Estimating phylogenetic trees from genome-scale data

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic methods known as "species tree methods" have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting or deep coalescence that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Although such methods are gaining in popularity, they are being adopted with caution in some quarters, in part because of an increasing number of examples of strong phylogenetic conflict between concatenation or supermatrix methods and species tree methods. Here we review theory and empirical examples that help clarify these conflicts. Thinking of concatenation as a special case of the more general model provided by the multispecies coalescent can help explain a number of differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences, base compositional heterogeneity and long branch attraction. We show that approaches such as binning, designed to augment the signal in species tree analyses, can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods that incorporate biological realism are a key to phylogenetic analysis of whole genome data.Comment: 39 pages, 3 figure

Terahertz spectra revealing the collective excitation mode in charge-density-wave single crystal LuFe2 O4

We report a low-energy collective excitation mode in charge-ordered multiferroic LuFe2O4 via terahertz time domain spectroscopy. Upon cooling from 300 K to 40 K, the central resonance frequency showed a pronounced hardening from 0.85 THz to 1.15 THz. In analogy to the well-known low-energy optical properties of LuFe2O4, we attributed this emerging resonance to the charge-density-wave (CDW) collective excitations. By using the Drude-Lorentz model fitting, we observe the CDW col-lective mode becomes increasingly damped with increasing the temperature. Furthermore, we analyze the kinks of the CDW collective mode at the magnetic transition temperature, which indicates the coupling of spin order with electric polarization

Anti-site-induced diverse diluted magnetism in LiMgPdSb-type CoMnTiSi alloy

The effect of three kinds of anti-site disorder to electronic structure and magnetic properties of the LiMgPdSb-type CoMnTiSi alloy are investigated. It was found the Mn-Ti anti-site disorder can induce the diluted magnetism in CoMnTiSi matrix. The magnetic structure has an oscillation between the ferromagnetic and antiferromagnetic states with the different degree of Mn-Ti anti-site disorder. Two novel characteristics: the diluted antiferromagnetic half-metallicity and the diluted zero-gap half-metallity are found in the different degree range of the Mn-Ti anti-site disorder. The Co-Mn and Co-Ti anti-site disorder have little effect on the magnetic properties. The width of energy gap and the intensity of DOS at the Fermi level can be adjusted by the degree of Co-Mn or Co-Ti anti-site disorder. The independent control to the carrier concentration and magnetization can be realized by introducing the different anti-site disorder

Superior intrinsic thermoelectric performance with zT of 1.8 in single-crystal and melt-quenched highly dense Cu2-xSe bulks

Practical applications of the high temperature thermoelectric materials developed so far are partially obstructed by the costly and complicated fabrication process. In this work, we put forward two additional important properties for thermoelectric materials, high crystal symmetry and congruent melting. We propose that the recently discovered thermoelectric material Cu2-xSe, with figure of merit, zT, over 1.5 at T of ~ 1000 K, should meet these requirements, based on our analysis of its crystal structure and the Cu-Se binary phase diagram. We found that its excellent thermoelectric performance is intrinsic, and less dependent on grain size, while highly dense samples can be easily fabricated by a melt-quenching approach. Our results reveal that the melt-quenched samples and single crystals exhibit almost the same superior thermoelectric performance, with zT as high as 1.7-1.8 at T of ~973 K. Our findings not only provide a cheap and fast fabrication method for highly dense Cu2-xSe bulks with superior thermoelectric performance, paving the way for possible commercialization of Cu2-xSe as an outstanding component in practical thermoelectric modules, but also provide guidance in searching for new classes of thermoelectric systems with high crystal symmetry or further improving the cost performance of other existing congruent-melting thermoelectric materials

Production of Biodiesel Using a Vegetable Oil from Swida wilsoniana Fruits

Energy demand is increasing dramatically due to the fast industrial development, rising population, expanding urbanization, and economic growth in the world and large amount of fossil fuels are widely used. The depletion of fossil fuel reserves and the environmental pollution caused by burning of fossil fuels stimulate development of alternative fuels. Biodiesel today is the most popular and promising biofuel and vegetable oils are one of the potential feedstocks for biodiesel production. In order to explore the wild oil plant sources in China, the fruit oil of Swida wilsoniana, a wild woody oil plant widely distributed in the mountainous regions of calcareous sandstone, was used to produce the biodiesel by transesterification method. The reaction parameters were optimized by an orthogonal experimental design. The results showed that Swida wilsoniana fruit oil (SWO) could be conversed to biodiesel at a wide range of reaction conditions. The optimum conditions for the reaction process were determined as: methanol/oil mole ratio 5:1, catalyst dosage 1.1%, reaction temperature 60 °C, and reaction time 120 min. The characteristics of Swida wilsoniana biodiesel (SDBD) were analyzed, which was similar to that of 0# diesel. Moreover, SDBD has the advantages of higher flash point (>105) and lower ash content (<0.003). Therefore, SDBD is a safe and clean biodiesel and a promising alternative biofuel

Development，Reliability and Validity of the Chinese Version of the Return-to-Work Self-Efficacy Questionnaire among Young and Middle-aged Stroke Patients

BackgroundThe prevalence of varying degrees of post-stroke dysfunctions commonly found in an increasing number of young and middle-aged stroke patients, has hindered them from returning to work quickly, and caused serious socioeconomic burdens. Return-to-work self-efficacy is an important predictor of returning to work, and the assessment of which may provide guidance for promoting patients to return to work. However, there is no scale measuring the return-to-work self-efficacy of Chinese stroke patients.ObjectiveTo develop a Chinese version of the Return-to-work Self-efficacy Questionnaire (RTW-SE) by translating the English version of the RTW-SE, then assess its reliability and validity in young and middle-aged Chinese stroke patients.MethodsBy use of forward and backward translation of the English version of the RTW-SE, the Chinese version of the scale was developed. Then the scale was tested in a sample of 130 cases, and was analyzed for item analysis and exploratory factor analysis. Then, the scale was retested in another sample (n=255) from November 2020 to April 2021 for confirmatory factor analysis. The Pearson correlation and critical ratio were used as parameters for item analysis, and the Cronbach's α and split-half reliability were used as parameters of the reliability of the scale. Content validity and structural validity were adopted as parameters of the scale validity. Content validity was expressed by scale- and item-level content validity indices. Structural validity was evaluated by factor analysis, including exploratory factor analysis and confirmatory factor analysis.ResultsThe response rates of the test, and retest for the scale were 93.1% (121/130) , and 96.1% (245/255) , respectively. The results of item analysis showed that item-total correlation coefficients ranged from 0.636 to 0.897, with critical ratios greater than 3 for all items (P<0.001) . Reliability analysis showed that the Cronbach's α and split-half reliability of the scale were 0.942, and 0.940, respectively. The scale- and item-level content validity indices were 0.95 and 0.80~1.00, respectively. By exploratory factor analysis, one common factor was extracted, and the factor loadings of items ranged from 0.628 to 0.901, with 63.919% as the percentage of explained total variance. The confirmatory factor analysis showed that the model fit was good.ConclusionThe Chinese version of RTW-SE may be a reliable and valid tool for measuring return-to-work self-efficacy in young and middle-aged Chinese patients with stroke

Recent Advances in Return-to-work Self-efficacy Assessment Tools

Returning to work is an important sign of recovery and returning to normal life for patients. Most patients have a strong desire to return to work, however, their confidence is low. Return-to-work self-efficacy is not only a reflection of patients' confidence in returning to work but also an important predictor of his readiness to get back to work. Based on the concept and meaning of return-to-work self-efficacy, this study introduces its related theoretical models, summarizes the contents, scoring criteria, validity and reliability of related assessment tools, and conducts a comparative analysis of the tools, to provide Chinese rehabilitation care workers with evidence contributing to the selection of an appropriate return-to-work self-efficacy assessment tool

Diversity patterns and conservation gaps of Magnoliaceae species in China

Postponed access: the file will be available after 2023-12-27Magnoliaceae, a primitive group of angiosperms and distinguished ornamental plants with more than 100 species in China, is one of the most threatened plant family in the wild due to logging, habitat loss, over-collection and climate change. To provide a scientific guide of its conservation for policymakers, we explore the diversity patterns of 114 Magnoliaceae species in China using three diversity indices (species richness, weighted endemism, β-diversity) with a spatial resolution of 10 km by 10 km. Two methods, the top 5% richness algorithm and complementary algorithm, are used to identify diversity hotspots. Conservation gaps are recognized by overlapping the diversity hotspots with Chinese nature reserves. Our results indicate that Magnoliaceae species richness and weighted endemism are high in tropical to subtropical low montane forests in southern China, exceptionally high in southernmost Yunnan and boundary of Guizhou, Guangxi and Hunan. The β-diversity are scattered in southern China, suggesting a different species composition among grid cells. We identify 2524 grids as diversity hotspots for Magnoliaceae species in China, with 24 grids covered by three diversity indices (first-level diversity hotspots), 561 grids covered by two indices (second-level diversity hotspots) simultaneously and 1939 grids (76.8%) covered by only one index (third-level diversity hotspots). The first-level diversity hotspots include over 70% of the critically endangered Magnoliaceae species and are the priority areas for Magnoliaceae conservation. However, only 24% of the diversity hotspots fall in nature reserves and only ten grids are from the first-level diversity hotspots. Zhejiang, Guizhou and Fujian have less than 20% of diversity hotspots covered by nature reserves and need attention in future Magnoliaceae conservation. Using multiple diversity indices and algorithms, our study identifies diversity hotspots and conservation gaps and provides scientific basis for Magnoliaceae conservation in future.acceptedVersio