TY - JOUR
AB - Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.
AU - Zhou, Liang-Zi
AU - Wang, Lele
AU - Chen, Xia
AU - Ge, Zengxiang
AU - Mergner, Julia
AU - Li, Xingli
AU - Küster, Bernhard
AU - Längst, Gernot
AU - Qu, Li-Jia
AU - Dresselhaus, Thomas
ID - 14726
JF - The Plant Cell
KW - Cell Biology
KW - Plant Science
SN - 1040-4651
TI - The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize
ER -
TY - JOUR
AB - The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.
AU - Biniaz, Ahmad
AU - Jain, Kshitij
AU - Lubiw, Anna
AU - Masárová, Zuzana
AU - Miltzow, Tillmann
AU - Mondal, Debajyoti
AU - Naredla, Anurag Murty
AU - Tkadlec, Josef
AU - Turcotte, Alexi
ID - 12833
IS - 2
JF - Discrete Mathematics and Theoretical Computer Science
SN - 1462-7264
TI - Token swapping on trees
VL - 24
ER -
TY - CONF
AB - Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.
If we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.
This “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs.
AU - Stefo, Christos
AU - Xiang, Zhuolun
AU - Kokoris Kogias, Eleftherios
ID - 14735
SN - 1611-3349
T2 - 27th International Conference on Financial Cryptography and Data Security
TI - Executing and proving over dirty ledgers
VL - 13950
ER -
TY - JOUR
AB - Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy.
AU - Jethwa, Rajesh B
AU - Hey, Dominic
AU - Kerber, Rachel N.
AU - Bond, Andrew D.
AU - Wright, Dominic S.
AU - Grey, Clare P.
ID - 14733
JF - ACS Applied Energy Materials
KW - Electrical and Electronic Engineering
KW - Materials Chemistry
KW - Electrochemistry
KW - Energy Engineering and Power Technology
KW - Chemical Engineering (miscellaneous)
TI - Exploring the landscape of heterocyclic quinones for redox flow batteries
ER -
TY - JOUR
AB - Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology.
AU - Wan, Shanhong
AU - Xiao, Shanshan
AU - Li, Mingquan
AU - Wang, Xin
AU - Lim, Khak Ho
AU - Hong, Min
AU - Ibáñez, Maria
AU - Cabot, Andreu
AU - Liu, Yu
ID - 14734
JF - Small Methods
TI - Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4
ER -
TY - JOUR
AB - John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies.
AU - Ivanov, Grigory
AU - Naszódi, Márton
ID - 14737
IS - 23
JF - International Mathematics Research Notices
KW - General Mathematics
SN - 1073-7928
TI - Functional John and Löwner conditions for pairs of log-concave functions
VL - 2023
ER -
TY - CONF
AB - Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks.
AU - Bastankhah, Mahsa
AU - Chatterjee, Krishnendu
AU - Maddah-Ali, Mohammad Ali
AU - Schmid, Stefan
AU - Svoboda, Jakub
AU - Yeo, Michelle X
ID - 14736
SN - 0302-9743
T2 - 27th International Conference on Financial Cryptography and Data Security
TI - R2: Boosting liquidity in payment channel networks with online admission control
VL - 13950
ER -
TY - JOUR
AB - Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods.
AU - Ali, Dashti
AU - Asaad, Aras
AU - Jimenez, Maria-Jose
AU - Nanda, Vidit
AU - Paluzo-Hidalgo, Eduardo
AU - Soriano Trigueros, Manuel
ID - 14739
IS - 12
JF - IEEE Transactions on Pattern Analysis and Machine Intelligence
KW - Applied Mathematics
KW - Artificial Intelligence
KW - Computational Theory and Mathematics
KW - Computer Vision and Pattern Recognition
KW - Software
SN - 0162-8828
TI - A survey of vectorization methods in topological data analysis
VL - 45
ER -
TY - JOUR
AB - Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.
While an important role for CRs in speciation has been suggested, evidence primarily stems
from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon
pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at
a macroevolutionary level has been supported by associations between species diversity and
rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of
CRs and taxa. Now that more broadly applicable and precise CR detection approaches have
become available, we address the challenges in filling some of the conceptual and empirical
gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We
synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
AU - Lucek, Kay
AU - Giménez, Mabel D.
AU - Joron, Mathieu
AU - Rafajlović, Marina
AU - Searle, Jeremy B.
AU - Walden, Nora
AU - Westram, Anja M
AU - Faria, Rui
ID - 14742
IS - 11
JF - Cold Spring Harbor Perspectives in Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 1943-0264
TI - The impact of chromosomal rearrangements in speciation: From micro- to macroevolution
VL - 15
ER -
TY - CONF
AB - Sharding distributed ledgers is a promising on-chain solution for scaling blockchains but lacks formal grounds, nurturing skepticism on whether such complex systems can scale blockchains securely. We fill this gap by introducing the first formal framework as well as a roadmap to robust sharding. In particular, we first define the properties sharded distributed ledgers should fulfill. We build upon and extend the Bitcoin backbone protocol by defining consistency and scalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system.
Using our model, we explore the limitations of sharding. We show that a sharded ledger with n participants cannot scale under a fully adaptive adversary, but it can scale up to m shards where n=c'm log m, under an epoch-adaptive adversary; the constant c' encompasses the trade-off between security and scalability. This is possible only if the sharded ledgers create succinct proofs of the valid state updates at every epoch. We leverage our results to identify the sufficient components for robust sharding, which we incorporate in a protocol abstraction termed Divide & Scale. To demonstrate the power of our framework, we analyze the most prominent sharded blockchains (Elastico, Monoxide, OmniLedger, RapidChain) and pinpoint where they fail to meet the desired properties.
AU - Avarikioti, Zeta
AU - Desjardins, Antoine
AU - Kokoris Kogias, Eleftherios
AU - Wattenhofer, Roger
ID - 14744
SN - 0302-9743
T2 - 30th International Colloquium on Structural Information and Communication Complexity
TI - Divide & Scale: Formalization and roadmap to robust sharding
VL - 13892
ER -
TY - JOUR
AB - We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry.
AU - Mishra, Umang
AU - Li, Vyacheslav
AU - Wald, Sebastian
AU - Agafonova, Sofya
AU - Diorico, Fritz R
AU - Hosten, Onur
ID - 14749
IS - 15
JF - Optics Letters
KW - Atomic and Molecular Physics
KW - and Optics
SN - 0146-9592
TI - Monitoring and active stabilization of laser injection locking using beam ellipticity
VL - 48
ER -
TY - JOUR
AB - Radiative cooling of the lowest atmospheric levels is of strong importance for modulating atmospheric circulations and organizing convection, but detailed observations and a robust theoretical understanding are lacking. Here we use unprecedented observational constraints from subsidence regimes in the tropical Atlantic to develop a theory for the shape and magnitude of low‐level longwave radiative cooling in clear‐sky, showing peaks larger than 5–10 K/day at the top of the boundary layer. A suite of novel scaling approximations is first developed from simplified spectral theory, in close agreement with the measurements. The radiative cooling peak height is set by the maximum lapse rate in water vapor path, and its magnitude is mainly controlled by the ratio of column relative humidity above and below the peak. We emphasize how elevated intrusions of moist air can reduce low‐level cooling, by sporadically shading the spectral range which effectively cools to space. The efficiency of this spectral shading depends both on water content and altitude of moist intrusions; its height dependence cannot be explained by the temperature difference between the emitting and absorbing layers, but by the decrease of water vapor extinction with altitude. This analytical work can help to narrow the search for low‐level cloud patterns sensitive to radiative‐convective feedbacks: the most organized patterns with largest cloud fractions occur in atmospheres below 10% relative humidity and feel the strongest low‐level cooling. This motivates further assessment of favorable conditions for radiative‐convective feedbacks and a robust quantification of corresponding shallow cloud dynamics in current and warmer climates.
AU - Fildier, B.
AU - Muller, Caroline J
AU - Pincus, R.
AU - Fueglistaler, S.
ID - 14752
IS - 3
JF - AGU Advances
KW - General Earth and Planetary Sciences
TI - How moisture shapes low‐level radiative cooling in subsidence regimes
VL - 4
ER -
TY - JOUR
AB - The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role.
AU - Wang, B.
AU - Mellibovsky, F.
AU - Ayats López, Roger
AU - Deguchi, K.
AU - Meseguer, A.
ID - 14754
IS - 2246
JF - Philosophical Transactions of the Royal Society A
KW - General Physics and Astronomy
KW - General Engineering
KW - General Mathematics
SN - 1364-503X
TI - Mean structure of the supercritical turbulent spiral in Taylor–Couette flow
VL - 381
ER -
TY - JOUR
AB - Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (PT), in three different frames, using different combinations of beam particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF 0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-PT
quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion.
AU - Faccioli, Pietro
AU - Krätschmer, Ilse
AU - Lourenço, Carlos
ID - 14753
JF - Physics Letters B
KW - Nuclear and High Energy Physics
SN - 0370-2693
TI - Low-pT quarkonium polarization measurements: Challenges and opportunities
VL - 840
ER -
TY - JOUR
AB - Consider the random matrix model A1/2UBU∗A1/2, where A and B are two N × N deterministic matrices and U is either an N × N Haar unitary or orthogonal random matrix. It is well known that on the macroscopic scale (Invent. Math. 104 (1991) 201–220), the limiting empirical spectral distribution (ESD) of the above model is given by the free multiplicative convolution
of the limiting ESDs of A and B, denoted as μα μβ, where μα and μβ are the limiting ESDs of A and B, respectively. In this paper, we study the asymptotic microscopic behavior of the edge eigenvalues and eigenvectors statistics. We prove that both the density of μA μB, where μA and μB are the ESDs of A and B, respectively and the associated subordination functions
have a regular behavior near the edges. Moreover, we establish the local laws near the edges on the optimal scale. In particular, we prove that the entries of the resolvent are close to some functionals depending only on the eigenvalues of A, B and the subordination functions with optimal convergence rates. Our proofs and calculations are based on the techniques developed for the additive model A+UBU∗ in (J. Funct. Anal. 271 (2016) 672–719; Comm. Math.
Phys. 349 (2017) 947–990; Adv. Math. 319 (2017) 251–291; J. Funct. Anal. 279 (2020) 108639), and our results can be regarded as the counterparts of (J. Funct. Anal. 279 (2020) 108639) for the multiplicative model.
AU - Ding, Xiucai
AU - Ji, Hong Chang
ID - 14750
IS - 4
JF - The Annals of Applied Probability
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
SN - 1050-5164
TI - Local laws for multiplication of random matrices
VL - 33
ER -
TY - JOUR
AB - We prove the r-spin cobordism hypothesis in the setting of (weak) 2-categories for every positive integer r: the 2-groupoid of 2-dimensional fully extended r-spin TQFTs with given target is equivalent to the homotopy fixed points of an induced Spin 2r -action. In particular, such TQFTs are classified by fully dualisable objects together with a trivialisation of the rth power of their Serre automorphisms. For r=1, we recover the oriented case (on which our proof builds), while ordinary spin structures correspond to r=2.
To construct examples, we explicitly describe Spin 2r-homotopy fixed points in the equivariant completion of any symmetric monoidal 2-category. We also show that every object in a 2-category of Landau–Ginzburg models gives rise to fully extended spin TQFTs and that half of these do not factor through the oriented bordism 2-category.
AU - Carqueville, Nils
AU - Szegedy, Lorant
ID - 14756
IS - 3
JF - Quantum Topology
KW - Geometry and Topology
KW - Mathematical Physics
SN - 1663-487X
TI - Fully extended r-spin TQFTs
VL - 14
ER -
TY - JOUR
AB - We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation.
AU - Zhang, Yihan
ID - 14751
IS - 7
JF - IEEE Transactions on Information Theory
KW - Computer Science Applications
KW - Information Systems
SN - 0018-9448
TI - Zero-error communication over adversarial MACs
VL - 69
ER -
TY - JOUR
AB - We consider the sharp interface limit for the scalar-valued and vector-valued Allen–Cahn equation with homogeneous Neumann boundary condition in a bounded smooth domain Ω of arbitrary dimension N ⩾ 2 in the situation when a two-phase diffuse interface has developed and intersects the boundary ∂ Ω. The limit problem is mean curvature flow with 90°-contact angle and we show convergence in strong norms for well-prepared initial data as long as a smooth solution to the limit problem exists. To this end we assume that the limit problem has a smooth solution on [ 0 , T ] for some time T > 0. Based on the latter we construct suitable curvilinear coordinates and set up an asymptotic expansion for the scalar-valued and the vector-valued Allen–Cahn equation. In order to estimate the difference of the exact and approximate solutions with a Gronwall-type argument, a spectral estimate for the linearized Allen–Cahn operator in both cases is required. The latter will be shown in a separate paper, cf. (Moser (2021)).
AU - Moser, Maximilian
ID - 14755
IS - 3-4
JF - Asymptotic Analysis
KW - General Mathematics
SN - 0921-7134
TI - Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result
VL - 131
ER -
TY - CHAP
AB - The cerebral cortex is comprised of a vast cell-type diversity sequentially generated by cortical progenitor cells. Faithful progenitor lineage progression requires the tight orchestration of distinct molecular and cellular mechanisms regulating proper progenitor proliferation behavior and differentiation. Correct execution of developmental programs involves a complex interplay of cell intrinsic and tissue-wide mechanisms. Many studies over the past decades have been able to determine a plethora of genes critically involved in cortical development. However, only a few made use of genetic paradigms with sparse and global gene deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter, we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide mechanisms to gain a precise understanding of gene function during radial glial progenitor lineage progression.
AU - Villalba Requena, Ana
AU - Amberg, Nicole
AU - Hippenmeyer, Simon
ED - Huttner, Wieland
ID - 14757
T2 - Neocortical Neurogenesis in Development and Evolution
TI - Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression
ER -
TY - JOUR
AB - Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB
relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.
AU - Wald, Sebastian
AU - Diorico, Fritz R
AU - Hosten, Onur
ID - 14759
IS - 1
JF - Applied Optics
KW - Atomic and Molecular Physics
KW - and Optics
KW - Engineering (miscellaneous)
KW - Electrical and Electronic Engineering
SN - 1559-128X
TI - Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone
VL - 62
ER -
TY - DATA
AB - 3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.
AU - Danzl, Johann G
ID - 12817
TI - Research data for the publication "Dense 4D nanoscale reconstruction of living brain tissue"
ER -
TY - JOUR
AB - Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue.
AU - Velicky, Philipp
AU - Miguel Villalba, Eder
AU - Michalska, Julia M
AU - Lyudchik, Julia
AU - Wei, Donglai
AU - Lin, Zudi
AU - Watson, Jake
AU - Troidl, Jakob
AU - Beyer, Johanna
AU - Ben Simon, Yoav
AU - Sommer, Christoph M
AU - Jahr, Wiebke
AU - Cenameri, Alban
AU - Broichhagen, Johannes
AU - Grant, Seth G.N.
AU - Jonas, Peter M
AU - Novarino, Gaia
AU - Pfister, Hanspeter
AU - Bickel, Bernd
AU - Danzl, Johann G
ID - 13267
JF - Nature Methods
SN - 1548-7091
TI - Dense 4D nanoscale reconstruction of living brain tissue
VL - 20
ER -
TY - CONF
AB - Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.
AU - Iofinova, Eugenia B
AU - Peste, Elena-Alexandra
AU - Alistarh, Dan-Adrian
ID - 14771
T2 - 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition
TI - Bias in pruned vision models: In-depth analysis and countermeasures
ER -
TY - JOUR
AB - We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.
AU - Danzl, Johann G
AU - Velicky, Philipp
ID - 14770
IS - 8
JF - Nature Methods
KW - Cell Biology
KW - Molecular Biology
KW - Biochemistry
KW - Biotechnology
SN - 1548-7091
TI - LIONESS enables 4D nanoscale reconstruction of living brain tissue
VL - 20
ER -
TY - JOUR
AB - Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.
AU - Harish, Rohit K
AU - Gupta, Mansi
AU - Zöller, Daniela
AU - Hartmann, Hella
AU - Gheisari, Ali
AU - Machate, Anja
AU - Hans, Stefan
AU - Brand, Michael
ID - 14774
IS - 19
JF - Development
KW - Developmental Biology
KW - Molecular Biology
SN - 0950-1991
TI - Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation
VL - 150
ER -
TY - JOUR
AB - Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.
AU - Teplova, Anastasiia
AU - Pigidanov, Artemii A.
AU - Serebryakova, Marina V.
AU - Golyshev, Sergei A.
AU - Galiullina, Raisa A.
AU - Chichkova, Nina V.
AU - Vartapetian, Andrey B.
ID - 14776
IS - 22
JF - International Journal of Molecular Sciences
KW - Inorganic Chemistry
KW - Organic Chemistry
KW - Physical and Theoretical Chemistry
KW - Computer Science Applications
KW - Spectroscopy
KW - Molecular Biology
KW - General Medicine
KW - Catalysis
SN - 1422-0067
TI - Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3
VL - 24
ER -
TY - JOUR
AB - We establish a quantitative version of the Tracy–Widom law for the largest eigenvalue of high-dimensional sample covariance matrices. To be precise, we show that the fluctuations of the largest eigenvalue of a sample covariance matrix X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N random matrix whose entries are independent real or complex random variables, assuming that both M and N tend to infinity at a constant rate. This result improves the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant expansions, the local laws for the Green function and asymptotic properties of the correlation kernel of the white Wishart ensemble.
AU - Schnelli, Kevin
AU - Xu, Yuanyuan
ID - 14775
IS - 1
JF - The Annals of Applied Probability
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
SN - 1050-5164
TI - Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices
VL - 33
ER -
TY - JOUR
AB - Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics.
AU - Muller, Caroline J
AU - Abramian, Sophie
ID - 14773
IS - 5
JF - Physics Today
KW - General Physics and Astronomy
SN - 0031-9228
TI - The cloud dynamics of convective storm systems
VL - 76
ER -
TY - JOUR
AB - The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators.
AU - Sato, Kosuke
AU - Singh, Saurabh
AU - Yamazaki, Itsuki
AU - Hirata, Keisuke
AU - Ang, Artoni Kevin R.
AU - Matsunami, Masaharu
AU - Takeuchi, Tsunehiro
ID - 14777
IS - 12
JF - AIP Advances
KW - General Physics and Astronomy
TI - Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag
VL - 13
ER -
TY - JOUR
AB - We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.
AU - Dymond, Michael
AU - Kaluza, Vojtech
ID - 9651
JF - Geometriae Dedicata
SN - 0046-5755
TI - Divergence of separated nets with respect to displacement equivalence
ER -
TY - CONF
AB - In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic k-median and k-means problems, there are no known deterministic dimensionality reduction procedure or coreset construction that avoid an exponential dependency on the input dimension d, the precision parameter $\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds with probability $1-1/n$ and whose size does not depend on the number of input points, n. This has led researchers in the area to ask what is the power of randomness for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly, the best approximation ratio achievable deterministically without a complexity exponential in the dimension are $1+\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari, Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani, Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when allowing a complexity FPT in the number of clusters k: this stands in sharp contrast with the $(1+\varepsilon)$-approximation achievable in that case, when allowing randomization.In this paper, we provide deterministic sketches constructions for clustering, whose size bounds are close to the best-known randomized ones. We show how to compute a dimension reduction onto $\varepsilon^{-O(1)} \log k$ dimensions in time $k^{O\left(\varepsilon^{-O(1)}+\log \log k\right)}$ poly $(n d)$, and how to build a coreset of size $O\left(k^{2} \log ^{3} k \varepsilon^{-O(1)}\right)$ in time $2^{\varepsilon^{O(1)} k \log ^{3} k}+k^{O\left(\varepsilon^{-O(1)}+\log \log k\right)}$ poly $(n d)$. In the case where k is small, this answers an open question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell. ’18] on whether it is possible to efficiently compute coresets deterministically.We also construct a deterministic algorithm for computing $(1+$ $\varepsilon)$-approximation to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2} \log ^{3} k / \varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized complexity of $2^{(k / \varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM 10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights on sketches also yield a randomized coreset construction that uses uniform sampling, that immediately improves over the recent results of [Braverman et al. FOCS ’22] by a factor k.
AU - Cohen-Addad, Vincent
AU - Saulpic, David
AU - Schwiegelshohn, Chris
ID - 14768
T2 - 2023 IEEE 64th Annual Symposium on Foundations of Computer Science
TI - Deterministic clustering in high dimensional spaces: Sketches and approximation
ER -
TY - JOUR
AB - The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.
AU - Gallardo-Dodd, Carlos J.
AU - Oertlin, Christian
AU - Record, Julien
AU - Galvani, Rômulo G.
AU - Sommerauer, Christian
AU - Kuznetsov, Nikolai V.
AU - Doukoumopoulos, Evangelos
AU - Ali, Liaqat
AU - Oliveira, Mariana M. S.
AU - Seitz, Christina
AU - Percipalle, Mathias
AU - Nikić, Tijana
AU - Sadova, Anastasia A.
AU - Shulgina, Sofia M.
AU - Shmarov, Vjacheslav A.
AU - Kutko, Olga V.
AU - Vlasova, Daria D.
AU - Orlova, Kseniya D.
AU - Rykova, Marina P.
AU - Andersson, John
AU - Percipalle, Piergiorgio
AU - Kutter, Claudia
AU - Ponomarev, Sergey A.
AU - Westerberg, Lisa S.
ID - 14784
IS - 34
JF - Science Advances
KW - Multidisciplinary
SN - 2375-2548
TI - Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells
VL - 9
ER -
TY - JOUR
AB - The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.
AU - Baldauf, Lucia
AU - Frey, Felix F
AU - Arribas Perez, Marcos
AU - Idema, Timon
AU - Koenderink, Gijsje H.
ID - 14782
IS - 11
JF - Biophysical Journal
KW - Biophysics
SN - 0006-3495
TI - Branched actin cortices reconstituted in vesicles sense membrane curvature
VL - 122
ER -
TY - JOUR
AB - Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.
AU - Cheung, Giselle T
AU - Chever, Oana
AU - Rollenhagen, Astrid
AU - Quenech’du, Nicole
AU - Ezan, Pascal
AU - Lübke, Joachim H. R.
AU - Rouach, Nathalie
ID - 14783
IS - 8
JF - Cells
KW - General Medicine
SN - 2073-4409
TI - Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses
VL - 12
ER -
TY - JOUR
AB - Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.
AU - Nies, Fabian
AU - Wein, Tanita
AU - Hanke, Dustin M.
AU - Springstein, Benjamin L
AU - Alcorta, Jaime
AU - Taubenheim, Claudia
AU - Dagan, Tal
ID - 14785
IS - 6
JF - Environmental Microbiology Reports
KW - Agricultural and Biological Sciences (miscellaneous)
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
TI - Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803
VL - 15
ER -
TY - JOUR
AB - In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix.
AU - Ding, Xiucai
AU - Ji, Hong Chang
ID - 14780
JF - Stochastic Processes and their Applications
KW - Applied Mathematics
KW - Modeling and Simulation
KW - Statistics and Probability
SN - 0304-4149
TI - Spiked multiplicative random matrices and principal components
VL - 163
ER -
TY - JOUR
AB - The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers.
AU - Shaw, Thomas E.
AU - Buri, Pascal
AU - McCarthy, Michael
AU - Miles, Evan S.
AU - Ayala, Álvaro
AU - Pellicciotti, Francesca
ID - 14779
IS - 11
JF - Geophysical Research Letters
KW - General Earth and Planetary Sciences
KW - Geophysics
SN - 0094-8276
TI - The decaying near‐surface boundary layer of a retreating alpine glacier
VL - 50
ER -
TY - JOUR
AB - Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency.
AU - Westerich, Kim Joana
AU - Tarbashevich, Katsiaryna
AU - Schick, Jan
AU - Gupta, Antra
AU - Zhu, Mingzhao
AU - Hull, Kenneth
AU - Romo, Daniel
AU - Zeuschner, Dagmar
AU - Goudarzi, Mohammad
AU - Gross-Thebing, Theresa
AU - Raz, Erez
ID - 14781
IS - 17
JF - Developmental Cell
KW - Developmental Biology
KW - Cell Biology
KW - General Biochemistry
KW - Genetics and Molecular Biology
KW - Molecular Biology
SN - 1534-5807
TI - Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1
VL - 58
ER -
TY - THES
AB - Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal
verification and control of finite state stochastic systems, a subfield of formal methods
also known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively
less attention. However, infinite state stochastic systems commonly arise in practice.
For instance, probabilistic models that contain continuous probability distributions such
as normal or uniform, or stochastic dynamical systems which are a classical model for
control under uncertainty, both give rise to infinite state systems.
The goal of this thesis is to contribute to laying theoretical and algorithmic foundations
of fully automated formal verification and control of infinite state stochastic systems,
with a particular focus on systems that may be executed over a long or infinite time.
We consider formal verification of infinite state stochastic systems in the setting of
static analysis of probabilistic programs and formal control in the setting of controller
synthesis in stochastic dynamical systems. For both problems, we present some of the
first fully automated methods for probabilistic (a.k.a. quantitative) reachability and
safety analysis applicable to infinite time horizon systems. We also advance the state
of the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.
Finally, for formal controller synthesis in stochastic dynamical systems, we present a
novel framework for learning neural network control policies in stochastic dynamical
systems with formal guarantees on correctness with respect to quantitative reachability,
safety or reach-avoid specifications.
AU - Zikelic, Dorde
ID - 14539
SN - 2663 - 337X
TI - Automated verification and control of infinite state stochastic systems
ER -
TY - JOUR
AB - Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.
Here, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.
AU - Mund, Markus
AU - Tschanz, Aline
AU - Wu, Yu-Le
AU - Frey, Felix F
AU - Mehl, Johanna L.
AU - Kaksonen, Marko
AU - Avinoam, Ori
AU - Schwarz, Ulrich S.
AU - Ries, Jonas
ID - 14788
IS - 3
JF - Journal of Cell Biology
KW - Cell Biology
SN - 0021-9525
TI - Clathrin coats partially preassemble and subsequently bend during endocytosis
VL - 222
ER -
TY - JOUR
AB - Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species.
AU - Filipović Marijić, Vlatka
AU - Subirana, Maria Angels
AU - Schaumlöffel, Dirk
AU - Barišić, Josip
AU - Gontier, Etienne
AU - Krasnici, Nesrete
AU - Mijošek, Tatjana
AU - Hernández-Orts, Jesús S.
AU - Scholz, Tomáš
AU - Erk, Marijana
ID - 14786
JF - Science of The Total Environment
KW - Pollution
KW - Waste Management and Disposal
KW - Environmental Chemistry
KW - Environmental Engineering
SN - 0048-9697
TI - First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS
VL - 887
ER -
TY - JOUR
AB - Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system.
AU - Stankowski, Sean
AU - Chase, Madeline A.
AU - McIntosh, Hanna
AU - Streisfeld, Matthew A.
ID - 14787
IS - 8
JF - Molecular Ecology
KW - Genetics
KW - Ecology
KW - Evolution
KW - Behavior and Systematics
SN - 0962-1083
TI - Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone
VL - 32
ER -
TY - JOUR
AB - Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues.
AU - Corominas-Murtra, Bernat
AU - Hannezo, Edouard B
ID - 12162
JF - Seminars in Cell & Developmental Biology
KW - Cell Biology
KW - Developmental Biology
SN - 1084-9521
TI - Modelling the dynamics of mammalian gut homeostasis
VL - 150-151
ER -
TY - JOUR
AB - We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations.
AU - Huybrechts, D.
AU - Mauri, Mirko
ID - 13268
IS - 1
JF - Mathematical Research Letters
SN - 1073-2780
TI - On type II degenerations of hyperkähler manifolds
VL - 30
ER -
TY - JOUR
AB - This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are "close to" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit.
AU - Carioni, Marcello
AU - Fischer, Julian L
AU - Schlömerkemper, Anja
ID - 14661
IS - 1
JF - Journal of Convex Analysis
SN - 0944-6532
TI - External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development
VL - 30
ER -
TY - JOUR
AB - A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population
mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.
AU - Pauw, Brian R.
AU - Smales, Glen J.
AU - Anker, Andy S.
AU - Annadurai, Venkatasamy
AU - Balazs, Daniel
AU - Bienert, Ralf
AU - Bouwman, Wim G.
AU - Breßler, Ingo
AU - Breternitz, Joachim
AU - Brok, Erik S.
AU - Bryant, Gary
AU - Clulow, Andrew J.
AU - Crater, Erin R.
AU - De Geuser, Frédéric
AU - Giudice, Alessandra Del
AU - Deumer, Jérôme
AU - Disch, Sabrina
AU - Dutt, Shankar
AU - Frank, Kilian
AU - Fratini, Emiliano
AU - Garcia, Paulo R.A.F.
AU - Gilbert, Elliot P.
AU - Hahn, Marc B.
AU - Hallett, James
AU - Hohenschutz, Max
AU - Hollamby, Martin
AU - Huband, Steven
AU - Ilavsky, Jan
AU - Jochum, Johanna K.
AU - Juelsholt, Mikkel
AU - Mansel, Bradley W.
AU - Penttilä, Paavo
AU - Pittkowski, Rebecca K.
AU - Portale, Giuseppe
AU - Pozzo, Lilo D.
AU - Rochels, Leonhard
AU - Rosalie, Julian M.
AU - Saloga, Patrick E.J.
AU - Seibt, Susanne
AU - Smith, Andrew J.
AU - Smith, Gregory N.
AU - Spiering, Glenn A.
AU - Stawski, Tomasz M.
AU - Taché, Olivier
AU - Thünemann, Andreas F.
AU - Toth, Kristof
AU - Whitten, Andrew E.
AU - Wuttke, Joachim
ID - 14799
IS - 6
JF - Journal of Applied Crystallography
SN - 0021-8898
TI - The human factor: Results of a small-angle scattering data analysis round robin
VL - 56
ER -
TY - JOUR
AB - We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.
AU - Chatterjee, Krishnendu
AU - Kafshdar Goharshady, Ehsan
AU - Novotný, Petr
AU - Zárevúcky, Jiří
AU - Zikelic, Dorde
ID - 14778
IS - 2
JF - Formal Aspects of Computing
KW - Theoretical Computer Science
KW - Software
SN - 0934-5043
TI - On lexicographic proof rules for probabilistic termination
VL - 35
ER -
TY - CONF
AB - A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display.
AU - Chen, Bin
AU - Jindal, Akshay
AU - Piovarci, Michael
AU - Wang, Chao
AU - Seidel, Hans Peter
AU - Didyk, Piotr
AU - Myszkowski, Karol
AU - Serrano, Ana
AU - Mantiuk, Rafał K.
ID - 14798
SN - 9798400703157
T2 - Proceedings of the SIGGRAPH Asia 2023 Conference
TI - The effect of display capabilities on the gloss consistency between real and virtual objects
ER -
TY - JOUR
AB - In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance.
AU - Beznosikov, Aleksandr
AU - Horvath, Samuel
AU - Richtarik, Peter
AU - Safaryan, Mher
ID - 14815
JF - Journal of Machine Learning Research
TI - On biased compression for distributed learning
VL - 24
ER -
TY - CONF
AB - In this paper, we present novel algorithms that efficiently compute a shortest reconfiguration sequence between two given dominating sets in trees and interval graphs under the TOKEN SLIDING model. In this problem, a graph is provided along with its two dominating sets, which can be imagined as tokens placed on vertices. The objective is to find a shortest sequence of dominating sets that transforms one set into the other, with each set in the sequence resulting from sliding a single token in the previous set. While identifying any sequence has been well studied, our work presents the first polynomial algorithms for this optimization variant in the context of dominating sets.
AU - Křišťan, Jan Matyáš
AU - Svoboda, Jakub
ID - 14456
SN - 0302-9743
T2 - 24th International Symposium on Fundamentals of Computation Theory
TI - Shortest dominating set reconfiguration under token sliding
VL - 14292
ER -
TY - CONF
AB - This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm.
AU - Cohen, Shir
AU - Goren, Guy
AU - Kokoris Kogias, Eleftherios
AU - Sonnino, Alberto
AU - Spiegelman, Alexander
ID - 14829
SN - 0302-9743
T2 - 27th International Conference on Financial Cryptography and Data Security
TI - Proof of availability and retrieval in a modular blockchain architecture
VL - 13951
ER -
TY - JOUR
AB - Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.
AU - Schwayer, Cornelia
AU - Brückner, David
ID - 14827
IS - 24
JF - Journal of Cell Science
KW - Cell Biology
SN - 0021-9533
TI - Connecting theory and experiment in cell and tissue mechanics
VL - 136
ER -
TY - CONF
AB - We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks.
AU - Zikelic, Dorde
AU - Lechner, Mathias
AU - Henzinger, Thomas A
AU - Chatterjee, Krishnendu
ID - 14830
IS - 10
KW - General Medicine
SN - 2159-5399
T2 - Proceedings of the 37th AAAI Conference on Artificial Intelligence
TI - Learning control policies for stochastic systems with reach-avoid guarantees
VL - 37
ER -
TY - JOUR
AB - Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.
AU - Stankowski, Sean
AU - Zagrodzka, Zuzanna B
AU - Galindo, Juan
AU - Montaño-Rendón, Mauricio
AU - Faria, Rui
AU - Mikhailova, Natalia
AU - Blakeslee, April M H
AU - Arnason, Einar
AU - Broquet, Thomas
AU - Morales, Hernán E
AU - Grahame, John W
AU - Westram, Anja M
AU - Johannesson, Kerstin
AU - Butlin, Roger K
ID - 14833
IS - 1
JF - Evolutionary Journal of the Linnean Society
TI - Whole-genome phylogeography of the intertidal snail Littorina saxatilis
VL - 2
ER -
TY - JOUR
AB - Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis.
AU - Sakref, Yann
AU - Muñoz Basagoiti, Maitane
AU - Zeravcic, Zorana
AU - Rivoire, Olivier
ID - 14831
IS - 51
JF - The Journal of Physical Chemistry B
KW - Materials Chemistry
KW - Surfaces
KW - Coatings and Films
KW - Physical and Theoretical Chemistry
SN - 1520-6106
TI - On kinetic constraints that catalysis imposes on elementary processes
VL - 127
ER -
TY - JOUR
AB - Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules.
AU - Azadbakht, Ali
AU - Meadowcroft, Billie
AU - Majek, Juraj
AU - Šarić, Anđela
AU - Kraft, Daniela J.
ID - 14844
JF - Biophysical Journal
SN - 0006-3495
TI - Nonadditivity in interactions between three membrane-wrapped colloidal spheres
ER -
TY - GEN
AB - Cover Page
AU - Becker, Lea Marie
AU - Berbon, Mélanie
AU - Vallet, Alicia
AU - Grelard, Axelle
AU - Morvan, Estelle
AU - Bardiaux, Benjamin
AU - Lichtenecker, Roman
AU - Ernst, Matthias
AU - Loquet, Antoine
AU - Schanda, Paul
ID - 14861
IS - 19
KW - General Chemistry
KW - Catalysis
SN - 1433-7851
T2 - Angewandte Chemie International Edition
TI - Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues
VL - 62
ER -
TY - JOUR
AB - We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal.
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
AU - Xu, Yuanyuan
ID - 14849
IS - 6
JF - The Annals of Probability
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
SN - 0091-1798
TI - On the rightmost eigenvalue of non-Hermitian random matrices
VL - 51
ER -
TY - JOUR
AB - Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht.
AU - Becker, Lea Marie
AU - Berbon, Mélanie
AU - Vallet, Alicia
AU - Grelard, Axelle
AU - Morvan, Estelle
AU - Bardiaux, Benjamin
AU - Lichtenecker, Roman
AU - Ernst, Matthias
AU - Loquet, Antoine
AU - Schanda, Paul
ID - 14835
IS - 19
JF - Angewandte Chemie
KW - General Medicine
SN - 0044-8249
TI - Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten
VL - 135
ER -
TY - CHAP
AB - Organization – or departure from a random pattern – in tropical deep convection is heavily studied due to its immediate relevance to climate sensitivity and extremes. Low-latitude convection has motivated numerical model idealizations, where the Coriolis force is removed and boundary conditions are simplified spatially and temporally. One of the most stunning aspects of such idealized simulated cloud organization is the spontaneous clumping of convection that can occur without any predetermining external perturbation, such as inhomogeneous surface boundary conditions or large-scale waves. Whereas individual convective rain cells measure only few kilometers in horizontal diameter, the clusters they form can often span hundreds or even thousands of kilometers. Hence, organization may emerge from the very small scales but can show effects at the synoptic scale. We refer to such emergent organization as convective self-organization. Convective self-organization thus features characteristics of emergence, such as non-trivial system-scale pattern formation or hysteresis. We summarize observational evidence for large-scale organization and briefly recap classical idealized modeling studies that yield convective self-aggregation – emergent organization under strongly idealized boundary conditions. We then focus on developing research, where temporal variation, such as the diurnal cycle, or two-way interactive surface properties yield distinct organizational modes. Convectively generated cold pools and mesoscale convective systems, both ubiquitous in nature, are thereby found to potentially play key roles in promoting – rather than suppressing – sustained system-scale organization.
AU - Haerter, Jan O.
AU - Muller, Caroline J
ED - Sullivan, Sylvia
ED - Hoose, Corinna
ID - 14853
SN - 2328-8779
T2 - Clouds and Their Climatic Impacts
TI - Mechanisms for the Self‐Organization of Tropical Deep Convection
ER -
TY - CHAP
AB - Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies.
AU - Sučec, I.
AU - Schanda, Paul
ED - Hiller, Sebastian
ED - Liu, Maili
ED - He, Lichun
ID - 14847
SN - 9781839162824
T2 - Biophysics of Molecular Chaperones
TI - Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies
VL - 29
ER -
TY - CHAP
AB - Regulating protein states is considered the core function of chaperones. However, despite their importance to all major cellular processes, the conformational changes that chaperones impart on polypeptide chains are difficult to study directly due to their heterogeneous, dynamic, and multi-step nature. Here, we review recent advances towards this aim using single-molecule manipulation methods, which are rapidly revealing new mechanisms of conformational control and helping to define a different perspective on the chaperone function.
AU - Wruck, F.
AU - Avellaneda Sarrió, Mario
AU - Naqvi, M. M.
AU - Koers, E. J.
AU - Till, K.
AU - Gross, L.
AU - Moayed, F.
AU - Roland, A.
AU - Heling, L. W. H. J.
AU - Mashaghi, A.
AU - Tans, S. J.
ED - Hiller, Sebastian
ED - Liu, Maili
ED - He, Lichun
ID - 14848
SN - 9781839162824
T2 - Biophysics of Molecular Chaperones
TI - Probing Single Chaperone Substrates
VL - 29
ER -
TY - JOUR
AB -
Abstract
We study the spectrum of the Fröhlich Hamiltonian for the polaron at fixed total momentum. We prove the existence of excited eigenvalues between the ground state energy and the essential spectrum at strong coupling. In fact, our main result shows that the number of excited energy bands diverges in the strong coupling limit. To prove this we derive upper bounds for the min-max values of the corresponding fiber Hamiltonians and compare them with the bottom of the essential spectrum, a lower bound on which was recently obtained by Brooks and Seiringer (Comm. Math. Phys. 404:1 (2023), 287–337). The upper bounds are given in terms of the ground state energy band shifted by momentum-independent excitation energies determined by an effective Hamiltonian of Bogoliubov type.
AU - Mitrouskas, David Johannes
AU - Seiringer, Robert
ID - 14854
IS - 4
JF - Pure and Applied Analysis
KW - General Medicine
SN - 2578-5885
TI - Ubiquity of bound states for the strongly coupled polaron
VL - 5
ER -
TY - CONF
AB - We entangled microwave and optical photons for the first time as verified by a measured two-mode vacuum squeezing of 0.7 dB. This electro-optic entanglement is the key resource needed to connect cryogenic quantum circuits.
AU - Sahu, Rishabh
AU - Qiu, Liu
AU - Hease, William J
AU - Arnold, Georg M
AU - Minoguchi, Yuri
AU - Rabl, Peter
AU - Fink, Johannes M
ID - 14872
SN - 9781957171296
T2 - Frontiers in Optics + Laser Science 2023
TI - Entangling microwaves and telecom wavelength light
ER -
TY - CONF
AB - Starting with the empty graph on $[n]$, at each round, a set of $K=K(n)$ edges is presented chosen uniformly at random from the ones that have not been presented yet. We are then asked to choose at most one of the presented edges and add it to the current graph. Our goal is to construct a Hamiltonian graph with $(1+o(1))n$ edges within as few rounds as possible. We show that in this process, one can build a Hamiltonian graph of size $(1+o(1))n$ in $(1+o(1))(1+(\log n)/2K) n$ rounds w.h.p. The case $K=1$ implies that w.h.p. one can build a Hamiltonian graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along the first $(0.5+o(1))n\log n$ rounds of the random graph process. This answers a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds is asymptotically optimal as the first $0.5n\log n$ edges do not span a Hamilton cycle w.h.p. The case $K=\Theta(\log n)$ implies that the Hamiltonicity threshold of the corresponding Achlioptas process is at most $(1+o(1))(1+(\log n)/2K) n$. This matches the $(1-o(1))(1+(\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky and Sudakov and resolves the problem of determining the Hamiltonicity threshold of the Achlioptas process with $K=\Theta(\log n)$. We also show that in the above process one can construct a graph $G$ that spans a matching of size $\lfloor V(G)/2) \rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\log n)/2K) n$ rounds w.h.p. Our proof relies on a robust Hamiltonicity property of the strong $4$-core of the binomial random graph which we use as a black-box. This property allows it to absorb paths covering vertices outside the strong $4$-core into a cycle.
AU - Anastos, Michael
ID - 14867
T2 - Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications
TI - Constructing Hamilton cycles and perfect matchings efficiently
ER -
TY - GEN
AU - Stöllner, Andrea
AU - Lenton, Isaac C
AU - Muller, Caroline J
AU - Waitukaitis, Scott R
ID - 14864
T2 - EGU General Assembly 2023
TI - Measuring spontaneous charging of single aerosol particles
ER -
TY - GEN
AU - Rella, Simon
AU - Kulikova, Y
AU - Minnegalieva, Aygul
AU - Kondrashov, Fyodor
ID - 14862
IS - Supplement_2
KW - Public Health
KW - Environmental and Occupational Health
SN - 1101-1262
T2 - European Journal of Public Health
TI - Complex vaccination strategies prevent the emergence of vaccine resistance
VL - 33
ER -
TY - GEN
AU - Polesello, Andrea
AU - Muller, Caroline J
AU - Pasquero, Claudia
AU - Meroni, Agostino N.
ID - 14863
T2 - EGU General Assembly 2023
TI - Intensification mechanisms of tropical cyclones
ER -
TY - GEN
AB - Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.
AU - Olusanya, Oluwafunmilola O
AU - Khudiakova, Kseniia
AU - Sachdeva, Himani
ID - 14732
T2 - bioRxiv
TI - Genetic load, eco-evolutionary feedback and extinction in a metapopulation
ER -
TY - JOUR
AB - We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of
established PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs.
Our approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.
Our technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs.
AU - Freire, Marco
AU - Bhargava, Manas
AU - Schreck, Camille
AU - Hugron, Pierre-Alexandre
AU - Bickel, Bernd
AU - Lefebvre, Sylvain
ID - 13049
IS - 4
JF - Transactions on Graphics
KW - PCB design and layout
KW - Mesh geometry models
SN - 0730-0301
TI - PCBend: Light up your 3D shapes with foldable circuit boards
VL - 42
ER -
TY - JOUR
AB - Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.
AU - Chen, Huihuang
AU - Li, Lanxin
AU - Zou, Minxia
AU - Qi, Linlin
AU - Friml, Jiří
ID - 13212
IS - 7
JF - Molecular Plant
SN - 1752-9867
TI - Distinct functions of TIR1 and AFB1 receptors in auxin signalling.
VL - 16
ER -
TY - JOUR
AB - Tattoos are a highly popular medium, with both artistic and medical applications. Although the mechanical process of tattoo application has evolved historically, the results are reliant on the artisanal skill of the artist. This can be especially challenging for some skin tones, or in cases where artists lack experience. We provide the first systematic overview of tattooing as a computational fabrication technique. We built an automated tattooing rig and a recipe for the creation of silicone sheets mimicking realistic skin tones, which allowed us to create an accurate model predicting tattoo appearance. This enables several exciting applications including tattoo previewing, color retargeting, novel ink spectra optimization, color-accurate prosthetics, and more.
AU - Piovarci, Michael
AU - Chapiro, Alexandre
AU - Bickel, Bernd
ID - 12984
IS - 4
JF - Transactions on Graphics
KW - appearance
KW - modeling
KW - reproduction
KW - tattoo
KW - skin color
KW - gamut mapping
KW - ink-optimization
KW - prosthetic
SN - 0730-0301
TI - Skin-Screen: A computational fabrication framework for color tattoos
VL - 42
ER -
TY - GEN
AB - Code and data necessary to reproduce the simulations and data analyses reported in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023.
AU - Feitosa Tomé, Douglas
ID - 14892
TI - douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation
ER -
TY - JOUR
AB - Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator.
AU - Mukhopadhyay, Soham
AU - Senior, Jorden L
AU - Saez Mollejo, Jaime
AU - Puglia, Denise
AU - Zemlicka, Martin
AU - Fink, Johannes M
AU - Higginbotham, Andrew P
ID - 14032
JF - Nature Physics
KW - General Physics and Astronomy
SN - 1745-2473
TI - Superconductivity from a melted insulator in Josephson junction arrays
VL - 19
ER -
TY - JOUR
AB - The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general.
AU - Qi, Linlin
AU - Friml, Jiří
ID - 13266
IS - 2
JF - New Phytologist
SN - 0028-646X
TI - Tale of cAMP as a second messenger in auxin signaling and beyond
VL - 240
ER -
TY - JOUR
AB - Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question.
AU - Minchington, Thomas
AU - Rus, Stefanie
AU - Kicheva, Anna
ID - 13136
JF - Current Opinion in Systems Biology
TI - Control of tissue dimensions in the developing neural tube and somites
VL - 35
ER -
TY - JOUR
AB - In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model.
AU - Agresti, Antonio
AU - Veraar, Mark
ID - 13135
IS - 9
JF - Journal of Differential Equations
SN - 0022-0396
TI - Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity
VL - 368
ER -
TY - JOUR
AB - Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0
such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)
. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses.
AU - Brunck, Florestan R
ID - 13270
IS - 3
JF - Discrete and Computational Geometry
SN - 0179-5376
TI - Iterated medial triangle subdivision in surfaces of constant curvature
VL - 70
ER -
TY - JOUR
AB - This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point.
AU - Polyanskii, Nikita
AU - Zhang, Yihan
ID - 13269
IS - 10
JF - IEEE Transactions on Information Theory
SN - 0018-9448
TI - Codes for the Z-channel
VL - 69
ER -
TY - JOUR
AB - Given A⊆GL2(Fq), we prove that there exist disjoint subsets B,C⊆A such that A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where
M(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.
We also study some related questions on moderate expanders over matrix rings, namely, for A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, ForumMath., 31, 951–970).
AU - Mohammadi, Ali
AU - Pham, Thang
AU - Wang, Yiting
ID - 13128
IS - 4
JF - Canadian Mathematical Bulletin
SN - 0008-4395
TI - An energy decomposition theorem for matrices and related questions
VL - 66
ER -
TY - JOUR
AB - The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture.
AU - Xia, Jing
AU - Kong, Mengjuan
AU - Yang, Zhisen
AU - Sun, Lianghanxiao
AU - Peng, Yakun
AU - Mao, Yanbo
AU - Wei, Hong
AU - Ying, Wei
AU - Gao, Yongxiao
AU - Friml, Jiří
AU - Weng, Jianping
AU - Liu, Xin
AU - Sun, Linfeng
AU - Tan, Shutang
ID - 13209
IS - 6
JF - Plant Communications
TI - Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen
VL - 4
ER -
TY - JOUR
AB - When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.
AU - Grober, Daniel
AU - Palaia, Ivan
AU - Ucar, Mehmet C
AU - Hannezo, Edouard B
AU - Šarić, Anđela
AU - Palacci, Jérémie A
ID - 13971
JF - Nature Physics
SN - 1745-2473
TI - Unconventional colloidal aggregation in chiral bacterial baths
VL - 19
ER -
TY - JOUR
AB - The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles.
AU - Cornalba, Federico
AU - Fischer, Julian L
ID - 10551
IS - 5
JF - Archive for Rational Mechanics and Analysis
SN - 0003-9527
TI - The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles
VL - 247
ER -
TY - JOUR
AB - Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure.
AU - Kueffner, Konstantin
AU - Lukina, Anna
AU - Schilling, Christian
AU - Henzinger, Thomas A
ID - 13234
JF - International Journal on Software Tools for Technology Transfer
SN - 1433-2779
TI - Into the unknown: Active monitoring of neural networks (extended version)
VL - 25
ER -
TY - JOUR
AB - Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.
AU - Napoli, Federico
AU - Becker, Lea Marie
AU - Schanda, Paul
ID - 14036
IS - 10
JF - Current Opinion in Structural Biology
SN - 0959-440X
TI - Protein dynamics detected by magic-angle spinning relaxation dispersion NMR
VL - 82
ER -
TY - JOUR
AB - Over the last two decades, a significant line of work in theoretical algorithms has made progress in solving linear systems of the form Lx=b, where L is the Laplacian matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x of the linear system can be interpreted as the potentials of an electrical flow in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013. https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time algorithm that maintains the Kirchoff Current Law, and gradually enforces the Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this paper, we consider a dual version of the algorithm that maintains the Kirchoff Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling: each iteration updates all potentials on one side of a fundamental cut of a spanning tree by the same amount. We prove that this dual algorithm also runs in a near-linear number of iterations. We show, however, that if we abstract cut toggling as a natural data structure problem, this problem can be reduced to the online vector–matrix-vector problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing, pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and thus a straightforward implementation of the cut-toggling algorithm requires essentially linear time per iteration. To circumvent the lower bound, we batch update steps, and perform them simultaneously instead of sequentially. An appropriate choice of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian systems. Furthermore, we show that if we sparsify the graph and call our algorithm recursively on the Laplacian system implied by batching and sparsifying, we can reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm can achieve (almost) the same running time as its primal cycle-toggling counterpart.
AU - Henzinger, Monika H
AU - Jin, Billy
AU - Peng, Richard
AU - Williamson, David P.
ID - 14043
JF - Algorithmica
SN - 0178-4617
TI - A combinatorial cut-toggling algorithm for solving Laplacian linear systems
VL - 85
ER -
TY - JOUR
AB - Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter.
AU - Rønning, Jonas
AU - Renaud, Julian B
AU - Doostmohammadi, Amin
AU - Angheluta, Luiza
ID - 14087
JF - Soft Matter
SN - 1744-683X
TI - Spontaneous flows and dynamics of full-integer topological defects in polar active matter
VL - 39
ER -
TY - JOUR
AB - We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule.
AU - Vernooij, Matthijs
AU - Wirth, Melchior
ID - 13319
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Derivations and KMS-symmetric quantum Markov semigroups
VL - 403
ER -
TY - JOUR
AB - Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition).
AU - Lombardi, Fabrizio
AU - Herrmann, Hans J.
AU - Parrino, Liborio
AU - Plenz, Dietmar
AU - Scarpetta, Silvia
AU - Vaudano, Anna Elisabetta
AU - De Arcangelis, Lucilla
AU - Shriki, Oren
ID - 14402
IS - 10
JF - Cell Reports
TI - Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state
VL - 42
ER -
TY - JOUR
AB - There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data.
AU - Ojavee, Sven E.
AU - Darrous, Liza
AU - Patxot, Marion
AU - Läll, Kristi
AU - Fischer, Krista
AU - Mägi, Reedik
AU - Kutalik, Zoltan
AU - Robinson, Matthew Richard
ID - 14258
IS - 9
JF - American Journal of Human Genetics
SN - 0002-9297
TI - Genetic insights into the age-specific biological mechanisms governing human ovarian aging
VL - 110
ER -
TY - JOUR
AB - In this paper, we determine the motivic class — in particular, the weight polynomial and conjecturally the Poincaré polynomial — of the open de Rham space, defined and studied by Boalch, of certain moduli spaces of irregular meromorphic connections on the trivial rank
bundle on P1. The computation is by motivic Fourier transform. We show that the result satisfies the purity conjecture, that is, it agrees with the pure part of the conjectured mixed Hodge polynomial of the corresponding wild character variety. We also identify the open de Rham spaces with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer. We finish with constructing natural complete hyperkähler metrics on them, which in the four-dimensional cases are expected to be of type ALF.
AU - Hausel, Tamás
AU - Wong, Michael Lennox
AU - Wyss, Dimitri
ID - 14244
IS - 4
JF - Proceedings of the London Mathematical Society
SN - 0024-6115
TI - Arithmetic and metric aspects of open de Rham spaces
VL - 127
ER -
TY - JOUR
AB - Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues. Here, we review the force-induced ERK activation in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive ERK activation. We conclude that mechanical forces are not merely passive factors shaping cells and tissues but also active regulators of cellular signaling pathways controlling collective cell behaviors.
AU - Hirashima, Tsuyoshi
AU - Hino, Naoya
AU - Aoki, Kazuhiro
AU - Matsuda, Michiyuki
ID - 14080
IS - 10
JF - Current Opinion in Cell Biology
SN - 0955-0674
TI - Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation
VL - 84
ER -
TY - JOUR
AB - A graph G=(V, E) is called fully regular if for every independent set I c V, the number of vertices in V\I that are not connected to any element of I depends only on the size of I. A linear ordering of the vertices of G is called successive if for every i, the first i vertices induce a connected subgraph of G. We give an explicit formula for the number of successive vertex orderings of a fully regular graph.
As an application of our results, we give alternative proofs of two theorems of Stanley and Gao & Peng, determining the number of linear edge orderings of complete graphs and complete bipartite graphs, respectively, with the property that the first i edges induce a connected subgraph.
As another application, we give a simple product formula for the number of linear orderings of the hyperedges of a complete 3-partite 3-uniform hypergraph such that, for every i, the first i hyperedges induce a connected subgraph. We found similar formulas for complete (non-partite) 3-uniform hypergraphs and in another closely related case, but we managed to verify them only when the number of vertices is small.
AU - Fang, Lixing
AU - Huang, Hao
AU - Pach, János
AU - Tardos, Gábor
AU - Zuo, Junchi
ID - 13165
IS - 10
JF - Journal of Combinatorial Theory. Series A
SN - 0097-3165
TI - Successive vertex orderings of fully regular graphs
VL - 199
ER -
TY - JOUR
AB - We present a photon- and metal-free approach for the radical fluorination of aliphatic oxalate-activated alcohols. The method relies on the spontaneous generation of the N-(chloromethyl)triethylenediamine radical dication, a potent single electron oxidant, from Selectfluor and 4-(dimethylamino)pyridine. The protocol is easily scalable and provides the desired fluorinated products within only a few minutes reaction time.
AU - Baunis, Haralds
AU - Pieber, Bartholomäus
ID - 14409
IS - 42
JF - European Journal of Organic Chemistry
SN - 1434-193X
TI - Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex
VL - 26
ER -
TY - JOUR
AB - In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a fermionic quantum system, with almost optimal (semi-classical) constant and a gradient correction term. We present a stronger version of this inequality, with a much simplified proof. As a corollary we obtain a simple proof of the original Lieb–Thirring inequality.
AU - Seiringer, Robert
AU - Solovej, Jan Philip
ID - 14254
IS - 10
JF - Journal of Functional Analysis
SN - 0022-1236
TI - A simple approach to Lieb-Thirring type inequalities
VL - 285
ER -
TY - JOUR
AB - We report on a simple surfactant/template free chemical route for the synthesis of semi-polycrystalline polyaniline-graphite (SPani-graphite) composite and its application as an electroactive material in electrochemical charge storage. The synthesized material exhibits well-defined poly-crystallographic lattices in high resolution transmission electron micrographs and sharp peaks in x-ray diffraction spectra suggesting crystalline nature of the material. The specific capacitance computed from the galvanostatic charge-discharge (GCD) data obtained from 3-electrode cell configuration using 1 M aq. Na2SO4 as an electrolyte was 111.4 F g−1 at a current density of 0.1 A g−1 which rises to 269 F g−1 at an elevated current density of 1.0 A g−1. A similar pattern of increase in the specific capacitance values with an increase in the current density was observed in the results obtained from 2-electrode symmetric device configuration using polymer gel electrolyte (xanthan gum in 1 M aq. Na2SO4). The specific capacitance computed from the GCD data obtained from the device configuration was 20 F g−1 at the current density of 1.0 A g−1. The device delivers an energy density of 1.7 Wh kg−1 and a power density of 2.48 kWh kg−1 at an applied current density of 0.5 A g−1 suggesting an excellent rate capability and power management. In addition, the device exhibits ⁓92 % specific capacitance retention up to 8000 continuous GCD cycles and ⁓80 % coulombic efficiency up to 10,000 continuous GCD cycles indicating excellent cycling stability. The unique feature of increasing specific capacitance with respect to applied current density is attributed to the presence of semi-polycrystalline phases in the SPani-graphite matrix. The material behaves as a surface redox supercapacitor and its unique mechanism of charge storage is discussed in detail in the article.
AU - Mahato, Neelima
AU - Singh, Saurabh
AU - Faisal, Mohammad
AU - Sreekanth, T. V.M.
AU - Majumder, Sutripto
AU - Yoo, Kisoo
AU - Kim, Jonghoon
ID - 14379
JF - Synthetic Metals
SN - 0379-6779
TI - Polycrystalline phases grown in-situ engendering unique mechanism of charge storage in polyaniline-graphite composite
VL - 299
ER -
TY - JOUR
AB - Motivated by recent applications to entropy theory in dynamical systems, we generalise notions introduced by Matthews and define weakly weighted and componentwise weakly weighted (generalised) quasi-metrics. We then systematise and extend to full generality the correspondences between these objects and other structures arising in theoretical computer science and dynamics. In particular, we study the correspondences with weak partial metrics and, if the underlying space is a semilattice, with invariant (generalised) quasi-metrics satisfying the descending path condition, and with strictly monotone semi(-co-)valuations.
We conclude discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation of both the known intrinsic semilattice entropy and the semigroup entropy.
AU - Castellano, Ilaria
AU - Giordano Bruno, Anna
AU - Zava, Nicolò
ID - 14362
JF - Theoretical Computer Science
SN - 0304-3975
TI - Weakly weighted generalised quasi-metric spaces and semilattices
VL - 977
ER -
TY - JOUR
AB - Background:
Pro-apoptotic BAX is a central mediator of retinal ganglion cell (RGC) death after optic nerve damage. BAX activation occurs in two stages including translocation of latent BAX to the mitochondrial outer membrane (MOM) and then permeabilization of the MOM to facilitate the release of apoptotic signaling molecules. As a critical component of RGC death, BAX is an attractive target for neuroprotective therapies and an understanding of the kinetics of BAX activation and the mechanisms controlling the two stages of this process in RGCs is potentially valuable in informing the development of a neuroprotective strategy.
Methods:
The kinetics of BAX translocation were assessed by both static and live-cell imaging of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC) protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX was assessed by staining with the 6A7 monoclonal antibody, which recognizes a conformational change in this protein after MOM insertion. Assessment of individual kinases associated with both stages of activation was made using small molecule inhibitors injected into the vitreous either independently or in concert with ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase cascade was evaluated using mice with a double conditional knock-out of both Mkk4 and Mkk7.
Results:
ONC induces the translocation of GFP-BAX in RGCs at a slower rate and with less intracellular synchronicity than 661W cells, but exhibits less variability among mitochondrial foci within a single cell. GFP-BAX was also found to translocate in all compartments of an RGC including the dendritic arbor and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation of BAX immediately following translocation. Unlike tissue culture cells, which exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant delay between these two stages, similar to detached cells undergoing anoikis. Translocation, with minimal permeabilization could be induced in a subset of RGCs using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor (sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.
Conclusions:
A comparison between BAX activation kinetics in tissue culture cells and in cells of a complex tissue environment shows distinct differences indicating that caution should be used when translating findings from one condition to the other. RGCs exhibit both a delay between translocation and permeabilization and the ability for translocated BAX to be retrotranslocated, suggesting several stages at which intervention of the activation process could be exploited in the design of a therapeutic strategy.
AU - Maes, Margaret E
AU - Donahue, Ryan J.
AU - Schlamp, Cassandra L.
AU - Marola, Olivia J.
AU - Libby, Richard T.
AU - Nickells, Robert W.
ID - 14401
JF - Molecular Neurodegeneration
TI - BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps
VL - 18
ER -
TY - JOUR
AB - Microwave-optics entanglement is a vital component for building hybrid quantum networks. Here, a new mechanism for preparing stationary entanglement between microwave and optical cavity fields in a cavity optomagnomechanical system is proposed. It consists of a magnon mode in a ferrimagnetic crystal that couples directly to a microwave cavity mode via the magnetic dipole interaction and indirectly to an optical cavity through the deformation displacement of the crystal. The mechanical displacement is induced by the magnetostrictive force and coupled to the optical cavity via radiation pressure. Both the opto- and magnomechanical couplings are dispersive. Magnon–phonon entanglement is created via magnomechanical parametric down-conversion, which is further distributed to optical and microwave photons via simultaneous optomechanical beamsplitter interaction and electromagnonic state-swap interaction, yielding stationary microwave-optics entanglement. The microwave-optics entanglement is robust against thermal noise, which will find broad potential applications in quantum networks and quantum information processing with hybrid quantum systems.
AU - Fan, Zhi Yuan
AU - Qiu, Liu
AU - Gröblacher, Simon
AU - Li, Jie
ID - 14489
IS - 12
JF - Laser and Photonics Reviews
SN - 1863-8880
TI - Microwave-optics entanglement via cavity optomagnomechanics
VL - 17
ER -
TY - JOUR
AB - Vertebrate movement is orchestrated by spinal inter- and motor neurons that, together with sensory and cognitive input, produce dynamic motor behaviors. These behaviors vary from the simple undulatory swimming of fish and larval aquatic species to the highly coordinated running, reaching and grasping of mice, humans and other mammals. This variation raises the fundamental question of how spinal circuits have changed in register with motor behavior. In simple, undulatory fish, exemplified by the lamprey, two broad classes of interneurons shape motor neuron output: ipsilateral-projecting excitatory neurons, and commissural-projecting inhibitory neurons. An additional class of ipsilateral inhibitory neurons is required to generate escape swim behavior in larval zebrafish and tadpoles. In limbed vertebrates, a more complex spinal neuron composition is observed. In this review, we provide evidence that movement elaboration correlates with an increase and specialization of these three basic interneuron types into molecularly, anatomically, and functionally distinct subpopulations. We summarize recent work linking neuron types to movement-pattern generation across fish, amphibians, reptiles, birds and mammals.
AU - Wilson, Alexia C
AU - Sweeney, Lora Beatrice Jaeger
ID - 13097
JF - Frontiers in Neural Circuits
SN - 1662-5110
TI - Spinal cords: Symphonies of interneurons across species
VL - 17
ER -