Collective Almost Synchronization in Complex Networks

This work introduces the phenomenon of Collective Almost Synchronization (CAS), which describes a universal way of how patterns can appear in complex networks even for small coupling strengths. The CAS phenomenon appears due to the existence of an approximately constant local mean field and is characterized by having nodes with trajectories evolving around periodic stable orbits. Common notion based on statistical knowledge would lead one to interpret the appearance of a local constant mean field as a consequence of the fact that the behavior of each node is not correlated to the behaviors of the others. Contrary to this common notion, we show that various well known weaker forms of synchronization (almost, time-lag, phase synchronization, and generalized synchronization) appear as a result of the onset of an almost constant local mean field. If the memory is formed in a brain by minimising the coupling strength among neurons and maximising the number of possible patterns, then the CAS phenomenon is a plausible explanation for it.Comment: 3 figure

Effects of Argonaute on gene expression in Thermus thermophilus.

This is the final version of the article. Available from the publisher via the DOI in this record.BACKGROUND: Eukaryotic Argonaute proteins mediate RNA-guided RNA interference, allowing both regulation of host gene expression and defense against invading mobile genetic elements. Recently, it has become evident that prokaryotic Argonaute homologs mediate DNA-guided DNA interference, and play a role in host defense. Argonaute of the bacterium Thermus thermophilus (TtAgo) targets invading plasmid DNA during and after transformation. Using small interfering DNA guides, TtAgo can cleave single and double stranded DNAs. Although TtAgo additionally has been demonstrated to cleave RNA targets complementary to its DNA guide in vitro, RNA targeting by TtAgo has not been demonstrated in vivo. METHODS: To investigate if TtAgo also has the potential to control RNA levels, we analyzed RNA-seq data derived from cultures of four T. thermophilus strain HB27 variants: wild type, TtAgo knockout (Δago), and either strain transformed with a plasmid. Additionally we determined the effect of TtAgo on expression of plasmid-encoded RNA and plasmid DNA levels. RESULTS: In the absence of exogenous DNA (plasmid), TtAgo presence or absence had no effect on gene expression levels. When plasmid DNA is present, TtAgo reduces plasmid DNA levels 4-fold, and a corresponding reduction of plasmid gene transcript levels was observed. We therefore conclude that TtAgo interferes with plasmid DNA, but not with plasmid-encoded RNA. Interestingly, TtAgo presence stimulates expression of specific endogenous genes, but only when exogenous plasmid DNA was present. Specifically, the presence of TtAgo directly or indirectly stimulates expression of CRISPR loci and associated genes, some of which are involved in CRISPR adaptation. This suggests that TtAgo-mediated interference with plasmid DNA stimulates CRISPR adaptation.Funding: This study was financially supported by a TOP grant from the Netherlands Organisation for Scientific Research (NWO) to John van der Oost (NWO-TOP 854.10.003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Core to surface excitations on GaAs(110)

We have carried out ab initio calculations of surface core excitations on finite cluster models of the GaAs(110) surface. For the Ga core excitation we find a localized excited state involving excitation into the empty Ga-4p orbital and bound with respect to the conduction band minimum (CBM) by 0.7 eV. This is in reasonable agreement with experiment (binding energy >~0.8 eV). This transition, which is not analogous to bulk core excitations, is termed a core surfaston to emphasize the character of the state. We find that the As core surfaston is above the CBM by 1.0 eV and hence should be difficult to observe

Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T)).

Syntrophobacter fumaroxidans strain MPOB(T) is the best-studied species of the genus Syntrophobacter. The species is of interest because of its anaerobic syntrophic lifestyle, its involvement in the conversion of propionate to acetate, H2 and CO2 during the overall degradation of organic matter, and its release of products that serve as substrates for other microorganisms. The strain is able to ferment fumarate in pure culture to CO2 and succinate, and is also able to grow as a sulfate reducer with propionate as an electron donor. This is the first complete genome sequence of a member of the genus Syntrophobacter and a member genus in the family Syntrophobacteraceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,990,251 bp long genome with its 4,098 protein-coding and 81 RNA genes is a part of the Microbial Genome Program (MGP) and the Genomes to Life (GTL) Program project

Perfluoro Alkyl Hypofluorites and Peroxides Revisited

A more convenient synthesis of the perfluoro alkyl hypofluorite (F3C)3COF as well as the hitherto unknown (C2F5)(F3C)2COF compound is reported. Both hypofluorites can be prepared by use of the corresponding tertiary alcohols RFOH and elemental fluorine in the presence of CsF. An appropriate access to these highly reactive hypofluorites is crucial. The hypofluorites are then transferred into their corresponding perfluoro bisalkyl peroxides RFOORF [RF=(F3C)3C, (C2F5)(F3C)2C] by treatment with partially fluorinated silver wool. NMR, gas‐phase infrared, and solid‐state Raman spectra of the perfluoro bisalkyl peroxides are presented and their chemical properties are discussed

Chemisorption of Al and Ga on the GaAs (110) surface

We have studied the initial stages of the chemisorption of Al and Ga on the clean GaAs (110) surface by applying quantum chemical methods to small clusters representing Al or Ga on GaAs (110). These calculations suggest that at smallest coverages Al or Ga bind to a surface Ga atom; for higher coverages Al and the surface Ga interchange positions. We have obtained the binding energy, the chemical shifts of the Ga–3d, As–3d and Al–2p states, and the microscopic dipole associated with chemisorption of Al or Ga on GaAs (110). These results are compared to experimental values and further experiments are suggested

Prolonged hypothyroidism severely reduces ovarian follicular reserve in adult rats

Background There is substantial evidence both in humans and in animals that a prolonged reduction in plasma thyroid hormone concentration leads to reproductive problems, including disturbed folliculogenesis, impaired ovulation and fertilization rates, miscarriage and pregnancy complications. The objective of the present study is to examine the consequences of chronic hypothyroidism, induced in adulthood, for the size of the ovarian follicle pool. In order to investigate this, adult female rats were provided either a control or an iodide deficient diet in combination with perchlorate supplementation to inhibit iodide uptake by the thyroid. Sixteen weeks later animals were sacrificed. Blood was collected for hormone analyses and ovaries were evaluated histologically. Results At the time of sacrifice, plasma thyroid-stimulating hormone concentrations were 20- to 40-fold increased, thyroxine concentrations were negligible while tri-iothyronin concentrations were decreased by 40% in the hypothyroid group, confirming that the animals were hypothyroid. Primordial, primary and preantral follicle numbers were significantly lower in the hypothyroid ovaries compared to the euthyroid controls, while a downward trend in antral follicle and corpora lutea numbers was observed. Surprisingly the percentage of atretic follicles was not significantly different between the two groups, suggesting that the reduced preantral and antral follicle numbers were presumably not the consequence of increased degeneration of these follicle types in the hypothyroid group. Plasma anti-Müllerian hormone (AMH) levels showed a significant correlation with the growing follicle population represented by the total ovarian number of primary, preantral and antral follicles, suggesting that also under hypothyroid conditions AMH can serve as a surrogate marker to assess the growing ovarian follicle population. Conclusions The induction of a chronic hypothyroid condition in adult female rats negatively affects the ovarian follicular reserve and the size of the growing follicle population, which may impact fertility