Using genotype abundance to improve phylogenetic inference

Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this paper, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation

Phenomena of fluorescence and phosphorescence

The present paper introduces the basic concepts of luminescence via defining, classifying and enumerating the applications of various types of luminescence. Two key aspects of luminescence- fluorescence and phosphorescence - have been dealt with theoretically for monomolecular and bimolecular materials. The rate equations of these materials have been derived and discussed. The rise and decay of luminescence intensities for both monomolecular and bimolecular materials have been discussed. &nbsp

Conductance at intermediate disorder strength

In a graphene pn junction at high magnetic field, unidirectional “snake states” are formed at the pn interface. In a clean pn junction, each snake state exists in one of the valleys of the graphene band structure, and the conductance of the junction as a whole is determined by microscopic details of the coupling between the snake states at the pn interface and quantum Hall edge states at the sample boundaries [Tworzydło et al., Phys. Rev. B 76, 035411 (2007)]. Disorder mixes and couples the snake states. We here report a calculation of the full conductance distribution in the crossover between the clean limit and the strong-disorder limit, in which the conductance distribution is given by random matrix theory [Abanin and Levitov, Science 317, 641 (2007)]. Our calculation involves an exact solution of the relevant scaling equation for the scattering matrix, and the results are formulated in terms of parameters describing the microscopic disorder potential in bulk graphene

Long-term monitoring of the broad-line region properties in a selected sample of AGN

We present the results of the long-term optical monitoring campaign of active galactic nuclei (AGN) coordinated by the Special Astrophysical Observatory of the Russian Academy of Science. This campaign has produced a remarkable set of optical spectra, since we have monitored for several decades different types of broad-line (type 1) AGN, from a Seyfert 1, double-peaked line, radio loud and radio quiet AGN, to a supermassive binary black hole candidate. Our analysis of the properties of the broad line region (BLR) of these objects is based on the variability of the broad emission lines. We hereby give a comparative review of the variability properties of the broad emission lines and the BLR of seven different type 1 AGNs, emphasizing some important results, such as the variability rate, the BLR geometry, and the presence of the intrinsic Baldwin effect. We are discussing the difference and similarity in the continuum and emission line variability, focusing on what is the impact of our results to the supermassive black hole mass determination from the BLR properties.Comment: Published in Frontiers in Astronomy and Space Scienc

Decay of phosphorescence and delayed fluorescence of organic materials

The Present paper reports the decay of phosphorescence and delayed fluorescence of organic material poly (2,7-(9,9-bis(2-ethyl-hexyle-flourene) (PF2/6). On the basis of the rate equation for the generation , recombination and diffusion of triplet excitons expressions are derived for the decay time of phosphorescence and delayed fluorescence of organic materials. The lifetime of phosphorescence is comes out to be twice the decay time of delayed fluorescence. The intensity of phosphorescence depends linearly on the intensity of the laser light used for exciton , however the intensity of light depends quadritically on the intensity of the laser light used for excitation. A compression is made between the theoretical and experimental results, in which a good agreement is found. &nbsp

Alloy formation by mg under-potential deposition on al from nitrate melts

Magnesium was underpotentially deposited on aluminium electrodes from magnesium nitrate-ammonium nitrate melts at temperatures ranging from 390 to 500 K. The electrochemical techniques used were linear sweep voltammetry and potential step. Electrodes were studied by scanning electron microscopy (SEM), energy dispersive spectrometry (EDS), energy dispersive X-ray spectroscopy (EDX) and X-ray diffraction (XRD). It was found that reduction processes of nitrate, nitrite and water (when present), in the underpotential range studied, took part simultaneously with magnesium underpotential deposition. Consequently, magnesium UPD reduction and stripping voltammetry peaks were not pronounced and well defined. Nevertheless, EDS, EDX and XRD measurements showed evidence of Mg2Al3, MgAl2 and Al12Mg17 alloys formed by underpotential deposition of magnesium onto aluminium substrate

Direct electrical modulation of surface response in a single plasmonic nanoresonator

Classical electrodynamics describes the optical response of macroscopic systems, where the boundaries between materials is treated as infinitesimally thin. However, due to the quantum nature of electrons, interfaces acquires a finite thickness. To include non-classical surface effects in the framework of Maxwell's equations, surface-response functions can be introduced, also known as Feibelman $d$-parameters. Surface response impacts systems with strong field localization at interfaces, which is encountered in noble metal nanoparticles supporting surface plasmon polaritons. However, studying surface response is challenging as it necessitates sub-nanometer control of geometric features, e.g. the gap size in a dimer antenna, while minimizing uncertainties in morphology. In contrast, electrical gating is convenient since the static screening charges are confined exclusively to the surface, which alleviates the need for precise control over the morphology. Here, we study the perturbation of Feibelman $d$-parameters by direct electric charging of a single plasmonic nanoresonator and investigate the resulting changes of the resonance in experiment and theory. The measured change of the resonance frequency matches the theory by assuming a perturbation of the tangential surface current. However, we also observe an unforeseen narrowing in the resonance width when adding electrons to the surface of a plasmonic nanoresonator. These reduced losses cannot be explained by electron spill-out within the local-response approximation (LRA). Such an effect is likely caused by nonlocality and the anisotropy of the perturbed local permittivity. Our findings open up possibilities to reduce losses in plasmonic resonators and to develop ultrafast and extremely small electrically driven plasmonic modulators and metasurfaces by leveraging electrical control over non-classical surface effects.Comment: 10 pages, 3 figures, 15 pages Supplementar

Treatment trends for muscle-invasive bladder cancer in Germany from 2006 to 2019

Purpose: To examine national treatment trends of muscle-invasive bladder cancer (MIBC) in Germany with a special focus on radical cystectomy (RC). Patients and methods: Population-based data were derived from the nationwide hospital billing database of the German Federal Statistical Office and institution-related information from the reimbursement.INFO tool based on hospitals’ quality reports from 2006 to 2019. Additionally, we used the German National Center for Cancer Registry data to analyze all cases of bladder cancer with stage ≥ T2 who received RC, chemotherapy, radiation therapy or a combination from 2006 to 2017. Results: The annual number of RC cases in Germany increased by 28% from 5627 cases in 2006 to 7292 cases in 2019 (p = 0.001). The proportion of patients undergoing RC remained constant at about 75% in all age groups between 2006 and 2017 (p = 0.3). Relative to all performed RC, the proportion of patients > 75 years increased from 25% in 2006 to 38% in 2019 (p = 0.03). The proportion of patients receiving a combination of RC and chemotherapy increased from 9% in 2006 to 13% in 2017 (p = 0.005). In 2006, 8 of 299 urology departments (2.7%) performed more than 50 RCs per year, which increased to 17 of 360 (4.7%) in 2019. In 2019, 107 departments (29%) performed 25–49 RCs and 236 (66%) departments performed < 25 RCs. Conclusion: In Germany, three out of four patients with MIBC receive RC and the proportion of patients > 75 years is increasing. The combination of surgery and chemotherapy is increasingly used. With overall increasing case numbers, there is a slight tendency towards centralization.Peer Reviewe

Genome sequences of human coronavirus OC43 and NL63, associated with respiratory infections in Kilifi, Kenya

Coding-complete genomes of two human coronavirus OC43 strains and one NL63 strain were obtained by metagenomic sequencing of clinical samples collected in 2017 and 2018 in Kilifi, Kenya. Maximum likelihood phylogenies showed that the OC43 strains were genetically dissimilar and that the NL63 strain was closely related to NL63 genotype B viruses. [Abstract copyright: Copyright © 2019 Kamau et al.