TY - JOUR
AB - We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory.
AU - Köse, Seyda
AU - Özbudak, Ferruh
ID - 10842
IS - 4
JF - Cryptography and Communications
KW - Applied Mathematics
KW - Computational Theory and Mathematics
KW - Computer Networks and Communications
SN - 1936-2447
TI - Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes
VL - 14
ER -
TY - JOUR
AB - Cellular metabolism must adapt to changing demands to enable homeostasis. During immune responses or cancer metastasis, cells leading migration into challenging environments require an energy boost, but what controls this capacity is unclear. Here, we study a previously uncharacterized nuclear protein, Atossa (encoded by CG9005), which supports macrophage invasion into the germband of Drosophila by controlling cellular metabolism. First, nuclear Atossa increases mRNA levels of Porthos, a DEAD-box protein, and of two metabolic enzymes, lysine-α-ketoglutarate reductase (LKR/SDH) and NADPH glyoxylate reductase (GR/HPR), thus enhancing mitochondrial bioenergetics. Then Porthos supports ribosome assembly and thereby raises the translational efficiency of a subset of mRNAs, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Mitochondrial respiration measurements, metabolomics, and live imaging indicate that Atossa and Porthos power up OxPhos and energy production to promote the forging of a path into tissues by leading macrophages. Since many crucial physiological responses require increases in mitochondrial energy output, this previously undescribed genetic program may modulate a wide range of cellular behaviors.
AU - Emtenani, Shamsi
AU - Martin, Elliot T
AU - György, Attila
AU - Bicher, Julia
AU - Genger, Jakob-Wendelin
AU - Köcher, Thomas
AU - Akhmanova, Maria
AU - Pereira Guarda, Mariana
AU - Roblek, Marko
AU - Bergthaler, Andreas
AU - Hurd, Thomas R
AU - Rangan, Prashanth
AU - Siekhaus, Daria E
ID - 10918
JF - The Embo Journal
TI - Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila
VL - 41
ER -
TY - JOUR
AB - The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.
AU - Obr, Martin
AU - Hagen, Wim J.H.
AU - Dick, Robert A.
AU - Yu, Lingbo
AU - Kotecha, Abhay
AU - Schur, Florian KM
ID - 11155
IS - 2
JF - Journal of Structural Biology
KW - Structural Biology
SN - 1047-8477
TI - Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs
VL - 214
ER -
TY - JOUR
AB - Direct numerical simulations (DNS) of turbulent channel flows up to Reτ≈1000 are conducted to investigate the three-dimensional (consisting of streamwise wavenumber, spanwise wavenumber and frequency) spectrum of wall pressure fluctuations. To develop a predictive model of the wavenumber–frequency spectrum from the wavenumber spectrum, the time decorrelation mechanisms of wall pressure fluctuations are investigated. It is discovered that the energy-containing part of the wavenumber–frequency spectrum of wall pressure fluctuations can be well predicted using a similar random sweeping model for streamwise velocity fluctuations. To refine the investigation, we further decompose the spectrum of the total wall pressure fluctuations into the autospectra of rapid and slow pressure fluctuations, and the cross-spectrum between them. We focus on evaluating the assumption applied in many predictive models, that is, the magnitude of the cross-spectrum is negligibly small. The present DNS shows that neglecting the cross-spectrum causes a maximum error up to 4.7 dB in the subconvective region for all Reynolds numbers under test. Our analyses indicate that the approximation of neglecting the cross-spectrum needs to be applied carefully in the investigations of acoustics at low Mach numbers, in which the subconvective components of wall pressure fluctuations make important contributions to the radiated acoustic power.
AU - Yang, Bowen
AU - Yang, Zixuan
ID - 10925
JF - Journal of Fluid Mechanics
SN - 0022-1120
TI - On the wavenumber-frequency spectrum of the wall pressure fluctuations in turbulent channel flow
VL - 937
ER -
TY - JOUR
AB - Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4,5,6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.
AU - Lukacisin, Martin
AU - Espinosa-Cantú, Adriana
AU - Bollenbach, Mark Tobias
ID - 11341
JF - Nature
SN - 0028-0836
TI - Intron-mediated induction of phenotypic heterogeneity
VL - 605
ER -
TY - JOUR
AB - Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.
AU - Freitas, Susana
AU - Westram, Anja M
AU - Schwander, Tanja
AU - Arakelyan, Marine
AU - Ilgaz, Çetin
AU - Kumlutas, Yusuf
AU - Harris, David James
AU - Carretero, Miguel A.
AU - Butlin, Roger K.
ID - 11334
IS - 5
JF - Evolution
SN - 0014-3820
TI - Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization
VL - 76
ER -
TY - JOUR
AB - We show that the fluctuations of the largest eigenvalue of a real symmetric or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws at a rate O(N^{-1/3+\omega }), as N tends to infinity. For Wigner matrices this improves the previous rate O(N^{-2/9+\omega }) obtained by Bourgade (J Eur Math Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515, 2012) to prove edge universality, on a finer spectral parameter scale with improved error estimates. The proof relies on the continuous Green function flow induced by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions from the third and fourth order moments of the matrix entries are obtained using iterative cumulant expansions and recursive comparisons for correlation functions, along with uniform convergence estimates for correlation kernels of the Gaussian invariant ensembles.
AU - Schnelli, Kevin
AU - Xu, Yuanyuan
ID - 11332
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner matrices
VL - 393
ER -
TY - JOUR
AB - Multistable systems are characterized by exhibiting domain coexistence, where each domain accounts for the different equilibrium states. In case these systems are described by vectorial fields, domains can be connected through topological defects. Vortices are one of the most frequent and studied topological defect points. Optical vortices are equally relevant for their fundamental features as beams with topological features and their applications in image processing, telecommunications, optical tweezers, and quantum information. A natural source of optical vortices is the interaction of light beams with matter vortices in liquid crystal cells. The rhythms that govern the emergence of matter vortices due to fluctuations are not established. Here, we investigate the nucleation mechanisms of the matter vortices in liquid crystal cells and establish statistical laws that govern them. Based on a stochastic amplitude equation, the law for the number of nucleated vortices as a function of anisotropy, voltage, and noise level intensity is set. Experimental observations in a nematic liquid crystal cell with homeotropic anchoring and a negative anisotropic dielectric constant under the influence of a transversal electric field show a qualitative agreement with the theoretical findings.
AU - Aguilera, Esteban
AU - Clerc, Marcel G.
AU - Zambra, Valeska
ID - 11343
JF - Nonlinear Dynamics
KW - Electrical and Electronic Engineering
KW - Applied Mathematics
KW - Mechanical Engineering
KW - Ocean Engineering
KW - Aerospace Engineering
KW - Control and Systems Engineering
SN - 0924-090X
TI - Vortices nucleation by inherent fluctuations in nematic liquid crystal cells
VL - 108
ER -
TY - JOUR
AB - Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I.
AU - Kampjut, Domen
AU - Sazanov, Leonid A
ID - 11167
JF - Current Opinion in Structural Biology
KW - Molecular Biology
KW - Structural Biology
SN - 0959-440X
TI - Structure of respiratory complex I – An emerging blueprint for the mechanism
VL - 74
ER -
TY - JOUR
AB - Adenosine triphosphate (ATP) is the energy source for various biochemical processes and biomolecular motors in living things. Development of ATP antagonists and their stimuli-controlled actions offer a novel approach to regulate biological processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins. The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated the axonemal dynein motor activity for the force generation in a demembranated model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of ATP antagonists significantly differ in their affinity to the ATP binding site.
AU - Thayyil, Sampreeth
AU - Nishigami, Yukinori
AU - Islam, Muhammad J
AU - Hashim, P. K.
AU - Furuta, Ken'Ya
AU - Oiwa, Kazuhiro
AU - Yu, Jian
AU - Yao, Min
AU - Nakagaki, Toshiyuki
AU - Tamaoki, Nobuyuki
ID - 11333
IS - 30
JF - Chemistry - A European Journal
SN - 09476539
TI - Dynamic control of microbial movement by photoswitchable ATP antagonists
VL - 28
ER -
TY - JOUR
AU - Chang, Cheng
AU - Qin, Bingchao
AU - Su, Lizhong
AU - Zhao, Li Dong
ID - 11356
IS - 11
JF - Science Bulletin
SN - 2095-9273
TI - Distinct electron and hole transports in SnSe crystals
VL - 67
ER -
TY - JOUR
AB - One hallmark of plant cells is their cell wall. They protect cells against the environment and high turgor and mediate morphogenesis through the dynamics of their mechanical and chemical properties. The walls are a complex polysaccharidic structure. Although their biochemical composition is well known, how the different components organize in the volume of the cell wall and interact with each other is not well understood and yet is key to the wall’s mechanical properties. To investigate the ultrastructure of the plant cell wall, we imaged the walls of onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling (cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution visualization of cellulose fibers in situ. We reveal the coexistence of dense fiber fields bathed in a reticulated matrix we termed “meshing,” which is more abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal angular distribution at all depths in the cell wall and bundled according to their orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan (HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting that it is—at least in part—composed of HG pectins. We propose the following model for the construction of the abaxial epidermal primary cell wall: the cell deposits successive layers of cellulose fibers at −45° and +45° relative to the cell’s long axis and secretes the surrounding HG-rich meshing proximal to the plasma membrane, which then migrates to more distal regions of the cell wall.
AU - Nicolas, William J.
AU - Fäßler, Florian
AU - Dutka, Przemysław
AU - Schur, Florian KM
AU - Jensen, Grant
AU - Meyerowitz, Elliot
ID - 11351
IS - 11
JF - Current Biology
KW - General Agricultural and Biological Sciences
KW - General Biochemistry
KW - Genetics and Molecular Biology
SN - 0960-9822
TI - Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose fibers and reticulated homogalacturonan networks
VL - 32
ER -
TY - JOUR
AB - We establish global-in-time existence results for thermodynamically consistent reaction-(cross-)diffusion systems coupled to an equation describing heat transfer. Our main interest is to model species-dependent diffusivities,
while at the same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal case lies in the intrinsic presence of cross-diffusion type phenomena like the Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic equilibria, a nonvanishing temperature gradient may drive a concentration flux even in a situation with constant concentrations; likewise, a nonvanishing concentration gradient may drive a heat flux even in a case of spatially constant temperature. We use time discretisation and regularisation techniques and derive a priori estimates based on a suitable entropy and the associated entropy production. Renormalised solutions are used in cases where non-integrable diffusion fluxes or reaction terms appear.
AU - Fischer, Julian L
AU - Hopf, Katharina
AU - Kniely, Michael
AU - Mielke, Alexander
ID - 10547
IS - 1
JF - SIAM Journal on Mathematical Analysis
KW - Energy-Reaction-Diffusion Systems
KW - Cross Diffusion
KW - Global-In-Time Existence of Weak/Renormalised Solutions
KW - Entropy Method
KW - Onsager System
KW - Soret/Dufour Effect
SN - 0036-1410
TI - Global existence analysis of energy-reaction-diffusion systems
VL - 54
ER -
TY - JOUR
AU - Stöllner, Andrea
ID - 11403
IS - 6
JF - Nature Reviews Earth and Environment
TI - Measuring airborne nanoplastics using aerosol physics
VL - 3
ER -
TY - JOUR
AB - The synthetic strigolactone (SL) analog, rac-GR24, has been instrumental in studying the role of SLs as well as karrikins because it activates the receptors DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2) of their signaling pathways, respectively. Treatment with rac-GR24 modifies the root architecture at different levels, such as decreasing the lateral root density (LRD), while promoting root hair elongation or flavonol accumulation. Previously, we have shown that the flavonol biosynthesis is transcriptionally activated in the root by rac-GR24 treatment, but, thus far, the molecular players involved in that response have remained unknown. To get an in-depth insight into the changes that occur after the compound is perceived by the roots, we compared the root transcriptomes of the wild type and the more axillary growth2 (max2) mutant, affected in both SL and karrikin signaling pathways, with and without rac-GR24 treatment. Quantitative reverse transcription (qRT)-PCR, reporter line analysis and mutant phenotyping indicated that the flavonol response and the root hair elongation are controlled by the ELONGATED HYPOCOTYL 5 (HY5) and MYB12 transcription factors, but HY5, in contrast to MYB12, affects the LRD as well. Furthermore, we identified the transcription factors TARGET OF MONOPTEROS 5 (TMO5) and TMO5 LIKE1 as negative and the Mediator complex as positive regulators of the rac-GR24 effect on LRD. Altogether, hereby, we get closer toward understanding the molecular mechanisms that underlay the rac-GR24 responses in the root.
AU - Struk, Sylwia
AU - Braem, Lukas
AU - Matthys, Cedrick
AU - Walton, Alan
AU - Vangheluwe, Nick
AU - Van Praet, Stan
AU - Jiang, Lingxiang
AU - Baster, Pawel
AU - De Cuyper, Carolien
AU - Boyer, Francois-Didier
AU - Stes, Elisabeth
AU - Beeckman, Tom
AU - Friml, Jiří
AU - Gevaert, Kris
AU - Goormachtig, Sofie
ID - 10583
IS - 1
JF - Plant & Cell Physiology
KW - flavonols
KW - MAX2
KW - rac-Gr24
KW - RNA-seq
KW - root development
KW - transcriptional regulation
SN - 0032-0781
TI - Transcriptional analysis in the Arabidopsis roots reveals new regulators that link rac-GR24 treatment with changes in flavonol accumulation, root hair elongation and lateral root density
VL - 63
ER -
TY - CONF
AB - We study the problem of specifying sequential information-flow properties of systems. Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL.
AU - Bartocci, Ezio
AU - Ferrere, Thomas
AU - Henzinger, Thomas A
AU - Nickovic, Dejan
AU - Da Costa, Ana Oliveira
ID - 10774
SN - 03029743
T2 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
TI - Flavors of sequential information flow
VL - 13182
ER -
TY - JOUR
AB - Directed percolation (DP) has recently emerged as a possible solution to the century old puzzle surrounding the transition to turbulence. Multiple model studies reported DP exponents, however, experimental evidence is limited since the largest possible observation times are orders of magnitude shorter than the flows’ characteristic timescales. An exception is cylindrical Couette flow where the limit is not temporal, but rather the realizable system size. We present experiments in a Couette setup of unprecedented azimuthal and axial aspect ratios. Approaching the critical point to within less than 0.1% we determine five critical exponents, all of which are in excellent agreement with the 2+1D DP universality class. The complex dynamics encountered at
the onset of turbulence can hence be fully rationalized within the framework of statistical mechanics.
AU - Klotz, Lukasz
AU - Lemoult, Grégoire M
AU - Avila, Kerstin
AU - Hof, Björn
ID - 10654
IS - 1
JF - Physical Review Letters
SN - 0031-9007
TI - Phase transition to turbulence in spatially extended shear flows
VL - 128
ER -
TY - JOUR
AB - Superconductor-semiconductor hybrid devices are at the heart of several proposed approaches to quantum information processing, but their basic properties remain to be understood. We embed a twodimensional Al-InAs hybrid system in a resonant microwave circuit, probing the breakdown of superconductivity due to an applied magnetic field. We find a fingerprint from the two-component nature of the hybrid system, and quantitatively compare with a theory that includes the contribution of intraband p±ip pairing in the InAs, as well as the emergence of Bogoliubov-Fermi surfaces due to magnetic field. Separately resolving the Al and InAs contributions allows us to determine the carrier density and mobility in the InAs.
AU - Phan, Duc T
AU - Senior, Jorden L
AU - Ghazaryan, Areg
AU - Hatefipour, M.
AU - Strickland, W. M.
AU - Shabani, J.
AU - Serbyn, Maksym
AU - Higginbotham, Andrew P
ID - 10851
IS - 10
JF - Physical Review Letters
KW - General Physics and Astronomy
SN - 0031-9007
TI - Detecting induced p±ip pairing at the Al-InAs interface with a quantum microwave circuit
VL - 128
ER -
TY - JOUR
AB - Idealized simulations of the tropical atmosphere have predicted that clouds can spontaneously clump together in space, despite perfectly homogeneous settings. This phenomenon has been called self-aggregation, and it results in a state where a moist cloudy region with intense deep convective storms is surrounded by extremely dry subsiding air devoid of deep clouds. We review here the main findings from theoretical work and idealized models of this phenomenon, highlighting the physical processes believed to play a key role in convective self-aggregation. We also review the growing literature on the importance and implications of this phenomenon for the tropical atmosphere, notably, for the hydrological cycle and for precipitation extremes, in our current and in a warming climate.
AU - Muller, Caroline J
AU - Yang, Da
AU - Craig, George
AU - Cronin, Timothy
AU - Fildier, Benjamin
AU - Haerter, Jan O.
AU - Hohenegger, Cathy
AU - Mapes, Brian
AU - Randall, David
AU - Shamekh, Sara
AU - Sherwood, Steven C.
ID - 10656
JF - Annual Review of Fluid Mechanics
SN - 0066-4189
TI - Spontaneous aggregation of convective storms
VL - 54
ER -
TY - CONF
AB - To maximize the performance of concurrent data structures, researchers have often turned to highly complex fine-grained techniques, resulting in efficient and elegant algorithms, which can however be often difficult to understand and prove correct. While simpler techniques exist, such as transactional memory, they can have limited performance or portability relative to their fine-grained counterparts. Approaches at both ends of this complexity-performance spectrum have been extensively explored, but relatively less is known about the middle ground: approaches that are willing to sacrifice some performance for simplicity, while remaining competitive with state-of-the-art handcrafted designs. In this paper, we explore this middle ground, and present PathCAS, a primitive that combines ideas from multi-word CAS (KCAS) and transactional memory approaches, while carefully avoiding overhead. We show how PathCAS can be used to implement efficient search data structures relatively simply, using an internal binary search tree as an example, then extending this to an AVL tree. Our best implementations outperform many handcrafted search trees: in search-heavy workloads, it rivals the BCCO tree [5], the fastest known concurrent binary tree in terms of search performance [3]. Our results suggest that PathCAS can yield concurrent data structures that are relatively easy to build and prove correct, while offering surprisingly high performance.
AU - Brown, Trevor A
AU - Sigouin, William
AU - Alistarh, Dan-Adrian
ID - 11181
SN - 9781450392044
T2 - Proceedings of the 27th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming
TI - PathCAS: An efficient middle ground for concurrent search data structures
ER -
TY - JOUR
AB - Conflict over reproduction between females and males exists because of anisogamy and promiscuity. Together they generate differences in fitness optima between the sexes and result in antagonistic coevolution of female and male reproductive traits. Mounting duration is likely to be a compromise between male and female interests whose outcome depends on the intensity of sexual selection. The timing of sperm transfer during mounting is critical. For example, mountings may be interrupted before sperm is transferred as a consequence of female or male choice, or they may be prolonged to function as mate guarding. In the highly promiscuous intertidal snail Littorina saxatilis, mountings vary substantially in duration, from less than a minute to more than an hour, and it has been assumed that mountings of a few minutes do not result in any sperm being transferred. Here, we examined the timing of sperm transfer, a reproductive trait that is likely affected by sexual conflict. We performed time-controlled mounting trials using L. saxatilis males and virgin females, aiming to examine indirectly when the transfer of sperm starts. We observed the relationship between mounting duration and the proportion of developing embryos out of all eggs and embryos in the brood pouch. Developing embryos were observed in similar proportions in all treatments (i.e. 1, 5 and 10 or more minutes at which mountings were artificially interrupted), suggesting that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short matings do not result in sperm shortage in the females. We discuss how the observed pattern can be influenced by predation risk, population density, and female status and receptivity.
AU - Perini, Samuel
AU - Butlin, Rogerk
AU - Westram, Anja M
AU - Johannesson, Kerstin
ID - 10926
IS - 1
JF - Journal of Molluscan Studies
SN - 0260-1230
TI - Very short mountings are enough for sperm transfer in Littorina saxatilis
VL - 88
ER -
TY - JOUR
AB - In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:
• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.
• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.
• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:
• the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;
• the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);
• the QC-Criterion and the Spreading Principle from KSS.
The purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.
• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:
• puzzle pieces shrink to points,
• (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.
• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings
are the analogues of Lattès maps in this setting.
• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.
AU - Clark, Trevor
AU - Drach, Kostiantyn
AU - Kozlovski, Oleg
AU - Strien, Sebastian Van
ID - 11553
IS - 2
JF - Arnold Mathematical Journal
SN - 2199-6792
TI - The dynamics of complex box mappings
VL - 8
ER -
TY - JOUR
AB - We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].
We consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition.
AU - Cooley, Oliver
AU - Del Giudice, Nicola
AU - Kang, Mihyun
AU - Sprüssel, Philipp
ID - 11740
IS - 3
JF - Electronic Journal of Combinatorics
TI - Phase transition in cohomology groups of non-uniform random simplicial complexes
VL - 29
ER -
TY - JOUR
AB - Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like electron band structure, making it a versatile solid state platform to observe and control nontrivial electrodynamic phenomena. Here we report an observation of universal terahertz (THz) transparency determined by fine-structure constant α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating phases with topologically different electronic band structure. Using THz spectroscopy in a magnetic field we obtain direct evidence of asymmetric spin splitting of the Dirac cone. This particle-hole asymmetry facilitates optical control of edge spin currents in the quantum wells.
AU - Dziom, Uladzislau
AU - Shuvaev, A.
AU - Gospodarič, J.
AU - Novik, E. G.
AU - Dobretsova, A. A.
AU - Mikhailov, N. N.
AU - Kvon, Z. D.
AU - Alpichshev, Zhanybek
AU - Pimenov, A.
ID - 11737
IS - 4
JF - Physical Review B
SN - 2469-9950
TI - Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells
VL - 106
ER -
TY - JOUR
AB - We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.
AU - Forkert, Dominik L
AU - Maas, Jan
AU - Portinale, Lorenzo
ID - 11739
IS - 4
JF - SIAM Journal on Mathematical Analysis
KW - Fokker--Planck equation
KW - gradient flow
KW - evolutionary $\Gamma$-convergence
SN - 0036-1410
TI - Evolutionary $\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions
VL - 54
ER -
TY - JOUR
AB - This paper introduces a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compiled a database from physical tests of several different knitted fabrics used in the textile industry. These data span different types of complex knit patterns, yarn compositions, and fabric finishes, and the results demonstrate diverse physical properties like stiffness, nonlinearity, and anisotropy.
We then develop a system for approximating these mechanical responses with yarn-level cloth simulation. To do so, we introduce an efficient pipeline for converting between fabric-level data and yarn-level simulation, including a novel swatch-level approximation for speeding up computation, and some small-but-necessary extensions to yarn-level models used in computer graphics. The dataset used for this paper can be found at http://mslab.es/projects/YarnLevelFabrics.
AU - Sperl, Georg
AU - Sánchez-Banderas, Rosa M.
AU - Li, Manwen
AU - Wojtan, Christopher J
AU - Otaduy, Miguel A.
ID - 11736
IS - 4
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - Estimation of yarn-level simulation models for production fabrics
VL - 41
ER -
TY - JOUR
AB - Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble.
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 11741
JF - Probability Theory and Related Fields
SN - 0178-8051
TI - Quenched universality for deformed Wigner matrices
ER -
TY - JOUR
AB - Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term.
AU - Li, Lanxin
AU - Chen, Huihuang
AU - Alotaibi, Saqer S.
AU - Pěnčík, Aleš
AU - Adamowski, Maciek
AU - Novák, Ondřej
AU - Friml, Jiří
ID - 11723
IS - 31
JF - Proceedings of the National Academy of Sciences
KW - Multidisciplinary
SN - 0027-8424
TI - RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis
VL - 119
ER -
TY - JOUR
AB - Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.
AU - Abualia, Rashed
AU - Ötvös, Krisztina
AU - Novák, Ondřej
AU - Bouguyon, Eleonore
AU - Domanegg, Kevin
AU - Krapp, Anne
AU - Nacry, Philip
AU - Gojon, Alain
AU - Lacombe, Benoit
AU - Benková, Eva
ID - 11734
IS - 31
JF - Proceedings of the National Academy of Sciences of the United States of America
TI - Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses
VL - 119
ER -
TY - JOUR
AB - Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h2SNP. We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.
AU - Orliac, Etienne J.
AU - Trejo Banos, Daniel
AU - Ojavee, Sven E.
AU - Läll, Kristi
AU - Mägi, Reedik
AU - Visscher, Peter M.
AU - Robinson, Matthew Richard
ID - 11733
IS - 31
JF - Proceedings of the National Academy of Sciences of the United States of America
TI - Improving GWAS discovery and genomic prediction accuracy in biobank data
VL - 119
ER -
TY - JOUR
AB - We study two interacting quantum particles forming a bound state in d-dimensional free
space, and constrain the particles in k directions to (0, ∞)k ×Rd−k, with Neumann boundary
conditions. First, we prove that the ground state energy strictly decreases upon going from k
to k+1. This shows that the particles stick to the corner where all boundary planes intersect.
Second, we show that for all k the resulting Hamiltonian, after removing the free part of the
kinetic energy, has only finitely many eigenvalues below the essential spectrum. This paper
generalizes the work of Egger, Kerner and Pankrashkin (J. Spectr. Theory 10(4):1413–1444,
2020) to dimensions d > 1.
AU - Roos, Barbara
AU - Seiringer, Robert
ID - 10850
IS - 12
JF - Journal of Functional Analysis
KW - Analysis
SN - 0022-1236
TI - Two-particle bound states at interfaces and corners
VL - 282
ER -
TY - JOUR
AB - Interlocking puzzles are intriguing geometric games where the puzzle pieces are held together based on their geometric arrangement, preventing the puzzle from falling apart. High-level-of-difficulty, or simply high-level, interlocking puzzles are a subclass of interlocking puzzles that require multiple moves to take out the first subassembly from the puzzle. Solving a high-level interlocking puzzle is a challenging task since one has to explore many different configurations of the puzzle pieces until reaching a configuration where the first subassembly can be taken out. Designing a high-level interlocking puzzle with a user-specified level of difficulty is even harder since the puzzle pieces have to be interlocking in all the configurations before the first subassembly is taken out.
In this paper, we present a computational approach to design high-level interlocking puzzles. The core idea is to represent all possible configurations of an interlocking puzzle as well as transitions among these configurations using a rooted, undirected graph called a disassembly graph and leverage this graph to find a disassembly plan that requires a minimal number of moves to take out the first subassembly from the puzzle. At the design stage, our algorithm iteratively constructs the geometry of each puzzle piece to expand the disassembly graph incrementally, aiming to achieve a user-specified level of difficulty. We show that our approach allows efficient generation of high-level interlocking puzzles of various shape complexities, including new solutions not attainable by state-of-the-art approaches.
AU - Chen, Rulin
AU - Wang, Ziqi
AU - Song, Peng
AU - Bickel, Bernd
ID - 11735
IS - 4
JF - ACM Transactions on Graphics
SN - 0730-0301
TI - Computational design of high-level interlocking puzzles
VL - 41
ER -
TY - JOUR
AB - We provide a definition of the effective mass for the classical polaron described by the Landau–Pekar (LP) equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by LP (1948 J. Exp. Theor. Phys. 18 419–423).
AU - Feliciangeli, Dario
AU - Rademacher, Simone Anna Elvira
AU - Seiringer, Robert
ID - 10755
IS - 1
JF - Journal of Physics A: Mathematical and Theoretical
SN - 1751-8113
TI - The effective mass problem for the Landau-Pekar equations
VL - 55
ER -
TY - JOUR
AB - We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix.
AU - Bossmann, Lea
ID - 11783
IS - 6
JF - Journal of Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0022-2488
TI - Low-energy spectrum and dynamics of the weakly interacting Bose gas
VL - 63
ER -
TY - JOUR
AB - We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature.
AU - Henheik, Sven Joscha
AU - Lauritsen, Asbjørn Bækgaard
ID - 11732
JF - Journal of Statistical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0022-4715
TI - The BCS energy gap at high density
VL - 189
ER -
TY - JOUR
AB - We consider the flow of two viscous and incompressible fluids within a bounded domain modeled by means of a two-phase Navier–Stokes system. The two fluids are assumed to be immiscible, meaning that they are separated by an interface. With respect to the motion of the interface, we consider pure transport by the fluid flow. Along the boundary of the domain, a complete slip boundary condition for the fluid velocities and a constant ninety degree contact angle condition for the interface are assumed. In the present work, we devise for the resulting evolution problem a suitable weak solution concept based on the framework of varifolds and establish as the main result a weak-strong uniqueness principle in 2D. The proof is based on a relative entropy argument and requires a non-trivial further development of ideas from the recent work of Fischer and the first author (Arch. Ration. Mech. Anal. 236, 2020) to incorporate the contact angle condition. To focus on the effects of the necessarily singular geometry of the evolving fluid domains, we work for simplicity in the regime of same viscosities for the two fluids.
AU - Hensel, Sebastian
AU - Marveggio, Alice
ID - 11842
IS - 3
JF - Journal of Mathematical Fluid Mechanics
SN - 1422-6928
TI - Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities
VL - 24
ER -
TY - JOUR
AB - Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.
AU - Toprakcioglu, Zenon
AU - Kamada, Ayaka
AU - Michaels, Thomas C.T.
AU - Xie, Mengqi
AU - Krausser, Johannes
AU - Wei, Jiapeng
AU - Šarić, Anđela
AU - Vendruscolo, Michele
AU - Knowles, Tuomas P.J.
ID - 11841
IS - 31
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
TI - Adsorption free energy predicts amyloid protein nucleation rates
VL - 119
ER -
TY - CONF
AB - The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible.
AU - Chambers, Erin
AU - Fillmore, Christopher D
AU - Stephenson, Elizabeth R
AU - Wintraecken, Mathijs
ED - Goaoc, Xavier
ED - Kerber, Michael
ID - 11428
SN - 1868-8969
T2 - 38th International Symposium on Computational Geometry
TI - A cautionary tale: Burning the medial axis is unstable
VL - 224
ER -
TY - JOUR
AB - A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.
AU - Tomasek, Kathrin
AU - Leithner, Alexander F
AU - Glatzová, Ivana
AU - Lukesch, Michael S.
AU - Guet, Calin C
AU - Sixt, Michael K
ID - 11843
JF - eLife
TI - Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14
VL - 11
ER -
TY - JOUR
AB - This paper is a continuation of Part I of this project, where we developed a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian noise. In the current Part II we consider blow-up criteria and regularization phenomena. As in Part I we can allow nonlinearities with polynomial growth and rough initial values from critical spaces. In the first main result we obtain several new blow-up criteria for quasi- and semilinear stochastic evolution equations. In particular, for semilinear equations we obtain a Serrin type blow-up criterium, which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074, 2018) to the stochastic setting. Blow-up criteria can be used to prove global well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights in time play a central role in the proofs. Our second contribution is a new method to bootstrap Sobolev and Hölder regularity in time and space, which does not require smoothness of the initial data. The blow-up criteria are at the basis of these new methods. Moreover, in applications the bootstrap results can be combined with our blow-up criteria, to obtain efficient ways to prove global existence. This gives new results even in classical 𝐿2-settings, which we illustrate for a concrete SPDE. In future works in preparation we apply the results of the current paper to obtain global well-posedness results and regularity for several concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into a more flexible framework, where less restrictions on the nonlinearities are needed, and we are able to treat rough initial values from critical spaces. Moreover, we will obtain higher-order regularity results.
AU - Agresti, Antonio
AU - Veraar, Mark
ID - 11858
IS - 2
JF - Journal of Evolution Equations
KW - Mathematics (miscellaneous)
SN - 1424-3199
TI - Nonlinear parabolic stochastic evolution equations in critical spaces part II
VL - 22
ER -
TY - CHAP
AB - Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating.
AU - Liu, Jianxin
AU - Marensi, Elena
AU - Wu, Xuesong
ED - Sherwin, Spencer
ED - Schmid, Peter
ED - Wu, Xuesong
ID - 10820
SN - 1875-3507
T2 - IUTAM Laminar-Turbulent Transition
TI - Effects of streaky structures on the instability of supersonic boundary layers
VL - 38
ER -
TY - JOUR
AB - We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods.
AU - Clozeau, Nicolas
ID - 10173
JF - Stochastics and Partial Differential Equations: Analysis and Computations
SN - 2194-0401
TI - Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields
ER -
TY - CONF
AB - In the stochastic population protocol model, we are given a connected graph with n nodes, and in every time step, a scheduler samples an edge of the graph uniformly at random and the nodes connected by this edge interact. A fundamental task in this model is stable leader election, in which all nodes start in an identical state and the aim is to reach a configuration in which (1) exactly one node is elected as leader and (2) this node remains as the unique leader no matter what sequence of interactions follows. On cliques, the complexity of this problem has recently been settled: time-optimal protocols stabilize in Θ(n log n) expected steps using Θ(log log n) states, whereas protocols that use O(1) states require Θ(n2) expected steps.
In this work, we investigate the complexity of stable leader election on general graphs. We provide the first non-trivial time lower bounds for leader election on general graphs, showing that, when moving beyond cliques, the complexity landscape of leader election becomes very diverse: the time required to elect a leader can range from O(1) to Θ(n3) expected steps. On the upper bound side, we first observe that there exists a protocol that is time-optimal on many graph families, but uses polynomially-many states. In contrast, we give a near-time-optimal protocol that uses only O(log2n) states that is at most a factor log n slower. Finally, we show that the constant-state protocol of Beauquier et al. [OPODIS 2013] is at most a factor n log n slower than the fast polynomial-state protocol. Moreover, among constant-state protocols, this protocol has near-optimal average case complexity on dense random graphs.
AU - Alistarh, Dan-Adrian
AU - Rybicki, Joel
AU - Voitovych, Sasha
ID - 11844
SN - 9781450392624
T2 - Proceedings of the Annual ACM Symposium on Principles of Distributed Computing
TI - Near-optimal leader election in population protocols on graphs
ER -
TY - JOUR
AB - We study the many-body dynamics of an initially factorized bosonic wave function in the mean-field regime. We prove large deviation estimates for the fluctuations around the condensate. We derive an upper bound extending a recent result to more general interactions. Furthermore, we derive a new lower bound which agrees with the upper bound in leading order.
AU - Rademacher, Simone Anna Elvira
AU - Seiringer, Robert
ID - 11917
JF - Journal of Statistical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0022-4715
TI - Large deviation estimates for weakly interacting bosons
VL - 188
ER -
TY - JOUR
AB - A domain is called Kac regular for a quadratic form on L2 if every functions vanishing almost everywhere outside the domain can be approximated in form norm by functions with compact support in the domain. It is shown that this notion is stable under domination of quadratic forms. As applications measure perturbations of quasi-regular Dirichlet forms, Cheeger energies on metric measure spaces and Schrödinger operators on manifolds are studied. Along the way a characterization of the Sobolev space with Dirichlet boundary conditions on domains in infinitesimally Riemannian metric measure spaces is obtained.
AU - Wirth, Melchior
ID - 11916
IS - 3
JF - Advances in Operator Theory
KW - Algebra and Number Theory
KW - Analysis
TI - Kac regularity and domination of quadratic forms
VL - 7
ER -
TY - GEN
AB - It is a highly desirable property for deep networks to be robust against
small input changes. One popular way to achieve this property is by designing
networks with a small Lipschitz constant. In this work, we propose a new
technique for constructing such Lipschitz networks that has a number of
desirable properties: it can be applied to any linear network layer
(fully-connected or convolutional), it provides formal guarantees on the
Lipschitz constant, it is easy to implement and efficient to run, and it can be
combined with any training objective and optimization method. In fact, our
technique is the first one in the literature that achieves all of these
properties simultaneously. Our main contribution is a rescaling-based weight
matrix parametrization that guarantees each network layer to have a Lipschitz
constant of at most 1 and results in the learned weight matrices to be close to
orthogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL).
Experiments and ablation studies in the context of image classification with
certified robust accuracy confirm that AOL layers achieve results that are on
par with most existing methods. Yet, they are simpler to implement and more
broadly applicable, because they do not require computationally expensive
matrix orthogonalization or inversion steps as part of the network
architecture. We provide code at https://github.com/berndprach/AOL.
AU - Prach, Bernd
AU - Lampert, Christoph
ID - 11839
T2 - arXiv
TI - Almost-orthogonal layers for efficient general-purpose Lipschitz networks
ER -
TY - DATA
AB - Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.
AU - Elkrewi, Marwan N
ID - 11653
TI - Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp"
ER -
TY - JOUR
AB - The infiltration of immune cells into tissues underlies the establishment of tissue-resident macrophages and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here, we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio, which are themselves required for invasion. Both the filamin and the tetraspanin enhance the cortical activity of Rho1 and the formin Diaphanous and thus the assembly of cortical actin, which is a critical function since expressing a dominant active form of Diaphanous can rescue the Dfos macrophage invasion defect. In vivo imaging shows that Dfos enhances the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the properties of the macrophage nucleus from affecting tissue entry. We thus identify strengthening the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.
AU - Belyaeva, Vera
AU - Wachner, Stephanie
AU - György, Attila
AU - Emtenani, Shamsi
AU - Gridchyn, Igor
AU - Akhmanova, Maria
AU - Linder, M
AU - Roblek, Marko
AU - Sibilia, M
AU - Siekhaus, Daria E
ID - 10614
IS - 1
JF - PLoS Biology
SN - 1544-9173
TI - Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila
VL - 20
ER -
TY - THES
AB - The infiltration of immune cells into tissues underlies the establishment of tissue-resident
macrophages and responses to infections and tumors. However, the mechanisms immune
cells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.
In this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to
overcome the tissue barrier of the germband in the embryo. One strategy is the strengthening
of the actin cortex through developmentally controlled transcriptional regulation induced by
the Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces
expression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the
activated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical
strength allows hemocytes to overcome the physical resistance of the surrounding tissue and
translocate their nucleus to move forward. This mechanism affects the speed of migration
when hemocytes face a confined environment in vivo.
Another aspect of the invasion process is the initial step of the leading hemocytes entering
the tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel
subpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads
penetration into the germband. Hemocytes that are deficient in BMP signaling activation
show impaired persistence at the tissue entry, while their migration speed remains
unaffected.
This suggests that there might be different mechanisms controlling immune cell migration
within the confined environment in vivo, one of these being the general ability to overcome
the resistance of the surrounding tissue and another affecting the order of hemocytes that
collectively invade the tissue in a stream of individual cells.
Together, my findings provide deeper insights into transcriptional changes in immune
cells that enable efficient tissue invasion and pave the way for future studies investigating the
early colonization of tissues by macrophages in higher organisms. Moreover, they extend the
current view of Drosophila immune cell heterogeneity and point toward a potentially
conserved role for canonical BMP signaling in specifying immune cells that lead the migration
of tissue resident macrophages during embryogenesis.
AU - Wachner, Stephanie
ID - 11193
SN - 2663-337X
TI - Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells
ER -
TY - JOUR
AB - Squall lines are known to be the consequence of the interaction of low-level shear with cold pools associated with convective downdrafts. Also, as the magnitude of the shear increases beyond a critical shear, squall lines tend to orient themselves. The existing literature suggests that this orientation reduces incoming wind shear to the squall line, and maintains equilibrium between wind shear and cold pool spreading. Although this theory is widely accepted, very few quantitative studies have been conducted on supercritical regime especially. Here, we test this hypothesis with tropical squall lines obtained by imposing a vertical wind shear in cloud resolving simulations in radiative convective equilibrium. In the sub-critical regime, squall lines are perpendicular to the shear. In the super-critical regime, their orientation maintain the equilibrium, supporting existing theories. We also find that as shear increases, cold pools become more intense. However, this intensification has little impact on squall line orientation.
AU - Abramian, Sophie
AU - Muller, Caroline J
AU - Risi, Camille
ID - 10653
IS - 1
JF - Geophysical Research Letters
SN - 0094-8276
TI - Shear-convection interactions and orientation of tropical squall lines
VL - 49
ER -
TY - THES
AB - In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.
Our main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.
For the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\in \mathbb{N}}$ and $(H_n)_{n\in\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).
Via the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\mathrm{PGL}_{d+2}(\mathbb{F}_q)$ for any $\varepsilon>0$ and sufficiently large $q=q(\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.
By improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\mathrm{PGL}_{2}(\mathbb{F}_q)$ is not tight.
In a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.
AU - Wild, Pascal
ID - 11777
SN - 2663-337X
TI - High-dimensional expansion and crossing numbers of simplicial complexes
ER -
TY - JOUR
AB - Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation.
AU - Benedikter, Niels P
ID - 7900
IS - 1
JF - Reviews in Mathematical Physics
SN - 0129-055X
TI - Bosonic collective excitations in Fermi gases
VL - 33
ER -
TY - CHAP
AB - Expansion microscopy is a recently developed super-resolution imaging technique, which provides an alternative to optics-based methods such as deterministic approaches (e.g. STED) or stochastic approaches (e.g. PALM/STORM). The idea behind expansion microscopy is to embed the biological sample in a swellable gel, and then to expand it isotropically, thereby increasing the distance between the fluorophores. This approach breaks the diffraction barrier by simply separating the emission point-spread-functions of the fluorophores. The resolution attainable in expansion microscopy is thus directly dependent on the separation that can be achieved, i.e. on the expansion factor. The original implementation of the technique achieved an expansion factor of fourfold, for a resolution of 70–80 nm. The subsequently developed X10 method achieves an expansion factor of 10-fold, for a resolution of 25–30 nm. This technique can be implemented with minimal technical requirements on any standard fluorescence microscope, and is more easily applied for multi-color imaging than either deterministic or stochastic super-resolution approaches. This renders X10 expansion microscopy a highly promising tool for new biological discoveries, as discussed here, and as demonstrated by several recent applications.
AU - Truckenbrodt, Sven M
AU - Rizzoli, Silvio O.
ID - 7941
SN - 0091-679X
T2 - Methods in Cell Biology
TI - Simple multi-color super-resolution by X10 microscopy
VL - 161
ER -
TY - JOUR
AB - We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system.
AU - Diringer, Asaf A.
AU - Gulden, Tobias
ID - 8198
IS - 21
JF - Physical Review B
SN - 24699950
TI - Impact of drive harmonics on the stability of Floquet many-body localization
VL - 103
ER -
TY - JOUR
AB - Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks.
AU - Zenke, Friedemann
AU - Vogels, Tim P
ID - 8253
IS - 4
JF - Neural Computation
SN - 0899-7667
TI - The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks
VL - 33
ER -
TY - JOUR
AB - We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a "gap covering" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor.
AU - Alistarh, Dan-Adrian
AU - Nadiradze, Giorgi
AU - Sabour, Amirmojtaba
ID - 8286
JF - Algorithmica
SN - 0178-4617
TI - Dynamic averaging load balancing on cycles
ER -
TY - JOUR
AB - When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability.
AU - Aichholzer, Oswin
AU - Akitaya, Hugo A.
AU - Cheung, Kenneth C.
AU - Demaine, Erik D.
AU - Demaine, Martin L.
AU - Fekete, Sándor P.
AU - Kleist, Linda
AU - Kostitsyna, Irina
AU - Löffler, Maarten
AU - Masárová, Zuzana
AU - Mundilova, Klara
AU - Schmidt, Christiane
ID - 8317
JF - Computational Geometry: Theory and Applications
SN - 09257721
TI - Folding polyominoes with holes into a cube
VL - 93
ER -
TY - JOUR
AB - It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim.
AU - Pitrik, József
AU - Virosztek, Daniel
ID - 8373
JF - Linear Algebra and its Applications
KW - Kubo-Ando mean
KW - weighted multivariate mean
KW - barycenter
SN - 0024-3795
TI - A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means
VL - 609
ER -
TY - JOUR
AB - While recent advancements in computation and modelling have improved the analysis of complex traits, our understanding of the genetic basis of the time at symptom onset remains limited. Here, we develop a Bayesian approach (BayesW) that provides probabilistic inference of the genetic architecture of age-at-onset phenotypes in a sampling scheme that facilitates biobank-scale time-to-event analyses. We show in extensive simulation work the benefits BayesW provides in terms of number of discoveries, model performance and genomic prediction. In the UK Biobank, we find many thousands of common genomic regions underlying the age-at-onset of high blood pressure (HBP), cardiac disease (CAD), and type-2 diabetes (T2D), and for the genetic basis of onset reflecting the underlying genetic liability to disease. Age-at-menopause and age-at-menarche are also highly polygenic, but with higher variance contributed by low frequency variants. Genomic prediction into the Estonian Biobank data shows that BayesW gives higher prediction accuracy than other approaches.
AU - Ojavee, Sven E
AU - Kousathanas, Athanasios
AU - Trejo Banos, Daniel
AU - Orliac, Etienne J
AU - Patxot, Marion
AU - Lall, Kristi
AU - Magi, Reedik
AU - Fischer, Krista
AU - Kutalik, Zoltan
AU - Robinson, Matthew Richard
ID - 8430
IS - 1
JF - Nature Communications
TI - Genomic architecture and prediction of censored time-to-event phenotypes with a Bayesian genome-wide analysis
VL - 12
ER -
TY - JOUR
AB - The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis.
AU - Takeo, Yukari H.
AU - Shuster, S. Andrew
AU - Jiang, Linnie
AU - Hu, Miley
AU - Luginbuhl, David J.
AU - Rülicke, Thomas
AU - Contreras, Ximena
AU - Hippenmeyer, Simon
AU - Wagner, Mark J.
AU - Ganguli, Surya
AU - Luo, Liqun
ID - 8544
IS - 4
JF - Neuron
TI - GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells
VL - 109
ER -
TY - JOUR
AB - Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors.
AU - Zhang, Tingting
AU - Liu, Tengyuan
AU - Mora, Natalia
AU - Guegan, Justine
AU - Bertrand, Mathilde
AU - Contreras, Ximena
AU - Hansen, Andi H
AU - Streicher, Carmen
AU - Anderle, Marica
AU - Danda, Natasha
AU - Tiberi, Luca
AU - Hippenmeyer, Simon
AU - Hassan, Bassem A.
ID - 8546
IS - 10
JF - Cell Reports
TI - Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum
VL - 35
ER -
TY - JOUR
AB - Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.
Here, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.
Pharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.
This study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems.
AU - Li, Hongjiang
AU - von Wangenheim, Daniel
AU - Zhang, Xixi
AU - Tan, Shutang
AU - Darwish-Miranda, Nasser
AU - Naramoto, Satoshi
AU - Wabnik, Krzysztof T
AU - de Rycke, Riet
AU - Kaufmann, Walter
AU - Gütl, Daniel J
AU - Tejos, Ricardo
AU - Grones, Peter
AU - Ke, Meiyu
AU - Chen, Xu
AU - Dettmer, Jan
AU - Friml, Jiří
ID - 8582
IS - 1
JF - New Phytologist
SN - 0028646X
TI - Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana
VL - 229
ER -
TY - JOUR
AB - Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics, pattern formation and active turbulence. However, how mechanical and chemical signalling are integrated at the cellular level to give rise to such collective behaviours remains unclear. We address this by focusing on the highly conserved phenomenon of spatiotemporal waves of density and extracellular signal-regulated kinase (ERK) activation, which appear both in vitro and in vivo during collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechanochemical coupling between active cellular tensions and the mechanosensitive ERK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce long-ranged order and migration in a desired orientation, and we determine the theoretically optimal wavelength and period for inducing maximal migration towards free edges, which fits well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatiotemporal instabilities and the design principles of robust and efficient long-ranged migration.
AU - Boocock, Daniel R
AU - Hino, Naoya
AU - Ruzickova, Natalia
AU - Hirashima, Tsuyoshi
AU - Hannezo, Edouard B
ID - 8602
JF - Nature Physics
SN - 17452473
TI - Theory of mechanochemical patterning and optimal migration in cell monolayers
VL - 17
ER -
TY - JOUR
AB - We consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem.
AU - Frank, Rupert
AU - Seiringer, Robert
ID - 8603
IS - 3
JF - Communications on Pure and Applied Mathematics
SN - 00103640
TI - Quantum corrections to the Pekar asymptotics of a strongly coupled polaron
VL - 74
ER -
TY - JOUR
AB - The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance, and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16‐1 and GhKNOX2‐1 genes might be potential regulators of leaf shape. We functionally characterized the auxin‐responsive factor ARF16‐1 acting upstream of GhKNOX2‐1 to determine leaf morphology in cotton. The transcription of GhARF16‐1 was significantly higher in lobed‐leaved cotton than in smooth‐leaved cotton. Furthermore, the overexpression of GhARF16‐1 led to the upregulation of GhKNOX2‐1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2‐1. We found that GhARF16‐1 specifically bound to the promoter of GhKNOX2‐1 to induce its expression. The heterologous expression of GhARF16‐1 and GhKNOX2‐1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2‐1 is epistatic to GhARF16‐1 in Arabidopsis, suggesting that the GhARF16‐1 and GhKNOX2‐1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16‐1 and its downstream‐activated gene KNOX2‐1, determines leaf morphology in eudicots.
AU - He, P
AU - Zhang, Yuzhou
AU - Li, H
AU - Fu, X
AU - Shang, H
AU - Zou, C
AU - Friml, Jiří
AU - Xiao, G
ID - 8606
IS - 3
JF - Plant Biotechnology Journal
SN - 1467-7644
TI - GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton
VL - 19
ER -
TY - JOUR
AB - To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments.
AU - Ke, M
AU - Ma, Z
AU - Wang, D
AU - Sun, Y
AU - Wen, C
AU - Huang, D
AU - Chen, Z
AU - Yang, L
AU - Tan, Shutang
AU - Li, R
AU - Friml, Jiří
AU - Miao, Y
AU - Chen, X
ID - 8608
IS - 2
JF - New Phytologist
SN - 0028-646x
TI - Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana
VL - 229
ER -
TY - JOUR
AB - The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber.
AU - Rychlewicz, Kamil P
ID - 6965
IS - 2
JF - Bulletin of the London Mathematical Society
SN - 0024-6093
TI - The positivity of local equivariant Hirzebruch class for toric varieties
VL - 53
ER -
TY - GEN
AB - Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.
AU - Samarasinghe, Ranmal A.
AU - Miranda, Osvaldo
AU - Buth, Jessie E.
AU - Mitchell, Simon
AU - Ferando, Isabella
AU - Watanabe, Momoko
AU - Kurdian, Arinnae
AU - Golshani, Peyman
AU - Plath, Kathrin
AU - Lowry, William E.
AU - Parent, Jack M.
AU - Mody, Istvan
AU - Novitch, Bennett G.
ID - 6995
SN - 1097-6256
TI - Identification of neural oscillations and epileptiform changes in human brain organoids
VL - 24
ER -
TY - JOUR
AB - Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.
AU - Lombardi, Fabrizio
AU - Shriki, Oren
AU - Herrmann, Hans J
AU - de Arcangelis, Lucilla
ID - 7463
JF - Neurocomputing
SN - 0925-2312
TI - Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches
VL - 461
ER -
TY - JOUR
AB - Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.
AU - Fredes Tolorza, Felipe A
AU - Silva Sifuentes, Maria A
AU - Koppensteiner, Peter
AU - Kobayashi, Kenta
AU - Jösch, Maximilian A
AU - Shigemoto, Ryuichi
ID - 7551
IS - 1
JF - Current Biology
TI - Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation
VL - 31
ER -
TY - JOUR
AB - Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.
AU - Mlynarski, Wiktor F
AU - Hledik, Michal
AU - Sokolowski, Thomas R
AU - Tkačik, Gašper
ID - 7553
IS - 7
JF - Neuron
TI - Statistical analysis and optimality of neural systems
VL - 109
ER -
TY - JOUR
AB - We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.
AU - Boccato, Chiara
ID - 7685
IS - 1
JF - Reviews in Mathematical Physics
SN - 0129-055X
TI - The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime
VL - 33
ER -
TY - CONF
AB - We study a class of convex-concave saddle-point problems of the form minxmaxy⟨Kx,y⟩+fP(x)−h∗(y) where K is a linear operator, fP is the sum of a convex function f with a Lipschitz-continuous gradient and the indicator function of a bounded convex polytope P, and h∗ is a convex (possibly nonsmooth) function. Such problem arises, for example, as a Lagrangian relaxation of various discrete optimization problems. Our main assumptions are the existence of an efficient linear minimization oracle (lmo) for fP and an efficient proximal map for h∗ which motivate the solution via a blend of proximal primal-dual algorithms and Frank-Wolfe algorithms. In case h∗ is the indicator function of a linear constraint and function f is quadratic, we show a O(1/n2) convergence rate on the dual objective, requiring O(nlogn) calls of lmo. If the problem comes from the constrained optimization problem minx∈Rd{fP(x)|Ax−b=0} then we additionally get bound O(1/n2) both on the primal gap and on the infeasibility gap. In the most general case, we show a O(1/n) convergence rate of the primal-dual gap again requiring O(nlogn) calls of lmo. To the best of our knowledge, this improves on the known convergence rates for the considered class of saddle-point problems. We show applications to labeling problems frequently appearing in machine learning and computer vision.
AU - Kolmogorov, Vladimir
AU - Pock, Thomas
ID - 10552
T2 - 38th International Conference on Machine Learning
TI - One-sided Frank-Wolfe algorithms for saddle problems
ER -
TY - CONF
AB - The popularity of permissioned blockchain systems demands BFT SMR protocols that are efficient under good network conditions (synchrony) and robust under bad network conditions (asynchrony). The state-of-the-art partially synchronous BFT SMR protocols provide optimal linear communication cost per decision under synchrony and good leaders, but lose liveness under asynchrony. On the other hand, the state-of-the-art asynchronous BFT SMR protocols are live even under asynchrony, but always pay quadratic cost even under synchrony. In this paper, we propose a BFT SMR protocol that achieves the best of both worlds -- optimal linear cost per decision under good networks and leaders, optimal quadratic cost per decision under bad networks, and remains always live.
AU - Gelashvili, Rati
AU - Kokoris Kogias, Eleftherios
AU - Spiegelman, Alexander
AU - Xiang, Zhuolun
ID - 10553
KW - optimal
KW - state machine replication
KW - fallback
KW - asynchrony
KW - byzantine faults
SN - 9-781-4503-8548-0
T2 - Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
TI - Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol
ER -
TY - CONF
AB - We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication.
AU - Keidar, Idit
AU - Kokoris Kogias, Eleftherios
AU - Naor, Oded
AU - Spiegelman, Alexander
ID - 10554
SN - 978-1-4503-8548-0
T2 - Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing
TI - All You Need is DAG
ER -
TY - CONF
AB - In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1