TY - JOUR
AB - Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.
AU - Marquès-Bueno, MM
AU - Armengot, L
AU - Noack, LC
AU - Bareille, J
AU - Rodriguez Solovey, Lesia
AU - Platre, MP
AU - Bayle, V
AU - Liu, M
AU - Opdenacker, D
AU - Vanneste, S
AU - Möller, BK
AU - Nimchuk, ZL
AU - Beeckman, T
AU - Caño-Delgado, AI
AU - Friml, Jiří
AU - Jaillais, Y
ID - 8824
IS - 1
JF - Current Biology
SN - 0960-9822
TI - Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism
VL - 31
ER -
TY - JOUR
AB - Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.
AU - Fredes Tolorza, Felipe A
AU - Silva Sifuentes, Maria A
AU - Koppensteiner, Peter
AU - Kobayashi, Kenta
AU - Jösch, Maximilian A
AU - Shigemoto, Ryuichi
ID - 7551
IS - 1
JF - Current Biology
TI - Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation
VL - 31
ER -
TY - JOUR
AB - We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.
AU - Boccato, Chiara
ID - 7685
IS - 1
JF - Reviews in Mathematical Physics
SN - 0129-055X
TI - The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime
VL - 33
ER -
TY - JOUR
AB - Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation.
AU - Benedikter, Niels P
ID - 7900
IS - 1
JF - Reviews in Mathematical Physics
SN - 0129-055X
TI - Bosonic collective excitations in Fermi gases
VL - 33
ER -
TY - JOUR
AB - The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19.
AU - Nardo, Alexander D.
AU - Schneeweiss-Gleixner, Mathias
AU - Bakail, May M
AU - Dixon, Emmanuel D.
AU - Lax, Sigurd F.
AU - Trauner, Michael
ID - 8927
IS - 1
JF - Liver International
SN - 14783223
TI - Pathophysiological mechanisms of liver injury in COVID-19
VL - 41
ER -
TY - JOUR
AB - Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear.
Here we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation.
The gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.
AU - Gelová, Zuzana
AU - Gallei, Michelle C
AU - Pernisová, Markéta
AU - Brunoud, Géraldine
AU - Zhang, Xixi
AU - Glanc, Matous
AU - Li, Lanxin
AU - Michalko, Jaroslav
AU - Pavlovicova, Zlata
AU - Verstraeten, Inge
AU - Han, Huibin
AU - Hajny, Jakub
AU - Hauschild, Robert
AU - Čovanová, Milada
AU - Zwiewka, Marta
AU - Hörmayer, Lukas
AU - Fendrych, Matyas
AU - Xu, Tongda
AU - Vernoux, Teva
AU - Friml, Jiří
ID - 8931
JF - Plant Science
KW - Agronomy and Crop Science
KW - Plant Science
KW - Genetics
KW - General Medicine
SN - 0168-9452
TI - Developmental roles of auxin binding protein 1 in Arabidopsis thaliana
VL - 303
ER -
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 - GEN
AB - We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of $\mathbb{P}^3$ outside certain planes using universal torsors.
AU - Wilsch, Florian Alexander
ID - 9034
T2 - arXiv
TI - Integral points of bounded height on a log Fano threefold
ER -
TY - JOUR
AB - We continue our study of ‘no‐dimension’ analogues of basic theorems in combinatorial and convex geometry in Banach spaces. We generalize some results of the paper (Adiprasito, Bárány and Mustafa, ‘Theorems of Carathéodory, Helly, and Tverberg without dimension’, Proceedings of the Thirtieth Annual ACM‐SIAM Symposium on Discrete Algorithms (Society for Industrial and Applied Mathematics, San Diego, California, 2019) 2350–2360) and prove no‐dimension versions of the colored Tverberg theorem, the selection lemma and the weak 𝜀 ‐net theorem in Banach spaces of type 𝑝>1 . To prove these results, we use the original ideas of Adiprasito, Bárány and Mustafa for the Euclidean case, our no‐dimension version of the Radon theorem and slightly modified version of the celebrated Maurey lemma.
AU - Ivanov, Grigory
ID - 9037
JF - Bulletin of the London Mathematical Society
SN - 00246093
TI - No-dimension Tverberg's theorem and its corollaries in Banach spaces of type p
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 - We study properties of the volume of projections of the n-dimensional
cross-polytope $\crosp^n = \{ x \in \R^n \mid |x_1| + \dots + |x_n| \leqslant 1\}.$ We prove that the projection of $\crosp^n$ onto a k-dimensional coordinate subspace has the maximum possible volume for k=2 and for k=3.
We obtain the exact lower bound on the volume of such a projection onto a two-dimensional plane. Also, we show that there exist local maxima which are not global ones for the volume of a projection of $\crosp^n$ onto a k-dimensional subspace for any n>k⩾2.
AU - Ivanov, Grigory
ID - 9098
IS - 5
JF - Discrete Mathematics
SN - 0012365X
TI - On the volume of projections of the cross-polytope
VL - 344
ER -
TY - JOUR
AB - We show that on an Abelian variety over an algebraically closed field of positive characteristic, the obstruction to lifting an automorphism to a field of characteristic zero as a morphism vanishes if and only if it vanishes for lifting it as a derived autoequivalence. We also compare the deformation space of these two types of deformations.
AU - Srivastava, Tanya K
ID - 9099
JF - Archiv der Mathematik
SN - 0003889X
TI - Lifting automorphisms on Abelian varieties as derived autoequivalences
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 - Behavioral predispositions are innate tendencies of animals to behave in a given way without the input of learning. They increase survival chances and, due to environmental and ecological challenges, may vary substantially even between closely related taxa. These differences are likely to be especially pronounced in long-lived species like crocodilians. This order is particularly relevant for comparative cognition due to its phylogenetic proximity to birds. Here we compared early life behavioral predispositions in two Alligatoridae species. We exposed American alligator and spectacled caiman hatchlings to three different novel situations: a novel object, a novel environment that was open and a novel environment with a shelter. This was then repeated a week later. During exposure to the novel environments, alligators moved around more and explored a larger range of the arena than the caimans. When exposed to the novel object, the alligators reduced the mean distance to the novel object in the second phase, while the caimans further increased it, indicating diametrically opposite ontogenetic development in behavioral predispositions. Although all crocodilian hatchlings face comparable challenges, e.g., high predation pressure, the effectiveness of parental protection might explain the observed pattern. American alligators are apex predators capable of protecting their offspring against most dangers, whereas adult spectacled caimans are frequently predated themselves. Their distancing behavior might be related to increased predator avoidance and also explain the success of invasive spectacled caimans in the natural habitats of other crocodilians.
AU - Reber, Stephan A.
AU - Oh, Jinook
AU - Janisch, Judith
AU - Stevenson, Colin
AU - Foggett, Shaun
AU - Wilkinson, Anna
ID - 9101
JF - Animal Cognition
SN - 14359448
TI - Early life differences in behavioral predispositions in two Alligatoridae species
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 - JOUR
AB - Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.
AU - Zhao, Y
AU - Wu, L
AU - Fu, Q
AU - Wang, D
AU - Li, J
AU - Yao, B
AU - Yu, S
AU - Jiang, L
AU - Qian, J
AU - Zhou, X
AU - Han, L
AU - Zhao, S
AU - Ma, C
AU - Zhang, Y
AU - Luo, C
AU - Dong, Q
AU - Li, S
AU - Zhang, L
AU - Jiang, X
AU - Li, Y
AU - Luo, H
AU - Li, K
AU - Yang, J
AU - Luo, Q
AU - Li, L
AU - Peng, S
AU - Huang, H
AU - Zuo, Z
AU - Liu, C
AU - Wang, L
AU - Li, C
AU - He, X
AU - Friml, Jiří
AU - Du, Y
ID - 9189
JF - Plant, Cell & Environment
SN - 0140-7791
TI - INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance
ER -
TY - GEN
AB - Formal design of embedded and cyber-physical systems relies on mathematical
modeling. In this paper, we consider the model class of hybrid automata whose
dynamics are defined by affine differential equations. Given a set of
time-series data, we present an algorithmic approach to synthesize a hybrid
automaton exhibiting behavior that is close to the data, up to a specified
precision, and changes in synchrony with the data. A fundamental problem in our
synthesis algorithm is to check membership of a time series in a hybrid
automaton. Our solution integrates reachability and optimization techniques for
affine dynamical systems to obtain both a sufficient and a necessary condition
for membership, combined in a refinement framework. The algorithm processes one
time series at a time and hence can be interrupted, provide an intermediate
result, and be resumed. We report experimental results demonstrating the
applicability of our synthesis approach.
AU - Garcia Soto, Miriam
AU - Henzinger, Thomas A
AU - Schilling, Christian
ID - 9200
KW - hybrid automaton
KW - membership
KW - system identification
T2 - arXiv
TI - Synthesis of hybrid automata with affine dynamics from time-series data
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 - JOUR
AB - Plant fitness is largely dependent on the root, the underground organ, which, besides its anchoring function, supplies the plant body with water and all nutrients necessary for growth and development. To exploit the soil effectively, roots must constantly integrate environmental signals and react through adjustment of growth and development. Important components of the root management strategy involve a rapid modulation of the root growth kinetics and growth direction, as well as an increase of the root system radius through formation of lateral roots (LRs). At the molecular level, such a fascinating growth and developmental flexibility of root organ requires regulatory networks that guarantee stability of the developmental program but also allows integration of various environmental inputs. The plant hormone auxin is one of the principal endogenous regulators of root system architecture by controlling primary root growth and formation of LR. In this review, we discuss recent progress in understanding molecular networks where auxin is one of the main players shaping the root system and acting as mediator between endogenous cues and environmental factors.
AU - Cavallari, Nicola
AU - Artner, Christina
AU - Benková, Eva
ID - 9212
JF - Cold Spring Harbor Perspectives in Biology
SN - 1943-0264
TI - Auxin-regulated lateral root organogenesis
ER -
TY - JOUR
AB - The Landau–Pekar equations describe the dynamics of a strongly coupled polaron.
Here, we provide a class of initial data for which the associated effective Hamiltonian
has a uniform spectral gap for all times. For such initial data, this allows us to extend the
results on the adiabatic theorem for the Landau–Pekar equations and their derivation
from the Fröhlich model obtained in previous works to larger times.
AU - Feliciangeli, Dario
AU - Rademacher, Simone Anna Elvira
AU - Seiringer, Robert
ID - 9225
JF - Letters in Mathematical Physics
SN - 03779017
TI - Persistence of the spectral gap for the Landau–Pekar equations
VL - 111
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 - JOUR
AB - Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned.
AU - Achakulvisut, Titipat
AU - Ruangrong, Tulakan
AU - Mineault, Patrick
AU - Vogels, Tim P
AU - Peters, Megan A.K.
AU - Poirazi, Panayiota
AU - Rozell, Christopher
AU - Wyble, Brad
AU - Goodman, Dan F.M.
AU - Kording, Konrad Paul
ID - 9228
JF - Trends in Cognitive Sciences
SN - 1364-6613
TI - Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences
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 - Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues.
AU - Pauler, Florian
AU - Hudson, Quanah
AU - Laukoter, Susanne
AU - Hippenmeyer, Simon
ID - 9188
IS - 5
JF - Neurochemistry International
KW - Cell Biology
KW - Cellular and Molecular Neuroscience
SN - 0197-0186
TI - Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond
VL - 145
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 - In this paper, we present two new inertial projection-type methods for solving multivalued variational inequality problems in finite-dimensional spaces. We establish the convergence of the sequence generated by these methods when the multivalued mapping associated with the problem is only required to be locally bounded without any monotonicity assumption. Furthermore, the inertial techniques that we employ in this paper are quite different from the ones used in most papers. Moreover, based on the weaker assumptions on the inertial factor in our methods, we derive several special cases of our methods. Finally, we present some experimental results to illustrate the profits that we gain by introducing the inertial extrapolation steps.
AU - Izuchukwu, Chinedu
AU - Shehu, Yekini
ID - 9234
JF - Networks and Spatial Economics
KW - Computer Networks and Communications
KW - Software
KW - Artificial Intelligence
SN - 1566-113X
TI - New inertial projection methods for solving multivalued variational inequality problems beyond monotonicity
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 -