Interaction between games give rise to the evolution of moral norms of cooperation.

In many biological populations, such as human groups, individuals face a complex strategic setting, where they need to make strategic decisions over a diverse set of issues and their behavior in one strategic context can affect their decisions in another. This raises the question of how the interaction between different strategic contexts affects individuals' strategic choices and social norms? To address this question, I introduce a framework where individuals play two games with different structures and decide upon their strategy in a second game based on their knowledge of their opponent's strategy in the first game. I consider both multistage games, where the same opponents play the two games consecutively, and reputation-based model, where individuals play their two games with different opponents but receive information about their opponent's strategy.

Detecting Tripartite Steering via Quantum Entanglement.

Einstein-Podolsky-Rosen steering is a kind of powerful nonlocal quantum resource in quantum information processing such as quantum cryptography and quantum communication. Many criteria have been proposed in the past few years to detect steerability, both analytically and numerically, for bipartite quantum systems. We propose effective criteria for tripartite steerability and genuine tripartite steerability of three-qubit quantum states by establishing connections between the tripartite steerability (resp.

What makes a reaction network "chemical"?

Background: Reaction networks (RNs) comprise a set X of species and a set [Formula: see text] of reactions [Formula: see text], each converting a multiset of educts [Formula: see text] into a multiset [Formula: see text] of products. RNs are equivalent to directed hypergraphs. However, not all RNs necessarily admit a chemical interpretation.

Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes.

Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts.

RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform.

We propose a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz. This heuristic is inspired by the kinetic partitioning mechanism, by which molecules follow alternative folding pathways to their native structure, some much faster than others. Similarly, our algorithm RAFFT starts by generating an ensemble of concurrent folding pathways ending in multiple metastable structures, which is in contrast with traditional thermodynamic approaches that find single structures with minimal free energies.

Consistent predator-prey biomass scaling in complex food webs.

The ratio of predator-to-prey biomass is a key element of trophic structure that is typically investigated from a food chain perspective, ignoring channels of energy transfer (e.g. omnivory) that may govern community structure.

Information conduction and convection in noiseless Vicsek flocks.

Physical interactions generally respect certain symmetries, such as reciprocity and energy conservation, which survive in coarse-grained isothermal descriptions. Active many-body systems usually break such symmetries intrinsically, on the particle level, so that their collective behavior is often more naturally interpreted as a result of information exchange. Here we study numerically how information spreads from a "leader" particle through an initially aligned flock, described by the Vicsek model without noise.

aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights.

Background: We study in this work the inverse folding problem for RNA, which is the discovery of sequences that fold into given target secondary structures.

Results: We implement a Lévy mutation scheme in an updated version of aRNAque an evolutionary inverse folding algorithm and apply it to the design of RNAs with and without pseudoknots. We find that the Lévy mutation scheme increases the diversity of designed RNA sequences and reduces the average number of evaluations of the evolutionary algorithm.

Diffusion approximations in population genetics and the rate of Muller's ratchet.

The Wright-Fisher binomial model of allele frequency change is often approximated by a scaling limit in which selection, mutation and drift all decrease at the same 1/N rate. This construction restricts the applicability of the resulting 'Wright-Fisher diffusion equation' to the weak selection, weak mutation regime of evolution. We argue that diffusion approximations of the Wright-Fisher model can be used more generally, for instance in cases where genetic drift is much weaker than selection.

The expansion of chemical space in 1826 and in the 1840s prompted the convergence to the periodic system.

The periodic system, which intertwines order and similarity among chemical elements, arose from knowledge about substances constituting the chemical space. Little is known, however, about how the expansion of the space contributed to the emergence of the system-formulated in the 1860s. Here, we show by analyzing the space between 1800 and 1869 that after an unstable period culminating around 1826, chemical space led the system to converge to a backbone structure clearly recognizable in the 1840s.

Uniform convergence guarantees for the deep Ritz method for nonlinear problems.

We provide convergence guarantees for the Deep Ritz Method for abstract variational energies. Our results cover nonlinear variational problems such as the -Laplace equation or the Modica-Mortola energy with essential or natural boundary conditions. Under additional assumptions, we show that the convergence is uniform across bounded families of right-hand sides.

Transfer learning of phase transitions in percolation and directed percolation.

The latest advances of statistical physics have shown remarkable performance of machine learning in identifying phase transitions. In this paper, we apply domain adversarial neural network (DANN) based on transfer learning to studying nonequilibrium and equilibrium phase transition models, which are percolation model and directed percolation (DP) model, respectively. With the DANN, only a small fraction of input configurations (two-dimensional images) needs to be labeled, which is automatically chosen, to capture the critical point.

Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.

Background: Calling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations induced by the chemical treatment. Nevertheless, SNP data is desirable both for genotyping and to understand the DNA methylome in the context of the genetic background. The confounding effect of bisulfite conversion however can be conceptually resolved by observing differences in allele counts on a per-strand basis, whereby artificial mutations are reflected by non-complementary base pairs.

Soft mode in the dynamics of over-realizable online learning for soft committee machines.

Overparametrized deep neural networks trained by stochastic gradient descent are successful in performing many tasks of practical relevance. One aspect of overparametrization is the possibility that the student network has a larger expressivity than the data generating process. In the context of a student-teacher scenario, this corresponds to the so-called over-realizable case, where the student network has a larger number of hidden units than the teacher.

Bi-alignments with affine gaps costs.

Background: Commonly, sequence and structure elements are assumed to evolve congruently, such that homologous sequence positions correspond to homologous structural features. Assuming congruent evolution, alignments based on sequence and structure similarity can therefore optimize both similarities at the same time in a single alignment. To model incongruent evolution, where sequence and structural features diverge positionally, we recently introduced bi-alignments.

Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair.

CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways, either by regulating their expression or via direct protein-protein contact and enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but an additional role in cellular DNA repair pathways has been proposed previously.

Small integral membrane protein 10 like 1 downregulation enhances differentiation of adipose progenitor cells.

Small integral membrane protein 10 like 1 (SMIM10L1) was identified by RNA sequencing as the most significantly downregulated gene in Phosphatase and Tensin Homologue (PTEN) knockdown adipose progenitor cells (APCs). PTEN is a tumor suppressor that antagonizes the growth promoting Phosphoinositide 3-kinase (PI3K)/AKT/mechanistic Target of Rapamycin (mTOR) cascade. Diseases caused by germline pathogenic variants in PTEN are summarized as PTEN Hamartoma Tumor Syndrome (PHTS).

Blindly verifying partially unknown entanglement.

Quantum entanglement has shown distinguished features beyond any classical state. Many methods have been presented to verify unknown entanglement with the complete information about the density matrices by quantum state tomography. In this work, we aim to identify unknown entanglement with only partial information of the state space.

ExceS-A: an exon-centric split aligner.

Spliced alignments are a key step in the construction of high-quality homology-based annotations of protein sequences. The exon/intron structure, which is computed as part of spliced alignment procedures, often conveys important information for the distinguishing paralogous members of gene families. Here we present an exon-centric pipeline for spliced alignment that is intended in particular for applications that involve exon-by-exon comparisons of coding sequences.

The cost of noise: Stochastic punishment falls short of sustaining cooperation in social dilemma experiments.

Identifying mechanisms able to sustain costly cooperation among self-interested agents is a central problem across social and biological sciences. One possible solution is peer punishment: when agents have an opportunity to sanction defectors, classical behavioral experiments suggest that cooperation can take root. Overlooked from standard experimental designs, however, is the fact that real-world human punishment-the administration of justice-is intrinsically noisy.

A Characterization of Maximally Entangled Two-Qubit States.

As already known by Rana's result, all eigenvalues of any partial-transposed bipartite state fall within the closed interval [-12,1]. In this note, we study a family of bipartite quantum states where the minimal eigenvalues of partial-transposed states are -12. For a two-qubit system, we find that the minimal eigenvalue of its partial-transposed state is -12 if and only if such a two-qubit state is maximally entangled.

Evolution of DNA Methylation Across Ecdysozoa.

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as Drosophila melanogaster and Caenorhabditis elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada.

Corrigendum: The Rise of Populism and the Reconfiguration of the German Political Space.

[This corrects the article DOI: 10.3389/fdata.2021.