TY - JOUR
AB - The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.
AU - Gupta, Chitrak
AU - Khaniya, Umesh
AU - Chan, Chun Kit
AU - Dehez, Francois
AU - Shekhar, Mrinal
AU - Gunner, M. R.
AU - Sazanov, Leonid A
AU - Chipot, Christophe
AU - Singharoy, Abhishek
ID - 8040
IS - 20
JF - Journal of the American Chemical Society
SN - 00027863
TI - Charge transfer and chemo-mechanical coupling in respiratory complex I
VL - 142
ER -
TY - JOUR
AB - When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.
AU - Collard, Ylona
AU - Grosjean, Galien M
AU - Vandewalle, Nicolas
ID - 8036
JF - Communications Physics
TI - Magnetically powered metachronal waves induce locomotion in self-assemblies
VL - 3
ER -
TY - JOUR
AB - With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain.
AU - Paranjape, Chaitanya S
AU - Duguet, Yohann
AU - Hof, Björn
ID - 8043
JF - Journal of Fluid Mechanics
SN - 00221120
TI - Oblique stripe solutions of channel flow
VL - 897
ER -
TY - GEN
AB - The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.
AU - Gupta, Chitrak
AU - Khaniya, Umesh
AU - Chan, Chun
AU - Dehez, Francois
AU - Shekhar, Mrinal
AU - Gunner, M. R.
AU - Sazanov, Leonid A
AU - Chipot, Christophe
AU - Singharoy, Abhishek
ID - 9326
TI - Charge transfer and chemo-mechanical coupling in respiratory complex I
ER -
TY - JOUR
AB - We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.
AU - Boccato, Chiara
AU - Brennecke, Christian
AU - Cenatiempo, Serena
AU - Schlein, Benjamin
ID - 8042
IS - 7
JF - Journal of the European Mathematical Society
SN - 14359855
TI - The excitation spectrum of Bose gases interacting through singular potentials
VL - 22
ER -
TY - GEN
AB - Additional analyses of the trajectories
AU - Gupta, Chitrak
AU - Khaniya, Umesh
AU - Chan, Chun Kit
AU - Dehez, Francois
AU - Shekhar, Mrinal
AU - Gunner, M.R.
AU - Sazanov, Leonid A
AU - Chipot, Christophe
AU - Singharoy, Abhishek
ID - 9713
TI - Supporting information
ER -
TY - GEN
AU - Gupta, Chitrak
AU - Khaniya, Umesh
AU - Chan, Chun Kit
AU - Dehez, Francois
AU - Shekhar, Mrinal
AU - Gunner, M.R.
AU - Sazanov, Leonid A
AU - Chipot, Christophe
AU - Singharoy, Abhishek
ID - 9878
TI - Movies
ER -
TY - JOUR
AB - Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment.
Methods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo.
Results: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system.
Conclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy.
AU - Hippe, Andreas
AU - Braun, Stephan Alexander
AU - Oláh, Péter
AU - Gerber, Peter Arne
AU - Schorr, Anne
AU - Seeliger, Stephan
AU - Holtz, Stephanie
AU - Jannasch, Katharina
AU - Pivarcsi, Andor
AU - Buhren, Bettina
AU - Schrumpf, Holger
AU - Kislat, Andreas
AU - Bünemann, Erich
AU - Steinhoff, Martin
AU - Fischer, Jens
AU - Lira, Sérgio A.
AU - Boukamp, Petra
AU - Hevezi, Peter
AU - Stoecklein, Nikolas Hendrik
AU - Hoffmann, Thomas
AU - Alves, Frauke
AU - Sleeman, Jonathan
AU - Bauer, Thomas
AU - Klufa, Jörg
AU - Amberg, Nicole
AU - Sibilia, Maria
AU - Zlotnik, Albert
AU - Müller-Homey, Anja
AU - Homey, Bernhard
ID - 8093
JF - British Journal of Cancer
SN - 0007-0920
TI - EGFR/Ras-induced CCL20 production modulates the tumour microenvironment
VL - 123
ER -
TY - JOUR
AB - In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.
AU - Seiringer, Robert
AU - Yngvason, Jakob
ID - 8091
JF - Journal of Statistical Physics
SN - 00224715
TI - Emergence of Haldane pseudo-potentials in systems with short-range interactions
VL - 181
ER -
TY - JOUR
AB - The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.
AU - Shehu, Yekini
AU - Iyiola, Olaniyi S.
ID - 8077
JF - Applied Numerical Mathematics
SN - 0168-9274
TI - Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence
VL - 157
ER -
TY - JOUR
AB - In the present work, we report a solution-based strategy to produce crystallographically textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric performance in the direction normal to the substrate. Our strategy is based on the formulation of a molecular precursor that can be continuously decomposed to produce a SnSe powder or printed into predefined patterns. The precursor formulation and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates. The printed layer and the bulk material obtained after hot press displays a clear preferential orientation of the crystallographic domains, resulting in an ultralow thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate. Such textured nanomaterials present highly anisotropic properties with the best thermoelectric performance in plane, i.e., in the directions parallel to the substrate, which coincide with the crystallographic bc plane of SnSe. This is an unfortunate characteristic because thermoelectric devices are designed to create/harvest temperature gradients in the direction normal to the substrate. We further demonstrate that this limitation can be overcome with the introduction of small amounts of tellurium in the precursor. The presence of tellurium allows one to reduce the band gap and increase both the charge carrier concentration and the mobility, especially the cross plane, with a minimal decrease of the Seebeck coefficient. These effects translate into record out of plane ZT values at 800 K.
AU - Zhang, Yu
AU - Liu, Yu
AU - Xing, Congcong
AU - Zhang, Ting
AU - Li, Mengyao
AU - Pacios, Mercè
AU - Yu, Xiaoting
AU - Arbiol, Jordi
AU - Llorca, Jordi
AU - Cadavid, Doris
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 8039
IS - 24
JF - ACS Applied Materials and Interfaces
TI - Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices
VL - 12
ER -
TY - JOUR
AB - The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.
AU - Hillary, Robert F.
AU - Trejo-Banos, Daniel
AU - Kousathanas, Athanasios
AU - Mccartney, Daniel L.
AU - Harris, Sarah E.
AU - Stevenson, Anna J.
AU - Patxot, Marion
AU - Ojavee, Sven Erik
AU - Zhang, Qian
AU - Liewald, David C.
AU - Ritchie, Craig W.
AU - Evans, Kathryn L.
AU - Tucker-Drob, Elliot M.
AU - Wray, Naomi R.
AU - Mcrae, Allan F.
AU - Visscher, Peter M.
AU - Deary, Ian J.
AU - Robinson, Matthew Richard
AU - Marioni, Riccardo E.
ID - 8133
IS - 1
JF - Genome Medicine
TI - Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults
VL - 12
ER -
TY - JOUR
AB - Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.
AU - Gonçalves, Pedro J.
AU - Lueckmann, Jan-Matthis
AU - Deistler, Michael
AU - Nonnenmacher, Marcel
AU - Öcal, Kaan
AU - Bassetto, Giacomo
AU - Chintaluri, Chaitanya
AU - Podlaski, William F.
AU - Haddad, Sara A.
AU - Vogels, Tim P
AU - Greenberg, David S.
AU - Macke, Jakob H.
ID - 8127
JF - eLife
TI - Training deep neural density estimators to identify mechanistic models of neural dynamics
VL - 9
ER -
TY - JOUR
AB - Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.
AU - Agnes, Everton J.
AU - Luppi, Andrea I.
AU - Vogels, Tim P
ID - 8126
IS - 50
JF - The Journal of Neuroscience
TI - Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields
VL - 40
ER -
TY - JOUR
AB - The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity.
AU - Salzer, Elisabeth
AU - Zoghi, Samaneh
AU - Kiss, Máté G.
AU - Kage, Frieda
AU - Rashkova, Christina
AU - Stahnke, Stephanie
AU - Haimel, Matthias
AU - Platzer, René
AU - Caldera, Michael
AU - Ardy, Rico Chandra
AU - Hoeger, Birgit
AU - Block, Jana
AU - Medgyesi, David
AU - Sin, Celine
AU - Shahkarami, Sepideh
AU - Kain, Renate
AU - Ziaee, Vahid
AU - Hammerl, Peter
AU - Bock, Christoph
AU - Menche, Jörg
AU - Dupré, Loïc
AU - Huppa, Johannes B.
AU - Sixt, Michael K
AU - Lomakin, Alexis
AU - Rottner, Klemens
AU - Binder, Christoph J.
AU - Stradal, Theresia E.B.
AU - Rezaei, Nima
AU - Boztug, Kaan
ID - 8132
IS - 49
JF - Science Immunology
TI - The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity
VL - 5
ER -
TY - GEN
AB - Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).
AU - Hillary, Robert F.
AU - Trejo-Banos, Daniel
AU - Kousathanas, Athanasios
AU - McCartney, Daniel L.
AU - Harris, Sarah E.
AU - Stevenson, Anna J.
AU - Patxot, Marion
AU - Ojavee, Sven Erik
AU - Zhang, Qian
AU - Liewald, David C.
AU - Ritchie, Craig W.
AU - Evans, Kathryn L.
AU - Tucker-Drob, Elliot M.
AU - Wray, Naomi R.
AU - McRae, Allan F.
AU - Visscher, Peter M.
AU - Deary, Ian J.
AU - Robinson, Matthew Richard
AU - Marioni, Riccardo E.
ID - 9706
TI - Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults
ER -
TY - JOUR
AB - We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.
AU - Mayer, Simon
AU - Seiringer, Robert
ID - 8134
IS - 6
JF - Journal of Mathematical Physics
SN - 00222488
TI - The free energy of the two-dimensional dilute Bose gas. II. Upper bound
VL - 61
ER -
TY - JOUR
AU - Barton, Nicholas H
ID - 8112
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
SN - 0962-8436
TI - On the completion of speciation
VL - 375
ER -
TY - JOUR
AB - In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.
AU - Laukoter, Susanne
AU - Pauler, Florian
AU - Beattie, Robert J
AU - Amberg, Nicole
AU - Hansen, Andi H
AU - Streicher, Carmen
AU - Penz, Thomas
AU - Bock, Christoph
AU - Hippenmeyer, Simon
ID - 8162
IS - 6
JF - Neuron
SN - 0896-6273
TI - Cell-type specificity of genomic imprinting in cerebral cortex
VL - 107
ER -
TY - JOUR
AB - Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.
AU - Zhang, J
AU - Mazur, E
AU - Balla, J
AU - Gallei, Michelle C
AU - Kalousek, P
AU - Medveďová, Z
AU - Li, Y
AU - Wang, Y
AU - Prat, Tomas
AU - Vasileva, Mina K
AU - Reinöhl, V
AU - Procházka, S
AU - Halouzka, R
AU - Tarkowski, P
AU - Luschnig, C
AU - Brewer, PB
AU - Friml, Jiří
ID - 8138
IS - 1
JF - Nature Communications
SN - 2041-1723
TI - Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization
VL - 11
ER -
TY - JOUR
AB - Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.
AU - Kulmuni, Jonna
AU - Butlin, Roger K.
AU - Lucek, Kay
AU - Savolainen, Vincent
AU - Westram, Anja M
ID - 8168
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological sciences
SN - 0962-8436
TI - Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers
VL - 375
ER -
TY - JOUR
AB - The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.
AU - Stankowski, Sean
AU - Westram, Anja M
AU - Zagrodzka, Zuzanna B.
AU - Eyres, Isobel
AU - Broquet, Thomas
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
ID - 8167
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - The evolution of strong reproductive isolation between sympatric intertidal snails
VL - 375
ER -
TY - JOUR
AB - Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function
of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct
peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and
centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For
CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the
gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in
detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in
helium droplets introduced here should apply to a range of molecules and complexes.
AU - Chatterley, Adam S.
AU - Christiansen, Lars
AU - Schouder, Constant A.
AU - Jørgensen, Anders V.
AU - Shepperson, Benjamin
AU - Cherepanov, Igor
AU - Bighin, Giacomo
AU - Zillich, Robert E.
AU - Lemeshko, Mikhail
AU - Stapelfeldt, Henrik
ID - 8170
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains
VL - 125
ER -
TY - CONF
AB - Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.
AU - Baranowski, Marek
AU - He, Shaobo
AU - Lechner, Mathias
AU - Nguyen, Thanh Son
AU - Rakamarić, Zvonimir
ID - 8194
SN - 03029743
T2 - Automated Reasoning
TI - An SMT theory of fixed-point arithmetic
VL - 12166
ER -
TY - JOUR
AB - Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.
AU - Shang, Huiying
AU - Hess, Jaqueline
AU - Pickup, Melinda
AU - Field, David
AU - Ingvarsson, Pär K.
AU - Liu, Jianquan
AU - Lexer, Christian
ID - 8169
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group
VL - 375
ER -
TY - JOUR
AB - Direct ethanol fuel cells (DEFCs) show a huge potential to power future electric vehicles and portable electronics, but their deployment is currently limited by the unavailability of proper electrocatalysis for the ethanol oxidation reaction (EOR). In this work, we engineer a new electrocatalyst by incorporating phosphorous into a palladium-tin alloy and demonstrate a significant performance improvement toward EOR. We first detail a synthetic method to produce Pd2Sn:P nanocrystals that incorporate 35% of phosphorus. These nanoparticles are supported on carbon black and tested for EOR. Pd2Sn:P/C catalysts exhibit mass current densities up to 5.03 A mgPd−1, well above those of Pd2Sn/C, PdP2/C and Pd/C reference catalysts. Furthermore, a twofold lower Tafel slope and a much longer durability are revealed for the Pd2Sn:P/C catalyst compared with Pd/C. The performance improvement is rationalized with the aid of density functional theory (DFT) calculations considering different phosphorous chemical environments. Depending on its oxidation state, surface phosphorus introduces sites with low energy OH− adsorption and/or strongly influences the electronic structure of palladium and tin to facilitate the oxidation of the acetyl to acetic acid, which is considered the EOR rate limiting step. DFT calculations also points out that the durability improvement of Pd2Sn:P/C catalyst is associated to the promotion of OH adsorption that accelerates the oxidation of intermediate poisoning COads, reactivating the catalyst surface.
AU - Yu, Xiaoting
AU - Liu, Junfeng
AU - Li, Junshan
AU - Luo, Zhishan
AU - Zuo, Yong
AU - Xing, Congcong
AU - Llorca, Jordi
AU - Nasiou, Déspina
AU - Arbiol, Jordi
AU - Pan, Kai
AU - Kleinhanns, Tobias
AU - Xie, Ying
AU - Cabot, Andreu
ID - 8189
IS - 11
JF - Nano Energy
SN - 2211-2855
TI - Phosphorous incorporation in Pd2Sn alloys for electrocatalytic ethanol oxidation
VL - 77
ER -
TY - JOUR
AB - Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.
AU - Corominas-Murtra, Bernat
AU - Scheele, Colinda L.G.J.
AU - Kishi, Kasumi
AU - Ellenbroek, Saskia I.J.
AU - Simons, Benjamin D.
AU - Van Rheenen, Jacco
AU - Hannezo, Edouard B
ID - 8220
IS - 29
JF - Proceedings of the National Academy of Sciences of the United States of America
TI - Stem cell lineage survival as a noisy competition for niche access
VL - 117
ER -
TY - JOUR
AB - We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.
AU - Gulden, Tobias
AU - Berg, Erez
AU - Rudner, Mark Spencer
AU - Lindner, Netanel
ID - 8199
JF - SciPost Physics
SN - 2542-4653
TI - Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps
VL - 9
ER -
TY - JOUR
AB - Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.
AU - Zhang, Xiaomin
AU - Schlögl, Alois
AU - Jonas, Peter M
ID - 8261
IS - 6
JF - Neuron
SN - 0896-6273
TI - Selective routing of spatial information flow from input to output in hippocampal granule cells
VL - 107
ER -
TY - JOUR
AB - Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.
AU - Gurel, Nezihe Merve
AU - Kara, Kaan
AU - Stojanov, Alen
AU - Smith, Tyler
AU - Lemmin, Thomas
AU - Alistarh, Dan-Adrian
AU - Puschel, Markus
AU - Zhang, Ce
ID - 8268
JF - IEEE Transactions on Signal Processing
SN - 1053587X
TI - Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications
VL - 68
ER -
TY - JOUR
AU - He, Peng
AU - Zhang, Yuzhou
AU - Xiao, Guanghui
ID - 8271
IS - 9
JF - Molecular Plant
SN - 16742052
TI - Origin of a subgenome and genome evolution of allotetraploid cotton species
VL - 13
ER -
TY - JOUR
AB - By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.
AU - Grosjean, Galien M
AU - Wald, Sebastian
AU - Sobarzo Ponce, Juan Carlos A
AU - Waitukaitis, Scott R
ID - 8101
IS - 8
JF - Physical Review Materials
KW - electric charge
KW - tribocharging
KW - soft matter
KW - granular materials
KW - polymers
SN - 2475-9953
TI - Quantitatively consistent scale-spanning model for same-material tribocharging
VL - 4
ER -
TY - JOUR
AB - Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes.
AU - Kalinin, Nikita
AU - Shkolnikov, Mikhail
ID - 8325
IS - 9
JF - Communications in Mathematical Physics
SN - 00103616
TI - Sandpile solitons via smoothing of superharmonic functions
VL - 378
ER -
TY - JOUR
AB - Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
AU - Gutierrez-Fernandez, Javier
AU - Kaszuba, Karol
AU - Minhas, Gurdeep S.
AU - Baradaran, Rozbeh
AU - Tambalo, Margherita
AU - Gallagher, David T.
AU - Sazanov, Leonid A
ID - 8318
IS - 1
JF - Nature Communications
TI - Key role of quinone in the mechanism of respiratory complex I
VL - 11
ER -
TY - JOUR
AB - The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.
AU - Mukba, S. A.
AU - Vlasov, Petr
AU - Kolosov, P. M.
AU - Shuvalova, E. Y.
AU - Egorova, T. V.
AU - Alkalaeva, E. Z.
ID - 8320
IS - 4
JF - Molecular Biology
SN - 00268933
TI - Expanding the genetic code: Unnatural base pairs in biological systems
VL - 54
ER -
TY - JOUR
AB - The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.
AU - Mukba, S. A.
AU - Vlasov, Petr
AU - Kolosov, P. M.
AU - Shuvalova, E. Y.
AU - Egorova, T. V.
AU - Alkalaeva, E. Z.
ID - 8321
IS - 4
JF - Molekuliarnaia biologiia
SN - 00268984
TI - Expanding the genetic code: Unnatural base pairs in biological systems
VL - 54
ER -
TY - JOUR
AU - Pach, János
ID - 8323
JF - Discrete and Computational Geometry
SN - 01795376
TI - A farewell to Ricky Pollack
VL - 64
ER -
TY - JOUR
AB - Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.
AU - Kubiasova, Karolina
AU - Montesinos López, Juan C
AU - Šamajová, Olga
AU - Nisler, Jaroslav
AU - Mik, Václav
AU - Semeradova, Hana
AU - Plíhalová, Lucie
AU - Novák, Ondřej
AU - Marhavý, Peter
AU - Cavallari, Nicola
AU - Zalabák, David
AU - Berka, Karel
AU - Doležal, Karel
AU - Galuszka, Petr
AU - Šamaj, Jozef
AU - Strnad, Miroslav
AU - Benková, Eva
AU - Plíhal, Ondřej
AU - Spíchal, Lukáš
ID - 8336
JF - Nature Communications
TI - Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum
VL - 11
ER -
TY - JOUR
AB - Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.
AU - Antoniadi, Ioanna
AU - Novák, Ondřej
AU - Gelová, Zuzana
AU - Johnson, Alexander J
AU - Plíhal, Ondřej
AU - Simerský, Radim
AU - Mik, Václav
AU - Vain, Thomas
AU - Mateo-Bonmatí, Eduardo
AU - Karady, Michal
AU - Pernisová, Markéta
AU - Plačková, Lenka
AU - Opassathian, Korawit
AU - Hejátko, Jan
AU - Robert, Stéphanie
AU - Friml, Jiří
AU - Doležal, Karel
AU - Ljung, Karin
AU - Turnbull, Colin
ID - 8337
JF - Nature Communications
TI - Cell-surface receptors enable perception of extracellular cytokinins
VL - 11
ER -
TY - GEN
AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the
mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.
AU - Varzi, Alberto
AU - Thanner, Katharina
AU - Scipioni, Roberto
AU - Di Lecce, Daniele
AU - Hassoun, Jusef
AU - Dörfler, Susanne
AU - Altheus, Holger
AU - Kaskel, Stefan
AU - Prehal, Christian
AU - Freunberger, Stefan Alexander
ID - 8067
KW - Battery
KW - Lithium metal
KW - Lithium-sulphur
KW - Lithium-air
KW - All-solid-state
SN - 2664-1690
TI - Current status and future perspectives of Lithium metal batteries
ER -
TY - JOUR
AB - With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.
AU - Varzi, Alberto
AU - Thanner, Katharina
AU - Scipioni, Roberto
AU - Di Lecce, Daniele
AU - Hassoun, Jusef
AU - Dörfler, Susanne
AU - Altheus, Holger
AU - Kaskel, Stefan
AU - Prehal, Christian
AU - Freunberger, Stefan Alexander
ID - 8361
IS - 12
JF - Journal of Power Sources
SN - 0378-7753
TI - Current status and future perspectives of lithium metal batteries
VL - 480
ER -
TY - JOUR
AB - Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.
AU - Arnold, Georg M
AU - Wulf, Matthias
AU - Barzanjeh, Shabir
AU - Redchenko, Elena
AU - Rueda Sanchez, Alfredo R
AU - Hease, William J
AU - Hassani, Farid
AU - Fink, Johannes M
ID - 8529
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface
VL - 11
ER -
TY - JOUR
AB - We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.
AU - Skrivan, Tomas
AU - Soderstrom, Andreas
AU - Johansson, John
AU - Sprenger, Christoph
AU - Museth, Ken
AU - Wojtan, Christopher J
ID - 8535
IS - 4
JF - ACM Transactions on Graphics
SN - 07300301
TI - Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces
VL - 39
ER -
TY - JOUR
AB - Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.
AU - Su, C.
AU - Zhao, Gufang
AU - Zhong, C.
ID - 8539
IS - 3
JF - Annales Scientifiques de l'Ecole Normale Superieure
SN - 0012-9593
TI - On the K-theory stable bases of the springer resolution
VL - 53
ER -
TY - GEN
AB - This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request.
AU - Arnold, Georg M
AU - Wulf, Matthias
AU - Barzanjeh, Shabir
AU - Redchenko, Elena
AU - Rueda Sanchez, Alfredo R
AU - Hease, William J
AU - Hassani, Farid
AU - Fink, Johannes M
ID - 13056
TI - Converting microwave and telecom photons with a silicon photonic nanomechanical interface
ER -
TY - JOUR
AB - Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.
AU - Andrei, Andreea
AU - Öztürk, Yavuz
AU - Khalfaoui-Hassani, Bahia
AU - Rauch, Juna
AU - Marckmann, Dorian
AU - Trasnea, Petru Iulian
AU - Daldal, Fevzi
AU - Koch, Hans-Georg
ID - 8579
IS - 9
JF - Membranes
TI - Cu homeostasis in bacteria: The ins and outs
VL - 10
ER -
TY - JOUR
AB - The majority of adenosine triphosphate (ATP) powering cellular processes in eukaryotes is produced by the mitochondrial F1Fo ATP synthase. Here, we present the atomic models of the membrane Fo domain and the entire mammalian (ovine) F1Fo, determined by cryo-electron microscopy. Subunits in the membrane domain are arranged in the ‘proton translocation cluster’ attached to the c-ring and a more distant ‘hook apparatus’ holding subunit e. Unexpectedly, this subunit is anchored to a lipid ‘plug’ capping the c-ring. We present a detailed proton translocation pathway in mammalian Fo and key inter-monomer contacts in F1Fo multimers. Cryo-EM maps of F1Fo exposed to calcium reveal a retracted subunit e and a disassembled c-ring, suggesting permeability transition pore opening. We propose a model for the permeability transition pore opening, whereby subunit e pulls the lipid plug out of the c-ring. Our structure will allow the design of drugs for many emerging applications in medicine.
AU - Pinke, Gergely
AU - Zhou, Long
AU - Sazanov, Leonid A
ID - 8581
IS - 11
JF - Nature Structural and Molecular Biology
SN - 15459993
TI - Cryo-EM structure of the entire mammalian F-type ATP synthase
VL - 27
ER -
TY - CONF
AB - We evaluate the usefulness of persistent homology in the analysis of heart rate variability. In our approach we extract several topological descriptors characterising datasets of RR-intervals, which are later used in classical machine learning algorithms. By this method we are able to differentiate the group of patients with the history of transient ischemic attack and the group of hypertensive patients.
AU - Graff, Grzegorz
AU - Graff, Beata
AU - Jablonski, Grzegorz
AU - Narkiewicz, Krzysztof
ID - 8580
SN - 9781728157511
T2 - 11th Conference of the European Study Group on Cardiovascular Oscillations: Computation and Modelling in Physiology: New Challenges and Opportunities,
TI - The application of persistent homology in the analysis of heart rate variability
ER -
TY - JOUR
AB - Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.
AU - Tian, Anhao
AU - Kang, Bo
AU - Li, Baizhou
AU - Qiu, Biying
AU - Jiang, Wenhong
AU - Shao, Fangjie
AU - Gao, Qingqing
AU - Liu, Rui
AU - Cai, Chengwei
AU - Jing, Rui
AU - Wang, Wei
AU - Chen, Pengxiang
AU - Liang, Qinghui
AU - Bao, Lili
AU - Man, Jianghong
AU - Wang, Yan
AU - Shi, Yu
AU - Li, Jin
AU - Yang, Minmin
AU - Wang, Lisha
AU - Zhang, Jianmin
AU - Hippenmeyer, Simon
AU - Zhu, Junming
AU - Bian, Xiuwu
AU - Wang, Ying‐Jie
AU - Liu, Chong
ID - 8592
IS - 21
JF - Advanced Science
KW - General Engineering
KW - General Physics and Astronomy
KW - General Materials Science
KW - Medicine (miscellaneous)
KW - General Chemical Engineering
KW - Biochemistry
KW - Genetics and Molecular Biology (miscellaneous)
SN - 2198-3844
TI - Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting
VL - 7
ER -
TY - JOUR
AB - Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.
AU - Prehal, Christian
AU - Fitzek, Harald
AU - Kothleitner, Gerald
AU - Presser, Volker
AU - Gollas, Bernhard
AU - Freunberger, Stefan Alexander
AU - Abbas, Qamar
ID - 8568
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Persistent and reversible solid iodine electrodeposition in nanoporous carbons
VL - 11
ER -
TY - JOUR
AB - The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.
AU - Deichler, Alfonso
AU - Carrasco, Denisse
AU - Lopez-Jury, Luciana
AU - Vega Zuniga, Tomas A
AU - Marquez, Natalia
AU - Mpodozis, Jorge
AU - Marin, Gonzalo
ID - 8643
JF - Scientific Reports
TI - A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents
VL - 10
ER -
TY - JOUR
AB - Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.
AU - Esteban, Laura A
AU - Lonishin, Lyubov R
AU - Bobrovskiy, Daniil M
AU - Leleytner, Gregory
AU - Bogatyreva, Natalya S
AU - Kondrashov, Fyodor
AU - Ivankov, Dmitry N
ID - 8645
IS - 6
JF - Bioinformatics
SN - 1367-4803
TI - HypercubeME: Two hundred million combinatorially complete datasets from a single experiment
VL - 36
ER -
TY - JOUR
AB - Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.
AU - Merrin, Jack
ID - 8597
IS - 6
JF - Physical Biology
TI - Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide
VL - 17
ER -
TY - JOUR
AB - Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.
AU - Henneberger, Christian
AU - Bard, Lucie
AU - Panatier, Aude
AU - Reynolds, James P.
AU - Kopach, Olga
AU - Medvedev, Nikolay I.
AU - Minge, Daniel
AU - Herde, Michel K.
AU - Anders, Stefanie
AU - Kraev, Igor
AU - Heller, Janosch P.
AU - Rama, Sylvain
AU - Zheng, Kaiyu
AU - Jensen, Thomas P.
AU - Sanchez-Romero, Inmaculada
AU - Jackson, Colin J.
AU - Janovjak, Harald L
AU - Ottersen, Ole Petter
AU - Nagelhus, Erlend Arnulf
AU - Oliet, Stephane H.R.
AU - Stewart, Michael G.
AU - Nägerl, U. VAlentin
AU - Rusakov, Dmitri A.
ID - 8674
IS - 5
JF - Neuron
SN - 08966273
TI - LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia
VL - 108
ER -
TY - JOUR
AB - Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules.
AU - Ghazaryan, Areg
AU - Lemeshko, Mikhail
AU - Volosniev, Artem
ID - 8652
JF - Communications Physics
SN - 2399-3650
TI - Filtering spins by scattering from a lattice of point magnets
VL - 3
ER -
TY - JOUR
AB - Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.
AU - Sznurkowska, Magdalena K.
AU - Hannezo, Edouard B
AU - Azzarelli, Roberta
AU - Chatzeli, Lemonia
AU - Ikeda, Tatsuro
AU - Yoshida, Shosei
AU - Philpott, Anna
AU - Simons, Benjamin D
ID - 8669
JF - Nature Communications
TI - Tracing the cellular basis of islet specification in mouse pancreas
VL - 11
ER -
TY - JOUR
AB - Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.
AU - Chaigne, Agathe
AU - Labouesse, Céline
AU - White, Ian J.
AU - Agnew, Meghan
AU - Hannezo, Edouard B
AU - Chalut, Kevin J.
AU - Paluch, Ewa K.
ID - 8672
IS - 2
JF - Developmental Cell
SN - 15345807
TI - Abscission couples cell division to embryonic stem cell fate
VL - 55
ER -
TY - JOUR
AB - In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.
AU - Fischer, Julian L
AU - Kniely, Michael
ID - 8697
IS - 11
JF - Nonlinearity
SN - 09517715
TI - Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model
VL - 33
ER -
TY - JOUR
AB - Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.
AU - Tsai, Tony Y.-C.
AU - Sikora, Mateusz K
AU - Xia, Peng
AU - Colak-Champollion, Tugba
AU - Knaut, Holger
AU - Heisenberg, Carl-Philipp J
AU - Megason, Sean G.
ID - 8680
IS - 6512
JF - Science
KW - Multidisciplinary
SN - 0036-8075
TI - An adhesion code ensures robust pattern formation during tissue morphogenesis
VL - 370
ER -
TY - JOUR
AB - Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data.
AU - Galan, Silvia
AU - Machnik, Nick N
AU - Kruse, Kai
AU - Díaz, Noelia
AU - Marti-Renom, Marc A
AU - Vaquerizas, Juan M
ID - 8707
JF - Nature Genetics
SN - 10614036
TI - CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction
VL - 52
ER -
TY - JOUR
AB - A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system.
AU - Lechner, Mathias
AU - Hasani, Ramin
AU - Amini, Alexander
AU - Henzinger, Thomas A
AU - Rus, Daniela
AU - Grosu, Radu
ID - 8679
JF - Nature Machine Intelligence
TI - Neural circuit policies enabling auditable autonomy
VL - 2
ER -
TY - JOUR
AB - The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].
AU - Zhang, Haonan
ID - 8670
IS - 10
JF - Journal of Mathematical Physics
SN - 00222488
TI - Equality conditions of data processing inequality for α-z Rényi relative entropies
VL - 61
ER -
TY - JOUR
AB - The brain represents and reasons probabilistically about complex stimuli and motor actions using a noisy, spike-based neural code. A key building block for such neural computations, as well as the basis for supervised and unsupervised learning, is the ability to estimate the surprise or likelihood of incoming high-dimensional neural activity patterns. Despite progress in statistical modeling of neural responses and deep learning, current approaches either do not scale to large neural populations or cannot be implemented using biologically realistic mechanisms. Inspired by the sparse and random connectivity of real neuronal circuits, we present a model for neural codes that accurately estimates the likelihood of individual spiking patterns and has a straightforward, scalable, efficient, learnable, and realistic neural implementation. This model’s performance on simultaneously recorded spiking activity of >100 neurons in the monkey visual and prefrontal cortices is comparable with or better than that of state-of-the-art models. Importantly, the model can be learned using a small number of samples and using a local learning rule that utilizes noise intrinsic to neural circuits. Slower, structural changes in random connectivity, consistent with rewiring and pruning processes, further improve the efficiency and sparseness of the resulting neural representations. Our results merge insights from neuroanatomy, machine learning, and theoretical neuroscience to suggest random sparse connectivity as a key design principle for neuronal computation.
AU - Maoz, Ori
AU - Tkačik, Gašper
AU - Esteki, Mohamad Saleh
AU - Kiani, Roozbeh
AU - Schneidman, Elad
ID - 8698
IS - 40
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 00278424
TI - Learning probabilistic neural representations with randomly connected circuits
VL - 117
ER -
TY - CONF
AB - Traditional robotic control suits require profound task-specific knowledge for designing, building and testing control software. The rise of Deep Learning has enabled end-to-end solutions to be learned entirely from data, requiring minimal knowledge about the application area. We design a learning scheme to train end-to-end linear dynamical systems (LDS)s by gradient descent in imitation learning robotic domains. We introduce a new regularization loss component together with a learning algorithm that improves the stability of the learned autonomous system, by forcing the eigenvalues of the internal state updates of an LDS to be negative reals. We evaluate our approach on a series of real-life and simulated robotic experiments, in comparison to linear and nonlinear Recurrent Neural Network (RNN) architectures. Our results show that our stabilizing method significantly improves test performance of LDS, enabling such linear models to match the performance of contemporary nonlinear RNN architectures. A video of the obstacle avoidance performance of our method on a mobile robot, in unseen environments, compared to other methods can be viewed at https://youtu.be/mhEsCoNao5E.
AU - Lechner, Mathias
AU - Hasani, Ramin
AU - Rus, Daniela
AU - Grosu, Radu
ID - 8704
SN - 10504729
T2 - Proceedings - IEEE International Conference on Robotics and Automation
TI - Gershgorin loss stabilizes the recurrent neural network compartment of an end-to-end robot learning scheme
ER -
TY - JOUR
AB - Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.
AU - Sokolova, E. E.
AU - Vlasov, Petr
AU - Egorova, T. V.
AU - Shuvalov, A. V.
AU - Alkalaeva, E. Z.
ID - 8700
IS - 5
JF - Molecular Biology
SN - 00268933
TI - The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes
VL - 54
ER -
TY - JOUR
AB - Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.
AU - Sokolova, E. E.
AU - Vlasov, Petr
AU - Egorova, T. V.
AU - Shuvalov, A. V.
AU - Alkalaeva, E. Z.
ID - 8701
IS - 5
JF - Molekuliarnaia biologiia
SN - 00268984
TI - The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes
VL - 54
ER -
TY - GEN
AB - A binary neutron star merger has been observed in a multi-messenger detection of gravitational wave (GW) and electromagnetic (EM) radiation. Binary neutron stars that merge within a Hubble time, as well as many other compact binaries, are expected to form via common envelope evolution. Yet five decades of research on common envelope evolution have not yet resulted in a satisfactory understanding of the multi-spatial multi-timescale evolution for the systems that lead to compact binaries. In this paper, we report on the first successful simulations of common envelope ejection leading to binary neutron star formation in 3D hydrodynamics. We simulate the dynamical inspiral phase of the interaction between a 12M⊙ red supergiant and a 1.4M⊙ neutron star for different initial separations and initial conditions. For all of our simulations, we find complete envelope ejection and final orbital separations of af≈1.3-5.1R⊙ depending on the simulation and criterion, leading to binary neutron stars that can merge within a Hubble time. We find αCE-equivalent efficiencies of ≈0.1-2.7 depending on the simulation and criterion, but this may be specific for these extended progenitors. We fully resolve the core of the star to ≲0.005R⊙ and our 3D hydrodynamics simulations are informed by an adjusted 1D analytic energy formalism and a 2D kinematics study in order to overcome the prohibitive computational cost of simulating these systems. The framework we develop in this paper can be used to simulate a wide variety of interactions between stars, from stellar mergers to common envelope episodes leading to GW sources.
AU - Jamie A. P. Law-Smith, Jamie A. P. Law-Smith
AU - Everson, Rosa Wallace
AU - Enrico Ramirez-Ruiz, Enrico Ramirez-Ruiz
AU - Mink, Selma E. de
AU - Son, Lieke A. C. van
AU - Götberg, Ylva Louise Linsdotter
AU - Zellmann, Stefan
AU - Alejandro Vigna-Gómez, Alejandro Vigna-Gómez
AU - Renzo, Mathieu
AU - Wu, Samantha
AU - Schrøder, Sophie L.
AU - Foley, Ryan J.
AU - Tenley Hutchinson-Smith, Tenley Hutchinson-Smith
ID - 14096
T2 - arXiv
TI - Successful common envelope ejection and binary neutron star formation in 3D hydrodynamics
ER -
TY - JOUR
AB - In the high spin–orbit-coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir–O bond geometry in Sr2IrO4 and perform momentum-dependent resonant inelastic X-ray scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low-energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven cross-over from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron–hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information toward the control of the ground state of complex oxides in the presence of high spin–orbit coupling.
AU - Paris, Eugenio
AU - Tseng, Yi
AU - Paerschke, Ekaterina
AU - Zhang, Wenliang
AU - Upton, Mary H
AU - Efimenko, Anna
AU - Rolfs, Katharina
AU - McNally, Daniel E
AU - Maurel, Laura
AU - Naamneh, Muntaser
AU - Caputo, Marco
AU - Strocov, Vladimir N
AU - Wang, Zhiming
AU - Casa, Diego
AU - Schneider, Christof W
AU - Pomjakushina, Ekaterina
AU - Wohlfeld, Krzysztof
AU - Radovic, Milan
AU - Schmitt, Thorsten
ID - 8699
IS - 40
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 00278424
TI - Strain engineering of the charge and spin-orbital interactions in Sr2IrO4
VL - 117
ER -
TY - JOUR
AB - Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
AU - Kampjut, Domen
AU - Sazanov, Leonid A
ID - 8737
IS - 6516
JF - Science
TI - The coupling mechanism of mammalian respiratory complex I
VL - 370
ER -
TY - CONF
AB - Load imbalance pervasively exists in distributed deep learning training systems, either caused by the inherent imbalance in learned tasks or by the system itself. Traditional synchronous Stochastic Gradient Descent (SGD)
achieves good accuracy for a wide variety of tasks, but relies on global synchronization to accumulate the gradients at every training step. In this paper, we propose eager-SGD, which relaxes the global synchronization for
decentralized accumulation. To implement eager-SGD, we propose to use two partial collectives: solo and majority. With solo allreduce, the faster processes contribute their gradients eagerly without waiting for the slower processes, whereas with majority allreduce, at least half of the participants must contribute gradients before continuing, all without using a central parameter server. We theoretically prove the convergence of the algorithms and describe the partial collectives in detail. Experimental results on load-imbalanced environments (CIFAR-10, ImageNet, and UCF101 datasets) show
that eager-SGD achieves 1.27x speedup over the state-of-the-art synchronous SGD, without losing accuracy.
AU - Li, Shigang
AU - Tal Ben-Nun, Tal Ben-Nun
AU - Girolamo, Salvatore Di
AU - Alistarh, Dan-Adrian
AU - Hoefler, Torsten
ID - 8722
T2 - Proceedings of the 25th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
TI - Taming unbalanced training workloads in deep learning with partial collective operations
ER -
TY - JOUR
AB - Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein γB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
AU - Schulte, Linda
AU - Mao, Jiafei
AU - Reitz, Julian
AU - Sreeramulu, Sridhar
AU - Kudlinzki, Denis
AU - Hodirnau, Victor-Valentin
AU - Meier-Credo, Jakob
AU - Saxena, Krishna
AU - Buhr, Florian
AU - Langer, Julian D.
AU - Blackledge, Martin
AU - Frangakis, Achilleas S.
AU - Glaubitz, Clemens
AU - Schwalbe, Harald
ID - 8744
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cysteine oxidation and disulfide formation in the ribosomal exit tunnel
VL - 11
ER -
TY - JOUR
AB - Appropriately designed nanocomposites allow improving the thermoelectric performance by several mechanisms, including phonon scattering, modulation doping and energy filtering, while additionally promoting better mechanical properties than those of crystalline materials. Here, a strategy for producing Bi2Te3–Cu2xTe nanocomposites based on the consolidation of heterostructured nanoparticles is described and the thermoelectric properties of the obtained materials are investigated. We first detail a two-step solution-based process to produce Bi2Te3–Cu2xTe heteronanostructures, based on the growth of Cu2xTe nanocrystals on the surface of Bi2Te3 nanowires. We characterize the structural and chemical properties of the synthesized nanostructures and of the nanocomposites
produced by hot-pressing the particles at moderate temperatures. Besides, the transport properties of the nanocomposites are investigated as a function of the amount of Cu introduced. Overall, the presence of Cu decreases the material thermal conductivity through promotion of phonon scattering, modulates the charge carrier concentration through electron spillover, and increases the Seebeck coefficient through filtering of charge carriers at energy barriers. These effects result in an improvement of over 50% of the thermoelectric figure of merit of Bi2Te3.
AU - Zhang, Yu
AU - Liu, Yu
AU - Calcabrini, Mariano
AU - Xing, Congcong
AU - Han, Xu
AU - Arbiol, Jordi
AU - Cadavid, Doris
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 8747
IS - 40
JF - Journal of Materials Chemistry C
TI - Bismuth telluride-copper telluride nanocomposites from heterostructured building blocks
VL - 8
ER -
TY - JOUR
AB - Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring.
AU - Kaveh, Kamran
AU - McAvoy, Alex
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 8767
IS - 11
JF - PLOS Computational Biology
KW - Ecology
KW - Modelling and Simulation
KW - Computational Theory and Mathematics
KW - Genetics
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
KW - Molecular Biology
KW - Cellular and Molecular Neuroscience
SN - 1553-734X
TI - The Moran process on 2-chromatic graphs
VL - 16
ER -
TY - CONF
AB - Efficiently handling time-triggered and possibly nondeterministic switches
for hybrid systems reachability is a challenging task. In this paper we present
an approach based on conservative set-based enclosure of the dynamics that can
handle systems with uncertain parameters and inputs, where the uncertainties
are bound to given intervals. The method is evaluated on the plant model of an
experimental electro-mechanical braking system with periodic controller. In
this model, the fast-switching controller dynamics requires simulation time
scales of the order of nanoseconds. Accurate set-based computations for
relatively large time horizons are known to be expensive. However, by
appropriately decoupling the time variable with respect to the spatial
variables, and enclosing the uncertain parameters using interval matrix maps
acting on zonotopes, we show that the computation time can be lowered to 5000
times faster with respect to previous works. This is a step forward in formal
verification of hybrid systems because reduced run-times allow engineers to
introduce more expressiveness in their models with a relatively inexpensive
computational cost.
AU - Forets, Marcelo
AU - Freire, Daniel
AU - Schilling, Christian
ID - 8750
SN - 9781728191485
T2 - 18th ACM-IEEE International Conference on Formal Methods and Models for System Design
TI - Efficient reachability analysis of parametric linear hybrid systems with time-triggered transitions
ER -
TY - JOUR
AB - We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where the microscopic system satisfies the detailed-balance condition. The latter allows us to enrich the systems with a gradient structure, i.e. the evolution is given by a gradient-flow equation. We present the arising links between the associated gradient structures that are driven by the relative entropy of the detailed-balance steady state. The limit of large volumes is studied in the sense of evolutionary Γ-convergence of gradient flows. Moreover, we use the gradient structures to derive hybrid models for coupling different modeling levels.
AU - Maas, Jan
AU - Mielke, Alexander
ID - 8758
IS - 6
JF - Journal of Statistical Physics
SN - 00224715
TI - Modeling of chemical reaction systems with detailed balance using gradient structures
VL - 181
ER -
TY - GEN
AB - This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request.
AU - Peruzzo, Matilda
AU - Trioni, Andrea
AU - Hassani, Farid
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 13070
TI - Surpassing the resistance quantum with a geometric superinductor
ER -
TY - JOUR
AB - Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets.
AU - Nicolai, Leo
AU - Schiefelbein, Karin
AU - Lipsky, Silvia
AU - Leunig, Alexander
AU - Hoffknecht, Marie
AU - Pekayvaz, Kami
AU - Raude, Ben
AU - Marx, Charlotte
AU - Ehrlich, Andreas
AU - Pircher, Joachim
AU - Zhang, Zhe
AU - Saleh, Inas
AU - Marel, Anna-Kristina
AU - Löf, Achim
AU - Petzold, Tobias
AU - Lorenz, Michael
AU - Stark, Konstantin
AU - Pick, Robert
AU - Rosenberger, Gerhild
AU - Weckbach, Ludwig
AU - Uhl, Bernd
AU - Xia, Sheng
AU - Reichel, Christoph Andreas
AU - Walzog, Barbara
AU - Schulz, Christian
AU - Zheden, Vanessa
AU - Bender, Markus
AU - Li, Rong
AU - Massberg, Steffen
AU - Gärtner, Florian R
ID - 8787
JF - Nature Communications
TI - Vascular surveillance by haptotactic blood platelets in inflammation and infection
VL - 11
ER -
TY - JOUR
AB - Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty.
AU - Kleshnina, Maria
AU - Streipert, Sabrina
AU - Filar, Jerzy
AU - Chatterjee, Krishnendu
ID - 8789
IS - 11
JF - Mathematics
TI - Prioritised learning in snowdrift-type games
VL - 8
ER -
TY - CONF
AB - Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.
AU - Bogomolov, Sergiy
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Potomkin, Kostiantyn
AU - Schilling, Christian
ID - 8287
KW - reachability
KW - hybrid systems
KW - decomposition
T2 - Proceedings of the International Conference on Embedded Software
TI - Reachability analysis of linear hybrid systems via block decomposition
ER -
TY - JOUR
AB - We consider a real-time setting where an environment releases sequences of firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute on a single processor so as to maximize cumulated utility. The competitive ratio is a well-known performance measure for the scheduler: it gives the worst-case ratio, among all possible choices for the environment, of the cumulated utility of the online scheduler versus an offline scheduler that knows these choices in advance. Traditionally, competitive analysis is performed by hand, while automated techniques are rare and only handle static environments with independent tasks. We present a quantitative-verification framework for precedence-aware competitive analysis, where task releases may depend on preceding scheduling choices, i.e., the environment can respond to scheduling decisions dynamically . We consider two general classes of precedences: 1) follower precedences force the release of a dependent task upon the completion of a set of precursor tasks, while and 2) pairing precedences modify the characteristics of a dependent task provided the completion of a set of precursor tasks. Precedences make competitive analysis challenging, as the online and offline schedulers operate on diverging sequences. We make a formal presentation of our framework, and use a GPU-based implementation to analyze ten well-known schedulers on precedence-based application examples taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching; 3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental results show that precedences and task parameters can vary drastically the best scheduler. Our framework thus supports application designers in choosing the best scheduler among a given set automatically.
AU - Pavlogiannis, Andreas
AU - Schaumberger, Nico
AU - Schmid, Ulrich
AU - Chatterjee, Krishnendu
ID - 8788
IS - 11
JF - IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
SN - 02780070
TI - Precedence-aware automated competitive analysis of real-time scheduling
VL - 39
ER -
TY - JOUR
AB - Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.
AU - Bogomolov, Sergiy
AU - Forets, Marcelo
AU - Frehse, Goran
AU - Potomkin, Kostiantyn
AU - Schilling, Christian
ID - 8790
IS - 11
JF - IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
SN - 02780070
TI - Reachability analysis of linear hybrid systems via block decomposition
VL - 39
ER -
TY - JOUR
AB - Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression.
AU - Nibau, Candida
AU - Dadarou, Despoina
AU - Kargios, Nestoras
AU - Mallioura, Areti
AU - Fernandez-Fuentes, Narcis
AU - Cavallari, Nicola
AU - Doonan, John H.
ID - 8924
JF - Frontiers in Plant Science
TI - A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis
VL - 11
ER -
TY - JOUR
AB - Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application.
AU - Irtem, Erdem
AU - Arenas Esteban, Daniel
AU - Duarte, Miguel
AU - Choukroun, Daniel
AU - Lee, Seungho
AU - Ibáñez, Maria
AU - Bals, Sara
AU - Breugelmans, Tom
ID - 8926
IS - 22
JF - ACS Catalysis
TI - Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction
VL - 10
ER -
TY - JOUR
AB - Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving
the system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2.
AU - Zemlicka, Martin
AU - Kopčík, M.
AU - Szabó, P.
AU - Samuely, T.
AU - Kačmarčík, J.
AU - Neilinger, P.
AU - Grajcar, M.
AU - Samuely, P.
ID - 8944
IS - 18
JF - Physical Review B
SN - 24699950
TI - Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field
VL - 102
ER -
TY - JOUR
AB - Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies.
AU - Rizzo, Rossella
AU - Zhang, Xiyun
AU - Wang, Jilin W.J.L.
AU - Lombardi, Fabrizio
AU - Ivanov, Plamen Ch
ID - 8955
JF - Frontiers in Physiology
TI - Network physiology of cortico–muscular interactions
VL - 11
ER -
TY - JOUR
AB - Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.
AU - Zhang, Xuying
AU - Mennicke, Christine V.
AU - Xiao, Guanxi
AU - Beattie, Robert J
AU - Haider, Mansoor
AU - Hippenmeyer, Simon
AU - Ghashghaei, H. Troy
ID - 8949
IS - 12
JF - Cells
SN - 2073-4409
TI - Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage
VL - 9
ER -
TY - JOUR
AB - The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.
AU - Fäßler, Florian
AU - Dimchev, Georgi A
AU - Hodirnau, Victor-Valentin
AU - Wan, William
AU - Schur, Florian KM
ID - 8971
JF - Nature Communications
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - General Physics and Astronomy
KW - General Chemistry
SN - 2041-1723
TI - Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction
VL - 11
ER -
TY - CONF
AB - Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.
Vaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that
(security) Provably prevents replay and (if location data is available) relay attacks.
(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.
(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).
Towards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message.
AU - Pietrzak, Krzysztof Z
ID - 8987
SN - 03029743
T2 - Progress in Cryptology
TI - Delayed authentication: Preventing replay and relay attacks in private contact tracing
VL - 12578
ER -
TY - JOUR
AB - Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation.
AU - Godard, Benoit G
AU - Dumollard, Rémi
AU - Munro, Edwin
AU - Chenevert, Janet
AU - Hebras, Céline
AU - Mcdougall, Alex
AU - Heisenberg, Carl-Philipp J
ID - 8957
IS - 6
JF - Developmental Cell
SN - 15345807
TI - Apical relaxation during mitotic rounding promotes tension-oriented cell division
VL - 55
ER -
TY - JOUR
AB - In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.
AU - Grah, Rok
AU - Zoller, Benjamin
AU - Tkačik, Gašper
ID - 9000
IS - 50
JF - PNAS
SN - 00278424
TI - Nonequilibrium models of optimal enhancer function
VL - 117
ER -
TY - JOUR
AB - Quantum illumination uses entangled signal-idler photon pairs to boost the detection efficiency of low-reflectivity objects in environments with bright thermal noise. Its advantage is particularly evident at low signal powers, a promising feature for applications such as noninvasive biomedical scanning or low-power short-range radar. Here, we experimentally investigate the concept of quantum illumination at microwave frequencies. We generate entangled fields to illuminate a room-temperature object at a distance of 1 m in a free-space detection setup. We implement a digital phase-conjugate receiver based on linear quadrature measurements that outperforms a symmetric classical noise radar in the same conditions, despite the entanglement-breaking signal path. Starting from experimental data, we also simulate the case of perfect idler photon number detection, which results in a quantum advantage compared with the relative classical benchmark. Our results highlight the opportunities and challenges in the way toward a first room-temperature application of microwave quantum circuits.
AU - Barzanjeh, Shabir
AU - Pirandola, S.
AU - Vitali, D
AU - Fink, Johannes M
ID - 7910
IS - 19
JF - Science Advances
TI - Microwave quantum illumination using a digital receiver
VL - 6
ER -
TY - CONF
AB - Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits.
AU - Barzanjeh, Shabir
AU - Pirandola, Stefano
AU - Vitali, David
AU - Fink, Johannes M
ID - 9001
IS - 9
SN - 1097-5659
T2 - IEEE National Radar Conference - Proceedings
TI - Microwave quantum illumination with a digital phase-conjugated receiver
VL - 2020
ER -
TY - JOUR
AB - Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.
AU - Browning, Timothy D
AU - Sawin, Will
ID - 9007
IS - 4
JF - Commentarii Mathematici Helvetici
SN - 00102571
TI - Free rational points on smooth hypersurfaces
VL - 95
ER -
TY - JOUR
AB - Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion
efficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication.
AU - Hease, William J
AU - Rueda Sanchez, Alfredo R
AU - Sahu, Rishabh
AU - Wulf, Matthias
AU - Arnold, Georg M
AU - Schwefel, Harald G.L.
AU - Fink, Johannes M
ID - 9114
IS - 2
JF - PRX Quantum
SN - 2691-3399
TI - Bidirectional electro-optic wavelength conversion in the quantum ground state
VL - 1
ER -
TY - JOUR
AB - Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future.
AU - Lauk, Nikolai
AU - Sinclair, Neil
AU - Barzanjeh, Shabir
AU - Covey, Jacob P
AU - Saffman, Mark
AU - Spiropulu, Maria
AU - Simon, Christoph
ID - 9194
IS - 2
JF - Quantum Science and Technology
SN - 2058-9565
TI - Perspectives on quantum transduction
VL - 5
ER -
TY - JOUR
AB - We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems.
AU - Fischer, Julian L
AU - Laux, Tim
AU - Simon, Theresa M.
ID - 9039
IS - 6
JF - SIAM Journal on Mathematical Analysis
SN - 00361410
TI - Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies
VL - 52
ER -
TY - JOUR
AB - We consider the free additive convolution of two probability measures μ and ν on the real line and show that μ ⊞ v is supported on a single interval if μ and ν each has single interval support. Moreover, the density of μ ⊞ ν is proven to vanish as a square root near the edges of its support if both μ and ν have power law behavior with exponents between −1 and 1 near their edges. In particular, these results show the ubiquity of the conditions in our recent work on optimal local law at the spectral edges for addition of random matrices [5].
AU - Bao, Zhigang
AU - Erdös, László
AU - Schnelli, Kevin
ID - 9104
JF - Journal d'Analyse Mathematique
SN - 00217670
TI - On the support of the free additive convolution
VL - 142
ER -
TY - GEN
AB - This dataset comprises all data shown in the plots of the main part of the submitted article "Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State". Additional raw data are available from the corresponding author on reasonable request.
AU - Hease, William J
AU - Rueda Sanchez, Alfredo R
AU - Sahu, Rishabh
AU - Wulf, Matthias
AU - Arnold, Georg M
AU - Schwefel, Harald
AU - Fink, Johannes M
ID - 13071
TI - Bidirectional electro-optic wavelength conversion in the quantum ground state
ER -
TY - JOUR
AB - Quantum information technology based on solid state qubits has created much interest in converting quantum states from the microwave to the optical domain. Optical photons, unlike microwave photons, can be transmitted by fiber, making them suitable for long distance quantum communication. Moreover, the optical domain offers access to a large set of very well‐developed quantum optical tools, such as highly efficient single‐photon detectors and long‐lived quantum memories. For a high fidelity microwave to optical transducer, efficient conversion at single photon level and low added noise is needed. Currently, the most promising approaches to build such systems are based on second‐order nonlinear phenomena such as optomechanical and electro‐optic interactions. Alternative approaches, although not yet as efficient, include magneto‐optical coupling and schemes based on isolated quantum systems like atoms, ions, or quantum dots. Herein, the necessary theoretical foundations for the most important microwave‐to‐optical conversion experiments are provided, their implementations are described, and the current limitations and future prospects are discussed.
AU - Lambert, Nicholas J.
AU - Rueda Sanchez, Alfredo R
AU - Sedlmeir, Florian
AU - Schwefel, Harald G. L.
ID - 9195
IS - 1
JF - Advanced Quantum Technologies
SN - 2511-9044
TI - Coherent conversion between microwave and optical photons - An overview of physical implementations
VL - 3
ER -
TY - JOUR
AB - Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.
Calypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees.
AU - Kokoris Kogias, Eleftherios
AU - Alp, Enis Ceyhun
AU - Gasser, Linus
AU - Jovanovic, Philipp
AU - Syta, Ewa
AU - Ford, Bryan
ID - 9011
IS - 4
JF - Proceedings of the VLDB Endowment
TI - CALYPSO: Private data management for decentralized ledgers
VL - 14
ER -