The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

High rate nitrogen removal by ANAMMOX internal circulation reactor (IC) for old landfill leachate treatment

© 2017 Elsevier Ltd This study aimed to evaluate the performance of a high rate nitrogen removal lab-scale ANAMMOX reactor, namely Internal Circulation (IC) reactor, for old landfill leachate treatment. The reactor was operated with pre-treated leachate from a pilot Partial Nitritation Reactor (PNR) using a high nitrogen loading rate ranging from 2 to 10 kg N m−3 d−1. High rate removal of nitrogen (9.52 ± 1.11 kg N m−3 d−1) was observed at an influent nitrogen concentration of 1500 mg N L−1. The specific ANAMMOX activity was found to be 0.598 ± 0.026 gN2-N gVSS−1 d−1. Analysis of ANAMMOX granules suggested that 0.5–1.0 mm size granular sludge was the dominant group. The results of DNA analysis revealed that Candidatus Kueneniastuttgartiensis was the dominant species (37.45%) in the IC reactor, whereas other species like uncultured Bacteroidetes bacterium only constituted 5.37% in the system, but they were still responsible for removing recalcitrant organic matter

Contribution of the cyclic nucleotide gated channel subunit, CNG-3, to olfactory plasticity in Caenorhabditis elegans.

In Caenorhabditis elegans, the AWC neurons are thought to deploy a cGMP signaling cascade in the detection of and response to AWC sensed odors. Prolonged exposure to an AWC sensed odor in the absence of food leads to reversible decreases in the animal's attraction to that odor. This adaptation exhibits two stages referred to as short-term and long-term adaptation. Previously, the protein kinase G (PKG), EGL-4/PKG-1, was shown necessary for both stages of adaptation and phosphorylation of its target, the beta-type cyclic nucleotide gated (CNG) channel subunit, TAX-2, was implicated in the short term stage. Here we uncover a novel role for the CNG channel subunit, CNG-3, in short term adaptation. We demonstrate that CNG-3 is required in the AWC for adaptation to short (thirty minute) exposures of odor, and contains a candidate PKG phosphorylation site required to tune odor sensitivity. We also provide in vivo data suggesting that CNG-3 forms a complex with both TAX-2 and TAX-4 CNG channel subunits in AWC. Finally, we examine the physiology of different CNG channel subunit combinations

Genetic interaction between two VNTRs in the MAOA gene is associated with the nicotine dependence

Nicotine dependence is an addiction to tobacco products and a global public health concern that in part would be influenced by our genetics. Smokers are reported to have reduced MAOA activity, but the results from genetic associations with this gene have been inconclusive. Two functionally relevant variable number tandem repeat (VNTR) domains, termed uVNTR and dVNTR, in the MAOA gene are well characterized transcriptional regulatory elements. In the present study, we analyzed uVNTR and dVNTR polymorphisms in the MAOA gene in the Vietnamese male population of smokers and non-smokers in order to assess the association of MAOA with the nicotine dependence measured by the Fagerström Test for Nicotine Dependence (FTND). Individual analysis of VNTRs separately identified uVNTR to be associated with the F6 question of the FTND indicating the stronger addiction to nicotine. No associations were found between the dVNTR and smoking behavior. The combination of dVNTR and uVNTR, that predicts low expression of MAOA (10–3 haplotypes), was significantly associated with the higher nicotine dependence (FTND score), longer smoking duration, and more persistent smoking behavior (fewer quit attempts). In conclusion, our study confirms that low MAOA expression is genetically predictive to the higher nicotine dependence

Diet and ovarian cancer risk: a case–control study in China

This case–control study, conducted in Zhejiang, China during 1999–2000, investigated whether dietary factors have an aetiological association with ovarian cancer. Cases were 254 patients with histologically confirmed epithelial ovary cancer. The 652 controls comprised 340 hospital visitors, 261 non-neoplasm hospital outpatients without long-term diet modifications and 51 women recruited from the community. A validated food frequency questionnaire was used to measure the habitual diet of cases and controls. The risks of ovarian cancer for the dietary factors were assessed by adjusted odds ratios based on multivariate logistic regression analysis, accounting for potential confounding demographic, lifestyle, familial factors and hormonal status, family ovarian cancer history and total energy intake. The ovarian cancer risk declined with increasing consumption of vegetables and fruits but vice versa with high intakes of animal fat and salted vegetables. The adjusted upper quartile odds ratio compared to the lower quartile was 0.24 (0.1–0.5) for vegetables, 0.36 (0.2–0.7) for fruits, 4.6 (2.2–9.3) for animal fat and 3.4 (2.0–5.8) for preserved (salted) vegetables with significant dose-response relationship. The risk of ovarian cancer also appeared to increase for those women preferring fat, fried, cured and smoked food

Institutional leadership—the historical case study of a religious organisation

In this chapter, I discuss institutional leadership vis-à-vis the value of poverty. To do so, I analyse how poverty has been conceptualised within a Catholic religious organisation, the Jesuits. The chapter shows that, in the Jesuit case, poverty is not strictly defined. Instead, poverty results from the constant dialogue between the individual Jesuit and their leader. This means that the understanding of what constitutes poverty is neither explicit nor implicit. The chapter contributes to our understanding of institutional leadership as the promotion and protection of values, as per Selznick’s classical definition. However, we discuss a less known part of Selznick’s work in which the ambiguous character of values is highlighted. In this sense, and after the Jesuit case, we advance the possibility that the promotion and protection of institutional values by institutional leaders does not necessarily imply the definition of what a value is. As values are not defined beforehand but the result of a constant dialogue between the leader and their followers, institutional leadership can be revisited and freed from the heroic view that has long characterised it

Direct determination of the solar neutrino fluxes from solar neutrino data

We determine the solar neutrino fluxes from a global analysis of the solar and terrestrial neutrino data in the framework of three-neutrino mixing. Using a Bayesian approach we reconstruct the posterior probability distribution function for the eight normalization parameters of the solar neutrino fluxes plus the relevant masses and mixing, with and without imposing the luminosity constraint. This is done by means of a Markov Chain Monte Carlo employing the Metropolis-Hastings algorithm. We also describe how these results can be applied to test the predictions of the Standard Solar Models. Our results show that, at present, both models with low and high metallicity can describe the data with good statistical agreement.Comment: 24 pages, 1 table, 7 figures. Acknowledgments correcte

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package