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Sökning: WFRF:(Fang Yue)

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2.
  • Beal, Jacob, et al. (författare)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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4.
  • Klionsky, Daniel J., et al. (författare)
  • Guidelines for the use and interpretation of assays for monitoring autophagy
  • 2012
  • Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
  • Forskningsöversikt (refereegranskat)abstract
    • In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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  • Jin, Ying-Hui, et al. (författare)
  • Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
  • 2020
  • Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
  • Tidskriftsartikel (refereegranskat)abstract
    • The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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8.
  • Li, Yuchen, et al. (författare)
  • Psychological distress among health professional students during the COVID-19 outbreak
  • 2021
  • Ingår i: Psychological Medicine. - : Cambridge University Press. - 0033-2917 .- 1469-8978. ; 51:11, s. 1952-1954
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Due to the drastic surge of COVID-19 patients, many countries are considering or already graduating health professional students early to aid professional resources. We aimed to assess outbreak-related psychological distress and symptoms of acute stress reaction (ASR) in health professional students and to characterize individuals with potential need for interventions.Methods: We conducted a prospective cohort study of 1442 health professional students at Sichuan University, China. At baseline (October 2019), participants were assessed for childhood adversity, stressful life events, internet addiction, and family functioning. Using multivariable logistic regression, we examined associations of the above exposures with subsequent psychological distress and ASR in response to the outbreak.Results: Three hundred and eighty-four (26.63%) participants demonstrated clinically significant psychological distress, while 160 (11.10%) met the criterion for a probable ASR. Individuals who scored high on both childhood adversity and stressful life event experiences during the past year were at increased risks of both distress (ORs 2.00-2.66) and probable ASR (ORs 2.23-3.10), respectively. Moreover, internet addiction was associated with elevated risks of distress (OR 2.05, 95% CI 1.60-2.64) and probable ASR (OR 2.15, 95% CI 1.50-3.10). By contrast, good family functioning was associated with decreased risks of distress (OR 0.43, 95% CI 0.33-0.55) and probable ASR (OR 0.48, 95% CI 0.33-0.69). All associations were independent of baseline psychological distress.Conclusions: Our findings suggest that COVID-19 related psychological distress and high symptoms burden of ASR are common among health professional students. Extended family and professional support should be considered for vulnerable individuals during these unprecedented times.
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9.
  • Ai, Yue-Jie, 1982-, et al. (författare)
  • Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase
  • 2011
  • Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:37, s. 10976-10982
  • Tidskriftsartikel (refereegranskat)abstract
    • Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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10.
  • Ai, Yue-Jie, et al. (författare)
  • Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
  • 2010
  • Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102
  • Tidskriftsartikel (refereegranskat)abstract
    • The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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11.
  • Ai, Yue-Jie, et al. (författare)
  • Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore
  • 2012
  • Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:38, s. 13409-13414
  • Tidskriftsartikel (refereegranskat)abstract
    • We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.
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12.
  • Ai, Yue-Jie, et al. (författare)
  • Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair : Similarities and differences
  • 2010
  • Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:6, s. 064302-
  • Tidskriftsartikel (refereegranskat)abstract
    • 2-aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed. (C) 2010 American Institute of Physics. [doi:10.1063/1.3464485]
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13.
  • Chang, Chiao-Nien, et al. (författare)
  • The Design, Structure–Activity, and Kinetic Studies of 3-Benzyl-5-oxa-1,2,3,4-Tetrahydro-2H-chromeno-(3,4-c)pyridin-8-yl Sulfamates as Steroid Sulfatase Inhibitors
  • 2022
  • Ingår i: Bioorganic chemistry. - : Elsevier BV. - 0045-2068.
  • Tidskriftsartikel (refereegranskat)abstract
    • Steroid sulfatase inhibitors block the local production of estrogenic steroids and are attractive agents for the treatment of estrogen-dependent cancers. Inspiration of coumarin-based inhibitors, we synthesized thirty-two 5-oxa-1,2,3,4-tetrahydro-2H-chromeno-(3,4-c)pyridin-8-yl sulfamates, focusing on the substitution derivatives on the adjacent phenyl ring and evaluated their abilities to block STS from human placenta and MCF-7 cells. SAR analysis revealed that the incorporation of chlorine at either meta and/or para position of the adjacent phenyl ring of the tricyclic skeleton enhanced STS inhibition. Di-substitutions at the adjacent phenyl ring were superior to mono and tri-substitutions. Further kinetic analysis of these compounds revealed that chloride-bearing compounds, such as 19m, 19v, and 19w, had KI of 0.02 to 0.11 nM and kinact/KI ratios of 8.8-17.5 nM-1min-1, a parameter indicated for the efficiency of irreversible inhibition. We also used the docking model to illustrate the difference in STS inhibitory potency of compounds. Finally, the safety and anti-cancer activity of selected compounds 19m, 19v, and 19w were also studied, showing the results of low cytotoxicity on NHDF cell line and being more potent than irosustat on ZR-75-1 cell, which was a hormone-dependent cancer cell line with high STS expression.
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14.
  • Cheng, Fang, et al. (författare)
  • Vimentin coordinates fibroblast proliferation and keratinocyte differentiation in wound healing via TGF-beta-Slug signaling
  • 2016
  • Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 113:30, s. E4320-E4327
  • Tidskriftsartikel (refereegranskat)abstract
    • Vimentin has been shown to be involved in wound healing, but its functional contribution to this process is poorly understood. Here we describe a previously unrecognized function of vimentin in coordinating fibroblast proliferation and keratinocyte differentiation during wound healing. Loss of vimentin led to a severe deficiency in fibroblast growth, which in turn inhibited the activation of two major initiators of epithelial-mesenchymal transition (EMT), TGF-beta 1 signaling and the Zinc finger transcriptional repressor protein Slug, in vimentin-deficient (VIM-/-) wounds. Correspondingly, VIM-/- wounds exhibited loss of EMT-like keratinocyte activation, limited keratinization, and slow reepithelialization. Furthermore, the fibroblast deficiency abolished collagen accumulation in the VIM-/- wounds. Vimentin reconstitution in VIM-/- fibroblasts restored both their proliferation and TGF-beta 1 production. Similarly, restoring paracrine TGF-beta-Slug-EMT signaling reactivated the transdifferentiation of keratinocytes, reviving their migratory properties, a critical feature for efficient healing. Our results demonstrate that vimentin orchestrates the healing by controlling fibroblast proliferation, TGF-beta 1-Slug signaling, collagen accumulation, and EMT processing, all of which in turn govern the required keratinocyte activation.
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15.
  • Dan, Lilin, et al. (författare)
  • Design of Offset Spatial Modulation OFDM
  • 2021
  • Ingår i: IEEE Transactions on Communications. - : Institute of Electrical and Electronics Engineers (IEEE). - 0090-6778 .- 1558-0857. ; 69:9, s. 6267-6280
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper, the idea of offset spatial modulation (OSM) is integrated with orthogonal frequency division multiplexing (OFDM), toward an efficient design to bridge their advantages. Compared to its conventional counterpart as spatial modulation (SM)-OFDM, the proposed OSM-OFDM scheme aims at providing a simplified implementation structure with less number of radio frequency (RF) chains, by introducing an offset between the RF chain and the index of the activated transmit antenna on each subcarrier. Specifically, three types of offset antenna selection (OAS) methods are developed to meet different scene requirements for different number of available RF chains. Furthermore, through theoretical analysis, we quantify the bit error rate upper bounds of OSM-OFDM with different types of OAS methods. Finally, extensive computer simulations demonstrate that OSM-OFDM provides a flexible tradeoff among implementation cost, computation complexity and error performance.
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16.
  • Elbediwi, M, et al. (författare)
  • Global Burden of Colistin-Resistant Bacteria: Mobilized Colistin Resistance Genes Study (1980-2018)
  • 2019
  • Ingår i: Microorganisms. - : MDPI AG. - 2076-2607. ; 7:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Colistin is considered to be an antimicrobial of last-resort for the treatment of multidrug-resistant Gram-negative bacterial infections. The recent global dissemination of mobilized colistin resistance (mcr) genes is an urgent public health threat. An accurate estimate of the global prevalence of mcr genes, their reservoirs and the potential pathways for human transmission are required to implement control and prevention strategies, yet such data are lacking. Publications from four English (PubMed, Scopus, the Cochrane Database of Systematic Reviews and Web of Science) and two Chinese (CNKI and WANFANG) databases published between 18 November 2015 and 30 December 2018 were identified. In this systematic review and meta-analysis, the prevalence of mcr genes in bacteria isolated from humans, animals, the environment and food products were investigated. A total of 974 publications were identified. 202 observational studies were included in the systematic review and 71 in the meta-analysis. mcr genes were reported from 47 countries across six continents and the overall average prevalence was 4.7% (0.1–9.3%). China reported the highest number of mcr-positive strains. Pathogenic Escherichia coli (54%), isolated from animals (52%) and harboring an IncI2 plasmid (34%) were the bacteria with highest prevalence of mcr genes. The estimated prevalence of mcr-1 pathogenic E. coli was higher in food-animals than in humans and food products, which suggests a role for foodborne transmission. This study provides a comprehensive assessment of prevalence of the mcr gene by source, organism, genotype and type of plasmid.
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17.
  • Fang, Ruisen, et al. (författare)
  • Late Ediacaran cavity-dwelling filamentous microorganisms accommodated in a valve-like organism from the uppermost Dengying Formation in eastern Yunnan of South China
  • 2022
  • Ingår i: Precambrian Research. - : Elsevier. - 0301-9268 .- 1872-7433. ; 379
  • Tidskriftsartikel (refereegranskat)abstract
    • The Ediacaran–Cambrian transition, one of the major turning points in Earth’s history, is characterized by an epoch-making change in biosphere. In South China, the late Ediacaran Dengying Formation (ca. 551–538 Ma) is an important stratigraphic unit yielding trace fossils, tubular skeletal fossils and some complex forms that represent possible bilateral animals. The fossil-bearing Ediacaran strata of eastern Yunnan is hitherto known from the Jiucheng Member containing the Jiangchuan Biota, together with the enigmatic cosmopolitan taxon Shaanxilithes. Here, we present for the first time cavity-dwelling filamentous microorganisms accommodated within a valve-like fossil from the upper Baiyanshao Member of the Dengying Formation at the Sujiawa Section in Huize County, eastern Yunnan of China. SEM scanning and Micro-CT reconstruction indicate that the well-preserved filaments were characterized by mycelial network structures with abundant branching pattern. Preservation of filamentous microorganisms might result from the decay process of soft parts that were originally accommodated and enclosed within the valve-like organism, and subsequently preserved by early diagenetic phosphatization, which obscures their original organic identity and chemical composition. This paper potentially presents the first fossil evidence of a saprophytic relationship between microorganisms as decomposers and a valve-like organism prior to the eve of the Cambrian Explosion of metazoan animals.
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18.
  • Fang, Shu, et al. (författare)
  • Offset Spatial Modulation and Offset Space Shift Keying : Efficient Designs for Single-RF MIMO Systems
  • 2019
  • Ingår i: IEEE Transactions on Communications. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 0090-6778 .- 1558-0857. ; 67:8, s. 5434-5444
  • Tidskriftsartikel (refereegranskat)abstract
    • Spatial modulation (SM) and space shift keying (SSK) techniques have the unique advantages of their single-radio-frequency (RF) structures compared with conventional multiple-input-multiple-output (MIMO) techniques. However, the transmission rates of these techniques are decided by the maximal switching frequency or by the minimal switching time between the RF chain and transmit antennas, which has been a bottleneck for their applications in future broadband wireless communications. To alleviate this problem, we propose a class of novel offset SM (OSM) and offset SSK (OSSK) schemes, with the aid of channel state information (CSI) at the transmitter. Compared with conventional SM and SSK, the proposed OSM and OSSK schemes can reduce the switching frequency of the RF chain, by introducing an offset between the connected RF chain and the index of the spatial modulated antenna. In extreme conditions, the proposed OSM and OSSK can work without RF switching while maintaining the single-RF advantage of conventional SM and SSK schemes. Through theoretical analysis, we also develop the bit-error rate (BER) performance bounds for the proposed two schemes. Finally, our simulation results demonstrate that the proposed OSM and OSSK outperform their counterparts, including conventional SM, SSK, CSI-aided SM, and CSI-aided SSK, while having a simplified RF-switching structure.
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19.
  • Fang, Xing, et al. (författare)
  • Microstructure and mechanical properties of the laser welded air-hardening steel joint
  • 2024
  • Ingår i: Materials Characterization. - : Elsevier BV. - 1044-5803 .- 1873-4189. ; 213
  • Tidskriftsartikel (refereegranskat)abstract
    • The decrease in mechanical properties of high-strength steel after welding is an important issue affecting the wide application of high-strength steel. Air-hardening steel is a high-strength steel suitable for lower body structural parts such as subframes. Its application process involves welding, hot forming and other processes. The present work investigates the microstructure and mechanical properties of the air-hardening steel laser welded joint that is air-cooled after hot forming in the two-phase zone (800 °C). The microstructure was characterized by electron backscattered diffraction (EBSD), scanning electron microscope (SEM) and transmission electron microscope (TEM). The results show that during hot forming, the welded joint transforms from martensite to ferrite and acicular martensite, and the base metal transforms from ferrite to polygonal martensite and ferrite. The difference in martensite morphology between the welded joint and the base metal is attributed to the nucleation positions of austenite. The structural evolution of the welded joint and the base metal is accompanied with the annihilation and reproduction of dislocations, which results in significant changes in hardness. The hardness value dropped from the highest 430 HV to 271 HV in the welded joint, while increased from the lowest 184 HV to 203 HV in the base metal. After hot forming, the tensile strength of the welded sample is reduced by only 36 MPa, and the total elongation is slightly decreased by about 1.5% compared with the unwelded sample. The welded joint and the base metal have similar plastic deformation capabilities, since the acicular martensite in the welded joint displays good plastic deformation ability, and the dislocation density of the welded joint and the base metal is similar. Overall, the microstructure and dislocation density of the air-hardening steel welded joint after hot forming are similar to those of the base metal, which is responsible for the good mechanical properties of air-hardening steel welded joint.
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20.
  • Hantson, Stijn, et al. (författare)
  • Quantitative assessment of fire and vegetation properties in simulations with fire-enabled vegetation models from the Fire Model Intercomparison Project
  • 2020
  • Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 13:7, s. 3299-3318
  • Tidskriftsartikel (refereegranskat)abstract
    • Global fire-vegetation models are widely used to assess impacts of environmental change on fire regimes and the carbon cycle and to infer relationships between climate, land use and fire. However, differences in model structure and parameterizations, in both the vegetation and fire components of these models, could influence overall model performance, and to date there has been limited evaluation of how well different models represent various aspects of fire regimes. The Fire Model Intercomparison Project (FireMIP) is coordinating the evaluation of state-of-the-art global fire models, in order to improve projections of fire characteristics and fire impacts on ecosystems and human societies in the context of global environmental change. Here we perform a systematic evaluation of historical simulations made by nine FireMIP models to quantify their ability to reproduce a range of fire and vegetation benchmarks. The FireMIP models simulate a wide range in global annual total burnt area (39-536 Mha) and global annual fire carbon emission (0.91-4.75 Pg C yr-1) for modern conditions (2002-2012), but most of the range in burnt area is within observational uncertainty (345-468 Mha). Benchmarking scores indicate that seven out of nine FireMIP models are able to represent the spatial pattern in burnt area. The models also reproduce the seasonality in burnt area reasonably well but struggle to simulate fire season length and are largely unable to represent interannual variations in burnt area. However, models that represent cropland fires see improved simulation of fire seasonality in the Northern Hemisphere. The three FireMIP models which explicitly simulate individual fires are able to reproduce the spatial pattern in number of fires, but fire sizes are too small in key regions, and this results in an underestimation of burnt area. The correct representation of spatial and seasonal patterns in vegetation appears to correlate with a better representation of burnt area. The two older fire models included in the FireMIP ensemble (LPJ-GUESS-GlobFIRM, MC2) clearly perform less well globally than other models, but it is difficult to distinguish between the remaining ensemble members; some of these models are better at representing certain aspects of the fire regime; none clearly outperforms all other models across the full range of variables assessed.
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21.
  • Hantson, Stijn, et al. (författare)
  • The status and challenge of global fire modelling
  • 2016
  • Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 13:11, s. 3359-3375
  • Tidskriftsartikel (refereegranskat)abstract
    • Biomass burning impacts vegetation dynamics, biogeochemical cycling, atmospheric chemistry, and climate, with sometimes deleterious socio-economic impacts. Under future climate projections it is often expected that the risk of wildfires will increase. Our ability to predict the magnitude and geographic pattern of future fire impacts rests on our ability to model fire regimes, using either well-founded empirical relationships or process-based models with good predictive skill. While a large variety of models exist today, it is still unclear which type of model or degree of complexity is required to model fire adequately at regional to global scales. This is the central question underpinning the creation of the Fire Model Intercomparison Project (FireMIP), an international initiative to compare and evaluate existing global fire models against benchmark data sets for present-day and historical conditions. In this paper we review how fires have been represented in fire-enabled dynamic global vegetation models (DGVMs) and give an overview of the current state of the art in fire-regime modelling. We indicate which challenges still remain in global fire modelling and stress the need for a comprehensive model evaluation and outline what lessons may be learned from FireMIP.
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22.
  • He, Lu-Jun, et al. (författare)
  • Genetic polymorphisms of N-acetyltransferase 2 and colorectal cancer risk.
  • 2005
  • Ingår i: World Journal of Gastroenterology. - 1007-9327 .- 2219-2840. ; 11:27, s. 4268-4271
  • Tidskriftsartikel (refereegranskat)abstract
    • AIM: To identify the distribution of N-acetyltrasferase 2(NAT2) polymorphism in Hebei Han Chinese and the effects of the polymorphism on the development of colorectal cancer. METHODS: We performed a hospital-based case-control study of 237 healthy individuals and 83 colorectal cancer patients of Hebei Han Chinese. DNA was extracted from peripheral blood and cancer tissues. The genotypes of the polymorphisms were assessed by PCR-restriction fragment length polymorphism (RFLP). RESULTS: There were four NAT2 alleles of WT, M1, M2, and M3 both in the healthy subjects and in the patients, and 10 genotypes of WT/WT, WT/M1, WT/M2, WT/M3, M1/M1, M1/M2, M1/M3, M2/M2, M2/M3, M3/M3. M2 allele was present in 15.61% of healthy subjects and 29.52% of patients (chi(2) = 15.31, P<0.0001), and M3 allele was present in 30.59% of healthy subjects and 16.87% of patients (chi(2) = 25.33, P<0.0001). There were more WT/M2 (chi(2) = 34.42, P<0.0001, odd ratio = 4.99, 95%CI = 2.27-9.38) and less WT/M3 (chi(2) = 3.80, P = 0.03) in the patients than in the healthy subjects. In 70.3% of the patients, there was a difference in NAT2 genotype between their tumors and blood cells. Patients had more WT/M2 (chi(2) = 5.11, P = 0.02) and less M2/M3 (chi(2) = 4.27, P = 0.039) in their blood cells than in the tumors. Furthermore, 53.8% (7/13) of M2/M3 in tumors were from WT/M2 of blood cells. CONCLUSION: There is a possible relationship between the NAT2 polymorphisms and colorectal cancer in Hebei Han Chinese. The genotype WT/M2 may be a risk factor for colorectal cancer.
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23.
  • Jing, Chun-lei, et al. (författare)
  • Avian malaria parasite infections do not affect personality in the chestnut thrush (Turdus rubrocanus) on the Qinghai-Tibet Plateau
  • 2023
  • Ingår i: Heliyon. - : Cell Press. - 2405-8440. ; 9:9
  • Tidskriftsartikel (refereegranskat)abstract
    • Personality traits, the consistent individual behavioral differences, are currently gaining much attention in studies of natural bird populations. However, associations between personality traits and parasite infections are not often investigated. Even less attention has been given to studies of birds in the high-elevation region such as the Tibetan plateau. This research aims to examine the relationship between avian malaria parasites and two personality traits in a population of the Chestnut Thrush (Turdus rubrocanus) breed in the Tibetan plateau. Our results revealed no evidence of sex bias in malaria parasite prevalence. Furthermore, we found no effect of infection status on two personality scores: activity and boldness. Additionally, no effects on the activity level or boldness were observed for different parasite lineages of Haemoproteus, Leucocytozoon, the sex of the birds, or their interactions. Similarly, we did not find any relationship between activity level and boldness with nestling numbers, sex, or their interactions. Notably, individuals with a larger number of offspring tended to display greater boldness. Our findings indicate that blood parasite infections are common in this population but do not significantly impact the personality of the birds.
  •  
24.
  • Kattge, Jens, et al. (författare)
  • TRY plant trait database - enhanced coverage and open access
  • 2020
  • Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
  • Tidskriftsartikel (refereegranskat)abstract
    • Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
  •  
25.
  •  
26.
  • Liang, Yue, et al. (författare)
  • Evolutionary contingency in lingulid brachiopods across mass extinctions
  • 2023
  • Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 33:8, s. 1565-1572.e3
  • Tidskriftsartikel (refereegranskat)abstract
    • Morphology usually serves as an effective proxy for functional ecology,1,2,3,4,5 and evaluating morphological, anatomical, and ecological changes permits a deeper understanding of the nature of diversification and macroevolution.5,6,7,8,9,10,11,12 Lingulid (order Lingulida) brachiopods are both diverse and abundant during the early Palaeozoic but decrease in diversity over time, with only a few genera of linguloids and discinoids present in modern marine ecosystems, resulting in them frequently being referred to as “living fossils.”13,14,15 The dynamics that drove this decline remain uncertain, and it has not been determined if there is an associated decline in morphological and ecological diversity. Here, we apply geometric morphometrics to reconstruct global morphospace occupation for lingulid brachiopods through the Phanerozoic, with results showing that maximum morphospace occupation was reached by the Early Ordovician. At this time of peak diversity, linguloids with a sub-rectangular shell shape already possessed several evolutionary features, such as the rearrangement of mantle canals and reduction of the pseudointerarea, common to all modern infaunal forms. The end Ordovician mass extinction has a differential effect on linguloids, disproportionally wiping out those forms with a rounded shell shape, while forms with sub-rectangular shells survived both the end Ordovician and the Permian-Triassic mass extinctions, leaving a fauna predominantly composed of infaunal forms. For discinoids, both morphospace occupation and epibenthic life strategies remain consistent through the Phanerozoic. Morphospace occupation over time, when considered using anatomical and ecological analyses, suggests that the limited morphological and ecological diversity of modern lingulid brachiopods reflects evolutionary contingency rather than deterministic processes.
  •  
27.
  • Liang, Yue, et al. (författare)
  • Late Ordovician lingulid brachiopods from the Pingliang Formation (Shaanxi Province, North China) : Morphological and ecological implications
  • 2024
  • Ingår i: Journal of Asian Earth Sciences. - : Elsevier. - 1367-9120 .- 1878-5786. ; 263
  • Tidskriftsartikel (refereegranskat)abstract
    • Brachiopods first appeared in the early Cambrian and persist till present. They are one of the main lineages of marine invertebrates that diversified throughout the Paleozoic and reached their maximum diversity of high-rank taxonomy during the Ordovician. During this time interval, brachiopods were mainly dominated by the articulated Orthida and Strophomenida, which represent major components of the Paleozoic Evolutionary Fauna; however, the inarticulated lingulid brachiopods (Order Lingulida) were comparatively less abundant and received less attention during this time period. Here, we report a new record of the lingulid brachiopod Anomaloglossa porca from the Upper Ordovician (Sandbian) Pingliang Formation of the Xilinggou Section, Shaanxi Province, North China. Collected specimens are preserved as calcium phosphatic shells with highly mineralization which preserve detailed morphology and shell ornamentation of both ventral and dorsal valves. The new occurrence of A. porca extends its paleogeographic distribution from Gondwana and Tarim to North China Platform. Moreover, comprehensive geometric morphometric analysis of A. porca is performed and the results indicate that both the shell shape and pseudointerarea are very close to the recent infaunal lingulids. If interpreted correctly, the fossils represent the first example of infaunal lifestyles achieved by Ordovician lingulids from North China, exhibiting the ecological complexities of the Late Ordovician benthos composed of epibenthos and infaunas as well.
  •  
28.
  • Liang, Yue, et al. (författare)
  • When lingulid brachiopods became infaunal(?) : Perspectives from the morphological and anatomical information
  • 2023
  • Ingår i: Estonian journal of earth sciences. - : Estonian Academy Publishers. - 1736-4728 .- 1736-7557. ; 72:1, s. 140-140
  • Tidskriftsartikel (refereegranskat)abstract
    • Morphology usually serves as an effective proxy for functional ecology, and the evaluation of morphological, anatomical, and ecological changes allows for a deeper understanding of the nature of diversification and macroevolution. Lingulid (Order Lingulida) brachiopods were diverse and abundant during the early Palaeozoic, but decreased in diversity over time, with only a few genera of linguloids and discinoids present in modern marine ecosystems, frequently referred to as 'living fossils'. The dynamics that drove this decline remain unclear and it has not been determined if there is an associated decline in morphological and ecological diversity. We applied geometric morphometrics to reconstruct global morphospace occupied by lingulid brachiopods through the Phanerozoic, with results showing that maximum morphospace occupation was reached in the Early Ordovician. At this time of peak diversity, linguloids with sub-rectangular shells already possessed several evolutionary features common to all modern infaunal forms such as the rearrangement of mantle canals and reduction of the pseudointerarea. The endOrdovician mass extinction had a differential effect on linguloids, disproportionally wiping out those with rounded shells whilst forms with sub-rectangular shells survived both the endOrdovician and the Permian-Triassic mass extinctions, with post-extinction faunas predomi nantly composed of infaunal forms. For discinoids, both morphospace occupation and epi-benthic life strategies remain consistent through the Phanerozoic. Analysis of the morphospace occupation of lingulids over time, taking into account their body size, anatomical features and ecological changes, suggests that the reduced morphological and ecological diversity observed in modern lingulid brachiopods reflects evolutionary contingency rather than deterministic processes.
  •  
29.
  • Liu, Chenjuan, 1988-, et al. (författare)
  • A free standing Ru–TiC nanowire array/carbon textile cathode with enhanced stability for Li–O2 batteries
  • 2018
  • Ingår i: Journal of Materials Chemistry A. - : Royal Society of Chemistry (RSC). - 2050-7488 .- 2050-7496. ; 6, s. 23659-23668
  • Tidskriftsartikel (refereegranskat)abstract
    • The instability of carbon cathode materials is one of the key problems that hinder the development of lithium–air/lithium–oxygen (Li–O2) batteries. In this contribution, a type of TiC-based cathode is developed as a suitable alternative to carbon based cathodes, and its stability with respect to its surface properties is investigated. Here, a free-standing TiC nanowire array cathode was in situ grown on a carbon textile, covering its exposed surface. The TiC nanowire array, via deposition with Ru nanoparticles, showed enhanced oxygen reduction/evolution activity and cyclability, compared to the one without Ru modification. The battery performance of the Li–O2cells with Ru–TiC was investigated by using in operando synchrotron radiation powder X-ray diffraction (SR-PXD) during a full cycle. With the aid of surface analysis, the role of the cathode substrate and surface modification is demonstrated. The presented results are a further step toward a wise design of stable cathodes for Li–O2 batteries.
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30.
  • Ma, Tao, et al. (författare)
  • Genomic insights into salt adaptation in a desert poplar
  • 2013
  • Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
  • Tidskriftsartikel (refereegranskat)abstract
    • Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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31.
  • Pellegrini, Adam F.A., et al. (författare)
  • Soil carbon storage capacity of drylands under altered fire regimes
  • 2023
  • Ingår i: Nature Climate Change. - 1758-678X. ; 13:10, s. 1089-1094
  • Tidskriftsartikel (refereegranskat)abstract
    • The determinants of fire-driven changes in soil organic carbon (SOC) across broad environmental gradients remains unclear, especially in global drylands. Here we combined datasets and field sampling of fire-manipulation experiments to evaluate where and why fire changes SOC and compared our statistical model to simulations from ecosystem models. Drier ecosystems experienced larger relative changes in SOC than humid ecosystems—in some cases exceeding losses from plant biomass pools—primarily explained by high fire-driven declines in tree biomass inputs in dry ecosystems. Many ecosystem models underestimated the SOC changes in drier ecosystems. Upscaling our statistical model predicted that soils in savannah–grassland regions may have gained 0.64 PgC due to net-declines in burned area over the past approximately two decades. Consequently, ongoing declines in fire frequencies have probably created an extensive carbon sink in the soils of global drylands that may have been underestimated by ecosystem models.
  •  
32.
  • Rabin, Sam S., et al. (författare)
  • The Fire Modeling Intercomparison Project (FireMIP), phase 1 : Experimental and analytical protocols with detailed model descriptions
  • 2017
  • Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 10:3, s. 1175-1197
  • Tidskriftsartikel (refereegranskat)abstract
    • The important role of fire in regulating vegetation community composition and contributions to emissions of greenhouse gases and aerosols make it a critical component of dynamic global vegetation models and Earth system models. Over 2 decades of development, a wide variety of model structures and mechanisms have been designed and incorporated into global fire models, which have been linked to different vegetation models. However, there has not yet been a systematic examination of how these different strategies contribute to model performance. Here we describe the structure of the first phase of the Fire Model Intercomparison Project (FireMIP), which for the first time seeks to systematically compare a number of models. By combining a standardized set of input data and model experiments with a rigorous comparison of model outputs to each other and to observations, we will improve the understanding of what drives vegetation fire, how it can best be simulated, and what new or improved observational data could allow better constraints on model behavior. In this paper, we introduce the fire models used in the first phase of FireMIP, the simulation protocols applied, and the benchmarking system used to evaluate the models. We have also created supplementary tables that describe, in thorough mathematical detail, the structure of each model.
  •  
33.
  • Rich, Rebecca L., et al. (författare)
  • A global benchmark study using affinity-based biosensors
  • 2009
  • Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
  • Tidskriftsartikel (refereegranskat)abstract
    • To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
  •  
34.
  • Song, Kai, 1988-, et al. (författare)
  • Conservation genomics in the boreal forest : Population structure and local adaptation in the sibling species Chinese Grouse and Hazel Grouse
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The climate of the world’s arctic regions, including the poles and the Tibetan plateau region, act as a bellwether for global change. On the Tibetan plateau, there are numerous species well adapted to cold environments. The Chinese Grouse and Hazel Grouse are sibling species distributed in the Eurasian subarctic forests of the Tibetan plateau respectively. Conservation genomics are transforming our understanding of organismal responses in a changing Arctic boreal forest. In this study, we used 29 individuals from the sister species Chinese Grouse and Hazel Grouse from the boreal forest in Eurasia.  Our results provide insights into the genetic diversity and differentiation in to different geographic populations of the two species. Full genome sequencing of samples covering the distribution area of grouse species throughout the Eurasian boreal forest has enabled us to provide the first analysis of the population structure and introgression. Through selective sweep analysis, we detected that the Chinese Grouse inhabiting the QTP high altitude environment show evidence of having evolved adaptations to hypobaric hypoxia and high ultraviolet radiation.
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35.
  •  
36.
  • Song, Kai, 1988-, et al. (författare)
  • Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change
  • 2021
  • Ingår i: BMC Ecology and Evolution. - : BioMed Central (BMC). - 2730-7182. ; 21:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46-3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species.
  •  
37.
  • Song, Kai, 1988-, et al. (författare)
  • Demographics and divergence of the sibling species Chinese Grouse and Hazel Grouse inferred from whole genome sequencing
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To provide insights into the role of recent ice ages in species divergence and population history in southern Eurasian boreal forests, we sequenced the genomes of 32 individuals from the sister species Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of outgroup species from Europe and China. Our results show very different population demographic histories between the sibling species. Using PSMC we show that the peak and bottleneck of effective population size (Ne) occurred at different times; the Hazel Grouse had a peak in the Mid-Pleistocene and a bottleneck during the Last Glacial Period, in contrast to the Chinese Grouse, which peaked with a larger population size after the Hazel Grouse. In addition, the northern population of Chinese Grouse inhabiting the Qilian Mountains became separated from the main population residing in the south and since then consistently showed lower effective population size than the southern population. The Hazel Grouse population in northern China had a higher effective population size at the peak of the Last Glacial Period compared to the European population, which appeared to have gone through a severe bottleneck. As revealed by MSMC modelling, both species have recently decreased and now have low effective population sizes. The results of this study, suggest that differences in the demographic processes that shaped the evolutionary history and distribution for both species, will contribute to the understanding of the biological processes affecting the fauna in boreal forests in Eurasia.
  •  
38.
  • Song, Kai, 1988-, et al. (författare)
  • Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowi
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Background: The Quaternary is characterized by marked climatic oscillations between glacial and interglacial periods that had worldwide consequences in forming the contemporary diversity of many populations, species and communities. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouse Tetrastes sewerzowi is a forest-dwelling species endemic to the mountains to the east of the Qinghai–Tibet Plateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. Understanding demographic history is important in placing current population status into a broader ecological and evolutionary context.Results: Analysis of the Chinese Grouse genome reveals fluctuation in effective population size throughout the Pleistocene. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene then followed a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that suitable habitat shift between high altitude regions to low altitude regions were due to a changing climate. The result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period and then a peak and a bottleneck occurring at the LGM. Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and will become highly fragmented if boreal forest cover restricts the ecological niche.Conclusions: The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck happened during the LGM, when the conifer forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support the historical population fluctuation. The distribution of the Chinese Grouse was strongly dependent on the boreal forest cover. To protect the fragmented boreal forest is an essential action to protect the Chinese Grouse.
  •  
39.
  • Song, Kai, 1988-, et al. (författare)
  • Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese GrouseTetrastes sewerzowi
  • 2020
  • Ingår i: BMC Genomics. - : BMC. - 1471-2164. ; 21:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background The Quaternary had worldwide consequences in forming the contemporary diversity of many populations, species and communities, which is characterized by marked climatic oscillations between glacial and interglacial periods. The origin and evolution of biodiversity in mountainous areas are highly dependent on historical orogenesis and associated climatic changes. The Chinese grouseTetrastes sewerzowiis a forest-dwelling species endemic to the mountains to the east of the Qinghai-TibetPlateau, which has been listed as Near Threatened with a decreasing trend by the IUCN because of ongoing deforestation and fragmentation of coniferous forests. It is important to place current population status into a broader ecological and evolutionary context to understand their demographic history. Results Analyses of the Chinese Grouse genome revealed fluctuations throughout the Pleistocene in effective population size. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene which was then followed by a sharp decline during the last glacial maximum (LGM). Ecological niche modeling indicated that a suitable habitat shift between high altitude regions to low altitude regions was due to a changing climate. This result parallels patterns of population size change in Chinese Grouse estimated from PSMC modelling, which suggested an expansion in population size from the last interglacial period (LIG) and then a peak and a bottleneck occurring at the last glacial maximum (LGM). Furthermore, the present-day distribution of Chinese Grouse is greatly reduced and fragmented. It will likely become even more fragmented in the future since coniferous forest cover is threatened in the region of their distribution and the availability of such habitat restricts their ecological niche. Conclusions The Chinese Grouse have experienced substantial population size changes from the beginning to the LIG and reached a peak before the LGM. A sharp decrease and bottleneck occurred during the LGM, when the coniferous forests were subjected to extensive loss. The results inferred from the whole genome sequencing and species distribution models both support historical population fluctuations. The distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. To protect the fragmented coniferous forests is an essential action to protect the Chinese Grouse.
  •  
40.
  • Song, Kai, 1988-, et al. (författare)
  • Inbreeding and genetic load in a pair of sibling grouse species : Tetrastes sewersowi and T. bonasia
  • 2024
  • Ingår i: Avian Research. - : Elsevier. - 2053-7166. ; 15
  • Tidskriftsartikel (refereegranskat)abstract
    • Genetic load and inbreeding are recognized as important factors to be considered in conservation programs. Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals, including humans (inbreeding depression). Genomic techniques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation. We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both. We found a large range of inbreeding measured as FROH (fraction of runs of homozygosity) in individuals from different populations of Chinese Grouse (Tetrastes sewerzowi) and Hazel Grouse (T. bonasia). FROH estimated from genome-wide runs of homozygosity (ROH) ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse. Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse (including samples from Sweden, Germany and Northeast Poland) were the most inbred (FROH ranged from 0.10 to 0.23 and 0.11 to 0.44, respectively). These levels are comparable to other highly inbred populations of birds. Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels. Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse. These results are possibly explained by higher fixation rates, mutational melt down, in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse. However, when we compared the relatively more severe class of loss-of-function mutations, Hazel Grouse had slightly higher levels than Chinese Grouse, a result which may indicate that purifying selection (purging) has been more efficient in Chinese Grouse on this class of mutations.
  •  
41.
  • Song, Kai, 1988-, et al. (författare)
  • Purifying selection in Grouse is more efficient in large populations
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Inbreeding depression and purging are recognized as essential factors to be considered in conservation programs. Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals, including humans. Genomic techniques are increasingly used in measuring and understanding inbreeding and inbreeding depression and their importance in evolution and conservation. We use whole genome resequencing data from isolated, bottlenecked, and outbred Tetrastes and Lagopus populations in subarctic Eurasia to quantify inbreeding depression and purifying selection. We found a large range of inbreeding measured as FROH in populations of Chinese Grouse (Tetrastes sewerzowi) and Hazel Grouse (T. bonasia). FROH estimated from genome-wide runs of homozygosity (ROH) ranged from 0.02 to 0.24 among Chinese Grouse populations and 0.01 to 0.44 in Hazel grouse. A population of Chinese Grouse residing in the Qilian mountains and the European populations of Hazel Grouse (including samples from Sweden, Germany and North East Poland) were both highly inbred (FROH ranged from 0.10 to 0.23 and 0.11 to 0.44, respectively). Hazel grouse from northern China and Chinese grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels. In addition, through comparison of the ratio between deleterious missense mutations and synonymous mutations, purifying selection was found to be more efficient in Hazel grouse and ptarmigan populations which hold larger population sizes than Chinese grouse. However, when we compared the ratio between loss-of-function and synonymous mutations, Hazel Grouse had slightly higher levels than Chinese Grouse while Willow Ptarmigan and Rock Ptarmigan had lower levels of genetic load. These results indicate that purifying selection has been more efficient in the wide ranging hazel grouse which thereby can sustain higher levels of inbreeding compared to Chinese grouse. Our study provides the first genetic evidence of inbreeding depression and purging patterns in boreal forest species in Eurasia from the respective sibling species and provide relevant information for future conservation and management of the species.
  •  
42.
  • Uitterlinden, André G, et al. (författare)
  • The association between common vitamin D receptor gene variations and osteoporosis : a participant-level meta-analysis
  • 2006
  • Ingår i: Annals of Internal Medicine. - 0003-4819. ; 145:4, s. 255-264
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Polymorphisms of the vitamin D receptor (VDR) gene have been implicated in the genetic regulation of bone mineral density (BMD). However, the clinical impact of these variants remains unclear.OBJECTIVE: To evaluate the relation between VDR polymorphisms, BMD, and fractures.DESIGN: Prospective multicenter large-scale association study.SETTING: The Genetic Markers for Osteoporosis consortium, involving 9 European research teams.PARTICIPANTS: 26,242 participants (18,405 women).MEASUREMENTS: Cdx2 promoter, FokI, BsmI, ApaI, and TaqI polymorphisms; BMD at the femoral neck and the lumbar spine by dual x-ray absorptiometry; and fractures.RESULTS: Comparisons of BMD at the lumbar spine and femoral neck showed nonsignificant differences less than 0.011 g/cm2 for any genotype with or without adjustments. A total of 6067 participants reported a history of fracture, and 2088 had vertebral fractures. For all VDR alleles, odds ratios for fractures were very close to 1.00 (range, 0.98 to 1.02) and collectively the 95% CIs ranged from 0.94 (lowest) to 1.07 (highest). For vertebral fractures, we observed a 9% (95% CI, 0% to 18%; P = 0.039) risk reduction for the Cdx2 A-allele (13% risk reduction in a dominant model).LIMITATIONS: The authors analyzed only selected VDR polymorphisms. Heterogeneity was detected in some analyses and may reflect some differences in collection of fracture data across cohorts. Not all fractures were related to osteoporosis.CONCLUSIONS: The FokI, BsmI, ApaI, and TaqI VDR polymorphisms are not associated with BMD or with fractures, but the Cdx2 polymorphism may be associated with risk for vertebral fractures.
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43.
  • Van Marle, Margreet J.E., et al. (författare)
  • Historic global biomass burning emissions for CMIP6 (BB4CMIP) based on merging satellite observations with proxies and fire models (1750-2015)
  • 2017
  • Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 10:9, s. 3329-3357
  • Forskningsöversikt (refereegranskat)abstract
    • Fires have influenced atmospheric composition and climate since the rise of vascular plants, and satellite data have shown the overall global extent of fires. Our knowledge of historic fire emissions has progressively improved over the past decades due mostly to the development of new proxies and the improvement of fire models. Currently, there is a suite of proxies including sedimentary charcoal records, measurements of fire-emitted trace gases and black carbon stored in ice and firn, and visibility observations. These proxies provide opportunities to extrapolate emission estimates back in time based on satellite data starting in 1997, but each proxy has strengths and weaknesses regarding, for example, the spatial and temporal extents over which they are representative. We developed a new historic biomass burning emissions dataset starting in 1750 that merges the satellite record with several existing proxies and uses the average of six models from the Fire Model Intercomparison Project (FireMIP) protocol to estimate emissions when the available proxies had limited coverage. According to our approach, global biomass burning emissions were relatively constant, with 10-year averages varying between 1.8 and 2.3 PgC yr-1. Carbon emissions increased only slightly over the full time period and peaked during the 1990s after which they decreased gradually. There is substantial uncertainty in these estimates, and patterns varied depending on choices regarding data representation, especially on regional scales. The observed pattern in fire carbon emissions is for a large part driven by African fires, which accounted for 58% of global fire carbon emissions. African fire emissions declined since about 1950 due to conversion of savanna to cropland, and this decrease is partially compensated for by increasing emissions in deforestation zones of South America and Asia. These global fire emission estimates are mostly suited for global analyses and will be used in the Coupled Model Intercomparison Project Phase 6 (CMIP6) simulations.
  •  
44.
  • Wang, Jianmin, et al. (författare)
  • Experimental Study on Abstract Expression of Human-Robot Emotional Communication
  • 2021
  • Ingår i: Symmetry. - : MDPI AG. - 2073-8994. ; 13:9
  • Tidskriftsartikel (refereegranskat)abstract
    • With the continuous development of intelligent product interaction technology, the facial expression design of virtual images on the interactive interface of intelligent products has become an important research topic. Based on the current research on facial expression design of existing intelligent products, we symmetrically mapped the PAD (pleasure-arousal-dominance) emotion value to the image design, explored the characteristics of abstract expressions and the principles of expression design, and evaluated them experimentally. In this study, the experiment of PAD scores was conducted on the emotion expression design of abstract expressions, and the data results were analyzed to iterate the expression design. The experimental results show that PAD values can effectively guide designers in expression design. Meanwhile, the efficiency and recognition accuracy of human communication with abstract expression design can be improved by facial auxiliary elements and eyebrows.
  •  
45.
  • Wang, Lu, et al. (författare)
  • Historical Soil Moisture Variability in High-Latitude Humid Regions: Insights From a Paleoclimate Data-Model Comparison
  • 2024
  • Ingår i: EARTHS FUTURE. - 2328-4277. ; 12:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Understanding historical soil moisture (SM) variations and their relationship with temperature in high-latitude humid regions is essential for predicting hot droughts under widespread warming. This paper presents the first-ever annual-resolution summer surface SM reconstruction (1736-2006 CE) in Sweden, located in northern Europe (NE). The reconstruction utilizes the paleoclimate proxy, tree-ring delta O-18, which exhibits a strong correlation with reanalysis SM data during 1948-2007 CE (r = -0.67, p < 0.001). In contrast to an unprecedented trend suggested by previous studies, our reconstruction exhibits a wetting trend in NE since the 1960s falling within the historical spectrum of trends. Both reanalysis SM data and our reconstruction show significant negative correlations with temperature at interannual timescales. However, Coupled Model Intercomparison Project Phase 6 climate models failed to capture the significant SM-temperature relationship during the historical (1850-1947 CE) and observation periods (1948-2006 CE). This proxy-model comparison represents a critical step toward enhancing our understanding of SM dynamics and the reliability of SM projections in high-latitude humid regions.
  •  
46.
  • Wen-Yu, Fang, et al. (författare)
  • Elastic constants, electronic structures and thermal conductivity of monolayer XO2 (X = Ni, Pd, Pt)
  • 2021
  • Ingår i: Wuli xuebao. - : Chinese Physical Society and Institute of Physics, Chinese Academy of Sciences. - 1000-3290. ; 70:24
  • Tidskriftsartikel (refereegranskat)abstract
    • Based on the first-principles calculations, the stability, elastic constants, electronic structure, and lattice thermal conductivity of monolayer XO2 (X = Ni, Pd, Pt) are investigated in this work. The results show that XO2 (X = Ni, Pd, Pt) have mechanical and dynamic stability at the same time. In addition, the Young's modulus of monolayer NiO2, PdO2 and PtO2 are 124.69 N.m(-1), 103.31 N.m(-1) and 116.51 N.m(-1), Poisson's ratio of monolayer NiO2, PdO2 and PtO2 are 0.25, 0.24 and 0.27, respectively, and each of them possesses high isotropy. The band structures show that monolayer XO2 (X = Ni, Pd, Pt) are indirect band-gap semiconductors with energy gap of 2.95 eV, 3.00 eV and 3.34 eV, respectively, and the energy levels near the valence band maximum and conduction band minimum are mainly composed of Ni-3d/Pd-4d/Pt-5d and O-2p orbital electrons. Based on deformation potential theory, the carrier mobility of each monolayer is calculated, and the results show that the effective mass and deformation potential of monolayer XO2 (X = Ni, Pd, Pt) along the armchair and zigzag directions show obvious anisotropy, and the highest electron and hole mobility are 13707.96 and 53.25 cm(2) .V-1.s(-1), 1288.12 and 19.18 cm(2).V-1.s(-1), and 404.71 and 270.60 cm(2) .V-1.s(-1) for NiO2, PdO(2 )and PtO2, respectively. Furthermore, the lattice thermal conductivity of monolayer XO2 (X = Ni, Pd, Pt) at 300 K are 53.55 W.m(-1).K-1, 19.06 W.m(-1).K-1 and 17.43 W.m(-1).K-1, respectively. These properties indicate that monolayer XO2 (X = Ni, Pd, Pt) have potential applications in nanometer electronic materials and thermal conductivity devices.
  •  
47.
  • Xie, Yukun, et al. (författare)
  • Behavioral Indicators Affecting Driving Performance in Human Machine Interface Assessments with Simulation
  • 2021
  • Ingår i: Advances in Human Aspects of Transportation. - Cham : Springer. - 9783030800116 ; , s. 246-252
  • Konferensbidrag (refereegranskat)abstract
    • Human-machine interface (HMI) is valued as a medium for information interaction between the digital cockpit and the driver, and simulated driving evaluation is an important method for assessing in-vehicle HMI. It is worth exploring how to select appropriate behavioral indicators for evaluation analysis and design iterations. The study selected six secondary tasks for HMI evaluation using touch screen interaction under a constant speed straight road driving scenario. Vehicle indicators including vertical and horizontal control and behavioral indicators related to the secondary tasks were collected. By performing stepwise regression analysis on the data from 26 participants, some behavioral indicators that have an impact on driving performance were extracted to provide suggestions for the simulation experimental evaluation and HMI design optimization iterations.
  •  
48.
  • Yang, Hui, et al. (författare)
  • Multicriteria evaluation of discharge simulation in Dynamic Global Vegetation Models
  • 2015
  • Ingår i: Journal of Geophysical Research: Atmospheres. - 2169-8996. ; 120:15, s. 7488-7505
  • Tidskriftsartikel (refereegranskat)abstract
    • In this study, we assessed the performance of discharge simulations by coupling the runoff from seven Dynamic Global Vegetation Models (DGVMs; LPJ, ORCHIDEE, Sheffield-DGVM, TRIFFID, LPJ-GUESS, CLM4CN, and OCN) to one river routing model for 16 large river basins. The results show that the seasonal cycle of river discharge is generally modeled well in the low and middle latitudes but not in the high latitudes, where the peak discharge (due to snow and ice melting) is underestimated. For the annual mean discharge, the DGVMs chained with the routing model show an underestimation. Furthermore, the 30year trend of discharge is also underestimated. For the interannual variability of discharge, a skill score based on overlapping of probability density functions (PDFs) suggests that most models correctly reproduce the observed variability (correlation coefficient higher than 0.5; i.e., models account for 50% of observed interannual variability) except for the Lena, Yenisei, Yukon, and the Congo river basins. In addition, we compared the simulated runoff from different simulations where models were forced with either fixed or varying land use. This suggests that both seasonal and annual mean runoff has been little affected by land use change but that the trend itself of runoff is sensitive to land use change. None of the models when considered individually show significantly better performances than any other and in all basins. This suggests that based on current modeling capability, a regional-weighted average of multimodel ensemble projections might be appropriate to reduce the bias in future projection of global river discharge.
  •  
49.
  • Yang, Xuan, et al. (författare)
  • Geochemical records and environmental analysis of the Ediacaran-Cambrian boundary in Eastern Yunnan, South China
  • 2023
  • Ingår i: Frontiers in Earth Science. - 2296-6463. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • The Ediacaran–Cambrian transition is characterized by an unprecedented change in biosphere, lithosphere, and atmosphere. However, the identification of this transition and its global correlation remains debated. East Yunnan is a region of utmost importance in the study of the Ediacaran-Cambrian transition. Although strata from this region have been well studied, recognition of the base of the Cambrian continues to be controversial. This paper presents, a carbon chemostratigraphic isotope and trace element profile through the Dengying and Zhujiaqing formations in the Sujiawa section in East Yunnan. Through carbon isotope and trace element analyses of the Dengying and Zhujiaqing formations we attempt to regionally correlate the section and discuss the paleo-marine redox environment changes during this period. The Fe content of samples is low and the Mn/Sr ratios of the majority of the Sujiawa section samples is lower than 10 and shows no correlations with δ13Ccarb and δ18Ocarb values, indicating that the samples retain near-primary δ13Ccarb characteristics. The carbon isotope profile from the Sujiawa section, shows a prominent negative δ13Ccarb in the basal Zhongyicun Member (N1’, −7.3‰) that most likely represents the prominent negative excursion recorded in Ediacaran-Cambrian strata across the world. REE patterns and Y/Ho ratios were used to screen samples, to ensure that the primary seawater REE features and Ce anomalies were preserved. The samples satisfying this screening process show seawater-like REE distribution patterns in leached carbonates and may have recorded Ce anomalies of the seawater from which the carbonates precipitated. These data show that the Baiyanshao Member has Ce/Ce* values between 0.57 and 0.88, the Daibu Member between 0.56 and 0.83, and the Zhongyicun Member between 0.60 and 0.96. The Ce anomalies through the section indicates that the region experienced suboxic-oxic-anoxic conditions throughout the Ediacaran-Cambrian period. Carbon isotope and trace element analyses indicate that the strata record a negative carbon isotope excursion event and anoxic conditions during the period of deposition. This study complements the carbon chemostratigraphic information and trace element data in the region and provides valuable clues for understanding the lithofacies changes through the Ediacaran and Cambrian in different regions of South China.
  •  
50.
  • Zhang, Feng, et al. (författare)
  • Nonadiabatic histidine dissociation of hexacoordinate heme in neuroglobin protein
  • 2010
  • Ingår i: Journal of Physical Chemistry A. - America : American Chemical Society. - 1089-5639 .- 1520-5215.
  • Tidskriftsartikel (refereegranskat)abstract
    • In the present work, density functional theory and canonical nonadiabatic Monte Carlo transition state theory have been used to investigate histidine dissociation process from the hexacoordinate heme in Ngb protein. The potential energy surfaces (PES) of the lowest singlet, triplet, and quintet states are calculated by stepwise optimization along with the histidine dissociation pathway. Based on the calculated two-dimensional PES, the histidine dissociation rates for the spin-forbidden processes via singlet to triplet and singlet to quintet transitions have been calculated by the nonadiabatic Monte Carlo transition state theory in canonical ensemble. The present study provides a quantitative description on spin-forbidden histidine dissociation processes.
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