Desynchronization of temporal solitons in Kerr cavities with pulsed injection.

A numerical and analytical study was conducted to investigate the bifurcation mechanisms that cause desynchronization between the soliton repetition frequency and the frequency of external pulsed injection in a Kerr cavity described by the Lugiato-Lefever equation (LLE). The results suggest that desynchronization typically occurs through an Andronov-Hopf (AH) bifurcation. Additionally, a simple and intuitive criterion for this bifurcation to occur is proposed.

Doubling of invariant curves and chaos in three-dimensional diffeomorphisms.

This paper gives a review of doubling bifurcations of closed invariant curves. We also discuss the role of the curve-doubling bifurcations in the formation of chaotic dynamics. In particular, we study scenarios of the emergence of discrete Lorenz and Shilnikov attractors in three-dimensional Hénon maps.

A criterion for mixed dynamics in two-dimensional reversible maps.

We give conditions for non-conservative dynamics in reversible maps with transverse and non-transverse homoclinic orbits.

Similarity and Strength of Glomerular Odor Representations Define a Neural Metric of Sniff-Invariant Discrimination Time.

The olfactory environment is first represented by glomerular activity patterns in the olfactory bulb. It remains unclear how these representations intersect with sampling behavior to account for the time required to discriminate odors. Using different chemical classes, we investigate glomerular representations and sniffing behavior during olfactory decision-making.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta.

Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays.

Remarkable charged particle dynamics near magnetic field null lines.

The study of charged-particle motion in electromagnetic fields is a rich source of problems, models, and new phenomena for nonlinear dynamics. The case of a strong magnetic field is well studied in the framework of a guiding center theory, which is based on conservation of an adiabatic invariant-the magnetic moment. This theory ceases to work near a line on which the magnetic field vanishes-the magnetic field null line.

The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals.

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3].

Reef invertebrate viromics: diversity, host specificity and functional capacity.

Recent metagenomic analyses have revealed a high diversity of viruses in the pelagic ocean and uncovered clear habitat-specific viral distribution patterns. Conversely, similar insights into the composition, host specificity and function of viruses associated with marine organisms have been limited by challenges associated with sampling and computational analysis. Here, we performed targeted viromic analysis of six coral reef invertebrate species and their surrounding seawater to deliver taxonomic and functional profiles of viruses associated with reef organisms.

Equilibration of energy in slow-fast systems.

Ergodicity is a fundamental requirement for a dynamical system to reach a state of statistical equilibrium. However, in systems with several characteristic timescales, the ergodicity of the fast subsystem impedes the equilibration of the whole system because of the presence of an adiabatic invariant. In this paper, we show that violation of ergodicity in the fast dynamics can drive the whole system to equilibrium.

Coral-associated viral communities show high levels of diversity and host auxiliary functions.

Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the dominate across all species examined, and ssDNA viruses, notably the , are also prevalent.

Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.

The gut microbiota generates a huge pool of unknown metabolites, and their identification and characterization is a key challenge in metabolomics. However, there are still gaps on the studies of gut microbiota and their chemical structures. In this investigation, an unusual class of bacterial sulfonolipids (SLs) is detected in mouse cecum, which was originally found in environmental microbes.

Unraveling the microbial processes of black band disease in corals through integrated genomics.

Coral disease outbreaks contribute to the ongoing degradation of reef ecosystems, however, microbial mechanisms underlying the onset and progression of most coral diseases are poorly understood. Black band disease (BBD) manifests as a cyanobacterial-dominated microbial mat that destroys coral tissues as it rapidly spreads over coral colonies. To elucidate BBD pathogenesis, we apply a comparative metagenomic and metatranscriptomic approach to identify taxonomic and functional changes within microbial lesions during in-situ development of BBD from a comparatively benign stage termed cyanobacterial patches.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow.

Exponential energy growth due to slow parameter oscillations in quantum mechanical systems.

It is shown that a periodic emergence and destruction of an additional quantum number leads to an exponential growth of energy of a quantum mechanical system subjected to a slow periodic variation of parameters. The main example is given by systems (e.g.

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies.

Background: The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood.

High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved.

The systems biology of microbial communities, organismal communities inhabiting all ecological niches on earth, has in recent years been strongly facilitated by the rapid development of experimental, sequencing and data analysis methods. Novel experimental approaches and binning methods in metagenomics render the semi-automatic reconstructions of near-complete genomes of uncultivable bacteria possible, while advances in high-resolution amplicon analysis allow for efficient and less biased taxonomic community characterization. This will also facilitate predictive modeling approaches, hitherto limited by the low resolution of metagenomic data.

The 5300-year-old Helicobacter pylori genome of the Iceman.

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H.

Leaky Fermi accelerators.

A Fermi accelerator is a billiard with oscillating walls. A leaky accelerator interacts with an environment of an ideal gas at equilibrium by exchange of particles through a small hole on its boundary. Such interaction may heat the gas: we estimate the net energy flow through the hole under the assumption that the particles inside the billiard do not collide with each other and remain in the accelerator for a sufficiently long time.

Exponential energy growth in adiabatically changing Hamiltonian systems.

We show that the mixed phase space dynamics of a typical smooth Hamiltonian system universally leads to a sustained exponential growth of energy at a slow periodic variation of parameters. We build a model for this process in terms of geometric Brownian motion with a positive drift, and relate it to the steady entropy increase after each period of the parameters variation.

A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes.

A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal. The microbial diversity was examined via 16S rRNA gene analysis. We generated more than 44,000 GS-FLX+454 reads for each animal.

The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.

Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale PPI networks of several model organisms were investigated. A number of theoretical models have been developed to explain both the network formation and the current structure.

Fermi acceleration and adiabatic invariants for non-autonomous billiards.

Recent results concerned with the energy growth of particles inside a container with slowly moving walls are summarized, augmented, and discussed. For breathing bounded domains with smooth boundaries, it is proved that for all initial conditions the acceleration is at most exponential. Anosov-Kasuga averaging theory is reviewed in the application to the non-autonomous billiards, and the results are corroborated by numerical simulations.

Long-range interaction and synchronization of oscillating dissipative solitons.

We study the interaction of well-separated oscillating localized structures (oscillons). We show that oscillons emit weakly decaying dispersive waves, which lead to the formation of bound states due to harmonic synchronization. We also show that in optical applications the Andronov-Hopf bifurcation of stationary localized structures leads to a drastic increase in their interaction strength.