scholarly journals Message Passing and Metabolism

Entropy ◽  
2021 ◽  
Vol 23 (5) ◽  
pp. 606
Author(s):  
Thomas Parr
Keyword(s):  
Steady State ◽  
Message Passing ◽  
Theoretical Biology ◽  
Biochemical Networks ◽  
Prior Beliefs ◽  
Inference Problem ◽  
Chemical Computation ◽  
Regulation Of Metabolism ◽  
Probability Mass

Active inference is an increasingly prominent paradigm in theoretical biology. It frames the dynamics of living systems as if they were solving an inference problem. This rests upon their flow towards some (non-equilibrium) steady state—or equivalently, their maximisation of the Bayesian model evidence for an implicit probabilistic model. For many models, these self-evidencing dynamics manifest as messages passed among elements of a system. Such messages resemble synaptic communication at a neuronal network level but could also apply to other network structures. This paper attempts to apply the same formulation to biochemical networks. The chemical computation that occurs in regulation of metabolism relies upon sparse interactions between coupled reactions, where enzymes induce conditional dependencies between reactants. We will see that these reactions may be viewed as the movement of probability mass between alternative categorical states. When framed in this way, the master equations describing such systems can be reformulated in terms of their steady-state distribution. This distribution plays the role of a generative model, affording an inferential interpretation of the underlying biochemistry. Finally, we see that—in analogy with computational neurology and psychiatry—metabolic disorders may be characterized as false inference under aberrant prior beliefs.

I. Intrazellulärer Transport von Zwischenprodukten der Photosynthese im Photosynthese-Gleichgewicht und im Dunkel-Licht-Dunkel-Wechsel

1967 ◽  
Vol 22 (11) ◽  
pp. 1189-1199 ◽  
Author(s):  
U. Heber ◽  
K. A. Santarius ◽  
M. A. Hudson ◽  
U. W. Hallier
Keyword(s):  
Steady State ◽  
Phosphate Esters ◽  
Dark Light ◽  
Regulation Of Metabolism ◽  
Large Fluctuations ◽  
Phosphoglyceric Acid ◽  
Intact Leaves ◽  
Sugar Phosphates ◽  
Kinetics Of

1. The distribution — before, during and after photosynthesis — of different phosphate esters in chloroplasts and cytoplasm of leaf cells of spinach and Elodea has been investigated. In steady state experiments intact leaves were fed, during illumination, with 14CO2. The kinetics of the distribution of labelled phosphate esters between chloroplasts and cytoplasm were determined. In further experiments with intact leaves fluctuations in the pool sizes of phosphate esters in chloroplasts and in the cytoplasm were recorded in the dark/light and the light/dark transient. Independent fluctuations served as an indication that little or no exchange between chloroplasts and cytoplasm takes place. Concomitant fluctuations suggest rapid exchange.2. Although labelling takes place in the chloroplasts, a number of labelled phosphorylated intermediates appear rapidly in the cytoplasm during steady state photosynthesis of intact leaves in the presence of 14CO2. This is particularly true for phosphoglyceric acid, glucose-6-phosphate, fructose-6-phosphate and fructose-1,6-diphosphate. On the other hand, labelled ribulosediphosphate, sedoheptulosediphosphate and sedoheptulosemonophosphate remain largely in the chloroplasts. This agrees with earlier work on the behaviour of phosphorylated intermediates during the induction period of photosynthesis.3. In the dark the level of the bulk of the sugar diphosphates is lower in the chloroplasts than in the cytoplasm of intact leaves. On illumination, a large accumulation occurs only in the chloroplasts. This behaviour suggests impermeability of the chloroplast membrane towards at least some of the sugar diphosphates. In contrast, concomitant large fluctuations in the levels of dihydroxyacetonephosphate and fructose-1,6-diphosphate have been observed during the transients from dark to light and vice versa in chloroplasts and cytoplasm alike indicating that at least one of these compounds functions as a transport metabolite. Changes in the concentrations of glucose-6-phosphate and fructose-6-phosphate were much smaller under the influence of light than those of other sugar phosphates.4. The results demonstrate the role of phosphorylated transport metabolites in carbon metabolism in chloroplasts and cytoplasm. Implications of these findings in relation to photosynthesis, respiration and the regulation of metabolism are discussed.

Reducing misperceptions through news stories with data visualization: The role of readers’ prior knowledge and prior beliefs

Journalism ◽  
2021 ◽  
pp. 146488492110287
Author(s):  
Paul Mena
Keyword(s):  
Experimental Design ◽  
Prior Knowledge ◽  
Data Visualization ◽  
Accurate Information ◽  
Graphical Representations ◽  
Prior Beliefs ◽  
News Stories ◽  
Issue Involvement

Amid the global discussion on ways to fight misinformation, journalists have been writing stories with graphical representations of data to expose misperceptions and provide readers with more accurate information. Employing an experimental design, this study explored to what extent news stories correcting misperceptions are effective in reducing them when the stories include data visualization and how influential readers’ prior beliefs, issue involvement and prior knowledge may be in that context. The study found that the presence of data visualization in news articles correcting misperceptions significantly enhanced the reduction of misperceptions among news readers with less than average prior knowledge about an issue. In addition, it was found that prior beliefs had a significant effect on news readers’ misperceptions regardless of the presence or absence of data visualization. In this way, this research offers some support for the notion that data visualization may be useful to decrease misperceptions under certain circumstances.

scholarly journals Modules or Mean-Fields?

Entropy ◽  
2020 ◽  
Vol 22 (5) ◽  
pp. 552 ◽  
Author(s):  
Thomas Parr ◽  
Noor Sajid ◽  
Karl J. Friston
Keyword(s):  
Steady State ◽  
Message Passing ◽  
Mean Field Theory ◽  
Functional Anatomy ◽  
Mean Field ◽  
State Density ◽  
Stochastic Dynamical Systems ◽  
Conditional Independency ◽  
The Brain ◽  
Non Equilibrium

The segregation of neural processing into distinct streams has been interpreted by some as evidence in favour of a modular view of brain function. This implies a set of specialised ‘modules’, each of which performs a specific kind of computation in isolation of other brain systems, before sharing the result of this operation with other modules. In light of a modern understanding of stochastic non-equilibrium systems, like the brain, a simpler and more parsimonious explanation presents itself. Formulating the evolution of a non-equilibrium steady state system in terms of its density dynamics reveals that such systems appear on average to perform a gradient ascent on their steady state density. If this steady state implies a sufficiently sparse conditional independency structure, this endorses a mean-field dynamical formulation. This decomposes the density over all states in a system into the product of marginal probabilities for those states. This factorisation lends the system a modular appearance, in the sense that we can interpret the dynamics of each factor independently. However, the argument here is that it is factorisation, as opposed to modularisation, that gives rise to the functional anatomy of the brain or, indeed, any sentient system. In the following, we briefly overview mean-field theory and its applications to stochastic dynamical systems. We then unpack the consequences of this factorisation through simple numerical simulations and highlight the implications for neuronal message passing and the computational architecture of sentience.

scholarly journals Optimistic amnesia: how online and offline processing shape belief updating and memory biases in immediate and long-term optimism biases

2021 ◽  
Author(s):  
Ziqing Yao ◽  
Xuanyi Lin ◽  
Xiaoqing Hu
Keyword(s):  
Active Role ◽  
Prior Beliefs ◽  
Belief Updating ◽  
Estimation Task ◽  
Memory Biases ◽  
Brain Potentials ◽  
Adverse Life Event ◽  
Offline Processing

Abstract When people are confronted with feedback that counters their prior beliefs, they preferentially rely on desirable rather than undesirable feedback in belief updating, i.e. an optimism bias. In two pre-registered EEG studies employing an adverse life event probability estimation task, we investigated the neurocognitive processes that support the formation and the change of optimism biases in immediate and 24 h delayed tests. We found that optimistic belief updating biases not only emerged immediately but also became significantly larger after 24 h, suggesting an active role of valence-dependent offline consolidation processes in the change of optimism biases. Participants also showed optimistic memory biases: they were less accurate in remembering undesirable than desirable feedback probabilities, with inferior memories of undesirable feedback associated with lower belief updating in the delayed test. Examining event-related brain potentials (ERPs) revealed that desirability of feedback biased initial encoding: desirable feedback elicited larger P300s than undesirable feedback, with larger P300 amplitudes predicting both higher belief updating and memory accuracies. These results suggest that desirability of feedback could bias both online and offline memory-related processes such as encoding and consolidation, with both processes contributing to the formation and change of optimism biases.

scholarly journals The critical role of T cells in glucocorticoid-induced osteoporosis

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Lin Song ◽  
Lijuan Cao ◽  
Rui Liu ◽  
Hui Ma ◽  
Yanan Li ◽  
...  
Keyword(s):  
Bone Marrow ◽  
T Cells ◽  
Steady State ◽  
Side Effects ◽  
Critical Role ◽  
Wild Type ◽  
Receptor Activator ◽  
Steady State Levels ◽  
Induced Apoptosis

AbstractGlucocorticoids (GC) are widely used clinically, despite the presence of significant side effects, including glucocorticoid-induced osteoporosis (GIOP). While GC are believed to act directly on osteoblasts and osteoclasts to promote osteoporosis, the detailed underlying molecular mechanism of GC-induced osteoporosis is still not fully elucidated. Here, we show that lymphocytes play a pivotal role in regulating GC-induced osteoporosis. We show that GIOP could not be induced in SCID mice that lack T cells, but it could be re-established by adoptive transfer of splenic T cells from wild-type mice. As expected, T cells in the periphery are greatly reduced by GC; instead, they accumulate in the bone marrow where they are protected from GC-induced apoptosis. These bone marrow T cells in GC-treated mice express high steady-state levels of NF-κB receptor activator ligand (RANKL), which promotes the formation and maturation of osteoclasts and induces osteoporosis. Taken together, these findings reveal a critical role for T cells in GIOP.

scholarly journals The role of noise on the steady state distributions of phytoplankton populations

2016 ◽  
Vol 2016 (5) ◽  
pp. 054044 ◽  
Author(s):  
D Valenti ◽  
G Denaro ◽  
F Conversano ◽  
C Brunet ◽  
A Bonanno ◽  
...  
Keyword(s):  
Steady State

scholarly journals Accumulation of Prostacyclin in Rat Brain during Haemorrhagic Hypotension—Possible Role of PGI2 in Autoregulation

1984 ◽  
Vol 4 (1) ◽  
pp. 107-109 ◽  
Author(s):  
E. Shohami ◽  
A. Sidi
Keyword(s):  
Blood Pressure ◽  
Steady State ◽  
Control Group ◽  
Prostaglandin E ◽  
Cortical Tissue ◽  
Arterial Blood ◽  
Haemorrhagic Hypotension ◽  
Potent Vasodilator ◽  
Prostaglandin F

The effect of haemorrhagic hypotension on the levels of prostaglandin E2 (PGE2), thromboxane B2 (TXB2), and 6-keto prostaglandin F1α (6-keto-PGF1α) in cortical tissue of rats was studied. Lightly anesthetized rats were subjected to steady-state hypotension for 15 min, with a mean arterial blood pressure of 80, 60, and 40 mm Hg, and compared to a control group of normotensive rats. No significant change was found in the levels of PGE2 and TXB2. The level of 6-keto-PGF1α increased from 7.8 ± 0.9 to 14.1 ± 1.9 pg/mg protein (p < 0.02) at 80 mm Hg. Our findings suggest that prostacyclin, which is a potent vasodilator, might play a role in setting the lower limit of the autoregulation range.

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