TY - JOUR
AB - The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.
AU - Düllberg, Christian F
AU - Auer, Albert
AU - Canigova, Nikola
AU - Loibl, Katrin
AU - Loose, Martin
ID - 8988
IS - 1
JF - PNAS
SN - 00278424
TI - In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1
VL - 118
ER -
TY - JOUR
AB - The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.
AU - Tan, Shutang
AU - Luschnig, Christian
AU - Friml, Jiří
ID - 8992
IS - 1
JF - Molecular Plant
SN - 16742052
TI - Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling
VL - 14
ER -
TY - JOUR
AB - N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.
AU - Abas, Lindy
AU - Kolb, Martina
AU - Stadlmann, Johannes
AU - Janacek, Dorina P.
AU - Lukic, Kristina
AU - Schwechheimer, Claus
AU - Sazanov, Leonid A
AU - Mach, Lukas
AU - Friml, Jiří
AU - Hammes, Ulrich Z.
ID - 8993
IS - 1
JF - PNAS
SN - 00278424
TI - Naphthylphthalamic acid associates with and inhibits PIN auxin transporters
VL - 118
ER -
TY - JOUR
AB - Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.
AU - Kavcic, Bor
AU - Tkačik, Gašper
AU - Bollenbach, Tobias
ID - 8997
JF - PLOS Computational Biology
KW - Modelling and Simulation
KW - Genetics
KW - Molecular Biology
KW - Antibiotics
KW - Drug interactions
SN - 1553-7358
TI - Minimal biophysical model of combined antibiotic action
VL - 17
ER -
TY - JOUR
AB - In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not
arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available.
AU - Avila, Kerstin
AU - Hof, Björn
ID - 8999
IS - 1
JF - Entropy
TI - Second-order phase transition in counter-rotating taylor-couette flow experiment
VL - 23
ER -
TY - JOUR
AB - Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field.
AU - Brooks, Morris
AU - Lemeshko, Mikhail
AU - Lundholm, D.
AU - Yakaboylu, Enderalp
ID - 9005
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Molecular impurities as a realization of anyons on the two-sphere
VL - 126
ER -
TY - JOUR
AB - Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.
AU - Ötvös, Krisztina
AU - Marconi, Marco
AU - Vega, Andrea
AU - O’Brien, Jose
AU - Johnson, Alexander J
AU - Abualia, Rashed
AU - Antonielli, Livio
AU - Montesinos López, Juan C
AU - Zhang, Yuzhou
AU - Tan, Shutang
AU - Cuesta, Candela
AU - Artner, Christina
AU - Bouguyon, Eleonore
AU - Gojon, Alain
AU - Friml, Jiří
AU - Gutiérrez, Rodrigo A.
AU - Wabnik, Krzysztof T
AU - Benková, Eva
ID - 9010
IS - 3
JF - EMBO Journal
SN - 02614189
TI - Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport
VL - 40
ER -
TY - JOUR
AB - We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels.
AU - Gulden, Tobias
AU - Kamenev, Alex
ID - 9020
IS - 1
JF - Entropy
TI - Dynamics of ion channels via non-hermitian quantum mechanics
VL - 23
ER -
TY - THES
AB - In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime.
In the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time
(up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions.
In the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result
improves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.
AU - Cipolloni, Giorgio
ID - 9022
TI - Fluctuations in the spectrum of random matrices
ER -
TY - JOUR
AB - Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices.
AU - Aguilar-Merino, Patricia
AU - Álvarez-Pérez, Gonzalo
AU - Taboada-Gutiérrez, Javier
AU - Duan, Jiahua
AU - Prieto Gonzalez, Ivan
AU - Álvarez-Prado, Luis Manuel
AU - Nikitin, Alexey Y.
AU - Martín-Sánchez, Javier
AU - Alonso-González, Pablo
ID - 9038
IS - 1
JF - Nanomaterials
TI - Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal
VL - 11
ER -
TY - JOUR
AU - Römhild, Roderich
AU - Andersson, Dan I.
ID - 9046
IS - 1
JF - PLoS Pathogens
SN - 15537366
TI - Mechanisms and therapeutic potential of collateral sensitivity to antibiotics
VL - 17
ER -
TY - JOUR
AB - This work analyzes the latency of the simplified successive cancellation (SSC) decoding scheme for polar codes proposed by Alamdar-Yazdi and Kschischang. It is shown that, unlike conventional successive cancellation decoding, where latency is linear in the block length, the latency of SSC decoding is sublinear. More specifically, the latency of SSC decoding is O(N1−1/μ) , where N is the block length and μ is the scaling exponent of the channel, which captures the speed of convergence of the rate to capacity. Numerical results demonstrate the tightness of the bound and show that most of the latency reduction arises from the parallel decoding of subcodes of rate 0 or 1.
AU - Mondelli, Marco
AU - Hashemi, Seyyed Ali
AU - Cioffi, John M.
AU - Goldsmith, Andrea
ID - 9047
IS - 1
JF - IEEE Transactions on Wireless Communications
SN - 15361276
TI - Sublinear latency for simplified successive cancellation decoding of polar codes
VL - 20
ER -
TY - JOUR
AB - The analogy between an equilibrium partition function and the return probability in many-body unitary dynamics has led to the concept of dynamical quantum phase transition (DQPT). DQPTs are defined by nonanalyticities in the return amplitude and are present in many models. In some cases, DQPTs can be related to equilibrium concepts, such as order parameters, yet their universal description is an open question. In this Letter, we provide first steps toward a classification of DQPTs by using a matrix product state description of unitary dynamics in the thermodynamic limit. This allows us to distinguish the two limiting cases of “precession” and “entanglement” DQPTs, which are illustrated using an analytical description in the quantum Ising model. While precession DQPTs are characterized by a large entanglement gap and are semiclassical in their nature, entanglement DQPTs occur near avoided crossings in the entanglement spectrum and can be distinguished by a complex pattern of nonlocal correlations. We demonstrate the existence of precession and entanglement DQPTs beyond Ising models, discuss observables that can distinguish them, and relate their interplay to complex DQPT phenomenology.
AU - De Nicola, Stefano
AU - Michailidis, Alexios
AU - Serbyn, Maksym
ID - 9048
IS - 4
JF - Physical Review Letters
KW - General Physics and Astronomy
SN - 0031-9007
TI - Entanglement view of dynamical quantum phase transitions
VL - 126
ER -
TY - THES
AB - In this thesis we study persistence of multi-covers of Euclidean balls and the geometric structures underlying their computation, in particular Delaunay mosaics and Voronoi tessellations.
The k-fold cover for some discrete input point set consists of the space where at least k balls of radius r around the input points overlap. Persistence is a notion that captures, in some sense, the topology of the shape underlying the input. While persistence is usually computed for the union of balls, the k-fold cover is of interest as it captures local density,
and thus might approximate the shape of the input better if the input data is noisy. To compute persistence of these k-fold covers, we need a discretization that is provided by higher-order Delaunay mosaics.
We present and implement a simple and efficient algorithm for the computation of higher-order Delaunay mosaics, and use it to give experimental results for their combinatorial properties. The algorithm makes use of a new geometric structure, the rhomboid tiling. It contains the higher-order Delaunay mosaics as slices, and by introducing a filtration
function on the tiling, we also obtain higher-order α-shapes as slices. These allow us to compute persistence of the multi-covers for varying radius r; the computation for varying k is less straight-foward and involves the rhomboid tiling directly. We apply our algorithms to experimental sphere packings to shed light on their structural properties. Finally, inspired by periodic structures in packings and materials, we propose and implement an algorithm for periodic Delaunay triangulations to be integrated into the Computational Geometry Algorithms Library (CGAL), and discuss
the implications on persistence for periodic data sets.
AU - Osang, Georg F
ID - 9056
SN - 2663-337X
TI - Multi-cover persistence and Delaunay mosaics
ER -
TY - JOUR
AB - The sensory and cognitive abilities of the mammalian neocortex are underpinned by intricate columnar and laminar circuits formed from an array of diverse neuronal populations. One approach to determining how interactions between these circuit components give rise to complex behavior is to investigate the rules by which cortical circuits are formed and acquire functionality during development. This review summarizes recent research on the development of the neocortex, from genetic determination in neural stem cells through to the dynamic role that specific neuronal populations play in the earliest circuits of neocortex, and how they contribute to emergent function and cognition. While many of these endeavors take advantage of model systems, consideration will also be given to advances in our understanding of activity in nascent human circuits. Such cross-species perspective is imperative when investigating the mechanisms underlying the dysfunction of early neocortical circuits in neurodevelopmental disorders, so that one can identify targets amenable to therapeutic intervention.
AU - Hanganu-Opatz, Ileana L.
AU - Butt, Simon J. B.
AU - Hippenmeyer, Simon
AU - De Marco García, Natalia V.
AU - Cardin, Jessica A.
AU - Voytek, Bradley
AU - Muotri, Alysson R.
ID - 9073
IS - 5
JF - The Journal of Neuroscience
KW - General Neuroscience
SN - 0270-6474
TI - The logic of developing neocortical circuits in health and disease
VL - 41
ER -
TY - GEN
AB - Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans.
AU - Anderson, Donovan J.
AU - Pauler, Florian
AU - McKenna, Aaron
AU - Shendure, Jay
AU - Hippenmeyer, Simon
AU - Horwitz, Marshall S.
ID - 9082
T2 - bioRxiv
TI - Simultaneous identification of brain cell type and lineage via single cell RNA sequencing
ER -
TY - JOUR
AB - We employ the Gross-Pitaevskii equation to study acoustic emission generated in a uniform Bose gas by a static impurity. The impurity excites a sound-wave packet, which propagates through the gas. We calculate the shape of this wave packet in the limit of long wave lengths, and argue that it is possible to extract properties of the impurity by observing this shape. We illustrate here this possibility for a Bose gas with a trapped impurity atom -- an example of a relevant experimental setup. Presented results are general for all one-dimensional systems described by the nonlinear Schrödinger equation and can also be used in nonatomic systems, e.g., to analyze light propagation in nonlinear optical media. Finally, we calculate the shape of the sound-wave packet for a three-dimensional Bose gas assuming a spherically symmetric perturbation.
AU - Marchukov, Oleksandr
AU - Volosniev, Artem
ID - 9093
IS - 2
JF - SciPost Physics
SN - 2542-4653
TI - Shape of a sound wave in a weakly-perturbed Bose gas
VL - 10
ER -
TY - JOUR
AB - Psoriasis is a chronic inflammatory skin disease clinically characterized by the appearance of red colored, well-demarcated plaques with thickened skin and with silvery scales. Recent studies have established the involvement of a complex signalling network of interactions between cytokines, immune cells and skin cells called keratinocytes. Keratinocytes form the cells of the outermost layer of the skin (epidermis). Visible plaques in psoriasis are developed due to the fast proliferation and unusual differentiation of keratinocyte cells. Despite that, the exact mechanism of the appearance of these plaques in the cytokine-immune cell network is not clear. A mathematical model embodying interactions between key immune cells believed to be involved in psoriasis, keratinocytes and relevant cytokines has been developed. The complex network formed of these interactions poses several challenges. Here, we choose to study subnetworks of this complex network and initially focus on interactions involving TNFα, IL-23/IL-17, and IL-15. These are chosen based on known evidence of their therapeutic efficacy. In addition, we explore the role of IL-15 in the pathogenesis of psoriasis and its potential as a future drug target for a novel treatment option. We perform steady state analyses for these subnetworks and demonstrate that the interactions between cells, driven by cytokines could cause the emergence of a psoriasis state (hyper-proliferation of keratinocytes) when levels of TNFα, IL-23/IL-17 or IL-15 are increased. The model results explain and support the clinical potentiality of anti-cytokine treatments. Interestingly, our results suggest different dynamic scenarios underpin the pathogenesis of psoriasis, depending upon the dominant cytokines of subnetworks. We observed that the increase in the level of IL-23/IL-17 and IL-15 could lead to psoriasis via a bistable route, whereas an increase in the level of TNFα would lead to a monotonic and gradual disease progression. Further, we demonstrate how this insight, bistability, could be exploited to improve the current therapies and develop novel treatment strategies for psoriasis.
AU - Pandey, Rakesh
AU - Al-Nuaimi, Yusur
AU - Mishra, Rajiv Kumar
AU - Spurgeon, Sarah K.
AU - Goodfellow, Marc
ID - 9097
JF - Scientific Reports
TI - Role of subnetworks mediated by TNF α, IL-23/IL-17 and IL-15 in a network involved in the pathogenesis of psoriasis
VL - 11
ER -
TY - JOUR
AB - Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.
AU - Faria, Rui
AU - Johannesson, Kerstin
AU - Stankowski, Sean
ID - 9100
IS - 1
JF - Journal of Evolutionary Biology
SN - 1010061X
TI - Speciation in marine environments: Diving under the surface
VL - 34
ER -
TY - JOUR
AB - We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.
AU - Fraisse, Christelle
AU - Popovic, Iva
AU - Mazoyer, Clément
AU - Spataro, Bruno
AU - Delmotte, Stéphane
AU - Romiguier, Jonathan
AU - Loire, Étienne
AU - Simon, Alexis
AU - Galtier, Nicolas
AU - Duret, Laurent
AU - Bierne, Nicolas
AU - Vekemans, Xavier
AU - Roux, Camille
ID - 9119
JF - Molecular Ecology Resources
SN - 1755098X
TI - DILS: Demographic inferences with linked selection by using ABC
ER -
TY - JOUR
AB - We show that the energy gap for the BCS gap equation is
Ξ=μ(8e−2+o(1))exp(π2μ−−√a)
in the low density limit μ→0. Together with the similar result for the critical temperature by Hainzl and Seiringer (Lett Math Phys 84: 99–107, 2008), this shows that, in the low density limit, the ratio of the energy gap and critical temperature is a universal constant independent of the interaction potential V. The results hold for a class of potentials with negative scattering length a and no bound states.
AU - Lauritsen, Asbjørn Bækgaard
ID - 9121
JF - Letters in Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0377-9017
TI - The BCS energy gap at low density
VL - 111
ER -
TY - JOUR
AB - While several tools have been developed to study the ground state of many-body quantum spin systems, the limitations of existing techniques call for the exploration of new approaches. In this manuscript we develop an alternative analytical and numerical framework for many-body quantum spin ground states, based on the disentanglement formalism. In this approach, observables are exactly expressed as Gaussian-weighted functional integrals over scalar fields. We identify the leading contribution to these integrals, given by the saddle point of a suitable effective action. Analytically, we develop a field-theoretical expansion of the functional integrals, performed by means of appropriate Feynman rules. The expansion can be truncated to a desired order to obtain analytical approximations to observables. Numerically, we show that the disentanglement approach can be used to compute ground state expectation values from classical stochastic processes. While the associated fluctuations grow exponentially with imaginary time and the system size, this growth can be mitigated by means of an importance sampling scheme based on knowledge of the saddle point configuration. We illustrate the advantages and limitations of our methods by considering the quantum Ising model in 1, 2 and 3 spatial dimensions. Our analytical and numerical approaches are applicable to a broad class of systems, bridging concepts from quantum lattice models, continuum field theory, and classical stochastic processes.
AU - De Nicola, Stefano
ID - 9158
IS - 1
JF - Journal of Statistical Mechanics: Theory and Experiment
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
KW - Statistical and Nonlinear Physics
SN - 1742-5468
TI - Disentanglement approach to quantum spin ground states: Field theory and stochastic simulation
VL - 2021
ER -
TY - JOUR
AB - We show that Hilbert schemes of points on supersingular Enriques surface in characteristic 2, Hilbn(X), for n ≥ 2 are simply connected, symplectic varieties but are not irreducible symplectic as the hodge number h2,0 > 1, even though a supersingular Enriques surface is an irreducible symplectic variety. These are the classes of varieties which appear only in characteristic 2 and they show that the hodge number formula for G¨ottsche-Soergel does not hold over haracteristic 2. It also gives examples of varieties with trivial canonical class which are neither irreducible symplectic nor Calabi-Yau, thereby showing that there are strictly more classes of simply connected varieties with trivial canonical class in characteristic 2 than over C as given by Beauville-Bogolomov decomposition theorem.
AU - Srivastava, Tanya K
ID - 9173
IS - 03
JF - Bulletin des Sciences Mathematiques
SN - 0007-4497
TI - Pathologies of the Hilbert scheme of points of a supersingular Enriques surface
VL - 167
ER -
TY - GEN
AB - We associate a certain tensor product lattice to any primitive integer lattice and ask about its typical shape. These lattices are related to the tangent bundle of Grassmannians and their study is motivated by Peyre's programme on "freeness" for rational points of bounded height on Fano
varieties.
AU - Browning, Timothy D
AU - Horesh, Tal
AU - Wilsch, Florian Alexander
ID - 9199
T2 - arXiv
TI - Equidistribution and freeness on Grassmannians
ER -
TY - JOUR
AB - Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins.
AU - Kampjut, Domen
AU - Steiner, Julia
AU - Sazanov, Leonid A
ID - 9205
IS - 3
JF - iScience
TI - Cryo-EM grid optimization for membrane proteins
VL - 24
ER -
TY - JOUR
AB - The precise engineering of thermoelectric materials using nanocrystals as their building blocks has proven to be an excellent strategy to increase energy conversion efficiency. Here we present a synthetic route to produce Sb-doped PbS colloidal nanoparticles. These nanoparticles are then consolidated into nanocrystalline PbS:Sb using spark plasma sintering. We demonstrate that the introduction of Sb significantly influences the size, geometry, crystal lattice and especially the carrier concentration of PbS. The increase of charge carrier concentration achieved with the introduction of Sb translates into an increase of the electrical and thermal conductivities and a decrease of the Seebeck coefficient. Overall, PbS:Sb nanomaterial were characterized by two-fold higher thermoelectric figures of merit than undoped PbS.
AU - Cadavid, Doris
AU - Wei, Kaya
AU - Liu, Yu
AU - Zhang, Yu
AU - Li, Mengyao
AU - Genç, Aziz
AU - Berestok, Taisiia
AU - Ibáñez, Maria
AU - Shavel, Alexey
AU - Nolas, George S.
AU - Cabot, Andreu
ID - 9206
IS - 4
JF - Materials
TI - Synthesis, bottom up assembly and thermoelectric properties of Sb-doped PbS nanocrystal building blocks
VL - 14
ER -
TY - CONF
AB - We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function.
AU - Garcia Soto, Miriam
AU - Prabhakar, Pavithra
ID - 9202
T2 - 2020 IEEE Real-Time Systems Symposium
TI - Hybridization for stability verification of nonlinear switched systems
ER -
TY - CONF
AB - In the multiway cut problem we are given a weighted undirected graph G=(V,E) and a set T⊆V of k terminals. The goal is to find a minimum weight set of edges E′⊆E with the property that by removing E′ from G all the terminals become disconnected. In this paper we present a simple local search approximation algorithm for the multiway cut problem with approximation ratio 2−2k . We present an experimental evaluation of the performance of our local search algorithm and show that it greatly outperforms the isolation heuristic of Dalhaus et al. and it has similar performance as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and Buchbinder et al. which have the currently best known approximation ratios for this problem.
AU - Bloch-Hansen, Andrew
AU - Samei, Nasim
AU - Solis-Oba, Roberto
ID - 9227
SN - 0302-9743
T2 - Conference on Algorithms and Discrete Applied Mathematics
TI - Experimental evaluation of a local search approximation algorithm for the multiway cut problem
VL - 12601
ER -
TY - JOUR
AB - Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?
AU - Tkačik, Gašper
AU - Gregor, Thomas
ID - 9226
IS - 2
JF - Development
TI - The many bits of positional information
VL - 148
ER -
TY - GEN
AB - We consider a model of the Riemann zeta function on the critical axis and study its maximum over intervals of length (log T)θ, where θ is either fixed or tends to zero at a suitable rate.
It is shown that the deterministic level of the maximum interpolates smoothly between the ones
of log-correlated variables and of i.i.d. random variables, exhibiting a smooth transition ‘from
3/4 to 1/4’ in the second order. This provides a natural context where extreme value statistics of
log-correlated variables with time-dependent variance and rate occur. A key ingredient of the
proof is a precise upper tail tightness estimate for the maximum of the model on intervals of
size one, that includes a Gaussian correction. This correction is expected to be present for the
Riemann zeta function and pertains to the question of the correct order of the maximum of
the zeta function in large intervals.
AU - Arguin, Louis-Pierre
AU - Dubach, Guillaume
AU - Hartung, Lisa
ID - 9230
T2 - arXiv
TI - Maxima of a random model of the Riemann zeta function over intervals of varying length
ER -
TY - JOUR
AB - Cesium lead halides have intrinsically unstable crystal lattices and easily transform within perovskite and nonperovskite structures. In this work, we explore the conversion of the perovskite CsPbBr3 into Cs4PbBr6 in the presence of PbS at 450 °C to produce doped nanocrystal-based composites with embedded Cs4PbBr6 nanoprecipitates. We show that PbBr2 is extracted from CsPbBr3 and diffuses into the PbS lattice with a consequent increase in the concentration of free charge carriers. This new doping strategy enables the adjustment of the density of charge carriers between 1019 and 1020 cm–3, and it may serve as a general strategy for doping other nanocrystal-based semiconductors.
AU - Calcabrini, Mariano
AU - Genc, Aziz
AU - Liu, Yu
AU - Kleinhanns, Tobias
AU - Lee, Seungho
AU - Dirin, Dmitry N.
AU - Akkerman, Quinten A.
AU - Kovalenko, Maksym V.
AU - Arbiol, Jordi
AU - Ibáñez, Maria
ID - 9118
IS - 2
JF - ACS Energy Letters
TI - Exploiting the lability of metal halide perovskites for doping semiconductor nanocomposites
VL - 6
ER -
TY - JOUR
AB - We consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem.
AU - Frank, Rupert
AU - Seiringer, Robert
ID - 8603
IS - 3
JF - Communications on Pure and Applied Mathematics
SN - 00103640
TI - Quantum corrections to the Pekar asymptotics of a strongly coupled polaron
VL - 74
ER -
TY - JOUR
AB - This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system.
AU - Marveggio, Alice
AU - Schimperna, Giulio
ID - 8792
IS - 2
JF - Journal of Differential Equations
SN - 00220396
TI - On a non-isothermal Cahn-Hilliard model based on a microforce balance
VL - 274
ER -
TY - CHAP
AB - Expansion microscopy is a recently developed super-resolution imaging technique, which provides an alternative to optics-based methods such as deterministic approaches (e.g. STED) or stochastic approaches (e.g. PALM/STORM). The idea behind expansion microscopy is to embed the biological sample in a swellable gel, and then to expand it isotropically, thereby increasing the distance between the fluorophores. This approach breaks the diffraction barrier by simply separating the emission point-spread-functions of the fluorophores. The resolution attainable in expansion microscopy is thus directly dependent on the separation that can be achieved, i.e. on the expansion factor. The original implementation of the technique achieved an expansion factor of fourfold, for a resolution of 70–80 nm. The subsequently developed X10 method achieves an expansion factor of 10-fold, for a resolution of 25–30 nm. This technique can be implemented with minimal technical requirements on any standard fluorescence microscope, and is more easily applied for multi-color imaging than either deterministic or stochastic super-resolution approaches. This renders X10 expansion microscopy a highly promising tool for new biological discoveries, as discussed here, and as demonstrated by several recent applications.
AU - Truckenbrodt, Sven M
AU - Rizzoli, Silvio O.
ID - 7941
SN - 0091-679X
T2 - Methods in Cell Biology
TI - Simple multi-color super-resolution by X10 microscopy
VL - 161
ER -
TY - JOUR
AB - Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.
AU - Fraisse, Christelle
AU - Sachdeva, Himani
ID - 9168
IS - 2
JF - Genetics
SN - 1943-2631
TI - The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes
VL - 217
ER -
TY - JOUR
AB - Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane.
AU - Grosser, Joshua A.
AU - Maes, Margaret E
AU - Nickells, Robert W.
ID - 9009
IS - 2
JF - Apoptosis
SN - 1360-8185
TI - Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis
VL - 26
ER -
TY - JOUR
AB - This paper continues the discussion started in [CK19] concerning Arnold's legacy on classical KAM theory and (some of) its modern developments. We prove a detailed and explicit `global' Arnold's KAM Theorem, which yields, in particular, the Whitney conjugacy of a non{degenerate, real{analytic, nearly-integrable Hamiltonian system to an integrable system on a closed, nowhere dense, positive measure subset of the phase space. Detailed measure estimates on the Kolmogorov's set are provided in the case the phase space is: (A) a uniform neighbourhood of an arbitrary (bounded) set times the d-torus and (B) a domain with C2 boundary times the d-torus. All constants are explicitly given.
AU - Chierchia, Luigi
AU - Koudjinan, Edmond
ID - 8689
IS - 1
JF - Regular and Chaotic Dynamics
KW - Nearly{integrable Hamiltonian systems
KW - perturbation theory
KW - KAM Theory
KW - Arnold's scheme
KW - Kolmogorov's set
KW - primary invariant tori
KW - Lagrangian tori
KW - measure estimates
KW - small divisors
KW - integrability on nowhere dense sets
KW - Diophantine frequencies.
SN - 1560-3547
TI - V.I. Arnold's ''Global'' KAM theorem and geometric measure estimates
VL - 26
ER -
TY - JOUR
AB - In this paper we experimentally study the transitional range of Reynolds numbers in
plane Couette–Poiseuille flow, focusing our attention on the localized turbulent structures
triggered by a strong impulsive jet and the large-scale flow generated around these
structures. We present a detailed investigation of the large-scale flow and show how
its amplitude depends on Reynolds number and amplitude perturbation. In addition,
we characterize the initial dynamics of the localized turbulent spot, which includes the
coupling between the small and large scales, as well as the dependence of the advection
speed on the large-scale flow generated around the spot. Finally, we provide the first
experimental measurements of the large-scale flow around an oblique turbulent band.
AU - Klotz, Lukasz
AU - Pavlenko, A. M.
AU - Wesfreid, J. E.
ID - 9207
JF - Journal of Fluid Mechanics
SN - 0022-1120
TI - Experimental measurements in plane Couette-Poiseuille flow: Dynamics of the large- and small-scale flow
VL - 912
ER -
TY - GEN
AB - Metabolic adaptation to changing demands underlies homeostasis. During inflammation or metastasis, cells leading migration into challenging environments require an energy boost, however what controls this capacity is unknown. We identify a previously unstudied nuclear protein, Atossa, as changing metabolism in Drosophila melanogaster immune cells to promote tissue invasion. Atossa’s vertebrate orthologs, FAM214A-B, can fully substitute for Atossa, indicating functional conservation from flies to mammals. Atossa increases mRNA levels of Porthos, an unstudied RNA helicase and two metabolic enzymes, LKR/SDH and GR/HPR. Porthos increases translation of a gene subset, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Respiration measurements and metabolomics indicate that Atossa and Porthos powers up mitochondrial oxidative phosphorylation to produce sufficient energy for leading macrophages to forge a path into tissues. As increasing oxidative phosphorylation enables many crucial physiological responses, this unique genetic program may modulate a wide range of cellular behaviors beyond migration.
AU - Emtenani, Shamsi
AU - Martin, Elliott T.
AU - György, Attila
AU - Bicher, Julia
AU - Genger, Jakob-Wendelin
AU - Hurd, Thomas R.
AU - Köcher, Thomas
AU - Bergthaler, Andreas
AU - Rangan, Prashanth
AU - Siekhaus, Daria E
ID - 9238
T2 - bioRxiv
TI - A genetic program boosts mitochondrial function to power macrophage tissue invasion
ER -
TY - JOUR
AB - Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.
AU - Hernández-Rocamora, Víctor M.
AU - Baranova, Natalia S.
AU - Peters, Katharina
AU - Breukink, Eefjan
AU - Loose, Martin
AU - Vollmer, Waldemar
ID - 9243
JF - eLife
TI - Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins
VL - 10
ER -
TY - JOUR
AB - A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games.
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Žikelić, Đorđe
ID - 9239
IS - 8
JF - Journal of Computer and System Sciences
SN - 0022-0000
TI - Bidding mechanisms in graph games
VL - 119
ER -
TY - JOUR
AB - Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.
AU - Hankeova, Simona
AU - Salplachta, Jakub
AU - Zikmund, Tomas
AU - Kavkova, Michaela
AU - Van Hul, Noémi
AU - Brinek, Adam
AU - Smekalova, Veronika
AU - Laznovsky, Jakub
AU - Dawit, Feven
AU - Jaros, Josef
AU - Bryja, Vítězslav
AU - Lendahl, Urban
AU - Ellis, Ewa
AU - Nemeth, Antal
AU - Fischler, Björn
AU - Hannezo, Edouard B
AU - Kaiser, Jozef
AU - Andersson, Emma Rachel
ID - 9244
JF - eLife
TI - DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome
VL - 10
ER -
TY - JOUR
AB - Volumetric light transport is a pervasive physical phenomenon, and therefore its accurate simulation is important for a broad array of disciplines. While suitable mathematical models for computing the transport are now available, obtaining the necessary material parameters needed to drive such simulations is a challenging task: direct measurements of these parameters from material samples are seldom possible. Building on the inverse scattering paradigm, we present a novel measurement approach which indirectly infers the transport parameters from extrinsic observations of multiple-scattered radiance. The novelty of the proposed approach lies in replacing structured illumination with a structured reflector bonded to the sample, and a robust fitting procedure that largely compensates for potential systematic errors in the calibration of the setup. We show the feasibility of our approach by validating simulations of complex 3D compositions of the measured materials against physical prints, using photo-polymer resins. As presented in this paper, our technique yields colorspace data suitable for accurate appearance reproduction in the area of 3D printing. Beyond that, and without fundamental changes to the basic measurement methodology, it could equally well be used to obtain spectral measurements that are useful for other application areas.
AU - Elek, Oskar
AU - Zhang, Ran
AU - Sumin, Denis
AU - Myszkowski, Karol
AU - Bickel, Bernd
AU - Wilkie, Alexander
AU - Křivánek, Jaroslav
AU - Weyrich, Tim
ID - 9241
IS - 5
JF - Optics Express
TI - Robust and practical measurement of volume transport parameters in solid photo-polymer materials for 3D printing
VL - 29
ER -
TY - JOUR
AB - We consider the Fröhlich Hamiltonian in a mean-field limit where many bosonic particles weakly couple to the quantized phonon field. For large particle numbers and a suitably small coupling, we show that the dynamics of the system is approximately described by the Landau–Pekar equations. These describe a Bose–Einstein condensate interacting with a classical polarization field, whose dynamics is effected by the condensate, i.e., the back-reaction of the phonons that are created by the particles during the time evolution is of leading order.
AU - Leopold, Nikolai K
AU - Mitrouskas, David Johannes
AU - Seiringer, Robert
ID - 9246
JF - Archive for Rational Mechanics and Analysis
SN - 00039527
TI - Derivation of the Landau–Pekar equations in a many-body mean-field limit
VL - 240
ER -
TY - JOUR
AB - In the recent years important experimental advances in resonant electro-optic modulators as high-efficiency sources for coherent frequency combs and as devices for quantum information transfer have been realized, where strong optical and microwave mode coupling were achieved. These features suggest electro-optic-based devices as candidates for entangled optical frequency comb sources. In the present work, I study the generation of entangled optical frequency combs in millimeter-sized resonant electro-optic modulators. These devices profit from the experimentally proven advantages such as nearly constant optical free spectral ranges over several gigahertz, and high optical and microwave quality factors. The generation of frequency multiplexed quantum channels with spectral bandwidth in the MHz range for conservative parameter values paves the way towards novel uses in long-distance hybrid quantum networks, quantum key distribution, enhanced optical metrology, and quantum computing.
AU - Rueda Sanchez, Alfredo R
ID - 9242
IS - 2
JF - Physical Review A
SN - 2469-9926
TI - Frequency-multiplexed hybrid optical entangled source based on the Pockels effect
VL - 103
ER -
TY - JOUR
AB - Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient.
AU - Vaahtomeri, Kari
AU - Moussion, Christine
AU - Hauschild, Robert
AU - Sixt, Michael K
ID - 9259
JF - Frontiers in Immunology
TI - Shape and function of interstitial chemokine CCL21 gradients are independent of heparan sulfates produced by lymphatic endothelium
VL - 12
ER -
TY - JOUR
AB - Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms.
AU - Hu, Yangjie
AU - Omary, Moutasem
AU - Hu, Yun
AU - Doron, Ohad
AU - Hörmayer, Lukas
AU - Chen, Qingguo
AU - Megides, Or
AU - Chekli, Ori
AU - Ding, Zhaojun
AU - Friml, Jiří
AU - Zhao, Yunde
AU - Tsarfaty, Ilan
AU - Shani, Eilon
ID - 9254
JF - Nature Communications
TI - Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing
VL - 12
ER -
TY - JOUR
AB - Our ability to trust that a random number is truly random is essential for fields as diverse as cryptography and fundamental tests of quantum mechanics. Existing solutions both come with drawbacks—device-independent quantum random number generators (QRNGs) are highly impractical and standard semi-device-independent QRNGs are limited to a specific physical implementation and level of trust. Here we propose a framework for semi-device-independent randomness certification, using a source of trusted vacuum in the form of a signal shutter. It employs a flexible set of assumptions and levels of trust, allowing it to be applied in a wide range of physical scenarios involving both quantum and classical entropy sources. We experimentally demonstrate our protocol with a photonic setup and generate secure random bits under three different assumptions with varying degrees of security and resulting data rates.
AU - Pivoluska, Matej
AU - Plesch, Martin
AU - Farkas, Máté
AU - Ruzickova, Natalia
AU - Flegel, Clara
AU - Valencia, Natalia Herrera
AU - Mccutcheon, Will
AU - Malik, Mehul
AU - Aguilar, Edgar A.
ID - 9255
JF - npj Quantum Information
TI - Semi-device-independent random number generation with flexible assumptions
VL - 7
ER -
TY - JOUR
AB - We consider the ferromagnetic quantum Heisenberg model in one dimension, for any spin S≥1/2. We give upper and lower bounds on the free energy, proving that at low temperature it is asymptotically equal to the one of an ideal Bose gas of magnons, as predicted by the spin-wave approximation. The trial state used in the upper bound yields an analogous estimate also in the case of two spatial dimensions, which is believed to be sharp at low temperature.
AU - Napiórkowski, Marcin M
AU - Seiringer, Robert
ID - 9256
IS - 2
JF - Letters in Mathematical Physics
SN - 03779017
TI - Free energy asymptotics of the quantum Heisenberg spin chain
VL - 111
ER -
TY - JOUR
AU - Pinkard, Henry
AU - Stuurman, Nico
AU - Ivanov, Ivan E.
AU - Anthony, Nicholas M.
AU - Ouyang, Wei
AU - Li, Bin
AU - Yang, Bin
AU - Tsuchida, Mark A.
AU - Chhun, Bryant
AU - Zhang, Grace
AU - Mei, Ryan
AU - Anderson, Michael
AU - Shepherd, Douglas P.
AU - Hunt-Isaak, Ian
AU - Dunn, Raymond L.
AU - Jahr, Wiebke
AU - Kato, Saul
AU - Royer, Loïc A.
AU - Thiagarajah, Jay R.
AU - Eliceiri, Kevin W.
AU - Lundberg, Emma
AU - Mehta, Shalin B.
AU - Waller, Laura
ID - 9258
IS - 3
JF - Nature Methods
SN - 1548-7091
TI - Pycro-Manager: Open-source software for customized and reproducible microscope control
VL - 18
ER -