Speciational view of macroevolution: are micro and macroevolution decoupled?

We introduce a simple computational model that, with a microscopic dynamics driven by natural selection and mutation alone, allows the description of true speciation events. A statistical analysis of the so generated evolutionary tree captures realistic features showing power laws for frequency distributions in time and size. Albeit these successful predictions, the difficulty in obtaining punctuated dynamics with mass extinctions suggests the necessity of decoupling micro and macro-evolutionary mechanisms in agreement with some ideas of Gould's and Eldredge's theory of punctuated equilibrium.Comment: Europhys. Lett. 75:342--34

Effects of Preference for Attachment to Low-degree Nodes on the Degree Distributions of a Growing Directed Network and a Simple Food-Web Model

We study the growth of a directed network, in which the growth is constrained by the cost of adding links to the existing nodes. We propose a new preferential-attachment scheme, in which a new node attaches to an existing node i with probability proportional to 1/k_i, where k_i is the number of outgoing links at i. We calculate the degree distribution for the outgoing links in the asymptotic regime (t->infinity), both analytically and by Monte Carlo simulations. The distribution decays like k c^k/Gamma(k) for large k, where c is a constant. We investigate the effect of this preferential-attachment scheme, by comparing the results to an equivalent growth model with a degree-independent probability of attachment, which gives an exponential outdegree distribution. Also, we relate this mechanism to simple food-web models by implementing it in the cascade model. We show that the low-degree preferential-attachment mechanism breaks the symmetry between in- and outdegree distributions in the cascade model. It also causes a faster decay in the tails of the outdegree distributions for both our network growth model and the cascade model.Comment: 10 pages, 7 figures. A new figure added. Minor modifications made in the tex

Robustness of One-Dimensional Photonic Bandgaps Under Random Variations of Geometrical Parameters

The supercell method is used to study the variation of the photonic bandgaps in one-dimensional photonic crystals under random perturbations to thicknesses of the layers. The results of both plane wave and analytical band structure and density of states calculations are presented along with the transmission cofficient as the level of randomness and the supercell size is increased. It is found that higher bandgaps disappear first as the randomness is gradually increased. The lowest bandgap is found to persist up to a randomness level of 55 percent.Comment: Submitted to Physical Review B on April 8 200

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel

Tangled Nature: A model of emergent structure and temporal mode among co-evolving agents

Understanding systems level behaviour of many interacting agents is challenging in various ways, here we'll focus on the how the interaction between components can lead to hierarchical structures with different types of dynamics, or causations, at different levels. We use the Tangled Nature model to discuss the co-evolutionary aspects connecting the microscopic level of the individual to the macroscopic systems level. At the microscopic level the individual agent may undergo evolutionary changes due to mutations of strategies. The micro-dynamics always run at a constant rate. Nevertheless, the system's level dynamics exhibit a completely different type of intermittent abrupt dynamics where major upheavals keep throwing the system between meta-stable configurations. These dramatic transitions are described by a log-Poisson time statistics. The long time effect is a collectively adapted of the ecological network. We discuss the ecological and macroevolutionary consequences of the adaptive dynamics and briefly describe work using the Tangled Nature framework to analyse problems in economics, sociology, innovation and sustainabilityComment: Invited contribution to Focus on Complexity in European Journal of Physics. 25 page, 1 figur

Dysfunction of endothelial progenitor cells is associated with the type I IFN pathway in patients with polymyositis and dermatomyositis

Objective. Alterations in phenotype and function of endothelial progenitor cells (EPCs) have been associated with poor vascular outcomes and impaired vascular repair in various conditions. Our hypothesis was that patients with PM and DM have dysregulation of EPCs driven by type I IFN and IL-18 similar to other autoimmune diseases. Methods. Quantification of circulating EPCs was performed by flow cytometry in patients with PM/DM and matched healthy controls. The ability of EPCs to differentiate into mature endothelial cells was investigated by light and fluorescence microscopy quantification in the presence or absence of PM/DM or control serum, neutralizing antibodies to type I IFN receptor or IL-18. Serum type I IFN activity was quantified by induction of type I IFN-inducible genes in HeLa cells. Circulating IL-18 concentrations were assessed by ELISA. Results. Circulating EPCs were significantly lower in PM/DM patients compared with controls. PM/DM EPCs displayed a decreased capacity to differentiate into mature endothelial cells and PM/DM serum significantly inhibited differentiation of control EPCs. This effect was reversed in the majority of samples with neutralizing antibodies to IL-18 or to type I IFN receptor or by a combination of these antibodies. Patients with associated impairments in EPC function had higher type I IFN serum activity. Conclusion. PM/DM is associated with dysregulation of EPC phenotype and function that may be attributed, at least in part, to aberrant IL-18 and type I IFN pathways. The implication of these vasculopathic findings for disease prognosis and complications remains to be determined

Effect of Aging Treatment on Surface Roughness, Mechanical Properties, and Fracture Behavior of 6xxx and 7xxx Aluminum Alloys

The effect of aging treatment on the surface roughness and mechanical properties of AA6061 and AA7075 alloys was studied. Microhardness and tensile tests were used to investigae the mechanical properties. X-ray diffraction analysis was used to investigate the surface of the specimens. Furthermore, after tensile tests fractured surfaces were examined with scanning electron microscopy. An atomic force microscope was employed for analysis of the effect of aging treatment on surface roughness. Higher surface roughness with an increase in the volume fraction of the precipitate was revealed.Исследовано влияние процесса старения на шероховатость поверхности и механические свойства алюминиевых сплавов AA6061 и AA7075. Механические свойства исследовали при испытаниях на микротвердость и растяжение. Поверхность образцов исследовали с помощью рентгеноструктурного анализа. После испытания на растяжение поверхность разрушения исследовали методом растровой электронной микроскопии. Влияние процесса старения на шероховатость поверхности изучали с помощью атомно-силового микроскопа. Показано, что с ростом шероховатости поверхности увеличивается количество выделившихся фаз.Досліджено вплив процесу старіння на шорсткість поверхні і механічні властивості алюмінієвих сплавів АА6061 та АА7075. Механічні властивості досліджували при випробуваннях на мікротвердість і розтяг. Поверхню зразків досліджували за допомогою рентгеноструктурного аналізу. Після випробувань на розтяг поверхню руйнування досліджували методом растрової електронної мікроскопії. Вплив процесу старіння на шорсткість поверхні вивчали за допомогою атомно-силового мікроскопа. Показано, що з ростом шорсткості поверхні збільшується кількість виділених фа

Magnetoelectric Effect in Hydrogen Harvesting: Magnetic Field as a Trigger of Catalytic Reactions (Adv. Mater. 19/2022)

Magnetic fields have been regarded as an additional stimulus for electro- and photocatalytic reactions, but not as a direct trigger for catalytic processes. Multiferroic/magnetoelectric materials, whose electrical polarization and surface charges can be magnetically altered, are especially suitable for triggering and control of catalytic reactions solely with magnetic fields. Here, we demonstrate that magnetic fields can be employed as an independent input energy source for hydrogen harvesting by means of the magnetoelectric effect. Composite multiferroic CoFe2O4-BiFeO3 core-shell nanoparticles act as catalysts for the hydrogen evolution reaction (HER) that is triggered when an alternating magnetic field is applied to an aqueous dispersion of the magnetoelectric nanocatalysts. Based on density functional calculations, we propose that the hydrogen evolution is driven by changes in the ferroelectric polarization direction of BiFeO3 caused by the magnetoelectric coupling. We believe our findings will open new avenues towards magnetically induced renewable energy harvesting

Photocatalytic Activity of Mesoporous Graphitic Carbon Nitride (mpg-C3N4) Towards Organic Chromophores Under UV and VIS Light Illumination

A template-assisted synthetic method including the thermal polycondensation of guanidine hydrochloride (GndCl) was utilized to synthesize highly-organized mesoporous graphitic carbon nitride (mpg-C3N4) photocatalysts. Comprehensive structural analysis of the mpg-C3N4 materials were performed by XPS, XRD, FT-IR, BET and solid-state NMR spectroscopy. Photocatalytic performance of the mpg-C3N4 materials was studied for the photodegradation of several dyes under visible and UV light illumination as a function of catalyst loading and the structure of mpg-C3N4 depending on the polycondensation temperature. Among all of the formerly reported performances in the literature (including the ones for Degussa P25 commercial benchmark), currently synthesized mpg-C3N4 photocatalysts exhibit a significantly superior visible light-induced photocatalytic activity towards rhodamine B (RhB) dye. Enhanced catalytic efficiency could be mainly attributed to the terminated polycondensation process, high specific surface area, and mesoporous structure with a wide pore size distribution. © 2016, Springer Science+Business Media New York