}, } @phdthesis{12358, abstract = {The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and visual complexity. The small-scale interactions of yarns colliding with and pulling on each other result in drastically different large-scale stretching and bending behavior, introducing anisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this complexity and match the quality of real fabric, it may be too computationally expensive for large fabrics. On the other hand, continuum-based approaches do not need to discretize the cloth at a stitch-level, but it is non-trivial to find a material model that would replicate the large-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis, we discuss three methods to try and bridge the gap between small-scale and large-scale yarn mechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively fitting yarn parameters to physical measurements of real fabric. To start, we present a method for animating yarn-level cloth effects using a thin-shell solver. We first use a large number of periodic yarn-level simulations to build a model of the potential energy density of the cloth, and then use it to compute forces in a thin-shell simulator. The resulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics and the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of full yarn-level simulation. While our thin-shell simulations are able to capture large-scale yarn mechanics, they lack the rich visual detail of yarn-level simulations. Therefore, we propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching at negligible cost. Finally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compile a database from physical tests of several knitted fabrics used in the textile industry spanning diverse physical properties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized shell models to speed up computation and adding some small-but-necessary extensions to yarn-level models used in computer graphics. }, author = {Sperl, Georg}, isbn = {978-3-99078-020-6}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting}}, doi = {10.15479/at:ista:12103}, year = {2022}, } @unpublished{11943, abstract = {Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full in-silico reconstruction1–5, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches6–12 facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy6,13 in extracellularly labelled tissue14 for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue.}, author = {Velicky, Philipp and Miguel Villalba, Eder and Michalska, Julia M and Wei, Donglai and Lin, Zudi and Watson, Jake and Troidl, Jakob and Beyer, Johanna and Ben Simon, Yoav and Sommer, Christoph M and Jahr, Wiebke and Cenameri, Alban and Broichhagen, Johannes and Grant, Seth G. N. and Jonas, Peter M and Novarino, Gaia and Pfister, Hanspeter and Bickel, Bernd and Danzl, Johann G}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{Saturated reconstruction of living brain tissue}}, doi = {10.1101/2022.03.16.484431}, year = {2022}, } @article{12244, abstract = {Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology.}, author = {Colombo, Gloria and Cubero, Ryan J and Kanari, Lida and Venturino, Alessandro and Schulz, Rouven and Scolamiero, Martina and Agerberg, Jens and Mathys, Hansruedi and Tsai, Li-Huei and Chachólski, Wojciech and Hess, Kathryn and Siegert, Sandra}, issn = {1546-1726}, journal = {Nature Neuroscience}, keywords = {General Neuroscience}, number = {10}, pages = {1379--1393}, publisher = {Springer Nature}, title = {{A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes}}, doi = {10.1038/s41593-022-01167-6}, volume = {25}, year = {2022}, } @phdthesis{11388, abstract = {In evolve and resequence experiments, a population is sequenced, subjected to selection and then sequenced again, so that genetic changes before and after selection can be observed at the genetic level. Here, I use these studies to better understand the genetic basis of complex traits - traits which depend on more than a few genes. In the first chapter, I discuss the first evolve and resequence experiment, in which a population of mice, the so-called "Longshanks" mice, were selected for tibia length while their body mass was kept constant. The full pedigree is known. We observed a selection response on all chromosomes and used the infinitesimal model with linkage, a model which assumes an infinite number of genes with infinitesimally small effect sizes, as a null model. Results implied a very polygenic basis with a few loci of major effect standing out and changing in parallel. There was large variability between the different chromosomes in this study, probably due to LD. In chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency based summary statistic, giving an equation based on the initial allele frequencies, average pairwise LD, and the first four moments of the haplotype block copy number distribution. I describe this distribution by referring back to the founder generation. I then demonstrate how to infer selection via a maximum likelihood scheme on the example of a single locus and discuss how to extend this to more realistic scenarios. In chapter three, I discuss the second evolve and resequence experiment, in which a small population of Drosophila melanogaster was selected for increased pupal case size over 6 generations. The experiment was highly replicated with 27 lines selected within family and a known pedigree. We observed a phenotypic selection response of over one standard deviation. I describe the patterns in allele frequency data, including allele frequency changes and patterns of heterozygosity, and give ideas for future work.}, author = {Belohlavy, Stefanie}, isbn = {978-3-99078-018-3}, pages = {98}, publisher = {Institute of Science and Technology Austria}, title = {{The genetic basis of complex traits studied via analysis of evolve and resequence experiments}}, doi = {10.15479/at:ista:11388}, 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{11522, abstract = {The decline in abundance of Lyman-α (Lyα) emitting galaxies at z ≳ 6 is a powerful and commonly used probe to constrain the progress of cosmic reionization. We use the CODAII simulation, which is a radiation hydrodynamic simulation featuring a box of ∼94 comoving Mpc side length, to compute the Lyα transmission properties of the intergalactic medium (IGM) at z ∼ 5.8 to 7. Our results mainly confirm previous studies, i.e. we find a declining Lyα transmission with redshift and a large sightline-to-sightline variation. However, motivated by the recent discovery of blue Lyα peaks at high redshift, we also analyse the IGM transmission on the blue side, which shows a rapid decline at z ≳ 6 of the blue transmission. This low transmission can be attributed not only to the presence of neutral regions but also to the residual neutral hydrogen within ionized regions, for which a density even as low as nHI∼10−9cm−3 (sometimes combined with kinematic effects) leads to a significantly reduced visibility. Still, we find that ∼1 per cent of sightlines towards M1600AB ∼ −21 galaxies at z ∼ 7 are transparent enough to allow a transmission of a blue Lyα peak. We discuss our results in the context of the interpretation of observations.}, author = {Gronke, Max and Ocvirk, Pierre and Mason, Charlotte and Matthee, Jorryt J and Bosman, Sarah E I and Sorce, Jenny G and Lewis, Joseph and Ahn, Kyungjin and Aubert, Dominique and Dawoodbhoy, Taha and Iliev, Ilian T and Shapiro, Paul R and Yepes, Gustavo}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {dark ages, reionization, first stars, intergalactic medium, galaxies: formation}, number = {3}, pages = {3697--3709}, publisher = {Oxford University Press}, title = {{Lyman-α transmission properties of the intergalactic medium in the CoDaII simulation}}, doi = {10.1093/mnras/stab2762}, volume = {508}, 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{11756, abstract = {We give two fully dynamic algorithms that maintain a (1 + ε)-approximation of the weight M of a minimum spanning forest (MSF) of an n-node graph G with edges weights in [1, W ], for any ε > 0. (1) Our deterministic algorithm takes O (W 2 log W /ε3) worst-case update time, which is O (1) if both W and ε are constants. (2) Our randomized (Monte-Carlo style) algorithm works with high probability and runs in worst-case O (log W /ε4) update time if W = O ((m∗)1/6/log2/3 n), where m∗ is the minimum number of edges in the graph throughout all the updates. It works even against an adaptive adversary. We complement our algorithmic results with two cell-probe lower bounds for dynamically maintaining an approximation of the weight of an MSF of a graph.}, author = {Henzinger, Monika H and Peng, Pan}, issn = {0890-5401}, journal = {Information and Computation}, number = {12}, publisher = {Elsevier}, title = {{Constant-time dynamic weight approximation for minimum spanning forest}}, doi = {10.1016/j.ic.2021.104805}, volume = {281}, year = {2021}, } @article{11886, abstract = {We present a deterministic (1+𝑜(1))-approximation (𝑛1/2+𝑜(1)+𝐷1+𝑜(1))-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the \sf CONGEST model); here 𝑛 is the number of nodes in the network, 𝐷 is its (hop) diameter, and edge weights are positive integers from 1 to poly(𝑛). This is the first nontrivial deterministic algorithm for this problem. It also improves (i) the running time of the randomized (1+𝑜(1))-approximation 𝑂̃ (𝑛√𝐷1/4+𝐷)-time algorithm of Nanongkai [in Proceedings of STOC, 2014, pp. 565--573] by a factor of as large as 𝑛1/8, and (ii) the 𝑂(𝜖−1log𝜖−1)-approximation factor of Lenzen and Patt-Shamir's 𝑂̃ (𝑛1/2+𝜖+𝐷)-time algorithm [in Proceedings of STOC, 2013, pp. 381--390] within the same running time. (Throughout, we use 𝑂̃ (⋅) to hide polylogarithmic factors in 𝑛.) Our running time matches the known time lower bound of Ω(𝑛/log𝑛‾‾‾‾‾‾‾√+𝐷) [M. Elkin, SIAM J. Comput., 36 (2006), pp. 433--456], thus essentially settling the status of this problem which was raised at least a decade ago [M. Elkin, SIGACT News, 35 (2004), pp. 40--57]. It also implies a (2+𝑜(1))-approximation (𝑛1/2+𝑜(1)+𝐷1+𝑜(1))-time algorithm for approximating a network's weighted diameter which almost matches the lower bound by Holzer and Pinsker [in Proceedings of OPODIS, 2015, Schloss Dagstuhl. Leibniz-Zent. Inform., Wadern, Germany, 2016, 6]. In achieving this result, we develop two techniques which might be of independent interest and useful in other settings: (i) a deterministic process that replaces the “hitting set argument” commonly used for shortest paths computation in various settings, and (ii) a simple, deterministic construction of an (𝑛𝑜(1),𝑜(1))-hop set of size 𝑛1+𝑜(1). We combine these techniques with many distributed algorithmic techniques, some of which are from problems that are not directly related to shortest paths, e.g., ruling sets [A. V. Goldberg, S. A. Plotkin, and G. E. Shannon, SIAM J. Discrete Math., 1 (1988), pp. 434--446], source detection [C. Lenzen and D. Peleg, in Proceedings of PODC, 2013, pp. 375--382], and partial distance estimation [C. Lenzen and B. Patt-Shamir, in Proceedings of PODC, 2015, pp. 153--162]. Our hop set construction also leads to single-source shortest paths algorithms in two other settings: (i) a (1+𝑜(1))-approximation 𝑛𝑜(1)-time algorithm on congested cliques, and (ii) a (1+𝑜(1))-approximation 𝑛𝑜(1)-pass 𝑛1+𝑜(1)-space streaming algorithm. The first result answers an open problem in [D. Nanongkai, in Proceedings of STOC, 2014, pp. 565--573]. The second result partially answers an open problem raised by McGregor in 2006 [List of Open Problems in Sublinear Algorithms: Problem 14].}, author = {Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon}, issn = {1095-7111}, journal = {SIAM Journal on Computing}, number = {3}, pages = {STOC16--98--STOC16--137}, publisher = {Society for Industrial & Applied Mathematics}, title = {{A deterministic almost-tight distributed algorithm for approximating single-source shortest paths}}, doi = {10.1137/16m1097808}, volume = {50}, year = {2021}, } @article{17900, abstract = {To rival the performance of modern integrated circuits, single-molecule devices must be designed to exhibit extremely nonlinear current–voltage (I–V) characteristics1,2,3,4. A common approach is to design molecular backbones where destructive quantum interference (QI) between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) produces a nonlinear energy-dependent tunnelling probability near the electrode Fermi energy (EF)5,6,7,8. However, tuning such systems is not straightforward, as aligning the frontier orbitals to EF is hard to control9. Here, we instead create a molecular system where constructive QI between the HOMO and LUMO is suppressed and destructive QI between the HOMO and strongly coupled occupied orbitals of opposite phase is enhanced. We use a series of fluorene oligomers containing a central benzothiadiazole10 unit to demonstrate that this strategy can be used to create highly nonlinear single-molecule circuits. Notably, we are able to reproducibly modulate the conductance of a 6-nm molecule by a factor of more than 10^4.}, author = {Greenwald, Julia E. and Cameron, Joseph and Findlay, Neil J. and Fu, Tianren and Gunasekaran, Suman and Skabara, Peter J. and Venkataraman, Latha}, issn = {1748-3395}, journal = {Nature Nanotechnology}, number = {3}, pages = {313--317}, publisher = {Springer Nature}, title = {{Highly nonlinear transport across single-molecule junctions via destructive quantum interference}}, doi = {10.1038/s41565-020-00807-x}, volume = {16}, year = {2021}, }