Neural networks and dynamical systems

AbstractModels for the identification and control of nonlinear dynamical systems using neural networks were introduced by Narendra and Parthasarathy in 1990, and methods for the adjustment of model parameters were also suggested. Simulation results of simple nonlinear systems were presented to demonstrate the feasibility of the schemes proposed. The concepts introduced at that time are investigated in this paper in greater detail. In particular, a number of questions that arise when the methods are applied to more complex systems are addressed. These include nonlinear systems of higher order as well as multivariable systems. The effect of using simpler models for both identification and control are discussed, and a new controller structure containing a linear part in addition to a multilayer neural network is introduced

Postaragonite phases of CaCO3 at lower mantle pressures

The stability, structure and properties of carbonate minerals at lower mantle conditions has significant impact on our understanding of the global carbon cycle and the composition of the interior of the Earth. In recent years, there has been significant interest in the behavior of carbonates at lower mantle conditions, specifically in their carbon hybridization, which has relevance for the storage of carbon within the deep mantle. Using high-pressure synchrotron X-ray diffraction in a diamond anvil cell coupled with direct laser heating of CaCO3 using a CO2 laser, we identify a crystalline phase of the material above 40 GPa − corresponding to a lower mantle depth of around 1,000 km − which has first been predicted by ab initio structure predictions. The observed sp2 carbon hybridized species at 40 GPa is monoclinic with P21/c symmetry and is stable up to 50 GPa, above which it transforms into a structure which cannot be indexed by existing known phases. A combination of ab initio random structure search (AIRSS) and quasi-harmonic approximation (QHA) calculations are used to re-explore the relative phase stabilities of the rich phase diagram of CaCO3. Nudged elastic band (NEB) calculations are used to investigate the reaction mechanisms between relevant crystal phases of CaCO3 and we postulate that the mineral is capable of undergoing sp2-sp3 hybridization change purely in the P21/c structure − forgoing the accepted post-aragonite Pmmn structure

Aluminum exposure at human dietary levels promotes vascular dysfunction and increases blood pressure in rats: a concerted action of NAD(P)H oxidase and COX-2

Abstract Aluminum (Al) is a non-essential metal and a significant environmental contaminant and is associated with a number of human diseases including cardiovascular disease. We investigated the effects of Al exposure at doses similar to human dietary levels on the cardiovascular system over a 60 day period. Wistar male rats were divided into two major groups and received orally: 1) Low aluminum level − rats were subdivided and treated for 60 days as follows: a) Untreated − ultrapure water; b) AlCl3 at a dose of 8.3 mg/kg bw for 60 days, representing human Al exposure by diet; and 2) High aluminum level − rats were subdivided and treated for 42 days as follows: C) Untreated − ultrapure water; d) AlCl3 at 100 mg/kg bw for 42 days, representing a high level of human exposure to Al. Effects on systolic blood pressure (SBP) and vascular function of aortic and mesenteric resistance arteries (MRA) were studied. Endothelium and smooth muscle integrity were evaluated by concentration-response curves to acetylcholine (ACh) and sodium nitroprusside. Vasoconstrictor responses to phenylephrine (Phe) in the presence and absence of endothelium and in the presence of the NOS inhibitor L-NAME, the potassium channels blocker TEA, the NAD(P)H oxidase inhibitor apocynin, superoxide dismutase (SOD), the non-selective COX inhibitor indomethacin and the selective COX-2 inhibitor NS 398 were analyzed. Vascular reactive oxygen species (ROS), lipid peroxidation and total antioxidant capacity, were measured. The mRNA expressions of eNOS, NAD(P)H oxidase 1 and 2, SOD1, COX-2 and thromboxane A2 receptor (TXA-2 R) were also investigated. Al exposure at human dietary levels impaired the cardiovascular system and these effects were almost the same as Al exposure at much higher levels. Al increased SBP, decreased ACh-induced relaxation, increased response to Phe, decreased endothelial modulation of vasoconstrictor responses, the bioavailability of nitric oxide (NO), the involvement of potassium channels on vascular responses, as well as increased ROS production from NAD(P)H oxidase and contractile prostanoids mainly from COX-2 in both aorta and mesenteric arteries. Al exposure increased vascular ROS production and lipid peroxidation as well as altered the antioxidant status in aorta and MRA. Al decreased vascular eNOS and SOD1 mRNA levels and increased the NAD(P)H oxidase 1, COX-2 and TXA-2 R mRNA levels. Our results point to an excess of ROS mainly from NAD(P)H oxidase after Al exposure and the increased vascular prostanoids from COX-2 acting in concert to decrease NO bioavailability, thus inducing vascular dysfunction and increasing blood pressure. Therefore, 60-day chronic exposure to Al, which reflects common human dietary Al intake, appears to pose a risk for the cardiovascular system

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation

Acute myeloid leukemia (AML) involves a block in terminal differentiation of the myeloid lineage and uncontrolled proliferation of a progenitor state. Using phorbol myristate acetate (PMA), it is possible to overcome this block in THP-1 cells (an M5-AML containing the MLL-MLLT3 fusion), resulting in differentiation to an adherent monocytic phenotype. As part of FANTOM4, we used microarrays to identify 23 microRNAs that are regulated by PMA. We identify four PMA-induced micro- RNAs (mir-155, mir-222, mir-424 and mir-503) that when overexpressed cause cell-cycle arrest and partial differentiation and when used in combination induce additional changes not seen by any individual microRNA. We further characterize these prodifferentiative microRNAs and show that mir-155 and mir-222 induce G2 arrest and apoptosis, respectively. We find mir-424 and mir-503 are derived from a polycistronic precursor mir-424-503 that is under repression by the MLL-MLLT3 leukemogenic fusion. Both of these microRNAs directly target cell-cycle regulators and induce G1 cell-cycle arrest when overexpressed in THP-1. We also find that the pro-differentiative mir-424 and mir-503 downregulate the anti-differentiative mir-9 by targeting a site in its primary transcript. Our study highlights the combinatorial effects of multiple microRNAs within cellular systems.Comment: 45 pages 5 figure

Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism

Objective: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism. Methods: Hypervariable V3–V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n=33 and n=25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profles using bioinformatics in order to identify diferences in taxonomy and metabolic pathways. Results: We identifed a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifdobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_ UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabo‑ lism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed diferences in key bacterial enzymes involved in urate synthesis, degradation, and elimination. Conclusion: Our fndings revealed that taxonomic variations in the gut microbiome of gout patients with and with‑ out tophi might have a functional impact on urate metabolism. Keywords: Gout, Gut microbiota, Uric acid metabolis

Visceral fat area and cardiometabolic risk: The Kardiovize study

BACKGROUND: Visceral fat is associated with adiposity-based complications. Bioimpedance measurement allows estimation of visceral fat area (VFA) in an easy manner. However, a validated cut-off value for VFA by bioimpedance associated with cardiometabolic risk is lacking in European population. AIM: To determine cut-off values of VFA measured via bioimpedance associated with cardiometabolic risk. METHODS: Random cross-sectional Czech population-based sample of 25-64 years old subjects. Receiver Operating Characteristic (ROC) curves were used and the area under the curve (AUC), sensitivity, and specificity were calculated. The Cardiometabolic Disease Staging System (CMDS) was used to classify cardiometabolic risk: Stage 1 - 1 or 2 metabolic syndrome (MetS) components, without impaired fasting glucose (IFG); Stage 2 - MetS or IFG; Stage 3 - MetS with IFG; Stage 4 - type 2 diabetes and/or cardiovascular disease. RESULTS: 2052 participants (54.5% females, median age 49 years) were included. Median VFA (inter-quartile range) were 82.2 cm2 (54.8) in men and 89.8 cm2 (55.6) in women. The best VFA cut-offs associated with Stage 1 in men and women were 71 cm2 (sensitivity = 0.654; specificity = 0.427) and 83 cm2 (sensitivity = 0.705; specificity = 0.556) ; Stage 2: 84 cm2 (sensitivity = 0.673; specificity = 0.551) and 98 cm2 (sensitivity = 0.702; specificity = 0.628) ; Stage 3: 90 cm2 (sensitivity = 0.886; specificity = 0.605) and 109 cm2 (sensitivity = 0.755; specificity = 0.704); Stage 4: 91 cm2 (sensitivity = 0.625; specificity = 0.611) and 81 cm2 (sensitivity = 0.695; specificity = 0.448), respectively. CONCLUSION: A cut-off value of VFA of 71 cm2 in men and 83 cm2 in women exhibited the earliest stage of cardiometabolic risk, and 90 cm2 in men and 109 cm2 in women showed the best performance to detect risk

Molecular phenotyping of single pancreatic islet leader beta cells by "Flash-Seq"

AIMS: Spatially-organized increases in cytosolic Ca2+ within pancreatic beta cells in the pancreatic islet underlie the stimulation of insulin secretion by high glucose. Recent data have revealed the existence of subpopulations of beta cells including "leaders" which initiate Ca2+ waves. Whether leader cells possess unique molecular features, or localisation, is unknown. MAIN METHODS: High speed confocal Ca2+ imaging was used to identify leader cells and connectivity analysis, running under MATLAB and Python, to identify highly connected "hub" cells. To explore transcriptomic differences between beta cell sub-groups, individual leaders or followers were labelled by photo-activation of the cryptic fluorescent protein PA-mCherry and subjected to single cell RNA sequencing ("Flash-Seq"). KEY FINDINGS: Distinct Ca2+ wave types were identified in individual islets, with leader cells present in 73 % (28 of 38 islets imaged). Scale-free, power law-adherent behaviour was also observed in 29 % of islets, though "hub" cells in these islets did not overlap with leaders. Transcripts differentially expressed (295; padj < 0.05) between leader and follower cells included genes involved in cilium biogenesis and transcriptional regulation. Providing some support for these findings, ADCY6 immunoreactivity tended to be higher in leader than follower cells, whereas cilia number and length tended to be lower in the former. Finally, leader cells were located significantly closer to delta, but not alpha, cells in Euclidian space than were follower cells. SIGNIFICANCE: The existence of both a discrete transcriptome and unique localisation implies a role for these features in defining the specialized function of leaders. These data also raise the possibility that localised signalling between delta and leader cells contributes to the initiation and propagation of islet Ca2+ waves

Echinoderms have bilateral tendencies

Echinoderms take many forms of symmetry. Pentameral symmetry is the major form and the other forms are derived from it. However, the ancestors of echinoderms, which originated from Cambrian period, were believed to be bilaterians. Echinoderm larvae are bilateral during their early development. During embryonic development of starfish and sea urchins, the position and the developmental sequence of each arm are fixed, implying an auxological anterior/posterior axis. Starfish also possess the Hox gene cluster, which controls symmetrical development. Overall, echinoderms are thought to have a bilateral developmental mechanism and process. In this article, we focused on adult starfish behaviors to corroborate its bilateral tendency. We weighed their central disk and each arm to measure the position of the center of gravity. We then studied their turning-over behavior, crawling behavior and fleeing behavior statistically to obtain the center of frequency of each behavior. By joining the center of gravity and each center of frequency, we obtained three behavioral symmetric planes. These behavioral bilateral tendencies might be related to the A/P axis during the embryonic development of the starfish. It is very likely that the adult starfish is, to some extent, bilaterian because it displays some bilateral propensity and has a definite behavioral symmetric plane. The remainder of bilateral symmetry may have benefited echinoderms during their evolution from the Cambrian period to the present