Stability of the replica symmetric solution for the information conveyed by by a neural network

The information that a pattern of firing in the output layer of a feedforward network of threshold-linear neurons conveys about the network's inputs is considered. A replica-symmetric solution is found to be stable for all but small amounts of noise. The region of instability depends on the contribution of the threshold and the sparseness: for distributed pattern distributions, the unstable region extends to higher noise variances than for very sparse distributions, for which it is almost nonexistant.Comment: 19 pages, LaTeX, 5 figures. Also available at http://www.mrc-bbc.ox.ac.uk/~schultz/papers.html . Submitted to Phys. Rev. E Minor change

Positive feedback induces switch between distributive and processive phosphorylation of Hog1

Cellular decision making often builds on ultrasensitive MAPK pathways. The phosphorylation mechanism of MAP kinase has so far been described as either distributive or processive, with distributive mechanisms generating ultrasensitivity in theoretical analyses. However, the in vivo mechanism of MAP kinase phosphorylation and its activation dynamics remain unclear. Here, we characterize the regulation of the MAP kinase Hog1 in Saccharomyces cerevisiae via topologically different ODE models, parameterized on multimodal activation data. Interestingly, our best fitting model switches between distributive and processive phosphorylation behavior regulated via a positive feedback loop composed of an affinity and a catalytic component targeting the MAP kinase-kinase Pbs2. Indeed, we show that Hog1 directly phosphorylates Pbs2 on serine 248 (S248), that cells expressing a non-phosphorylatable (S248A) or phosphomimetic (S248E) mutant show behavior that is consistent with simulations of disrupted or constitutively active affinity feedback and that Pbs2-S248E shows significantly increased affinity to Hog1 in vitro. Simulations further suggest that this mixed Hog1 activation mechanism is required for full sensitivity to stimuli and to ensure robustness to different perturbations.© 2023. The Author(s)

Statistical distribution of quantum entanglement for a random bipartite state

We compute analytically the statistics of the Renyi and von Neumann entropies (standard measures of entanglement), for a random pure state in a large bipartite quantum system. The full probability distribution is computed by first mapping the problem to a random matrix model and then using a Coulomb gas method. We identify three different regimes in the entropy distribution, which correspond to two phase transitions in the associated Coulomb gas. The two critical points correspond to sudden changes in the shape of the Coulomb charge density: the appearance of an integrable singularity at the origin for the first critical point, and the detachement of the rightmost charge (largest eigenvalue) from the sea of the other charges at the second critical point. Analytical results are verified by Monte Carlo numerical simulations. A short account of some of these results appeared recently in Phys. Rev. Lett. {\bf 104}, 110501 (2010).Comment: 7 figure

Ask yeast how to burn your fats: lessons learned from the metabolic adaptation to salt stress

[EN] Here, we review and update the recent advances in the metabolic control during the adaptive response of budding yeast to hyperosmotic and salt stress, which is one of the best understood signaling events at the molecular level. This environmental stress can be easily applied and hence has been exploited in the past to generate an impressively detailed and comprehensive model of cellular adaptation. It is clear now that this stress modulates a great number of different physiological functions of the cell, which altogether contribute to cellular survival and adaptation. Primary defense mechanisms are the massive induction of stress tolerance genes in the nucleus, the activation of cation transport at the plasma membrane, or the production and intracellular accumulation of osmolytes. At the same time and in a coordinated manner, the cell shuts down the expression of housekeeping genes, delays the progression of the cell cycle, inhibits genomic replication, and modulates translation efficiency to optimize the response and to avoid cellular damage. To this fascinating interplay of cellular functions directly regulated by the stress, we have to add yet another layer of control, which is physiologically relevant for stress tolerance. Salt stress induces an immediate metabolic readjustment, which includes the up-regulation of peroxisomal biomass and activity in a coordinated manner with the reinforcement of mitochondrial respiratory metabolism. Our recent findings are consistent with a model, where salt stress triggers a metabolic shift from fermentation to respiration fueled by the enhanced peroxisomal oxidation of fatty acids. We discuss here the regulatory details of this stress-induced metabolic shift and its possible roles in the context of the previously known adaptive functions.The work of the authors was supported by grants from Ministerio de Economía y Competitividad (BFU2011- 23326 and BFU2016-75792-R).Pascual-Ahuir Giner, MD.; Manzanares-Estreder, S.; Timón Gómez, A.; Proft ., MH. (2017). Ask yeast how to burn your fats: lessons learned from the metabolic adaptation to salt stress. Current Genetics. 64(1):63-69. https://doi.org/10.1007/s00294-017-0724-5S6369641Aguilera J, Prieto JA (2001) The Saccharomyces cerevisiae aldose reductase is implied in the metabolism of methylglyoxal in response to stress conditions. Curr Genet 39:273–283Albertyn J, Hohmann S, Thevelein JM, Prior BA (1994) GPD1, which encodes glycerol-3-phosphate dehydrogenase, is essential for growth under osmotic stress in Saccharomyces cerevisiae, and its expression is regulated by the high-osmolarity glycerol response pathway. 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Nature 493:116–119Escote X, Zapater M, Clotet J, Posas F (2004) Hog1 mediates cell-cycle arrest in G1 phase by the dual targeting of Sic1. Nat Cell Biol 6:997–1002Ferreira C, van Voorst F, Martins A, Neves L, Oliveira R, Kielland-Brandt MC, Lucas C, Brandt A (2005) A member of the sugar transporter family, Stl1p is the glycerol/H+ symporter in Saccharomyces cerevisiae. Mol Biol Cell 16:2068–2076Gonzalez R, Morales P, Tronchoni J, Cordero-Bueso G, Vaudano E, Quiros M, Novo M, Torres-Perez R, Valero E (2016) New genes involved in osmotic stress tolerance in Saccharomyces cerevisiae. Front Microbiol 7:1545Ho YH, Gasch AP (2015) Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling. Curr Genet 61:503–511Hohmann S (2015) An integrated view on a eukaryotic osmoregulation system. Curr Genet 61:373–382Hohmann S, Krantz M, Nordlander B (2007) Yeast osmoregulation. 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RNA 15:600–614Nadal-Ribelles M, Conde N, Flores O, Gonzalez-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F (2012) Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol 13:R106Pastor MM, Proft M, Pascual-Ahuir A (2009) Mitochondrial function is an inducible determinant of osmotic stress adaptation in yeast. J Biol Chem 284:30307–30317Petelenz-Kurdziel E, Kuehn C, Nordlander B, Klein D, Hong KK, Jacobson T, Dahl P, Schaber J, Nielsen J, Hohmann S, Klipp E (2013) Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress. PLoS Comput Biol 9:e1003084Posas F, Chambers JR, Heyman JA, Hoeffler JP, de Nadal E, Arino J (2000) The transcriptional response of yeast to saline stress. J Biol Chem 275:17249–17255Proft M, Struhl K (2002) Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. 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A recovery-explicit error estimator in energy norm for linear elasticity

[EN] Significant research effort has been devoted to produce one-sided error estimates for Finite Element Analyses, in particular to provide upper bounds of the actual error. Typically, this has been achieved using residual-type estimates. One of the most popular and simpler (in terms of implementation) techniques used in commercial codes is the recovery-based error estimator. This technique produces accurate estimations of the exact error but is not designed to naturally produce upper bounds of the error in energy norm. Some attempts to remedy this situation provide bounds depending on unknown constants. Here, a new step towards obtaining error bounds from the recovery-based estimates is proposed. The idea is (1) to use a locally equilibrated recovery technique to obtain an accurate estimation of the exact error, (2) to add an explicit-type error bound of the lack of equilibrium of the recovered stresses in order to guarantee a bound of the actual error and (3) to efficiently and accurately evaluate the constants appearing in the bounding expressions, thus providing asymptotic bounds. The numerical tests with h-adaptive refinement process show that the bounding property holds even for coarse meshes, providing upper bounds in practical applications.The authors also thank the support of the Framework Programme 7 Initial Training Network Funding under grant number 289361 "Integrating Numerical Simulation and Geometric Design Technology".Nadal Soriano, E.; Díez, P.; Ródenas, J.; Tur Valiente, M.; Fuenmayor Fernández, FJ. (2015). A recovery-explicit error estimator in energy norm for linear elasticity. Computer Methods in Applied Mechanics and Engineering. 287:172-190. https://doi.org/10.1016/j.cma.2015.01.013S17219028

Computing Naturally in the Billiard Ball Model

Fredkin's Billiard Ball Model (BBM) is considered one of the fundamental models of collision-based computing, and it is essentially based on elastic collisions of mobile billiard balls. Moreover, fixed mirrors or reflectors are brought into the model to deflect balls to complete the computation. However, the use of fixed mirrors is "physically unrealistic" and makes the BBM not perfectly momentum conserving from a physical point of view, and it imposes an external architecture onto the computing substrate which is not consistent with the concept of "architectureless" in collision-based computing. In our initial attempt to reduce mirrors in the BBM, we present a class of gates: the m-counting gate, and show that certain circuits can be realized with few mirrors using this gate. We envisage that our findings can be useful in future research of collision-based computing in novel chemical and optical computing substrates.Comment: 10 pages, 7 figure

Circulating CD5L is associated with cardiovascular events and all-cause mortality in individuals with chronic kidney disease

This study assessed the association of CD5L and soluble CD36 (sCD36) with the risk of a cardiovascular event (CVE), including CV death and all-cause mortality in CKD. We evaluated the association of CD5L and sCD36 with a predefined composite CV endpoint (unstable angina, myocardial infarction, transient ischemic attack, cerebrovascular accident, congestive heart failure, arrhythmia, peripheral arterial disease [PAD] or amputation by PAD, aortic aneurysm, or death from CV causes) and all-cause mortality using Cox proportional hazards regression, adjusted for CV risk factors. The analysis included 1,516 participants free from pre-existing CV disease followed up for 4 years. The median age was 62 years, 38.8% were female, and 26.8% had diabetes. There were 98 (6.5%) CVEs and 72 (4.8%) deaths, of which 26 (36.1%) were of CV origin. Higher baseline CD5L concentration was associated with increased risk of CVE (HR, 95% CI, 1.17, 1.0-1.36), and all-cause mortality (1.22, 1.01-1.48) after adjusting for age, sex, diabetes, systolic blood pressure, dyslipidemia, waist circumference, smoking, and CKD stage. sCD36 showed no association with adverse CV outcomes or mortality. Our study showed for the first time that higher concentrations of CD5L are associated with future CVE and all-cause mortality in individuals with CKD

Design, Synthesis and Characterization of a Highly Effective Inhibitor for Analog-Sensitive (as) Kinases

Highly selective, cell-permeable and fast-acting inhibitors of individual kinases are sought-after as tools for studying the cellular function of kinases in real time. A combination of small molecule synthesis and protein mutagenesis, identified a highly potent inhibitor (1-Isopropyl-3-(phenylethynyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine) of a rationally engineered Hog1 serine/threonine kinase (Hog1T100G). This inhibitor has been successfully used to study various aspects of Hog1 signaling, including a transient cell cycle arrest and gene expression changes mediated by Hog1 in response to stress. This study also underscores that the general applicability of this approach depends, in part, on the selectivity of the designed the inhibitor with respect to activity versus the engineered and wild type kinases. To explore this specificity in detail, we used a validated chemogenetic assay to assess the effect of this inhibitor on all gene products in yeast in parallel. The results from this screen emphasize the need for caution and for case-by-case assessment when using the Analog-Sensitive Kinase Allele technology to assess the physiological roles of kinases

Moonlighting Proteins Hal3 and Vhs3 Form a Heteromeric PPCDC with Ykl088w in Yeast CoA Biosynthesis

Premi a l'excel·lència investigadora. 2010Unlike most other organisms, the essential five-step Coenzyme A biosynthetic pathway has not been fully resolved in yeast. Specifically, the gene(s) encoding the phosphopantothenoylcysteine decarboxylase (PPCDC) activity still remains unidentified. Sequence homology analyses suggest three candidates, namely Ykl088w, Hal3 and Vhs3, as putative PPCDC enzymes in Saccharomyces cerevisiae. Interestingly, Hal3 and Vhs3 have been characterized as negative regulatory subunits of the Ppz1 protein phosphatase. Here we show that YKL088w does not encode a third Ppz1 regulatory subunit, and that the essential roles of Ykl088w and the Hal3/Vhs3 pair are complementary, cannot be interchanged and can be attributed to PPCDC-related functions. We demonstrate that while known eukaryotic PPCDCs are homotrimers, the active yeast enzyme is a heterotrimer which consists of Ykl088w and Hal3/Vhs3 monomers that separately provides two essential catalytic residues. Our results unveil Hal3/Vhs3 as moonlighting proteins, involved in both CoA biosynthesis and protein phosphatase regulation

Impact of smoking status on the relative efficacy of the EGFR TKI/angiogenesis inhibitor combination therapy in advanced NSCLC-a systematic review and meta-analysis.

BACKGROUND The ETOP 10-16 BOOSTER trial failed to demonstrate a progression-free survival (PFS) benefit for adding bevacizumab to osimertinib in second line. An exploratory subgroup analysis, however, suggested a PFS benefit of the combination in patients with a smoking history and prompted us to do this study. METHODS A systematic review and meta-analysis to evaluate the differential effect of smoking status on the benefit of adding an angiogenesis inhibitor to epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor therapy was carried out. All relevant randomized controlled trials appearing in main oncology congresses or in PubMed as of 1 November 2021 were used according to the Preferred Reporting Items for Systematic Review and Meta-Analyses statement. Primarily PFS according to smoking status, and secondarily overall survival (OS) were of interest. Pooled and interaction hazard ratios (HRs) were estimated by fixed or random effects models, depending on the detected degree of heterogeneity. Bias was assessed using the revised Cochrane tool for randomized controlled trials (RoB 2). RESULTS Information by smoking was available for 1291 patients for PFS (seven studies) and 678 patients for OS (four studies). The risk of bias was low for all studies. Combination treatment significantly prolonged PFS for smokers [n = 502, HR = 0.55, 95% confidence interval (CI): 0.44-0.69] but not for nonsmokers (n = 789, HR = 0.92, 95% CI: 0.66-1.27; treatment-by-smoking interaction P = 0.02). Similarly, a significant OS benefit was found for smokers (n = 271, HR = 0.66, 95% CI: 0.47-0.93) but not for nonsmokers (n = 407, HR = 1.07, 95% CI: 0.82-1.42; treatment-by-smoking interaction P = 0.03). CONCLUSION In advanced EGFR-non-small-cell lung cancer patients, the addition of an angiogenesis inhibitor to EGFR-tyrosine kinase inhibitor therapy provides a statistically significant PFS and OS benefit in smokers, but not in non-smokers. The biological basis for this observation should be pursued and could determine whether this might be due to a specific co-mutational pattern produced by tobacco exposure