Parallelizations in Weihrauch Reducibility and Constructive Reverse Mathematics
Ontology highlight
ABSTRACT:
SUBMITTER: Anselmo M
PROVIDER: S-EPMC7309481 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Hybrid games combine discrete, continuous, and adversarial dynamics. Differential game logic (
| S-EPMC7324283 | biostudies-literature
Project description:The ability of macromolecules to transduce stimulus information at one site into conformational changes at a distant site, termed "allostery," is vital for cellular signaling. Here, we propose a link between the sensitivity of allosteric macromolecules to their underlying biophysical parameters, the interrelationships between these parameters, and macromolecular adaptability. We demonstrate that the parameters of a canonical model of the mSlo large-conductance Ca2+-activated K+ (BK) ion channel are non-identifiable with respect to the equilibrium open probability-voltage relationship, a common functional assay. We construct a reduced model with emergent parameters that are identifiable and expressed as combinations of the original mechanistic parameters. These emergent parameters indicate which coordinated changes in mechanistic parameters can leave assay output unchanged. We predict that these coordinated changes are used by allosteric macromolecules to adapt, and we demonstrate how this prediction can be tested experimentally. We show that these predicted parameter compensations are used in the first reported allosteric phenomena: the Bohr effect, by which hemoglobin adapts to varying pH.
| S-EPMC5412534 | biostudies-literature
Project description:Gene regulatory networks (GRNs) control biological processes like pluripotency, differentiation, and apoptosis. Omics methods can identify a large number of putative network components (on the order of hundreds or thousands) but it is possible that in many cases a small subset of genes control the state of GRNs. Here, we explore how the topology of the interactions between network components may indicate whether the effective state of a GRN can be represented by a small subset of genes. We use methods from information theory to model the regulatory interactions in GRNs as cascading and superposing information channels. We propose an information loss function that enables identification of the conditions by which a small set of genes can represent the state of all the other genes in the network. This information-theoretic analysis extends to a measure of free energy change due to communication within the network, which provides a new perspective on the reducibility of GRNs. Both the information loss and relative free energy depend on the density of interactions and edge communication error in a network. Therefore, this work indicates that a loss in mutual information between genes in a GRN is directly coupled to a thermodynamic cost, i.e., a reduction of relative free energy, of the system.
| S-EPMC7824329 | biostudies-literature
Project description:Fe-MCM-41 materials were prepared by different methods. The Fe was both incorporated into the structure and formed crystallites attached to the silica. High Fe content MCM-41 (~16 wt%) with retention of mesoporosity and long-range order was achieved by a range of new synthetic methodologies: (i) by delaying the addition of Fe3+(aq) to the stirred synthesis gel by 2 h, (ii) by addition of Fe3+ precursor as a freshly-precipitated aqueous slurry, (iii) by exploiting a secondary synthesis with Si-MCM-41 as SiO2 source. For comparative purposes the MCM-41 was also prepared by incipient wetness impregnation (IWI). Although all these synthesis methods preserved mesoporosity and long-range order of the SiO2 matrix, the hydrothermally-fabricated Fe materials prepared via the secondary synthesis route has the most useful properties for exploitation as a catalyst, in terms of hydrothermal stability of the resulting support. Temperature-programmed reduction (TPR) studies revealed a three-peak reduction pattern for this material instead of the commonly observed two-peak reduction pattern. The three peaks showed variable intensity that related to the presence of two components: crystalline Fe2O3 and Fe embedded in the SiO2 matrix (on the basis of ESR studies). The role of secondary synthesis of Si-MCM-41 on the iron reducibility was also demonstrated in IWI of sec-Si-MCM-41.
| S-EPMC5513583 | biostudies-literature
Project description:The author reviews research showing that repetitive thought (RT) can have constructive or unconstructive consequences. The main unconstructive consequences of RT are (a) depression, (b) anxiety, and (c) difficulties in physical health. The main constructive consequences of RT are (a) recovery from upsetting and traumatic events, (b) adaptive preparation and anticipatory planning, (c) recovery from depression, and (d) uptake of health-promoting behaviors. Several potential principles accounting for these distinct consequences of RT are identified within this review: (a) the valence of thought content, (b) the intrapersonal and situational context in which RT occurs, and (c) the level of construal (abstract vs. concrete processing) adopted during RT. Of the existing models of RT, it is proposed that an elaborated version of the control theory account provides the best theoretical framework to account for its distinct consequences.
| S-EPMC2672052 | biostudies-other
Project description:The construction of well-controllable in vitro models of physiological and pathological vascular endothelium remains a fundamental challenge in tissue engineering and drug development. Here, we present an approach for forming a synthetic endothelial extracellular matrix (ECM) that closely resembles that of the native structure by locally depositing basement membrane materials onto type 1 collagen nanofibers only in a region adjacent to the endothelial cell (EC) monolayer. Culturing the EC monolayer on this synthetic endothelial ECM remarkably enhanced its physiological properties, reducing its vascular permeability, and promoting a stabilized, quiescent phenotype. We demonstrated that the EC monolayer on the synthetic endothelial ECM neither creates non-physiological barriers to cell-cell or cell-ECM interactions, nor hinders molecular diffusion of growth factors and other molecules. The synthetic endothelial ECM and vascular endothelium on it may help us enter in a new phase of research in which various models of the biological barrier behavior can be tested experimentally.
| S-EPMC4685304 | biostudies-literature
Project description:UnlabelledConstructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution.ReviewersAlex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article.
| S-EPMC3534586 | biostudies-literature
Project description:BackgroundThe pigment melanin is produced by specialized cells, called melanocytes. In healthy skin, melanocytes are sparsely spread among the other cell types in the basal layer of the epidermis. Sun tanning results from an UV-induced increase in the release of melanin to neighbouring keratinocytes, the major cell type component of the epidermis as well as redistribution of melanin among these cells. Here we provide a mathematical conceptualization of our current knowledge of the tanning response, in terms of a dynamic model. The resolution level of the model is tuned to available data, and its primary focus is to describe the tanning response following UV exposure.ResultsThe model appears capable of accounting for available experimental data on the tanning response in different skin and photo types. It predicts that the thickness of the epidermal layer and how far the melanocyte dendrites grow out in the epidermal layers after UV exposure influence the tanning response substantially.ConclusionDespite the paucity of experimental validation data the model is constrained enough to serve as a foundation for the establishment of a theoretical-experimental research programme aimed at elucidating the more fine-grained regulatory anatomy underlying the tanning response.
| S-EPMC2714304 | biostudies-literature
Project description:Developments of the PDB_REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB_REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB_REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12?000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R(free) and in terms of widely accepted geometric validation criteria. It is concluded that PDB_REDO is useful to update the otherwise `static' structures in the PDB to modern crystallographic standards. The publically available PDB_REDO database provides better model statistics and contributes to better refinement and validation targets.
| S-EPMC3322608 | biostudies-literature
Project description:Market timing is an investment technique that tries to continuously switch investment into assets forecast to have better returns. What is the likelihood of having a successful market timing strategy? With an emphasis on modeling simplicity, I calculate the feasible set of market timing portfolios using index mutual fund data for perfectly timed (by hindsight) all or nothing quarterly switching between two asset classes, US stocks and bonds over the time period 1993-2017. The historical optimal timing path of switches is shown to be indistinguishable from a random sequence. The key result is that the probability distribution function of market timing returns is asymmetric, that the highest probability outcome for market timing is a below median return. Put another way, simple math says market timing is more likely to lose than to win-even before accounting for costs. The median of the market timing return probability distribution can be directly calculated as a weighted average of the returns of the model assets with the weights given by the fraction of time each asset has a higher return than the other. For the time period of the data the median return was close to, but not identical with, the return of a static 60:40 stock:bond portfolio. These results are illustrated through Monte Carlo sampling of timing paths within the feasible set and by the observed return paths of several market timing mutual funds.
| S-EPMC6051602 | biostudies-literature