Analytic relationship of relative synchronizability to network structure and motifs.

Synchronization phenomena on networks have attracted much attention in studies of neural, social, economic, and biological systems, yet we still lack a systematic understanding of how relative synchronizability relates to underlying network structure. Indeed, this question is of central importance to the key theme of how dynamics on networks relate to their structure more generally. We present an analytic technique to directly measure the relative synchronizability of noise-driven time-series processes on networks, in terms of the directed network structure.

RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions.

The differentiation of regions with coding potential from non-coding regions remains a key task in computational biology. Methods such as RNAcode that exploit patterns of sequence conservation for this task have a substantial advantage in classification accuracy in particular for short coding sequences, compared to methods that rely on a single input sequence. However, they require sequence alignments as input.

Stable cooperation emerges in stochastic multiplicative growth.

Understanding the evolutionary stability of cooperation is a central problem in biology, sociology, and economics. There exist only a few known mechanisms that guarantee the existence of cooperation and its robustness to cheating. Here, we introduce a mechanism for the emergence of cooperation in the presence of fluctuations.

Clustering systems of phylogenetic networks.

Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set X of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization that cannot be captured by trees. A variety of classes of such networks have been discussed in the literature, including phylogenetic, level-1, tree-child, tree-based, galled tree, regular, or normal networks as models of different types of evolutionary processes. Clusters arise in models of phylogeny as the sets [Formula: see text] of descendant taxa of a vertex v.

Battery Capacity of Energy-Storing Quantum Systems.

The quantum battery capacity is introduced in this Letter as a figure of merit that expresses the potential of a quantum system to store and supply energy. It is defined as the difference between the highest and the lowest energy that can be reached by means of the unitary evolution of the system. This function is closely connected to the ergotropy, but it does not depend on the temporary level of energy of the system.

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.

Background: RNA features a highly negatively charged phosphate backbone that attracts a cloud of counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a large influence on folding and stability of RNA structures. Despite their well-documented effects, salt effects are not handled consistently by currently available secondary structure prediction algorithms.

Modelling Spirals of Silence and Echo Chambers by Learning from the Feedback of Others.

What are the mechanisms by which groups with certain opinions gain public voice and force others holding a different view into silence? Furthermore, how does social media play into this? Drawing on neuroscientific insights into the processing of social feedback, we develop a theoretical model that allows us to address these questions. In repeated interactions, individuals learn whether their opinion meets public approval and refrain from expressing their standpoint if it is socially sanctioned. In a social network sorted around opinions, an agent forms a distorted impression of public opinion enforced by the communicative activity of the different camps.

Order-disorder transition in the zero-temperature Ising model on random graphs.

The zero-temperature Ising model is known to reach a fully ordered ground state in sufficiently dense random graphs. In sparse random graphs, the dynamics gets absorbed in disordered local minima at magnetization close to zero. Here, we find that the nonequilibrium transition between the ordered and the disordered regime occurs at an average degree that slowly grows with the graph size.

Discrete Ricci curvatures capture age-related changes in human brain functional connectivity networks.

Introduction: Geometry-inspired notions of discrete Ricci curvature have been successfully used as markers of disrupted brain connectivity in neuropsychiatric disorders, but their ability to characterize age-related changes in functional connectivity is unexplored.

Methods: We apply Forman-Ricci curvature and Ollivier-Ricci curvature to compare functional connectivity networks of healthy young and older subjects from the Max Planck Institute Leipzig Study for Mind-Body-Emotion Interactions (MPI-LEMON) dataset ( = 225).

Results: We found that both Forman-Ricci curvature and Ollivier-Ricci curvature can capture whole-brain and region-level age-related differences in functional connectivity.

Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.

Background: Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes. Given the exact locations of their genes, the breakpoints can be computed without much effort. However, often, existing gene annotations are erroneous, or only nucleotide sequences are available.

The Uncertain Role of Nominations for the Nobel Prize in Chemistry.

The solicitation of nominations for the Nobel Prizes in Chemistry (NPch) is and has been the first step in the selection process since the very first awards were made in 1901. The number of nominations solicited by and provided to the Nobel Committee for Chemistry supports the belief by the nominators that their nominations are meaningful. In this publication, we examine data culled from the Nobel Prize Nomination Archives for the period 1901-1970 of the variable role of nominations in the selection process for the Nobel Prize in Chemistry.

The six stages of the convergence of the periodic system to its final structure.

The periodic system encodes order and similarity among chemical elements arising from known substances at a given time that constitute the chemical space. Although the system has incorporated new elements, the connection with the remaining space is still to be analysed, which leads to the question of how the exponentially growing space has affected the periodic system. Here we show, by analysing the space between 1800 and 2021, that the system has converged towards its current stable structure through six stages, respectively characterised by the finding of elements (1800-1826), the emergence of the core structure of the system (1826-1860), its organic chemistry bias (1860-1900) and its further stabilisation (1900-1948), World War 2 new chemistry (1948-1980) and the system final stabilisation (1980-).

Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.

Structural analysis of RNA is an important and versatile tool to investigate the function of this type of molecules in the cell as well as in vitro. Several robust and reliable procedures are available, relying on chemical modification inducing RT stops or nucleotide misincorporations during reverse transcription. Others are based on cleavage reactions and RT stop signals.

Quick Estimate of Information Decomposition for Text Style Transfer.

A growing number of papers on style transfer for texts rely on information decomposition. The performance of the resulting systems is usually assessed empirically in terms of the output quality or requires laborious experiments. This paper suggests a straightforward information theoretical framework to assess the quality of information decomposition for latent representations in the context of style transfer.

Identifying Risk Factors for Blindness From Glaucoma at First Presentation to a Tertiary Clinic.

Purpose: Glaucoma is the leading cause of irreversible blindness, a crippling disability resulting in higher risks of chronic health conditions. To better understand disparities in blindness risk, we identified risk factors of blindness on first presentation to a glaucoma clinic using a large clinical database.

Design: Retrospective cross-sectional study.

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing.

The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring combinations of eight genomic segments from distinct parental viruses. Existing data indicate that reassortant genotypes are not equiprobable; however, the low throughput of available virology techniques does not allow quantitative analysis. Here, we have developed a high-throughput single-cell droplet microfluidic system allowing encapsulation of IAV-infected cells, each cell being infected by a single progeny virion resulting from a coinfection process.

Diversity enables the jump towards cooperation for the Traveler's Dilemma.

Social dilemmas are situations in which collective welfare is at odds with individual gain. One widely studied example, due to the conflict it poses between human behaviour and game theoretic reasoning, is the Traveler's Dilemma. The dilemma relies on the players' incentive to undercut their opponent at the expense of losing a collective high payoff.

Dynamics of Quantum Networks in Noisy Environments.

Noise exists inherently in realistic quantum systems and affects the evolution of quantum systems. We investigate the dynamics of quantum networks in noisy environments by using the fidelity of the quantum evolved states and the classical percolation theory. We propose an analytical framework that allows us to characterize the stability of quantum networks in terms of quantum noises and network topologies.

Unveiling Charge-Transport Mechanisms in Electronic Devices Based on Defect-Engineered MoS Covalent Networks.

Device performance of solution-processed 2D semiconductors in printed electronics has been limited so far by structural defects and high interflake junction resistance. Covalently interconnected networks of transition metal dichalcogenides potentially represent an efficient strategy to overcome both limitations simultaneously. Yet, the charge-transport properties in such systems have not been systematically researched.

Opinion manipulation on Farsi Twitter.

For Iranians and the Iranian diaspora, the Farsi Twittersphere provides an important alternative to state media and an outlet for political discourse. But this understudied online space has become an opinion manipulation battleground, with diverse actors using inauthentic accounts to advance their goals and shape online narratives. Examining trending discussions crossing social cleavages in Iran, we explore how the dynamics of opinion manipulation differ across diverse issue areas.

A combinatorial view of stochastic processes: White noise.

White noise is a fundamental and fairly well understood stochastic process that conforms to the conceptual basis for many other processes, as well as for the modeling of time series. Here, we push a fresh perspective toward white noise that, grounded on combinatorial considerations, contributes to giving new interesting insights both for modeling and theoretical purposes. To this aim, we incorporate the ordinal pattern analysis approach, which allows us to abstract a time series as a sequence of patterns and their associated permutations, and introduce a simple functional over permutations that partitions them into classes encoding their level of asymmetry.

Signal propagation and linear response in the delay Vicsek model.

Retardation between sensation and action is an inherent biological trait. Here we study its effect in the Vicsek model, which is a paradigmatic swarm model. We find that (1) a discrete time delay in the orientational interactions diminishes the ability of strongly aligned swarms to follow a leader and, in return, increases their stability against random orientation fluctuations; (2) both longer delays and higher speeds favor ballistic over diffusive spreading of information (orientation) through the swarm; (3) for short delays, the mean change in the total orientation (the order parameter) scales linearly in a small orientational bias of the leaders and inversely in the delay time, while its variance first increases and then saturates with increasing delays; and (4) the linear response breaks down when orientation conservation is broken.

Moderate-density parity-check codes from projective bundles.

New constructions for moderate-density parity-check (MDPC) codes using finite geometry are proposed. We design a parity-check matrix for the main family of binary codes as the concatenation of two matrices: the incidence matrix between points and lines of the Desarguesian projective plane and the incidence matrix between points and ovals of a projective bundle. A projective bundle is a special collection of ovals which pairwise meet in a unique point.

The effects of social feedback on private opinions. Empirical evidence from the laboratory.

The question of how people change their opinions through social interactions has been on the agenda of social scientific research for many decades. Now that the Internet has led to an ever greater interconnectedness and new forms of exchange that seem to go hand in hand with increasing political polarization, it is once again gaining in relevance. Most recently, the field of opinion dynamics has been complemented by social feedback theory, which explains opinion polarization phenomena by means of a reinforcement learning mechanism.