@article{8741, abstract = {In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions on the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of these qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements.}, author = {Klose, Ann Kristin and Karle, Volker and Winkelmann, Ricarda and Donges, Jonathan F.}, issn = {20545703}, journal = {Royal Society Open Science}, number = {6}, publisher = {The Royal Society}, title = {{Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements}}, doi = {10.1098/rsos.200599}, volume = {7}, year = {2020}, } @article{7687, abstract = {A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.}, author = {Ernst, Doris and Novotny, Gertraud and Schönher, Eva Maria}, issn = {1022-2588}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, number = {1}, pages = {46--59}, publisher = {Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare}, title = {{(Core Trust) Seal your repository!}}, doi = {10.31263/voebm.v73i1.3491}, volume = {73}, year = {2020}, } @inproceedings{15071, abstract = {A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6 T (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism.}, author = {Oshurkova, Viktoriia and Troshina, Olga and Trubitsyn, Vladimir and Ryzhmanova, Yana and Bochkareva, Olga and Shcherbakova, Viktoria}, booktitle = {Proceedings of 1st International Electronic Conference on Microbiology}, location = {Virtual}, publisher = {MDPI}, title = {{Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T}}, doi = {10.3390/ecm2020-07116}, year = {2020}, } @article{15153, abstract = {Mammalian circadian rhythms are generated by a transcription-based feedback loop in which CLOCK:BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which ultimately interact with CLOCK:BMAL1 to close the feedback loop with ~24 hr periodicity. Here we pinpoint a key difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. Both cryptochromes bind the BMAL1 transactivation domain similarly to sequester it from coactivators and repress CLOCK:BMAL1 activity. However, we find that CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We discovered a dynamic serine-rich loop adjacent to the secondary pocket in the photolyase homology region (PHR) domain that regulates differential binding of cryptochromes to the PAS domain core of CLOCK:BMAL1. Notably, binding of the co-repressor PER2 remodels the serine loop of CRY2, making it more CRY1-like and enhancing its affinity for CLOCK:BMAL1.}, author = {Fribourgh, Jennifer L and Srivastava, Ashutosh and Sandate, Colby R and Michael, Alicia Kathleen and Hsu, Peter L and Rakers, Christin and Nguyen, Leslee T and Torgrimson, Megan R and Parico, Gian Carlo G and Tripathi, Sarvind and Zheng, Ning and Lander, Gabriel C and Hirota, Tsuyoshi and Tama, Florence and Partch, Carrie L}, issn = {2050-084X}, journal = {eLife}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience}, publisher = {eLife Sciences Publications}, title = {{Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing}}, doi = {10.7554/elife.55275}, volume = {9}, year = {2020}, } @phdthesis{7525, abstract = {The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. In the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. On electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b. In summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain. }, author = {Bhandari, Pradeep}, issn = {2663-337X}, keywords = {Cav2.3, medial habenula (MHb), interpeduncular nucleus (IPN)}, pages = {79}, publisher = {Institute of Science and Technology Austria}, title = {{Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway}}, doi = {10.15479/AT:ISTA:7525}, year = {2020}, } @article{8586, abstract = {Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.}, author = {Fäßler, Florian and Zens, Bettina and Hauschild, Robert and Schur, Florian KM}, issn = {1047-8477}, journal = {Journal of Structural Biology}, keywords = {electron microscopy, cryo-EM, EM sample preparation, 3D printing, cell culture}, number = {3}, publisher = {Elsevier}, title = {{3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy}}, doi = {10.1016/j.jsb.2020.107633}, volume = {212}, year = {2020}, } @phdthesis{8657, abstract = {Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery. Perturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency). In the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression. In the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions. We extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters. In the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate. This thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation.}, author = {Kavcic, Bor}, isbn = {978-3-99078-011-4}, issn = {2663-337X}, pages = {271}, publisher = {Institute of Science and Technology Austria}, title = {{Perturbations of protein synthesis: from antibiotics to genetics and physiology}}, doi = {10.15479/AT:ISTA:8657}, year = {2020}, } @article{7473, abstract = {How structural and functional properties of synapses relate to each other is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms of synaptic transmission, and electron microscopy (EM) has provided insight into morphological properties of synapses. Here we describe an enhanced method for functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure freezing. We demonstrate that the improved method can be applied to intact networks in acute brain slices and organotypic slice cultures from mice. As a proof of concept, we probed vesicle pool changes during synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked vesicle pool and the functionally defined readily releasable pool and provide evidence of fast endocytosis at this synapse. Functional EM with acute slices and slice cultures has the potential to reveal the structural and functional mechanisms of transmission in intact, genetically perturbed, and disease-affected synapses.}, author = {Borges Merjane, Carolina and Kim, Olena and Jonas, Peter M}, issn = {0896-6273}, journal = {Neuron}, pages = {992--1006}, publisher = {Elsevier}, title = {{Functional electron microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain slices}}, doi = {10.1016/j.neuron.2019.12.022}, volume = {105}, year = {2020}, } @article{8250, abstract = {Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by “translation bottlenecks”: points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of “continuous epistasis” in bacterial physiology.}, author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Mechanisms of drug interactions between translation-inhibiting antibiotics}}, doi = {10.1038/s41467-020-17734-z}, volume = {11}, year = {2020}, } @unpublished{7673, abstract = {Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions.}, author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias}, booktitle = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, title = {{A minimal biophysical model of combined antibiotic action}}, doi = {10.1101/2020.04.18.047886}, year = {2020}, } @article{8002, abstract = {Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.}, author = {Hörmayer, Lukas and Montesinos López, Juan C and Marhavá, Petra and Benková, Eva and Yoshida, Saiko and Friml, Jiří}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {26}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots}}, doi = {10.1073/pnas.2003346117}, volume = {117}, year = {2020}, } @phdthesis{7680, abstract = {Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone. In optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability. Most optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry. This work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment. CBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo.}, author = {Kainrath, Stephanie}, issn = {2663-337X}, pages = {98}, publisher = {Institute of Science and Technology Austria}, title = {{Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals}}, doi = {10.15479/AT:ISTA:7680}, year = {2020}, } @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}, } @phdthesis{8340, abstract = {Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven proton pumping machines which establish a proton motive force across the inner mitochondrial membrane. This electrochemical proton gradient is used to drive ATP synthesis, which powers the majority of cellular processes such as protein synthesis, locomotion and signalling. In this thesis I investigate the structures and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory complex I and transhydrogenase. I present the first high-resolution structure of the full transhydrogenase from any species, and a significantly improved structure of complex I. Improving the resolution from 3.3 Å available previously to up to 2.3 Å in this thesis allowed us to model bound water molecules, crucial in the proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different substrates and inhibitors bound were solved to delineate the catalytic cycle and understand the proton pumping mechanism. In transhydrogenase, the proton channel is gated by reversible detachment of the NADP(H)-binding domain which opens the proton channel to the opposite sites of the membrane. In complex I, the proton channels are gated by reversible protonation of key glutamate and lysine residues and breaking of the water wire connecting the proton pumps with the quinone reduction site. The tight coupling between the redox and the proton pumping reactions in transhydrogenase is achieved by controlling the NADP(H) exchange which can only happen when the NADP(H)-binding domain interacts with the membrane domain. In complex I, coupling is achieved by cycling of the whole complex between the closed state, in which quinone can get reduced, and the open state, in which NADH can induce quinol ejection from the binding pocket. On the basis of these results I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex I that are consistent with a large amount of previous work. In both enzymes, conformational and electrostatic mechanisms contribute to the overall catalytic process. Results presented here could be used for better understanding of the human pathologies arising from deficiencies of complex I or transhydrogenase and could be used to develop novel therapies.}, author = {Kampjut, Domen}, isbn = {978-3-99078-008-4}, issn = {2663-337X}, pages = {242}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes}}, doi = {10.15479/AT:ISTA:8340}, 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{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 = {18790380}, 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{8434, abstract = {Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin-binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex, an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.This article has an associated First Person interview with the first author of the paper. }, author = {Dimchev, Georgi A and Amiri, Behnam and Humphries, Ashley C. and Schaks, Matthias and Dimchev, Vanessa and Stradal, Theresia E. B. and Faix, Jan and Krause, Matthias and Way, Michael and Falcke, Martin and Rottner, Klemens}, issn = {1477-9137}, journal = {Journal of Cell Science}, keywords = {Cell Biology}, number = {7}, publisher = {The Company of Biologists}, title = {{Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation}}, doi = {10.1242/jcs.239020}, volume = {133}, year = {2020}, } @article{7889, abstract = {Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants.}, author = {Mitiouchkina, Tatiana and Mishin, Alexander S. and Gonzalez Somermeyer, Louisa and Markina, Nadezhda M. and Chepurnyh, Tatiana V. and Guglya, Elena B. and Karataeva, Tatiana A. and Palkina, Kseniia A. and Shakhova, Ekaterina S. and Fakhranurova, Liliia I. and Chekova, Sofia V. and Tsarkova, Aleksandra S. and Golubev, Yaroslav V. and Negrebetsky, Vadim V. and Dolgushin, Sergey A. and Shalaev, Pavel V. and Shlykov, Dmitry and Melnik, Olesya A. and Shipunova, Victoria O. and Deyev, Sergey M. and Bubyrev, Andrey I. and Pushin, Alexander S. and Choob, Vladimir V. and Dolgov, Sergey V. and Kondrashov, Fyodor and Yampolsky, Ilia V. and Sarkisyan, Karen S.}, issn = {1546-1696}, journal = {Nature Biotechnology}, pages = {944--946}, publisher = {Springer Nature}, title = {{Plants with genetically encoded autoluminescence}}, doi = {10.1038/s41587-020-0500-9}, volume = {38}, year = {2020}, } @unpublished{9750, abstract = {Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.}, author = {Slovakova, Jana and Sikora, Mateusz K and Caballero Mancebo, Silvia and Krens, Gabriel and Kaufmann, Walter and Huljev, Karla and Heisenberg, Carl-Philipp J}, booktitle = {bioRxiv}, pages = {41}, publisher = {Cold Spring Harbor Laboratory}, title = {{Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion}}, doi = {10.1101/2020.11.20.391284}, year = {2020}, } @article{7426, abstract = {This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the state–space, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the state–space in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method.}, author = {Garcia Soto, Miriam and Prabhakar, Pavithra}, issn = {1751-570X}, journal = {Nonlinear Analysis: Hybrid Systems}, number = {5}, publisher = {Elsevier}, title = {{Abstraction based verification of stability of polyhedral switched systems}}, doi = {10.1016/j.nahs.2020.100856}, volume = {36}, year = {2020}, } @phdthesis{8983, abstract = {Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers.}, author = {Emtenani, Shamsi}, issn = {2663-337X}, pages = {141}, publisher = {Institute of Science and Technology Austria}, title = {{Metabolic regulation of Drosophila macrophage tissue invasion}}, doi = {10.15479/AT:ISTA:8983}, year = {2020}, } @unpublished{8557, abstract = {The infiltration of immune cells into tissues underlies the establishment of tissue resident macrophages, and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio which are themselves required for invasion. Cortical F-actin levels are critical as expressing a dominant active form of Diaphanous, a actin polymerizing Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo imaging shows that Dfos is required to enhance the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the mechanical properties of the macrophage nucleus from affecting tissue entry. We thus identify tuning the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.}, author = {Belyaeva, Vera and Wachner, Stephanie and Gridchyn, Igor and Linder, Markus and Emtenani, Shamsi and György, Attila and Sibilia, Maria and Siekhaus, Daria E}, booktitle = {bioRxiv}, title = {{Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance}}, doi = {10.1101/2020.09.18.301481}, year = {2020}, } @unpublished{8831, abstract = {Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.}, author = {Aggarwal, Kushagra and Hofmann, Andrea C and Jirovec, Daniel and Prieto Gonzalez, Ivan and Sammak, Amir and Botifoll, Marc and Marti-Sanchez, Sara and Veldhorst, Menno and Arbiol, Jordi and Scappucci, Giordano and Katsaros, Georgios}, booktitle = {arXiv}, title = {{Enhancement of proximity induced superconductivity in planar Germanium}}, year = {2020}, } @article{8532, abstract = {The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography.}, author = {Kleindienst, David and Montanaro-Punzengruber, Jacqueline-Claire and Bhandari, Pradeep and Case, Matthew J and Fukazawa, Yugo and Shigemoto, Ryuichi}, issn = {14220067}, journal = {International Journal of Molecular Sciences}, number = {18}, publisher = {MDPI}, title = {{Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses}}, doi = {10.3390/ijms21186737}, volume = {21}, 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 = {16113349}, 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 = {09518320}, 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{7161, abstract = {In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature.}, author = {Shehu, Yekini and Gibali, Aviv and Sagratella, Simone}, issn = {1573-2878}, journal = {Journal of Optimization Theory and Applications}, pages = {877–894}, publisher = {Springer Nature}, title = {{Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces}}, doi = {10.1007/s10957-019-01616-6}, volume = {184}, year = {2020}, } @article{7652, abstract = {Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature.}, author = {Tomanek, Isabella and Grah, Rok and Lagator, M. and Andersson, A. M. C. and Bollback, Jonathan P and Tkačik, Gašper and Guet, Calin C}, issn = {2397-334X}, journal = {Nature Ecology & Evolution}, number = {4}, pages = {612--625}, publisher = {Springer Nature}, title = {{Gene amplification as a form of population-level gene expression regulation}}, doi = {10.1038/s41559-020-1132-7}, volume = {4}, year = {2020}, } @phdthesis{7258, abstract = {Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings.}, author = {Scarselli, Davide}, issn = {2663-337X}, pages = {174}, publisher = {Institute of Science and Technology Austria}, title = {{New approaches to reduce friction in turbulent pipe flow}}, doi = {10.15479/AT:ISTA:7258}, year = {2020}, } @phdthesis{8653, abstract = {Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. Gene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments.  }, author = {Tomanek, Isabella}, issn = {2663-337X}, keywords = {duplication, amplification, promoter, CNV, AMGET, experimental evolution, Escherichia coli}, pages = {117}, publisher = {Institute of Science and Technology Austria}, title = {{The evolution of gene expression by copy number and point mutations}}, doi = {10.15479/AT:ISTA:8653}, year = {2020}, } @article{7427, abstract = {Plants, like other multicellular organisms, survive through a delicate balance between growth and defense against pathogens. Salicylic acid (SA) is a major defense signal in plants, and the perception mechanism as well as downstream signaling activating the immune response are known. Here, we identify a parallel SA signaling that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase 2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin transporter is hyperphosphorylated in response to SA, leading to changed activity of this important growth regulator. Accordingly, auxin transport and auxin-mediated root development, including growth, gravitropic response, and lateral root organogenesis, are inhibited. This study reveals how SA, besides activating immunity, concomitantly attenuates growth through crosstalk with the auxin distribution network. Further analysis of this dual role of SA and characterization of additional SA-regulated PP2A targets will provide further insights into mechanisms maintaining a balance between growth and defense.}, author = {Tan, Shutang and Abas, Melinda F and Verstraeten, Inge and Glanc, Matous and Molnar, Gergely and Hajny, Jakub and Lasák, Pavel and Petřík, Ivan and Russinova, Eugenia and Petrášek, Jan and Novák, Ondřej and Pospíšil, Jiří and Friml, Jiří}, issn = {09609822}, journal = {Current Biology}, number = {3}, pages = {381--395.e8}, publisher = {Cell Press}, title = {{Salicylic acid targets protein phosphatase 2A to attenuate growth in plants}}, doi = {10.1016/j.cub.2019.11.058}, volume = {30}, year = {2020}, } @article{7500, abstract = {Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited. In the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application. Our methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling. Further studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.}, author = {Mazur, E and Kulik, Ivan and Hajny, Jakub and Friml, Jiří}, issn = {1469-8137}, journal = {New Phytologist}, number = {5}, pages = {1375--1383}, publisher = {Wiley}, title = {{Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis}}, doi = {10.1111/nph.16446}, volume = {226}, year = {2020}, } @phdthesis{8822, abstract = {Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23). Next, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization.}, author = {Hajny, Jakub}, issn = {2663-337X}, pages = {249}, publisher = {Institute of Science and Technology Austria}, title = {{Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration}}, doi = {10.15479/AT:ISTA:8822}, year = {2020}, } @phdthesis{8350, abstract = {Cytoplasm is a gel-like crowded environment composed of tens of thousands of macromolecules, organelles, cytoskeletal networks and cytosol. The structure of the cytoplasm is thought to be highly organized and heterogeneous due to the crowding of its constituents and their effective compartmentalization. In such an environment, the diffusive dynamics of the molecules is very restricted, an effect that is further amplified by clustering and anchoring of molecules. Despite the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization of cytoplasm is essential for important cellular functions, such as nuclear positioning and cell division. How such mesoscale reorganization of the cytoplasm is achieved, especially for very large cells such as oocytes or syncytial tissues that can span hundreds of micrometers in size, has only begun to be understood. In this thesis, I focus on the recent advances in elucidating the molecular, cellular and biophysical principles underlying cytoplasmic organization across different scales, structures and species. First, I outline which of these principles have been identified by reductionist approaches, such as in vitro reconstitution assays, where boundary conditions and components can be modulated at ease. I then describe how the theoretical and experimental framework established in these reduced systems have been applied to their more complex in vivo counterparts, in particular oocytes and embryonic syncytial structures, and discuss how such complex biological systems can initiate symmetry breaking and establish patterning. Specifically, I examine an example of large-scale reorganizations taking place in zebrafish embryos, where extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk granules along the animal-vegetal axis of the embryo. Using biophysical experimentation and theory, I investigate the forces underlying this process, to show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the embryo. This wave functions in segregation by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm pulling is mediated by bulk actin network flows exerting friction forces on the cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. This study defines a novel role of bulk actin polymerization waves in embryo polarization via cytoplasmic segregation. Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish oocyte maturation, where the initial segregation of the cytoplasm and yolk granules occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster formation, traveling the oocyte along the animal-vegetal axis. Further research is required to determine the role of such microtubule structures in cytoplasmic reorganizations therein. Collectively, these studies provide further evidence for the coupling between cell cytoskeleton and cell cycle machinery, which can underlie a core self-organizing mechanism for orchestrating large-scale reorganizations in a cell-cycle-tunable manner, where the modulations of the force-generating machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions.}, author = {Shamipour, Shayan}, issn = {2663-337X}, pages = {107}, publisher = {Institute of Science and Technology Austria}, title = {{Bulk actin dynamics drive phase segregation in zebrafish oocytes }}, doi = {10.15479/AT:ISTA:8350}, year = {2020}, } @article{8569, abstract = {Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final target lamina, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating the specific sequential steps of radial neuronal migration in vivo are however still unclear, let alone the effects and interactions with the extracellular environment. In any in vivo context, cells will always be exposed to a complex extracellular environment consisting of (1) secreted factors acting as potential signaling cues, (2) the extracellular matrix, and (3) other cells providing cell–cell interaction through receptors and/or direct physical stimuli. Most studies so far have described and focused mainly on intrinsic cell-autonomous gene functions in neuronal migration but there is accumulating evidence that non-cell-autonomous-, local-, systemic-, and/or whole tissue-wide effects substantially contribute to the regulation of radial neuronal migration. These non-cell-autonomous effects may differentially affect cortical neuron migration in distinct cellular environments. However, the cellular and molecular natures of such non-cell-autonomous mechanisms are mostly unknown. Furthermore, physical forces due to collective migration and/or community effects (i.e., interactions with surrounding cells) may play important roles in neocortical projection neuron migration. In this concise review, we first outline distinct models of non-cell-autonomous interactions of cortical projection neurons along their radial migration trajectory during development. We then summarize experimental assays and platforms that can be utilized to visualize and potentially probe non-cell-autonomous mechanisms. Lastly, we define key questions to address in the future.}, author = {Hansen, Andi H and Hippenmeyer, Simon}, issn = {2296-634X}, journal = {Frontiers in Cell and Developmental Biology}, number = {9}, publisher = {Frontiers}, title = {{Non-cell-autonomous mechanisms in radial projection neuron migration in the developing cerebral cortex}}, doi = {10.3389/fcell.2020.574382}, volume = {8}, 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}, } @article{8190, author = {Sixt, Michael K and Huttenlocher, Anna}, issn = {1540-8140}, journal = {The Journal of Cell Biology}, number = {8}, publisher = {Rockefeller University Press}, title = {{Zena Werb (1945-2020): Cell biology in context}}, doi = {10.1083/jcb.202007029}, volume = {219}, 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 = {14220067}, 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{8139, abstract = {Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.}, author = {Johnson, Alexander J and Gnyliukh, Nataliia and Kaufmann, Walter and Narasimhan, Madhumitha and Vert, G and Bednarek, SY and Friml, Jiří}, issn = {1477-9137}, journal = {Journal of Cell Science}, number = {15}, publisher = {The Company of Biologists}, title = {{Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis}}, doi = {10.1242/jcs.248062}, volume = {133}, year = {2020}, } @article{9160, abstract = {Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.}, author = {Semeradova, Hana and Montesinos López, Juan C and Benková, Eva}, issn = {2590-3462}, journal = {Plant Communications}, number = {3}, publisher = {Elsevier}, title = {{All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways}}, doi = {10.1016/j.xplc.2020.100048}, volume = {1}, year = {2020}, } @article{10354, abstract = {Background ESCRT-III is a membrane remodelling filament with the unique ability to cut membranes from the inside of the membrane neck. It is essential for the final stage of cell division, the formation of vesicles, the release of viruses, and membrane repair. Distinct from other cytoskeletal filaments, ESCRT-III filaments do not consume energy themselves, but work in conjunction with another ATP-consuming complex. Despite rapid progress in describing the cell biology of ESCRT-III, we lack an understanding of the physical mechanisms behind its force production and membrane remodelling. Results Here we present a minimal coarse-grained model that captures all the experimentally reported cases of ESCRT-III driven membrane sculpting, including the formation of downward and upward cones and tubules. This model suggests that a change in the geometry of membrane bound ESCRT-III filaments—from a flat spiral to a 3D helix—drives membrane deformation. We then show that such repetitive filament geometry transitions can induce the fission of cargo-containing vesicles. Conclusions Our model provides a general physical mechanism that explains the full range of ESCRT-III-dependent membrane remodelling and scission events observed in cells. This mechanism for filament force production is distinct from the mechanisms described for other cytoskeletal elements discovered so far. The mechanistic principles revealed here suggest new ways of manipulating ESCRT-III-driven processes in cells and could be used to guide the engineering of synthetic membrane-sculpting systems.}, author = {Harker-Kirschneck, Lena and Baum, Buzz and Šarić, Anđela}, issn = {1741-7007}, journal = {BMC Biology}, keywords = {cell biology}, number = {1}, publisher = {Springer Nature}, title = {{Changes in ESCRT-III filament geometry drive membrane remodelling and fission in silico}}, doi = {10.1186/s12915-019-0700-2}, volume = {17}, year = {2019}, } @article{10355, abstract = {The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.}, author = {Hafner, Anne E and Krausser, Johannes and Šarić, Anđela}, issn = {0959-440X}, journal = {Current Opinion in Structural Biology}, keywords = {molecular biology, structural biology}, pages = {43--52}, publisher = {Elsevier}, title = {{Minimal coarse-grained models for molecular self-organisation in biology}}, doi = {10.1016/j.sbi.2019.05.018}, volume = {58}, year = {2019}, } @article{10621, abstract = {Twisted bilayer graphene has recently emerged as a platform for hosting correlated phenomena. For twist angles near θ ≈ 1.1°, the low-energy electronic structure of twisted bilayer graphene features isolated bands with a flat dispersion1,2. Recent experiments have observed a variety of low-temperature phases that appear to be driven by electron interactions, including insulating states, superconductivity and magnetism3,4,5,6. Here we report electrical transport measurements up to room temperature for twist angles varying between 0.75° and 2°. We find that the resistivity, ρ, scales linearly with temperature, T, over a wide range of T before falling again owing to interband activation. The T-linear response is much larger than observed in monolayer graphene for all measured devices, and in particular increases by more than three orders of magnitude in the range where the flat band exists. Our results point to the dominant role of electron–phonon scattering in twisted bilayer graphene, with possible implications for the origin of the observed superconductivity.}, author = {Polshyn, Hryhoriy and Yankowitz, Matthew and Chen, Shaowen and Zhang, Yuxuan and Watanabe, K. and Taniguchi, T. and Dean, Cory R. and Young, Andrea F.}, issn = {1745-2481}, journal = {Nature Physics}, keywords = {general physics and astronomy}, number = {10}, pages = {1011--1016}, publisher = {Springer Nature}, title = {{Large linear-in-temperature resistivity in twisted bilayer graphene}}, doi = {10.1038/s41567-019-0596-3}, volume = {15}, year = {2019}, } @article{10622, abstract = {We demonstrate a method for manipulating small ensembles of vortices in multiply connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux through the superconducting structure. By scanning the tip over the surface of the device and by utilizing the dynamical coupling between the vortices and the cantilever, a high-resolution spatial map of the different vortex configurations is obtained. Moving the tip to a particular location in the map stabilizes a distinct multivortex configuration. Thus, the scanning of the tip over a particular trajectory in space permits nontrivial operations to be performed, such as braiding of individual vortices within a larger vortex ensemble—a key capability required by many proposals for topological quantum computing.}, author = {Polshyn, Hryhoriy and Naibert, Tyler and Budakian, Raffi}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {mechanical engineering, condensed matter physics, general materials science, general chemistry, bioengineering}, number = {8}, pages = {5476--5482}, publisher = {American Chemical Society}, title = {{Manipulating multivortex states in superconducting structures}}, doi = {10.1021/acs.nanolett.9b01983}, volume = {19}, year = {2019}, } @article{10625, abstract = {The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures.}, author = {Yankowitz, Matthew and Chen, Shaowen and Polshyn, Hryhoriy and Zhang, Yuxuan and Watanabe, K. and Taniguchi, T. and Graf, David and Young, Andrea F. and Dean, Cory R.}, issn = {1095-9203}, journal = {Science}, keywords = {multidisciplinary}, number = {6431}, pages = {1059--1064}, publisher = {American Association for the Advancement of Science (AAAS)}, title = {{Tuning superconductivity in twisted bilayer graphene}}, doi = {10.1126/science.aav1910}, volume = {363}, year = {2019}, } @article{10664, abstract = {Since the discovery of correlated insulators and superconductivity in magic-angle twisted bilayer graphene (tBLG) ([1, 2], JCCM April 2018), theorists have been excitedly pursuing the alluring mix of band topology, symmetry breaking, Mott insulators and superconductivity at play, as well as the potential relation (if any) to high-Tc physics. Now a new stream of experimental work is arriving which further enriches the story. To briefly recap Episodes 1 and 2 (JCCM April and November 2018), when two graphene layers are stacked with a small rotational mismatch θ, the resulting long-wavelength moire pattern leads to a superlattice potential which reconstructs the low energy band structure. When θ approaches the “magic-angle” θM ∼ 1 ◦, the band structure features eight nearly-flat bands which fill when the electron number per moire unit cell, n/n0, lies between −4 < n/n0 < 4. The bands can be counted as 8 = 2 × 2 × 2: for each spin (2×) and valley (2×) characteristic of monolayergraphene, tBLG has has 2× flat bands which cross at mini-Dirac points.}, author = {Yankowitz, Mathew and Chen, Shaowen and Polshyn, Hryhoriy and Watanabe, K. and Taniguchi, T. and Graf, David and Young, Andrea F. and Dean, Cory R. and Sharpe, Aaron L. and Fox, E.J. and Barnard, A.W. and Finney, Joe}, journal = {Journal Club for Condensed Matter Physics}, publisher = {Simons Foundation ; University of California, Riverside}, title = {{New correlated phenomena in magic-angle twisted bilayer graphene/s}}, doi = {10.36471/jccm_february_2019_03}, volume = {03}, year = {2019}, } @article{10619, abstract = {The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory.}, author = {Serlin, M. and Tschirhart, C. L. and Polshyn, Hryhoriy and Zhang, Y. and Zhu, J. and Watanabe, K. and Taniguchi, T. and Balents, L. and Young, A. F.}, issn = {1095-9203}, journal = {Science}, keywords = {multidisciplinary}, number = {6480}, pages = {900--903}, publisher = {American Association for the Advancement of Science}, title = {{Intrinsic quantized anomalous Hall effect in a moiré heterostructure}}, doi = {10.1126/science.aay5533}, volume = {367}, year = {2019}, } @inproceedings{10724, abstract = {Twisted bilayer graphene (tBLG) near the flat band condition is a versatile new platform for the study of correlated physics in 2D. Resistive states have been observed at several commensurate fillings of the flat miniband, along with superconducting states near half filling. To better understand the electronic structure of this system, we study electronic transport of graphite gated superconducting tBLG devices in the normal regime. At high magnetic fields, we observe full lifting of the spin and valley degeneracy. The transitions in the splitting of this four-fold degeneracy as a function of carrier density indicate Landau level (LL) crossings, which tilted field measurements show occur between LLs with different valley polarization. Similar LL structure measured in two devices, one with twist angle θ=1.08° at ambient pressure and one at θ=1.27° and 1.33GPa, suggests that the dimensionless combination of twist angle and interlayer coupling controls the relevant details of the band structure. In addition, we find that the temperature dependence of the resistance at B=0 shows linear growth at several hundred Ohm/K in a broad range of temperatures. We discuss the implications for modeling the scattering processes in this system.}, author = {Polshyn, Hryhoriy and Zhang, Yuxuan and Yankowitz, Matthew and Chen, Shaowen and Taniguchi, Takashi and Watanabe, Kenji and Graf, David E. and Dean, Cory R. and Young, Andrea}, booktitle = {APS March Meeting 2019}, issn = {0003-0503}, location = {Boston, MA, United States}, number = {2}, publisher = {American Physical Society}, title = {{Normal state transport in superconducting twisted bilayer graphene}}, volume = {64}, year = {2019}, } @inproceedings{10722, abstract = {Bilayer graphene, rotationally faulted to ~1.1 degree misalignment, has recently been shown to host superconducting and resistive states associated with the formation of a flat electronic band. While numerous theories exist for the origins of both states, direct validation of these theories remains an outstanding experimental problem. Here, we focus on the resistive states occurring at commensurate filling (1/2, 1/4, and 3/4) of the two lowest superlattice bands. We test theoretical proposals that these states arise due to broken spin—and/or valley—symmetry by performing direct magnetic imaging with nanoscale SQUID-on-tip microscopy. This technique provides single-spin resolved magnetometry on sub-100nm length scales. I will present imaging data from our 4.2K nSOT microscope on graphite-gated twisted bilayers near the flat band condition and discuss the implications for the physics of the commensurate resistive states.}, author = {Serlin, Marec and Tschirhart, Charles and Polshyn, Hryhoriy and Zhu, Jiacheng and Huber, Martin E. and Young, Andrea}, booktitle = {APS March Meeting 2019}, issn = {0003-0503}, location = {Boston, MA, United States}, number = {2}, publisher = {American Physical Society}, title = {{Direct Imaging of magnetic structure in twisted bilayer graphene with scanning nanoSQUID-On-Tip microscopy}}, volume = {64}, year = {2019}, } @inproceedings{10725, abstract = {Bilayer graphene with ~ 1.1 degrees twist mismatch between the layers hosts a low energy flat band in which the Coulomb interaction is large relative to the bandwidth, promoting correlated insulating states at half band filling, and superconducting (SC) phases with dome-like structure neighboring correlated insulating states. Here we show measurements of a dual-graphite-gated twisted bilayer graphene device, which minimizes charge inhomogeneity. We observe new correlated phases, including for the first time a SC pocket near half-filling of the electron-doped band and resistive states at quarter-filling of both bands that emerge in a magnetic field. Changing the layer polarization with vertical electric field reveals an unexpected competition between SC and correlated insulator phases, which we interpret to result from differences in disorder of each graphene layer and underscores the spatial inhomogeneity like twist angle as a significant source of disorder in these devices [1].}, author = {Chen, Shaowen and Yankowitz, Matthew and Polshyn, Hryhoriy and Watanabe, Kenji and Taniguchi, Takashi and Graf, David E. and Young, Andrea and Dean, Cory R.}, booktitle = {APS March Meeting 2019}, issn = {0003-0503}, location = {Boston, MA, United States}, number = {2}, publisher = {American Physical Society}, title = {{Correlated insulating and superconducting phases in twisted bilayer graphene}}, volume = {64}, year = {2019}, } @inproceedings{10723, abstract = {In monolayer graphene, the interplay of electronic correlations with the internal spin- and valley- degrees of freedom leads to a complex phase diagram of isospin symmetry breaking at high magnetic fields. Recently, Wei et al. (Science (2018)) demonstrated that spin waves can be electrically generated and detected in graphene heterojunctions, allowing direct experiment access to the spin degree of freedom. Here, we apply this technique to high quality graphite-gated graphene devices showing robust fractional quantum Hall phases and isospin phase transitions. We use an edgeless Corbino geometry to eliminate the contributions of edge states to the spin-wave mediated nonlocal voltage, allowing unambiguous identification of spin wave transport signatures. Our data reveal two phases within the ν = 1 plateau. For exactly ν=1, charge is localized but spin waves propagate freely while small carrier doping completely quenches the low-energy spin-wave transport, even as those charges remain localized. We identify this new phase as a spin textured electron solid. We also find that spin-wave transport is modulated by phase transitions in the valley order that preserve spin polarization, suggesting that this technique is sensitive to both spin and valley order.}, author = {Zhou, Haoxin and Polshyn, Hryhoriy and Tanaguchi, Takashi and Watanabe, Kenji and Young, Andrea}, booktitle = {APS March Meeting 2019}, issn = {0003-0503}, location = {Boston, MA, United States}, number = {2}, publisher = {American Physical Society}, title = {{Spin wave transport through electron solids and fractional quantum Hall liquids in graphene}}, volume = {64}, year = {2019}, } @inproceedings{10877, abstract = {This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with piecewise constant dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been applied to solve five different benchmark problems in the category for piecewise constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL. Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results probably provide the most complete assessment of tools for the safety verification of continuous and hybrid systems with piecewise constant dynamics up to this date.}, author = {Frehse, Goran and Abate, Alessandro and Adzkiya, Dieky and Becchi, Anna and Bu, Lei and Cimatti, Alessandro and Giacobbe, Mirco and Griggio, Alberto and Mover, Sergio and Mufid, Muhammad Syifa'ul and Riouak, Idriss and Tonetta, Stefano and Zaffanella, Enea}, booktitle = {ARCH19. 6th International Workshop on Applied Verification of Continuous and Hybrid Systems}, editor = {Frehse, Goran and Althoff, Matthias}, issn = {2398-7340}, location = {Montreal, Canada}, pages = {1--13}, publisher = {EasyChair}, title = {{ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics}}, doi = {10.29007/rjwn}, volume = {61}, year = {2019}, } @article{11061, abstract = {Many adult tissues contain postmitotic cells as old as the host organism. The only organelle that does not turn over in these cells is the nucleus, and its maintenance represents a formidable challenge, as it harbors regulatory proteins that persist throughout adulthood. Here we developed strategies to visualize two classes of such long-lived proteins, histones and nucleoporins, to understand the function of protein longevity in nuclear maintenance. Genome-wide mapping of histones revealed specific enrichment of long-lived variants at silent gene loci. Interestingly, nuclear pores are maintained by piecemeal replacement of subunits, resulting in mosaic complexes composed of polypeptides with vastly different ages. In contrast, nondividing quiescent cells remove old nuclear pores in an ESCRT-dependent manner. Our findings reveal distinct molecular strategies of nuclear maintenance, linking lifelong protein persistence to gene regulation and nuclear integrity.}, author = {Toyama, Brandon H. and Arrojo e Drigo, Rafael and Lev-Ram, Varda and Ramachandra, Ranjan and Deerinck, Thomas J. and Lechene, Claude and Ellisman, Mark H. and HETZER, Martin W}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {2}, pages = {433--444}, publisher = {Rockefeller University Press}, title = {{Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells}}, doi = {10.1083/jcb.201809123}, volume = {218}, year = {2019}, } @article{11062, abstract = {Most neurons are not replaced during an animal’s lifetime. This nondividing state is characterized by extreme longevity and age-dependent decline of key regulatory proteins. To study the lifespans of cells and proteins in adult tissues, we combined isotope labeling of mice with a hybrid imaging method (MIMS-EM). Using 15N mapping, we show that liver and pancreas are composed of cells with vastly different ages, many as old as the animal. Strikingly, we also found that a subset of fibroblasts and endothelial cells, both known for their replicative potential, are characterized by the absence of cell division during adulthood. In addition, we show that the primary cilia of beta cells and neurons contains different structural regions with vastly different lifespans. Based on these results, we propose that age mosaicism across multiple scales is a fundamental principle of adult tissue, cell, and protein complex organization.}, author = {Arrojo e Drigo, Rafael and Lev-Ram, Varda and Tyagi, Swati and Ramachandra, Ranjan and Deerinck, Thomas and Bushong, Eric and Phan, Sebastien and Orphan, Victoria and Lechene, Claude and Ellisman, Mark H. and HETZER, Martin W}, issn = {1550-4131}, journal = {Cell Metabolism}, keywords = {Cell Biology, Molecular Biology, Physiology}, number = {2}, pages = {343--351.e3}, publisher = {Elsevier}, title = {{Age mosaicism across multiple scales in adult tissues}}, doi = {10.1016/j.cmet.2019.05.010}, volume = {30}, year = {2019}, } @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{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}, } @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{11517, abstract = {To understand star formation in galaxies, we investigate the star formation rate (SFR) surface density (ΣSFR) profiles for galaxies, based on a well-defined sample of 976 star-forming MaNGA galaxies. We find that the typical ΣSFR profiles within 1.5Re of normal SF galaxies can be well described by an exponential function for different stellar mass intervals, while the sSFR profile shows positive gradients, especially for more massive SF galaxies. This is due to the more pronounced central cores or bulges rather than the onset of a `quenching' process. While galaxies that lie significantly above (or below) the star formation main sequence (SFMS) show overall an elevation (or suppression) of ΣSFR at all radii, this central elevation (or suppression) is more pronounced in more massive galaxies. The degree of central enhancement and suppression is quite symmetric, suggesting that both the elevation and suppression of star formation are following the same physical processes. Furthermore, we find that the dispersion in ΣSFR within and across the population is found to be tightly correlated with the inferred gas depletion time, whether based on the stellar surface mass density or the orbital dynamical time. This suggests that we are seeing the response of a simple gas-regulator system to variations in the accretion rate. This is explored using a heuristic model that can quantitatively explain the dependence of σ(ΣSFR) on gas depletion timescale. Variations in accretion rate are progressively more damped out in regions of low star-formation efficiency leading to a reduced amplitude of variations in star-formation.}, author = {Wang, Enci and Lilly, Simon J. and Pezzulli, Gabriele and Matthee, Jorryt J}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {IOP Publishing}, title = {{On the elevation and suppression of star formation within galaxies}}, doi = {10.3847/1538-4357/ab1c5b}, volume = {877}, year = {2019}, } @article{11535, abstract = {We investigate the clustering and halo properties of ∼5000 Ly α-selected emission-line galaxies (LAEs) from the Slicing COSMOS 4K (SC4K) and from archival NB497 imaging of SA22 split in 15 discrete redshift slices between z ∼ 2.5 and 6. We measure clustering lengths of r0 ∼ 3–6 h−1 Mpc and typical halo masses of ∼1011 M⊙ for our narrowband-selected LAEs with typical LLy α ∼ 1042–43 erg s−1. The intermediate-band-selected LAEs are observed to have r0 ∼ 3.5–15 h−1 Mpc with typical halo masses of ∼1011–12 M⊙ and typical LLy α ∼ 1043–43.6 erg s−1. We find a strong, redshift-independent correlation between halo mass and Ly α luminosity normalized by the characteristic Ly α luminosity, L⋆(z). The faintest LAEs (L ∼ 0.1 L⋆(z)) typically identified by deep narrowband surveys are found in 1010 M⊙ haloes and the brightest LAEs (L ∼ 7 L⋆(z)) are found in ∼5 × 1012 M⊙ haloes. A dependency on the rest-frame 1500 Å UV luminosity, MUV, is also observed where the halo masses increase from 1011 to 1013 M⊙ for MUV ∼ −19 to −23.5 mag. Halo mass is also observed to increase from 109.8 to 1012 M⊙ for dust-corrected UV star formation rates from ∼0.6 to 10 M⊙ yr−1 and continues to increase up to 1013 M⊙ in halo mass, where the majority of those sources are active galactic nuclei. All the trends we observe are found to be redshift independent. Our results reveal that LAEs are the likely progenitors of a wide range of galaxies depending on their luminosity, from dwarf-like, to Milky Way-type, to bright cluster galaxies. LAEs therefore provide unique insight into the early formation and evolution of the galaxies we observe in the local Universe.}, author = {Khostovan, A A and Sobral, D and Mobasher, B and Matthee, Jorryt J and Cochrane, R K and Chartab, N and Jafariyazani, M and Paulino-Afonso, A and Santos, S and Calhau, J}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, galaxies: evolution, galaxies: haloes, galaxies: high-redshift, galaxies: star formation, cosmology: observations, large-scale structure of Universe}, number = {1}, pages = {555--573}, publisher = {Oxford University Press}, title = {{The clustering of typical Ly α emitters from z ∼ 2.5–6: Host halo masses depend on Ly α and UV luminosities}}, doi = {10.1093/mnras/stz2149}, volume = {489}, year = {2019}, } @article{11541, abstract = {We present new Hubble Space Telescope (HST)/WFC3 observations and re-analyse VLT data to unveil the continuum, variability, and rest-frame ultraviolet (UV) lines of the multiple UV clumps of the most luminous Lyα emitter at z = 6.6, CR7 (COSMOS Redshift 7). Our re-reduced, flux-calibrated X-SHOOTER spectra of CR7 reveal an He II emission line in observations obtained along the major axis of Lyα emission with the best seeing conditions. He II is spatially offset by ≈+0.8 arcsec from the peak of Lyα emission, and it is found towards clump B. Our WFC3 grism spectra detects the UV continuum of CR7’s clump A, yielding a power law with β=−2.5+0.6−0.7 and MUV=−21.87+0.25−0.20⁠. No significant variability is found for any of the UV clumps on their own, but there is tentative (≈2.2 σ) brightening of CR7 in F110W as a whole from 2012 to 2017. HST grism data fail to robustly detect rest-frame UV lines in any of the clumps, implying fluxes ≲2×10−17 erg s−1 cm−2 (3σ). We perform CLOUDY modelling to constrain the metallicity and the ionizing nature of CR7. CR7 seems to be actively forming stars without any clear active galactic nucleus activity in clump A, consistent with a metallicity of ∼0.05–0.2 Z⊙. Component C or an interclump component between B and C may host a high ionization source. Our results highlight the need for spatially resolved information to study the formation and assembly of early galaxies.}, author = {Sobral, David and Matthee, Jorryt J and Brammer, Gabriel and Ferrara, Andrea and Alegre, Lara and Röttgering, Huub and Schaerer, Daniel and Mobasher, Bahram and Darvish, Behnam}, 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, cosmology: observations, dark ages, reionization, first stars, early Universe}, number = {2}, pages = {2422--2441}, publisher = {Oxford University Press}, title = {{On the nature and physical conditions of the luminous Ly α emitter CR7 and its rest-frame UV components}}, doi = {10.1093/mnras/sty2779}, volume = {482}, year = {2019}, } @article{11540, abstract = {Observations have revealed that the star formation rate (SFR) and stellar mass (Mstar) of star-forming galaxies follow a tight relation known as the galaxy main sequence. However, what physical information is encoded in this relation is under debate. Here, we use the EAGLE cosmological hydrodynamical simulation to study the mass dependence, evolution, and origin of scatter in the SFR–Mstar relation. At z = 0, we find that the scatter decreases slightly with stellar mass from 0.35 dex at Mstar ≈ 109 M⊙ to 0.30 dex at Mstar ≳ 1010.5 M⊙. The scatter decreases from z = 0 to z = 5 by 0.05 dex at Mstar ≳ 1010 M⊙ and by 0.15 dex for lower masses. We show that the scatter at z = 0.1 originates from a combination of fluctuations on short time-scales (ranging from 0.2–2 Gyr) that are presumably associated with self-regulation from cooling, star formation, and outflows, but is dominated by long time-scale (∼10 Gyr) variations related to differences in halo formation times. Shorter time-scale fluctuations are relatively more important for lower mass galaxies. At high masses, differences in black hole formation efficiency cause additional scatter, but also diminish the scatter caused by different halo formation times. While individual galaxies cross the main sequence multiple times during their evolution, they fluctuate around tracks associated with their halo properties, i.e. galaxies above/below the main sequence at z = 0.1 tend to have been above/below the main sequence for ≫1 Gyr.}, author = {Matthee, Jorryt J and Schaye, Joop}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics : galaxies: evolution, galaxies: formation, galaxies: star formation, cosmology: theory}, number = {1}, pages = {915--932}, publisher = {Oxford University Press}, title = {{The origin of scatter in the star formation rate–stellar mass relation}}, doi = {10.1093/mnras/stz030}, volume = {484}, year = {2019}, } @article{11616, abstract = {We present the discovery of HD 221416 b, the first transiting planet identified by the Transiting Exoplanet Survey Satellite (TESS) for which asteroseismology of the host star is possible. HD 221416 b (HIP 116158, TOI-197) is a bright (V = 8.2 mag), spectroscopically classified subgiant that oscillates with an average frequency of about 430 μHz and displays a clear signature of mixed modes. The oscillation amplitude confirms that the redder TESS bandpass compared to Kepler has a small effect on the oscillations, supporting the expected yield of thousands of solar-like oscillators with TESS 2 minute cadence observations. Asteroseismic modeling yields a robust determination of the host star radius (R⋆ = 2.943 ± 0.064 R⊙), mass (M⋆ = 1.212 ± 0.074 M⊙), and age (4.9 ± 1.1 Gyr), and demonstrates that it has just started ascending the red-giant branch. Combining asteroseismology with transit modeling and radial-velocity observations, we show that the planet is a "hot Saturn" (Rp = 9.17 ± 0.33 R⊕) with an orbital period of ∼14.3 days, irradiance of F = 343 ± 24 F⊕, and moderate mass (Mp = 60.5 ± 5.7 M⊕) and density (ρp = 0.431 ± 0.062 g cm−3). The properties of HD 221416 b show that the host-star metallicity–planet mass correlation found in sub-Saturns (4–8 R⊕) does not extend to larger radii, indicating that planets in the transition between sub-Saturns and Jupiters follow a relatively narrow range of densities. With a density measured to ∼15%, HD 221416 b is one of the best characterized Saturn-size planets to date, augmenting the small number of known transiting planets around evolved stars and demonstrating the power of TESS to characterize exoplanets and their host stars using asteroseismology.}, author = {Huber, Daniel and Chaplin, William J. and Chontos, Ashley and Kjeldsen, Hans and Christensen-Dalsgaard, Jørgen and Bedding, Timothy R. and Ball, Warrick and Brahm, Rafael and Espinoza, Nestor and Henning, Thomas and Jordán, Andrés and Sarkis, Paula and Knudstrup, Emil and Albrecht, Simon and Grundahl, Frank and Andersen, Mads Fredslund and Pallé, Pere L. and Crossfield, Ian and Fulton, Benjamin and Howard, Andrew W. and Isaacson, Howard T. and Weiss, Lauren M. and Handberg, Rasmus and Lund, Mikkel N. and Serenelli, Aldo M. and Rørsted Mosumgaard, Jakob and Stokholm, Amalie and Bieryla, Allyson and Buchhave, Lars A. and Latham, David W. and Quinn, Samuel N. and Gaidos, Eric and Hirano, Teruyuki and Ricker, George R. and Vanderspek, Roland K. and Seager, Sara and Jenkins, Jon M. and Winn, Joshua N. and Antia, H. M. and Appourchaux, Thierry and Basu, Sarbani and Bell, Keaton J. and Benomar, Othman and Bonanno, Alfio and Buzasi, Derek L. and Campante, Tiago L. and Çelik Orhan, Z. and Corsaro, Enrico and Cunha, Margarida S. and Davies, Guy R. and Deheuvels, Sebastien and Grunblatt, Samuel K. and Hasanzadeh, Amir and Di Mauro, Maria Pia and A. García, Rafael and Gaulme, Patrick and Girardi, Léo and Guzik, Joyce A. and Hon, Marc and Jiang, Chen and Kallinger, Thomas and Kawaler, Steven D. and Kuszlewicz, James S. and Lebreton, Yveline and Li, Tanda and Lucas, Miles and Lundkvist, Mia S. and Mann, Andrew W. and Mathis, Stéphane and Mathur, Savita and Mazumdar, Anwesh and Metcalfe, Travis S. and Miglio, Andrea and F. G. Monteiro, Mário J. P. and Mosser, Benoit and Noll, Anthony and Nsamba, Benard and Joel Ong, Jia Mian and Örtel, S. and Pereira, Filipe and Ranadive, Pritesh and Régulo, Clara and Rodrigues, Thaíse S. and Roxburgh, Ian W. and Aguirre, Victor Silva and Smalley, Barry and Schofield, Mathew and Sousa, Sérgio G. and Stassun, Keivan G. and Stello, Dennis and Tayar, Jamie and White, Timothy R. and Verma, Kuldeep and Vrard, Mathieu and Yıldız, M. and Baker, David and Bazot, Michaël and Beichmann, Charles and Bergmann, Christoph and Bugnet, Lisa Annabelle and Cale, Bryson and Carlino, Roberto and Cartwright, Scott M. and Christiansen, Jessie L. and Ciardi, David R. and Creevey, Orlagh and Dittmann, Jason A. and Nascimento, Jose-Dias Do and Eylen, Vincent Van and Fürész, Gabor and Gagné, Jonathan and Gao, Peter and Gazeas, Kosmas and Giddens, Frank and Hall, Oliver J. and Hekker, Saskia and Ireland, Michael J. and Latouf, Natasha and LeBrun, Danny and Levine, Alan M. and Matzko, William and Natinsky, Eva and Page, Emma and Plavchan, Peter and Mansouri-Samani, Masoud and McCauliff, Sean and Mullally, Susan E. and Orenstein, Brendan and Soto, Aylin Garcia and Paegert, Martin and van Saders, Jennifer L. and Schnaible, Chloe and Soderblom, David R. and Szabó, Róbert and Tanner, Angelle and Tinney, C. G. and Teske, Johanna and Thomas, Alexandra and Trampedach, Regner and Wright, Duncan and Yuan, Thomas T. and Zohrabi, Farzaneh}, issn = {0004-6256}, journal = {The Astronomical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {6}, publisher = {IOP Publishing}, title = {{A hot Saturn orbiting an oscillating late subgiant discovered by TESS}}, doi = {10.3847/1538-3881/ab1488}, volume = {157}, year = {2019}, } @article{11613, abstract = {Over 2,000 stars were observed for 1 month with a high enough cadence in order to look for acoustic modes during the survey phase of the Kepler mission. Solar-like oscillations have been detected in about 540 stars. The question of why no oscillations were detected in the remaining stars is still open. Previous works explained the non-detection of modes with the high level of magnetic activity of the stars. However, the sample of stars studied contained some classical pulsators and red giants that could have biased the results. In this work, we revisit this analysis on a cleaner sample of main-sequence solar-like stars that consists of 1,014 stars. First we compute the predicted amplitude of the modes of that sample and for the stars with detected oscillation and compare it to the noise at high frequency in the power spectrum. We find that the stars with detected modes have an amplitude to noise ratio larger than 0.94. We measure reliable rotation periods and the associated photometric magnetic index for 684 stars out of the full sample and in particular for 323 stars where the amplitude of the modes is predicted to be high enough to be detected. We find that among these 323 stars 32% of them have a level of magnetic activity larger than the Sun during its maximum activity, explaining the non-detection of acoustic modes. Interestingly, magnetic activity cannot be the primary reason responsible for the absence of detectable modes in the remaining 68% of the stars without acoustic modes detected and with reliable rotation periods. Thus, we investigate metallicity, inclination angle of the rotation axis, and binarity as possible causes of low mode amplitudes. Using spectroscopic observations for a subsample, we find that a low metallicity could be the reason for suppressed modes. No clear correlation with binarity nor inclination is found. We also derive the lower limit for our photometric activity index (of 20–30 ppm) below which rotation and magnetic activity are not detected. Finally, with our analysis we conclude that stars with a photometric activity index larger than 2,000 ppm have 98.3% probability of not having oscillations detected.}, author = {Mathur, Savita and García, Rafael A. and Bugnet, Lisa Annabelle and Santos, Ângela R.G. and Santiago, Netsha and Beck, Paul G.}, issn = {2296-987X}, journal = {Frontiers in Astronomy and Space Sciences}, keywords = {Astronomy and Astrophysics}, publisher = {Frontiers Media}, title = {{Revisiting the impact of stellar magnetic activity on the detectability of solar-like oscillations by Kepler}}, doi = {10.3389/fspas.2019.00046}, volume = {6}, year = {2019}, } @article{11615, abstract = {The recently published Kepler mission Data Release 25 (DR25) reported on ∼197 000 targets observed during the mission. Despite this, no wide search for red giants showing solar-like oscillations have been made across all stars observed in Kepler’s long-cadence mode. In this work, we perform this task using custom apertures on the Kepler pixel files and detect oscillations in 21 914 stars, representing the largest sample of solar-like oscillating stars to date. We measure their frequency at maximum power, νmax, down to νmax≃4μHz and obtain log (g) estimates with a typical uncertainty below 0.05 dex, which is superior to typical measurements from spectroscopy. Additionally, the νmax distribution of our detections show good agreement with results from a simulated model of the Milky Way, with a ratio of observed to predicted stars of 0.992 for stars with 10<νmax<270μHz. Among our red giant detections, we find 909 to be dwarf/subgiant stars whose flux signal is polluted by a neighbouring giant as a result of using larger photometric apertures than those used by the NASA Kepler science processing pipeline. We further find that only 293 of the polluting giants are known Kepler targets. The remainder comprises over 600 newly identified oscillating red giants, with many expected to belong to the Galactic halo, serendipitously falling within the Kepler pixel files of targeted stars.}, author = {Hon, Marc and Stello, Dennis and García, Rafael A and Mathur, Savita and Sharma, Sanjib and Colman, Isabel L and Bugnet, Lisa Annabelle}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, asteroseismology, methods: data analysis, techniques: image processing, stars: oscillations, stars: statistics}, number = {4}, pages = {5616--5630}, publisher = {Oxford University Press}, title = {{A search for red giant solar-like oscillations in all Kepler data}}, doi = {10.1093/mnras/stz622}, volume = {485}, year = {2019}, } @article{11614, abstract = {The NASA Transiting Exoplanet Survey Satellite (TESS) is about to provide full-frame images of almost the entire sky. The amount of stellar data to be analysed represents hundreds of millions stars, which is several orders of magnitude more than the number of stars observed by the Convection, Rotation and planetary Transits satellite (CoRoT), and NASA Kepler and K2 missions. We aim at automatically classifying the newly observed stars with near real-time algorithms to better guide the subsequent detailed studies. In this paper, we present a classification algorithm built to recognise solar-like pulsators among classical pulsators. This algorithm relies on the global amount of power contained in the power spectral density (PSD), also known as the flicker in spectral power density (FliPer). Because each type of pulsating star has a characteristic background or pulsation pattern, the shape of the PSD at different frequencies can be used to characterise the type of pulsating star. The FliPer classifier (FliPerClass) uses different FliPer parameters along with the effective temperature as input parameters to feed a ML algorithm in order to automatically classify the pulsating stars observed by TESS. Using noisy TESS-simulated data from the TESS Asteroseismic Science Consortium (TASC), we classify pulsators with a 98% accuracy. Among them, solar-like pulsating stars are recognised with a 99% accuracy, which is of great interest for a further seismic analysis of these stars, which are like our Sun. Similar results are obtained when we trained our classifier and applied it to 27-day subsets of real Kepler data. FliPerClass is part of the large TASC classification pipeline developed by the TESS Data for Asteroseismology (T’DA) classification working group.}, author = {Bugnet, Lisa Annabelle and García, R. A. and Mathur, S. and Davies, G. R. and Hall, O. J. and Lund, M. N. and Rendle, B. M.}, issn = {1432-0746}, journal = {Astronomy & Astrophysics}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, publisher = {EDP Science}, title = {{FliPerClass: In search of solar-like pulsators among TESS targets}}, doi = {10.1051/0004-6361/201834780}, volume = {624}, year = {2019}, } @article{11623, abstract = {Brightness variations due to dark spots on the stellar surface encode information about stellar surface rotation and magnetic activity. In this work, we analyze the Kepler long-cadence data of 26,521 main-sequence stars of spectral types M and K in order to measure their surface rotation and photometric activity level. Rotation-period estimates are obtained by the combination of a wavelet analysis and autocorrelation function of the light curves. Reliable rotation estimates are determined by comparing the results from the different rotation diagnostics and four data sets. We also measure the photometric activity proxy Sph using the amplitude of the flux variations on an appropriate timescale. We report rotation periods and photometric activity proxies for about 60% of the sample, including 4431 targets for which McQuillan et al. did not report a rotation period. For the common targets with rotation estimates in this study and in McQuillan et al., our rotation periods agree within 99%. In this work, we also identify potential polluters, such as misclassified red giants and classical pulsator candidates. Within the parameter range we study, there is a mild tendency for hotter stars to have shorter rotation periods. The photometric activity proxy spans a wider range of values with increasing effective temperature. The rotation period and photometric activity proxy are also related, with Sph being larger for fast rotators. Similar to McQuillan et al., we find a bimodal distribution of rotation periods.}, author = {Santos, A. R. G. and García, R. A. and Mathur, S. and Bugnet, Lisa Annabelle and van Saders, J. L. and Metcalfe, T. S. and Simonian, G. V. A. and Pinsonneault, M. H.}, issn = {0067-0049}, journal = {The Astrophysical Journal Supplement Series}, keywords = {Space and Planetary Science, Astronomy and Astrophysics, methods: data analysis, stars: activity, stars: low-mass, stars: rotation, starspots, techniques: photometric}, number = {1}, publisher = {IOP Publishing}, title = {{Surface rotation and photometric activity for Kepler targets. I. M and K main-sequence stars}}, doi = {10.3847/1538-4365/ab3b56}, volume = {244}, year = {2019}, } @unpublished{11627, abstract = {For a solar-like star, the surface rotation evolves with time, allowing in principle to estimate the age of a star from its surface rotation period. Here we are interested in measuring surface rotation periods of solar-like stars observed by the NASA mission Kepler. Different methods have been developed to track rotation signals in Kepler photometric light curves: time-frequency analysis based on wavelet techniques, autocorrelation and composite spectrum. We use the learning abilities of random forest classifiers to take decisions during two crucial steps of the analysis. First, given some input parameters, we discriminate the considered Kepler targets between rotating MS stars, non-rotating MS stars, red giants, binaries and pulsators. We then use a second classifier only on the MS rotating targets to decide the best data analysis treatment.}, author = {Breton, S. N. and Bugnet, Lisa Annabelle and Santos, A. R. G. and Saux, A. Le and Mathur, S. and Palle, P. L. and Garcia, R. A.}, booktitle = {arXiv}, keywords = {asteroseismology, rotation, solar-like stars, kepler, machine learning, random forest}, title = {{Determining surface rotation periods of solar-like stars observed by the Kepler mission using machine learning techniques}}, doi = {10.48550/arXiv.1906.09609}, year = {2019}, } @unpublished{11630, abstract = {The second mission of NASA’s Kepler satellite, K2, has collected hundreds of thousands of lightcurves for stars close to the ecliptic plane. This new sample could increase the number of known pulsating stars and then improve our understanding of those stars. For the moment only a few stars have been properly classified and published. In this work, we present a method to automaticly classify K2 pulsating stars using a Machine Learning technique called Random Forest. The objective is to sort out the stars in four classes: red giant (RG), main-sequence Solar-like stars (SL), classical pulsators (PULS) and Other. To do this we use the effective temperatures and the luminosities of the stars as well as the FliPer features, that measures the amount of power contained in the power spectral density. The classifier now retrieves the right classification for more than 80% of the stars.}, author = {Saux, A. Le and Bugnet, Lisa Annabelle and Mathur, S. and Breton, S. N. and Garcia, R. A.}, booktitle = {arXiv}, keywords = {asteroseismology - methods, data analysis - thecniques, machine learning - stars, oscillations}, title = {{Automatic classification of K2 pulsating stars using machine learning techniques}}, doi = {10.48550/arXiv.1906.09611}, year = {2019}, } @inproceedings{11826, abstract = {The diameter, radius and eccentricities are natural graph parameters. While these problems have been studied extensively, there are no known dynamic algorithms for them beyond the ones that follow from trivial recomputation after each update or from solving dynamic All-Pairs Shortest Paths (APSP), which is very computationally intensive. This is the situation for dynamic approximation algorithms as well, and even if only edge insertions or edge deletions need to be supported. This paper provides a comprehensive study of the dynamic approximation of Diameter, Radius and Eccentricities, providing both conditional lower bounds, and new algorithms whose bounds are optimal under popular hypotheses in fine-grained complexity. Some of the highlights include: - Under popular hardness hypotheses, there can be no significantly better fully dynamic approximation algorithms than recomputing the answer after each update, or maintaining full APSP. - Nearly optimal partially dynamic (incremental/decremental) algorithms can be achieved via efficient reductions to (incremental/decremental) maintenance of Single-Source Shortest Paths. For instance, a nearly (3/2+epsilon)-approximation to Diameter in directed or undirected n-vertex, m-edge graphs can be maintained decrementally in total time m^{1+o(1)}sqrt{n}/epsilon^2. This nearly matches the static 3/2-approximation algorithm for the problem that is known to be conditionally optimal.}, author = {Ancona, Bertie and Henzinger, Monika H and Roditty, Liam and Williams, Virginia Vassilevska and Wein, Nicole}, booktitle = {46th International Colloquium on Automata, Languages, and Programming}, isbn = {978-3-95977-109-2}, issn = {1868-8969}, location = {Patras, Greece}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Algorithms and hardness for diameter in dynamic graphs}}, doi = {10.4230/LIPICS.ICALP.2019.13}, volume = {132}, year = {2019}, } @inproceedings{11850, abstract = {Modern networked systems are increasingly reconfigurable, enabling demand-aware infrastructures whose resources can be adjusted according to the workload they currently serve. Such dynamic adjustments can be exploited to improve network utilization and hence performance, by moving frequently interacting communication partners closer, e.g., collocating them in the same server or datacenter. However, dynamically changing the embedding of workloads is algorithmically challenging: communication patterns are often not known ahead of time, but must be learned. During the learning process, overheads related to unnecessary moves (i.e., re-embeddings) should be minimized. This paper studies a fundamental model which captures the tradeoff between the benefits and costs of dynamically collocating communication partners on l servers, in an online manner. Our main contribution is a distributed online algorithm which is asymptotically almost optimal, i.e., almost matches the lower bound (also derived in this paper) on the competitive ratio of any (distributed or centralized) online algorithm.}, author = {Henzinger, Monika H and Neumann, Stefan and Schmid, Stefan}, booktitle = {SIGMETRICS'19: International Conference on Measurement and Modeling of Computer Systems}, isbn = {978-1-4503-6678-6}, location = {Phoenix, AZ, United States}, pages = {43–44}, publisher = {Association for Computing Machinery}, title = {{Efficient distributed workload (re-)embedding}}, doi = {10.1145/3309697.3331503}, year = {2019}, } @inproceedings{11853, abstract = {We present a deterministic dynamic algorithm for maintaining a (1+ε)f-approximate minimum cost set cover with O(f log(Cn)/ε^2) amortized update time, when the input set system is undergoing element insertions and deletions. Here, n denotes the number of elements, each element appears in at most f sets, and the cost of each set lies in the range [1/C, 1]. Our result, together with that of Gupta~et~al.~[STOC'17], implies that there is a deterministic algorithm for this problem with O(f log(Cn)) amortized update time and O(min(log n, f)) -approximation ratio, which nearly matches the polynomial-time hardness of approximation for minimum set cover in the static setting. Our update time is only O(log (Cn)) away from a trivial lower bound. Prior to our work, the previous best approximation ratio guaranteed by deterministic algorithms was O(f^2), which was due to Bhattacharya~et~al.~[ICALP`15]. In contrast, the only result that guaranteed O(f) -approximation was obtained very recently by Abboud~et~al.~[STOC`19], who designed a dynamic algorithm with (1+ε)f-approximation ratio and O(f^2 log n/ε) amortized update time. Besides the extra O(f) factor in the update time compared to our and Gupta~et~al.'s results, the Abboud~et~al.~algorithm is randomized, and works only when the adversary is oblivious and the sets are unweighted (each set has the same cost). We achieve our result via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. This approach was pursued previously by Bhattacharya~et~al.~and Gupta~et~al., but not in the recent paper by Abboud~et~al. Unlike previous primal-dual algorithms that try to satisfy some local constraints for individual sets at all time, our algorithm basically waits until the dual solution changes significantly globally, and fixes the solution only where the fix is needed.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Nanongkai, Danupon}, booktitle = {60th Annual Symposium on Foundations of Computer Science}, isbn = {978-1-7281-4953-0}, issn = {2575-8454}, location = {Baltimore, MD, United States}, pages = {406--423}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{A new deterministic algorithm for dynamic set cover}}, doi = {10.1109/focs.2019.00033}, year = {2019}, } @inproceedings{11865, abstract = {We present the first sublinear-time algorithm that can compute the edge connectivity λ of a network exactly on distributed message-passing networks (the CONGEST model), as long as the network contains no multi-edge. We present the first sublinear-time algorithm for a distributed message-passing network sto compute its edge connectivity λ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm takes Õ(n1−1/353D1/353+n1−1/706) time to compute λ and a cut of cardinality λ with high probability, where n and D are the number of nodes and the diameter of the network, respectively, and Õ hides polylogarithmic factors. This running time is sublinear in n (i.e. Õ(n1−є)) whenever D is. Previous sublinear-time distributed algorithms can solve this problem either (i) exactly only when λ=O(n1/8−є) [Thurimella PODC’95; Pritchard, Thurimella, ACM Trans. Algorithms’11; Nanongkai, Su, DISC’14] or (ii) approximately [Ghaffari, Kuhn, DISC’13; Nanongkai, Su, DISC’14]. To achieve this we develop and combine several new techniques. First, we design the first distributed algorithm that can compute a k-edge connectivity certificate for any k=O(n1−є) in time Õ(√nk+D). The previous sublinear-time algorithm can do so only when k=o(√n) [Thurimella PODC’95]. In fact, our algorithm can be turned into the first parallel algorithm with polylogarithmic depth and near-linear work. Previous near-linear work algorithms are essentially sequential and previous polylogarithmic-depth algorithms require Ω(mk) work in the worst case (e.g. [Karger, Motwani, STOC’93]). Second, we show that by combining the recent distributed expander decomposition technique of [Chang, Pettie, Zhang, SODA’19] with techniques from the sequential deterministic edge connectivity algorithm of [Kawarabayashi, Thorup, STOC’15], we can decompose the network into a sublinear number of clusters with small average diameter and without any mincut separating a cluster (except the “trivial” ones). This leads to a simplification of the Kawarabayashi-Thorup framework (except that we are randomized while they are deterministic). This might make this framework more useful in other models of computation. Finally, by extending the tree packing technique from [Karger STOC’96], we can find the minimum cut in time proportional to the number of components. As a byproduct of this technique, we obtain an Õ(n)-time algorithm for computing exact minimum cut for weighted graphs.}, author = {Daga, Mohit and Henzinger, Monika H and Nanongkai, Danupon and Saranurak, Thatchaphol}, booktitle = {Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing}, isbn = {978-1-4503-6705-9}, issn = {0737-8017}, location = {Phoenix, AZ, United States}, pages = {343–354}, publisher = {Association for Computing Machinery}, title = {{Distributed edge connectivity in sublinear time}}, doi = {10.1145/3313276.3316346}, year = {2019}, } @inproceedings{11871, abstract = {Many dynamic graph algorithms have an amortized update time, rather than a stronger worst-case guarantee. But amortized data structures are not suitable for real-time systems, where each individual operation has to be executed quickly. For this reason, there exist many recent randomized results that aim to provide a guarantee stronger than amortized expected. The strongest possible guarantee for a randomized algorithm is that it is always correct (Las Vegas), and has high-probability worst-case update time, which gives a bound on the time for each individual operation that holds with high probability. In this paper we present the first polylogarithmic high-probability worst-case time bounds for the dynamic spanner and the dynamic maximal matching problem. 1. For dynamic spanner, the only known o(n) worst-case bounds were O(n3/4) high-probability worst-case update time for maintaining a 3-spanner, and O(n5/9) for maintaining a 5-spanner. We give a O(1)k log3(n) high-probability worst-case time bound for maintaining a (2k – 1)-spanner, which yields the first worst-case polylog update time for all constant k. (All the results above maintain the optimal tradeoff of stretch 2k – 1 and Õ(n1+1/k) edges.) 2. For dynamic maximal matching, or dynamic 2-approximate maximum matching, no algorithm with o(n) worst-case time bound was known and we present an algorithm with O(log5 (n)) high-probability worst-case time; similar worst-case bounds existed only for maintaining a matching that was (2 + ∊)-approximate, and hence not maximal. Our results are achieved using a new approach for converting amortized guarantees to worst-case ones for randomized data structures by going through a third type of guarantee, which is a middle ground between the two above: an algorithm is said to have worst-case expected update time α if for every update σ, the expected time to process σ is at most α. Although stronger than amortized expected, the worst-case expected guarantee does not resolve the fundamental problem of amortization: a worst-case expected update time of O(1) still allows for the possibility that every 1/f(n) updates requires Θ(f(n)) time to process, for arbitrarily high f(n). In this paper we present a black-box reduction that converts any data structure with worst-case expected update time into one with a high-probability worst-case update time: the query time remains the same, while the update time increases by a factor of O(log2(n)). Thus we achieve our results in two steps: (1) First we show how to convert existing dynamic graph algorithms with amortized expected polylogarithmic running times into algorithms with worst-case expected polylogarithmic running times. (2) Then we use our black-box reduction to achieve the polylogarithmic high-probability worst-case time bound. All our algorithms are Las-Vegas-type algorithms.}, author = {Bernstein, Aaron and Forster, Sebastian and Henzinger, Monika H}, booktitle = {30th Annual ACM-SIAM Symposium on Discrete Algorithms}, location = {San Diego, CA, United States}, pages = {1899--1918}, publisher = {Society for Industrial and Applied Mathematics}, title = {{A deamortization approach for dynamic spanner and dynamic maximal matching}}, doi = {10.1137/1.9781611975482.115}, year = {2019}, } @article{11898, abstract = {We build upon the recent papers by Weinstein and Yu (FOCS'16), Larsen (FOCS'12), and Clifford et al. (FOCS'15) to present a general framework that gives amortized lower bounds on the update and query times of dynamic data structures. Using our framework, we present two concrete results. (1) For the dynamic polynomial evaluation problem, where the polynomial is defined over a finite field of size n1+Ω(1) and has degree n, any dynamic data structure must either have an amortized update time of Ω((lgn/lglgn)2) or an amortized query time of Ω((lgn/lglgn)2). (2) For the dynamic online matrix vector multiplication problem, where we get an n×n matrix whose entires are drawn from a finite field of size nΘ(1), any dynamic data structure must either have an amortized update time of Ω((lgn/lglgn)2) or an amortized query time of Ω(n⋅(lgn/lglgn)2). For these two problems, the previous works by Larsen (FOCS'12) and Clifford et al. (FOCS'15) gave the same lower bounds, but only for worst case update and query times. Our bounds match the highest unconditional lower bounds known till date for any dynamic problem in the cell-probe model.}, author = {Bhattacharya, Sayan and Henzinger, Monika H and Neumann, Stefan}, issn = {0304-3975}, journal = {Theoretical Computer Science}, pages = {72--87}, publisher = {Elsevier}, title = {{New amortized cell-probe lower bounds for dynamic problems}}, doi = {10.1016/j.tcs.2019.01.043}, volume = {779}, year = {2019}, } @article{11984, abstract = {Differentially protected galactosamine building blocks are key components for the synthesis of human and bacterial oligosaccharides. The azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal provides straightforward access to the corresponding 2-nitrogenated glycoside. Poor reproducibility and the use of azides that lead to the formation of potentially explosive and toxic species limit the scalability of this reaction and render it a bottleneck for carbohydrate synthesis. Here, we present a method for the safe, efficient, and reliable azidophenylselenylation of 3,4,6-tri-O-acetyl-d-galactal at room temperature, using continuous flow chemistry. Careful analysis of the transformation resulted in reaction conditions that produce minimal side products while the reaction time was reduced drastically when compared to batch reactions. The flow setup is readily scalable to process 5 mmol of galactal in 3 h, producing 1.2 mmol/h of product.}, author = {Guberman, Mónica and Pieber, Bartholomäus and Seeberger, Peter H.}, issn = {1520-586X}, journal = {Organic Process Research and Development}, number = {12}, pages = {2764--2770}, publisher = {American Chemical Society}, title = {{Safe and scalable continuous flow azidophenylselenylation of galactal to prepare galactosamine building blocks}}, doi = {10.1021/acs.oprd.9b00456}, volume = {23}, year = {2019}, } @article{11982, abstract = {A carbon nitride material can be combined with homogeneous nickel catalysts for light-mediated cross-couplings of aryl bromides with alcohols under mild conditions. The metal-free heterogeneous semiconductor is fully recyclable and couples a broad range of electron-poor aryl bromides with primary and secondary alcohols as well as water. The application for intramolecular reactions and the synthesis of active pharmaceutical ingredients was demonstrated. The catalytic protocol is applicable for the coupling of aryl iodides with thiols as well.}, author = {Cavedon, Cristian and Madani, Amiera and Seeberger, Peter H. and Pieber, Bartholomäus}, issn = {1523-7052}, journal = {Organic Letters}, number = {13}, pages = {5331--5334}, publisher = {American Chemical Society}, title = {{Semiheterogeneous dual nickel/photocatalytic (thio)etherification using carbon nitrides}}, doi = {10.1021/acs.orglett.9b01957}, volume = {21}, year = {2019}, } @article{170, abstract = {Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ .}, author = {Browning, Timothy D and Sofos, Efthymios}, journal = {Mathematische Annalen}, number = {3-4}, pages = {977--1016}, publisher = {Springer Nature}, title = {{Counting rational points on quartic del Pezzo surfaces with a rational conic}}, doi = {10.1007/s00208-018-1716-6}, volume = {373}, year = {2019}, } @article{441, author = {Kalinin, Nikita and Shkolnikov, Mikhail}, issn = {2199-6768}, journal = {European Journal of Mathematics}, number = {3}, pages = {909–928}, publisher = {Springer Nature}, title = {{Tropical formulae for summation over a part of SL(2,Z)}}, doi = {10.1007/s40879-018-0218-0}, volume = {5}, year = {2019}, } @article{5887, abstract = {Cryptographic security is usually defined as a guarantee that holds except when a bad event with negligible probability occurs, and nothing is guaranteed in that bad case. However, in settings where such failure can happen with substantial probability, one needs to provide guarantees even for the bad case. A typical example is where a (possibly weak) password is used instead of a secure cryptographic key to protect a session, the bad event being that the adversary correctly guesses the password. In a situation with multiple such sessions, a per-session guarantee is desired: any session for which the password has not been guessed remains secure, independently of whether other sessions have been compromised. A new formalism for stating such gracefully degrading security guarantees is introduced and applied to analyze the examples of password-based message authentication and password-based encryption. While a natural per-message guarantee is achieved for authentication, the situation of password-based encryption is more delicate: a per-session confidentiality guarantee only holds against attackers for which the distribution of password-guessing effort over the sessions is known in advance. In contrast, for more general attackers without such a restriction, a strong, composable notion of security cannot be achieved.}, author = {Demay, Gregory and Gazi, Peter and Maurer, Ueli and Tackmann, Bjorn}, issn = {0926227X}, journal = {Journal of Computer Security}, number = {1}, pages = {75--111}, publisher = {IOS Press}, title = {{Per-session security: Password-based cryptography revisited}}, doi = {10.3233/JCS-181131}, volume = {27}, year = {2019}, } @article{6515, abstract = {We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature.}, author = {Dyer, Ramsay and Vegter, Gert and Wintraecken, Mathijs}, issn = {1920-180X}, journal = {Journal of Computational Geometry }, number = {1}, pages = {223–256}, publisher = {Carleton University}, title = {{Simplices modelled on spaces of constant curvature}}, doi = {10.20382/jocg.v10i1a9}, volume = {10}, year = {2019}, } @inproceedings{6528, abstract = {We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism.}, author = {Pietrzak, Krzysztof Z}, booktitle = {10th Innovations in Theoretical Computer Science Conference}, isbn = {978-3-95977-095-8}, issn = {1868-8969}, location = {San Diego, CA, United States}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Simple verifiable delay functions}}, doi = {10.4230/LIPICS.ITCS.2019.60}, volume = {124}, year = {2019}, } @inproceedings{6565, abstract = {In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example.}, author = {Kundu, Atreyee and Garcia Soto, Miriam and Prabhakar, Pavithra}, booktitle = {5th Indian Control Conference Proceedings}, isbn = {978-153866246-5}, location = {Delhi, India}, publisher = {IEEE}, title = {{Formal synthesis of stabilizing controllers for periodically controlled linear switched systems}}, doi = {10.1109/INDIANCC.2019.8715598}, year = {2019}, } @inproceedings{6628, abstract = {Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space.}, author = {Vegter, Gert and Wintraecken, Mathijs}, booktitle = {The 31st Canadian Conference in Computational Geometry}, location = {Edmonton, Canada}, pages = {275--279}, title = {{The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds}}, year = {2019}, } @inproceedings{6648, abstract = {Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.}, author = {Edelsbrunner, Herbert and Virk, Ziga and Wagner, Hubert}, booktitle = {35th International Symposium on Computational Geometry}, isbn = {9783959771047}, location = {Portland, OR, United States}, pages = {31:1--31:14}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Topological data analysis in information space}}, doi = {10.4230/LIPICS.SOCG.2019.31}, volume = {129}, year = {2019}, } @article{6659, abstract = {Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research.}, author = {Zenmyo, Naoki and Tokumaru, Hiroki and Uchinomiya, Shohei and Fuchida, Hirokazu and Tabata, Shigekazu and Hamachi, Itaru and Shigemoto, Ryuichi and Ojida, Akio}, issn = {00092673}, journal = {Bulletin of the Chemical Society of Japan}, number = {5}, pages = {995--1000}, publisher = {Bulletin of the Chemical Society of Japan}, title = {{Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins}}, doi = {10.1246/bcsj.20190034}, volume = {92}, year = {2019}, } @article{6662, abstract = {In phase retrieval, we want to recover an unknown signal 𝑥∈ℂ𝑑 from n quadratic measurements of the form 𝑦𝑖=|⟨𝑎𝑖,𝑥⟩|2+𝑤𝑖, where 𝑎𝑖∈ℂ𝑑 are known sensing vectors and 𝑤𝑖 is measurement noise. We ask the following weak recovery question: What is the minimum number of measurements n needed to produce an estimator 𝑥^(𝑦) that is positively correlated with the signal 𝑥? We consider the case of Gaussian vectors 𝑎𝑎𝑖. We prove that—in the high-dimensional limit—a sharp phase transition takes place, and we locate the threshold in the regime of vanishingly small noise. For 𝑛≤𝑑−𝑜(𝑑), no estimator can do significantly better than random and achieve a strictly positive correlation. For 𝑛≥𝑑+𝑜(𝑑), a simple spectral estimator achieves a positive correlation. Surprisingly, numerical simulations with the same spectral estimator demonstrate promising performance with realistic sensing matrices. Spectral methods are used to initialize non-convex optimization algorithms in phase retrieval, and our approach can boost the performance in this setting as well. Our impossibility result is based on classical information-theoretic arguments. The spectral algorithm computes the leading eigenvector of a weighted empirical covariance matrix. We obtain a sharp characterization of the spectral properties of this random matrix using tools from free probability and generalizing a recent result by Lu and Li. Both the upper bound and lower bound generalize beyond phase retrieval to measurements 𝑦𝑖 produced according to a generalized linear model. As a by-product of our analysis, we compare the threshold of the proposed spectral method with that of a message passing algorithm.}, author = {Mondelli, Marco and Montanari, Andrea}, issn = {1615-3383}, journal = {Foundations of Computational Mathematics}, number = {3}, pages = {703--773}, publisher = {Springer}, title = {{Fundamental limits of weak recovery with applications to phase retrieval}}, doi = {10.1007/s10208-018-9395-y}, volume = {19}, year = {2019}, } @article{6672, abstract = {The construction of anisotropic triangulations is desirable for various applications, such as the numerical solving of partial differential equations and the representation of surfaces in graphics. To solve this notoriously difficult problem in a practical way, we introduce the discrete Riemannian Voronoi diagram, a discrete structure that approximates the Riemannian Voronoi diagram. This structure has been implemented and was shown to lead to good triangulations in $\mathbb{R}^2$ and on surfaces embedded in $\mathbb{R}^3$ as detailed in our experimental companion paper. In this paper, we study theoretical aspects of our structure. Given a finite set of points $\mathcal{P}$ in a domain $\Omega$ equipped with a Riemannian metric, we compare the discrete Riemannian Voronoi diagram of $\mathcal{P}$ to its Riemannian Voronoi diagram. Both diagrams have dual structures called the discrete Riemannian Delaunay and the Riemannian Delaunay complex. We provide conditions that guarantee that these dual structures are identical. It then follows from previous results that the discrete Riemannian Delaunay complex can be embedded in $\Omega$ under sufficient conditions, leading to an anisotropic triangulation with curved simplices. Furthermore, we show that, under similar conditions, the simplices of this triangulation can be straightened.}, author = {Boissonnat, Jean-Daniel and Rouxel-Labbé, Mael and Wintraecken, Mathijs}, issn = {1095-7111}, journal = {SIAM Journal on Computing}, number = {3}, pages = {1046--1097}, publisher = {Society for Industrial & Applied Mathematics (SIAM)}, title = {{Anisotropic triangulations via discrete Riemannian Voronoi diagrams}}, doi = {10.1137/17m1152292}, volume = {48}, year = {2019}, } @inproceedings{6725, abstract = {A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. Recent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.}, author = {Kolmogorov, Vladimir}, booktitle = {46th International Colloquium on Automata, Languages and Programming}, isbn = {978-3-95977-109-2}, issn = {1868-8969}, location = {Patras, Greece}, pages = {77:1--77:12}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Testing the complexity of a valued CSP language}}, doi = {10.4230/LIPICS.ICALP.2019.77}, volume = {132}, year = {2019}, } @inbook{6726, abstract = {Randomness is an essential part of any secure cryptosystem, but many constructions rely on distributions that are not uniform. This is particularly true for lattice based cryptosystems, which more often than not make use of discrete Gaussian distributions over the integers. For practical purposes it is crucial to evaluate the impact that approximation errors have on the security of a scheme to provide the best possible trade-off between security and performance. Recent years have seen surprising results allowing to use relatively low precision while maintaining high levels of security. A key insight in these results is that sampling a distribution with low relative error can provide very strong security guarantees. Since floating point numbers provide guarantees on the relative approximation error, they seem a suitable tool in this setting, but it is not obvious which sampling algorithms can actually profit from them. While previous works have shown that inversion sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES 2014; Prest, ASIACRYPT 2017), other works have called into question if this is possible for other sampling techniques (Zheng et al., Eprint report 2018/309). In this work, we consider all sampling algorithms that are popular in the cryptographic setting and analyze the relationship of floating point precision and the resulting relative error. We show that all of the algorithms either natively achieve a low relative error or can be adapted to do so.}, author = {Walter, Michael}, booktitle = {Progress in Cryptology – AFRICACRYPT 2019}, editor = {Buchmann, J and Nitaj, A and Rachidi, T}, isbn = {978-3-0302-3695-3}, issn = {0302-9743}, location = {Rabat, Morocco}, pages = {157--180}, publisher = {Springer Nature}, title = {{Sampling the integers with low relative error}}, doi = {10.1007/978-3-030-23696-0_9}, volume = {11627}, year = {2019}, } @article{6663, abstract = {Consider the problem of constructing a polar code of block length N for a given transmission channel W. Previous approaches require one to compute the reliability of the N synthetic channels and then use only those that are sufficiently reliable. However, we know from two independent works by Schürch and by Bardet et al. that the synthetic channels are partially ordered with respect to degradation. Hence, it is natural to ask whether the partial order can be exploited to reduce the computational burden of the construction problem. We show that, if we take advantage of the partial order, we can construct a polar code by computing the reliability of roughly a fraction 1/ log 3/2 N of the synthetic channels. In particular, we prove that N/ log 3/2 N is a lower bound on the number of synthetic channels to be considered and such a bound is tight up to a multiplicative factor log log N. This set of roughly N/ log 3/2 N synthetic channels is universal, in the sense that it allows one to construct polar codes for any W, and it can be identified by solving a maximum matching problem on a bipartite graph. Our proof technique consists of reducing the construction problem to the problem of computing the maximum cardinality of an antichain for a suitable partially ordered set. As such, this method is general, and it can be used to further improve the complexity of the construction problem, in case a refined partial order on the synthetic channels of polar codes is discovered.}, author = {Mondelli, Marco and Hassani, Hamed and Urbanke, Rudiger}, journal = {IEEE}, number = {5}, pages = {2782--2791}, publisher = {IEEE}, title = {{Construction of polar codes with sublinear complexity}}, doi = {10.1109/tit.2018.2889667}, volume = {65}, year = {2019}, } @inproceedings{6747, abstract = {We establish connections between the problem of learning a two-layer neural network and tensor decomposition. We consider a model with feature vectors x∈ℝd, r hidden units with weights {wi}1≤i≤r and output y∈ℝ, i.e., y=∑ri=1σ(w𝖳ix), with activation functions given by low-degree polynomials. In particular, if σ(x)=a0+a1x+a3x3, we prove that no polynomial-time learning algorithm can outperform the trivial predictor that assigns to each example the response variable 𝔼(y), when d3/2≪r≪d2. Our conclusion holds for a `natural data distribution', namely standard Gaussian feature vectors x, and output distributed according to a two-layer neural network with random isotropic weights, and under a certain complexity-theoretic assumption on tensor decomposition. Roughly speaking, we assume that no polynomial-time algorithm can substantially outperform current methods for tensor decomposition based on the sum-of-squares hierarchy. We also prove generalizations of this statement for higher degree polynomial activations, and non-random weight vectors. Remarkably, several existing algorithms for learning two-layer networks with rigorous guarantees are based on tensor decomposition. Our results support the idea that this is indeed the core computational difficulty in learning such networks, under the stated generative model for the data. As a side result, we show that under this model learning the network requires accurate learning of its weights, a property that does not hold in a more general setting. }, author = {Mondelli, Marco and Montanari, Andrea}, booktitle = {Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics}, location = {Naha, Okinawa, Japan}, pages = {1051--1060}, publisher = {Proceedings of Machine Learning Research}, title = {{On the connection between learning two-layers neural networks and tensor decomposition}}, volume = {89}, year = {2019}, } @article{6750, abstract = {Polar codes have gained extensive attention during the past few years and recently they have been selected for the next generation of wireless communications standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC list (SCL) and SC flip (SCF), provide a reasonable error performance for polar codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC, Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code graph off-line, produce a list of operations, store the list in memory, and feed the list to the decoder to decode the constituent codes in order efficiently, thus increasing the decoding speed. However, the list of operations is dependent on the code rate and as the rate changes, a new list is produced, making fast SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible fast SC-based decoder by creating the list of operations directly in hardware, with low implementation complexity. We further propose a hardware architecture implementing the proposed method and show that the area occupation of the rate-flexible fast SC-based decoder in this paper is only 38% of the total area of the memory-based base-line decoder when 5G code rates are supported. }, author = {Hashemi, Seyyed Ali and Condo, Carlo and Mondelli, Marco and Gross, Warren J}, issn = {1053587X}, journal = {IEEE Transactions on Signal Processing}, number = {22}, publisher = {IEEE}, title = {{Rate-flexible fast polar decoders}}, doi = {10.1109/TSP.2019.2944738}, volume = {67}, year = {2019}, } @article{6759, abstract = {We consider the graph class Grounded-L corresponding to graphs that admit an intersection representation by L-shaped curves, where additionally the topmost points of each curve are assumed to belong to a common horizontal line. We prove that Grounded-L graphs admit an equivalent characterisation in terms of vertex ordering with forbidden patterns. We also compare this class to related intersection classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max point-tolerance graphs), or the outer-1-string graphs. We give constructions showing that these classes are all distinct and satisfy only trivial or previously known inclusions.}, author = {Jelínek, Vít and Töpfer, Martin}, issn = {10778926}, journal = {Electronic Journal of Combinatorics}, number = {3}, publisher = {Electronic Journal of Combinatorics}, title = {{On grounded L-graphs and their relatives}}, doi = {10.37236/8096}, volume = {26}, year = {2019}, }