Anthropocenic culturecide: an epitaph

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Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria - evolution of the Sox sulfur-oxidizing enzyme system

The soxB gene encodes the SoxB component of the periplasmic thiosulfate-oxidizing Sox enzyme complex, which has been proposed to be widespread among the various phylogenetic groups of sulfur-oxidizing bacteria (SOB) that convert thiosulfate to sulfate with and without the formation of sulfur globules as intermediate. Indeed, the comprehensive genetic and genomic analyses presented in the present study identified the soxB gene in 121 phylogenetically and physiologically divergent SOB, including several species for which thiosulfate utilization has not been reported yet. In first support of the previously postulated general involvement of components of the Sox enzyme complex in the thiosulfate oxidation process of sulfur-storing SOB, the soxB gene was detected in all investigated photo- and chemotrophic species that form sulfur globules during thiosulfate oxidation (Chromatiaceae, Chlorobiaceae, Ectothiorhodospiraceae, Thiothrix, Beggiatoa, Thiobacillus, invertebrate symbionts and free-living relatives). The SoxB phylogeny reflected the major 16S rRNA gene-based phylogenetic lineages of the investigated SOB, although topological discrepancies indicated several events of lateral soxB gene transfer among the SOB, e.g. its independent acquisition by the anaerobic anoxygenic phototrophic lineages from different chemotrophic donor lineages. A putative scenario for the proteobacterial origin and evolution of the Sox enzyme system in SOB is presented considering the phylogenetic, genomic (sox gene cluster composition) and geochemical data

Quality program plan

This report describes a quality program plan for the Mound laboratory. Areas include variation engineering, technical manual process control systems, process performance data, product index system, promotional marketing program, quality engineering staff, ultimate use education, and management reporting

Near-field optical power transmission of dipole nano-antennas

Nano-antennas in functional plasmonic applications require high near-field optical power transmission. In this study, a model is developed to compute the near-field optical power transmission in the vicinity of a nano-antenna. To increase the near-field optical power transmission from a nano-antenna, a tightly focused beam of light is utilized to illuminate a metallic nano-antenna. The modeling and simulation of these structures is performed using 3-D finite element method based full-wave solutions of Maxwell’s equations. Using the optical power transmission model, the interaction of a focused beam of light with plasmonic nanoantennas is investigated. In addition, the tightly focused beam of light is passed through a band-pass filter to identify the effect of various regions of the angular spectrum to the near-field radiation of a dipole nano-antenna. An extensive parametric study is performed to quantify the effects of various parameters on the transmission efficiency of dipole nano-antennas, including length, thickness, width, and the composition of the antenna, as well as the wavelength and half-beam angle of incident light. An optimal dipole nanoantenna geometry is identified based on the parameter studies in this work. In addition, the results of this study show the interaction of the optimized dipole nano-antenna with a magnetic recording medium when it is illuminated with a focused beam of light

Quantifying the 2.5D imaging performance of digital holographic systems

Digital holographic systems are a class of two step, opto-numerical, three-dimensional imaging techniques. The role of the digital camera in limiting the resolution and field of view of the reconstructed image, and the interaction of these limits with a general optical system is poorly understood. The linear canonical transform describes any optical system consisting of lenses and/or free space in a unified manner. Expressions derived using it are parametrised in terms of the parameters of the optical system, as well as those of the digital camera: aperture size, pixel size and pixel pitch. We develop rules of thumb for selecting an optical system to minimise mean squared error for given input and digital camera parameters. In the limit, our results constitute a point spread function analysis. The results presented in this paper will allow digital holography practitioners to select an optical system to maximise the quality of their reconstructed image using a priori knowledge of the camera and object

Proximity effect at superconducting Sn-Bi2Se3 interface

We have investigated the conductance spectra of Sn-Bi2Se3 interface junctions down to 250 mK and in different magnetic fields. A number of conductance anomalies were observed below the superconducting transition temperature of Sn, including a small gap different from that of Sn, and a zero-bias conductance peak growing up at lower temperatures. We discussed the possible origins of the smaller gap and the zero-bias conductance peak. These phenomena support that a proximity-effect-induced chiral superconducting phase is formed at the interface between the superconducting Sn and the strong spin-orbit coupling material Bi2Se3.Comment: 7 pages, 8 figure

A Practical Guide to Digital Holography and Generalized Sampling

The theorems of Nyquist, Shannon and Whittaker have long held true for sampling optical signals. They showed that a signal (with finite bandwidth) should be sampled at a rate at least as fast as twice the maximum spatial frequency of the signal. They proceeded to show how the continuous signal could be reconstructed perfectly from its well sampled counterpart by convolving a Sinc function with the sampled signal. Recent years have seen the emergence of a new generalized sampling theorem of which Nyquist Shannon is a special case. This new theorem suggests that it is possible to sample and reconstruct certain signals at rates much slower than those predicted by Nyquist-Shannon. One application in which this new theorem is of considerable interest is Fresnel Holography. A number of papers have recently suggested that the sampling rate for the digital recording of Fresnel holograms can be relaxed considerably. This may allow the positioning of the object closer to the camera allowing for a greater numerical aperture and thus an improved range of 3D perspective. In this paper we: (i) Review generalized sampling for Fresnel propagated signals, (ii) Investigate the effect of the twin image, always present in recording, on the generalized sampling theorem and (iii) Discuss the effect of finite pixel size for the first time

Formation of dense partonic matter in relativistic nucleus-nucleus collisions at RHIC: Experimental evaluation by the PHENIX collaboration

Extensive experimental data from high-energy nucleus-nucleus collisions were recorded using the PHENIX detector at the Relativistic Heavy Ion Collider (RHIC). The comprehensive set of measurements from the first three years of RHIC operation includes charged particle multiplicities, transverse energy, yield ratios and spectra of identified hadrons in a wide range of transverse momenta (p_T), elliptic flow, two-particle correlations, non-statistical fluctuations, and suppression of particle production at high p_T. The results are examined with an emphasis on implications for the formation of a new state of dense matter. We find that the state of matter created at RHIC cannot be described in terms of ordinary color neutral hadrons.Comment: 510 authors, 127 pages text, 56 figures, 1 tables, LaTeX. Submitted to Nuclear Physics A as a regular article; v3 has minor changes in response to referee comments. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review

Mediating effect of pubertal stages on the family environment and neurodevelopment: An open-data replication and multiverse analysis of an ABCD Study®

Contains fulltext : 285495.pdf (Publisher’s version ) (Open Access)Increasing evidence demonstrates that environmental factors meaningfully impact the development of the brain (Hyde et al., 2020; McEwen and Akil, 2020). Recent work from the Adolescent Brain Cognitive Development (ABCD) Study® suggests that puberty may indirectly account for some association between the family environment and brain structure and function (Thijssen et al., 2020). However, a limited number of large studies have evaluated what, how, and why environmental factors impact neurodevelopment. When these topics are investigated, there is typically inconsistent operationalization of variables between studies which may be measuring different aspects of the environment and thus different associations in the analytic models. Multiverse analyses (Steegen et al., 2016) are an efficacious technique for investigating the effect of different operationalizations of the same construct on underlying interpretations. While one of the assets of Thijssen et al. (2020) was its large sample from the ABCD data, the authors used an early release that contained 38% of the full ABCD sample. Then, the analyses used several 'researcher degrees of freedom' (Gelman and Loken, 2014) to operationalize key independent, mediating and dependent variables, including but not limited to, the use of a latent factor of preadolescents' environment comprised of different subfactors, such as parental monitoring and child-reported family conflict. While latent factors can improve reliability of constructs, the nuances of each subfactor and measure that comprise the environment may be lost, making the latent factors difficult to interpret in the context of individual differences. This study extends the work of Thijssen et al. (2020) by evaluating the extent to which the analytic choices in their study affected their conclusions. In Aim 1, using the same variables and models, we replicate findings from the original study using the full sample in Release 3.0. Then, in Aim 2, using a multiverse analysis we extend findings by considering nine alternative operationalizations of family environment, three of puberty, and five of brain measures (total of 135 models) to evaluate the impact on conclusions from Aim 1. In these results, 90% of the directions of effects and 60% of the p-values (e.g. p > .05 and p < .05) across effects were comparable between the two studies. However, raters agreed that only 60% of the effects had replicated. Across the multiverse analyses, there was a degree of variability in beta estimates across the environmental variables, and lack of consensus between parent reported and child reported pubertal development for the indirect effects. This study demonstrates the challenge in defining which effects replicate, the nuance across environmental variables in the ABCD data, and the lack of consensus across parent and child reported puberty scales in youth.16 p