TY - CONF AB - The family of feedback alignment (FA) algorithms aims to provide a more biologically motivated alternative to backpropagation (BP), by substituting the computations that are unrealistic to be implemented in physical brains. While FA algorithms have been shown to work well in practice, there is a lack of rigorous theory proofing their learning capabilities. Here we introduce the first feedback alignment algorithm with provable learning guarantees. In contrast to existing work, we do not require any assumption about the size or depth of the network except that it has a single output neuron, i.e., such as for binary classification tasks. We show that our FA algorithm can deliver its theoretical promises in practice, surpassing the learning performance of existing FA methods and matching backpropagation in binary classification tasks. Finally, we demonstrate the limits of our FA variant when the number of output neurons grows beyond a certain quantity. AU - Lechner, Mathias ID - 10672 T2 - 8th International Conference on Learning Representations TI - Learning representations for binary-classification without backpropagation ER - TY - CONF AB - A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that gives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to generate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on depth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking. AU - Henderson, Paul M AU - Lampert, Christoph ID - 8188 SN - 9781713829546 T2 - 34th Conference on Neural Information Processing Systems TI - Unsupervised object-centric video generation and decomposition in 3D VL - 33 ER - TY - JOUR AB - Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states. AU - Bloomer, Rebecca H. AU - Hutchison, Claire E. AU - Bäurle, Isabel AU - Walker, James AU - Fang, Xiaofeng AU - Perera, Pumi AU - Velanis, Christos N. AU - Gümüs, Serin AU - Spanos, Christos AU - Rappsilber, Juri AU - Feng, Xiaoqi AU - Goodrich, Justin AU - Dean, Caroline ID - 12188 IS - 28 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2 VL - 117 ER - TY - JOUR AB - Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells. AU - Christophorou, Nicolas AU - She, Wenjing AU - Long, Jincheng AU - Hurel, Aurélie AU - Beaubiat, Sébastien AU - Idir, Yassir AU - Tagliaro-Jahns, Marina AU - Chambon, Aurélie AU - Solier, Victor AU - Vezon, Daniel AU - Grelon, Mathilde AU - Feng, Xiaoqi AU - Bouché, Nicolas AU - Mézard, Christine ID - 12189 IS - 6 JF - PLOS Genetics KW - Cancer Research KW - Genetics (clinical) KW - Genetics KW - Molecular Biology KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 1553-7404 TI - AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization VL - 16 ER - TY - JOUR AB - Let be a sequence of points on an elliptic curve defined over a number field K. In this paper, we study the denominators of the x-coordinates of this sequence. We prove that, if Q is a torsion point of prime order, then for n large enough there always exists a primitive divisor. Later on, we show the link between the study of the primitive divisors and a Lang-Trotter conjecture. Indeed, given two points P and Q on the elliptic curve, we prove a lower bound for the number of primes p such that P is in the orbit of Q modulo p. AU - Verzobio, Matteo ID - 12310 IS - 4 JF - Journal of Number Theory KW - Algebra and Number Theory SN - 0022-314X TI - Primitive divisors of sequences associated to elliptic curves VL - 209 ER - TY - GEN AB - We investigate the structural similarities between liquid water and 53 ices, including 20 known crystalline phases. We base such similarity comparison on the local environments that consist of atoms within a certain cutoff radius of a central atom. We reveal that liquid water explores the local environments of the diverse ice phases, by directly comparing the environments in these phases using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, the lattice energies, and vibrational properties of the ices. The finding that the local environments characterising the different ice phases are found in water sheds light on water phase behaviors, and rationalizes the transferability of water models between different phases. AU - Monserrat, Bartomeu AU - Brandenburg, Jan Gerit AU - Engel, Edgar A. AU - Cheng, Bingqing ID - 9699 T2 - arXiv TI - Extracting ice phases from liquid water: Why a machine-learning water model generalizes so well ER - TY - JOUR AB - Desorption electrospray ionization (DESI), easy ambient sonic-spray ionization (EASI) and low-temperature plasma (LTP) ionization are powerful ambient ionization techniques for mass spectrometry. However, every single method has its limitation in terms of polarity and molecular weight of analyte molecules. After the miniaturization of every possible component of the different ion sources, we finally were able to embed two emitters and an ion transfer tubing into a small, hand-held device. The pen-like interface is connected to the mass spectrometer and a separate control unit via a bundle of flexible tubing and cables. The novel device allows the user to ionize an extended range of chemicals by simple switching between DESI, voltage-free EASI, or LTP ionization as well as to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The interface was successfully tested using different types of chemicals, pharmaceuticals, and real life samples. Moreover, the combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging mass spectrometry, which we name “interactive mass spectrometry imaging (IMSI)”. AU - Meisenbichler, Christina AU - Kluibenschedl, Florian AU - Müller, Thomas ID - 12940 IS - 21 JF - Analytical Chemistry KW - Analytical Chemistry SN - 0003-2700 TI - A 3-in-1 hand-held ambient mass spectrometry interface for identification and 2D localization of chemicals on surfaces VL - 92 ER - TY - JOUR AB - Linear tetrapyrroles, called phyllobilins, are obtained as major catabolites upon chlorophyll degradation. Primarily, colorless phylloleucobilins featuring four deconjugated pyrrole units were identified. Their yellow counterparts, phylloxanthobilins, were discovered more recently. Although the two catabolites differ only by one double bond, physicochemical properties are very distinct. Moreover, the presence of the double bond seems to enhance physiologically relevant bioactivities: in contrast to phylloleucobilin, we identified a potent anti-proliferative activity for a phylloxanthobilin, and show that this natural product induces apoptotic cell death and a cell cycle arrest in cancer cells. Interestingly, upon modifying inactive phylloleucobilin by esterification, an anti-proliferative activity can be observed that increases with the chain lengths of the alkyl esters. We provide first evidence for anti-cancer activity of phyllobilins, report a novel plant source for a phylloxanthobilin, and by using paper spray MS, show that these bioactive yellow chlorophyll catabolites are more prevalent in Nature than previously assumed. AU - Karg, Cornelia A. AU - Wang, Pengyu AU - Kluibenschedl, Florian AU - Müller, Thomas AU - Allmendinger, Lars AU - Vollmar, Angelika M. AU - Moser, Simone ID - 12939 IS - 29 JF - European Journal of Organic Chemistry KW - Organic Chemistry KW - Physical and Theoretical Chemistry SN - 1434-193X TI - Phylloxanthobilins are abundant linear tetrapyrroles from chlorophyll breakdown with activities against cancer cells VL - 2020 ER - TY - BOOK AB - This booklet is a collection of abstracts presented at the AHPC conference. ED - Schlögl, Alois ED - Kiss, Janos ED - Elefante, Stefano ID - 7474 SN - 978-3-99078-004-6 TI - Austrian High-Performance-Computing meeting (AHPC2020) ER - TY - CONF AB - Quantization converts neural networks into low-bit fixed-point computations which can be carried out by efficient integer-only hardware, and is standard practice for the deployment of neural networks on real-time embedded devices. However, like their real-numbered counterpart, quantized networks are not immune to malicious misclassification caused by adversarial attacks. We investigate how quantization affects a network’s robustness to adversarial attacks, which is a formal verification question. We show that neither robustness nor non-robustness are monotonic with changing the number of bits for the representation and, also, neither are preserved by quantization from a real-numbered network. For this reason, we introduce a verification method for quantized neural networks which, using SMT solving over bit-vectors, accounts for their exact, bit-precise semantics. We built a tool and analyzed the effect of quantization on a classifier for the MNIST dataset. We demonstrate that, compared to our method, existing methods for the analysis of real-numbered networks often derive false conclusions about their quantizations, both when determining robustness and when detecting attacks, and that existing methods for quantized networks often miss attacks. Furthermore, we applied our method beyond robustness, showing how the number of bits in quantization enlarges the gender bias of a predictor for students’ grades. AU - Giacobbe, Mirco AU - Henzinger, Thomas A AU - Lechner, Mathias ID - 7808 SN - 03029743 T2 - International Conference on Tools and Algorithms for the Construction and Analysis of Systems TI - How many bits does it take to quantize your neural network? VL - 12079 ER - TY - CONF AB - Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary. AU - Boissonnat, Jean-Daniel AU - Wintraecken, Mathijs ID - 7952 SN - 1868-8969 T2 - 36th International Symposium on Computational Geometry TI - The topological correctness of PL-approximations of isomanifolds VL - 164 ER - TY - JOUR AB - Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs) are of growing interest for highly sensitive quantitative imaging of magnetic, spintronic, and transport properties of low-dimensional systems. Utilizing specifically designed grooved quartz capillaries pulled into a sharp pipette, we have fabricated the smallest SQUID-on-tip (SOT) devices with effective diameters down to 39 nm. Integration of a resistive shunt in close proximity to the pipette apex combined with self-aligned deposition of In and Sn, have resulted in SOT with a flux noise of 42 n$\Phi_0$Hz$^{-1/2}$, yielding a record low spin noise of 0.29 $\mu_B$Hz$^{-1/2}$. In addition, the new SOTs function at sub-Kelvin temperatures and in high magnetic fields of over 2.5 T. Integrating the SOTs into a scanning probe microscope allowed us to image the stray field of a single Fe$_3$O$_4$ nanocube at 300 mK. Our results show that the easy magnetization axis direction undergoes a transition from the (111) direction at room temperature to an in-plane orientation, which could be attributed to the Verwey phase transition in Fe$_3$O$_4$. AU - Anahory, Y. AU - Naren, H. R. AU - Lachman, E. O. AU - Sinai, S. Buhbut AU - Uri, A. AU - Embon, L. AU - Yaakobi, E. AU - Myasoedov, Y. AU - Huber, M. E. AU - Klajn, Rafal AU - Zeldov, E. ID - 13341 IS - 5 JF - Nanoscale TI - SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging VL - 12 ER - TY - CONF AB - Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction). AU - Wagner, Uli AU - Welzl, Emo ID - 7990 SN - 18688969 T2 - 36th International Symposium on Computational Geometry TI - Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips) VL - 164 ER - TY - CONF AB - In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity. For sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra). A corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part. AU - Wagner, Uli AU - Welzl, Emo ID - 7807 SN - 9781611975994 T2 - Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms TI - Connectivity of triangulation flip graphs in the plane (Part I: Edge flips) VL - 2020-January ER - TY - GEN AB - The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact. AU - Simon, Alexis AU - Fraisse, Christelle AU - El Ayari, Tahani AU - Liautard-Haag, Cathy AU - Strelkov, Petr AU - Welch, John AU - Bierne, Nicolas ID - 13073 TI - How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels ER - TY - GEN AB - Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available. AU - Arnoux, Stephanie AU - Fraisse, Christelle AU - Sauvage, Christopher ID - 13065 TI - VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species ER - TY - JOUR AB - In nature, light is harvested by photoactive proteins to drive a range of biological processes, including photosynthesis, phototaxis, vision, and ultimately life. Bacteriorhodopsin, for example, is a protein embedded within archaeal cell membranes that binds the chromophore retinal within its hydrophobic pocket. Exposure to light triggers regioselective photoisomerization of the confined retinal, which in turn initiates a cascade of conformational changes within the protein, triggering proton flux against the concentration gradient, providing the microorganisms with the energy to live. We are inspired by these functions in nature to harness light energy using synthetic photoswitches under confinement. Like retinal, synthetic photoswitches require some degree of conformational flexibility to isomerize. In nature, the conformational change associated with retinal isomerization is accommodated by the structural flexibility of the opsin host, yet it results in steric communication between the chromophore and the protein. Similarly, we strive to design systems wherein isomerization of confined photoswitches results in steric communication between a photoswitch and its confining environment. To achieve this aim, a balance must be struck between molecular crowding and conformational freedom under confinement: too much crowding prevents switching, whereas too much freedom resembles switching of isolated molecules in solution, preventing communication. In this Account, we discuss five classes of synthetic light-switchable compounds—diarylethenes, anthracenes, azobenzenes, spiropyrans, and donor–acceptor Stenhouse adducts—comparing their behaviors under confinement and in solution. The environments employed to confine these photoswitches are diverse, ranging from planar surfaces to nanosized cavities within coordination cages, nanoporous frameworks, and nanoparticle aggregates. The trends that emerge are primarily dependent on the nature of the photoswitch and not on the material used for confinement. In general, we find that photoswitches requiring less conformational freedom for switching are, as expected, more straightforward to isomerize reversibly under confinement. Because these compounds undergo only small structural changes upon isomerization, however, switching does not propagate into communication with their environment. Conversely, photoswitches that require more conformational freedom are more challenging to switch under confinement but also can influence system-wide behavior. Although we are primarily interested in the effects of geometric constraints on photoswitching under confinement, additional effects inevitably emerge when a compound is removed from solution and placed within a new, more crowded environment. For instance, we have found that compounds that convert to zwitterionic isomers upon light irradiation often experience stabilization of these forms under confinement. This effect results from the mutual stabilization of zwitterions that are brought into close proximity on surfaces or within cavities. Furthermore, photoswitches can experience preorganization under confinement, influencing the selectivity and efficiency of their photoreactions. Because intermolecular interactions arising from confinement cannot be considered independently from the effects of geometric constraints, we describe all confinement effects concurrently throughout this Account. AU - Grommet, Angela B. AU - Lee, Lucia M. AU - Klajn, Rafal ID - 13361 IS - 11 JF - Accounts of Chemical Research KW - General Medicine KW - General Chemistry SN - 0001-4842 TI - Molecular photoswitching in confined spaces VL - 53 ER - TY - JOUR AB - Aggregation of organic molecules can drastically affect their physicochemical properties. For instance, the optical properties of BODIPY dyes are inherently related to the degree of aggregation and the mutual orientation of BODIPY units within these aggregates. Whereas the noncovalent aggregation of various BODIPY dyes has been studied in diverse media, the ill-defined nature of these aggregates has made it difficult to elucidate the structure–property relationships. Here, we studied the encapsulation of three structurally simple BODIPY derivatives within the hydrophobic cavity of a water-soluble, flexible PdII6L4 coordination cage. The cavity size allowed for the selective encapsulation of two dye molecules, irrespective of the substitution pattern on the BODIPY core. Working with a model, a pentamethyl-substituted derivative, we found that the mutual orientation of two BODIPY units in the cage’s cavity was remarkably similar to that in the crystalline state of the free dye, allowing us to isolate and characterize the smallest possible noncovalent H-type BODIPY aggregate, namely, an H-dimer. Interestingly, a CF3-substituted BODIPY, known for forming J-type aggregates, was also encapsulated as an H-dimer. Taking advantage of the dynamic nature of encapsulation, we developed a system in which reversible switching between H- and J-aggregates can be induced for multiple cycles simply by addition and subsequent destruction of the cage. We expect that the ability to rapidly and reversibly manipulate the optical properties of supramolecular inclusion complexes in aqueous media will open up avenues for developing detection systems that operate within biological environments. AU - Gemen, Julius AU - Ahrens, Johannes AU - Shimon, Linda J. W. AU - Klajn, Rafal ID - 13362 IS - 41 JF - Journal of the American Chemical Society KW - Colloid and Surface Chemistry KW - Biochemistry KW - General Chemistry KW - Catalysis SN - 0002-7863 TI - Modulating the optical properties of BODIPY dyes by noncovalent dimerization within a flexible coordination cage VL - 142 ER - TY - JOUR AB - Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions. AU - Canton, Martina AU - Grommet, Angela B. AU - Pesce, Luca AU - Gemen, Julius AU - Li, Shiming AU - Diskin-Posner, Yael AU - Credi, Alberto AU - Pavan, Giovanni M. AU - Andréasson, Joakim AU - Klajn, Rafal ID - 13364 IS - 34 JF - Journal of the American Chemical Society KW - Colloid and Surface Chemistry KW - Biochemistry KW - General Chemistry KW - Catalysis SN - 0002-7863 TI - Improving fatigue resistance of dihydropyrene by encapsulation within a coordination cage VL - 142 ER - TY - JOUR AB - Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions. AU - Pesce, Luca AU - Perego, Claudio AU - Grommet, Angela B. AU - Klajn, Rafal AU - Pavan, Giovanni M. ID - 13365 IS - 21 JF - Journal of the American Chemical Society KW - Colloid and Surface Chemistry KW - Biochemistry KW - General Chemistry KW - Catalysis SN - 0002-7863 TI - Molecular factors controlling the isomerization of Azobenzenes in the cavity of a flexible coordination cage VL - 142 ER - TY - JOUR AB - Scanning nanoscale superconducting quantum interference devices (nanoSQUIDs) are of growing interest for highly sensitive quantitative imaging of magnetic, spintronic, and transport properties of low-dimensional systems. Utilizing specifically designed grooved quartz capillaries pulled into a sharp pipette, we have fabricated the smallest SQUID-on-tip (SOT) devices with effective diameters down to 39 nm. Integration of a resistive shunt in close proximity to the pipette apex combined with self-aligned deposition of In and Sn, has resulted in SOTs with a flux noise of 42 nΦ0 Hz−1/2, yielding a record low spin noise of 0.29 μB Hz−1/2. In addition, the new SOTs function at sub-Kelvin temperatures and in high magnetic fields of over 2.5 T. Integrating the SOTs into a scanning probe microscope allowed us to image the stray field of a single Fe3O4 nanocube at 300 mK. Our results show that the easy magnetization axis direction undergoes a transition from the 〈111〉 direction at room temperature to an in-plane orientation, which could be attributed to the Verwey phase transition in Fe3O4. AU - Anahory, Y. AU - Naren, H. R. AU - Lachman, E. O. AU - Buhbut Sinai, S. AU - Uri, A. AU - Embon, L. AU - Yaakobi, E. AU - Myasoedov, Y. AU - Huber, M. E. AU - Klajn, Rafal AU - Zeldov, E. ID - 13368 IS - 5 JF - Nanoscale KW - General Materials Science SN - 2040-3364 TI - SQUID-on-tip with single-electron spin sensitivity for high-field and ultra-low temperature nanomagnetic imaging VL - 12 ER - TY - JOUR AB - Temporal activation of biological processes by visible light and subsequent return to an inactive state in the absence of light is an essential characteristic of photoreceptor cells. Inspired by these phenomena, light-responsive materials are very attractive due to the high spatiotemporal control of light irradiation, with light being able to precisely orchestrate processes repeatedly over many cycles. Herein, it is reported that light-driven proton transfer triggered by a merocyanine-based photoacid can be used to modulate the permeability of pH-responsive polymersomes through cyclic, temporally controlled protonation and deprotonation of the polymersome membrane. The membranes can undergo repeated light-driven swelling–contraction cycles without losing functional effectiveness. When applied to enzyme loaded-nanoreactors, this membrane responsiveness is used for the reversible control of enzymatic reactions. This combination of the merocyanine-based photoacid and pH-switchable nanoreactors results in rapidly responding and versatile supramolecular systems successfully used to switch enzymatic reactions ON and OFF on demand. AU - Moreno, Silvia AU - Sharan, Priyanka AU - Engelke, Johanna AU - Gumz, Hannes AU - Boye, Susanne AU - Oertel, Ulrich AU - Wang, Peng AU - Banerjee, Susanta AU - Klajn, Rafal AU - Voit, Brigitte AU - Lederer, Albena AU - Appelhans, Dietmar ID - 13363 IS - 37 JF - Small KW - Biomaterials KW - Biotechnology KW - General Materials Science KW - General Chemistry SN - 1613-6810 TI - Light‐driven proton transfer for cyclic and temporal switching of enzymatic nanoreactors VL - 16 ER - TY - JOUR AB - Confining molecules can fundamentally change their chemical and physical properties. Confinement effects are considered instrumental at various stages of the origins of life, and life continues to rely on layers of compartmentalization to maintain an out-of-equilibrium state and efficiently synthesize complex biomolecules under mild conditions. As interest in synthetic confined systems grows, we are realizing that the principles governing reactivity under confinement are the same in abiological systems as they are in nature. In this Review, we categorize the ways in which nanoconfinement effects impact chemical reactivity in synthetic systems. Under nanoconfinement, chemical properties can be modulated to increase reaction rates, enhance selectivity and stabilize reactive species. Confinement effects also lead to changes in physical properties. The fluorescence of light emitters, the colours of dyes and electronic communication between electroactive species can all be tuned under confinement. Within each of these categories, we elucidate design principles and strategies that are widely applicable across a range of confined systems, specifically highlighting examples of different nanocompartments that influence reactivity in similar ways. AU - Grommet, Angela B. AU - Feller, Moran AU - Klajn, Rafal ID - 13367 JF - Nature Nanotechnology KW - Electrical and Electronic Engineering KW - Condensed Matter Physics KW - General Materials Science KW - Biomedical Engineering KW - Atomic and Molecular Physics KW - and Optics KW - Bioengineering SN - 1748-3387 TI - Chemical reactivity under nanoconfinement VL - 15 ER - TY - CONF AB - This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N 1−1/µ ), where N is the block length and µ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 and 1. AU - Mondelli, Marco AU - Hashemi, Seyyed Ali AU - Cioffi, John AU - Goldsmith, Andrea ID - 8536 SN - 21578095 T2 - IEEE International Symposium on Information Theory - Proceedings TI - Simplified successive cancellation decoding of polar codes has sublinear latency VL - 2020-June ER - TY - JOUR AB - Context. A majority of massive stars are part of binary systems, a large fraction of which will inevitably interact during their lives. Binary-interaction products (BiPs), that is, stars affected by such interaction, are expected to be commonly present in stellar populations. BiPs are thus a crucial ingredient in the understanding of stellar evolution. Aims. We aim to identify and characterize a statistically significant sample of BiPs by studying clusters of 10 − 40 Myr, an age at which binary population models predict the abundance of BiPs to be highest. One example of such a cluster is NGC 330 in the Small Magellanic Cloud. Methods. Using MUSE WFM-AO observations of NGC 330, we resolved the dense cluster core for the first time and were able to extract spectra of its entire massive star population. We developed an automated spectral classification scheme based on the equivalent widths of spectral lines in the red part of the spectrum. Results. We characterize the massive star content of the core of NGC 330, which contains more than 200 B stars, 2 O stars, 6 A-type supergiants, and 11 red supergiants. We find a lower limit on the Be star fraction of 32 ± 3% in the whole sample. It increases to at least 46 ± 10% when we only consider stars brighter than V = 17 mag. We estimate an age of the cluster core between 35 and 40 Myr and a total cluster mass of 88−18+17 × 103 M⊙. Conclusions. We find that the population in the cluster core is different than the population in the outskirts: while the stellar content in the core appears to be older than the stars in the outskirts, the Be star fraction and the observed binary fraction are significantly higher. Furthermore, we detect several BiP candidates that will be subject of future studies. AU - Bodensteiner, J. AU - Sana, H. AU - Mahy, L. AU - Patrick, L. R. AU - de Koter, A. AU - de Mink, S. E. AU - Evans, C. J. AU - Götberg, Ylva Louise Linsdotter AU - Langer, N. AU - Lennon, D. J. AU - Schneider, F. R. N. AU - Tramper, F. ID - 13466 JF - Astronomy & Astrophysics KW - stars: massive / stars: emission-line / Be / binaries: spectroscopic / blue stragglers / Magellanic Clouds SN - 0004-6361 TI - The young massive SMC cluster NGC 330 seen by MUSE VL - 634 ER - TY - JOUR AB - Gravitational-wave detections are now probing the black hole (BH) mass distribution, including the predicted pair-instability mass gap. These data require robust quantitative predictions, which are challenging to obtain. The most massive BH progenitors experience episodic mass ejections on time-scales shorter than the convective turnover time-scale. This invalidates the steady-state assumption on which the classic mixing length theory relies. We compare the final BH masses computed with two different versions of the stellar evolutionary code MESA ⁠: (i) using the default implementation of Paxton et al. (2018) and (ii) solving an additional equation accounting for the time-scale for convective deceleration. In the second grid, where stronger convection develops during the pulses and carries part of the energy, we find weaker pulses. This leads to lower amounts of mass being ejected and thus higher final BH masses of up to ∼5M⊙ ⁠. The differences are much smaller for the progenitors that determine the maximum mass of BHs below the gap. This prediction is robust at MBH,max≃48M⊙ ⁠, at least within the idealized context of this study. This is an encouraging indication that current models are robust enough for comparison with the present-day gravitational-wave detections. However, the large differences between individual models emphasize the importance of improving the treatment of convection in stellar models, especially in the light of the data anticipated from the third generation of gravitational-wave detectors. AU - Renzo, M AU - Farmer, R J AU - Justham, S AU - de Mink, S E AU - Götberg, Ylva Louise Linsdotter AU - Marchant, P ID - 13465 IS - 3 JF - Monthly Notices of the Royal Astronomical Society KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0035-8711 TI - Sensitivity of the lower edge of the pair-instability black hole mass gap to the treatment of time-dependent convection VL - 493 ER - TY - JOUR AB - Massive stars are often found in binary systems, and it has been argued that binary products boost the ionizing radiation of stellar populations. Accurate predictions for binary products are needed to understand and quantify their contribution to cosmic reionization. We investigate the contribution of stars stripped in binaries because (1) they are, arguably, the best-understood products of binary evolution, (2) we recently produced the first radiative transfer calculations for the atmospheres of these stripped stars that predict their ionizing spectra, and (3) they are very promising sources because they boost the ionizing emission of stellar populations at late times. This allows stellar feedback to clear the surroundings such that a higher fraction of their photons can escape and ionize the intergalactic medium. Combining our detailed predictions for the ionizing spectra with a simple cosmic reionization model, we estimate that stripped stars contributed tens of percent of the photons that caused cosmic reionization of hydrogen, depending on the assumed escape fractions. More importantly, stripped stars harden the ionizing emission. We estimate that the spectral index for the ionizing part of the spectrum can increase to −1 compared to ≲ − 2 for single stars. At high redshift, stripped stars and massive single stars combined dominate the He II-ionizing emission, but we expect that active galactic nuclei drive cosmic helium reionization. Further observational consequences we expect are (1) high ionization states for the intergalactic gas surrounding stellar systems, such as C IV and Si IV, and (2) additional heating of the intergalactic medium of up to a few thousand Kelvin. Quantifying these warrants the inclusion of accurate models for stripped stars and other binary products in full cosmological simulations. AU - Götberg, Ylva Louise Linsdotter AU - de Mink, S. E. AU - McQuinn, M. AU - Zapartas, E. AU - Groh, J. H. AU - Norman, C. ID - 13467 JF - Astronomy & Astrophysics KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-6361 TI - Contribution from stars stripped in binaries to cosmic reionization of hydrogen and helium VL - 634 ER - TY - JOUR AB - Present and upcoming time-domain astronomy efforts, in part driven by gravitational-wave follow-up campaigns, will unveil a variety of rare explosive transients in the sky. Here, we focus on pulsational pair-instability evolution, which can result in signatures that are observable with electromagnetic and gravitational waves. We simulated grids of bare helium stars to characterize the resulting black hole (BH) masses together with the ejecta composition, velocity, and thermal state. We find that the stars do not react “elastically” to the thermonuclear ignition in the core: there is not a one-to-one correspondence between pair-instability driven ignition and mass ejections, which causes ambiguity as to what is an observable pulse. In agreement with previous studies, we find that for initial helium core masses of 37.5 M⊙ ≲ MHe, init ≲ 41 M⊙, corresponding to carbon-oxygen core masses 27.5 M⊙ ≲ MCO ≲ 30.1 M⊙, the explosions are not strong enough to affect the surface. With increasing initial helium core mass, they become progressively stronger causing first large radial expansion (41 M⊙ ≲ MHe, init ≲ 42 M⊙, corresponding to 30.1 M⊙ ≲ MCO ≲ 30.8 M⊙) and, finally, also mass ejection episodes (for MHe, init ≳ 42 M⊙, or MCO ≳ 30.8 M⊙). The lowest mass helium core to be fully disrupted in a pair-instability supernova is MHe, init ≃ 80 M⊙, corresponding to MCO ≃ 55 M⊙. Models with MHe, init ≳ 200 M⊙ (MCO ≳ 114 M⊙) reach the photodisintegration regime, resulting in BHs with masses of MBH ≳ 125 M⊙. Although this is currently considered unlikely, if BHs from these models form via (weak) explosions, the previously-ejected material might be hit by the blast wave and convert kinetic energy into observable electromagnetic radiation. We characterize the hydrogen-free circumstellar material from the pulsational pair-instability of helium cores by simply assuming that the ejecta maintain a constant velocity after ejection. We find that our models produce helium-rich ejecta with mass of 10−3 M⊙ ≲ MCSM ≲ 40 M⊙, the larger values corresponding to the more massive progenitor stars. These ejecta are typically launched at a few thousand km s−1 and reach distances of ∼1012 − 1015 cm before the core-collapse of the star. The delays between mass ejection events and the final collapse span a wide and mass-dependent range (from subhour to 104 years), and the shells ejected can also collide with each other, powering supernova impostor events before the final core-collapse. The range of properties we find suggests a possible connection with (some) type Ibn supernovae. AU - Renzo, M. AU - Farmer, R. AU - Justham, S. AU - Götberg, Ylva Louise Linsdotter AU - de Mink, S. E. AU - Zapartas, E. AU - Marchant, P. AU - Smith, N. ID - 13463 JF - Astronomy & Astrophysics KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-6361 TI - Predictions for the hydrogen-free ejecta of pulsational pair-instability supernovae VL - 640 ER - TY - JOUR AB - High-resolution numerical simulations including feedback and aimed at calculating the escape fraction (fesc) of hydrogen-ionizing photons often assume stellar radiation based on single-stellar population synthesis models. However, strong evidence suggests the binary fraction of massive stars is ≳70%. Moreover, simulations so far have yielded values of fesc falling only on the lower end of the ∼10%–20% range, the amount presumed necessary to reionize the universe. Analyzing a high-resolution (4 pc) cosmological radiation-hydrodynamic simulation, we study how fesc changes when we include two different products of binary stellar evolution—stars stripped of their hydrogen envelopes and massive blue stragglers. Both produce significant amounts of ionizing photons 10–200 Myr after each starburst. We find the relative importance of these photons to be amplified with respect to escaped ionizing photons, because peaks in star formation rates (SFRs) and fesc are often out of phase by this 10–200 Myr. Additionally, low-mass, bursty galaxies emit Lyman continuum radiation primarily from binary products when SFRs are low. Observations of these galaxies by the James Webb Space Telescope could provide crucial information on the evolution of binary stars as a function of redshift. Overall, including stripped stars and massive blue stragglers increases our photon-weighted mean escape fraction ($\langle {f}_{\mathrm{esc}}\rangle $) by ∼13% and ∼10%, respectively, resulting in $\langle {f}_{\mathrm{esc}}\rangle =17 \% $. Our results emphasize that using updated stellar population synthesis models with binary stellar evolution provides a more sound physical basis for stellar reionization. AU - Secunda, Amy AU - Cen, Renyue AU - Kimm, Taysun AU - Götberg, Ylva Louise Linsdotter AU - de Mink, Selma E. ID - 13461 IS - 1 JF - The Astrophysical Journal KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-637X TI - Delayed photons from binary evolution help reionize the universe VL - 901 ER - TY - JOUR AB - Massive binaries that merge as compact objects are the progenitors of gravitational-wave sources. Most of these binaries experience one or more phases of mass transfer, during which one of the stars loses all or part of its outer envelope and becomes a stripped-envelope star. The evolution of the size of these stripped stars is crucial in determining whether they experience further interactions and understanding their ultimate fate. We present new calculations of stripped-envelope stars based on binary evolution models computed with MESA. We use these to investigate their radius evolution as a function of mass and metallicity. We further discuss their pre-supernova observable characteristics and potential consequences of their evolution on the properties of supernovae from stripped stars. At high metallicity, we find that practically all of the hydrogen-rich envelope is removed, which is in agreement with earlier findings. Only progenitors with initial masses below 10 M⊙ expand to large radii (up to 100 R⊙), while more massive progenitors remain compact. At low metallicity, a substantial amount of hydrogen remains and the progenitors can, in principle, expand to giant sizes (> 400 R⊙) for all masses we consider. This implies that they can fill their Roche lobe anew. We show that the prescriptions commonly used in population synthesis models underestimate the stellar radii by up to two orders of magnitude. We expect that this has consequences for the predictions for gravitational-wave sources from double neutron star mergers, particularly with regard to their metallicity dependence. AU - Laplace, E. AU - Götberg, Ylva Louise Linsdotter AU - de Mink, S. E. AU - Justham, S. AU - Farmer, R. ID - 13464 JF - Astronomy & Astrophysics KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-6361 TI - The expansion of stripped-envelope stars: Consequences for supernovae and gravitational-wave progenitors VL - 637 ER - TY - JOUR AU - Avvakumov, Sergey AU - Wagner, Uli AU - Mabillard, Isaac AU - Skopenkov, A. B. ID - 9308 IS - 6 JF - Russian Mathematical Surveys SN - 0036-0279 TI - Eliminating higher-multiplicity intersections, III. Codimension 2 VL - 75 ER - TY - JOUR AB - We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates. AU - Carlen, Eric A. AU - Maas, Jan ID - 6358 IS - 2 JF - Journal of Statistical Physics SN - 00224715 TI - Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems VL - 178 ER - TY - CHAP AB - We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean space, motivated by the famous theorem of Gromov about the waist of radially symmetric Gaussian measures. In particular, it turns our possible to extend Gromov’s original result to the case of not necessarily radially symmetric Gaussian measure. We also provide examples of measures having no t-neighborhood waist property, including a rather wide class of compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2. We use a simpler form of Gromov’s pancake argument to produce some estimates of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian measures. AU - Akopyan, Arseniy AU - Karasev, Roman ED - Klartag, Bo'az ED - Milman, Emanuel ID - 74 SN - 00758434 T2 - Geometric Aspects of Functional Analysis TI - Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures VL - 2256 ER - TY - JOUR AB - We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree. AU - Browning, Timothy D AU - Sawin, Will ID - 177 IS - 3 JF - Annals of Mathematics TI - A geometric version of the circle method VL - 191 ER - TY - JOUR AB - While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials. AU - Benedikter, Niels P AU - Nam, Phan Thành AU - Porta, Marcello AU - Schlein, Benjamin AU - Seiringer, Robert ID - 6649 JF - Communications in Mathematical Physics SN - 0010-3616 TI - Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime VL - 374 ER - TY - JOUR AB - Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses. AU - Stella, Federico AU - Urdapilleta, Eugenio AU - Luo, Yifan AU - Treves, Alessandro ID - 6796 IS - 4 JF - Hippocampus SN - 10509631 TI - Partial coherence and frustration in self-organizing spherical grids VL - 30 ER - TY - JOUR AB - In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability. AU - Avni, Guy AU - Henzinger, Thomas A AU - Kupferman, Orna ID - 6761 JF - Theoretical Computer Science SN - 03043975 TI - Dynamic resource allocation games VL - 807 ER - TY - JOUR AB - We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising. AU - Shehu, Yekini AU - Li, Xiao-Huan AU - Dong, Qiao-Li ID - 6593 JF - Numerical Algorithms SN - 1017-1398 TI - An efficient projection-type method for monotone variational inequalities in Hilbert spaces VL - 84 ER - TY - JOUR AB - Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions. AU - Jahr, Wiebke AU - Velicky, Philipp AU - Danzl, Johann G ID - 6808 IS - 3 JF - Methods SN - 1046-2023 TI - Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens VL - 174 ER - TY - JOUR AB - This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋. AU - Filakovský, Marek AU - Vokřínek, Lukas ID - 6563 JF - Foundations of Computational Mathematics SN - 16153375 TI - Are two given maps homotopic? An algorithmic viewpoint VL - 20 ER - TY - JOUR AB - We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn. AU - Henderson, Paul M AU - Ferrari, Vittorio ID - 6952 JF - International Journal of Computer Vision SN - 0920-5691 TI - Learning single-image 3D reconstruction by generative modelling of shape, pose and shading VL - 128 ER - TY - JOUR AB - In the cerebellum, GluD2 is exclusively expressed in Purkinje cells, where it regulates synapse formation and regeneration, synaptic plasticity, and motor learning. Delayed cognitive development in humans with GluD2 gene mutations suggests extracerebellar functions of GluD2. However, extracerebellar expression of GluD2 and its relationship with that of GluD1 are poorly understood. GluD2 mRNA and protein were widely detected, with relatively high levels observed in the olfactory glomerular layer, medial prefrontal cortex, cingulate cortex, retrosplenial granular cortex, olfactory tubercle, subiculum, striatum, lateral septum, anterodorsal thalamic nucleus, and arcuate hypothalamic nucleus. These regions were also enriched for GluD1, and many individual neurons coexpressed the two GluDs. In the retrosplenial granular cortex, GluD1 and GluD2 were selectively expressed at PSD‐95‐expressing glutamatergic synapses, and their coexpression on the same synapses was shown by SDS‐digested freeze‐fracture replica labeling. Biochemically, GluD1 and GluD2 formed coimmunoprecipitable complex formation in HEK293T cells and in the cerebral cortex and hippocampus. We further estimated the relative protein amount by quantitative immunoblotting using GluA2/GluD2 and GluA2/GluD1 chimeric proteins as standards for titration of GluD1 and GluD2 antibodies. Intriguingly, the relative amount of GluD2 was almost comparable to that of GluD1 in the postsynaptic density fraction prepared from the cerebral cortex and hippocampus. In contrast, GluD2 was overwhelmingly predominant in the cerebellum. Thus, we have determined the relative extracerebellar expression of GluD1 and GluD2 at regional, neuronal, and synaptic levels. These data provide a molecular–anatomical basis for possible competitive and cooperative interactions of GluD family members at synapses in various brain regions. AU - Nakamoto, Chihiro AU - Konno, Kohtarou AU - Miyazaki, Taisuke AU - Nakatsukasa, Ena AU - Natsume, Rie AU - Abe, Manabu AU - Kawamura, Meiko AU - Fukazawa, Yugo AU - Shigemoto, Ryuichi AU - Yamasaki, Miwako AU - Sakimura, Kenji AU - Watanabe, Masahiko ID - 7148 IS - 6 JF - Journal of Comparative Neurology SN - 0021-9967 TI - Expression mapping, quantification, and complex formation of GluD1 and GluD2 glutamate receptors in adult mouse brain VL - 528 ER - TY - JOUR AB - Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality. AU - Donahue, RJ AU - Maes, Margaret E AU - Grosser, JA AU - Nickells, RW ID - 7033 IS - 2 JF - Molecular Neurobiology SN - 0893-7648 TI - BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage VL - 57 ER - TY - JOUR AU - Zhang, Yuzhou AU - Friml, Jiří ID - 6997 IS - 3 JF - New Phytologist SN - 0028-646x TI - Auxin guides roots to avoid obstacles during gravitropic growth VL - 225 ER - TY - JOUR AB - In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways. AU - Avagliano, Laura AU - Parenti, Ilaria AU - Grazioli, Paolo AU - Di Fede, Elisabetta AU - Parodi, Chiara AU - Mariani, Milena AU - Kaiser, Frank J. AU - Selicorni, Angelo AU - Gervasini, Cristina AU - Massa, Valentina ID - 7149 IS - 1 JF - Clinical Genetics SN - 0009-9163 TI - Chromatinopathies: A focus on Cornelia de Lange syndrome VL - 97 ER - TY - JOUR AB - We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds. AU - Rapcak, Miroslav AU - Soibelman, Yan AU - Yang, Yaping AU - Zhao, Gufang ID - 7004 JF - Communications in Mathematical Physics SN - 0010-3616 TI - Cohomological Hall algebras, vertex algebras and instantons VL - 376 ER - TY - JOUR AB - Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin. AU - Li, Yang AU - Wang, Yaping AU - Tan, Shutang AU - Li, Zhen AU - Yuan, Zhi AU - Glanc, Matous AU - Domjan, David AU - Wang, Kai AU - Xuan, Wei AU - Guo, Yan AU - Gong, Zhizhong AU - Friml, Jiří AU - Zhang, Jing ID - 7204 IS - 3 JF - Advanced Science TI - Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex VL - 7 ER - TY - JOUR AB - BACKGROUND:The introduction of image-guided methods to bypass surgery has resulted in optimized preoperative identification of the recipients and excellent patency rates. However, the recently presented methods have also been resource-consuming. In the present study, we have reported a cost-efficient planning workflow for extracranial-intracranial (EC-IC) revascularization combined with transdural indocyanine green videoangiography (tICG-VA). METHODS:We performed a retrospective review at a single tertiary referral center from 2011 to 2018. A novel software-derived workflow was applied for 25 of 92 bypass procedures during the study period. The precision and accuracy were assessed using tICG-VA identification of the cortical recipients and a comparison of the virtual and actual data. The data from a control group of 25 traditionally planned procedures were also matched. RESULTS:The intraoperative transfer time of the calculated coordinates averaged 0.8 minute (range, 0.4-1.9 minutes). The definitive recipients matched the targeted branches in 80%, and a neighboring branch was used in 16%. Our workflow led to a significant craniotomy size reduction in the study group compared with that in the control group (P = 0.005). tICG-VA was successfully applied in 19 cases. An average of 2 potential recipient arteries were identified transdurally, resulting in tailored durotomy and 3 craniotomy adjustments. Follow-up patency results were available for 49 bypass surgeries, comprising 54 grafts. The overall patency rate was 91% at a median follow-up period of 26 months. No significant difference was found in the patency rate between the study and control groups (P = 0.317). CONCLUSIONS:Our clinical results have validated the presented planning and surgical workflow and support the routine implementation of tICG-VA for recipient identification before durotomy. AU - Dodier, Philippe AU - Auzinger, Thomas AU - Mistelbauer, Gabriel AU - Wang, Wei Te AU - Ferraz-Leite, Heber AU - Gruber, Andreas AU - Marik, Wolfgang AU - Winter, Fabian AU - Fischer, Gerrit AU - Frischer, Josa M. AU - Bavinzski, Gerhard ID - 7220 IS - 2 JF - World Neurosurgery SN - 1878-8750 TI - Novel software-derived workflow in extracranial–intracranial bypass surgery validated by transdural indocyanine green videoangiography VL - 134 ER - TY - JOUR AB - The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin. AU - Gallei, Michelle C AU - Luschnig, Christian AU - Friml, Jiří ID - 7142 IS - 2 JF - Current Opinion in Plant Biology SN - 1369-5266 TI - Auxin signalling in growth: Schrödinger's cat out of the bag VL - 53 ER - TY - JOUR AB - In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors. AU - Ucar, Mehmet C AU - Lipowsky, Reinhard ID - 7166 IS - 1 JF - Nano Letters SN - 1530-6984 TI - Collective force generation by molecular motors is determined by strain-induced unbinding VL - 20 ER -