TY - JOUR
AB - Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.
AU - Alanko, Jonna H
AU - Ucar, Mehmet C
AU - Canigova, Nikola
AU - Stopp, Julian A
AU - Schwarz, Jan
AU - Merrin, Jack
AU - Hannezo, Edouard B
AU - Sixt, Michael K
ID - 14274
IS - 87
JF - Science Immunology
KW - General Medicine
KW - Immunology
SN - 2470-9468
TI - CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration
VL - 8
ER -
TY - JOUR
AB - The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system.
AU - Sorichetti, Valerio
AU - Ninarello, Andrea
AU - Ruiz-Franco, José
AU - Hugouvieux, Virginie
AU - Zaccarelli, Emanuela
AU - Micheletti, Cristian
AU - Kob, Walter
AU - Rovigatti, Lorenzo
ID - 12705
IS - 7
JF - Journal of Chemical Physics
SN - 0021-9606
TI - Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks
VL - 158
ER -
TY - JOUR
AB - We study turn-based stochastic zero-sum games with lexicographic preferences over objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as controllable and adversarial non-determinism. Lexicographic order allows one to consider multiple objectives with a strict preference order. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. For a mixture of reachability and safety objectives, we show that deterministic lexicographically optimal strategies exist and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP, matching the current known bound for single objectives; and in general the decision problem is PSPACE-hard and can be solved in NEXPTIME∩coNEXPTIME. We present an algorithm that computes the lexicographically optimal strategies via a reduction to the computation of optimal strategies in a sequence of single-objectives games. For omega-regular objectives, we restrict our analysis to one-player games, also known as Markov decision processes. We show that lexicographically optimal strategies exist and need either randomization or finite memory. We present an algorithm that solves the relevant decision problem in polynomial time. We have implemented our algorithms and report experimental results on various case studies.
AU - Chatterjee, Krishnendu
AU - Katoen, Joost P
AU - Mohr, Stefanie
AU - Weininger, Maximilian
AU - Winkler, Tobias
ID - 12738
JF - Formal Methods in System Design
TI - Stochastic games with lexicographic objectives
ER -
TY - GEN
AB - The zip file includes source data used in the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.
A sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.
AU - Ucar, Mehmet C
ID - 14279
TI - Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration"
ER -
TY - JOUR
AB - We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32].
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 10405
IS - 5
JF - Communications on Pure and Applied Mathematics
SN - 0010-3640
TI - Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices
VL - 76
ER -
TY - JOUR
AB - Mathematical models often aim to describe a complicated mechanism in a cohesive and simple manner. However, reaching perfect balance between being simple enough or overly simplistic is a challenging task. Frequently, game-theoretic models have an underlying assumption that players, whenever they choose to execute a specific action, do so perfectly. In fact, it is rare that action execution perfectly coincides with intentions of individuals, giving rise to behavioural mistakes. The concept of incompetence of players was suggested to address this issue in game-theoretic settings. Under the assumption of incompetence, players have non-zero probabilities of executing a different strategy from the one they chose, leading to stochastic outcomes of the interactions. In this article, we survey results related to the concept of incompetence in classic as well as evolutionary game theory and provide several new results. We also suggest future extensions of the model and argue why it is important to take into account behavioural mistakes when analysing interactions among players in both economic and biological settings.
AU - Graham, Thomas
AU - Kleshnina, Maria
AU - Filar, Jerzy A.
ID - 10770
JF - Dynamic Games and Applications
SN - 2153-0785
TI - Where do mistakes lead? A survey of games with incompetent players
VL - 13
ER -
TY - JOUR
AB - We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique.
AU - Dello Schiavo, Lorenzo
ID - 10145
JF - Potential Analysis
SN - 0926-2601
TI - Ergodic decomposition of Dirichlet forms via direct integrals and applications
VL - 58
ER -
TY - JOUR
AB - The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
AU - Manavella, Pablo A
AU - Godoy Herz, Micaela A
AU - Kornblihtt, Alberto R
AU - Sorenson, Reed
AU - Sieburth, Leslie E
AU - Nakaminami, Kentaro
AU - Seki, Motoaki
AU - Ding, Yiliang
AU - Sun, Qianwen
AU - Kang, Hunseung
AU - Ariel, Federico D
AU - Crespi, Martin
AU - Giudicatti, Axel J
AU - Cai, Qiang
AU - Jin, Hailing
AU - Feng, Xiaoqi
AU - Qi, Yijun
AU - Pikaard, Craig S
ID - 12669
IS - 6
JF - The Plant Cell
KW - Cell Biology
KW - Plant Science
SN - 1040-4651
TI - Beyond transcription: compelling open questions in plant RNA biology
VL - 35
ER -
TY - JOUR
AB - We say that (Formula presented.) if, in every edge coloring (Formula presented.), we can find either a 1-colored copy of (Formula presented.) or a 2-colored copy of (Formula presented.). The well-known states that the threshold for the property (Formula presented.) is equal to (Formula presented.), where (Formula presented.) is given by (Formula presented.) for any pair of graphs (Formula presented.) and (Formula presented.) with (Formula presented.). In this article, we show the 0-statement of the Kohayakawa–Kreuter conjecture for every pair of cycles and cliques.
AU - Liebenau, Anita
AU - Mattos, Letícia
AU - Mendonca Dos Santos, Walner
AU - Skokan, Jozef
ID - 11706
IS - 4
JF - Random Structures and Algorithms
SN - 1042-9832
TI - Asymmetric Ramsey properties of random graphs involving cliques and cycles
VL - 62
ER -
TY - JOUR
AB - We establish precise right-tail small deviation estimates for the largest eigenvalue of real symmetric and complex Hermitian matrices whose entries are independent random variables with uniformly bounded moments. The proof relies on a Green function comparison along a continuous interpolating matrix flow for a long time. Less precise estimates are also obtained in the left tail.
AU - Erdös, László
AU - Xu, Yuanyuan
ID - 12707
IS - 2
JF - Bernoulli
SN - 1350-7265
TI - Small deviation estimates for the largest eigenvalue of Wigner matrices
VL - 29
ER -
TY - JOUR
AB - As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.
AU - Bocanegra, Laura
AU - Singh, Amrita
AU - Hannezo, Edouard B
AU - Zagórski, Marcin P
AU - Kicheva, Anna
ID - 12837
JF - Nature Physics
SN - 1745-2473
TI - Cell cycle dynamics control fluidity of the developing mouse neuroepithelium
VL - 19
ER -
TY - THES
AB - During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.
AU - Bocanegra, Laura
ID - 13081
SN - 2663 - 337X
TI - Epithelial dynamics during mouse neural tube development
ER -
TY - JOUR
AB - In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.
AU - Filipović Marijić, Vlatka
AU - Krasnici, Nesrete
AU - Valić, Damir
AU - Kapetanović, Damir
AU - Vardić Smrzlić, Irena
AU - Jordanova, Maja
AU - Rebok, Katerina
AU - Ramani, Sheriban
AU - Kostov, Vasil
AU - Nastova, Rodne
AU - Dragun, Zrinka
ID - 12863
JF - Environmental Science and Pollution Research
SN - 0944-1344
TI - Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish
VL - 30
ER -
TY - JOUR
AB - Coherent control and manipulation of quantum degrees of freedom such as spins forms the basis of emerging quantum technologies. In this context, the robust valley degree of freedom and the associated valley pseudospin found in two-dimensional transition metal dichalcogenides is a highly attractive platform. Valley polarization and coherent superposition of valley states have been observed in these systems even up to room temperature. Control of valley coherence is an important building block for the implementation of valley qubit. Large magnetic fields or high-power lasers have been used in the past to demonstrate the control (initialization and rotation) of the valley coherent states. Here, the control of layer–valley coherence via strong coupling of valley excitons in bilayer WS2 to microcavity photons is demonstrated by exploiting the pseudomagnetic field arising in optical cavities owing to the transverse electric–transverse magnetic (TE–TM)mode splitting. The use of photonic structures to generate pseudomagnetic fields which can be used to manipulate exciton-polaritons presents an attractive approach to control optical responses without the need for large magnets or high-intensity optical pump powers.
AU - Khatoniar, Mandeep
AU - Yama, Nicholas
AU - Ghazaryan, Areg
AU - Guddala, Sriram
AU - Ghaemi, Pouyan
AU - Majumdar, Kausik
AU - Menon, Vinod
ID - 12836
IS - 13
JF - Advanced Optical Materials
TI - Optical manipulation of Layer–Valley coherence via strong exciton–photon coupling in microcavities
VL - 11
ER -
TY - JOUR
AB - We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory.
AU - Zhang, Yihan
AU - Vatedka, Shashank
ID - 12838
IS - 7
JF - IEEE Transactions on Information Theory
SN - 0018-9448
TI - Multiple packing: Lower bounds via infinite constellations
VL - 69
ER -
TY - JOUR
AB - This paper deals with the large-scale behaviour of dynamical optimal transport on Zd
-periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ
-convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs.
AU - Gladbach, Peter
AU - Kopfer, Eva
AU - Maas, Jan
AU - Portinale, Lorenzo
ID - 12959
IS - 5
JF - Calculus of Variations and Partial Differential Equations
SN - 0944-2669
TI - Homogenisation of dynamical optimal transport on periodic graphs
VL - 62
ER -
TY - JOUR
AB - Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K.
AU - Xing, Congcong
AU - Zhang, Yu
AU - Xiao, Ke
AU - Han, Xu
AU - Liu, Yu
AU - Nan, Bingfei
AU - Ramon, Maria Garcia
AU - Lim, Khak Ho
AU - Li, Junshan
AU - Arbiol, Jordi
AU - Poudel, Bed
AU - Nozariasbmarz, Amin
AU - Li, Wenjie
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 12915
IS - 9
JF - ACS Nano
SN - 1936-0851
TI - Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites
VL - 17
ER -
TY - JOUR
AB - Two notes separated by a doubling in frequency sound similar to humans. This “octave equivalence” is critical to perception and production of music and speech and occurs early in human development. Because it also occurs cross-culturally, a biological basis of octave equivalence has been hypothesized. Members of our team previousy suggested four human traits are at the root of this phenomenon: (1) vocal learning, (2) clear octave information in vocal harmonics, (3) differing vocal ranges, and (4) vocalizing together. Using cross-species studies, we can test how relevant these respective traits are, while controlling for enculturation effects and addressing questions of phylogeny. Common marmosets possess forms of three of the four traits, lacking differing vocal ranges. We tested 11 common marmosets by adapting an established head-turning paradigm, creating a parallel test to an important infant study. Unlike human infants, marmosets responded similarly to tones shifted by an octave or other intervals. Because previous studies with the same head-turning paradigm produced differential results to discernable acoustic stimuli in common marmosets, our results suggest that marmosets do not perceive octave equivalence. Our work suggests differing vocal ranges between adults and children and men and women and the way they are used in singing together may be critical to the development of octave equivalence.
AU - Wagner, Bernhard
AU - Šlipogor, Vedrana
AU - Oh, Jinook
AU - Varga, Marion
AU - Hoeschele, Marisa
ID - 12961
IS - 5
JF - Developmental Science
SN - 1363-755X
TI - A comparison between common marmosets (Callithrix jacchus) and human infants sheds light on traits proposed to be at the root of human octave equivalence
VL - 26
ER -
TY - JOUR
AB - We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.
AU - De Simoi, Jacopo
AU - Kaloshin, Vadim
AU - Leguil, Martin
ID - 12877
JF - Inventiones Mathematicae
SN - 0020-9910
TI - Marked Length Spectral determination of analytic chaotic billiards with axial symmetries
VL - 233
ER -
TY - JOUR
AB - Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.
AU - Gupta, Divyansh
AU - Mlynarski, Wiktor F
AU - Sumser, Anton L
AU - Symonova, Olga
AU - Svaton, Jan
AU - Jösch, Maximilian A
ID - 12349
JF - Nature Neuroscience
SN - 1097-6256
TI - Panoramic visual statistics shape retina-wide organization of receptive fields
VL - 26
ER -
TY - DATA
AB - Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.
AU - Gupta, Divyansh
AU - Sumser, Anton L
AU - Jösch, Maximilian A
ID - 12370
TI - Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields
ER -
TY - JOUR
AB - The deployment of direct formate fuel cells (DFFCs) relies on the development of active and stable catalysts for the formate oxidation reaction (FOR). Palladium, providing effective full oxidation of formate to CO2, has been widely used as FOR catalyst, but it suffers from low stability, moderate activity, and high cost. Herein, we detail a colloidal synthesis route for the incorporation of P on Pd2Sn nanoparticles. These nanoparticles are dispersed on carbon black and the obtained composite is used as electrocatalytic material for the FOR. The Pd2Sn0.8P-based electrodes present outstanding catalytic activities with record mass current densities up to 10.0 A mgPd-1, well above those of Pd1.6Sn/C reference electrode. These high current densities are further enhanced by increasing the temperature from 25 °C to 40 °C. The Pd2Sn0.8P electrode also allows for slowing down the rapid current decay that generally happens during operation and can be rapidly re-activated through potential cycling. The excellent catalytic performance obtained is rationalized using density functional theory (DFT) calculations.
AU - Montaña-Mora, Guillem
AU - Qi, Xueqiang
AU - Wang, Xiang
AU - Chacón-Borrero, Jesus
AU - Martinez-Alanis, Paulina R.
AU - Yu, Xiaoting
AU - Li, Junshan
AU - Xue, Qian
AU - Arbiol, Jordi
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 12829
JF - Journal of Electroanalytical Chemistry
SN - 1572-6657
TI - Phosphorous incorporation into palladium tin nanoparticles for the electrocatalytic formate oxidation reaction
VL - 936
ER -
TY - JOUR
AB - We study a new discretization of the Gaussian curvature for polyhedral surfaces. This discrete Gaussian curvature is defined on each conical singularity of a polyhedral surface as the quotient of the angle defect and the area of the Voronoi cell corresponding to the singularity. We divide polyhedral surfaces into discrete conformal classes using a generalization of discrete conformal equivalence pioneered by Feng Luo. We subsequently show that, in every discrete conformal class, there exists a polyhedral surface with constant discrete Gaussian curvature. We also provide explicit examples to demonstrate that this surface is in general not unique.
AU - Kourimska, Hana
ID - 12764
JF - Discrete and Computational Geometry
SN - 0179-5376
TI - Discrete yamabe problem for polyhedral surfaces
VL - 70
ER -
TY - THES
AB - The extension of extremal combinatorics to the setting of exterior algebra is a work
in progress that gained attention recently. In this thesis, we study the combinatorial structure of exterior algebra by introducing a dictionary that translates the notions from the set systems into the framework of exterior algebra. We show both generalizations of celebrated Erdös--Ko--Rado theorem and Hilton--Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms.
AU - Köse, Seyda
ID - 13331
SN - 2791-4585
TI - Exterior algebra and combinatorics
ER -
TY - JOUR
AB - Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection.
Because they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group.
Here, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals.
We discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the expression and evolution of behavioural strategies.
Finally, we outline avenues for further investigation such as approaches to quantify group-level responses, and the connection of the physiological and behavioural response to parasites in different social contexts.
AU - Stockmaier, Sebastian
AU - Ulrich, Yuko
AU - Albery, Gregory F.
AU - Cremer, Sylvia
AU - Lopes, Patricia C.
ID - 12765
IS - 4
JF - Functional Ecology
SN - 0269-8463
TI - Behavioural defences against parasites across host social structures
VL - 37
ER -
TY - JOUR
AB - The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.
AU - Ivanov, Grigory
AU - Köse, Seyda
ID - 12680
IS - 6
JF - Discrete Mathematics
SN - 0012-365X
TI - Erdős-Ko-Rado and Hilton-Milner theorems for two-forms
VL - 346
ER -
TY - JOUR
AB - In the physics literature the spectral form factor (SFF), the squared Fourier transform of the empirical eigenvalue density, is the most common tool to test universality for disordered quantum systems, yet previous mathematical results have been restricted only to two exactly solvable models (Forrester in J Stat Phys 183:33, 2021. https://doi.org/10.1007/s10955-021-02767-5, Commun Math Phys 387:215–235, 2021. https://doi.org/10.1007/s00220-021-04193-w). We rigorously prove the physics prediction on SFF up to an intermediate time scale for a large class of random matrices using a robust method, the multi-resolvent local laws. Beyond Wigner matrices we also consider the monoparametric ensemble and prove that universality of SFF can already be triggered by a single random parameter, supplementing the recently proven Wigner–Dyson universality (Cipolloni et al. in Probab Theory Relat Fields, 2021. https://doi.org/10.1007/s00440-022-01156-7) to larger spectral scales. Remarkably, extensive numerics indicates that our formulas correctly predict the SFF in the entire slope-dip-ramp regime, as customarily called in physics.
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 12792
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - On the spectral form factor for random matrices
VL - 401
ER -
TY - JOUR
AB - Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness.
AU - Corbet, René
AU - Kerber, Michael
AU - Lesnick, Michael
AU - Osang, Georg F
ID - 12709
JF - Discrete and Computational Geometry
SN - 0179-5376
TI - Computing the multicover bifiltration
VL - 70
ER -
TY - JOUR
AB - Kleinjohann (Archiv der Mathematik 35(1):574–582, 1980; Mathematische Zeitschrift 176(3), 327–344, 1981) and Bangert (Archiv der Mathematik 38(1):54–57, 1982) extended the reach rch(S) from subsets S of Euclidean space to the reach rchM(S) of subsets S of Riemannian manifolds M, where M is smooth (we’ll assume at least C3). Bangert showed that sets of positive reach in Euclidean space and Riemannian manifolds are very similar. In this paper we introduce a slight variant of Kleinjohann’s and Bangert’s extension and quantify the similarity between sets of positive reach in Euclidean space and Riemannian manifolds in a new way: Given p∈M and q∈S, we bound the local feature size (a local version of the reach) of its lifting to the tangent space via the inverse exponential map (exp−1p(S)) at q, assuming that rchM(S) and the geodesic distance dM(p,q) are bounded. These bounds are motivated by the importance of the reach and local feature size to manifold learning, topological inference, and triangulating manifolds and the fact that intrinsic approaches circumvent the curse of dimensionality.
AU - Boissonnat, Jean Daniel
AU - Wintraecken, Mathijs
ID - 12763
JF - Journal of Applied and Computational Topology
SN - 2367-1726
TI - The reach of subsets of manifolds
VL - 7
ER -
TY - THES
AB - Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome.
A previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?
We found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism.
Following up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased.
We propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.
AU - Radler, Philipp
ID - 14280
KW - Cell Division
KW - Reconstitution
KW - FtsZ
KW - FtsA
KW - Divisome
KW - E.coli
SN - 2663-337X
TI - Spatiotemporal signaling during assembly of the bacterial divisome
ER -
TY - CONF
AB - The safety-liveness dichotomy is a fundamental concept in formal languages which plays a key role in verification. Recently, this dichotomy has been lifted to quantitative properties, which are arbitrary functions from infinite words to partially-ordered domains. We look into harnessing the dichotomy for the specific classes of quantitative properties expressed by quantitative automata. These automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totallyordered domain of real numbers. In this automata-theoretic setting, we establish a connection between quantitative safety and topological continuity and provide an alternative characterization of quantitative safety and liveness in terms of their boolean counterparts. For all common value functions, we show how the safety closure of a quantitative automaton can be constructed in PTime, and we provide PSpace-complete checks of whether a given quantitative automaton is safe or live, with the exception of LimInfAvg and LimSupAvg automata, for which the safety check is in ExpSpace. Moreover, for deterministic Sup, LimInf, and LimSup automata, we give PTime decompositions into safe and live automata. These decompositions enable the separation of techniques for safety and liveness verification for quantitative specifications.
AU - Boker, Udi
AU - Henzinger, Thomas A
AU - Mazzocchi, Nicolas Adrien
AU - Sarac, Naci E
ID - 13221
SN - 9783959772990
T2 - 34th International Conference on Concurrency Theory
TI - Safety and liveness of quantitative automata
VL - 279
ER -
TY - CONF
AB - Partially specified Boolean networks (PSBNs) represent a promising framework for the qualitative modelling of biological systems in which the logic of interactions is not completely known. Phenotype control aims to stabilise the network in states exhibiting specific traits.
In this paper, we define the phenotype control problem in the context of asynchronous PSBNs and propose a novel semi-symbolic algorithm for solving this problem with permanent variable perturbations.
AU - Beneš, Nikola
AU - Brim, Luboš
AU - Pastva, Samuel
AU - Šafránek, David
AU - Šmijáková, Eva
ID - 14411
SN - 0302-9743
T2 - International Conference on Computational Methods in Systems Biology
TI - Phenotype control of partially specified boolean networks
VL - 14137
ER -
TY - JOUR
AB - Recently, a concept of generalized multifractality, which characterizes fluctuations and correlations of critical eigenstates, was introduced and explored for all 10 symmetry classes of disordered systems. Here, by using the nonlinear sigma-model (
NL
σ
M
) field theory, we extend the theory of generalized multifractality to boundaries of systems at criticality. Our numerical simulations on two-dimensional systems of symmetry classes A, C, and AII fully confirm the analytical predictions of pure-scaling observables and Weyl symmetry relations between critical exponents of surface generalized multifractality. This demonstrates the validity of the
NL
σ
M
for the description of Anderson-localization critical phenomena, not only in the bulk but also on the boundary. The critical exponents strongly violate generalized parabolicity, in analogy with earlier results for the bulk, corroborating the conclusion that the considered Anderson-localization critical points are not described by conformal field theories. We further derive relations between generalized surface multifractal spectra and linear combinations of Lyapunov exponents of a strip in quasi-one-dimensional geometry, which hold under the assumption of invariance with respect to a logarithmic conformal map. Our numerics demonstrate that these relations hold with an excellent accuracy. Taken together, our results indicate an intriguing situation: the conformal invariance is broken but holds partially at critical points of Anderson localization.
AU - Babkin, Serafim
AU - Karcher, Jonas F.
AU - Burmistrov, Igor S.
AU - Mirlin, Alexander D.
ID - 14406
IS - 10
JF - Physical Review B
SN - 2469-9950
TI - Generalized surface multifractality in two-dimensional disordered systems
VL - 108
ER -
TY - CONF
AB - This paper focuses on the implementation details of the baseline methods and a recent lightweight conditional model extrapolation algorithm LIMES [5] for streaming data under class-prior shift. LIMES achieves superior performance over the baseline methods, especially concerning the minimum-across-day accuracy, which is important for the users of the system. In this work, the key measures to facilitate reproducibility and enhance the credibility of the results are described.
AU - Tomaszewska, Paulina
AU - Lampert, Christoph
ID - 14410
SN - 0302-9743
T2 - International Workshop on Reproducible Research in Pattern Recognition
TI - On the implementation of baselines and lightweight conditional model extrapolation (LIMES) under class-prior shift
VL - 14068
ER -
TY - JOUR
AB - Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis.
AU - Scarpetta, Silvia
AU - Morrisi, Niccolò
AU - Mutti, Carlotta
AU - Azzi, Nicoletta
AU - Trippi, Irene
AU - Ciliento, Rosario
AU - Apicella, Ilenia
AU - Messuti, Giovanni
AU - Angiolelli, Marianna
AU - Lombardi, Fabrizio
AU - Parrino, Liborio
AU - Vaudano, Anna Elisabetta
ID - 12487
IS - 10
JF - iScience
TI - Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture
VL - 26
ER -
TY - CONF
AB - We introduce hypernode automata as a new specification formalism for hyperproperties of concurrent systems. They are finite automata with nodes labeled with hypernode logic formulas and transitions labeled with actions. A hypernode logic formula specifies relations between sequences of variable values in different system executions. Unlike HyperLTL, hypernode logic takes an asynchronous view on execution traces by constraining the values and the order of value changes of each variable without correlating the timing of the changes. Different execution traces are synchronized solely through the transitions of hypernode automata. Hypernode automata naturally combine asynchronicity at the node level with synchronicity at the transition level. We show that the model-checking problem for hypernode automata is decidable over action-labeled Kripke structures, whose actions induce transitions of the specification automata. For this reason, hypernode automaton is a suitable formalism for specifying and verifying asynchronous hyperproperties, such as declassifying observational determinism in multi-threaded programs.
AU - Bartocci, Ezio
AU - Henzinger, Thomas A
AU - Nickovic, Dejan
AU - Oliveira da Costa, Ana
ID - 14405
SN - 18688969
T2 - 34th International Conference on Concurrency Theory
TI - Hypernode automata
VL - 279
ER -
TY - JOUR
AB - Background:
Pro-apoptotic BAX is a central mediator of retinal ganglion cell (RGC) death after optic nerve damage. BAX activation occurs in two stages including translocation of latent BAX to the mitochondrial outer membrane (MOM) and then permeabilization of the MOM to facilitate the release of apoptotic signaling molecules. As a critical component of RGC death, BAX is an attractive target for neuroprotective therapies and an understanding of the kinetics of BAX activation and the mechanisms controlling the two stages of this process in RGCs is potentially valuable in informing the development of a neuroprotective strategy.
Methods:
The kinetics of BAX translocation were assessed by both static and live-cell imaging of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC) protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX was assessed by staining with the 6A7 monoclonal antibody, which recognizes a conformational change in this protein after MOM insertion. Assessment of individual kinases associated with both stages of activation was made using small molecule inhibitors injected into the vitreous either independently or in concert with ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase cascade was evaluated using mice with a double conditional knock-out of both Mkk4 and Mkk7.
Results:
ONC induces the translocation of GFP-BAX in RGCs at a slower rate and with less intracellular synchronicity than 661W cells, but exhibits less variability among mitochondrial foci within a single cell. GFP-BAX was also found to translocate in all compartments of an RGC including the dendritic arbor and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation of BAX immediately following translocation. Unlike tissue culture cells, which exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant delay between these two stages, similar to detached cells undergoing anoikis. Translocation, with minimal permeabilization could be induced in a subset of RGCs using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor (sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.
Conclusions:
A comparison between BAX activation kinetics in tissue culture cells and in cells of a complex tissue environment shows distinct differences indicating that caution should be used when translating findings from one condition to the other. RGCs exhibit both a delay between translocation and permeabilization and the ability for translocated BAX to be retrotranslocated, suggesting several stages at which intervention of the activation process could be exploited in the design of a therapeutic strategy.
AU - Maes, Margaret E
AU - Donahue, Ryan J.
AU - Schlamp, Cassandra L.
AU - Marola, Olivia J.
AU - Libby, Richard T.
AU - Nickells, Robert W.
ID - 14401
JF - Molecular Neurodegeneration
TI - BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps
VL - 18
ER -
TY - JOUR
AB - We consider the problem of computing the maximal probability of satisfying an
-regular specification for stochastic, continuous-state, nonlinear systems evolving in discrete time. The problem reduces, after automata-theoretic constructions, to finding the maximal probability of satisfying a parity condition on a (possibly hybrid) state space. While characterizing the exact satisfaction probability is open, we show that a lower bound on this probability can be obtained by (I) computing an under-approximation of the qualitative winning region, i.e., states from which the parity condition can be enforced almost surely, and (II) computing the maximal probability of reaching this qualitative winning region.
The heart of our approach is a technique to symbolically compute the under-approximation of the qualitative winning region in step (I) via a finite-state abstraction of the original system as a
-player parity game. Our abstraction procedure uses only the support of the probabilistic evolution; it does not use precise numerical transition probabilities. We prove that the winning set in the abstract -player game induces an under-approximation of the qualitative winning region in the original synthesis problem, along with a policy to solve it. By combining these contributions with (a) a symbolic fixpoint algorithm to solve
-player games and (b) existing techniques for reachability policy synthesis in stochastic nonlinear systems, we get an abstraction-based algorithm for finding a lower bound on the maximal satisfaction probability.
We have implemented the abstraction-based algorithm in Mascot-SDS, where we combined the outlined abstraction step with our tool Genie (Majumdar et al., 2023) that solves
-player parity games (through a reduction to Rabin games) more efficiently than existing algorithms. We evaluated our implementation on the nonlinear model of a perturbed bistable switch from the literature. We show empirically that the lower bound on the winning region computed by our approach is precise, by comparing against an over-approximation of the qualitative winning region. Moreover, our implementation outperforms a recently proposed tool for solving this problem by a large margin.
AU - Majumdar, Rupak
AU - Mallik, Kaushik
AU - Schmuck, Anne Kathrin
AU - Soudjani, Sadegh
ID - 14400
JF - Nonlinear Analysis: Hybrid Systems
SN - 1751-570X
TI - Symbolic control for stochastic systems via finite parity games
VL - 51
ER -
TY - JOUR
AB - Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition).
AU - Lombardi, Fabrizio
AU - Herrmann, Hans J.
AU - Parrino, Liborio
AU - Plenz, Dietmar
AU - Scarpetta, Silvia
AU - Vaudano, Anna Elisabetta
AU - De Arcangelis, Lucilla
AU - Shriki, Oren
ID - 14402
IS - 10
JF - Cell Reports
TI - Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state
VL - 42
ER -
TY - JOUR
AB - We prove that the mesoscopic linear statistics ∑if(na(σi−z0)) of the eigenvalues {σi}i of large n×n non-Hermitian random matrices with complex centred i.i.d. entries are asymptotically Gaussian for any H20-functions f around any point z0 in the bulk of the spectrum on any mesoscopic scale 01+N−1/3+ϵ, for any ϵ>0. The study of this natural process combines elements of Hermitian and non-Hermitian analysis, and illustrates some aspects of the intrinsic instability of (even weakly) non-Hermitian matrices.
AU - Dubach, Guillaume
AU - Erdös, László
ID - 12683
JF - Electronic Communications in Probability
TI - Dynamics of a rank-one perturbation of a Hermitian matrix
VL - 28
ER -
TY - JOUR
AB - We consider the fluctuations of regular functions f of a Wigner matrix W viewed as an entire matrix f (W). Going beyond the well-studied tracial mode, Trf (W), which is equivalent to the customary linear statistics of eigenvalues, we show that Trf (W)A is asymptotically normal for any nontrivial bounded deterministic matrix A. We identify three different and asymptotically independent modes of this fluctuation, corresponding to the tracial part, the traceless diagonal part and the off-diagonal part of f (W) in the entire mesoscopic regime, where we find that the off-diagonal modes fluctuate on a much smaller scale than the tracial mode. As a main motivation to study CLT in such generality on small mesoscopic scales, we determine
the fluctuations in the eigenstate thermalization hypothesis (Phys. Rev. A 43 (1991) 2046–2049), that is, prove that the eigenfunction overlaps with any deterministic matrix are asymptotically Gaussian after a small spectral averaging. Finally, in the macroscopic regime our result also generalizes (Zh. Mat. Fiz. Anal. Geom. 9 (2013) 536–581, 611, 615) to complex W and to all crossover ensembles in between. The main technical inputs are the recent
multiresolvent local laws with traceless deterministic matrices from the companion paper (Comm. Math. Phys. 388 (2021) 1005–1048).
AU - Cipolloni, Giorgio
AU - Erdös, László
AU - Schröder, Dominik J
ID - 12761
IS - 1
JF - Annals of Applied Probability
SN - 1050-5164
TI - Functional central limit theorems for Wigner matrices
VL - 33
ER -
TY - JOUR
AB - We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.
AU - Dello Schiavo, Lorenzo
AU - Lytvynov, Eugene
ID - 13145
JF - Electronic Communications in Probability
TI - A Mecke-type characterization of the Dirichlet–Ferguson measure
VL - 28
ER -
TY - JOUR
AB - It is known that the Brauer--Manin obstruction to the Hasse principle is vacuous for smooth Fano hypersurfaces of dimension at least 3 over any number field. Moreover, for such varieties it follows from a general conjecture of Colliot-Thélène that the Brauer--Manin obstruction to the Hasse principle should be the only one, so that the Hasse principle is expected to hold. Working over the field of rational numbers and ordering Fano hypersurfaces of fixed degree and dimension by height, we prove that almost every such hypersurface satisfies the Hasse principle provided that the dimension is at least 3. This proves a conjecture of Poonen and Voloch in every case except for cubic surfaces.
AU - Browning, Timothy D
AU - Boudec, Pierre Le
AU - Sawin, Will
ID - 8682
IS - 3
JF - Annals of Mathematics
SN - 0003-486X
TI - The Hasse principle for random Fano hypersurfaces
VL - 197
ER -
TY - JOUR
AB - Allometric settings of population dynamics models are appealing due to their parsimonious nature and broad utility when studying system level effects. Here, we parameterise the size-scaled Rosenzweig-MacArthur differential equations to eliminate prey-mass dependency, facilitating an in depth analytic study of the equations which incorporates scaling parameters’ contributions to coexistence. We define the functional response term to match empirical findings, and examine situations where metabolic theory derivations and observation diverge. The dynamical properties of the Rosenzweig-MacArthur system, encompassing the distribution of size-abundance equilibria, the scaling of period and amplitude of population cycling, and relationships between predator and prey abundances, are consistent with empirical observation. Our parameterisation is an accurate minimal model across 15+ orders of mass magnitude.
AU - Mckerral, Jody C.
AU - Kleshnina, Maria
AU - Ejov, Vladimir
AU - Bartle, Louise
AU - Mitchell, James G.
AU - Filar, Jerzy A.
ID - 12706
IS - 2
JF - PLoS One
TI - Empirical parameterisation and dynamical analysis of the allometric Rosenzweig-MacArthur equations
VL - 18
ER -
TY - JOUR
AB - High entropy alloys (HEAs) are highly suitable candidate catalysts for oxygen evolution and reduction reactions (OER/ORR) as they offer numerous parameters for optimizing the electronic structure and catalytic sites. Herein, FeCoNiMoW HEA nanoparticles are synthesized using a solution‐based low‐temperature approach. Such FeCoNiMoW nanoparticles show high entropy properties, subtle lattice distortions, and modulated electronic structure, leading to superior OER performance with an overpotential of 233 mV at 10 mA cm−2 and 276 mV at 100 mA cm−2. Density functional theory calculations reveal the electronic structures of the FeCoNiMoW active sites with an optimized d‐band center position that enables suitable adsorption of OOH* intermediates and reduces the Gibbs free energy barrier in the OER process. Aqueous zinc–air batteries (ZABs) based on this HEA demonstrate a high open circuit potential of 1.59 V, a peak power density of 116.9 mW cm−2, a specific capacity of 857 mAh gZn−1, and excellent stability for over 660 h of continuous charge–discharge cycles. Flexible and solid ZABs are also assembled and tested, displaying excellent charge–discharge performance at different bending angles. This work shows the significance of 4d/5d metal‐modulated electronic structure and optimized adsorption ability to improve the performance of OER/ORR, ZABs, and beyond.
AU - He, Ren
AU - Yang, Linlin
AU - Zhang, Yu
AU - Jiang, Daochuan
AU - Lee, Seungho
AU - Horta, Sharona
AU - Liang, Zhifu
AU - Lu, Xuan
AU - Ostovari Moghaddam, Ahmad
AU - Li, Junshan
AU - Ibáñez, Maria
AU - Xu, Ying
AU - Zhou, Yingtang
AU - Cabot, Andreu
ID - 14434
JF - Advanced Materials
KW - Mechanical Engineering
KW - Mechanics of Materials
KW - General Materials Science
SN - 0935-9648
TI - A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries
ER -
TY - JOUR
AB - Low‐cost, safe, and environmental‐friendly rechargeable aqueous zinc‐ion batteries (ZIBs) are promising as next‐generation energy storage devices for wearable electronics among other applications. However, sluggish ionic transport kinetics and the unstable electrode structure during ionic insertion/extraction hampers their deployment. Herein, we propose a new cathode material based on a layered metal chalcogenide (LMC), bismuth telluride (Bi2Te3), coated with polypyrrole (PPy). Taking advantage of the PPy coating, the Bi2Te3@PPy composite presents strong ionic absorption affinity, high oxidation resistance, and high structural stability. The ZIBs based on Bi2Te3@PPy cathodes exhibit high capacities and ultra‐long lifespans of over 5000 cycles. They also present outstanding stability even under bending. In addition, we analyze here the reaction mechanism using in situ X‐ray diffraction, X‐ray photoelectron spectroscopy, and computational tools and demonstrate that, in the aqueous system, Zn2+ is not inserted into the cathode as previously assumed. In contrast, proton charge storage dominates the process. Overall, this work not only shows the great potential of LMCs as ZIBs cathode materials and the advantages of PPy coating, but also clarifies the charge/discharge mechanism in rechargeable ZIBs based on LMCs.
AU - Zeng, Guifang
AU - Sun, Qing
AU - Horta, Sharona
AU - Wang, Shang
AU - Lu, Xuan
AU - Zhang, Chaoyue
AU - Li, Jing
AU - Li, Junshan
AU - Ci, Lijie
AU - Tian, Yanhong
AU - Ibáñez, Maria
AU - Cabot, Andreu
ID - 14435
JF - Advanced Materials
KW - Mechanical Engineering
KW - Mechanics of Materials
KW - General Materials Science
SN - 0935-9648
TI - A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries
ER -
TY - JOUR
AB - Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) plays an essential role in neuronal activities through interaction with various proteins involved in signaling at membranes. However, the distribution pattern of PI(4,5)P2 and the association with these proteins on the neuronal cell membranes remain elusive. In this study, we established a method for visualizing PI(4,5)P2 by SDS-digested freeze-fracture replica labeling (SDS-FRL) to investigate the quantitative nanoscale distribution of PI(4,5)P2 in cryo-fixed brain. We demonstrate that PI(4,5)P2 forms tiny clusters with a mean size of ∼1000 nm2 rather than randomly distributed in cerebellar neuronal membranes in male C57BL/6J mice. These clusters show preferential accumulation in specific membrane compartments of different cell types, in particular, in Purkinje cell (PC) spines and granule cell (GC) presynaptic active zones. Furthermore, we revealed extensive association of PI(4,5)P2 with CaV2.1 and GIRK3 across different membrane compartments, whereas its association with mGluR1α was compartment specific. These results suggest that our SDS-FRL method provides valuable insights into the physiological functions of PI(4,5)P2 in neurons.
AU - Eguchi, Kohgaku
AU - Le Monnier, Elodie
AU - Shigemoto, Ryuichi
ID - 13202
IS - 23
JF - The Journal of Neuroscience
SN - 0270-6474
TI - Nanoscale phosphoinositide distribution on cell membranes of mouse cerebellar neurons
VL - 43
ER -
TY - JOUR
AB - We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface.
AU - Bonolis, Dante
AU - Browning, Timothy D
ID - 12916
IS - 1
JF - Annali della Scuola Normale Superiore di Pisa - Classe di Scienze
SN - 0391-173X
TI - Uniform bounds for rational points on hyperelliptic fibrations
VL - 24
ER -
TY - JOUR
AB - We characterize critical points of 1-dimensional maps paired in persistent homology
geometrically and this way get elementary proofs of theorems about the symmetry
of persistence diagrams and the variation of such maps. In particular, we identify
branching points and endpoints of networks as the sole source of asymmetry and
relate the cycle basis in persistent homology with a version of the stable marriage
problem. Our analysis provides the foundations of fast algorithms for maintaining a
collection of sorted lists together with its persistence diagram.
AU - Biswas, Ranita
AU - Cultrera Di Montesano, Sebastiano
AU - Edelsbrunner, Herbert
AU - Saghafian, Morteza
ID - 13182
JF - Journal of Applied and Computational Topology
SN - 2367-1726
TI - Geometric characterization of the persistence of 1D maps
ER -
TY - THES
AB - Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of
changes in the brain throughout adulthood, regrouped under the term "plasticity". Some cells
in the brain —neurons— and specifically changes in the connections between neurons, the
synapses, were shown to be crucial for the formation, selection, and consolidation of memories
from past experiences. These ongoing changes of synapses across time are called synaptic
plasticity. Understanding how a myriad of biochemical processes operating at individual
synapses can somehow work in concert to give rise to meaningful changes in behavior is a
fascinating problem and an active area of research.
However, the experimental search for the precise plasticity mechanisms at play in the brain
is daunting, as it is difficult to control and observe synapses during learning. Theoretical
approaches have thus been the default method to probe the plasticity-behavior connection. Such
studies attempt to extract unifying principles across synapses and model all observed synaptic
changes using plasticity rules: equations that govern the evolution of synaptic strengths across
time in neuronal network models. These rules can use many relevant quantities to determine
the magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic
action potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.
However, analytical studies rely heavily on human intuition and are forced to make simplifying
assumptions about plasticity rules.
In this thesis, we aim to assist and augment human intuition in this search for plasticity rules.
We explore whether a numerical approach could automatically discover the plasticity rules
that elicit desired behaviors in large networks of interconnected neurons. This approach is
dubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make
neuronal networks learn how to solve a desired task. We first write all the potential plasticity
mechanisms to consider using a single expression with adjustable parameters. We then optimize
these plasticity parameters using evolutionary strategies or Bayesian inference on tasks known
to involve synaptic plasticity, such as familiarity detection and network stabilization.
We show that these automated approaches are powerful tools, able to complement established
analytical methods. By comprehensively screening plasticity rules at all synapse types in
realistic, spiking neuronal network models, we discover entire sets of degenerate plausible
plasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more
robust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity
rules, and provide fresh insights on synaptic plasticity in spiking network models.
AU - Confavreux, Basile J
ID - 14422
SN - 2663 - 337X
TI - Synapseek: Meta-learning synaptic plasticity rules
ER -
TY - THES
AB - Superconductivity has many important applications ranging from levitating trains over qubits to MRI scanners. The phenomenon is successfully modeled by Bardeen-Cooper-Schrieffer (BCS) theory. From a mathematical perspective, BCS theory has been studied extensively for systems without boundary. However, little is known in the presence of boundaries. With the help of numerical methods physicists observed that the critical temperature may increase in the presence of a boundary. The goal of this thesis is to understand the influence of boundaries on the critical temperature in BCS theory and to give a first rigorous justification of these observations. On the way, we also study two-body Schrödinger operators on domains with boundaries and prove additional results for superconductors without boundary.
BCS theory is based on a non-linear functional, where the minimizer indicates whether the system is superconducting or in the normal, non-superconducting state. By considering the Hessian of the BCS functional at the normal state, one can analyze whether the normal state is possibly a minimum of the BCS functional and estimate the critical temperature. The Hessian turns out to be a linear operator resembling a Schrödinger operator for two interacting particles, but with more complicated kinetic energy. As a first step, we study the two-body Schrödinger operator in the presence of boundaries.
For Neumann boundary conditions, we prove that the addition of a boundary can create new eigenvalues, which correspond to the two particles forming a bound state close to the boundary.
Second, we need to understand superconductivity in the translation invariant setting. While in three dimensions this has been extensively studied, there is no mathematical literature for the one and two dimensional cases. In dimensions one and two, we compute the weak coupling asymptotics of the critical temperature and the energy gap in the translation invariant setting. We also prove that their ratio is independent of the microscopic details of the model in the weak coupling limit; this property is referred to as universality.
In the third part, we study the critical temperature of superconductors in the presence of boundaries. We start by considering the one-dimensional case of a half-line with contact interaction. Then, we generalize the results to generic interactions and half-spaces in one, two and three dimensions. Finally, we compare the critical temperature of a quarter space in two dimensions to the critical temperatures of a half-space and of the full space.
AU - Roos, Barbara
ID - 14374
SN - 2663 - 337X
TI - Boundary superconductivity in BCS theory
ER -
TY - JOUR
AB - We consider the linear BCS equation, determining the BCS critical temperature, in the presence of a boundary, where Dirichlet boundary conditions are imposed. In the one-dimensional case with point interactions, we prove that the critical temperature is strictly larger than the bulk value, at least at weak coupling. In particular, the Cooper-pair wave function localizes near the boundary, an effect that cannot be modeled by effective Neumann boundary conditions on the order parameter as often imposed in Ginzburg–Landau theory. We also show that the relative shift in critical temperature vanishes if the coupling constant either goes to zero or to infinity.
AU - Hainzl, Christian
AU - Roos, Barbara
AU - Seiringer, Robert
ID - 13207
IS - 4
JF - Journal of Spectral Theory
SN - 1664-039X
TI - Boundary superconductivity in the BCS model
VL - 12
ER -
TY - JOUR
AB - The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices.
AU - D’Elia, Domenica
AU - Truu, Jaak
AU - Lahti, Leo
AU - Berland, Magali
AU - Papoutsoglou, Georgios
AU - Ceci, Michelangelo
AU - Zomer, Aldert
AU - Lopes, Marta B.
AU - Ibrahimi, Eliana
AU - Gruca, Aleksandra
AU - Nechyporenko, Alina
AU - Frohme, Marcus
AU - Klammsteiner, Thomas
AU - Pau, Enrique Carrillo De Santa
AU - Marcos-Zambrano, Laura Judith
AU - Hron, Karel
AU - Pio, Gianvito
AU - Simeon, Andrea
AU - Suharoschi, Ramona
AU - Moreno-Indias, Isabel
AU - Temko, Andriy
AU - Nedyalkova, Miroslava
AU - Apostol, Elena Simona
AU - Truică, Ciprian Octavian
AU - Shigdel, Rajesh
AU - Telalović, Jasminka Hasić
AU - Bongcam-Rudloff, Erik
AU - Przymus, Piotr
AU - Jordamović, Naida Babić
AU - Falquet, Laurent
AU - Tarazona, Sonia
AU - Sampri, Alexia
AU - Isola, Gaetano
AU - Pérez-Serrano, David
AU - Trajkovik, Vladimir
AU - Klucar, Lubos
AU - Loncar-Turukalo, Tatjana
AU - Havulinna, Aki S.
AU - Jansen, Christian
AU - Bertelsen, Randi J.
AU - Claesson, Marcus Joakim
ID - 14449
JF - Frontiers in Microbiology
TI - Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action
VL - 14
ER -
TY - JOUR
AB - Squall lines are substantially influenced by the interaction of low-level shear with cold pools associated with convective downdrafts. Beyond an optimal shear amplitude, squall lines tend to orient themselves at an angle with respect to the low-level shear. While the mechanisms behind squall line orientation seem to be increasingly well understood, uncertainties remain on the implications of this orientation. Roca and Fiolleau (2020, https://doi.org/10.1038/s43247-020-00015-4) show that long lived mesoscale convective systems, including squall lines, are disproportionately involved in rainfall extremes in the tropics. This article investigates the influence of the interaction between low-level shear and squall line outflow on squall line generated precipitation extrema in the tropics. Using a cloud resolving model, simulated squall lines in radiative convective equilibrium amid a shear-dominated regime (super optimal), a balanced regime (optimal), and an outflow dominated regime (suboptimal). Our results show that precipitation extremes in squall lines are 40% more intense in the case of optimal shear and remain 30% superior in the superoptimal regime relative to a disorganized case. With a theoretical scaling of precipitation extremes (C. Muller & Takayabu, 2020, https://doi.org/10.1088/1748-9326/ab7130), we show that the condensation rates control the amplification of precipitation extremes in tropical squall lines, mainly due to its change in vertical mass flux (dynamic component). The reduction of dilution by entrainment explains half of this change, consistent with Mulholland et al. (2021, https://doi.org/10.1175/jas-d-20-0299.1). The other half is explained by increased cloud-base velocity intensity in optimal and superoptimal squall lines.
AU - Abramian, Sophie
AU - Muller, Caroline J
AU - Risi, Camille
ID - 14453
IS - 10
JF - Journal of Advances in Modeling Earth Systems
TI - Extreme precipitation in tropical squall lines
VL - 15
ER -
TY - JOUR
AB - The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√. We illustrate our results with some numerical examples.
AU - Barton, Nicholas H
AU - Etheridge, Alison M.
AU - Véber, Amandine
ID - 14452
IS - 2
JF - Genetics
SN - 0016-6731
TI - The infinitesimal model with dominance
VL - 225
ER -
TY - JOUR
AB - The first long-lived turbulent structures observable in planar shear flows take the form of localized stripes, inclined with respect to the mean flow direction. The dynamics of these stripes is central to transition, and recent studies proposed an analogy to directed percolation where the stripes’ proliferation is ultimately responsible for the turbulence becoming sustained. In the present study we focus on the internal stripe dynamics as well as on the eventual stripe expansion, and we compare the underlying mechanisms in pressure- and shear-driven planar flows, respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities of the overall laminar–turbulence patterns, the stripe proliferation processes in the two cases are fundamentally different. Starting from the growth and sustenance of individual stripes, we find that in plane-Couette flow new streaks are created stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation is deterministic and occurs locally at the downstream tip. Because of the up/downstream symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and two strong laminar turbulent interfaces. These differences in symmetry as well as in internal growth give rise to two fundamentally different stripe splitting mechanisms. In plane-Poiseuille flow splitting is connected to the elongational growth of the original stripe, and it results from a break-off/shedding of the stripe's tail. In plane-Couette flow splitting follows from a broadening of the original stripe and a division along the stripe into two slimmer stripes.
AU - Marensi, Elena
AU - Yalniz, Gökhan
AU - Hof, Björn
ID - 14466
JF - Journal of Fluid Mechanics
KW - turbulence
KW - transition to turbulence
KW - patterns
SN - 0022-1120
TI - Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows
VL - 974
ER -
TY - DATA
AB - The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.
AU - Barton, Nicholas H
ID - 12949
KW - Quantitative genetics
KW - infinitesimal model
TI - The infinitesimal model with dominance
ER -
TY - JOUR
AB - Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.
AU - Reeve, James
AU - Butlin, Roger K.
AU - Koch, Eva L.
AU - Stankowski, Sean
AU - Faria, Rui
ID - 14463
JF - Molecular Ecology
SN - 0962-1083
TI - Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)
ER -
TY - JOUR
AU - Narzisi, Antonio
AU - Halladay, Alycia
AU - Masi, Gabriele
AU - Novarino, Gaia
AU - Lord, Catherine
ID - 14455
JF - Frontiers in Psychiatry
TI - Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment
VL - 14
ER -
TY - JOUR
AB - Given a triangle Δ, we study the problem of determining the smallest enclosing and largest embedded isosceles triangles of Δ with respect to area and perimeter. This problem was initially posed by Nandakumar [17, 22] and was first studied by Kiss, Pach, and Somlai [13], who showed that if Δ′ is the smallest area isosceles triangle containing Δ, then Δ′ and Δ share a side and an angle. In the present paper, we prove that for any triangle Δ, every maximum area isosceles triangle embedded in Δ and every maximum perimeter isosceles triangle embedded in Δ shares a side and an angle with Δ. Somewhat surprisingly, the case of minimum perimeter enclosing triangles is different: there are infinite families of triangles Δ whose minimum perimeter isosceles containers do not share a side and an angle with Δ.
AU - Ambrus, Áron
AU - Csikós, Mónika
AU - Kiss, Gergely
AU - Pach, János
AU - Somlai, Gábor
ID - 14464
IS - 7
JF - International Journal of Foundations of Computer Science
SN - 0129-0541
TI - Optimal embedded and enclosing isosceles triangles
VL - 34
ER -
TY - CONF
AB - Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model’s weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.
AU - Markov, Ilia
AU - Vladu, Adrian
AU - Guo, Qi
AU - Alistarh, Dan-Adrian
ID - 14461
T2 - Proceedings of the 40th International Conference on Machine Learning
TI - Quantized distributed training of large models with convergence guarantees
VL - 202
ER -
TY - CONF
AB - We study fine-grained error bounds for differentially private algorithms for counting under continual observation. Our main insight is that the matrix mechanism when using lower-triangular matrices can be used in the continual observation model. More specifically, we give an explicit factorization for the counting matrix Mcount and upper bound the error explicitly. We also give a fine-grained analysis, specifying the exact constant in the upper bound. Our analysis is based on upper and lower bounds of the completely bounded norm (cb-norm) of Mcount
. Along the way, we improve the best-known bound of 28 years by Mathias (SIAM Journal on Matrix Analysis and Applications, 1993) on the cb-norm of Mcount for a large range of the dimension of Mcount. Furthermore, we are the first to give concrete error bounds for various problems under continual observation such as binary counting, maintaining a histogram, releasing an approximately cut-preserving synthetic graph, many graph-based statistics, and substring and episode counting. Finally, we note that our result can be used to get a fine-grained error bound for non-interactive local learning and the first lower bounds on the additive error for (ϵ,δ)-differentially-private counting under continual observation. Subsequent to this work, Henzinger et al. (SODA, 2023) showed that our factorization also achieves fine-grained mean-squared error.
AU - Fichtenberger, Hendrik
AU - Henzinger, Monika H
AU - Upadhyay, Jalaj
ID - 14462
T2 - Proceedings of the 40th International Conference on Machine Learning
TI - Constant matters: Fine-grained error bound on differentially private continual observation
VL - 202
ER -
TY - CONF
AB - Autoencoders are a popular model in many branches of machine learning and lossy data compression. However, their fundamental limits, the performance of gradient methods and the features learnt during optimization remain poorly understood, even in the two-layer setting. In fact, earlier work has considered either linear autoencoders or specific training regimes (leading to vanishing or diverging compression rates). Our paper addresses this gap by focusing on non-linear two-layer autoencoders trained in the challenging proportional regime in which the input dimension scales linearly with the size of the representation. Our results characterize the minimizers of the population risk, and show that such minimizers are achieved by gradient methods; their structure is also unveiled, thus leading to a concise description of the features obtained via training. For the special case of a sign activation function, our analysis establishes the fundamental limits for the lossy compression of Gaussian sources via (shallow) autoencoders. Finally, while the results are proved for Gaussian data, numerical simulations on standard datasets display the universality of the theoretical predictions.
AU - Shevchenko, Aleksandr
AU - Kögler, Kevin
AU - Hassani, Hamed
AU - Mondelli, Marco
ID - 14459
T2 - Proceedings of the 40th International Conference on Machine Learning
TI - Fundamental limits of two-layer autoencoders, and achieving them with gradient methods
VL - 202
ER -
TY - CONF
AB - We provide an efficient implementation of the backpropagation algorithm, specialized to the case where the weights of the neural network being trained are sparse. Our algorithm is general, as it applies to arbitrary (unstructured) sparsity and common layer types (e.g., convolutional or linear). We provide a fast vectorized implementation on commodity CPUs, and show that it can yield speedups in end-to-end runtime experiments, both in transfer learning using already-sparsified networks, and in training sparse networks from scratch. Thus, our results provide the first support for sparse training on commodity hardware.
AU - Nikdan, Mahdi
AU - Pegolotti, Tommaso
AU - Iofinova, Eugenia B
AU - Kurtic, Eldar
AU - Alistarh, Dan-Adrian
ID - 14460
T2 - Proceedings of the 40th International Conference on Machine Learning
TI - SparseProp: Efficient sparse backpropagation for faster training of neural networks at the edge
VL - 202
ER -
TY - JOUR
AB - We prove the following quantitative Borsuk–Ulam-type result (an equivariant analogue of Gromov’s Topological Overlap Theorem): Let X be a free ℤ/2-complex of dimension d with coboundary expansion at least ηk in dimension 0 ≤ k < d. Then for every equivariant map F: X →ℤ/2 ℝd, the fraction of d-simplices σ of X with 0 ∈ F (σ) is at least 2−d Π d−1k=0ηk.
As an application, we show that for every sufficiently thick d-dimensional spherical building Y and every map f: Y → ℝ2d, we have f(σ) ∩ f(τ) ≠ ∅ for a constant fraction μd > 0 of pairs {σ, τ} of d-simplices of Y. In particular, such complexes are non-embeddable into ℝ2d, which proves a conjecture of Tancer and Vorwerk for sufficiently thick spherical buildings.
We complement these results by upper bounds on the coboundary expansion of two families of simplicial complexes; this indicates some limitations to the bounds one can obtain by straighforward applications of the quantitative Borsuk–Ulam theorem. Specifically, we prove
• an upper bound of (d + 1)/2d on the normalized (d − 1)-th coboundary expansion constant of complete (d + 1)-partite d-dimensional complexes (under a mild divisibility assumption on the sizes of the parts); and
• an upper bound of (d + 1)/2d + ε on the normalized (d − 1)-th coboundary expansion of the d-dimensional spherical building associated with GLd+2(Fq) for any ε > 0 and sufficiently large q. This disproves, in a rather strong sense, a conjecture of Lubotzky, Meshulam and Mozes.
AU - Wagner, Uli
AU - Wild, Pascal
ID - 14445
IS - 2
JF - Israel Journal of Mathematics
SN - 0021-2172
TI - Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes
VL - 256
ER -
TY - CONF
AB - Threshold secret sharing allows a dealer to split a secret s into n shares, such that any t shares allow for reconstructing s, but no t-1 shares reveal any information about s. Leakage-resilient secret sharing requires that the secret remains hidden, even when an adversary additionally obtains a limited amount of leakage from every share. Benhamouda et al. (CRYPTO’18) proved that Shamir’s secret sharing scheme is one bit leakage-resilient for reconstruction threshold t≥0.85n and conjectured that the same holds for t = c.n for any constant 0≤c≤1. Nielsen and Simkin (EUROCRYPT’20) showed that this is the best one can hope for by proving that Shamir’s scheme is not secure against one-bit leakage when t0c.n/log(n).
In this work, we strengthen the lower bound of Nielsen and Simkin. We consider noisy leakage-resilience, where a random subset of leakages is replaced by uniformly random noise. We prove a lower bound for Shamir’s secret sharing, similar to that of Nielsen and Simkin, which holds even when a constant fraction of leakages is replaced by random noise. To this end, we first prove a lower bound on the share size of any noisy-leakage-resilient sharing scheme. We then use this lower bound to show that there exist universal constants c1, c2, such that for sufficiently large n it holds that Shamir’s secret sharing scheme is not noisy-leakage-resilient for t≤c1.n/log(n), even when a c2 fraction of leakages are replaced by random noise.
AU - Hoffmann, Charlotte
AU - Simkin, Mark
ID - 14457
SN - 0302-9743
T2 - 8th International Conference on Cryptology and Information Security in Latin America
TI - Stronger lower bounds for leakage-resilient secret sharing
VL - 14168
ER -
TY - CONF
AB - We show for the first time that large-scale generative pretrained transformer (GPT) family models can be pruned to at least 50% sparsity in one-shot, without any retraining, at minimal loss of accuracy. This is achieved via a new pruning method called SparseGPT, specifically designed to work efficiently and accurately on massive GPT-family models. We can execute SparseGPT on the largest available open-source models, OPT-175B and BLOOM-176B, in under 4.5 hours, and can reach 60% unstructured sparsity with negligible increase in perplexity: remarkably, more than 100 billion weights from these models can be ignored at inference time. SparseGPT generalizes to semi-structured (2:4 and 4:8) patterns, and is compatible with weight quantization approaches. The code is available at: https://github.com/IST-DASLab/sparsegpt.
AU - Frantar, Elias
AU - Alistarh, Dan-Adrian
ID - 14458
T2 - Proceedings of the 40th International Conference on Machine Learning
TI - SparseGPT: Massive language models can be accurately pruned in one-shot
VL - 202
ER -
TY - JOUR
AB - Auxin belongs among major phytohormones and governs multiple aspects of plant growth and development. The establishment of auxin concentration gradients, determines, among other processes, plant organ positioning and growth responses to environmental stimuli.
Herein we report the synthesis of new NBD- or DNS-labelled IAA derivatives and the elucidation of their biological activity, fluorescence properties and subcellular accumulation patterns in planta. These novel compounds did not show auxin-like activity, but instead antagonized physiological auxin effects. The DNS-labelled derivatives FL5 and FL6 showed strong anti-auxin activity in roots and hypocotyls, which also occurred at the level of gene transcription as confirmed by quantitative PCR analysis. The auxin antagonism of our derivatives was further demonstrated in vitro using an SPR-based binding assay. The NBD-labelled compound FL4 with the best fluorescence properties proved to be unsuitable to study auxin accumulation patterns in planta. On the other hand, the strongest anti-auxin activity possessing compounds FL5 and FL6 could be useful to study binding mechanisms to auxin receptors and for manipulations of auxin-regulated processes.
AU - Bieleszová, Kristýna
AU - Hladík, Pavel
AU - Kubala, Martin
AU - Napier, Richard
AU - Brunoni, Federica
AU - Gelová, Zuzana
AU - Fiedler, Lukas
AU - Kulich, Ivan
AU - Strnad, Miroslav
AU - Doležal, Karel
AU - Novák, Ondřej
AU - Friml, Jiří
AU - Žukauskaitė, Asta
ID - 14447
JF - Plant Growth Regulation
SN - 0167-6903
TI - New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana
ER -
TY - CONF
AB - In this paper, we present novel algorithms that efficiently compute a shortest reconfiguration sequence between two given dominating sets in trees and interval graphs under the TOKEN SLIDING model. In this problem, a graph is provided along with its two dominating sets, which can be imagined as tokens placed on vertices. The objective is to find a shortest sequence of dominating sets that transforms one set into the other, with each set in the sequence resulting from sliding a single token in the previous set. While identifying any sequence has been well studied, our work presents the first polynomial algorithms for this optimization variant in the context of dominating sets.
AU - Křišťan, Jan Matyáš
AU - Svoboda, Jakub
ID - 14456
SN - 0302-9743
T2 - 24th International Symposium on Fundamentals of Computation Theory
TI - Shortest dominating set reconfiguration under token sliding
VL - 14292
ER -
TY - JOUR
AB - We investigate the potential of Multi-Objective, Deep Reinforcement Learning for stock and cryptocurrency single-asset trading: in particular, we consider a Multi-Objective algorithm which generalizes the reward functions and discount factor (i.e., these components are not specified a priori, but incorporated in the learning process). Firstly, using several important assets (BTCUSD, ETHUSDT, XRPUSDT, AAPL, SPY, NIFTY50), we verify the reward generalization property of the proposed Multi-Objective algorithm, and provide preliminary statistical evidence showing increased predictive stability over the corresponding Single-Objective strategy. Secondly, we show that the Multi-Objective algorithm has a clear edge over the corresponding Single-Objective strategy when the reward mechanism is sparse (i.e., when non-null feedback is infrequent over time). Finally, we discuss the generalization properties with respect to the discount factor. The entirety of our code is provided in open-source format.
AU - Cornalba, Federico
AU - Disselkamp, Constantin
AU - Scassola, Davide
AU - Helf, Christopher
ID - 14451
JF - Neural Computing and Applications
SN - 0941-0643
TI - Multi-objective reward generalization: improving performance of Deep Reinforcement Learning for applications in single-asset trading
ER -
TY - JOUR
AB - In the presence of an obstacle, active particles condensate into a surface “wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of “fast” and “slow” active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion “diversity,” defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter.
AU - Rojas Vega, Mauricio Nicolas
AU - De Castro, Pablo
AU - Soto, Rodrigo
ID - 14442
IS - 10
JF - The European Physical Journal E
SN - 1292-8941
TI - Mixtures of self-propelled particles interacting with asymmetric obstacles
VL - 46
ER -
TY - JOUR
AB - We prove several results about substructures in Latin squares. First, we explain how to adapt our recent work on high-girth Steiner triple systems to the setting of Latin squares, resolving a conjecture of Linial that there exist Latin squares with arbitrarily high girth. As a consequence, we see that the number of order- n Latin squares with no intercalate (i.e., no 2×2 Latin subsquare) is at least (e−9/4n−o(n))n2. Equivalently, P[N=0]≥e−n2/4−o(n2)=e−(1+o(1))EN
, where N is the number of intercalates in a uniformly random order- n Latin square.
In fact, extending recent work of Kwan, Sah, and Sawhney, we resolve the general large-deviation problem for intercalates in random Latin squares, up to constant factors in the exponent: for any constant 0<δ≤1 we have P[N≤(1−δ)EN]=exp(−Θ(n2)) and for any constant δ>0 we have P[N≥(1+δ)EN]=exp(−Θ(n4/3logn)).
Finally, as an application of some new general tools for studying substructures in random Latin squares, we show that in almost all order- n Latin squares, the number of cuboctahedra (i.e., the number of pairs of possibly degenerate 2×2 submatrices with the same arrangement of symbols) is of order n4, which is the minimum possible. As observed by Gowers and Long, this number can be interpreted as measuring ``how associative'' the quasigroup associated with the Latin square is.
AU - Kwan, Matthew Alan
AU - Sah, Ashwin
AU - Sawhney, Mehtaab
AU - Simkin, Michael
ID - 14444
IS - 2
JF - Israel Journal of Mathematics
SN - 0021-2172
TI - Substructures in Latin squares
VL - 256
ER -
TY - DATA
AB - The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.
AU - Dunajova, Zuzana
AU - Prats Mateu, Batirtze
AU - Radler, Philipp
AU - Lim, Keesiang
AU - Brandis, Dörte
AU - Velicky, Philipp
AU - Danzl, Johann G
AU - Wong, Richard W.
AU - Elgeti, Jens
AU - Hannezo, Edouard B
AU - Loose, Martin
ID - 13116
TI - Chiral and nematic phases of flexible active filaments
ER -
TY - CONF
AB - As AI and machine-learned software are used increasingly for making decisions that affect humans, it is imperative that they remain fair and unbiased in their decisions. To complement design-time bias mitigation measures, runtime verification techniques have been introduced recently to monitor the algorithmic fairness of deployed systems. Previous monitoring techniques assume full observability of the states of the (unknown) monitored system. Moreover, they can monitor only fairness properties that are specified as arithmetic expressions over the probabilities of different events. In this work, we extend fairness monitoring to systems modeled as partially observed Markov chains (POMC), and to specifications containing arithmetic expressions over the expected values of numerical functions on event sequences. The only assumptions we make are that the underlying POMC is aperiodic and starts in the stationary distribution, with a bound on its mixing time being known. These assumptions enable us to estimate a given property for the entire distribution of possible executions of the monitored POMC, by observing only a single execution. Our monitors observe a long run of the system and, after each new observation, output updated PAC-estimates of how fair or biased the system is. The monitors are computationally lightweight and, using a prototype implementation, we demonstrate their effectiveness on several real-world examples.
AU - Henzinger, Thomas A
AU - Kueffner, Konstantin
AU - Mallik, Kaushik
ID - 14454
SN - 0302-9743
T2 - 23rd International Conference on Runtime Verification
TI - Monitoring algorithmic fairness under partial observations
VL - 14245
ER -
TY - JOUR
AB - The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.
AU - Dunajova, Zuzana
AU - Prats Mateu, Batirtze
AU - Radler, Philipp
AU - Lim, Keesiang
AU - Brandis, Dörte
AU - Velicky, Philipp
AU - Danzl, Johann G
AU - Wong, Richard W.
AU - Elgeti, Jens
AU - Hannezo, Edouard B
AU - Loose, Martin
ID - 13314
JF - Nature Physics
SN - 1745-2473
TI - Chiral and nematic phases of flexible active filaments
ER -
TY - JOUR
AB - Recent work has paid close attention to the first principle of Granger causality, according to which cause precedes effect. In this context, the question may arise whether the detected direction of causality also reverses after the time reversal of unidirectionally coupled data. Recently, it has been shown that for unidirectionally causally connected autoregressive (AR) processes X → Y, after time reversal of data, the opposite causal direction Y → X is indeed detected, although typically as part of the bidirectional X↔ Y link. As we argue here, the answer is different when the measured data are not from AR processes but from linked deterministic systems. When the goal is the usual forward data analysis, cross-mapping-like approaches correctly detect X → Y, while Granger causality-like approaches, which should not be used for deterministic time series, detect causal independence X → Y. The results of backward causal analysis depend on the predictability of the reversed data. Unlike AR processes, observables from deterministic dynamical systems, even complex nonlinear ones, can be predicted well forward, while backward predictions can be difficult (notably when the time reversal of a function leads to one-to-many relations). To address this problem, we propose an approach based on models that provide multiple candidate predictions for the target, combined with a loss function that consideres only the best candidate. The resulting good forward and backward predictability supports the view that unidirectionally causally linked deterministic dynamical systems X → Y can be expected to detect the same link both before and after time reversal.
AU - Jakubík, Jozef
AU - Bui Thi Mai, Phuong
AU - Chvosteková, Martina
AU - Krakovská, Anna
ID - 14446
IS - 4
JF - Measurement Science Review
TI - Against the flow of time with multi-output models
VL - 23
ER -
TY - JOUR
AB - Importance Climate change, pollution, urbanization, socioeconomic inequality, and psychosocial effects of the COVID-19 pandemic have caused massive changes in environmental conditions that affect brain health during the life span, both on a population level as well as on the level of the individual. How these environmental factors influence the brain, behavior, and mental illness is not well known.
Observations A research strategy enabling population neuroscience to contribute to identify brain mechanisms underlying environment-related mental illness by leveraging innovative enrichment tools for data federation, geospatial observation, climate and pollution measures, digital health, and novel data integration techniques is described. This strategy can inform innovative treatments that target causal cognitive and molecular mechanisms of mental illness related to the environment. An example is presented of the environMENTAL Project that is leveraging federated cohort data of over 1.5 million European citizens and patients enriched with deep phenotyping data from large-scale behavioral neuroimaging cohorts to identify brain mechanisms related to environmental adversity underlying symptoms of depression, anxiety, stress, and substance misuse.
Conclusions and Relevance This research will lead to the development of objective biomarkers and evidence-based interventions that will significantly improve outcomes of environment-related mental illness.
AU - Schumann, Gunter
AU - Andreassen, Ole A.
AU - Banaschewski, Tobias
AU - Calhoun, Vince D.
AU - Clinton, Nicholas
AU - Desrivieres, Sylvane
AU - Brandlistuen, Ragnhild Eek
AU - Feng, Jianfeng
AU - Hese, Soeren
AU - Hitchen, Esther
AU - Hoffmann, Per
AU - Jia, Tianye
AU - Jirsa, Viktor
AU - Marquand, Andre F.
AU - Nees, Frauke
AU - Nöthen, Markus M.
AU - Novarino, Gaia
AU - Polemiti, Elli
AU - Ralser, Markus
AU - Rapp, Michael
AU - Schepanski, Kerstin
AU - Schikowski, Tamara
AU - Slater, Mel
AU - Sommer, Peter
AU - Stahl, Bernd Carsten
AU - Thompson, Paul M.
AU - Twardziok, Sven
AU - Van Der Meer, Dennis
AU - Walter, Henrik
AU - Westlye, Lars
ID - 14443
IS - 10
JF - JAMA Psychiatry
TI - Addressing global environmental challenges to mental health using population neuroscience: A review
VL - 80
ER -
TY - JOUR
AB - We study the Fröhlich polaron model in R3, and establish the subleading term in the strong coupling asymptotics of its ground state energy, corresponding to the quantum corrections to the classical energy determined by the Pekar approximation.
AU - Brooks, Morris
AU - Seiringer, Robert
ID - 14441
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - The Fröhlich Polaron at strong coupling: Part I - The quantum correction to the classical energy
VL - 404
ER -
TY - CONF
AB - We consider the problem of solving LP relaxations of MAP-MRF inference problems, and in particular the method proposed recently in [16], [35]. As a key computational subroutine, it uses a variant of the Frank-Wolfe (FW) method to minimize a smooth convex function over a combinatorial polytope. We propose an efficient implementation of this subroutine based on in-face Frank-Wolfe directions, introduced in [4] in a different context. More generally, we define an abstract data structure for a combinatorial subproblem that enables in-face FW directions, and describe its specialization for tree-structured MAP-MRF inference subproblems. Experimental results indicate that the resulting method is the current state-of-art LP solver for some classes of problems. Our code is available at pub.ist.ac.at/~vnk/papers/IN-FACE-FW.html.
AU - Kolmogorov, Vladimir
ID - 14448
SN - 1063-6919
T2 - Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition
TI - Solving relaxations of MAP-MRF problems: Combinatorial in-face Frank-Wolfe directions
VL - 2023
ER -
TY - JOUR
AB - Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation.
AU - Lyons, David B.
AU - Briffa, Amy
AU - He, Shengbo
AU - Choi, Jaemyung
AU - Hollwey, Elizabeth
AU - Colicchio, Jack
AU - Anderson, Ian
AU - Feng, Xiaoqi
AU - Howard, Martin
AU - Zilberman, Daniel
ID - 12672
IS - 3
JF - Cell Reports
TI - Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons
VL - 42
ER -
TY - JOUR
AB - Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.
AU - Leonard, Thomas A.
AU - Loose, Martin
AU - Martens, Sascha
ID - 14039
IS - 15
JF - Developmental Cell
SN - 1534-5807
TI - The membrane surface as a platform that organizes cellular and biochemical processes
VL - 58
ER -
TY - JOUR
AB - We consider the large polaron described by the Fröhlich Hamiltonian and study its energy-momentum relation defined as the lowest possible energy as a function of the total momentum. Using a suitable family of trial states, we derive an optimal parabolic upper bound for the energy-momentum relation in the limit of strong coupling. The upper bound consists of a momentum independent term that agrees with the predicted two-term expansion for the ground state energy of the strongly coupled polaron at rest and a term that is quadratic in the momentum with coefficient given by the inverse of twice the classical effective mass introduced by Landau and Pekar.
AU - Mitrouskas, David Johannes
AU - Mysliwy, Krzysztof
AU - Seiringer, Robert
ID - 13178
JF - Forum of Mathematics
TI - Optimal parabolic upper bound for the energy-momentum relation of a strongly coupled polaron
VL - 11
ER -
TY - JOUR
AB - In this paper, we determine the motivic class — in particular, the weight polynomial and conjecturally the Poincaré polynomial — of the open de Rham space, defined and studied by Boalch, of certain moduli spaces of irregular meromorphic connections on the trivial rank
bundle on P1. The computation is by motivic Fourier transform. We show that the result satisfies the purity conjecture, that is, it agrees with the pure part of the conjectured mixed Hodge polynomial of the corresponding wild character variety. We also identify the open de Rham spaces with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer. We finish with constructing natural complete hyperkähler metrics on them, which in the four-dimensional cases are expected to be of type ALF.
AU - Hausel, Tamás
AU - Wong, Michael Lennox
AU - Wyss, Dimitri
ID - 14244
JF - Proceedings of the London Mathematical Society
SN - 0024-6115
TI - Arithmetic and metric aspects of open de Rham spaces
ER -
TY - JOUR
AB - Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies.
AU - Napoli, Federico
AU - Becker, Lea Marie
AU - Schanda, Paul
ID - 14036
JF - Current Opinion in Structural Biology
SN - 0959-440X
TI - Protein dynamics detected by magic-angle spinning relaxation dispersion NMR
VL - 82
ER -