3,072 research outputs found
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 mâ3 dâ1. High rate removal of nitrogen (9.52 ± 1.11 kg N mâ3 dâ1) was observed at an influent nitrogen concentration of 1500 mg N Lâ1. The specific ANAMMOX activity was found to be 0.598 ± 0.026 gN2-N gVSSâ1 dâ1. Analysis of ANAMMOX granules suggested that 0.5â1.0 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 (10â3 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 caseâcontrol study in China
This caseâcontrol study, conducted in Zhejiang, China during 1999â2000, 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 (0.1â0.5) for vegetables, 0.36 (0.2â0.7) for fruits, 4.6 (2.2â9.3) for animal fat and 3.4 (2.0â5.8) 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 leadershipâthe historical case study of a religious organisation
In this chapter, I discuss institutional leadership vis-Ă -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 Selznickâs classical definition. However, we discuss a less known part of Selznickâs 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
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