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  • 1
    Online Resource
    Online Resource
    Alteration of functional connectivity network in population of objectively-defined subtle cognitive decline
    Oxford University Press (OUP) ; 2024
    In:  Brain Communications
    Details
    In: Brain Communications, Oxford University Press (OUP)
    Abstract: The objectively-defined subtle cognitive decline individuals had higher progression rates of cognitive decline and pathological deposition than healthy elderly, indicating a higher risk of progressing to Alzheimer’s disease. However, little is known about the brain functional alterations during this stage. Thus, we aimed to investigate the functional network patterns in objectively-defined subtle cognitive decline cohort. Forty-two cognitive normal, 29 objectively-defined subtle cognitive decline and 55 mild cognitive impairment subjects were included based on neuropsychological measures from the Alzheimer's Disease Neuroimaging Initiative dataset. Thirty cognitive normal, 22 objectively-defined subtle cognitive decline and 48 mild cognitive impairment had longitudinal MR data. The degree centrality and eigenvector centrality for each participant were calculated by using resting-state functional MRI. For cross-sectional data, analysis of covariance (ANCOVA) was performed to detect between-group differences of degree centrality and eigenvector centrality after controlling age, sex, and education. For longitudinal data, repeated measurement ANCOVA was used for comparing the alterations during follow-up period among three groups. In order to classify the clinical significance, we correlated degree centrality and eigenvector centrality values to Alzheimer’s disease biomarkers and cognitive function. The results of ANCOVA showed significant between-group differences of eigenvector centrality and degree centrality in left superior temporal gyrus and left precuneus respectively. Across groups, the eigenvector centrality value of left superior temporal gyrus was positively related with recognition scores in auditory verbal learning test, whereas the degree centrality value of left precuneus was positively associated with Mini-mental State Examination total score. For longitudinal data, the results of repeated measurement ANCOVA indicated objectively-defined subtle cognitive decline group had the highest declined rate of both eigenvector centrality and degree centrality values than other groups. Our study showed an increased brain functional connectivity in objectively-defined subtle cognitive decline individuals at both local and global level, which were associated with Alzheimer’s disease pathology and neuropsychological assessment. Moreover, we also observed a faster declined rate of functional network matrix in objectively-defined subtle cognitive decline individuals during the follow-ups.
    Type of Medium: Online Resource
    ISSN: 2632-1297
    URL: Article
    DOI: 10.1093/braincomms/fcae033
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 3020013-1
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  • 2
    Online Resource
    Online Resource
    Comparison of gefitinib-induced skin adverse reactions (SAR) in C57BL/6 and FVB/N mice
    Oxford University Press (OUP) ; 2021
    In:  Toxicology Research Vol. 10, No. 2 ( 2021-04-13), p. 334-344
    Details
    In: Toxicology Research, Oxford University Press (OUP), Vol. 10, No. 2 ( 2021-04-13), p. 334-344
    Abstract: Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as gefitinib, erlotinib, and afatinib, are widely used in clinical practice and remarkably effective in treatment of advanced non-small cell lung cancer. However, there are some adverse effects while taking EGFR-TKIs, among which skin adverse reactions (SAR) are the most common events. At present, the poor outcome of SAR and insufficient research on SAR models need to be addressed. In this study we focused on the SAR models to lay a foundation for mechanism researches. Gefitinib, one of the EGFR-TKIs, was used as SAR inducing agents. We chose C57BL/6 and FVB/N mice as experimental model and they were divided into four groups. The weight and skin moisture of mice were detected every 7 days, itching behavior and abnormal eyelids were tested at 35th day after gavage, and survival rate was also recorded. The weight of unit area hair, length of whiskers and inflammatory cells were evaluated after mice sacrificed. C57BL/6 animals treated with gefitinib showed significant differences in survival rate, weight of unit area hair, skin moisture changes, skin dryness, itching behavior, whisker irregular growth, abnormal eyelids, and inflammatory cells; FVB/N animals treated with gefitinib only showed significant differences in survival rate, whisker irregular growth and abnormal eyelids, compared with the control group, respectively. In this study, we compared the similarities and differences of gefitinib-induced SAR between C57BL/6 and FVB/N mice, which illustrated different patients probably showing different symptoms clinically and provided experimental basis for researching mechanism of EGFR-TKIs induced SAR.
    Type of Medium: Online Resource
    ISSN: 2045-4538
    URL: Article
    DOI: 10.1093/toxres/tfab008
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2684701-2
    SSG: 15,3
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  • 3
    Online Resource
    Online Resource
    Baicalin protects mice from infection with methicillin-resistant Staphylococcus aureus via alleviating inflammatory response
    Oxford University Press (OUP) ; 2020
    In:  Journal of Leukocyte Biology Vol. 108, No. 6 ( 2020-12-01), p. 1829-1839
    Details
    In: Journal of Leukocyte Biology, Oxford University Press (OUP), Vol. 108, No. 6 ( 2020-12-01), p. 1829-1839
    Abstract: Sepsis was redefined as life-threatening organ dysfunction caused by a dysregulated host response to infection in 2016. One of its most common causes is Staphylococcus aureus, especially methicillin-resistant Staphylococcus aureus (MRSA), which leads to a significant increase in morbidity and mortality. Therefore, innovative and effective approaches to combat MRSA infection are urgently needed. Recently, host-directed therapy (HDT) has become a new strategy in the treatment of infectious diseases, especially those caused by antibiotic-resistant bacteria. Baicalin (BAI) is the predominant flavonoid and bioactive compound isolated from the roots of Radix Scutellariae (Huang Qin), a kind of traditional Chinese medicine. It has been reported that BAI exhibits multiple biological properties such as anti-oxidant, antitumor, and anti-inflammatory activities. However, the therapeutic role of BAI in MRSA infection is still unknown. In this study, it is found that BAI treatment inhibited the production of IL-6, TNF-α, and other cytokines from MRSA- or bacterial mimics-stimulated Mϕs and dendritic cells (DCs). BAI played an anti-inflammatory role by inhibiting the activation of ERK, JNK MAPK, and NF-κB pathways. Moreover, the serum level of TNF-α was decreased, whereas IL-10 was increased, in mice injected with MRSA. Furthermore, the bacterial load in livers and kidneys were further decreased by the combination of BAI and vancomycin (VAN), which might account for the amelioration of tissue damage. BAI reduced the high mortality rate caused by MRSA infection. Collectively, the results suggested that BAI may be a viable candidate of HDT strategy against severe sepsis caused by antibiotic-resistant bacteria such as MRSA.
    Type of Medium: Online Resource
    ISSN: 0741-5400 , 1938-3673
    URL: Article
    DOI: 10.1002/JLB.3AB0820-576RRR
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2026833-6
    SSG: 12
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  • 4
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    Online Resource
    Physiological and biomass partitioning shifts to water stress under distinct soil types in Populus deltoides saplings
    Oxford University Press (OUP) ; 2020
    In:  Journal of Plant Ecology Vol. 13, No. 5 ( 2020-10-01), p. 545-553
    Details
    In: Journal of Plant Ecology, Oxford University Press (OUP), Vol. 13, No. 5 ( 2020-10-01), p. 545-553
    Abstract: Although soil environments exist extensive heterogeneity for many plants with a wide range of distribution, researches about effects of soil conditions on plants’ tolerance and adaptation are particularly inadequate. In our study, the aims are to reveal physiological strategies of Populus deltoides against drought stress under different soil conditions and to select the most suitable soil type for P. deltoides plantation. Methods Under controlled conditions, we used P. deltoides as a model species to detect differences in gas exchange rate, antioxidative capacity, nitrogen metabolism and biomass accumulation and partitioning in response to drought stress under three mineral soil types with distinct physicochemical characters, i.e. red soil (RS), yellow soil (YS) and yellow-brown soil (BS). Important Findings Exposure to 25% of field water holding capacity in soil for 3 months had significantly decreased biomass of all organs, photosynthetic rate, enzyme activities related to N assimilation, but increased H2O2, malondialdehyde and content of both NO3− and NH4+, when P. deltoides was planted in both RS and YS. In contrast, under BS, there are slightly negative effects exerted by water deficit on total biomass, gas exchange rate, activities of enzymes related to nitrogen metabolism and membrane damage caused by reactive oxygen species, which can be associated with a consistent increase in superoxide dismutase, peroxidase and catalase, and a higher ratio of root mass to shoot mass. It is concluded that, such higher capacity in tolerance and adaptation against drought stress under BS relative to both RS and YS could be accounted for more sufficient nutrient provision in soil parental materials and better soil aeration conditions which play a vital role in plant acclimation to water shortage. Our study also revealed that, distribution areas of BS might be preferable for cultivation of P. deltoides, when compared with those of RS and YS.
    Type of Medium: Online Resource
    ISSN: 1752-993X
    URL: Article
    DOI: 10.1093/jpe/rtaa042
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2381013-0
    SSG: 12
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  • 5
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    Online Resource
    Effects of drought and nutrient deficiencies on the allocation of recently fixed carbon in a plant–soil–microbe system
    Oxford University Press (OUP) ; 2023
    In:  Tree Physiology ( 2023-08-16)
    Details
    In: Tree Physiology, Oxford University Press (OUP), ( 2023-08-16)
    Abstract: Carbon (C) allocation plays an important role in plant adaptation to water and nutrient stresses. However, the effects of drought and nutrient deficiencies on the allocation of recently fixed C in the plant–soil–microbe system remain largely unknown. Herein, we studied the response of C allocation of Sophora moorcroftiana (an indigenous pioneer shrub in Tibet) to drought, nitrogen (N) deficiency and phosphorus (P) deficiency using a microcosm experiment. The 13CO2 continuous labeling was used to trace C allocation in the plant–soil–microbe system. We found that drought significantly reduced plant 13C, but it increased 13C accumulation in soil. The decreased plant 13C under drought was attributed to the decrease of 13C in stem and root rather than that in leaf. The excess 13C fraction in the microbial biomass (MB13C) was reduced by N deficiency, but it was not affected by the combination of drought and N deficiency, indicating that drought weakened the effects of N deficiency on MB13C. By contrast, MB13C increased under the combination of drought and P deficiency, suggesting that drought enhanced the effects of P deficiency on MB13C. Drought and nutrient deficiencies regulated the belowground 13C allocation. Specifically, drought and P deficiency increased the allocation of 13C to root and N deficiency regulated the allocation of 13C to microbial biomass C and dissolved organic C in soil. Notably, soil 13C decreased with increasing plant 13C, while MB13C first decreased and then increased with increasing plant 13C. Overall, our study demonstrated that drought and nutrient deficiencies interactively affected C allocation in a plant–soil–microbe system and provided insights into C allocation strategies in response to multiple resource (water and nutrient) stresses under environmental changes.
    Type of Medium: Online Resource
    ISSN: 1758-4469
    URL: Article
    DOI: 10.1093/treephys/tpad098
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1473475-8
    SSG: 12
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  • 6
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    Novel equations for estimating intraperitoneal pressure among peritoneal dialysis patients
    Oxford University Press (OUP) ; 2023
    In:  Clinical Kidney Journal Vol. 16, No. 9 ( 2023-08-31), p. 1447-1456
    Details
    In: Clinical Kidney Journal, Oxford University Press (OUP), Vol. 16, No. 9 ( 2023-08-31), p. 1447-1456
    Abstract: Increased intraperitoneal pressure (IPP) is associated with abdominal wall complications and technical failure in peritoneal dialysis (PD). Since the standard measurement of IPP is limited due to its cumbersome procedures, we aimed to develop and validate equations for estimating IPP. Methods We performed a cross-sectional study with a total of 200 prevalent PD patients who were divided into development and validation datasets after random sampling matched by body mass index. The IPPs were measured using the Durand method, with whole-body and abdominal anthropometry indices collected. Equations with 2.0-L and 1.5-L fill volumes were generated by stepwise linear regression modelling. The bias, accuracy and precision of the estimated IPP (eIPP) with 2-L and 1.5-L fill volumes were compared with actual IPPs by the Durand method. The eIPP for the 2-L fill volume was also compared with other existing equations. Results Two new equations incorporating waist circumference and height from the decubitus plane to mid-axillary line were generated. The eIPPs exhibited small biases in relation to the Durand method , with median differences of −0.24 cmH2O and −0.10 cmH2O for 2 L and 1.5 L, respectively. The precisions evaluated by the standard deviation of the absolute value of the differences were 2.59 cmH2O and 2.50 cmH2O, respectively. The accuracies evaluated by the value of the percentage of estimates that differed by & gt;20% for the eIPP were 26% for 2.0 L and 27% for 1.5 L. Better bias, precision and accuracy were observed for the eIPP equation compared with other existing equations for the 2.0-L fill volume. Conclusions We provided two new equations developed from abdominal anthropometry indices to accurately estimate the IPP in the PD population.
    Type of Medium: Online Resource
    ISSN: 2048-8505 , 2048-8513
    URL: Article
    DOI: 10.1093/ckj/sfad021
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2656786-6
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  • 7
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    Online Resource
    AB-Gen: Antibody Library Design with Generative Pre-Trained Transformer and Deep Reinforcement Learning
    Oxford University Press (OUP) ; 2023
    In:  Genomics, Proteomics & Bioinformatics Vol. 21, No. 5 ( 2023-10-01), p. 1043-1053
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 21, No. 5 ( 2023-10-01), p. 1043-1053
    Abstract: Antibody leads must fulfill multiple desirable properties to be clinical candidates. Primarily due to the low throughput in the experimental procedure, the need for such multi-property optimization causes the bottleneck in preclinical antibody discovery and development, because addressing one issue usually causes another. We developed a reinforcement learning (RL) method, named AB-Gen, for antibody library design using a generative pre-trained transformer (GPT) as the policy network of the RL agent. We showed that this model can learn the antibody space of heavy chain complementarity determining region 3 (CDRH3) and generate sequences with similar property distributions. Besides, when using human epidermal growth factor receptor-2 (HER2) as the target, the agent model of AB-Gen was able to generate novel CDRH3 sequences that fulfill multi-property constraints. Totally, 509 generated sequences were able to pass all property filters, and three highly conserved residues were identified. The importance of these residues was further demonstrated by molecular dynamics simulations, consolidating that the agent model was capable of grasping important information in this complex optimization task. Overall, the AB-Gen method is able to design novel antibody sequences with an improved success rate than the traditional propose-then-filter approach. It has the potential to be used in practical antibody design, thus empowering the antibody discovery and development process. The source code of AB-Gen is freely available at Zenodo (https://doi.org/10.5281/zenodo.7657016) and BioCode (https://ngdc.cncb.ac.cn/biocode/tools/BT007341).
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2023.03.004
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2233708-8
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  • 8
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    Detecting and characterizing microRNAs of diverse genomic origins via miRvial
    Oxford University Press (OUP) ; 2017
    In:  Nucleic Acids Research Vol. 45, No. 21 ( 2017-12-01), p. e176-e176
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 45, No. 21 ( 2017-12-01), p. e176-e176
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkx834
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 9
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    Online Resource
    AaWRKY17, a positive regulator of artemisinin biosynthesis, is involved in resistance to Pseudomonas syringae in Artemisia annua
    Oxford University Press (OUP) ; 2021
    In:  Horticulture Research Vol. 8, No. 1 ( 2021-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 8, No. 1 ( 2021-12)
    Abstract: Artemisia annua , a traditional Chinese medicinal plant, remains the only plant source for artemisinin production, yet few genes have been identified to be involved in both the response to biotic stresses, such as pathogens, and artemisinin biosynthesis. Here, we isolated and identified the WRKY transcription factor (TF) AaWRKY17, which could significantly increase the artemisinin content and resistance to Pseudomonas syringae in A. annua . Yeast one-hybrid (Y1H), dual-luciferase (dual-LUC), and electrophoretic mobility shift assay (EMSA) results showed that AaWRKY17 directly bound to the W-box motifs in the promoter region of the artemisinin biosynthetic pathway gene amorpha-4,11-diene synthase ( ADS ) and promoted its expression. Real-time quantitative PCR (RT-qPCR) analysis revealed that the transcript levels of two defense marker genes, Pathogenesis-Related 5 ( PR5 ) and NDR1/HIN1-LIKE 10 ( NHL10 ), were greatly increased in AaWRKY17- overexpressing transgenic A. annua plants. Additionally, overexpression of AaWRKY17 in A. annua resulted in decreased susceptibility to P. syringae . These results indicated that AaWRKY17 acted as a positive regulator in response to P. syringae infection. Together, our findings demonstrated that the novel WRKY transcription factor AaWRKY17 could potentially be used in transgenic breeding to improve the content of artemisinin and pathogen tolerance in A. annua .
    Type of Medium: Online Resource
    ISSN: 2662-6810 , 2052-7276
    URL: Article
    DOI: 10.1038/s41438-021-00652-6
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2781828-7
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  • 10
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    The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation
    Oxford University Press (OUP) ; 2023
    In:  Genomics, Proteomics & Bioinformatics Vol. 21, No. 3 ( 2023-06-01), p. 483-500
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 21, No. 3 ( 2023-06-01), p. 483-500
    Abstract: The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assembl  ies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2023.08.002
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2233708-8
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