79 research outputs found
Louse (Insecta : Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable
Lice are ectoparasitic insects hosted by birds and mammals. Mitochondrial 12S rRNA sequences obtained from lice show considerable length variation and are very difficult to align. We show that the louse 12S rRNA domain III secondary structure displays considerable variation compared to other insects, in both the shape and number of stems and loops. Phylogenetic trees constructed from tree edit distances between louse 12S rRNA structures do not closely resemble trees constructed from sequence data, suggesting that at least some of this structural variation has arisen independently in different louse lineages. Taken together with previous work on mitochondrial gene order and elevated rates of substitution in louse mitochondrial sequences, the structural variation in louse 12S rRNA confirms the highly distinctive nature of molecular evolution in these insects
Unifying Parsimonious Tree Reconciliation
Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach to address this research problem is to describe each individual
evolution as a phylogenetic tree and construct a tree reconciliation which is
parsimonious with respect to a given event model. Unfortunately, most of the
previous approaches are designed only either for host-parasite systems, for
gene tree/species tree reconciliation, or biogeography. Hence, a method is
desirable, which addresses the general problem of mapping phylogenetic trees
and covering all varieties of coevolving systems, including e.g., predator-prey
and symbiotic relationships. To overcome this gap, we introduce a generalized
cophylogenetic event model considering the combinatorial complete set of local
coevolutionary events. We give a dynamic programming based heuristic for
solving the maximum parsimony reconciliation problem in time O(n^2), for two
phylogenies each with at most n leaves. Furthermore, we present an exact
branch-and-bound algorithm which uses the results from the dynamic programming
heuristic for discarding partial reconciliations. The approach has been
implemented as a Java application which is freely available from
http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence
This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement:
A copy of the source data and R code used in this study have been deposited at figshare.com: https://doi.org/10.6084/m9.figshare.14393309
This article has earned Open Data and Open Materials badges. Data and materials are available at: https://figshare.com/articles/dataset/Dataset_for_ELE_EV_ELE13757/14393309?file=27503576 and https://figshare.com/articles/dataset/Dataset_for_ELE_EV_ELE13757/14393309?file=27503579Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.Kungliga Fysiografiska Sällskapet i LundAustralian Research Council (ARC
Atovaquone Compared with Dapsone for the Prevention of Pneumocystis carinii Pneumonia in Patients with HIV Infection Who Cannot Tolerate Trimethoprim, Sulfonamides, or Both
BACKGROUND
Although trimethoprim–sulfamethoxazole is the drug of choice for the prevention of Pneumocystis carinii pneumonia, many patients cannot tolerate it and must switch to an alternative agent. METHODS
We conducted a multicenter, open-label, randomized trial comparing daily atovaquone (1500-mg suspension) with daily dapsone (100 mg) for the prevention of P. carinii pneumonia among patients infected with the human immunodeficiency virus who could not tolerate trimethoprim–sulfamethoxazole. The median follow-up period was 27 months. RESULTS
Of 1057 patients enrolled, 298 had a history of P. carinii pneumonia.P. cariniipneumonia developed in 122 of 536 patients assigned to atovaquone (15.7 cases per 100 person-years), as compared with 135 of 521 in the dapsone group (18.4 cases per 100 person-years; relative risk for atovaquone vs. dapsone, 0.85; 95 percent confidence interval, 0.67 to 1.09; P=0.20). The relative risk of death was 1.07 (95 percent confidence interval, 0.89 to 1.30; P=0.45), and the relative risk of discontinuation of the assigned medication because of adverse events was 0.94 (95 percent confidence interval, 0.74 to 1.19; P=0.59). Among the 546 patients who were receiving dapsone at base line, the relative risk of discontinuation because of adverse events was 3.78 for atovaquone as compared with dapsone (95 percent confidence interval, 2.37 to 6.01; P CONCLUSIONS
Among patients who cannot tolerate trimethoprim–sulfamethoxazole, atovaquone and dapsone are similarly effective for the prevention ofP. carinii pneumonia. Our results support the continuation of dapsone prophylaxis among patients who are already receiving it. However, among those not receiving dapsone, atovaquone is better tolerated and may be the preferred choice for prophylaxis against P. cariniipneumonia
Ionic and electronic structure of sodium clusters up to N=59
We determined the ionic and electronic structure of sodium clusters with even
electron numbers and 2 to 59 atoms in axially averaged and three-dimensional
density functional calculations. A local, phenomenological pseudopotential that
reproduces important bulk and atomic properties and facilitates structure
calculations has been developed. Photoabsorption spectra have been calculated
for , , and to
. The consistent inclusion of ionic structure considerably
improves agreement with experiment. An icosahedral growth pattern is observed
for to . This finding is supported by
photoabsorption data.Comment: To appear in Phys. Rev. B 62. Version with figures in better quality
can be requested from the author
Bridging the Gap between Quantum Mechanics and Large-Scale Atomistic Simulation
The prospect of modeling across disparate length and time scales to achieve a predictive multiscale description of real materials properties has attracted widespread research interest in the last decade. To be sure, the challenges in such multiscale modeling are many, and in demanding cases, such as mechanical properties or dynamic phase transitions, multiple bridges extending from the atomic level all the way to the continuum level must be built. Although often overlooked in this process, one of the most fundamental and important problems in multiscale modeling is that of bridging the gap between first-principles quantum mechanics, from which true predictive power for real materials emanates, and the large-scale atomistic simulation of thousands or millions of atoms, which is usually essential to describe the complex atomic processes that link to higher length and time scales. For example, to model single-crystal plasticity at micron length scales via dislocation-dynamics simulations that evolve the detailed dislocation microstructure requires accurate large-scale atomistic information on the mobility and interaction of individual dislocations. Similarly, modeling the kinetics of structural phase transitions requires linking accurate large-scale atomistic information on nucleation processes with higher length and time scale growth processes
Time-integrated luminosity recorded by the BABAR detector at the PEP-II e+e- collider
This article is the Preprint version of the final published artcile which can be accessed at the link below.We describe a measurement of the time-integrated luminosity of the data collected by the BABAR experiment at the PEP-II asymmetric-energy e+e- collider at the ϒ(4S), ϒ(3S), and ϒ(2S) resonances and in a continuum region below each resonance. We measure the time-integrated luminosity by counting e+e-→e+e- and (for the ϒ(4S) only) e+e-→μ+μ- candidate events, allowing additional photons in the final state. We use data-corrected simulation to determine the cross-sections and reconstruction efficiencies for these processes, as well as the major backgrounds. Due to the large cross-sections of e+e-→e+e- and e+e-→μ+μ-, the statistical uncertainties of the measurement are substantially smaller than the systematic uncertainties. The dominant systematic uncertainties are due to observed differences between data and simulation, as well as uncertainties on the cross-sections. For data collected on the ϒ(3S) and ϒ(2S) resonances, an additional uncertainty arises due to ϒ→e+e-X background. For data collected off the ϒ resonances, we estimate an additional uncertainty due to time dependent efficiency variations, which can affect the short off-resonance runs. The relative uncertainties on the luminosities of the on-resonance (off-resonance) samples are 0.43% (0.43%) for the ϒ(4S), 0.58% (0.72%) for the ϒ(3S), and 0.68% (0.88%) for the ϒ(2S).This work is supported by the US Department of Energy and National Science Foundation, the Natural Sciences and Engineering Research Council (Canada), the Commissariat à l’Energie Atomique and Institut National de Physique Nucléaire et de Physiquedes Particules (France), the Bundesministerium für Bildung und Forschung and Deutsche Forschungsgemeinschaft (Germany), the Istituto Nazionale di Fisica Nucleare (Italy), the Foundation for Fundamental Research on Matter (The Netherlands), the Research Council of Norway, the Ministry of Education and Science of the Russian Federation, Ministerio de Ciencia e Innovación (Spain), and the Science and Technology Facilities Council (United Kingdom). Individuals have received support from the Marie-Curie IEF program (European Union) and the A.P. Sloan Foundation (USA)
Observation of the baryonic decay B \uaf 0 \u2192 \u39bc+ p \uaf K-K+
We report the observation of the baryonic decay B\uaf0\u2192\u39bc+p\uafK-K+ using a data sample of 471
7106 BB\uaf pairs produced in e+e- annihilations at s=10.58GeV. This data sample was recorded with the BABAR detector at the PEP-II storage ring at SLAC. We find B(B\uaf0\u2192\u39bc+p\uafK-K+)=(2.5\ub10.4(stat)\ub10.2(syst)\ub10.6B(\u39bc+))
710-5, where the uncertainties are statistical, systematic, and due to the uncertainty of the \u39bc+\u2192pK-\u3c0+ branching fraction, respectively. The result has a significance corresponding to 5.0 standard deviations, including all uncertainties. For the resonant decay B\uaf0\u2192\u39bc+p\uaf\u3c6, we determine the upper limit B(B\uaf0\u2192\u39bc+p\uaf\u3c6)<1.2
710-5 at 90% confidence level
Search for Darkonium in e+e- Collisions
Collider searches for dark sectors, new particles interacting only feebly with ordinary matter, have largely focused on identifying signatures of new mediators, leaving much of dark sector structures unexplored. In particular, the existence of dark matter bound states (darkonia) remains to be investigated. This possibility could arise in a simple model in which a dark photon (A0 ) is light enough to generate an attractive force between dark fermions. We report herein a search for a JPC ¼ 1−− darkonium state, the ϒD, produced in the reaction eþe− → γϒD, ϒD → A0 A0 A0 , where the dark photons subsequently decay into pairs of leptons or pions, using 514 fb−1 of data collected with the BABAR detector. No significant signal is observed, and we set bounds on the γ − A0 kinetic mixing as a function of the dark sector coupling constant for 0.001 < mA0 < 3.16 GeV and 0.05 < mϒD < 9.5 GeV.publishedVersio
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