KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions.

Molecular property prediction has become essential in accelerating advancements in drug discovery and materials science. Graph Neural Networks have recently demonstrated remarkable success in molecular representation learning; however, their broader adoption is impeded by two significant challenges: (1) data scarcity and constrained model generalization due to the expensive and time-consuming task of acquiring labeled data and (2) inadequate initial node and edge features that fail to incorporate comprehensive chemical domain knowledge, notably orbital information. To address these limitations, we introduce a Knowledge-Guided Graph (KGG) framework employing self-supervised learning to pretrain models using orbital-level features in order to mitigate reliance on extensive labeled data sets.

Prediction of Circular RNA Secondary Structures and Their Targets.

At the level of secondary structure, circular RNAs (circRNAs) can be understood in terms of base pairing, base-pair stacking, and entropic loop contribution in the same way as linear RNAs and intermolecular RNA-RNA interactions. The folding problem of circular RNAs can thus be solved by dynamic programming algorithms in essentially the same manner. In this chapter, we review the similarities and differences between circular and linear RNAs with a focus on the software tools provided by the ViennaRNA package.

Exploring the space of self-reproducing ribozymes using generative models.

Estimating the plausibility of RNA self-reproduction is central to origin-of-life scenarios. However, this property has been shown in only a handful of catalytic RNAs. Here, we compare models for their generative power in diversifying a reference ribozyme, based on statistical covariation and secondary structure prediction, and experimentally test model predictions using high-throughput sequencing.

Adenosine kinase and ADAL coordinate detoxification of modified adenosines to safeguard metabolism.

RNA contains diverse post-transcriptional modifications, and its catabolic breakdown yields numerous modified nucleosides requiring correct processing, but the mechanisms remain unknown. Here, we demonstrate that three RNA-derived modified adenosines, N-methyladenosine (mA), N,N-dimethyladenosine (mA), and N-isopentenyladenosine (iA), are sequentially metabolized into inosine monophosphate (IMP) to mitigate their intrinsic cytotoxicity. After phosphorylation by adenosine kinase (ADK), they undergo deamination by adenosine deaminase-like (ADAL).

The path-label reconciliation (PLR) dissimilarity measure for gene trees.

Background: In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies differences in the topology of reconciled gene trees, but also considers discrepancies in predicted ancestral gene-species maps and speciation/duplication events, offering a refinement of existing metrics such as Robinson-Foulds (RF) and their labeled extensions LRF and ELRF. A tunable parameter also allows users to adjust the balance between its species map and event labeling components.

Experimental Characterization of Quantumness Using the Uncertainty Principle, Coherence, and Nonlocality.

Heisenberg's uncertainty principle, coherence, and Bell nonlocality have been individually examined through many experiments. In this Letter, we systematically characterize all of this quantumness in a unified manner. We first construct universal uncertainty relations to reveal intrinsic features of incompatible measurements, which include all the state-independent uncertainties as special cases.

Recently Evolved, Stage-Specific Genes Are Enriched at Life-Stage Transitions in Flies.

Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal, and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster (D.

Impact of symmetry in local learning rules on predictive neural representations and generalization in spatial navigation.

In spatial cognition, the Successor Representation (SR) from reinforcement learning provides a compelling candidate of how predictive representations are used to encode space. In particular, hippocampal place cells are hypothesized to encode the SR. Here, we investigate how varying the temporal symmetry in learning rules influences those representations.

Crossover operators for molecular graphs with an application to virtual drug screening.

Genetic algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for searching over spaces of graphs.

Parity Property of Hexagonal Sliding Puzzles.

We study the puzzle graphs of hexagonal sliding puzzles of various shapes, and with various numbers of holes. The puzzle graph is a combinatorial model which captures the solvability and the complexity of sequential mechanical puzzles. Questions relating to the puzzle graph have been previously studied and resolved for the 15 Puzzle, which is the most famous-and unsolvable-square sliding puzzle of all time.

How the Nobel Committee for Chemistry Has Shaped the Nobel Prize: Historical Trends Based on the Nobel Prize Nomination Archive.

The Nobel Prize in Chemistry is governed by the Nobel Foundation's rules and managed by the Royal Swedish Academy of Sciences via its Nobel Committee for Chemistry. Despite 125 years of awarding these prizes and increased transparency from the Nobel Foundation, many aspects of the selection process remain obscure. Our analysis of the Nobel Prize Nomination Archive from 1901 to 1970 reveals that the decisions were heavily influenced by the personal and professional biases of the members of the Nobel Committee for Chemistry, who were not only responsible for inviting and assessing nominations but also for presenting recommendations to the Academy.

Cholesterol allosteric modulation of the oxytocin receptor.

G-protein coupled receptors are critical components in cellular signaling, mediating various physiological responses to external stimuli. Here, we investigate the intricate relationship between cholesterol and the oxytocin receptor (OXTR), focusing on the binding mechanisms and the allosteric cross talk of bound cholesterol to the orthosteric ligand binding pocket. Utilizing molecular docking and molecular dynamics simulations, we identify cholesterol binding sites both on the agonist-bound and antagonist-bound state, which show differing distributions and residence times of the cholesterol molecules.

Unbiased anchors for reliable genome-wide synteny detection.

Orthology inference lies at the foundation of comparative genomics research. The correct identification of loci which descended from a common ancestral sequence is not only complicated by sequence divergence but also duplication and other genome rearrangements. The conservation of gene order, i.

SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases.

Reaction templates are graphs that represent the reaction center as well as the surrounding context in order to specify salient features of chemical reactions. They are subgraphs of , which are equivalent to double pushout graph rewriting rules and thus can be applied directly to predict reaction outcomes at the structural formula level. We introduce here SynTemp, a framework designed to extract and hierarchically cluster reaction templates from large-scale reaction data repositories.

Universal conservation laws of the wave-particle-entanglement triad: theory and experiment.

When observed, a quantum system exhibits either wave-like or particle-like properties, depending on how it is measured. However, this duality is affected by the entanglement of the system with its quantum memory, raising a fundamental question: how are wave-particle duality and entanglement related? Here, we broaden the scope of wave-particle duality to include entanglement, introduce universal conservation laws for the wave-particle-entanglement triad, and perform demonstrations on silicon-integrated nanophotonic quantum chips. Our experiments not only mark the first confirmation of universal conservation laws but also highlight the potential of integrated photonics for exploring complex quantum phenomena in high-dimensional systems.

Pathway Realizability in Chemical Networks.

The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realizable, or can be made realizable, is missing. Realizable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway.

Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments.

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of identical-by-descent DNA segments (IBD) yield the most precise relatedness estimates.

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mitochondrial tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mitochondrial tRNAs with a uniform workflow.

Non-uniqueness of Admissible Solutions for the 2D Euler Equation with Vortex Data.

For any we prove that there exists an initial velocity field with vorticity for which there are infinitely many bounded admissible solutions to the 2D Euler equation. This shows sharpness of the weak-strong uniqueness principle, as well as sharpness of Yudovich's proof of uniqueness in the class of bounded admissible solutions. The initial data are truncated power-law vortices.

Spaces of mathematical chemistry.

In an effort to expand the domain of mathematical chemistry and inspire research beyond the realms of graph theory and quantum chemistry, we explore five mathematical chemistry spaces and their interconnectedness. These spaces comprise the chemical space, which encompasses substances and reactions; the space of reaction conditions, spanning the physical and chemical aspects involved in chemical reactions; the space of reaction grammars, which encapsulates the rules for creating and breaking chemical bonds; the space of substance properties, covering all documented measurements regarding substances; and the space of substance representations, composed of the various ontologies for characterising substances.

Oscillatory-Quality of sleep spindles links brain state with sleep regulation and function.

Here, we characterized the dynamics of sleep spindles, focusing on their damping, which we estimated using a metric called oscillatory-Quality (o-Quality), derived by fitting an autoregressive model to electrophysiological signals, recorded from the cortex in mice. The o-Quality of sleep spindles correlates weakly with their amplitude, shows marked laminar differences and regional topography across cortical regions, reflects the level of synchrony within and between cortical networks, is strongly modulated by sleep-wake history, reflects the degree of sensory disconnection, and correlates with the strength of coupling between spindles and slow waves. As most spindle events are highly localized and not detectable with conventional low-density recording approaches, o-Quality thus emerges as a valuable metric that allows us to infer the spread and dynamics of spindle activity across the brain and directly links their spatiotemporal dynamics with local and global regulation of brain states, sleep regulation, and function.

Evolution of neuropeptide Y/RFamide-like receptors in nematodes.

The Neuropeptide Y/RFamide-like receptors belong to the Rhodopsin-like G protein-coupled receptors G protein-coupled receptors (GPCRs) and are involved in functions such as locomotion, feeding and reproduction. With 41 described receptors they form the best-studied group of neuropeptide GPCRs in . In order to understand the expansion of the Neuropeptide Y/RFamide-like receptor family in nematodes, we started from the sequences of selected receptor paralogs in as query and surveyed the corresponding orthologous sequences in another 159 representative nematode target genomes.

Lengths of factorizations of integer-valued polynomials on Krull domains with prime elements.

Let be a Krull domain admitting a prime element with finite residue field and let be its quotient field. We show that for all positive integers and , there exists an integer-valued polynomial on , that is, an element of , which has precisely essentially different factorizations into irreducible elements of whose lengths are exactly . Using this, we characterize lengths of factorizations when is a unique factorization domain and therefore also in case is a discrete valuation domain.