Conditioning in Tropical Probability Theory.

We define a natural operation of conditioning of tropical diagrams of probability spaces and show that it is Lipschitz continuous with respect to the asymptotic entropy distance.

Arrow Contraction and Expansion in Tropical Diagrams.

Arrow contraction applied to a tropical diagram of probability spaces is a modification of the diagram, replacing one of the morphisms with an isomorphism while preserving other parts of the diagram. It is related to the rate regions introduced by Ahlswede and Körner. In a companion article, we use arrow contraction to derive information about the shape of the entropic cone.

Master regulators of biological systems in higher dimensions.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present, generating higher-order interactions.

MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy.

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination.

Generalized Bayes approach to inverse problems with model misspecification.

We propose a general framework for obtaining probabilistic solutions to PDE-based inverse problems. Bayesian methods are attractive for uncertainty quantification but assume knowledge of the likelihood model or data generation process. This assumption is difficult to justify in many inverse problems, where the specification of the data generation process is not obvious.

Relative timing information and orthology in evolutionary scenarios.

Background: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event.

The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.

Background: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward.

Evolution as a result of resource flow in ecosystems: Ecological dynamics can drive evolution.

To see how the flow of energy across ecosystems can derive evolution, I introduce a framework in which individuals interact with their peers and environment to accumulate resources, and use the resources to pay for their metabolic costs, grow and reproduce. I show that two conservation principles determine the system's equilibrium state: conservation of resources- a physical principle stating that in the equilibrium, resource production and consumption should balance, and payoff equality- an economic principle, stating that the payoffs of different types in equilibrium should equal. Besides the equilibrium state, the system shows non-equilibrium fluctuations derived by the exponential growth of the individuals in which the payoff equality principle does not hold.

The human cell count and size distribution.

Cell size and cell count are adaptively regulated and intimately linked to growth and function. Yet, despite their widespread relevance, the relation between cell size and count has never been formally examined over the whole human body. Here, we compile a comprehensive dataset of cell size and count over all major cell types, with data drawn from >1,500 published sources.

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.