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| Open AccessA genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity
Local activity of the DNA methylation machinery remains poorly understood. Here, the authors present a theoretical and experimental framework to infer methylation and demethylation rates at genome scale in mouse embryonic stem cells, finding that maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies.
- Paul Adrian Ginno
- , Dimos Gaidatzis
- & Dirk Schübeler
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| Open AccessNatural rhythms of periodic temporal attention
That attention is a rhythmic process has received abundant evidence. Here, the authors reveal the natural sampling rate of auditory and visual periodic temporal attention. Both are antagonistically modulated by overt motor activity, a result generalised in a dynamical model of coupled oscillators.
- Arnaud Zalta
- , Spase Petkoski
- & Benjamin Morillon
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| Open AccessIn vitro implementation of robust gene regulation in a synthetic biomolecular integral controller
Feedback mechanisms for synthetic gene circuits are necessary to provide robustness to external perturbations. Here the authors validate a biomolecular controller based on a sigma and anti-sigma factor to achieve stable gene expression in the face of external disturbances in an in vitro synthetic gene circuit.
- Deepak K. Agrawal
- , Ryan Marshall
- & Eduardo D Sontag
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Article
| Open AccessEmergence of collective oscillations in adaptive cells
There are many examples of cell populations exhibiting density-dependent collective oscillatory behaviour. Here, the authors show that sustained collective oscillations emerge when cells anticipate variation in signal and attempt to amplify it, a property that can be linked to adaptation.
- Shou-Wen Wang
- & Lei-Han Tang
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Article
| Open AccessSenescent cell turnover slows with age providing an explanation for the Gompertz law
One of the underlying causes of aging is the accumulation of senescent cells, but their turnover rates and dynamics during ageing are unknown. Here the authors measure and model senescent cell production and removal and explore implications for mortality.
- Omer Karin
- , Amit Agrawal
- & Uri Alon
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| Open AccessInferring and validating mechanistic models of neural microcircuits based on spike-train data
It is difficult to fit mechanistic, biophysically constrained circuit models to spike train data from in vivo extracellular recordings. Here the authors present analytical methods that enable efficient parameter estimation for integrate-and-fire circuit models and inference of the underlying connectivity structure in subsampled networks.
- Josef Ladenbauer
- , Sam McKenzie
- & Srdjan Ostojic
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Article
| Open AccessStable memory with unstable synapses
How are stable memories maintained in the brain despite significant ongoing fluctuations in synaptic strengths? Here, the authors show that a model consistent with fluctuations, homeostasis and biologically plausible learning rules, naturally leads to memories implemented as dynamic attractors.
- Lee Susman
- , Naama Brenner
- & Omri Barak
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| Open AccessPropagation of temporal and rate signals in cultured multilayer networks
The nature of the signals that propagate through feedforward networks is not well understood. Here, the authors combine microfabrication, multilayer cortical cultures, and optogenetic stimulation to show that NMDA-mediated synaptic current generates a sustained phase of activity that propagates firing rate signals.
- Jérémie Barral
- , Xiao-Jing Wang
- & Alex D. Reyes
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| Open AccessParallels in the sequential organization of birdsong and human speech
By examining the organization of bird song and human speech, the authors show that the two types of communication signals have similar sequential structures, following both hierarchical and Markovian organization.
- Tim Sainburg
- , Brad Theilman
- & Timothy Q. Gentner
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Article
| Open AccessError-correcting dynamics in visual working memory
Neural representations in working memory are susceptible to internal noise, which scales with memory load. Here, the authors show that attractor dynamics mitigate the influence of internal noise by pulling memories towards a few stable representations.
- Matthew F. Panichello
- , Brian DePasquale
- & Timothy J. Buschman
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| Open AccessSimultaneous motor preparation and execution in a last-moment reach correction task
Motor preparation processes guide movement. Here, by recording neural activity in monkeys reaching toward targets that can change location, the authors provide evidence that changing a prepared movement midway through completion reengages motor preparation.
- K. Cora Ames
- , Stephen I. Ryu
- & Krishna V. Shenoy
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| Open AccessNREM sleep in the rodent neocortex and hippocampus reflects excitable dynamics
NREM sleep in rodents is characterized by internal dynamics in the form of UP/DOWN states in the neocortex and SWRs in the hippocampus. Here, the authors report that a mean field model with excitable dynamics captures the transition probabilities between these states from rodent sleep data.
- Daniel Levenstein
- , György Buzsáki
- & John Rinzel
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Article
| Open AccessA neural circuit model of decision uncertainty and change-of-mind
We make decisions with varying degrees of confidence and, if our confidence in a decision falls, we may change our mind. Here, the authors present a neuronal circuit model to account for how change of mind occurs under particular low-confidence conditions.
- Nadim A. A. Atiya
- , Iñaki Rañó
- & KongFatt Wong-Lin
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Article
| Open AccessKingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida
The diurnal cycle exerts influences on various aspects of plant biology. Here, the authors generate and compare diurnal transcriptomics data from nine members of Archaeplastida representing major clades.
- Camilla Ferrari
- , Sebastian Proost
- & Marek Mutwil
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| Open AccessBrain songs framework used for discovering the relevant timescale of the human brain
An unresolved problem in neuroscience is to determine the relevant timescale for understanding spatiotemporal dynamics of the brain. Here, the authors introduce a new framework to study the different timescales through binning the output of a generative model of neural activity.
- Gustavo Deco
- , Josephine Cruzat
- & Morten L. Kringelbach
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| Open AccessAn orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability
To explain the neural correlates of behavior and its variability, one must analyze single-trial population dynamics. Here, the authors develop a statistical method that extracts low-dimensional dynamics that explain behavior better than high-dimensional neural activity revealing unexpected structure.
- Ziqiang Wei
- , Hidehiko Inagaki
- & Shaul Druckmann
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| Open AccessEscherichia coli can survive stress by noisy growth modulation
Noisy gene expression leading to phenotypic variability can help organisms to survive in changing environments. Here, Patange et al. show that noisy expression of a stress response regulator, RpoS, allows E. coli cells to modulate their growth rates to survive future adverse environments.
- Om Patange
- , Christian Schwall
- & James C. W. Locke
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Article
| Open AccessCausal decomposition in the mutual causation system
Causality inference in time series analysis based on temporal precedence principle between cause and effect fails to detect mutual causal interactions. Here, Yang et al. introduce a causal decomposition approach based on the covariation principle of cause and effect that overcomes this limitation.
- Albert C. Yang
- , Chung-Kang Peng
- & Norden E. Huang
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Article
| Open AccessSpontaneous cortical activity transiently organises into frequency specific phase-coupling networks
Coordination of neural activity between distant brain areas is necessary for cognition. Here, the authors report using MEG that various brain networks show dynamic phase coupling through specific frequency bands in the alpha and delta/theta range transiently during the resting state.
- Diego Vidaurre
- , Laurence T. Hunt
- & Mark W. Woolrich
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| Open AccessUncovering hidden brain state dynamics that regulate performance and decision-making during cognition
Brain activity is driven, in part, by external stimuli and demands, but internal brain states also change over time. Here, the authors use a novel Bayesian algorithm to track dynamic transitions between hidden neural states in human brain activity and to relate brain dynamics with behavior.
- Jalil Taghia
- , Weidong Cai
- & Vinod Menon
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| Open AccessPredicting the spatiotemporal diversity of seizure propagation and termination in human focal epilepsy
A major goal of epilepsy research is understanding the spatiotemporal dynamics of seizure. Here, the authors extend the Epileptor neural mass model into a neural field model, in order to provide a unified and patient-specific model of seizure initiation, propagation, and termination.
- Timothée Proix
- , Viktor K. Jirsa
- & Wilson Truccolo
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| Open AccessSupervised learning in spiking neural networks with FORCE training
FORCE training is a . Here the authors implement FORCE training in models of spiking neuronal networks and demonstrate that these networks can be trained to exhibit different dynamic behaviours.
- Wilten Nicola
- & Claudia Clopath
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| Open AccessFluctuations in instantaneous frequency predict alpha amplitude during visual perception
Though the amplitude and frequency of neural oscillations in the alpha band are related to dissociable visual processes, they are not independent mathematically. Here, the authors show that fluctuations in instantaneous frequency predict alpha amplitude during visual discrimination tasks.
- Stephanie Nelli
- , Sirawaj Itthipuripat
- & John T. Serences
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| Open AccessBalancing a genetic toggle switch by real-time feedback control and periodic forcing
Cybergenetics aims to monitor and regulate cellular processes in real-time using computer monitoring and feedback of biological readouts. Here the authors use a feedback loop and periodic forcing to maintain cells with a bistable synthetic circuit near its unstable state.
- Jean-Baptiste Lugagne
- , Sebastián Sosa Carrillo
- & Pascal Hersen
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| Open AccessSensorimotor computation underlying phototaxis in zebrafish
Active locomotion requires closed-loop sensorimotor co ordination between perception and action. Here the authors show using behavioural, imaging and modelling approaches that gaze orientation during phototaxis behaviour in larval zebrafish is related to oscillatory dynamics of a neuronal population in the hindbrain.
- Sébastien Wolf
- , Alexis M. Dubreuil
- & Georges Debrégeas
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Article
| Open AccessFocal cortical seizures start as standing waves and propagate respecting homotopic connectivity
Focal cortical seizures result from local and widespread propagation of excitatory activity. Here the authors employ widefield calcium imaging in mouse visual areas to demonstrate that these seizures start as local synchronous activation and then propagate along the connectivity that underlies normal sensory processing.
- L. Federico Rossi
- , Robert C. Wykes
- & Matteo Carandini
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| Open AccessCentral insulin modulates food valuation via mesolimbic pathways
The influence of insulin on food preference and the corresponding underlying neural circuits are unknown in humans. Here, the authors show that increasing insulin changes food preference by modulating mesolimbic neural circuits, and that this pattern is changed in insulin-resistant individuals.
- Lena J. Tiedemann
- , Sebastian M. Schmid
- & Stefanie Brassen
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Article
| Open AccessKinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress
Protein RNA interactions are dynamic and regulated in response to environmental changes. Here the authors describe ‘kinetic CRAC’, an approach that allows time resolved analyses of protein RNA interactions with minute time point resolution and apply it to gain insight into the function of the RNA-binding protein Nab3.
- Rob van Nues
- , Gabriele Schweikert
- & Sander Granneman
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| Open AccessDesigning attractive models via automated identification of chaotic and oscillatory dynamical regimes
Modelling of chaos and oscillations is usually done indirectly and quantitatively by fitting models to a finite number of data-points. Here, a qualitative framework is developed where the characteristics of the underlying dynamical system are directly specified, revealing new properties of such systems.
- Daniel Silk
- , Paul D.W. Kirk
- & Michael P.H. Stumpf
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| Open AccessInformation processing using a single dynamical node as complex system
The paradigm of reservoir computing shows that, like the human brain, complex networks can perform efficient information processing. Here, a simple delay dynamical system is demonstrated that can efficiently perform computations capable of replacing a complex network in reservoir computing.
- L. Appeltant
- , M.C. Soriano
- & I. Fischer