Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure

Who needs a stapling device for haemorrhoidectomy, if one has the radiofrequency device?

Peer reviewedPublisher PD

Fluctuations of radiation from a chaotic laser below threshold

Radiation from a chaotic cavity filled with gain medium is considered. A set of coupled equations describing the photon density and the population of gain medium is proposed and solved. The spectral distribution and fluctuations of the radiation are found. The full noise is a result of a competition between positive correlations of photons with equal frequencies (due to stimulated emission and chaotic scattering) which increase fluctuations, and a suppression due to interaction with a gain medium which leads to negative correlations between photons. The latter effect is responsible for a pronounced suppression of the photonic noise as compared to the linear theory predictions.Comment: 7 pages, 5 figures; expanded version, to appear in Phys. Rev.

The TIGRE gamma-ray telescope

TIGRE is an advanced telescope for gamma-ray astronomy with a few arcmin resolution. From 0.3 to 10 MeV it is a Compton telescope. Above 1 MeV, its multi-layers of double sided silicon strip detectors allow for Compton recoil electron tracking and the unique determination for incident photon direction. From 10 to 100 MeV the tracking feature is utilized for gamma-ray pair event reconstruction. Here we present TIGRE energy resolutions, background simulations and the development of the electronics readout system

Prospectus, December 8, 1993

https://spark.parkland.edu/prospectus_1993/1019/thumbnail.jp

Towards Better Integrators for Dissipative Particle Dynamics Simulations

Coarse-grained models that preserve hydrodynamics provide a natural approach to study collective properties of soft-matter systems. Here, we demonstrate that commonly used integration schemes in dissipative particle dynamics give rise to pronounced artifacts in physical quantities such as the compressibility and the diffusion coefficient. We assess the quality of these integration schemes, including variants based on a recently suggested self-consistent approach, and examine their relative performance. Implications of integrator-induced effects are discussed.Comment: 4 pages, 3 figures, 2 tables, accepted for publication in Phys. Rev. E (Rapid Communication), tentative publication issue: 01 Dec 200

Freezing by Monte Carlo Phase-Switch

We describe a Monte Carlo procedure which allows sampling of the disjoint configuration spaces associated with crystalline and fluid phases, within a single simulation. The method utilises biased sampling techniques to enhance the probabilities of gateway states (in each phase) which are such that a global switch (to the other phase) can be implemented. Equilibrium freezing-point parameters can be determined directly; statistical uncertainties prescribed transparently; and finite-size effects quantified systematically. The method is potentially quite general; we apply it to the freezing of hard spheres.Comment: 5 pages, 2 figure

Designing Chatbots for Crises: A Case Study Contrasting Potential and Reality

Chatbots are becoming ubiquitous technologies, and their popularity and adoption are rapidly spreading. The potential of chatbots in engaging people with digital services is fully recognised. However, the reputation of this technology with regards to usefulness and real impact remains rather questionable. Studies that evaluate how people perceive and utilise chatbots are generally lacking. During the last Kenyan elections, we deployed a chatbot on Facebook Messenger to help people submit reports of violence and misconduct experienced in the polling stations. Even though the chatbot was visited by more than 3,000 times, there was a clear mismatch between the users’ perception of the technology and its design. In this paper, we analyse the user interactions and content generated through this application and discuss the challenges and directions for designing more effective chatbots

Detection of non-thermal X-ray emission in the lobes and jets of Cygnus A

This article has been published in Monthly Notices of the Royal Astronomical Society © 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. 21 pages, 8 figuresWe present a spectral analysis of the lobes and X-ray jets of Cygnus A, using more than 2 Ms of $\textit{Chandra}$ observations. The X-ray jets are misaligned with the radio jets and significantly wider. We detect non-thermal emission components in both lobes and jets. For the eastern lobe and jet, we find 1 keV flux densities of $71_{-10}^{+10}$ nJy and $24_{-4}^{+4}$ nJy, and photon indices of $1.72_{-0.03}^{+0.03}$ and $1.64_{-0.04}^{+0.04}$ respectively. For the western lobe and jet, we find flux densities of $50_{-13}^{+12}$ nJy and $13_{-5}^{+5}$ nJy, and photon indices of $1.97_{-0.10}^{+0.23}$ and $1.86_{-0.12}^{+0.18}$ respectively. Using these results, we modeled the electron energy distributions of the lobes as broken power laws with age breaks. We find that a significant population of non-radiating particles is required to account for the total pressure of the eastern lobe. In the western lobe, no such population is required and the low energy cutoff to the electron distribution there needs to be raised to obtain pressures consistent with observations. This discrepancy is a consequence of the differing X-ray photon indices, which may indicate that the turnover in the inverse-Compton spectrum of the western lobe is at lower energies than in the eastern lobe. We modeled the emission from both jets as inverse-Compton emission. There is a narrow region of parameter space for which the X-ray jet can be a relic of an earlier active phase, although lack of knowledge about the jet's electron distribution and particle content makes the modelling uncertain.Peer reviewedFinal Published versio

Random Resonators and Prelocalized Modes in Disordered Dielectric Films

Areal density of disorder-induced resonators with a high quality factor, $Q\gg 1$, in a film with fluctuating refraction index is calculated theoretically. We demonstrate that for a given $kl>1$, where $k$ is the light wave vector, and $l$ is the transport mean free path, when {\em on average} the light propagation is diffusive, the likelihood for finding a random resonator increases dramatically with increasing the correlation radius of the disorder. Parameters of {\em most probable} resonators as functions of $Q$ and $kl$ are found.Comment: 6 pages including 2 figure