@misc{9898, abstract = {All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808859.v1}, year = {2019}, } @misc{9901, abstract = {Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808907.v1}, year = {2019}, } @misc{9899, abstract = {Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808865.v1}, year = {2019}, } @misc{9900, abstract = {Pan-genome statistics by species. (CSV 3 kb)}, author = {Sigalova, Olga M. and Chaplin, Andrei V. and Bochkareva, Olga and Shelyakin, Pavel V. and Filaretov, Vsevolod A. and Akkuratov, Evgeny E. and Burskaia, Valentina and Gelfand, Mikhail S.}, publisher = {Springer Nature}, title = {{Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction}}, doi = {10.6084/m9.figshare.9808886.v1}, year = {2019}, } @article{6936, abstract = {A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them. }, author = {Ovaskainen, Otso and Rybicki, Joel and Abrego, Nerea}, issn = {1600-0587}, journal = {Ecography}, number = {11}, pages = {1877--1886}, publisher = {Wiley}, title = {{What can observational data reveal about metacommunity processes?}}, doi = {10.1111/ecog.04444}, volume = {42}, year = {2019}, } @article{6857, abstract = {Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems. The recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.}, author = {Giese, B and Friess, J L and Schetelig, M F and Barton, Nicholas H and Messer, Philip and Debarre, Florence and Meimberg, H and Windbichler, N and Boete, C}, issn = {1521-1878}, journal = {BioEssays}, number = {11}, publisher = {Wiley}, title = {{Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna}}, doi = {10.1002/bies.201900151}, volume = {41}, year = {2019}, } @article{6940, abstract = {We study the effect of a linear tunneling coupling between two-dimensional systems, each separately exhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there are two phases: one where the one-body correlation functions are algebraically decaying and the other with exponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law decay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite temperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is present. We provide a picture of the phase diagram using a renormalization group approach.}, author = {Bighin, Giacomo and Defenu, Nicolò and Nándori, István and Salasnich, Luca and Trombettoni, Andrea}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {10}, publisher = {American Physical Society}, title = {{Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models}}, doi = {10.1103/physrevlett.123.100601}, volume = {123}, year = {2019}, } @article{6919, author = {Qi, Chao and Minin, Giulio Di and Vercellino, Irene and Wutz, Anton and Korkhov, Volodymyr M.}, issn = {23752548}, journal = {Science Advances}, number = {9}, publisher = {American Association for the Advancement of Science}, title = {{Structural basis of sterol recognition by human hedgehog receptor PTCH1}}, doi = {10.1126/sciadv.aaw6490}, volume = {5}, year = {2019}, } @article{6983, abstract = {Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver.}, author = {Kelemen, Réka K and Rajakaruna, H and Cockburn, IA and Ganusov, VV}, issn = {1664-3224}, journal = {Frontiers in Immunology}, publisher = {Frontiers}, title = {{Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells}}, doi = {10.3389/fimmu.2019.02153}, volume = {10}, year = {2019}, } @article{6972, abstract = {We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to f> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential.}, author = {Schmickler, C.H. and Hammer, H.-W. and Volosniev, Artem}, issn = {0370-2693}, journal = {Physics Letters B}, publisher = {Elsevier}, title = {{Universal physics of bound states of a few charged particles}}, doi = {10.1016/j.physletb.2019.135016}, volume = {798}, year = {2019}, } @article{7005, abstract = {Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes.}, author = {Cheung, Giselle T and Cousin, Michael A.}, issn = {1471-4159}, journal = {Journal of Neurochemistry}, number = {5}, pages = {570--583}, publisher = {Wiley}, title = {{Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction}}, doi = {10.1111/jnc.14862}, volume = {151}, year = {2019}, } @article{7000, abstract = {The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.}, author = {Shehu, Yekini and Iyiola, Olaniyi S. and Li, Xiao-Huan and Dong, Qiao-Li}, issn = {1807-0302}, journal = {Computational and Applied Mathematics}, number = {4}, publisher = {Springer Nature}, title = {{Convergence analysis of projection method for variational inequalities}}, doi = {10.1007/s40314-019-0955-9}, volume = {38}, year = {2019}, } @article{6978, abstract = {In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.}, author = {Budanur, Nazmi B and Dogra, Akshunna and Hof, Björn}, journal = {Physical Review Fluids}, number = {10}, pages = {102401}, publisher = {American Physical Society}, title = {{Geometry of transient chaos in streamwise-localized pipe flow turbulence}}, doi = {10.1103/PhysRevFluids.4.102401}, volume = {4}, year = {2019}, } @article{7026, abstract = {Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information.}, author = {Lukacisin, Martin and Bollenbach, Tobias}, issn = {2405-4712}, journal = {Cell Systems}, number = {5}, pages = {423--433.e1--e3}, publisher = {Cell Press}, title = {{Emergent gene expression responses to drug combinations predict higher-order drug interactions}}, doi = {10.1016/j.cels.2019.10.004}, volume = {9}, year = {2019}, } @article{7034, abstract = {We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus.}, author = {Fulek, Radoslav and Kynčl, Jan}, issn = {1439-6912}, journal = {Combinatorica}, number = {6}, pages = {1267--1279}, publisher = {Springer Nature}, title = {{Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4}}, doi = {10.1007/s00493-019-3905-7}, volume = {39}, year = {2019}, } @article{7095, abstract = {BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells.}, author = {Maes, Margaret E and Grosser, J. A. and Fehrman, R. L. and Schlamp, C. L. and Nickells, R. W.}, issn = {2045-2322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{Completion of BAX recruitment correlates with mitochondrial fission during apoptosis}}, doi = {10.1038/s41598-019-53049-w}, volume = {9}, year = {2019}, } @article{7097, abstract = {Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway.}, author = {Nagano, Makoto and Toshima, Junko Y. and Siekhaus, Daria E and Toshima, Jiro}, issn = {2399-3642}, journal = {Communications Biology}, number = {1}, publisher = {Springer Nature}, title = {{Rab5-mediated endosome formation is regulated at the trans-Golgi network}}, doi = {10.1038/s42003-019-0670-5}, volume = {2}, year = {2019}, } @article{7099, author = {Kasugai, Yu and Vogel, Elisabeth and Hörtnagl, Heide and Schönherr, Sabine and Paradiso, Enrica and Hauschild, Markus and Göbel, Georg and Milenkovic, Ivan and Peterschmitt, Yvan and Tasan, Ramon and Sperk, Günther and Shigemoto, Ryuichi and Sieghart, Werner and Singewald, Nicolas and Lüthi, Andreas and Ferraguti, Francesco}, issn = {0896-6273}, journal = {Neuron}, number = {4}, pages = {781--794.e4}, publisher = {Elsevier}, title = {{Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning}}, doi = {10.1016/j.neuron.2019.08.013}, volume = {104}, year = {2019}, } @article{6455, abstract = {During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity.}, author = {Telley, L and Agirman, G and Prados, J and Amberg, Nicole and Fièvre, S and Oberst, P and Bartolini, G and Vitali, I and Cadilhac, C and Hippenmeyer, Simon and Nguyen, L and Dayer, A and Jabaudon, D}, issn = {1095-9203}, journal = {Science}, number = {6440}, publisher = {AAAS}, title = {{Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex}}, doi = {10.1126/science.aav2522}, volume = {364}, year = {2019}, } @article{6586, abstract = {The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe.}, author = {Ibáñez, Maria and Hasler, Roger and Genç, Aziz and Liu, Yu and Kuster, Beatrice and Schuster, Maximilian and Dobrozhan, Oleksandr and Cadavid, Doris and Arbiol, Jordi and Cabot, Andreu and Kovalenko, Maksym V.}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {20}, pages = {8025--8029}, publisher = {American Chemical Society}, title = {{Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion}}, doi = {10.1021/jacs.9b01394}, volume = {141}, year = {2019}, } @article{6174, abstract = {We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture.}, author = {Dumitrescu, Philipp T. and Goremykina, Anna and Parameswaran, Siddharth A. and Serbyn, Maksym and Vasseur, Romain}, issn = {2469-9969}, journal = {Physical Review B}, number = {9}, publisher = {American Physical Society}, title = {{Kosterlitz-Thouless scaling at many-body localization phase transitions}}, doi = {10.1103/physrevb.99.094205}, volume = {99}, year = {2019}, } @article{6366, abstract = {Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.}, author = {Bellstaedt, Julia and Trenner, Jana and Lippmann, Rebecca and Poeschl, Yvonne and Zhang, Xixi and Friml, Jiří and Quint, Marcel and Delker, Carolin}, issn = {1532-2548}, journal = {Plant Physiology}, number = {2}, pages = {757--766}, publisher = {ASPB}, title = {{A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls}}, doi = {10.1104/pp.18.01377}, volume = {180}, year = {2019}, } @article{6986, abstract = {Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. }, author = {Li, Penghui}, issn = {1088-6826}, journal = {Proceedings of the American Mathematical Society}, number = {11}, pages = {4597--4604}, publisher = {AMS}, title = {{A colimit of traces of reflection groups}}, doi = {10.1090/proc/14586}, volume = {147}, year = {2019}, } @article{6454, abstract = {Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.}, author = {Ortiz-Álvarez, G and Daclin, M and Shihavuddin, A and Lansade, P and Fortoul, A and Faucourt, M and Clavreul, S and Lalioti, ME and Taraviras, S and Hippenmeyer, Simon and Livet, J and Meunier, A and Genovesio, A and Spassky, N}, issn = {1097-4199}, journal = {Neuron}, number = {1}, pages = {159--172.e7}, publisher = {Elsevier}, title = {{Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members}}, doi = {10.1016/j.neuron.2019.01.051}, volume = {102}, year = {2019}, } @article{6980, abstract = {Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development.}, author = {Petridou, Nicoletta and Heisenberg, Carl-Philipp J}, issn = {1460-2075}, journal = {The EMBO Journal}, number = {20}, publisher = {EMBO}, title = {{Tissue rheology in embryonic organization}}, doi = {10.15252/embj.2019102497}, volume = {38}, year = {2019}, } @article{6554, abstract = {Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it.}, author = {Xian, Yongqin and Lampert, Christoph and Schiele, Bernt and Akata, Zeynep}, issn = {1939-3539}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {9}, pages = {2251 -- 2265}, publisher = {Institute of Electrical and Electronics Engineers (IEEE)}, title = {{Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly}}, doi = {10.1109/tpami.2018.2857768}, volume = {41}, year = {2019}, } @article{6259, abstract = {The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes.}, author = {Cao, Min and Chen, Rong and Li, Pan and Yu, Yongqiang and Zheng, Rui and Ge, Danfeng and Zheng, Wei and Wang, Xuhui and Gu, Yangtao and Gelová, Zuzana and Friml, Jiří and Zhang, Heng and Liu, Renyi and He, Jun and Xu, Tongda}, issn = {1476-4687}, journal = {Nature}, pages = {240--243}, publisher = {Springer Nature}, title = {{TMK1-mediated auxin signalling regulates differential growth of the apical hook}}, doi = {10.1038/s41586-019-1069-7}, volume = {568}, year = {2019}, } @inbook{6987, abstract = {Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern.}, author = {McDougall, Alex and Chenevert, Janet and Godard, Benoit G and Dumollard, Remi}, booktitle = {Evo-Devo: Non-model species in cell and developmental biology}, editor = {Tworzydlo, Waclaw and Bilinski, Szczepan M.}, isbn = {9783030234584}, issn = {1861-0412}, pages = {127--154}, publisher = {Springer Nature}, title = {{Emergence of embryo shape during cleavage divisions}}, doi = {10.1007/978-3-030-23459-1_6}, volume = {68}, year = {2019}, } @article{6762, abstract = {We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level of theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size.}, author = {Friesecke, Gero and Kniely, Michael}, issn = {15403467}, journal = {Multiscale Modeling and Simulation}, number = {3}, pages = {926--947}, publisher = {SIAM}, title = {{New optimal control problems in density functional theory motivated by photovoltaics}}, doi = {10.1137/18M1207272}, volume = {17}, year = {2019}, } @article{10874, abstract = {In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM.}, author = {Ionica, Sorina and Kılıçer, Pınar and Lauter, Kristin and Lorenzo García, Elisa and Manzateanu, Maria-Adelina and Massierer, Maike and Vincent, Christelle}, issn = {2363-9555}, journal = {Research in Number Theory}, keywords = {Algebra and Number Theory}, publisher = {Springer Nature}, title = {{Modular invariants for genus 3 hyperelliptic curves}}, doi = {10.1007/s40993-018-0146-6}, volume = {5}, year = {2019}, } @article{7100, abstract = {We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.}, author = {Jeblick, Maximilian and Leopold, Nikolai K and Pickl, Peter}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {1--69}, publisher = {Springer Nature}, title = {{Derivation of the time dependent Gross–Pitaevskii equation in two dimensions}}, doi = {10.1007/s00220-019-03599-x}, volume = {372}, year = {2019}, } @article{7106, abstract = {PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.}, author = {Skokan, Roman and Medvecká, Eva and Viaene, Tom and Vosolsobě, Stanislav and Zwiewka, Marta and Müller, Karel and Skůpa, Petr and Karady, Michal and Zhang, Yuzhou and Janacek, Dorina P. and Hammes, Ulrich Z. and Ljung, Karin and Nodzyński, Tomasz and Petrášek, Jan and Friml, Jiří}, issn = {2055-0278}, journal = {Nature Plants}, number = {11}, pages = {1114--1119}, publisher = {Springer Nature}, title = {{PIN-driven auxin transport emerged early in streptophyte evolution}}, doi = {10.1038/s41477-019-0542-5}, volume = {5}, year = {2019}, } @article{7105, abstract = {Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.}, author = {Yolland, Lawrence and Burki, Mubarik and Marcotti, Stefania and Luchici, Andrei and Kenny, Fiona N. and Davis, John Robert and Serna-Morales, Eduardo and Müller, Jan and Sixt, Michael K and Davidson, Andrew and Wood, Will and Schumacher, Linus J. and Endres, Robert G. and Miodownik, Mark and Stramer, Brian M.}, issn = {1476-4679}, journal = {Nature Cell Biology}, number = {11}, pages = {1370--1381}, publisher = {Springer Nature}, title = {{Persistent and polarized global actin flow is essential for directionality during cell migration}}, doi = {10.1038/s41556-019-0411-5}, volume = {21}, year = {2019}, } @article{7108, abstract = {We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable.}, author = {Goaoc, Xavier and Patak, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli}, issn = {0004-5411}, journal = {Journal of the ACM}, number = {3}, publisher = {ACM}, title = {{Shellability is NP-complete}}, doi = {10.1145/3314024}, volume = {66}, year = {2019}, } @inproceedings{7136, abstract = {It is well established that the notion of min-entropy fails to satisfy the \emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers. We show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, "information can't hurt" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X> k, this suggests that the overheads of relaxation will be outweighed by the improved scalability of the relaxed scheduler. On the negative side, we provide lower bounds showing that certain algorithms will inherently incur a non-trivial amount of wasted work due to scheduler relaxation, even for relatively benign relaxed schedulers.}, author = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Koval, Nikita}, booktitle = {31st ACM Symposium on Parallelism in Algorithms and Architectures}, isbn = {9781450361842}, location = {Phoenix, AZ, United States}, pages = {145--154}, publisher = {ACM Press}, title = {{Efficiency guarantees for parallel incremental algorithms under relaxed schedulers}}, doi = {10.1145/3323165.3323201}, year = {2019}, } @article{7398, abstract = {Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation.}, author = {Erdem, Fatma Asli and Ilic, Marija and Koppensteiner, Peter and Gołacki, Jakub and Lubec, Gert and Freissmuth, Michael and Sandtner, Walter}, issn = {1540-7748}, journal = {The Journal of General Physiology}, number = {8}, pages = {1035--1050}, publisher = {Rockefeller University Press}, title = {{A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2}}, doi = {10.1085/jgp.201912318}, volume = {151}, year = {2019}, } @article{7395, abstract = {The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.}, author = {Letts, James A and Fiedorczuk, Karol and Degliesposti, Gianluca and Skehel, Mark and Sazanov, Leonid A}, issn = {1097-2765}, journal = {Molecular Cell}, number = {6}, pages = {1131--1146.e6}, publisher = {Cell Press}, title = {{Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk}}, doi = {10.1016/j.molcel.2019.07.022}, volume = {75}, year = {2019}, } @article{7405, abstract = {Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.}, author = {Dura-Bernal, Salvador and Suter, Benjamin and Gleeson, Padraig and Cantarelli, Matteo and Quintana, Adrian and Rodriguez, Facundo and Kedziora, David J and Chadderdon, George L and Kerr, Cliff C and Neymotin, Samuel A and McDougal, Robert A and Hines, Michael and Shepherd, Gordon MG and Lytton, William W}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{NetPyNE, a tool for data-driven multiscale modeling of brain circuits}}, doi = {10.7554/elife.44494}, volume = {8}, year = {2019}, } @article{7400, abstract = {Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.}, author = {Veltsos, Paris and Ridout, Kate E. and Toups, Melissa A and González-Martínez, Santiago C. and Muyle, Aline and Emery, Olivier and Rastas, Pasi and Hudzieczek, Vojtech and Hobza, Roman and Vyskot, Boris and Marais, Gabriel A. B. and Filatov, Dmitry A. and Pannell, John R.}, issn = {1943-2631}, journal = {Genetics}, number = {3}, pages = {815--835}, publisher = {Genetics Society of America}, title = {{Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua}}, doi = {10.1534/genetics.119.302045}, volume = {212}, year = {2019}, } @article{7404, abstract = {The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.}, author = {Stürner, Tomke and Tatarnikova, Anastasia and Müller, Jan and Schaffran, Barbara and Cuntz, Hermann and Zhang, Yun and Nemethova, Maria and Bogdan, Sven and Small, Vic and Tavosanis, Gaia}, issn = {1477-9129}, journal = {Development}, number = {7}, publisher = {The Company of Biologists}, title = {{Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo}}, doi = {10.1242/dev.171397}, volume = {146}, year = {2019}, } @inproceedings{7402, abstract = {Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans.}, author = {Chatterjee, Krishnendu and Doyen, Laurent}, booktitle = {34th Annual ACM/IEEE Symposium on Logic in Computer Science}, isbn = {9781728136080}, location = {Vancouver, BC, Canada}, pages = {1--13}, publisher = {IEEE}, title = {{Graph planning with expected finite horizon}}, doi = {10.1109/lics.2019.8785706}, year = {2019}, } @article{7451, abstract = {We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition.}, author = {Vukics, A. and Dombi, A. and Fink, Johannes M and Domokos, P.}, issn = {2521-327X}, journal = {Quantum}, publisher = {Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften}, title = {{Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition}}, doi = {10.22331/q-2019-06-03-150}, volume = {3}, year = {2019}, } @inproceedings{7468, abstract = {We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems.}, author = {Swoboda, Paul and Kolmogorov, Vladimir}, booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, isbn = {9781728132938}, issn = {10636919}, location = {Long Beach, CA, United States}, publisher = {IEEE}, title = {{Map inference via block-coordinate Frank-Wolfe algorithm}}, doi = {10.1109/CVPR.2019.01140}, volume = {2019-June}, year = {2019}, } @inproceedings{7479, abstract = {Multi-exit architectures, in which a stack of processing layers is interleaved with early output layers, allow the processing of a test example to stop early and thus save computation time and/or energy. In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities. Experiments on CIFAR100 and ImageNet show that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy for late ones. The method is particularly beneficial when training data is limited and it allows a straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. Moreover, it takes only afew lines to implement and incurs almost no computational overhead at training time, and none at all at test time.}, author = {Bui Thi Mai, Phuong and Lampert, Christoph}, booktitle = {IEEE International Conference on Computer Vision}, isbn = {9781728148038}, issn = {15505499}, location = {Seoul, Korea}, pages = {1355--1364}, publisher = {IEEE}, title = {{Distillation-based training for multi-exit architectures}}, doi = {10.1109/ICCV.2019.00144}, volume = {2019-October}, year = {2019}, } @inproceedings{7542, abstract = {We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs.}, author = {Wendler, Chris and Alistarh, Dan-Adrian and Püschel, Markus}, issn = {1049-5258}, location = {Vancouver, Canada}, pages = {927--938}, publisher = {Neural Information Processing Systems Foundation}, title = {{Powerset convolutional neural networks}}, volume = {32}, year = {2019}, } @inproceedings{7640, abstract = {We propose a new model for detecting visual relationships, such as "person riding motorcycle" or "bottle on table". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results.}, author = {Kolesnikov, Alexander and Kuznetsova, Alina and Lampert, Christoph and Ferrari, Vittorio}, booktitle = {Proceedings of the 2019 International Conference on Computer Vision Workshop}, isbn = {9781728150239}, location = {Seoul, South Korea}, publisher = {IEEE}, title = {{Detecting visual relationships using box attention}}, doi = {10.1109/ICCVW.2019.00217}, year = {2019}, } @unpublished{8184, abstract = {Denote by ∆N the N-dimensional simplex. A map f : ∆N → Rd is an almost r-embedding if fσ1∩. . .∩fσr = ∅ whenever σ1, . . . , σr are pairwise disjoint faces. A counterexample to the topological Tverberg conjecture asserts that if r is not a prime power and d ≥ 2r + 1, then there is an almost r-embedding ∆(d+1)(r−1) → Rd. This was improved by Blagojevi´c–Frick–Ziegler using a simple construction of higher-dimensional counterexamples by taking k-fold join power of lower-dimensional ones. We improve this further (for d large compared to r): If r is not a prime power and N := (d+ 1)r−r l d + 2 r + 1 m−2, then there is an almost r-embedding ∆N → Rd. For the r-fold van Kampen–Flores conjecture we also produce counterexamples which are stronger than previously known. Our proof is based on generalizations of the Mabillard–Wagner theorem on construction of almost r-embeddings from equivariant maps, and of the Ozaydin theorem on existence of equivariant maps. }, author = {Avvakumov, Sergey and Karasev, R. and Skopenkov, A.}, booktitle = {arXiv}, publisher = {arXiv}, title = {{Stronger counterexamples to the topological Tverberg conjecture}}, year = {2019}, } @inproceedings{6430, abstract = {A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure. All existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in Open image in new window , rendering the result meaningless already for moderate Open image in new window . Jafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications. Our results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14).}, author = {Fuchsbauer, Georg and Kamath Hosdurg, Chethan and Klein, Karen and Pietrzak, Krzysztof Z}, isbn = {9783030172589}, issn = {16113349}, location = {Beijing, China}, pages = {317--346}, publisher = {Springer Nature}, title = {{Adaptively secure proxy re-encryption}}, doi = {10.1007/978-3-030-17259-6_11}, volume = {11443}, year = {2019}, } @article{6069, abstract = {Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments.}, author = {Mayzel, Jonathan and Steinberg, Victor and Varshney, Atul}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Stokes flow analogous to viscous electron current in graphene}}, doi = {10.1038/s41467-019-08916-5}, volume = {10}, year = {2019}, } @article{6014, abstract = {Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity.}, author = {Varshney, Atul and Steinberg, Victor}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Elastic alfven waves in elastic turbulence}}, doi = {10.1038/s41467-019-08551-0}, volume = {10}, year = {2019}, } @article{6451, abstract = {Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis.}, author = {Amberg, Nicole and Sotiropoulou, Panagiota A. and Heller, Gerwin and Lichtenberger, Beate M. and Holcmann, Martin and Camurdanoglu, Bahar and Baykuscheva-Gentscheva, Temenuschka and Blanpain, Cedric and Sibilia, Maria}, issn = {2589-0042}, journal = {iScience}, pages = {243--256}, publisher = {Elsevier}, title = {{EGFR controls hair shaft differentiation in a p53-independent manner}}, doi = {10.1016/j.isci.2019.04.018}, volume = {15}, year = {2019}, }