Abstract
The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the ...character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.
We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server.
The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
We theoretically investigate mechanisms of higher-order harmonic generation in solid-state materials under a high-intensity ac electric field. A new theoretical framework presented in this Letter ...holds the legitimacy of Bloch's theorem even under the influence of the high-intensity electric field and provides an exact treatment of the diabatic processes of Bloch electrons. Utilizing this framework, we first discovered that the diabatic processes, namely, ac Zener tunneling and semimetallization of semiconductors, are key factors for nonperturbative mechanisms of HHG. These mechanisms are classified by the field intensity and could be understood by an extended simple man model based on an analogy between tunnel ionization in gaseous media and Zener tunneling in semiconductors. These conclusions would stimulate the universal understanding of HHG mechanisms in both atomic and solid cases.
Highly efficient ammonia synthesis at a low temperature is desirable for future energy and material sources. We accomplished efficient electrocatalytic low-temperature ammonia synthesis with the ...highest yield ever reported. The maximum ammonia synthesis rate was 30 099 μmol g
h
over a 9.9 wt% Cs/5.0 wt% Ru/SrZrO
catalyst, which is a very high rate. Proton hopping on the surface of the heterogeneous catalyst played an important role in the reaction, revealed by
IR measurements. Hopping protons activate N
even at low temperatures, and they moderate the harsh reaction condition requirements. Application of an electric field to the catalyst resulted in a drastic decrease in the apparent activation energy from 121 kJ mol
to 37 kJ mol
. N
dissociative adsorption is markedly promoted by the application of the electric field, as evidenced by DFT calculations. The process described herein opens the door for small-scale, on-demand ammonia synthesis.
This paper presents a full simulation study of the measurement of the production cross section (σZH) of the Higgsstrahlung process e+e−→ZH and the Higgs boson mass (MH) at the International Linear ...Collider (ILC), using events in which a Higgs boson recoils against a Z boson decaying into a pair of muons or electrons. The analysis is carried out for three center-of-mass energies s=250, 350, and 500 GeV, and two beam polarizations eL−eR+ and eR−eL+, for which the polarizations of e− and e+ are (Pe−,Pe+)=(−80%,+30%) and (+80%, −30%), respectively. Assuming an integrated luminosity of 250 fb−1 for each beam polarization at s=250 GeV, where the best lepton momentum resolution is obtainable, σZH and MH can be determined with a precision of 2.5% and 37 MeV for eL−eR+ and 2.9% and 41 MeV for eR−eL+, respectively. Regarding a 20 year ILC physics program, the expected precisions for the HZZ coupling and MH are estimated to be 0.4% and 14 MeV, respectively. The event selection is designed to optimize the precisions of σZH and MH while minimizing the bias on the measured σZH due to discrepancy in signal efficiencies among Higgs decay modes. For the first time, model independence has been demonstrated to a sub-percent level for the σZH measurement at each of the three center-of-mass energies. The results presented show the impact of center-of-mass energy and beam polarization on the evaluated precisions and serve as a benchmark for the planning of the ILC run scenario.
The formation of the Ontong Java Nui super oceanic plateau (OJN), which is based on the model that the submarine Ontong Java Plateau (OJP), Manihiki Plateau (MP), and Hikurangi Plateau (HP) were once ...its contiguous fragments, could have been the largest globally consequential volcanic event in Earth's history. This OJN hypothesis has been debated given the paucity of evidence, for example, the differences in crustal thickness, the compositional gap between MP and OJP basalts and the apparent older age of both plateaus relative to HP remain unresolved. Here we investigate the geochemical and
Ar-
Ar ages of dredged rocks recovered from the OJP's eastern margin. Volcanic rocks having compositions that match the low-Ti MP basalts are reported for the first time on the OJP and new ~ 96-116 Ma and 67-68 Ma
Ar-
Ar age data bridge the temporal gap between OJP and HP. These results provide new evidence for the Ontong Java Nui hypothesis and a framework for an integrated tectonomagmatic evolution of the OJP, MP, and HP. The isotopic data imply four mantle components in the source of OJN that are also expressed in present-day Pacific hotspots sources, indicating origin from (and longevity of) the Pacific Large Low Shear-wave Velocity Province.
Summary
An F2 population of 239 chickens was obtained by an intercross between Nagoya (NAG), a native Japanese breed with low growth, and White Plymouth Rock (WPR), a Western breed with high growth. ...Using SNP markers obtained by restriction site‐associated DNA sequencing, genome‐wide QTL analysis was performed and it revealed three QTL for early postnatal growth in the F2 population at genome‐wide 5% significance levels. The most highly significant QTL affecting body weights at 2–4 weeks of age and weight gains at 2–3 and 0–4 weeks was located on GGA4 between 34.0 and 65.6 Mb with LOD scores of 3.9–5.9 and it explained 4.9–9.9% of the total variance of the traits. The analysis provided evidence for significant QTL on GGA2 between 105.6 and 125.2 Mb (LOD = 4.6) and on GGA1 between 51.1 and 61.6 Mb (LOD = 4.0) which had effects on body weight at 3 weeks and body weight gain at 0–1 week respectively. These two genomic regions explained 6.6 and 6.9% of the phenotypic F2 variance of the corresponding traits respectively. The allele derived from WPR at all QTL increased the corresponding traits. Neither sex‐specific nor epistatic QTL was detected. The results showed that the GGA4 QTL affecting multiple traits is a key locus responsible for early growth in our chicken cross, suggesting that this QTL may make a great contribution to genetic improvement of growth performance of the NAG breed with a low growth rate.
Silent aspiration of oropharyngeal pathogenic organisms is a significant risk factor causing pneumonia in the elderly. We hypothesized that regular oral hygiene care will affect the presence of ...oropharyngeal bacteria. Professional cleaning of the oral cavity and/or the gargling of a disinfectant liquid solution was performed over a five-month period in three facilities for the dependent elderly. Total oropharyngeal bacteria, streptococci, staphylococci, Candida, Pseudomonas, and black-pigmented Bacteroides species were monitored. The levels of these oropharyngeal bacteria decreased or disappeared after weekly professional oral health care, i.e., cleaning of teeth, dentures, tongue, and oral mucous membrane by dental hygienists. After lunch, gargling with povidone iodine was shown to be less effective than professional oral care. These findings indicate that weekly professional mechanical cleaning of the oral cavity, rather than a daily chemical disinfection of the mouth, can be an important strategy to prevent aspiration pneumonia in the dependent elderly.
1. Comprehensive knowledge of innate fear in chickens has important implications for understanding the adaptation of native Japanese chickens in modern production and behavioural changes caused by ...modern breeding goals. Innate fear behaviour seen in chicks from six native Japanese chicken breeds;, Ingie (IG), Nagoya (NAG), Oh-Shamo (OSM), Tosa-Jidori (TJI), Tosa-Kukin (TKU) and Ukokkei (UK), were compared with those in two lines of White Leghorn (WL-G and WL-T) in tonic immobility (TI) and open field (OF) tests.
2. TI and OF tests were conducted for 267 chicks at 0-1 days of age in the eight breeds. Raw data for four TI traits and 13 OF traits were corrected for environmental factors. Breed differences were analysed by the Kruskal-Wallis test followed by the Steel Dwass post hoc test. Principal component (PC) analyses were conducted.
3. The results showed that OSM was the least sensitive to fear in both the TI and OF tests. The WL-G birds showed higher sensitivity to TI fear but lower sensitivity to OF fear. The PC analysis of OF traits classified the tested breeds into three groups: least (OSM and WL-G), moderate (IG, WL-T, NAG, TJI and TKU) and most sensitive (UK).
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