Ingredients for robustness.

A core property of robust systems is given by the invariance of their function against the removal of some of their structural components. This intuition has been formalised in the context of input-output maps, thereby introducing the notion of exclusion independence. We review work on how this formalisation allows us to derive characterisation theorems that provide a basis for the design of robust systems.

Inter-Eye Association of Visual Field Defects in Glaucoma and Its Clinical Utility.

Purpose: To investigate intereye associations of visual field (VF) defects.

Methods: We selected 24-2 VF pairs of both eyes from 63,604 patients tested on the same date with mean deviation (MD) ≥ -12 dB. VFs were decomposed into one normal and 15 defect patterns previously identified using archetypal analysis.

Are spliced ncRNA host genes distinct classes of lncRNAs?

Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload.

Edge-based analysis of networks: curvatures of graphs and hypergraphs.

The relations, rather than the elements, constitute the structure of networks. We therefore develop a systematic approach to the analysis of networks, modelled as graphs or hypergraphs, that is based on structural properties of (hyper)edges, instead of vertices. For that purpose, we utilize so-called network curvatures.

Dynamics of opinion expression.

Modeling efforts in opinion dynamics have to a large extent ignored that opinion exchange between individuals can also have an effect on how willing they are to express their opinion publicly. Here, we introduce a model of public opinion expression. Two groups of agents with different opinion on an issue interact with each other, changing the willingness to express their opinion according to whether they perceive themselves as part of the majority or minority opinion.

Coevolution of cooperation and language.

As a cooperative act decreases an individual's fitness for others to benefit, it is expected to be selected against by natural selection. That, how contrary to this naive expectation cooperation has evolved, is a fundamental problem in evolutionary biology and social sciences. Here, by introducing a mathematical model, we show that coevolution of cooperation and language can provide an avenue through which both cooperation and language evolve.

Biological information.

In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology. Nevertheless, I argue that Shannon's concept of information is useful in biology, although its application is not as straightforward as many people think.

DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial.

Background: One of the major challenges in obesity treatment is to explain the high variability in the individual's response to specific dietary and physical activity interventions. With this study, we tested the hypothesis that specific DNA methylation changes reflect individual responsiveness to lifestyle intervention and may serve as epigenetic predictors for a successful weight-loss.

Methods: We conducted an explorative genome-wide DNA methylation analysis in blood samples from 120 subjects (90% men, mean ± SD age = 49 ± 9 years, body mass-index (BMI) = 30.

Proteomics reveals sex-specific heat shock response of Baikal amphipod Eulimnogammarus cyaneus.

The ancient Lake Baikal is the largest source of liquid freshwater on Earth and home to a unique fauna. Several hundred mostly cold-adapted endemic amphipod species inhabit Baikal, an ecosystem that is already being influenced by global change. In this study, we characterized the core proteome and heat stress-induced changes in a temperature-tolerant endemic amphipod, Eulimnogammarus cyaneus, using a proteogenomic approach (PRIDE dataset PXD013237) to unravel the molecular mechanisms of the observed adverse effects.

An Artificial Intelligence Approach to Assess Spatial Patterns of Retinal Nerve Fiber Layer Thickness Maps in Glaucoma.

Purpose: The purpose of this study was to classify the spatial patterns of retinal nerve fiber layer thickness (RNFLT) and assess their associations with visual field (VF) loss in glaucoma.

Methods: We used paired reliable 24-2 VFs and optical coherence tomography scans of 691 eyes from 691 patients. The RNFLT maps were used to determine the RNFLT patterns (RPs) by non-negative matrix factorization (NMF).

Beyond Plug and Pray: Context Sensitivity and Design of Artificial Neomycin Riboswitches.

Gene regulation in prokaryotes often depends on RNA elements such as riboswitches or RNA thermometers located in the 5' untranslated region of mRNA. Rearrangements of the RNA structure in response, e.g.

Tailoring Echo State Networks for Optimal Learning.

As one of the most important paradigms of recurrent neural networks, the echo state network (ESN) has been applied to a wide range of fields, from robotics to medicine, finance, and language processing. A key feature of the ESN paradigm is its reservoir-a directed and weighted network of neurons that projects the input time series into a high-dimensional space where linear regression or classification can be applied. By analyzing the dynamics of the reservoir we show that the ensemble of eigenvalues of the network contributes to the ESN memory capacity.

Ollivier Ricci curvature of directed hypergraphs.

Many empirical networks incorporate higher order relations between elements and therefore are naturally modelled as, possibly directed and/or weighted, hypergraphs, rather than merely as graphs. In order to develop a systematic tool for the statistical analysis of such hypergraph, we propose a general definition of Ricci curvature on directed hypergraphs and explore the consequences of that definition. The definition generalizes Ollivier's definition for graphs.

Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in .

, the model organism for the evolutionary supergroup of Amoebozoa, is a social amoeba that, upon starvation, undergoes transition from a unicellular to a multicellular organism. In its genome, we identified two genes encoding for tRNA nucleotidyltransferases. Such pairs of tRNA nucleotidyltransferases usually represent collaborating partial activities catalyzing CC- and A-addition to the tRNA 3'-end, respectively.

Coupled dynamics on hypergraphs: Master stability of steady states and synchronization.

In the study of dynamical systems on networks or graphs, a key theme is how the network topology influences stability for steady states or synchronized states. Ideally, one would like to derive conditions for stability or instability that, instead of microscopic details of the individual nodes or vertices, rather make the influence of the network coupling topology visible. The master stability function is an important such tool to achieve this goal.

Event-Based Computation for Touch Localization Based on Precise Spike Timing.

Precise spike timing and temporal coding are used extensively within the nervous system of insects and in the sensory periphery of higher order animals. However, conventional Artificial Neural Networks (ANNs) and machine learning algorithms cannot take advantage of this coding strategy, due to their rate-based representation of signals. Even in the case of artificial Spiking Neural Networks (SNNs), identifying applications where temporal coding outperforms the rate coding strategies of ANNs is still an open challenge.

Caring for the future can turn tragedy into comedy for long-term collective action under risk of collapse.

We will need collective action to avoid catastrophic climate change, and this will require valuing the long term as well as the short term. Shortsightedness and uncertainty have hindered progress in resolving this collective action problem and have been recognized as important barriers to cooperation among humans. Here, we propose a coupled social-ecological dilemma to investigate the interdependence of three well-identified components of this cooperation problem: 1) timescales of collapse and recovery in relation to time preferences regarding future outcomes, 2) the magnitude of the impact of collapse, and 3) the number of actors in the collective.

Deriving pairwise transfer entropy from network structure and motifs.

Transfer entropy (TE) is an established method for quantifying directed statistical dependencies in neuroimaging and complex systems datasets. The pairwise (or bivariate) TE from a source to a target node in a network does not depend solely on the local source-target link weight, but on the wider network structure that the link is embedded in. This relationship is studied using a discrete-time linearly coupled Gaussian model, which allows us to derive the TE for each link from the network topology.

A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution.

Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al.

Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity.

Subcutaneous (sc) and visceral (vis) adipose tissue (AT) contribute to the variability in pathophysiological consequences of obesity and adverse fat distribution. To gain insights into the molecular mechanisms distinguishing vis and sc fat, we compared the transcriptome during differentiation of immortalized adipocytes from murine epididymal (epi) and inguinal (ing) AT. RNA was extracted on different days of adipogenesis (-2, 0, 2, 4, 6, 8) and analyzed using Clariom™ D mouse assays (Affymetrix) covering >214,900 transcripts in >66,100 genes.

Adaptive Bet-Hedging Revisited: Considerations of Risk and Time Horizon.

Models of adaptive bet-hedging commonly adopt insights from Kelly's famous work on optimal gambling strategies and the financial value of information. In particular, such models seek evolutionary solutions that maximize long-term average growth rate of lineages, even in the face of highly stochastic growth trajectories. Here, we argue for extensive departures from the standard approach to better account for evolutionary contingencies.

Splicing conservation signals in plant long noncoding RNAs.

Long noncoding RNAs (lncRNAs) have recently emerged as prominent regulators of gene expression in eukaryotes. LncRNAs often drive the modification and maintenance of gene activation or gene silencing states via chromatin conformation rearrangements. In plants, lncRNAs have been shown to participate in gene regulation, and are essential to processes such as vernalization and photomorphogenesis.

Rolf Huisgen, Eminent Chemist and Polymath (1920-2020): In His Own Words and In His Publication Metrics.

As a compliment to several other publications that present and honor Rolf Huisgen's research achievements, the first part of this paper reveals the human side of this eminent chemist. From excerpts from many of his personal and professional writings, Huisgen's personality and philosophies of life are revealed. Also revealed is Huisgen functioning as a historian of chemistry.

The information theory of individuality.

Despite the near universal assumption of individuality in biology, there is little agreement about what individuals are and few rigorous quantitative methods for their identification. Here, we propose that individuals are aggregates that preserve a measure of temporal integrity, i.e.

Alzheimer-related genes show accelerated evolution.

Alzheimer's disease (AD) is a neurodegenerative disorder of unknown cause with complex genetic and environmental traits. While AD is extremely prevalent in human elderly, it hardly occurs in non-primate mammals and even non-human-primates develop only an incomplete form of the disease. This specificity of AD to human clearly implies a phylogenetic aspect.