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  • 1
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Genome Biology and Evolution Vol. 12, No. 6 ( 2020-06-01), p. 860-866
    In: Genome Biology and Evolution, Oxford University Press (OUP), Vol. 12, No. 6 ( 2020-06-01), p. 860-866
    Abstract: Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera.
    Type of Medium: Online Resource
    ISSN: 1759-6653
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2495328-3
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  • 2
    In: Insect Science, Wiley, Vol. 29, No. 6 ( 2022-12), p. 1819-1833
    Abstract: The halictid genus Lasioglossum , as one of the most species‐rich bee groups with persistently contentious subgeneric boundaries, is one of the most challenging bee groups from a systematic standpoint. An enduring question is the relationship of Lasioglossum and Homalictus , whether all halictine bees with weakened distal wing venation comprise one or multiple genera. Here, we analyzed the phylogenetic relationships among the subgroups within Lasioglossum s.l . based on thousands of single‐copy orthologs and ultraconserved elements, which were extracted from 23 newly sequenced low‐coverage whole genomes alongside a published genome (22 ingroups plus 2 outgroups). Both marker sets provided consistent results across maximum likelihood and coalescent‐based species tree approaches. The phylogenetic and topology test results show that the Lasioglossum and Hemihalictus series are reciprocally monophyletic and Homalictus and Rostrohalictus are valid subgenera of Lasioglossum . Consequently, we lower Homalictus to subgenus status within Lasioglossum again, and we also raise Rostrohalictus to subgenus status from its prior synonymy with subgenus Hemihalictus . Lasioglossum przewalskyi is also transferred to the subgenus Hemihalictus . Ultimately, we redefine Lasioglossum to include all halictine bees with weakened distal wing venation.
    Type of Medium: Online Resource
    ISSN: 1672-9609 , 1744-7917
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2179775-4
    SSG: 12
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  • 3
    In: Acta Physica Sinica, Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences, Vol. 71, No. 19 ( 2022), p. 195201-
    Abstract: The effects of electric-quadrupole (E2) transitions on ion energy-level populations in plasma are studied by constructing the collisional radiative model of a three-level atomic system in the steady-state approximation. It is found that the influence is non-negligible at the low electron density, and becomes larger when the E2 transition rate grows with atomic number increasing. Furthermore, we investigate the E2-transition effects on the populations of levels in the ground configuration for Fe-like Mo〈sup〉16+〈/sup〉 and U〈sup〉66+〈/sup〉 ions in an electron-beam ion-trap plasma. The level populations are obtained by solving the large-scale rate equation numerically. On this basis, we discuss the influence of the E2 transition on the line intensity ratio of the magnetic dipole (M1) lines. In addition, we point out the significance of the E2 transitions on the intensity ratio of the M1 lines that can be used to diagnose the electron density of plasma.
    Type of Medium: Online Resource
    ISSN: 1000-3290 , 1000-3290
    Language: Unknown
    Publisher: Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences
    Publication Date: 2022
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  • 4
    Online Resource
    Online Resource
    IOP Publishing ; 2022
    In:  Chinese Physics B Vol. 31, No. 1 ( 2022-01-01), p. 013101-
    In: Chinese Physics B, IOP Publishing, Vol. 31, No. 1 ( 2022-01-01), p. 013101-
    Abstract: Systematic calculations and assessments are performed for the magnetic dipole (M1) transition energies and rates between the F 5 / 2 , 7 / 2 o 2 levels in the ground configuration 4d 10 4f along the Ag-like isoelectronic sequence with 62 ⩽ Z ⩽ 94 based on the second-order many-body perturbation theory implemented in the Flexible Atomic Code. The electron correlations, Breit interaction and quantum electrodynamics effects are taken into account in the present calculations. The accuracy and reliability of our results are evaluated through comprehensive comparisons with available measurements and other theoretical results. For transition energies, our results are in good agreement with the recent experimental data obtained from the electron beam ion traps within 0.18%. The maximum discrepancy between our results and those obtained with the large-scale multiconfiguration Dirac–Hartee–Fock calculations by Grumer et al. [ Phys. Rev. A 89 062501 (2014)] is less than 0.13% along the isoelectronic sequence. Furthermore, the corresponding M1 transition rates are also reported. The present results can be used as the benchmark and useful for spectra simulation and diagnostics of astrophysical and fusion plasmas.
    Type of Medium: Online Resource
    ISSN: 1674-1056
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2022
    detail.hit.zdb_id: 2412147-2
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  • 5
    Online Resource
    Online Resource
    Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences ; 2021
    In:  Acta Physica Sinica Vol. 70, No. 11 ( 2021), p. 115202-
    In: Acta Physica Sinica, Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences, Vol. 70, No. 11 ( 2021), p. 115202-
    Abstract: Aiming at the requirement of the on-line detailed atomic model in radiation hydrodynamic simulations, we propose a general model, multi-average ion collisional-radiative model (MAICRM), to rapidly simulate the ionization and charge state distribution of hot dense plasma under non-local thermal equilibrium (NLTE) conditions. In this model, an average ion is used to characterize the features of all the atomic states at one single charge state, including the average orbital occupation and the total population of the atomic states. The rate equations for the orbital occupations and the population are derived from the rate equations of the detailed configurations and separated into two sets under the two assumptions: one is the single orbital rate coefficients (including no occupation nor hole number of the relative orbital) that are only dependent on the charge state, and the other is the coupling of the excitation/de-excitation process and ionization/recombination process, which are weak. Namely, the orbital occupation of an average ion is mainly determined by the excitation/de-excitation process under a certain density and temperature; the population of the average ions is determined by the ionization/recombination process with the fixed orbital occupation. The two sets of rate equations are solved sequentially and iteratively until a set of converged orbital occupation and population values is obtained. The interplay between the occupation and the population is implicit in the excitation/de-excitation rate coefficient and ionization/recombination rate coefficient, each of which is a function of electron density and temperature as well as occupation. In this work, using the newly developed method and codes, the mean ionizations and charge state distributions of Fe, Xe and Au plasmas under different plasma conditions are calculated and in good agreement with the experimental results and DCA/SCA calculations. Meanwhile, compared with the DCA/SCA calculations, in which hundreds or thousands of detailed atomic states at each charge state are considered to obtain a converged ionization balance, MAICRM only considers one kind of ion at one single charge state, thus the computational cost of MAICRM is much reduced and lower than that of DCA/SCA. Due to its good degree of accuracy for ionization balance and its low computational cost, MAICRM is expected to be incorporated into the radiation hydrodynamic program to realize the online calculation of detailed nonequilibrium atomic models in the future.
    Type of Medium: Online Resource
    ISSN: 1000-3290 , 1000-3290
    Language: Unknown
    Publisher: Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences
    Publication Date: 2021
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  • 6
    In: Fuel Processing Technology, Elsevier BV, Vol. 146 ( 2016-06), p. 90-98
    Type of Medium: Online Resource
    ISSN: 0378-3820
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
    detail.hit.zdb_id: 1483666-X
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  • 7
    Online Resource
    Online Resource
    Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences ; 2021
    In:  Acta Physica Sinica Vol. 70, No. 7 ( 2021), p. 075201-
    In: Acta Physica Sinica, Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences, Vol. 70, No. 7 ( 2021), p. 075201-
    Abstract: 〈sec〉Radiative shock is an important phenomenon both in astrophysics and in inertial confinement fusion. In this paper, the radiation properties of X-ray heated radiatve shock in xenon is studied with the simulation method. The radiative shock is described by a one-dimensional, multi-group radiation hydrodynamics model proposed by Zinn [Zinn J 1973 〈i〉 J. Comput. Phys.〈/i〉 〈b〉13〈/b〉 569]. To conduct computation, the opacity and equation-of-state data of xenon are calculated and put into the model. The reliabilities of the model and the physical parameters of xenon are verified by comparing the temperature and velocity of the radiative shock calculated by the model with those measured experimentally. 〈/sec〉〈sec〉The evolution of the radiative shock involves abundant physical processes. The core of the xenon can be heated up to 100 eV, resulting in a thermal wave and forming an expanding high-temperature-core. Shortly, the hydrodynamic disturbances reach the thermal wave front, generating a shock. As the thermal wave slows down, the shock gradually exceeds the high-temperature-core, forming a double-step distribution in the temperature profile. 〈/sec〉〈sec〉The time evolution of the effective temperature of the radiative shock shows two maximum values and one minimum value, and the radiation spectra often deviate from blackbody spectrum. By analyzing the radiation and absorption properties at different positions of the shock, it can be found that the optical property of the shock is highly dynamic and can generate the above-mentioned radiation characteristics. When the radiative shock is just formed, the radiation comes from the shock surface and the shock precursor has a significant absorption of the radiation. As the shock temperature falls during expansion, the shock precursor disappears and the radiation inside the shock can come out owing to absorption coefficient decreases. When the shock becomes transparent, the radiation surface reaches the outside edge of the high-temperature-core. Then, the temperature of the high-temperature-core decreases further, making this region also optically thin, and the radiation from the inner region can come out. Finally, the radiation strength falls because of temperature decreasing. 〈/sec〉
    Type of Medium: Online Resource
    ISSN: 1000-3290 , 1000-3290
    Language: Unknown
    Publisher: Acta Physica Sinica, Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences
    Publication Date: 2021
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  • 8
    Online Resource
    Online Resource
    Ovid Technologies (Wolters Kluwer Health) ; 2023
    In:  Reproductive and Developmental Medicine Vol. 7, No. 3 ( 2023-09), p. 156-165
    In: Reproductive and Developmental Medicine, Ovid Technologies (Wolters Kluwer Health), Vol. 7, No. 3 ( 2023-09), p. 156-165
    Abstract: Inflammatory response plays a crucial role in the development and treatment of cancer. However, the role of inflammatory response in triple-negative breast cancer (TNBC) remains unclear. Based on the heterogeneity of the inflammatory response, we classified TNBC, elucidated its subtype features, and revealed potential therapeutic strategies. Methods: We established inflammatory response subtyping based on the RNA sequencing data of TNBCs derived from a cohort at the Fudan University Shanghai Cancer Center (FUSCC). Next, we explored the features and potential therapeutic strategies for each subgroup by analyzing transcriptome data. Using a machine-learning method, we validated and generalized the TNBC inflammatory response subtypes in an external dataset. Results: A total of 360 TNBC samples and 88 normal tissues were collected from a cohort at FUSCC. Patients with TNBC were divided into four inflammatory response groups (IRGs) based on the expression of inflammatory response genes: high inflammatory response gene expression with pronounced pyroptosis phenotype and high immune cell infiltration (IRG 1), low inflammatory response gene expression and low immune cell infiltration (IRG 2), ITGB8 specific inflammatory response with a predominant proliferation phenotype (IRG 3), and low M1/M2 ratio with a marked angiogenesis phenotype (IRG 4). Relapse-free survival (RFS) was better in IRG 1 and 2 and worse in IRG 3 and 4. Owing to their poor prognosis, we mainly focused on IRG 3 and IRG 4 to investigate potential treatment strategies. ITGB8 was highly expressed in IRG 3; thus, targeting ITGB8 may be a potential therapeutic strategy for patients in IRG 3. IRG 4 had a lower M1/M2 ratio and a marked angiogenesis phenotype; therefore, therapeutic strategies, such as anti-angiogenesis or M2 to M1 repolarization of macrophages, could be recommended for these patients. Additionally, we validated and generalized the TNBC inflammatory response subtyping in an external dataset using a machine-learning method. Conclusion: TNBC patients with different inflammatory response subtypes have different characteristics and may need subtype-specific treatment strategies.
    Type of Medium: Online Resource
    ISSN: 2096-2924
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2023
    detail.hit.zdb_id: 3046168-6
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  • 9
    Online Resource
    Online Resource
    Elsevier BV ; 2014
    In:  Journal of Ethnopharmacology Vol. 154, No. 1 ( 2014-05), p. 206-217
    In: Journal of Ethnopharmacology, Elsevier BV, Vol. 154, No. 1 ( 2014-05), p. 206-217
    Type of Medium: Online Resource
    ISSN: 0378-8741
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2014
    detail.hit.zdb_id: 1491279-X
    SSG: 15,3
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  • 10
    In: Life Sciences, Elsevier BV, Vol. 267 ( 2021-02), p. 118831-
    Type of Medium: Online Resource
    ISSN: 0024-3205
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
    detail.hit.zdb_id: 2013911-1
    SSG: 12
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