The discrepancy between experimental data and theoretical calculations in one-nucleon removal reactions at intermediate energies (quantified by the so-called “quenching factors”) and its dependence ...on the isospin asymmetry of the nuclei has been an open problem in nuclear physics for the last fifteen years. In this work, we propose an explanation for this long-standing problem, which relies on the inclusion of the process of core destruction due to its interaction with the removed nucleon. To include this effect, we extend the commonly used eikonal formalism via an effective nucleon density, and apply it to a series of nucleon knockout reactions. The effect of core destruction is found to depend strongly on the binding energy of the removed nucleon, leading to a significant reduction of the cross section for deeply bound nucleons, which reduces the isospin dependence of the “quenching factors”, making them more consistent with the trends found in transfer and (p,pN) reactions.
In this work, we present an extension of the Continuum-Discretized Coupled-Channel formalism to include the effects of absorption and excitation of the core through its interaction with the removed ...particle in the description of nuclear breakup reactions. This extension is performed via the inclusion of a complex energy-dependent interaction between core and removed particle and the use of a binormal basis to ensure orthogonality. The formalism is applied to neutron breakup reactions with a 12C target at 70 MeV per nucleon for the loosely-bound 11Be nucleus and the more deeply-bound 41Ca nucleus, finding a moderate reduction in the cross section for the weakly-bound case and a strong reduction for the more deeply-bound case. Possible implications for the interpretation of intermediate-energy knockout reactions are discussed.
The concept of Selection Mosaic is central to the Geographic Mosaic Theory of Coevolution. Most information on coevolving interactions, however, comes from specialized organisms. In contrast, an ...accurate understanding of the effect of geographically varying evolutionary dynamics on the evolution of generalist organisms is lacking, although these kinds of organisms are the most frequent in nature. In flowering plants, pollinators and herbivores are important selective agents. In this study we investigate whether a geographic selection mosaic for floral traits in a generalist plant, Erysimum mediohispanicum (Brassicaceae), can be mediated by the interplay of mutualistic and antagonistic interacting organisms. In eight populations we quantified the selection exerted by these organisms on several plant traits. We found significant spatial variation in pollinator assemblage. In different populations, the main pollinators belonged to different functional groups (beeflies, large bees, small bees, and beetles). Damage by ungulates also varied among populations. Consequently, we found that different populations were under different selective regimes, and the traits affected by selection depended on the local interaction intensity with pollinators and mammal herbivores. Some traits, such as flower number and stalk height, were selected similarly in most populations. Other traits, such as corolla diameter and tube length, were selected only in some populations. Finally, we found divergent selection for some traits, such as corolla tube width and corolla shape, which were selected in contrasting directions in different localities. This spatial variation in selective scenarios results in populations with strong selective regimes (hot spots) intermingled with populations with weak selective regimes (cold spots). Four important outcomes emerge from the E. mediohispanicum selection mosaic. (1) Interactions with generalist organisms may produce strong selection. (2) Spatial changes in main pollinators result in divergent selection across populations. (3) Geographic mosaics depend on a balance between mutualistic and antagonistic selection. (4) Selection mosaics operate at fairly small spatial scales. These findings will surely contribute to expanding the conceptual framework of the Geographic Mosaic Theory of Coevolution.
Increasing surface ozone is a main concern for crop production in the Global Change framework, especially in the Mediterranean basin where climate conditions favor its photochemical formation. ...Meanwhile, increasing common crop diseases, such as yellow rust, one of the most important pathogens affecting global wheat production has been detected in the area in recent decades. However, the impact of O3 on the occurrence and impact of fungal diseases is scarcely understood.
A close-to-field-conditions assay (Open Top Chamber facility) situated in a Mediterranean cereal rainfed farming area was carried out to study the impact of increasing O3 levels and N-fertilization on spontaneous fungal outbreaks in wheat. Four O3-fumigation levels reproducing pre-industrial to future pollutant atmospheres with additional 20 and 40 nL L−1 over the ambient levels were considered (7 h-mean ranging from 28 to 86 nL L−1). Two top N-fertilization supplementations (100 and 200 kg ha−1) were nested within the O3 treatments; foliar damage, pigment content and gas exchange parameters were measured. Pre-industrial natural background O3 levels strongly favored the yellow rust infection, where the O3-polluted levels currently observed at the farm highly benefited the crop, mitigating the presence of rust by 22 %. However, future expected high O3-levels neutralized the beneficial infection-controlling effect by inducing early wheat senescence, decreasing the chlorophyll index of the older leaves by up to 43 % under the higher O3 exposure. Nitrogen promoted the rust infection by up to 49.5 % without interacting with the O3-factor. Achieving future air quality standards might require considering new varietal improvement programs, to be able to adapt crops to an increased pathogen tolerance without requiring the assistance provided by O3-pollution.
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•Pre-industrial O3 levels favor yellow rust infection in modern Mediterranean wheat.•Current O3-polluted Mediterranean atmospheres mitigate wheat rust damage by 22 %.•Projected O3-levels induced early senescence decreasing the rust control benefit.•Nitrogen fertilization increases rust incidence but did not interact with O3.•Achieving air quality standards might require improvements in pathogen tolerance.
•We compared the new REGA version 3, with other seven subtyping tools.•Reproducibility was 100% with similarity-based tools and statistical-based tools.•Sensitivity and specificity was ∼ 96% with ...seven tools for B and C subtypes.•COMET, jpHMM, REGAv3 and SCUEAL had the best performance for other pure subtypes.•Performance was variable for CRFs, but COMET and REGAv3 identified most of them.
To investigate differences in pathogenesis, diagnosis and resistance pathways between HIV-1 subtypes, an accurate subtyping tool for large datasets is needed. We aimed to evaluate the performance of automated subtyping tools to classify the different subtypes and circulating recombinant forms using pol, the most sequenced region in clinical practice. We also present the upgraded version 3 of the Rega HIV subtyping tool (REGAv3).
HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. The performance of these tools, for pol, and for PR and RT separately, was compared in terms of reproducibility, sensitivity and specificity with respect to the gold standard which was manual phylogenetic analysis of the pol region.
The sensitivity and specificity for subtypes B and C was more than 96% for seven tools, but was variable for other subtypes such as A, D, F and G. With regard to the most common circulating recombinant forms (CRFs), the sensitivity and specificity for CRF01_AE was ∼99% with statistical-based tools, with phylogenetic-based tools and with Stanford, one of the similarity based tools. CRF02_AG was correctly identified for more than 96% by COMET, REGAv3, Stanford and STAR. All the tools reached a specificity of more than 97% for most of the subtypes and the two main CRFs (CRF01_AE and CRF02_AG). Other CRFs were identified only by COMET, REGAv2, REGAv3, and SCUEAL and with variable sensitivity. When analyzing sequences for PR and RT separately, the performance for PR was generally lower and variable between the tools. Similarity and statistical-based tools were 100% reproducible, but this was lower for phylogenetic-based tools such as REGA (∼99%) and SCUEAL (∼96%).
REGAv3 had an improved performance for subtype B and CRF02_AG compared to REGAv2 and is now able to also identify all epidemiologically relevant CRFs. In general the best performing tools, in alphabetical order, were COMET, jpHMM, REGAv3, and SCUEAL when analyzing pure subtypes in the pol region, and COMET and REGAv3 when analyzing most of the CRFs. Based on this study, we recommend to confirm subtyping with 2 well performing tools, and be cautious with the interpretation of short sequences.
An adaptive role of corolla shape has been often asserted without an empirical demonstration of how natural selection acts on this trait. In generalist plants, in which flowers are visited by diverse ...pollinator fauna that commonly vary spatially, detecting pollinator-mediated selection on corolla shape is even more difficult. In this study, we explore the mechanisms promoting selection on corolla shape in the generalist crucifer Erysimum mediohispanicum Polatschek (Brassicaceae). We found that the main pollinators of E. mediohispanicum (large bees, small bees and bee flies) discriminate between different corolla shapes when offered artificial flowers without reward. Importantly, different pollinators prefer different shapes: bees prefer flowers with narrow petals, whereas bee flies prefer flowers with rounded overlapping petals. We also found that flowers with narrow petals (those preferred by bees) produce both more pollen and nectar than those with rounded petals. Finally, different plant populations were visited by different faunas. As a result, we found spatial variation in the selection acting on corolla shape. Selection favoured flowers with narrow petals in the populations where large or small bees are the most abundant pollinator groups. Our study suggests that pollinators, by preferring flowers with high reward, exert strong selection on the E. mediohispanicum corolla shape. The geographical variation in the pollinator-mediated selection on E. mediohispanicum corolla shape suggests that phenotypic evolution and diversification can occur in this complex floral trait even without specialization.
An algebraic approach based on the unitary
algebra is proposed to describe 3D systems for effective potentials. Our approach is based on the 3D vibron model where the addition of a scalar boson is ...introduced into the space of a 3D harmonic oscillator. Our approach is based on the mapping between the
dynamical symmetry and the harmonic oscillator states. A minimisation procedure is used in order to determine the coefficients involved in the algebraic expansions. This allows the kets associated with the different subgroup chains to be linked to energy, coordinate and momentum representations. As an application of this approach the eigensystem of the 3D-Morse potential is analysed in detail. The analyses of inertia moments as well as the dipole moment strengths are also included. To show the convenience of this approach, a comparison with one ab-initio calculation for vibrational and rotational levels for O
is presented in the framework of an analytical potential. In addition, a notch test is done to show how the formalism allows to check the sensitivity of the ro-vibrational results as a function of the precise structure of the potential energy surface as a function of r.
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