pwc-archive/papers-with-abstracts huggingface dataset:
Social dilemmas in off-lattice populations
Authors: B. F. de Oliveira, A. Szolnoki
Date: 2021-02-07 00:00:00

Exploring the possible consequences of spatial reciprocity on the evolution of cooperation is an intensively studied research avenue. Related works assumed a certain interaction graph of competing players and studied how particular topologies may influence the dynamical behavior. In this paper we apply a numerically more demanding off-lattice population approach which could be potentially relevant especially in microbiological environments. As expected, results are conceptually similar to those which were obtained for lattice-type interaction graphs, but some spectacular differences can also be revealed. On one hand, in off-lattice populations spatial reciprocity may work more efficiently than for a lattice-based system. On the other hand, competing strategies may separate from each other in the continuous space concept, which gives a chance for cooperators to survive even at relatively high temptation values. Furthermore, the lack of strict neighborhood results in soft borders between competing patches which jeopardizes the long term stability of homogeneous domains. We survey the major social dilemma games based on pair interactions of players and reveal all analogies and differences compared to on-lattice simulations.
Hybrid reaction-diffusion and clock-and-wavefront model for the arrest of oscillations in the somitogenesis segmentation clock
Authors: Jesús Pantoja-Hernández, Víctor F. Breña-Medina, Moisés Santillán
Date: 2020-09-04 00:00:00

The clock and wavefront paradigm is arguably the most widely accepted model for explaining the embryonic process of somitogenesis. According to this model, somitogenesis is based upon the interaction between a genetic oscillator, known as segmentation clock, and a differentiation wavefront, which provides the positional information indicating where each pair of somites is formed. Shortly after the clock and wavefront paradigm was introduced, Meinhardt presented a conceptually different mathematical model for morphogenesis in general, and somitogenesis in particular. Recently, Cotterell et al. rediscovered an equivalent model by systematically enumerating and studying small networks performing segmentation. Cotterell et al. called it a progressive oscillatory reaction-diffusion (PORD) model. In the Meinhardt- PORD model, somitogenesis is driven by short-range interactions and the posterior movement of the front is a local, emergent phenomenon, which is not controlled by global positional information. With this model, it is possible to explain some experimental observations that are incompatible with the clock and wavefront model. However the Meinhardt-PORD model has some important disadvantages of its own. Namely, it is quite sensitive to fluctuations and depends on very specific initial conditions (which are not biologically realistic). In this work, we propose an equivalent Meinhardt-PORD model, and then amend it to couple it with a wavefront consisting of a receding morphogen gradient. By doing so, we get a hybrid model between the Meinhardt-PORD and the clock-and-wavefront ones, which overcomes most of the deficiencies of the two originating models.
Cities in a world of diminishing transport costs
Authors: Tomoya Mori, Minoru Osawa
Date: 2020-12-23 00:00:00

Economic activities favor mutual geographical proximity and concentrate spatially to form cities. In a world of diminishing transport costs, however, the advantage of physical proximity is fading, and the role of cities in the economy may be declining. To provide insights into the long-run evolution of cities, we analyzed Japan's census data over the 1970--2015 period. We found that fewer and larger cities thrived at the national scale, suggesting an eventual mono-centric economy with a single megacity; simultaneously, each larger city flattened out at the local scale, suggesting an eventual extinction of cities. We interpret this multi-scale phenomenon as an instance of pattern formation by self-organization, which is widely studied in mathematics and biology. However, cities' dynamics are distinct from mathematical or biological mechanisms because they are governed by economic interactions mediated by transport costs between locations. Our results call for the synthesis of knowledge in mathematics, biology, and economics to open the door for a general pattern formation theory that is applicable to socioeconomic phenomena.
Enhanced species coexistence in Lotka-Volterra competition models due to nonlocal interactions
Authors: Gabriel Andreguetto Maciel, Ricardo Martinez-Garcia
Date: 2020-12-11 00:00:00
Tasks: Diversity

We introduce and analyze a spatial Lotka-Volterra competition model with local and nonlocal interactions. We study two alternative classes of nonlocal competition that differ in how each species' characteristics determine the range of the nonlocal interactions. In both cases, nonlocal interactions can create spatial patterns of population densities in which highly populated clumps alternate with unpopulated regions. This non-populated regions provide spatial niches for a weaker competitor to establish in the community and persist in conditions in which local models predict competitive exclusion. Moreover, depending on the balance between local and nonlocal competition intensity, the clumps of the weaker competitor vary from M-like structures with higher densities of individuals accumulating at the edges of each clump to triangular structures with most individuals occupying their centers. These results suggest that long-range competition, through the creation of spatial patterns in population densities, might be an important driving force behind the rich diversity of species observed in real ecological communities.
Action potential propagation and block in a model of atrial tissue with myocyte-fibroblast coupling
Authors: Peter Mortensen, Hao Gao, Godfrey Smith, Radostin D. Simitev
Date: 2020-12-09 00:00:00

The electrical coupling between myocytes and fibroblasts and the spacial distribution of fibroblasts within myocardial tissues are significant factors in triggering and sustaining cardiac arrhythmias but their roles are poorly understood. This article describes both direct numerical simulations and an asymptotic theory of propagation and block of electrical excitation in a model of atrial tissue with myocyte-fibroblast coupling. In particular, three idealised fibroblast distributions are introduced: uniform distribution, fibroblast barrier and myocyte strait, all believed to be constituent blocks of realistic fibroblast distributions. Primary action potential biomarkers including conduction velocity, peak potential and triangulation index are estimated from direct simulations in all cases. Propagation block is found to occur at certain critical values of the parameters defining each idealised fibroblast distribution and these critical values are accurately determined. An asymptotic theory proposed earlier is extended and applied to the case of a uniform fibroblast distribution. Biomarker values are obtained from hybrid analytical-numerical solutions of coupled fast-time and slow-time periodic boundary value problems and compare well to direct numerical simulations. The boundary of absolute refractoriness is determined solely by the fast-time problem and is found to depend on the values of the myocyte potential and on the slow inactivation variable of the sodium current ahead of the propagating pulse. In turn, these quantities are estimated from the slow-time problem using a regular perturbation expansion to find the steady state of the coupled myocyte-fibroblast kinetics. The asymptotic theory gives a simple analytical expression that captures with remarkable accuracy the block of propagation in the presence of fibroblasts.
Multi-Array Electron Beam Stabilization using Block-Circulant Transformation and Generalized Singular Value Decomposition
Authors: Idris Kempf, Stephen R. Duncan, Paul J. Goulart, Guenther Rehm
Date: 2020-09-01 00:00:00

We introduce a novel structured controller design for the electron beam stabilization problem of the UK's national synchrotron light source. Because changes to the synchrotron will not allow the application of existing control approaches, we develop a novel method to diagonalize the multi-input multi-output (MIMO) system. A generalized singular value decomposition (GSVD) is used to simultaneously diagonalize the actuator response matrices, which is applicable to an arbitrary number of actuator dynamics in a cross-directional setting. The resulting decoupled systems are regulated using mid-ranged control and the controller gains derived as a function of the generalized singular values. In addition, we exploit the inherent block-circulant symmetry of the system. The performance of our controller is demonstrated using simulations that involve machine data.
Proof that the Kalman gain minimizes the generalized variance
Authors: Eviatar Bach
Date: 2021-03-11 00:00:00

The optimal gain matrix of the Kalman filter is often derived by minimizing the trace of the posterior covariance matrix. Here, I show that the Kalman gain also minimizes the determinant of the covariance matrix, a quantity known as the generalized variance. When the error distributions are Gaussian, the differential entropy is also minimized.
Full reconstruction of acoustic wavefields by means of pointwise measurements
Authors: Denis V. Makarov, Pavel S. Petrov
Date: 2021-03-10 00:00:00

Sound propagation in the ocean is considered. We demonstrate a novel algorithm for full wavefield reconstruction using pointwise measurements by means of a vertical array. The algorithm is based on the so-called discrete variable representation and can be implemented both for tonal and pulse signals. It is shown that the algorithm is robust against array distortions and ambient noise of moderate amplitude. Efficiency of reconstruction is verified by means of numerical simulation with a model of a shallow-sea waveguide. It is found that the effect of bottom sound attenuation enables accurate reconstruction with arrays having relatively low density of hydrophones.
STAR-RISs: Simultaneous Transmitting and Reflecting Reconfigurable Intelligent Surfaces
Authors: Jiaqi Xu, Yuanwei Liu, Xidong Mu, Octavia A. Dobre
Date: 2021-01-24 00:00:00
Tasks: Diversity

In this letter, simultaneous transmitting and reflecting reconfigurable intelligent surfaces (STAR-RISs) are studied. Compared with the conventional reflecting-only RISs, the coverage of STAR-RISs is extended to 360 degrees via simultaneous transmission and reflection. A general hardware model for STAR-RISs is presented. Then, channel models are proposed for the near-field and the far-field scenarios, base on which the diversity gain of the STAR-RISs is analyzed and compared with that of the conventional RISs. Numerical simulations are provided to verify analytical results and to demonstrate that full diversity order can be achieved on both sides of the STAR-RIS.
Sustainable improvement of seeds vigor using dry atmospheric plasma priming: evidence through coating wettability, water uptake and plasma reactive chemistry
Authors: T. Dufour, Q. Gutierrez, C. Bailly
Date: 2021-03-05 00:00:00

Lentil seeds have been packed in a dielectric barrier device and exposed for several minutes to a cold atmospheric plasma generated in helium with/without a reactive gas (nitrogen or oxygen). While no impact is evidenced on germination rates (caping nearly at 100% with/without plasma exposure), seeds vigor is clearly improved with a median germination time decreasing from 1850 min (31h) to 1500 min (26 h), hence representing a time saving of at least 5 hours. We show that the admixture of nitrogen to helium can further increase this time saving up to 8 hours. Contrarily, we demonstrate that the addition of molecular oxygen to the helium discharge does not promote seeds vigor. Whatever the plasma chemistry utilized, these biological effects are accompanied with strong hydrophilization of the seed coating (with a decrease in contact angles from 118{\deg} to 25{\deg}) as well as increased water absorption (water uptakes measured 8 hours after imbibition are close to 50% for plasma-treated seeds instead of 37% for seeds from the control group). A follow-up of the seeds over a 45-days ageing period shows the sustainability of the plasma-triggered biological effects: whatever the plasma treatment, seeds vigor remains stable and much higher than for seeds unexposed to plasma). For these reasons, the seed-packed dielectric barrier device (SP-DBD) supplied with a He-N2 gas mixture can be considered as a relevant dry atmospheric priming plasma (DAPP) in the same way as those used in routine by seed companies.
Ultrasound Matrix Imaging-Part II: The distortion matrix for aberration correction over multiple isoplanatic patches
Authors: William Lambert, Laura A. Cobus, Justine Robin, Mathias Fink, Alexandre Aubry
Date: 2021-03-02 00:00:00

This is the second article in a series of two which report on a matrix approach for ultrasound imaging in heterogeneous media. This article describes the quantification and correction of aberration, i.e. the distortion of an image caused by spatial variations in the medium speed-of-sound. Adaptive focusing can compensate for aberration, but is only effective over a restricted area called the isoplanatic patch. Here, we use an experimentally-recorded matrix of reflected acoustic signals tosynthesize a set of virtual transducers. We then examine wave propagation between these virtual transducers and an arbitrary correction plane. Such wave-fronts consist of two components: (i) An ideal geometric wave-front linked to diffraction and the input focusing point, and; (ii) Phase distortions induced by the speed-of-sound variations. These distortions are stored in a so-called distortion matrix, the singular value decomposition of which gives access to an optimized focusing law at any point. We show that, by decoupling the aberrations undergone by the outgoing and incoming waves and applying an iterative strategy, compensation for even high-order and spatially-distributed aberrations can be achieved. After a numerical validation of the process, ultrasound matrix imaging (UMI) is applied to the in-vivo imaging of a gallbladder. A map of isoplanatic modes is retrieved and is shown to be strongly correlated with the arrangement of tissues constituting the medium. The corresponding focusing laws yield an ultrasound image with drastically improved contrast and transverse resolution. UMI thus provides a flexible and powerful route towards computational ultrasound.
Transcription-translation machinery -- an autocatalytic network coupling all cellular cycles and generating a plethora of growth laws
Authors: Anjan Roy, Dotan Goberman, Rami Pugatch
Date: 2021-03-29 00:00:00
Tasks: All, Translation

Recently discovered simple quantitative relations, known as bacterial growth laws, hint on the existence of simple underlying principles at the heart of bacterial growth. In this work, we provide a unifying picture on how these known relations, as well as new relations that we derive, stems from a universal autocatalytic network common to all bacteria, facilitating balanced exponential growth of individual cells. We show that the core of the cellular autocatalytic network is the transcription -- translation machinery -- in itself an autocatalytic network comprising several coupled autocatalytic cycles, including the ribosome, RNA polymerase, and tRNA charging cycles. We derive two types of growth laws per autocatalytic cycle, one relating growth rate to the relative fraction of the catalyst and its catalysis rate, and the other relating growth rate to all the time scales in the cycle. The structure of the autocatalytic network generates numerous regimes in state space, determined by the limiting components, while the number of growth laws can be much smaller. We also derive a growth law that accounts for the RNA polymerase autocatalytic cycle, which we use to explain how growth rate depends on the inducible expression of the rpoB and rpoC genes, which code for the RpoB and C protein subunits of RNA polymerase, and how the concentration of rifampicin, which targets RNA polymerase, affects growth rate without changing the RNA-to-protein ratio. We derive growth laws for tRNA synthesis and charging, and predict how growth rate depends on temperature, perturbation to ribosome assembly, and membrane synthesis.
Theta, alpha and gamma traveling waves in a multi-item working memory model
Authors: Gustavo Soroka, Marco Idiart
Date: 2021-03-29 00:00:00
Tasks: Blocking

Brain oscillations are believed to be involved in the different operations necessary to manipulate information during working memory tasks. We propose a modular variant of the Lisman-Idiart model for short-term memory, where theta, alpha and gamma oscillations are traveling waves. Using this model we show that the interactions between theta and gamma determine the allocation of multiple information in distinct modules, while the interference between theta and alpha disrupts the maintenance of current stored information. The effect of alpha in erasing or blocking storage is robust and seems fairly independent of the frequency, as long as it stays within the alpha range. The model help us to understand why the alpha and theta oscillations, which have close frequency bands, could have opposite roles in working memory.
Unifying deterministic and stochastic ecological dynamics via a landscape-flux approach
Authors: Li Xu, Denis Patterson, Ann Carla Staver, Simon Asher Levin, Jin Wang
Date: 2021-03-15 00:00:00

We develop a landscape-flux framework to investigate observed frequency distributions of vegetation and the stability of these ecological systems under fluctuations. The frequency distributions can characterize the population-potential landscape related to the stability of ecological states. We illustrate the practical utility of this approach by analyzing a forest-savanna model. Savanna, and Forest states coexist under certain conditions, consistent with past theoretical work and empirical observations. However, a new Grassland state, unseen in the corresponding deterministic model, emerges as an alternative quasi-stable state under fluctuations, providing a novel theoretical basis for the appearance of widespread grasslands in some empirical analyses. The ecological dynamics are determined by both the population-potential landscape gradient and the steady-state probability flux. The flux quantifies the net input/output to the ecological system and therefore the degree of nonequilibriumness. Landscape and flux together determine the transitions between stable states characterized by dominant paths and switching rates. The intrinsic potential landscape admits a Lyapunov function, which provides a quantitative measure of global stability. We find that the average flux, entropy production rate, and free energy have significant changes near bifurcations under both finite and zero fluctuation. These may provide both dynamical and thermodynamic origins of the bifurcations. We identified the variances in observed frequency time traces, fluctuations and time irreversibility as kinematic measures for bifurcations. This new framework opens the way to characterize ecological systems globally, to uncover how they change among states, and to quantify the emergence of new quasi-stable states under stochastic fluctuations.
Dynamic sampling bias and overdispersion induced by skewed offspring distributions
Authors: Takashi Okada, Oskar Hallatschek
Date: 2021-03-10 00:00:00

Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions, leading to so-called `jackpot' events. The resulting allele frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the dynamics forward in time, especially with selection. Here, we employ an exact asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law $~n^{-(1+\alpha)}$. To demonstrate that this coarse-grained model captures a wide variety of non-equilibrium dynamics, we validate our results in traveling waves, where the phenomenon of 'gene surfing' can produce any exponent $1<\alpha <2$. We argue that the concept of a dynamic sampling bias is useful generally to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history.
Mesoporous bioactive glass/e-polycaprolactone scaffolds promote bone regeneration in osteoporotic sheep
Authors: N. Gomez-Cerezo, L. Casarrubios, M. Saiz-Pardo, L. Ortega, D. de Pablo, I. Diaz-Guemes, B. Fernandez-Tome, S. Enciso, F. M. Sanchez-Margallo, M. T. Portoles, D. Arcos, M. Vallet-Regi
Date: 2021-03-24 00:00:00

Macroporous scaffolds made of a SiO2-CaO-P2O5 mesoporous bioactive glass (MBG) and epolycaprolactone (PCL) have been prepared by robocasting. These scaffolds showed an excellent in vitro biocompatibility in contact with osteoblast like cells (Saos 2) and osteoclasts derived from RAW 264.7 macrophages. In vivo studies were carried out by implantation into cavitary defects drilled in osteoporotic sheep. The scaffolds evidenced excellent bone regeneration properties, promoting new bone formation at both the peripheral and the inner parts of the scaffolds, thick trabeculae, high vascularization and high presence of osteoblasts and osteoclasts. In order to evaluate the effects of the local release of an antiosteoporotic drug, 1% (%wt) of zoledronic acid was incorporated to the scaffolds. The scaffolds loaded with zoledronic acid induced apoptosis in Saos 2 cells, impeded osteoclast differentiation in a time dependent manner and inhibited bone healing, promoting an intense inflammatory response in osteoporotic sheep.