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.

Unambiguous State Discrimination with Intrinsic Coherence.

We investigate the discrimination of pure-mixed (quantum filtering) and mixed-mixed states and compare their optimal success probability with the one for discriminating other pairs of pure states superposed by the vectors included in the mixed states. We prove that under the equal-fidelity condition, the pure-pure state discrimination scheme is superior to the pure-mixed (mixed-mixed) one. With respect to quantum filtering, the coherence exists only in one pure state and is detrimental to the state discrimination for lower dimensional systems; while it is the opposite for the mixed-mixed case with symmetrically distributed coherence.

Finite-Size Scaling at the Edge of Disorder in a Time-Delay Vicsek Model.

Living many-body systems often exhibit scale-free collective behavior reminiscent of thermal critical phenomena. But their mutual interactions are inevitably retarded due to information processing and delayed actuation. We numerically investigate the consequences for the finite-size scaling in the Vicsek model of motile active matter.

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae.

The Genome of the "Sea Vomit" .

Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt , commonly known as "sea vomit", is a colonial tunicate considered an invasive species with substantial ecological and economical risk.

Common Features in lncRNA Annotation and Classification: A Survey.

Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast majority is poorly described beyond the existence of their transcripts.

Foundation of One-Particle Reduced Density Matrix Functional Theory for Excited States.

In . , , 023001 a reduced density matrix functional theory (RDMFT) was proposed for calculating energies of selected eigenstates of interacting many-Fermion systems. Here, we develop a solid foundation for this so-called -RDMFT and present the details of various derivations.

How Morphological Computation Shapes Integrated Information in Embodied Agents.

The Integrated Information Theory provides a quantitative approach to consciousness and can be applied to neural networks. An embodied agent controlled by such a network influences and is being influenced by its environment. This involves, on the one hand, morphological computation within goal directed action and, on the other hand, integrated information within the controller, the agent's brain.

cyPhyRNA-seq: a genome-scale RNA-seq method to detect active self-cleaving ribozymes by capturing RNAs with 2',3' clic hosphates and 5' droxyl ends.

Self-cleaving ribozymes are catalytically active RNAs that cleave themselves into a 5'-fragment with a 2',3'-cyclic phosphate and a 3'-fragment with a 5'-hydroxyl. They are widely applied for the construction of synthetic RNA devices and RNA-based therapeutics. However, the targeted discovery of self-cleaving ribozymes remains a major challenge.

Evolution of cooperation and consistent personalities in public goods games.

The evolution of cooperation has remained an important problem in evolutionary theory and social sciences. In this regard, a curious question is why consistent cooperative and defective personalities exist and if they serve a role in the evolution of cooperation? To shed light on these questions, here, I consider a population of individuals who possibly play two consecutive rounds of public goods game, with different enhancement factors. Importantly, individuals have independent strategies in the two rounds.

A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set.

Background: The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics.

Evolution of cooperation in costly institutions exhibits Red Queen and Black Queen dynamics in heterogeneous public goods.

Public goods are often subject to heterogeneous costs, such as the necessary costs to maintain the public goods infrastructure. However, the extent to which heterogeneity in participation cost can affect groups' ability to provide public goods is unclear. Here, by introducing a mathematical model, I show that when individuals face a costly institution and a free institution to perform a collective action task, the existence of a participation cost promotes cooperation in the costly institution.

An atlas of fragrance chemicals in children's products.

Exposure to environmental chemicals during early childhood is a potential health concern. At a tender age, children are exposed to fragrance chemicals used in toys and child care products. Although there are few initiatives in Europe and United States towards monitoring and regulation of fragrance chemicals in children's products, such efforts are still lacking elsewhere.

The global ocean size spectrum from bacteria to whales.

It has long been hypothesized that aquatic biomass is evenly distributed among logarithmic body mass size classes. Although this community structure has been observed regionally, mostly among plankton groups, its generality has never been formally tested across all marine life over the global ocean, nor have the impacts of humans on it been globally assessed. Here, we bring together data at the global scale to test the hypothesis from bacteria to whales.

Natural Selection beyond Life? A Workshop Report.

Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of "heritable variation in fitness among individuals". Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological framework, where properties are typically examined in light of their putative functions.

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

The paper explores the notion of a reconfiguration of political space in the context of the rise of populism and its effects on the political system. We focus on Germany and the appearance of the new right wing party "Alternative for Germany" (AfD). The idea of a political space is closely connected to the ubiquitous use of spatial metaphors in political talk.

Modeling the emergence of affective polarization in the social media society.

Rising political polarization in recent decades has hampered and gridlocked policymaking, as well as weakened trust in democratic institutions. These developments have been linked to the idea that new media technology fosters extreme views and political conflict by facilitating self-segregation into "echo chambers" where opinions are isolated and reinforced. This opinion-centered picture has recently been challenged by an emerging political science literature on "affective polarization", which suggests that current polarization is better understood as driven by partisanship emerging as a strong social identity.

Multiomics reveal unique signatures of human epiploic adipose tissue related to systemic insulin resistance.

Objective: Human white adipose tissue (AT) is a metabolically active organ with distinct depot-specific functions. Despite their locations close to the gastrointestinal tract, mesenteric AT and epiploic AT (epiAT) have only scarcely been investigated. Here, we aim to characterise these ATs in-depth and estimate their contribution to alterations in whole-body metabolism.