Keeping it cool: Soil sample cold pack storage and DNA shipment up to 1 month does not impact metabarcoding results

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.With the advances of sequencing tools, the fields of environmental microbiology and soil ecology have been transformed. Today, the unculturable majority of soil microbes can be sequenced. Although these tools give us tremendous power and open many doors to answer important questions, we must understand how sample processing may impact our results and interpretations. Here, we test the impacts of four soil storage methods on downstream amplicon metabarcoding and qPCR analyses for fungi and bacteria. We further investigate the impact of thaw time on extracted DNA to determine a safe length of time during which this can occur with minimal impact on study results. Overall, we find that storage using standard cold packs with subsequent storage at −20°C is little different than immediate storage in liquid nitrogen, suggesting that the historical and current method is adequate. We further find evidence that storage at room temperature or with aid of RNAlater can lead to changes in community composition and in the case of RNAlater, lower gene copies. We therefore advise against these storage methods for metabarcoding analyses. Finally, we show that over 1 month, DNA extract thaw time does not impact diversity or qPCR metrics. We hope that this work will help researchers working with soil bacteria and fungi make informed decisions about soil storage and transport to ensure repeatability and accuracy of results and interpretations.National Science Foundation (DEB- 1738041, OIA 1656006)National Geographic Society (WW-036ER-17

Mixing among light scalar mesons and L=1 q\bar{q} scalar mesons

Following the re-establishment of the \sigma(600) and the \kappa(900), the light scalar mesons a_0(980) and f_0(980) together with the \sigma(600) and the \kappa(900) are considered as the chiral scalar partner of pseudoscalar nonet in SU(3) chiral symmetry, and the high mass scalar mesons a_0(1450), K^*_0(1430), f_0(1370) and f_0(1710) turned out to be considered as the L=1 q\bar{q} scalar mesons. We assume that the high mass of the L=1 q\bar{q} scalar mesons is caused by the mixing with the light scalar mesons. For the structure of the light scalar mesons, we adopted the qq\bar{q}\bar{q} model in order to explain the "scalar meson puzzle". The inter-mixing between the light scalar nonet and the high mass L=1 q\bar{q} nonet and the intra-mixing among each nonet are analyzed by including the glueball into the high mass scalar nonet.Comment: 16 pages, 5 figure

Effects to Scalar Meson Decays of Strong Mixing between Low and High Mass Scalar Mesons

We analyze the mass spectroscopy of low and high mass scalar mesons and get the result that the coupling strengths of the mixing between low and high mass scalar mesons are very strong and the strengths of mixing for $I=1, 1/2$ scalar mesons and those of I=0 scalar mesons are almost same. Next, we analyze the decay widths and decay ratios of these mesons and get the results that the coupling constants $A'$ for $I=1, 1/2$ which represents the coupling of high mass scalar meson $N'$ -> two pseudoscalar mesons $PP$ are almost same as the coupling $A'$ for the I=0. On the other hand, the coupling constant $A$ for $I=1, I=1/2$ which represents the low mass scalar meson $N$ -> $PP$ are far from the coupling constant $A$ for I=0. We consider a resolution for this discrepancy. Coupling constant $A''$ for glueball $G$ -> $PP$ is smaller than the coupling $A'$. $\theta_P$ is $40^\circ \sim 50^\circ$.Comment: 15 pages, 6 figure

Effects of vessel traffic on relative abundance and behaviour of cetaceans : the case of the bottlenose dolphins in the Archipelago de La Maddalena, north-western Mediterranean sea

Acknowledgements This study was part of the Tursiops Project of the Dolphin Research Centre of Caprera, La Maddalena. Financial and logistical support was provided by the Centro Turistico Studentesco (CTS) and by the National Park of the Archipelago de La Maddalena. We thank the Natural Reserve of Bocche di Bonifacio for the support provided during data collection. The authors thank the numerous volunteers of the Caprera Dolphin Research Centre and especially Marco Ferraro, Mirko Ugo, Angela Pira and Maurizio Piras whose assistance during field observation and skills as a boat driver were invaluable.Peer reviewedPostprin

Tri-meson-mixing of π\pi-η\eta-η′\eta' and ρ\rho-ω\omega-ϕ\phi in the light-cone quark model

The radiative transition form factors of the pseudoscalar mesons {$\pi$, $\eta$, $\eta'$} and the vector mesons {$\rho$, $\omega$, $\phi$} are restudied with $\pi$-$\eta$-$\eta'$ and $\rho$-$\omega$-$\phi$ in tri-meson-mixing pattern, which is described by tri-mixing matrices in the light-cone constituent quark model. The experimental transition decay widths are better reproduced with tri-meson-mixing than previous results in a two-mixing-angle scenario of only two-meson $\eta$-$\eta'$ mixing and $\omega$-$\phi$ mixing.Comment: 8 pages, 6 figures, final version to appear in EPJ

Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.National Science Foundation (NSF) [DEB-0608178]U.S. Environmental Protection AgencyDepartment of EducationSigma XiUniversity of ChicagoFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)(CAPES) Coordenacao de Aperfeicoamento de Pessoal de Nivel Superiori

J/psi->VP decays and the quark and gluon content of the eta and eta'

The $\eta$-$\eta^\prime$ pseudoscalar mixing angle and the gluonium content of the $\eta^\prime$ meson are deduced from an updated phenomenological analysis of $J/\psi$ decays into a vector and a pseudoscalar meson. In absence of gluonium, the value of the mixing angle in the quark-flavour basis is found to be $\phi_P=(40.7\pm 2.3)^\circ$. In presence of gluonium, the values for the mixing angle and the gluonic content of the $\eta^\prime$ wave function are $\phi_P=(44.6\pm 4.4)^\circ$ and $Z^2_{\eta^\prime}=0.29^{+0.18}_{-0.26}$, respectively. The newly reported values of $B(J/\psi\to\rho\pi)$ by the BABAR and BES Collaborations are crucial to get a consistent description of data.Comment: 7 pages, 1 figure, uses svjour style. Comments on the relationship between J/psi to VP and V to Pgamma decays and on the neglected contributions together with an asymmetric treatment of errors are include

Illustrations and guidelines for selecting statistical methods for quantifying spatial pattern in ecological data

This paper aims to provide guidance to ecologists with limited experience in spatial analysis to help in their choice of techniques, It uses examples to compare methods of spatial analysis for ecological field data. A taxonomy of different data types is presented, including point- and area-referenced data, with and without attributes. Spatially and non-spatially explicit data are distinguished. The effects of sampling and other transformations that convert one data type to another are discussed; the possible loss of spatial information is considered. Techniques for analyzing spatial pattern, developed in plant ecology, animal ecology, landscape ecology, geostatistics and applied statistics are reviewed briefly and their overlap in methodology and philosophy noted. The techniques are categorized according to their output and the inferences that may be drawn from them, in a discursive style without formulae. Methods are compared for four case studies with field data covering a range of types. These are: 1) percentage cover of three shrubs along a line transect 2) locations and volume of a desert plant in a I ha area: 3) a remotely-sensed spectral index and elevation from 10(5) km(2) of a mountainous region; and 4) land cover from three rangeland types within 800 km2 of a coastal region. Initial approaches utilize mapping, frequency distributions and variance-mean indices. Analysis techniques we compare include: local quadrat variance, block, quadrat variance, correlograms, variograms, angular correlation, directional variograms, wavelets, SADIE, nearest neighbour methods, Ripley's L(t), and various landscape ecology metrics. Our advice to ecologists is to use simple visualization techniques for initial analysis, and subsequently to select methods that are appropriate for the data type and that answer their specific questions of interest, It is usually prudent to employ several different techniques

Gaze fixation improves the stability of expert juggling

Novice and expert jugglers employ different visuomotor strategies: whereas novices look at the balls around their zeniths, experts tend to fixate their gaze at a central location within the pattern (so-called gaze-through). A gaze-through strategy may reflect visuomotor parsimony, i.e., the use of simpler visuomotor (oculomotor and/or attentional) strategies as afforded by superior tossing accuracy and error corrections. In addition, the more stable gaze during a gaze-through strategy may result in more accurate movement planning by providing a stable base for gaze-centered neural coding of ball motion and movement plans or for shifts in attention. To determine whether a stable gaze might indeed have such beneficial effects on juggling, we examined juggling variability during 3-ball cascade juggling with and without constrained gaze fixation (at various depths) in expert performers (n = 5). Novice jugglers were included (n = 5) for comparison, even though our predictions pertained specifically to expert juggling. We indeed observed that experts, but not novices, juggled significantly less variable when fixating, compared to unconstrained viewing. Thus, while visuomotor parsimony might still contribute to the emergence of a gaze-through strategy, this study highlights an additional role for improved movement planning. This role may be engendered by gaze-centered coding and/or attentional control mechanisms in the brain