The Intransitive Logic of Directed Cycles and Flipons Enhances the Evolution of Molecular Computers by Augmenting the Kolmogorov Complexity of Genomes
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PROVIDER: S-EPMC10671625 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.
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Project description:Based on 774 argumentative writings produced by Chinese English as a foreign language (EFL) learners, this study examined the extent to which Kolmogorov complexity metrics can distinguish the proficiency levels of beginner, lower-intermediate, and upper-intermediate second language (L2) English learners. Kolmogorov complexity metric is a holistic information-theoretic approach, which measures three facets of linguistic complexity, i.e., overall, syntactic, and morphological complexity simultaneously. To assess its validity in distinguishing L2 proficiency, Kolmogorov complexity metric is compared with traditional syntactic and morphological complexity metrics as well as fine-grained syntactic complexity metrics. Results showed that Kolmogorov overall and syntactic complexity could significantly distinguish any adjacent pair of L2 levels, serving as the best separators explored in the present study. Neither Kolmogorov morphological complexity nor other complexity metrics at both the syntactic and morphological levels can distinguish between all pairs of adjacent levels. Results of correlation analysis showed that Kolmogorov syntactic complexity was not or weakly correlated with all the fine-grained syntactic complexity metrics, indicating that they may address distinct linguistic features and can complement each other to better predict different proficiency levels.
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Project description:BackgroundLogic models are commonly used in evaluations to represent the causal processes through which interventions produce outcomes, yet significant debate is currently taking place over whether they can describe complex interventions which adapt to context. This paper assesses the logic models used in healthcare research from a complexity perspective. A typology of existing logic models is proposed, as well as a formal methodology for deriving more flexible and dynamic logic models.AnalysisVarious logic model types were tested as part of an evaluation of a complex Patient Experience Toolkit (PET) intervention, developed and implemented through action research across six hospital wards/departments in the English NHS. Three dominant types of logic model were identified, each with certain strengths but ultimately unable to accurately capture the dynamics of PET. Hence, a fourth logic model type was developed to express how success hinges on the adaption of PET to its delivery settings. Aspects of the Promoting Action on Research Implementation in Health Services (PARIHS) model were incorporated into a traditional logic model structure to create a dynamic "type 4" logic model that can accommodate complex interventions taking on a different form in different settings.ConclusionLogic models can be used to model complex interventions that adapt to context but more flexible and dynamic models are required. An implication of this is that how logic models are used in healthcare research may have to change. Using logic models to forge consensus among stakeholders and/or provide precise guidance across different settings will be inappropriate in the case of complex interventions that adapt to context. Instead, logic models for complex interventions may be targeted at facilitators to enable them to prospectively assess the settings they will be working in and to develop context-sensitive facilitation strategies. Researchers should be clear as to why they are using a logic model and experiment with different models to ensure they have the correct type.
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Project description:Newborn mice emit signals that promote parenting from mothers and fathers but trigger aggressive responses from virgin males. Although pup-directed attacks by males require vomeronasal function, the specific infant cues that elicit this behavior are unknown. We developed a behavioral paradigm based on reconstituted pup cues and showed that discrete infant morphological features combined with salivary chemosignals elicit robust male aggression. Seven vomeronasal receptors were identified based on infant-mediated activity, and the involvement of two receptors, Vmn2r65 and Vmn2r88, in infant-directed aggression was demonstrated by genetic deletion. Using the activation of these receptors as readouts for biochemical fractionation, we isolated two pheromonal compounds, the submandibular gland protein C and hemoglobins. Unexpectedly, none of the identified vomeronasal receptors and associated cues were specific to pups. Thus, infant-mediated aggression by virgin males relies on the recognition of pup's physical traits in addition to parental and infant chemical cues.
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Project description:Atrial fibrillation (AF) is related to a very complex local electrical activity reflected in the rich morphology of intracardiac electrograms. The link between electrogram complexity and efficacy of the catheter ablation is unclear. We test the hypothesis that the Kolmogorov complexity of a single atrial bipolar electrogram recorded during AF within the coronary sinus (CS) at the beginning of the catheter ablation may predict AF termination directly after pulmonary vein isolation (PVI). The study population consisted of 26 patients for whom 30 s baseline electrograms were recorded. In all cases PVI was performed. If AF persisted after PVI, ablation was extended beyond PVs. Kolmogorov complexity estimated by Lempel–Ziv complexity and the block decomposition method was calculated and compared with other measures: Shannon entropy, AF cycle length, dominant frequency, regularity, organization index, electrogram fractionation, sample entropy and wave morphology similarity index. A 5 s window length was chosen as optimal in calculations. There was a significant difference in Kolmogorov complexity between patients with AF termination directly after PVI compared to patients undergoing additional ablation (p < 0.01). No such difference was seen for remaining complexity parameters. Kolmogorov complexity of CS electrograms measured at baseline before PVI can predict self-termination of AF directly after PVI.
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Project description:BackgroundViruses are among the shortest yet highly abundant species that harbor minimal instructions to infect cells, adapt, multiply, and exist. However, with the current substantial availability of viral genome sequences, the scientific repertory lacks a complexity landscape that automatically enlights viral genomes' organization, relation, and fundamental characteristics.ResultsThis work provides a comprehensive landscape of the viral genome's complexity (or quantity of information), identifying the most redundant and complex groups regarding their genome sequence while providing their distribution and characteristics at a large and local scale. Moreover, we identify and quantify inverted repeats abundance in viral genomes. For this purpose, we measure the sequence complexity of each available viral genome using data compression, demonstrating that adequate data compressors can efficiently quantify the complexity of viral genome sequences, including subsequences better represented by algorithmic sources (e.g., inverted repeats). Using a state-of-the-art genomic compressor on an extensive viral genomes database, we show that double-stranded DNA viruses are, on average, the most redundant viruses while single-stranded DNA viruses are the least. Contrarily, double-stranded RNA viruses show a lower redundancy relative to single-stranded RNA. Furthermore, we extend the ability of data compressors to quantify local complexity (or information content) in viral genomes using complexity profiles, unprecedently providing a direct complexity analysis of human herpesviruses. We also conceive a features-based classification methodology that can accurately distinguish viral genomes at different taxonomic levels without direct comparisons between sequences. This methodology combines data compression with simple measures such as GC-content percentage and sequence length, followed by machine learning classifiers.ConclusionsThis article presents methodologies and findings that are highly relevant for understanding the patterns of similarity and singularity between viral groups, opening new frontiers for studying viral genomes' organization while depicting the complexity trends and classification components of these genomes at different taxonomic levels. The whole study is supported by an extensive website (https://asilab.github.io/canvas/) for comprehending the viral genome characterization using dynamic and interactive approaches.
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Project description:The properties of random Boolean networks have been investigated extensively as models of regulation in biological systems. However, the Boolean functions (BFs) specifying the associated logical update rules should not be expected to be random. In this contribution, we focus on biologically meaningful types of BFs, and perform a systematic study of their preponderance in a compilation of 2,687 functions extracted from published models. A surprising feature is that most of these BFs have odd "bias", that is they produce "on" outputs for a total number of input combinations that is odd. Upon further analysis, we are able to explain this observation, along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of 2 complexity measures: Boolean complexity based on string lengths in formal logic, which is yet unexplored in biological contexts, and the so-called average sensitivity. RoFs minimize Boolean complexity and all such functions have odd bias. Furthermore, NCFs minimize not only the Boolean complexity but also the average sensitivity. These results reveal the importance of minimum complexity in the regulatory logic of biological networks.
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