35 results on '"Hu, Yunyun"'
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2. Tb 3+ assisted dithioerythritol stabilized copper nanocluster with AIE behavior for ratiometric fluorescent determination of fluoroquinolones.
- Author
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Liu W, Wang K, Liu P, Jiang W, Feng Y, Hu Y, Zheng M, Zhou Y, Xiao Y, and Liu Y
- Subjects
- Spectrometry, Fluorescence, Metal Nanoparticles chemistry, Animals, Limit of Detection, Copper chemistry, Copper analysis, Fluoroquinolones analysis, Fluoroquinolones chemistry, Fluorescent Dyes chemistry, Terbium chemistry
- Abstract
Background: Fluoroquinolones (FQs) are widely used in livestock and poultry industry because of their satisfactory effects in preventing and treating bacterial infection. However, due to irrational use and poor biodegradability, FQs can easily remain in food animals and further enter the human body through the food chain. Therefore, accurate and sensitive detection of FQs residues in animal-origin food is significant. The traditional methods commonly used for FQs detection have some limitations. Ratiometric fluorescence detection technology has the advantages of fast, sensitive, self-correcting, and easy visualization. However, the reports on the use of ratiometric fluorescence probes for FQs detection are limited., Results: In this work, a novel probe was proposed for ratiometric fluorescent analysis of FQs. In this probe, the fluorescence of dithioerythritol stabilized copper nanoclusters (DTE-Cu NCs) was significantly enhanced due to the Tb
3+ triggered aggregation-induced emission effect. FQs bound Tb3+ in Tb3+ /DTE-Cu NCs through carboxyl and carbonyl groups, so that Tb3+ was effectively sensitized to emit green fluorescence. However, the red fluorescence of DTE-Cu NCs was not interfered. The fluorescence of the probe transformed from red to green with the increase of FQs concentration. Using norfloxacin (NOR), difloxacin (DIF), and enrofloxacin (ENR) as FQs simulants, this probe showed a sensitive linear response ranged from 0.025 to 22.5 μM, with the limits of detection of 9.6 nM, 9.3 nM, and 7.7 nM. The application potential for FQs detection was verified via a standard addition assay of egg samples with the recovery rate of 90.4 %-114.7 %., Significant: The fluorescence probe based on Tb3+ /DTE-Cu NCs is expected to realize the ratiometric fluorescence sensitive detection of FQs. The establishment of this simple, effective, and rapid detection platform opens up a new way for the detection of FQs residues in animal-origin foods, and also provides a new idea for the design of rapid detection platforms for other hazard factors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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3. Mechanisms of mitophagy and oxidative stress in cerebral ischemia-reperfusion, vascular dementia, and Alzheimer's disease.
- Author
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Lyu Y, Meng Z, Hu Y, Jiang B, Yang J, Chen Y, Zhou J, Li M, and Wang H
- Abstract
Neurological diseases have consistently represented a significant challenge in both clinical treatment and scientific research. As research has progressed, the significance of mitochondria in the pathogenesis and progression of neurological diseases has become increasingly prominent. Mitochondria serve not only as a source of energy, but also as regulators of cellular growth and death. Both oxidative stress and mitophagy are intimately associated with mitochondria, and there is mounting evidence that mitophagy and oxidative stress exert a pivotal regulatory influence on the pathogenesis of neurological diseases. In recent years, there has been a notable rise in the prevalence of cerebral ischemia/reperfusion injury (CI/RI), vascular dementia (VaD), and Alzheimer's disease (AD), which collectively represent a significant public health concern. Reduced levels of mitophagy have been observed in CI/RI, VaD and AD. The improvement of associated pathology has been demonstrated through the increase of mitophagy levels. CI/RI results in cerebral tissue ischemia and hypoxia, which causes oxidative stress, disruption of the blood-brain barrier (BBB) and damage to the cerebral vasculature. The BBB disruption and cerebral vascular injury may induce or exacerbate VaD to some extent. In addition, inadequate cerebral perfusion due to vascular injury or altered function may exacerbate the accumulation of amyloid β (Aβ) thereby contributing to or exacerbating AD pathology. Intravenous tissue plasminogen activator (tPA; alteplase) and endovascular thrombectomy are effective treatments for stroke. However, there is a narrow window of opportunity for the administration of tPA and thrombectomy, which results in a markedly elevated incidence of disability among patients with CI/RI. It is regrettable that there are currently no there are still no specific drugs for VaD and AD. Despite the availability of the U.S. Food and Drug Administration (FDA)-approved clinical first-line drugs for AD, including memantine, donepezil hydrochloride, and galantamine, these agents do not fundamentally block the pathological process of AD. In this paper, we undertake a review of the mechanisms of mitophagy and oxidative stress in neurological disorders, a summary of the clinical trials conducted in recent years, and a proposal for a new strategy for targeted treatment of neurological disorders based on both mitophagy and oxidative stress., Competing Interests: ML was employed by China RongTong Medical Healthcare Group Co. Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Lyu, Meng, Hu, Jiang, Yang, Chen, Zhou, Li and Wang.)
- Published
- 2024
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4. Models for depression recognition and efficacy assessment based on clinical and sequencing data.
- Author
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Hu Y, Chen J, Li J, and Xu Z
- Abstract
Major depression is a complex psychiatric disorder that includes genetic, neurological, and cognitive factors. Early detection and intervention can prevent progression, and help select the best treatment. Traditional clinical diagnosis tends to be subjective and misdiagnosed. Based on this, this study leverages clinical scale assessments and sequencing data to construct disease prediction models. Firstly, data undergoes preprocessing involving normalization and other requisite procedures. Feature engineering is then applied to curate subsets of features, culminating in the construction of a model through the implementation of machine learning and deep learning algorithms. In this study, 18 features with significant differences between patients and healthy controls were selected. The depression recognition model was constructed by deep learning with an accuracy of 87.26 % and an AUC of 91.56 %, which can effectively distinguish patients with depression from healthy controls. In addition, 33 features selected by recursive feature elimination method were used to construct a prognostic effect model of patients after 2 weeks of treatment, with an accuracy of 75.94 % and an AUC of 83.33 %. The results show that the deep learning algorithm based on clinical and sequencing data has good accuracy and provides an objective and accurate method for the diagnosis and pharmacodynamic prediction of depression. Furthermore, the selected differential features can serve as candidate biomarkers to provide valuable clues for diagnosis and efficacy prediction., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)
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- 2024
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5. Fluorescent responsive membrane based on terbium coordination polymer and carbon dots with AIE effect for rapid and visual detection of fluoroquinolone.
- Author
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Hu Y, Chen X, Wang K, Jiang C, Liu W, Zhang S, Zheng M, Zhou Y, Xiao Y, and Liu Y
- Subjects
- Animals, Fluoroquinolones, Terbium chemistry, Carbon chemistry, Polymers chemistry, Reproducibility of Results, Fluorescent Dyes chemistry, Quantum Dots chemistry, Biosensing Techniques
- Abstract
In this study, based on aggregation-induced emission (AIE) effect and antenna effect, a novel portable fluorescent responsive membrane was constructed with red carbon dots (R-CDs) as reference signal and terbium coordination polymer (Tb-AMP CPs) as response signal for visual, instrument-free, and sensitive detection of fluoroquinolones (FQs). Specifically, the fluorescent responsive membrane (R-T membrane) was prepared by physically depositing R-CDs with AIE property and Tb-AMP CPs on the surface of polyvinylidene fluoride filter membranes at ambient temperature. In the presence of FQs, Tb
3+ in the Tb-AMP CPs of the prepared membrane coordinated with the β-diketone structure of FQs, which turned on the yellow-green fluorescence through the "antenna effect". As the concentration of FQs increased, the R-T membrane achieved a fluorescent color transition from bright pink to yellow-green. Its visual detection sensitivity for three FQs, including ciprofloxacin, difloxacin, and enrofloxacin, was 0.01 μM, and the detection limits were 7.4 nM, 7.8 nM, and 9.2 nM, respectively, by analyzing the color parameter green. In the residue analysis of FQs in real samples, the constructed membrane also exhibited remarkable anti-interference and reliability, which is of great significance for ensuring the safety of animal-derived food., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)- Published
- 2024
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6. Nano-flow cytometry unveils mitochondrial permeability transition process and multi-pathway cell death induction for cancer therapy.
- Author
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Su L, Xu J, Lu C, Gao K, Hu Y, Xue C, and Yan X
- Abstract
Mitochondrial permeability transition (mPT)-mediated mitochondrial dysfunction plays a pivotal role in various human diseases. However, the intricate details of its mechanisms and the sequence of events remain elusive, primarily due to the interference caused by Bax/Bak-induced mitochondrial outer membrane permeabilization (MOMP). To address these, we have developed a methodology that utilizes nano-flow cytometry (nFCM) to quantitatively analyze the opening of mitochondrial permeability transition pore (mPTP), dissipation of mitochondrial membrane potential ( Δ Ψ
m ), release of cytochrome c (Cyt c), and other molecular alternations of isolated mitochondria in response to mPT induction at the single-mitochondrion level. It was identified that betulinic acid (BetA) and antimycin A can directly induce mitochondrial dysfunction through mPT-mediated mechanisms, while cisplatin and staurosporine cannot. In addition, the nFCM analysis also revealed that BetA primarily induces mPTP opening through a reduction in Bcl-2 and Bcl-xL protein levels, along with an elevation in ROS content. Employing dose and time-dependent strategies of BetA, for the first time, we experimentally verified the sequential occurrence of mPTP opening and Δ Ψm depolarization prior to the release of Cyt c during mPT-mediated mitochondrial dysfunction. Notably, our study uncovers a simultaneous release of cell-death-associated factors, including Cyt c, AIF, PNPT1, and mtDNA during mPT, implying the initiation of multiple cell death pathways. Intriguingly, BetA induces caspase-independent cell death, even in the absence of Bax/Bak, thereby overcoming drug resistance. The presented findings offer new insights into mPT-mediated mitochondrial dysfunction using nFCM, emphasizing the potential for targeting such dysfunction in innovative cancer therapies and interventions., (© 2024. The Author(s).)- Published
- 2024
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7. Microbiome analysis reveals the differences in gut fungal community between Dutch Warmblood and Mongolian horses.
- Author
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Lan Y, Hu Y, Guo Y, Ali F, Amjad N, Ouyang Q, Almutairi MH, and Wang D
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- Humans, Animals, Horses, Plant Breeding, Ethnicity, Bacteria, Mycobiome, Microbiota, Gastrointestinal Microbiome genetics
- Abstract
Similar to gut bacterial community, gut fungal community are also an important part of the gut microbiota and play crucial roles in host immune regulation and metabolism. However, most studies have focused on the gut bacterial community, and research on the gut fungal community has been limited. Dutch Warmblood (DWH) and Mongolian horses (MGH) are important equine breeds, but little research has been done on their gut fungal community. Here, we assessed differences in gut fungal community between two horse species. Results showed that a total of 2159 OTUs were found in the Dutch Warmblood and Mongolian horses, of which 308 were common. Between-group analyzes of microbial diversity showed no differences in the alpha and beta diversity of gut fungal community between the two horse species. Microbiological taxonomic surveys showed that the dominant fungal phyla (Neocallimastigomycota and Ascomycota) and genera (unclassified_Neocallimastigaceae and Anaeromyces) were the same without being affected by species. Although the types of dominant fungal phyla did not change, the abundances of some fungal genera changed significantly. Results of Metastats analysis showed that there were a total of 206 fungal genera that were significantly different between the two horses, among which 78 genera showed an increase and 127 genera significantly decreased in Dutch Warmblood horses compared with Mongolian horses. In conclusion, this study investigated the composition and structure of the gut fungal community of Dutch Warmblood and Mongolian horses and found significant differences in gut fungal community between both breeds. Notably, this is the first exploration of the differences in the gut fungal community of both breeds, which may help to understand the distribution characteristics of the gut fungal community of different breeds of horses and reveal the differences in the traits of different horses., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)
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- 2024
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8. A bimetallic organic framework based fluorescent aptamer probe for the detection of zearalenone in cereals.
- Author
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Zhu L, Liu W, Tong F, Zhang S, Xu Y, Hu Y, Zheng M, Zhou Y, Zhang Z, Li X, and Liu Y
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- Fluorescent Dyes, Edible Grain chemistry, Zea mays, Food Contamination analysis, Gold, Limit of Detection, Zearalenone analysis, Aptamers, Nucleotide, Biosensing Techniques methods
- Abstract
In this work, a bimetallic organic framework (Cu/UiO-66) based "turn on" fluorescent aptamer probe was designed for the high-efficiency detection of zearalenone (ZEN). In the probe, the 6-carboxyfluorescein-labeled aptamer (FAM-Apt) was used as the recognition element, and the electrostatic interaction, coordination effect, and photoinduced electron transfer effect between FAM-Apt and Cu/UiO-66 caused fluorescence quenching. When ZEN existed, FAM-Apt recognized ZEN specifically, causing FAM-Apt to separate from the surface of Cu/UiO-66 and recovery of fluorescence. Under the optimal conditions, the probe had a linear detection range of 0.5 ng/mL-60 ng/mL, and the detection limit was 0.048 ng/mL. The application potential of the probe was verified by real detection of various cereals and their products, with a standard recovery from 83.67 %-106.8 %. The development of this efficient, rapid, and sensitive ZEN detection method provides a new platform for the quality control of cereals and their products., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)
- Published
- 2024
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9. Study on the Mechanism of Estrogen Regulating Endometrial Fibrosis After Mechanical Injury Via MIR-21-5P/PPARΑ/FAO Axis.
- Author
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Ding S, Hu Y, Mao P, Lin Q, and Yao Z
- Subjects
- Female, Animals, Mice, Humans, Stromal Cells metabolism, Stromal Cells drug effects, Signal Transduction drug effects, Fatty Acids metabolism, Estradiol pharmacology, Tissue Adhesions metabolism, Tissue Adhesions pathology, Tissue Adhesions genetics, MicroRNAs genetics, MicroRNAs metabolism, Endometrium metabolism, Endometrium pathology, Endometrium drug effects, Fibrosis, Estrogens pharmacology, Estrogens metabolism, PPAR alpha metabolism, PPAR alpha genetics
- Abstract
Background: Intrauterine adhesion (IUA) caused by endometrial mechanical injury has been found as a substantial risk factor for female infertility (e.g., induced abortion). Estrogen is a classic drug for the repair of endometrial injury, but its action mechanism in the clinical application of endometrial fibrosis is still unclear., Objective: To explore the specific action mechanism of estrogen treatment on IUA., Methods: The IUA model in vivo and the isolated endometrial stromal cells (ESCs) model in vitro were built. Then CCK8 assay, Real-Time PCR, Western Blot and Dual- Luciferase Reporter Gene assay were applied to determine the targeting action of estrogen on ESCs., Results: It was found that 17β-estradiol inhibited fibrosis of ESCs by down-regulating miR-21-5p level and activating PPARα signaling. Mechanistically, miR-21-5p significantly reduced the inhibitory effect of 17β-estradiol on fibrotic ESCs (ESCs-F) and its maker protein (e.g., α-SMA, collagen I, and fibronectin), where targeting to PPARα 3'- UTR and blocked its activation and transcription, thus lowering expressions of fatty acid oxidation (FAO) associated key enzyme, provoking fatty accumulation and reactive oxygen species (ROS) production, resulting in endometrial fibrosis. Nevertheless, the PPARα agonist caffeic acid counteracted the facilitation action of miR-21-5p on ESCs-F, which is consistent with the efficacy of estrogen intervention., Conclusion: In brief, the above findings revealed that the miR-21-5p/PPARα signal axis played an important role in the fibrosis of endometrial mechanical injury and suggested that estrogen might be a promising agent for its progression., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)
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- 2024
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10. Development of antioxidant and smart NH 3 -sensing packaging film by incorporating bilirubin into κ-carrageenan matrix.
- Author
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Liu Y, Tong F, Xu Y, Hu Y, Liu W, Yang Z, Yu Z, Xiong G, Zhou Y, and Xiao Y
- Subjects
- Carrageenan, Food Packaging, Amines, Anthocyanins, Hydrogen-Ion Concentration, Antioxidants, Bilirubin
- Abstract
Background: Active and smart food packaging based on natural polymers and pH-sensitive dyes as indicators has attracted widespread attention. In the present study, an antioxidant and amine-response color indicator film was developed by incorporating bilirubin (BIL) into the κ-carrageenan (Carr) matrix., Results: It was found that the introduction of BIL had no effect on the crystal/chemical structure, water sensitivity and mechanical performance of the Carr-based films. However, the barrier properties to light and the thermal stability were significantly improved after the addition BIL. The Carr/BIL composite films exhibited excellent 1,1-diphenyl-2-picryl-hydrazyl (i.e. DPPH)/2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (i.e. ABTS) free radical scavenging abilities and color responsiveness to different concentrations of ammonia. The application assay reflected that the Carr/BIL
0.0075 film was effective in delaying the oxidative deterioration of shrimp during storage and realizing the color response of its freshness through the change of b* value., Conclusion: Active and smart packaging films were successfully prepared by incorporating different contents of BIL into the Carr matrix. The present study helps to further encourage the design and development of a multi-functional packaging material. © 2023 Society of Chemical Industry., (© 2023 Society of Chemical Industry.)- Published
- 2023
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11. Relationship of body mass index and visceral fat area combination with arterial stiffness and cardiovascular risk in cardiovascular disease-free people: NHANES (2011-2018).
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Huang Y, Hu Y, and Bao B
- Abstract
Background: Obesity and arterial stiffness are strongly associated with cardiovascular disease; however, their relationship remains controversial., Methods: Body mass index was measured using anthropometric evaluation, and visceral fat area was calculated using an absorptiometry scan., Results: The data of 5309 participants were collected from NHANES (National Health and Nutrition Examination Survey) (2011-2018). Based on the normal-weight normal visceral fat group that was considered as a reference, ePWV increased in all other groups, with the obese grade 2 visceral obesity group increasing the most by 26.35 cm/s (95% CI: 13.52, 39.18, P < 0.001), followed by normal-weight visceral obesity group 24.43 cm/s (95% CI: 1.88, 46.98, P = 0.035), which was even higher than obese grade 1 visceral obesity (β: 21.16, 95% CI: 9.24, 33.07, P = 0.001), obese grade 2 normal visceral fat group (β: 13.8; 95% CI: 0.10, 27.5, P = 0.048) and overweight visceral obesity group (β: 10.23; 95% CI: 1.89, 18.57, P = 0.018). For the 10-year cardiovascular risk, the obese grade 2 visceral obesity group had a 9.56-fold increase in compared with the control (OR: 10.56, 95% CI: 4.06, 27.51, P < 0.0001). Normal-weight visceral obesity, obese grade 1 visceral obesity, and overweight visceral obesity groups increased by 8.03-fold (OR: 9.03, 95% CI: 2.66, 30.69; P < 0.001), 7.91-fold (OR: 8.91, 95% CI: 3.82, 20.79, P < 0.001), and 7.28-fold (OR: 8.28, 95% CI: 3.19, 21.46, P < 0.001). The risk was lower in the normal visceral fat group. Except for the obese grade 2 normal visceral fat group, there was no significant difference in other groups., Conclusions: Normal-weight visceral obesity was associated with higher arterial stiffness and 10-year cardiovascular risk.
- Published
- 2023
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12. Quantitative assessment of lipophilic membrane dye-based labelling of extracellular vesicles by nano-flow cytometry.
- Author
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Chen C, Cai N, Niu Q, Tian Y, Hu Y, and Yan X
- Subjects
- Micelles, Fluorescent Dyes analysis, Fluorescent Dyes chemistry, Fluorescent Dyes metabolism, Extracellular Vesicles metabolism
- Abstract
Although lipophilic membrane dyes (LMDs) or probes (LMPs) are widely used to label extracellular vesicles (EVs) for detection and purification, their labelling performance has not been systematically characterized. Through concurrent side scattering and fluorescence detection of single EVs as small as 40 nm in diameter by a laboratory-built nano-flow cytometer (nFCM), present study identified that (1) PKH67 and PKH26 could maximally label ∼60%-80% of EVs isolated from the conditioned cell culture medium (purity of ∼88%) and ∼40%-70% of PFP-EVs (purity of ∼73%); (2) excessive PKH26 could cause damage to the EV structure; (3) di-8-ANEPPS and high concentration of DiI could achieve efficient and uniform labelling of EVs with nearly 100% labelling efficiency for di-8-ANEPPS and 70%-100% for DiI; (4) all the four tested LMDs can aggregate and form micelles that exhibit comparable side scatter and fluorescence intensity with those of labelled EVs and thus hardly be differentiate from each other; (5) as the LMD concentration went up, the particle number of self-aggregates increased while the fluorescence intensity of aggregates remained constant; (6) PKH67 and PKH26 tend to form more aggregated micelles than di-8-ANEPPS and DiI, and the effect of LMD self-aggregation can be negligible at optimal staining conditions. (7) All the four tested LMDs can label almost all the very-low-density lipoprotein (VLDL) particles, indicating potential confounding factor in plasma-EV labelling. Besides, it was discovered that DSPE-PEG
2000 -biotin can only label ∼50% of plasma-EVs. The number of LMP inserted into the membrane of single EVs was measured for the first time and it was confirmed that membrane labelling by lipophilic dyes did not interfere with the immunophenotyping of EVs. nFCM provides a unique perspective for a better understanding of EV labelling by LMD/LMP., (© 2023 The Authors. Journal of Extracellular Vesicles published by Wiley Periodicals, LLC on behalf of the International Society for Extracellular Vesicles.)- Published
- 2023
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13. Quantitative analysis of fucosylated glycoproteins by immobilized lectin-affinity fluorescent labeling.
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Gao Z, Chen S, Du J, Wu Z, Ge W, Gao S, Zhou Z, Yang X, Xing Y, Shi M, Hu Y, Tang W, Xia J, Zhang X, Jiang J, and Yang S
- Abstract
Human biofluids are often used to discover disease-specific glycosylation, since abnormal changes in protein glycosylation can discern physiopathological states. Highly glycosylated proteins in biofluids make it possible to identify disease signatures. Glycoproteomic studies on saliva glycoproteins showed that fucosylation was significantly increased during tumorigenesis and that glycoproteins became hyperfucosylated in lung metastases, and tumor stage is associated with fucosylation. Quantification of salivary fucosylation can be achieved by mass spectrometric analysis of fucosylated glycoproteins or fucosylated glycans; however, the use of mass spectrometry is non-trivial for clinical practice. Here, we developed a high-throughput quantitative method, lectin-affinity fluorescent labeling quantification (LAFLQ), to quantify fucosylated glycoproteins without relying on mass spectrometry. Lectins with a specific affinity for fucoses are immobilized on the resin and effectively capture fluorescently labeled fucosylated glycoproteins, which are further quantitatively characterized by fluorescence detection in a 96-well plate. Our results demonstrated that serum IgG can be accurately quantified by lectin and fluorescence detection. Quantification in saliva showed significantly higher fucosylation in lung cancer patients compared to healthy controls or other non-cancer diseases, suggesting that this method has the potential to quantify stage-related fucosylation in lung cancer saliva., Competing Interests: The authors declare no competing financial interest., (This journal is © The Royal Society of Chemistry.)
- Published
- 2023
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14. Using structural analysis to clarify the impact of single nucleotide variants in neurexin/neuroligin revealed in clinical genomic sequencing.
- Author
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Xue K, Hu Y, Gu S, Wang C, Kong R, Xie W, and Li J
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- Cell Adhesion Molecules, Genomics, Nucleotides, Membrane Proteins genetics, Synapses
- Abstract
The synapse is a highly specialized and dynamic structure, which is involved in regulating neurotransmission. Nerve cell adhesion molecule is a kind of transmembrane protein that mediates the interaction between cells and cells, cells and extracellular matrix, and plays a role in cell recognition, metastasis, and transmembrane signal transduction. Among nerve cell adhesion molecules, Neurexins (NRXNs) and Neuroligins (NLGNs) have been focused due to the relation with autism and other neuropsychiatric diseases. The previous research discovered numerous variants in NRXNs and NLGNs reported in neurodevelopmental disorders by genomic sequencing. However, structural variants in synaptic molecules caused by genome variants still prevent us from understanding the molecular mechanism of diseases. Thus, we sought to conduct a comprehensive risk assessment of the known NRXN and NLGN gene variants by protein structure analysis. In this study, we analyzed the structural properties of the NRXN/NLGN complex by calculating free energy in residue scanning, in combination with existing risk evaluation tools to focus on candidate missense mutations. Our calculations show that five candidate missense mutations in NLGNs can reduce the stability of NLGNs and even prevent the formation of NRXN/NLGN complexes, namely R87W, R204H, R437H, R437C and R583W. In addition, we found that the affinity of the amino acid substitution (Leu593Phe) (ΔΔ G
(affinity) ) changes the affinity of the NLGN dimer. Overall, we have identified important potential pathological variants that provide clues to biomarkers. Communicated by Ramaswamy H. Sarma.- Published
- 2022
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15. Noninvasive Diagnosis of Nasopharyngeal Carcinoma Based on Phenotypic Profiling of Viral and Tumor Markers on Plasma Extracellular Vesicles.
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Hu Y, Tian Y, Di H, Xue C, Zheng Y, Hu B, Lin Q, and Yan X
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- Biomarkers, Tumor, Herpesvirus 4, Human, Humans, Nasopharyngeal Carcinoma diagnosis, Epstein-Barr Virus Infections metabolism, Extracellular Vesicles metabolism, Nasopharyngeal Neoplasms diagnosis
- Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor commonly associated with Epstein-Barr virus (EBV) infection, and its early diagnosis as well as its differentiation from nasopharyngitis (NPG) remains challenging due to the insufficient sensitivity of routine screening methods in clinical practice. To date, circulating extracellular vesicles (EVs, 40-1000 nm) have shown appealing potential in liquid biopsy for cancer diagnosis and prognosis. Herein, nanoflow cytometry (nFCM) capable of single EV analysis was applied to examine the expression of surface proteins with very low copy numbers on individual EVs as small as 40 nm. The particle concentrations of five EV subsets exposing EBV-encoded latent membrane proteins (LMP1 and LMP2A) and tumor markers (PD-L1, EGFR, and EpCAM) in plasma were determined rapidly via single-particle enumeration. We identified a five-marker panel named EV
SUM5 (an unweighted sum of the concentration of the five individual EV subsets) that significantly surpassed the traditional VCA-IgA assay in discriminating NPC patients from both healthy donors and NPG patients with accuracies of 96.3 and 83.1%, respectively. Moreover, EVSUM2 (an unweighted sum of virus-specific LMP1- and LMP2A-positive EVs) could achieve the diagnosis of NPG with an accuracy of 82.6%. Collectively, the work presented a rapid, reliable, and noninvasive method as well as two diagnostic markers to help more accurately differentiate NPC from NPG patients and healthy donors in clinical practice.- Published
- 2022
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16. A Predictive Model of Risk Factors for Conversion From Major Depressive Disorder to Bipolar Disorder Based on Clinical Characteristics and Circadian Rhythm Gene Polymorphisms.
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Xu Z, Chen L, Hu Y, Shen T, Chen Z, Tan T, Gao C, Chen S, Chen W, Chen B, Yuan Y, and Zhang Z
- Abstract
Background: Bipolar disorder (BD) is easy to be misdiagnosed as major depressive disorder (MDD), which may contribute to a delay in treatment and affect prognosis. Circadian rhythm dysfunction is significantly associated with conversion from MDD to BD. So far, there has been no study that has revealed a relationship between circadian rhythm gene polymorphism and MDD-to-BD conversion. Furthermore, the prediction of MDD-to-BD conversion has not been made by integrating multidimensional data. The study combined clinical and genetic factors to establish a predictive model through machine learning (ML) for MDD-to-BD conversion., Method: By following up for 5 years, 70 patients with MDD and 68 patients with BD were included in this study at last. Single nucleotide polymorphisms (SNPs) of the circadian rhythm genes were selected for detection. The R software was used to operate feature screening and establish a predictive model. The predictive model was established by logistic regression, which was performed by four evaluation methods., Results: It was found that age of onset was a risk factor for MDD-to-BD conversion. The younger the age of onset, the higher the risk of BD. Furthermore, suicide attempts and the number of hospitalizations were associated with MDD-to-BD conversion. Eleven circadian rhythm gene polymorphisms were associated with MDD-to-BD conversion by feature screening. These factors were used to establish two models, and 4 evaluation methods proved that the model with clinical characteristics and SNPs had the better predictive ability., Conclusion: The risk factors for MDD-to-BD conversion have been found, and a predictive model has been established, with a specific guiding significance for clinical diagnosis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Xu, Chen, Hu, Shen, Chen, Tan, Gao, Chen, Chen, Chen, Yuan and Zhang.)
- Published
- 2022
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17. Assessment of Microcirculation in the Type 2 Diabetic and Impaired Glucose Tolerance Feet of Elderly Men by CEUS.
- Author
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Li X, Wu L, Yang Z, Hu Y, Zhou C, and Ji R
- Abstract
Objective: To evaluate the foot microcirculation in type 2 diabetes mellitus (T2DM) and impaired glucose tolerance patients (IGT) with contrast-enhanced ultrasound (CEUS)., Methods: The study included 37 patients with T2DM but without diabetic foot (DM group), 15 patients with impaired glucose tolerance (IGT group) and 10 elderly males with normal fasting blood glucose (FBS) and negative glucose tolerance tests (control group). Color Doppler flow imaging (CDFI) and CEUS were performed on the right foot great toes for detecting the blood perfusion performance. CEUS images were recorded and parameters of CDFI and flow time-intensity curves (TICs) were analyzed by the Student's t -test., Results: There was no significant difference in CDFI parameters pulse index and peak systolic blood flow velocity (PSV) among the three groups (P >0.05). Compared with control group, CEUS images of IGT and DM groups showed lower microvascular density and were pale. Peak intensity (PI) and area under time-intensity curve (AUC) in control, IGT and DM groups were decreased gradually (PI 46.36±10.96 vs 35.26±11.65 vs 28.15±7.94, P = 0.001, AUC 5.12±1.02 vs 3.25±1.60 vs 2.81±1.20, P = 0.001). The arrival times (AT) and time to peak (TTP) tended to be increased with the extension of DM course, but the difference was not statistically significant (AT, P = 0.260, TTP, P = 0.481)., Conclusion: CEUS, as a noninvasive and valuable technique, could detect the alterations in foot microcirculation of DM and IGT patients., Competing Interests: The authors declare that they have no competing interests., (© 2021 Li et al.)
- Published
- 2021
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18. kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing.
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Lin X, Hua Y, Gu S, Lv L, Li X, Chen P, Dai P, Hu Y, Liu A, and Li J
- Subjects
- Mutation, Software, Genomics, High-Throughput Nucleotide Sequencing
- Abstract
Background: Genomic localized hypermutation regions were found in cancers, which were reported to be related to the prognosis of cancers. This genomic localized hypermutation is quite different from the usual somatic mutations in the frequency of occurrence and genomic density. It is like a mutations "violent storm", which is just what the Greek word "kataegis" means., Results: There are needs for a light-weighted and simple-to-use toolkit to identify and visualize the localized hypermutation regions in genome. Thus we developed the R package "kataegis" to meet these needs. The package used only three steps to identify the genomic hypermutation regions, i.e., i) read in the variation files in standard formats; ii) calculate the inter-mutational distances; iii) identify the hypermutation regions with appropriate parameters, and finally one step to visualize the nucleotide contents and spectra of both the foci and flanking regions, and the genomic landscape of these regions., Conclusions: The kataegis package is available on Bionconductor/Github ( https://github.com/flosalbizziae/kataegis ), which provides a light-weighted and simple-to-use toolkit for quickly identifying and visualizing the genomic hypermuation regions.
- Published
- 2021
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19. Dynamic variations of dissolved organic matter from treated wastewater effluent in the receiving water: Photo- and bio-degradation kinetics and its environmental implications.
- Author
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Wang Y, Gao Y, Ye T, Hu Y, and Yang C
- Subjects
- Biodegradation, Environmental, Kinetics, Wastewater, Water, Water Pollutants, Chemical analysis, Water Purification
- Abstract
Dissolved effluent organic matter (dEfOM) from wastewater treatment plants (WWTPs) is bound to encounter photo- and bio-degradation as discharged into the receiving water body. However, the comprehensive variations of dEfOM by photo- and bio-degradation are not well unveiled because of its compositional heterogeneity. In this work, dissolved organic carbon (DOC) concentrations, UV-Vis and fluorescent spectra combined with fluorescence regional integration (FRI) analysis were used to investigate the changes in bulk dEfOM and its fluorescent components during photo- and bio-degradation processes in the receiving water body. Results showed that 48.49%-69.62% of the discharged dEfOM was decomposed by ultra violet (UV)-irradiation and indigenous microbes, while the others (33%-45%) were recalcitrant and stable in the receiving water body. Specifically, the photo- and bio-degradation of chromophoric, fluorescent dEfOM and its components were found to follow the single or double exponential kinetic model, and the differences in photo- and bio-degradability of each components shifted its composition. Furthermore, results of bio-degradation after UV-irradiated dEfOM indicated that there was overlapping of photo- and bio-degradable fractions in dEfOM, and photoreactions could improve the self-production of natural organic matter in the receiving water body. These results could improve the understanding the fate of discharged dEfOM in the receiving water body, and we proposed some cost-effective strategies for discharging WWTPs effluent., (Copyright © 2021 Elsevier Inc. All rights reserved.)
- Published
- 2021
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20. Magnetic-Separation-Assisted Magnetic Relaxation Switching Assay for Mercury Ion Based on the Concentration Change of Oligonucleotide-Functionalized Magnetic Nanoparticle.
- Author
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Hu Y, Guo X, Wang H, Luo Q, Song Y, and Song E
- Abstract
Magnetic-separation-assisted magnetic relaxation switching (MRS) assay based on the concentration change of magnetic nanoparticles switches has been designed for bacteria, biological macromolecules, and small molecules detection because of its better analysis performance. As one of the most hazardous pollutants and highly dangerous elements, mercury ion (Hg
2+ ) was employed as a model to further investigate the applicability of nanoparticle switches concentration change-based MRS assay mode for detecting metal ions in this study. The principle is based on the specific and strong interaction between mercury ion with the thymine-thymine(T-T) mismatch in double-stranded DNA duplexes by employing oligonucleotide functionalized magnetic nanoparticle as magnetic capture probe and MRS signal probe, respectively. The result shows that magnetic nanoparticles concentration-dependent MRS sensing mode could be facile applied to detect metal ion of Hg2+ in tap water, lake water and serum with wider detection range and higher accuracy. The as-presented magnetic-separation-assisted MRS assay of Hg2+ in complicated samples shows potential application values for Hg2+ assay in clinical and environmental monitoring, which broadens its application.- Published
- 2020
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21. Potential role of genomic imprinted genes and brain developmental related genes in autism.
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Li J, Lin X, Wang M, Hu Y, Xue K, Gu S, Lv L, Huang S, and Xie W
- Subjects
- Computational Biology, Genomics, Humans, Male, Autistic Disorder genetics, Autistic Disorder metabolism, Autistic Disorder pathology, Brain growth & development, Brain pathology, Chromosomes, Human genetics, Chromosomes, Human metabolism, Databases, Genetic, Gene Expression Regulation, Genomic Imprinting
- Abstract
Background: Autism is a complex disease involving both environmental and genetic factors. Recent efforts have implicated the correlation of genomic imprinting and brain development in autism, however the pathogenesis of autism is not completely clear. Here, we used bioinformatic tools to provide a comprehensive analysis of the autism-related genes, genomic imprinted genes and the spatially and temporally differentially expressed genes of human brain, aiming to explore the relationship between autism, brain development and genomic imprinting., Methods: This study analyzed the distribution correlation between autism-related genes and imprinted genes on chromosomes using sliding windows and statistical methods. The normal brains' gene expression microarray data were reanalyzed to construct a spatio-temporal coordinate system of gene expression during brain development. Finally, we intersected the autism-related genes, imprinted genes and brain spatio-temporally differentially expressed genes for further analysis to find the major biological processes that these genes involved., Results: We found a positive correlation between the autism-related genes' and imprinted genes' distribution on chromosomes. Through the analysis of the normal brain microarray data, we constructed a spatio-temporal coordinate system of gene expression during human brain development, and obtained 13 genes that are differentially expressed in the process of brain development, which are both autism-related genes and imprinted genes. Furthermore, enrichment analysis illustrated that these genes are mainly involved in the biological processes, such as gamma-aminobutyric acid signaling pathway, neuron recognition, learning or memory, and regulation of synaptic transmission. Bioinformatic analysis implied that imprinted genes regulate the development and behavior of the brain. And its own mutation or changes in the epigenetic modification state of the imprinted control region could lead to some diseases, indicating that imprinted genes and brain development play an important role in diagnosis and prognosis of autism., Conclusion: This study systematically correlates brain development and genomic imprinting with autism, which provides a new perspective for the study of genetic mechanisms of autism, and selected the potential candidate biomarkers for early diagnosis of autism in clinic.
- Published
- 2020
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22. Quality and efficiency assessment of six extracellular vesicle isolation methods by nano-flow cytometry.
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Tian Y, Gong M, Hu Y, Liu H, Zhang W, Zhang M, Hu X, Aubert D, Zhu S, Wu L, and Yan X
- Abstract
Extracellular vesicles (EVs) have sparked tremendous interest owing to their prominent potential in diagnostics and therapeutics. Isolation of EVs from complex biological fluids with high purity is essential to the accurate analysis of EV cargo. Unfortunately, generally used isolation techniques do not offer good separation of EVs from non-EV contaminants. Hence, it is important to have a standardized method to characterise the properties of EV preparations, including size distribution, particle concentration, purity and phenotype. Employing a laboratory-built nano-flow cytometer (nFCM) that enables multiparameter analysis of single EVs as small as 40 nm, here we report a new benchmark to the quality and efficiency assessment of EVs isolated from plasma, one of the most difficult body fluids to work with. The performance of five widely used commercial isolation kits was examined and compared with the traditional differential ultracentrifugation (UC). Two to four orders of magnitude higher particle concentrations were observed for EV preparations from platelet-free plasma (PFP) by kits when compared with the EV preparation by UC, yet the purity was much lower. Meanwhile, the particle size distribution profiles of EV preparations by kits closely resembled those of PFP whereas the EV preparation by UC showed a broader size distribution at relatively large particle size. When these kits were used to isolate EVs from vesicle-depleted PFP (VD-PFP), comparable particle counts were obtained with their corresponding EV preparations from PFP, which confirmed again the isolation of a large quantity of non-vesicular contaminants. As CD9, CD63 and CD81 also exist in the plasma matrix, single-particle phenotyping of EVs offers distinct advantage in the validation of EVs compared with ensemble-averaged approaches, such as Western blot analysis. nFCM allows us to compare different isolation techniques without prejudice., (© 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group on behalf of The International Society for Extracellular Vesicles.)
- Published
- 2019
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23. Variations of DOM quantity and compositions along WWTPs-river-lake continuum: Implications for watershed environmental management.
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Wang Y, Hu Y, Yang C, Wang Q, and Jiang D
- Subjects
- Carbon analysis, China, Environmental Monitoring methods, Spectrometry, Fluorescence methods, Waste Disposal Facilities, Wastewater, Lakes analysis, Rivers chemistry, Waste Disposal, Fluid
- Abstract
Wastewater effluent makes up an increasingly large percentage of surface water supplies, but the impacts of discharge of effluent organic matter (EfOM) on receiving riverine and lacustrine dissolved organic matter (DOM) is still largely unknown. In the present study, we investigated variations of DOM quantity and quality along wastewater treatment plants (WWTPs)-river-lake continuum during drought periods, and made a tentative discussion on its implications for watershed environmental management. We used dissolved organic carbon (DOC) concentrations, UV absorption coefficients and excitation-emission-matrixs (EEMs) fluorescence spectroscopy combined with fluorescence regional integration (FRI) to characterize EfOM and riverine and lacustrine DOM along WWTPs-river-Chaohu Lake continuum. Our results showed that changes in DOM quantity and quality in receiving waterbodies were related to EfOM discharged from WWTPs and external input of DOM along inflowing river. Specifically, we found that the ratio of protein-like/humic-like notably decreased (P < 0.05), and %humic-like increased (P < 0.01) along WWTPs-river-lake continuum. Furthermore, the recent autochthonous contribution index (BIX) and the humification index (HIX) values showed that these variations of DOM composition were attributed to microbial degradations in receiving waterbodies. We concluded that the changes of DOM quantity and quality along WWTPs-river-lake continuum had important implications for DOM behaviors, and offered some novel ideas for watershed environmental management., (Copyright © 2018 Elsevier Ltd. All rights reserved.)
- Published
- 2019
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24. Effects of vegetation types on water-extracted soil organic matter (WSOM) from riparian wetland and its impacts on riverine water quality: Implications for riparian wetland management.
- Author
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Wang Y, Hu Y, Yang C, and Chen Y
- Abstract
Riparian wetlands play important roles in the enhancement of water quality by controlling nonpoint source pollution and protecting aquatic ecosystems. In the present study, we surveyed and identified vegetation types in riparian wetlands, evaluated how vegetation types influence spatial patterns of water-extracted soil organic matter (WSOM) from riparian wetland, and probed the impacts of riparian fluorescent WSOM on fluorescent dissolved organic matter (FDOM) and water trophic states in river ecosystems. We used absorption and excitation-emission-matrix (EEM) fluorescence spectroscopy to characterize the optical properties of riparian WSOM and riverine DOM from Chongming Island, China, the largest alluvial plain island in the world. Our results showed that fifty-eight spermatophytes in riparian wetland were clustered into five vegetation types, including warm coniferous forest (WCF), deciduous broad leaf forest (DBF), evergreen broad leaf forest (EBF), aquatic plants (AP) and herbaceous plants (HP). Absorption spectra revealed the effects of vegetation types on riparian chromophoric WSOM quantity. Although no difference in water-extracted soil organic carbon (WSOC) contents was observed, deciduous broad leaf forest (DBF) and evergreen broad leaf forest (EBF) fed more fluorescent WSOM quantity than did the other vegetation (AP, HP and WCF), and deciduous broad leaf forest (DBF) and aquatic plants (AP) provided more humic-like (RC.1 and RC.2) and fulvic-like (RC.3) substances into riparian wetland (P<0.05 or P<0.01). In addition, we noted that humic-like and protein-like substances (RC.4) transported from riparian wetland into a river water body, and riverine terrestrial-originated components (FC.1 and FC.2) were significantly related to the four riparian fluorescent WSOM components (P<0.05). Furthermore, the riverine trophic state was significantly higher when the fluvial DOM and its component quantity increased (P<0.05). We concluded that riparian wetland can control the quantity and quality of riparian WSOM and reshaped riverine DOM compositions and riverine water quality with important management implications., (Copyright © 2018 Elsevier B.V. All rights reserved.)
- Published
- 2018
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25. Size and Ultrasound Features Affecting Results of Ultrasound-Guided Fine-Needle Aspiration of Thyroid Nodules.
- Author
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Dong Y, Mao M, Zhan W, Zhou J, Zhou W, Yao J, Hu Y, Wang Y, and Ye T
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Biopsy, Fine-Needle, Female, Humans, Male, Middle Aged, Reproducibility of Results, Retrospective Studies, Sensitivity and Specificity, Severity of Illness Index, Thyroid Gland diagnostic imaging, Thyroid Gland pathology, Thyroid Gland surgery, Thyroid Nodule surgery, Young Adult, Thyroid Nodule diagnostic imaging, Thyroid Nodule pathology, Ultrasonography, Interventional methods
- Abstract
Objectives: Our goal was to assess the diagnostic efficacy of ultrasound (US)-guided fine-needle aspiration (FNA) of thyroid nodules according to size and US features., Methods: A retrospective correlation was made with 1745 whole thyroidectomy and hemithyroidectomy specimens with preoperative US-guided FNA results. All cases were divided into 5 groups according to nodule size (≤5, 5.1-10, 10.1-15, 15.1-20, and >20 mm). For target nodules, static images and cine clips of conventional US and color Doppler were obtained. Ultrasound images were reviewed and evaluated by two radiologists with at least 5 years US working experience without knowing the results of pathology, and then agreement was achieved., Results: The Bethesda category I rate was higher in nodules larger than 15 mm (P < .05). The diagnostic accuracy was best in nodules of 5 to 10 mm in diameter. The sensitivity, accuracy, PPV, and LR for negative US-guided FNA results were better in nodules with a size range of 5 to 15 mm. The specificity, negative predictive value (NPV), and LR for positive results and the Youden index rose with increasing nodule size. Seventeen false-positive and 60 false-negative results were found in this study. The false-negative rate rose with increasing nodule size. However, the false-positive rate was highest in the group containing the smallest nodules. Nodules with circumscribed margins and those that were nonsolid and nonhypoechoic and had no microcalcifications correlated with Bethesda I FNA results. Nodules with circumscribed margins and those that were nonsolid, heterogeneous, and nonhypoechoic and had increased vascularity correlated with false-negative FNA results. Borders correlated with Bethesda I false-negative and false-positive FNA results., Conclusions: Tiny nodules (≤5 mm) with obscure borders tended to yield false-positive FNA results. Large nodules (>20 mm) with several US features tended to yield false-negative FNA results., (© 2017 by the American Institute of Ultrasound in Medicine.)
- Published
- 2018
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26. Quality evaluation of randomized controlled trials reports of laparoscopy compared with open colorectal resection for colorectal cancer.
- Author
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Huang D, Jin X, Gao J, Li Y, Lu L, Sun F, Chen D, Zhao W, Luo W, Li H, Hu Y, and Hu F
- Subjects
- China, Colorectal Neoplasms pathology, Humans, Randomized Controlled Trials as Topic methods, Research Design, Colorectal Neoplasms surgery, Laparoscopy methods, Randomized Controlled Trials as Topic standards
- Abstract
Objectives: Previously, there were no data looking at the quality evaluation of randomized controlled trials (RCTs) on effect comparison of laparoscopic surgery and open surgery for colorectal cancer in China. Here, we evaluate the completeness and transparency of RCT reports in this field., Methods: The following databases were searched: Medline, EMbase, SCI Expanded, China National Knowledge Infrastructure, the Chinese Biological Medicine Database, VIP database and Wan Fang databases) to search RCT reports on the effect comparison of laparoscopic surgery and open surgery for colorectal cancer in China. Our study evaluated the reporting quality of RCTs based on 22 standards of Consolidated Standards for Reporting Trials (CONSORT) 2010 Statement. Two reviewers responded with 'yes' or 'no' to each standard to judge whether the authors had reported or had recorded concrete details of the reports accomplished in accordance with the requirement of each standard., Results: A total of 40 relevant RCTs were included in the final analysis. For the 'Title and abstract', only three articles (7.5%) could be identified directly from its title as the report of RCTs. For the 'Methods', only three articles (7.5%) applied the method of random allocation of sequences; only two articles (5%) mentioned the type of randomization or gave the description of the mechanism of allocation concealment; no article referred the concrete implementation of random method. Only one article (2.5%) applied the method of blinding or sample size calculation; no article had analysis about the metaphase of an experiment or an explanation of its interruption. For 'results', only one article (2.5%) described participant flow, primary and secondary outcomes with estimated effect size or ancillary analyses. Only 13 articles (32.5%) showed baseline demographic and clinical characteristics, 10 (25%) referred to intention-to-treat analysis, and 12 (30%) mentioned important harms or unintended effects. For the 'discussion', only eight articles (20%) gave the description of trials' limitations and 13 (32.5%) presented the generalizability (external validity, applicability) of the trial findings., Conclusion: The quality of the RCT reports on effect comparison of laparoscopic surgery and open surgery for colorectal cancer in China is poor. The reporting of RCTs in this field should be standardized, according to the specifications of the CONSORT 2010.
- Published
- 2015
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27. Quality of reporting on randomized controlled trials on recurrent spontaneous abortion in China.
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Gao J, Deng G, Hu Y, Huang Y, Lu L, Huang D, Li Y, Zhu L, Liu X, Jin X, and Luo S
- Subjects
- Bibliometrics, China epidemiology, Double-Blind Method, Female, Humans, Practice Guidelines as Topic, Pregnancy, Quality Control, Randomized Controlled Trials as Topic economics, Research Support as Topic, Sample Size, Single-Blind Method, Abortion, Habitual diagnosis, Abortion, Habitual epidemiology, Abortion, Habitual prevention & control, Periodicals as Topic standards, Randomized Controlled Trials as Topic standards, Research Design standards, Writing standards
- Abstract
Background: Despite increasing numbers of RCTs done in China, detailed information on the quality of Chinese RCTs is still missing. The aim of this study was to assess the reporting quality of RSA RCTs and to identify significant predictors of reporting quality., Methods: A literature review was conducted with the aim of identifying published RCTs on RSA conducted in China. In order to rate the report quality, we scored 1 for the item of CONSORT 2010 if it was reported and 0 if it was not stated or unclear. An overall quality score (OQS) with a range of 0-15 and a key methodological index score (MIS) with a range of 0-3 were calculated for each trial., Results: A total of 98 relevant RCTs were included in the final analysis. The median OQS was 7, with a minimum of 1 and maximum of 12. The general level of OQS was not high, especially among 'sample size,' 'baseline data,' 'outcomes and estimation,' and 'ancillary analyses,' all of which had a positive rate of less than 10%. The median MIS was 1 with a minimum of 0 and maximum of 1. 'Allocation concealment,' 'blinding,' and 'intention-to-treat analysis' were mentioned in 1 (1%), 1 (1%) and 69 (70%) of the studies, respectively. In univariate analysis, funding was the only factor associated with an increased OQS. Specifically, the mean OQS increased by approximately 1.52 for manuscripts supported by funding (95% CI: 0.12 - 2.92; p = 0.03). With regard to the MIS, no association was found for any variable., Conclusion: RCTs of RSA conducted in China need improvement in order to meet the level of "reporting quality" required by the CONSORT statement.
- Published
- 2015
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28. Ancient horizontal transfer of transaldolase-like protein gene and its role in plant vascular development.
- Author
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Yang Z, Zhou Y, Huang J, Hu Y, Zhang E, Xie Z, Ma S, Gao Y, Song S, Xu C, and Liang G
- Subjects
- Biological Evolution, Embryophyta growth & development, Gene Transfer, Horizontal, Introns genetics, Oryza growth & development, Phylogeny, Plant Proteins genetics, Plant Vascular Bundle genetics, Plant Vascular Bundle growth & development, Plants, Genetically Modified, Bacteria genetics, Embryophyta genetics, Oryza genetics, Transaldolase genetics
- Abstract
A major event in land plant evolution is the origin of vascular tissues, which ensure the long-distance transport of water, nutrients and organic compounds. However, the molecular basis for the origin and evolution of plant vascular tissues remains largely unknown. Here, we investigate the evolution of the land plant TAL-type transaldolase (TAL) gene and its potential function in rice (Oryza sativa) based on phylogenetic analyses and transgenic experiments, respectively. TAL genes are only present in land plants and bacteria. Phylogenetic analyses suggest that land plant TAL genes are derived from Actinobacteria through an ancient horizontal gene transfer (HGT) event. Further evidence reveals that land plant TAL genes have undergone positive selection and gained several introns following its acquisition by the most recent common ancestor of land plants. Transgenic plant experiments show that rice TAL is specifically expressed in vascular tissues and that knockdown of TAL expression leads to changes in both the number and pattern of vascular bundles. Our findings show that the ancient HGT of TAL from bacteria probably plays an important role in plant vascular development and adaptation to land environments., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)
- Published
- 2015
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29. Adaptive evolution and divergent expression of heat stress transcription factors in grasses.
- Author
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Yang Z, Wang Y, Gao Y, Zhou Y, Zhang E, Hu Y, Yuan Y, Liang G, and Xu C
- Subjects
- Amino Acid Sequence, Cold Temperature, DNA-Binding Proteins chemistry, Droughts, Gene Duplication, Gene Expression, Heat Shock Transcription Factors, Heat-Shock Proteins chemistry, Molecular Sequence Data, Multigene Family, Phylogeny, Plant Proteins chemistry, Poaceae classification, Poaceae physiology, Sequence Alignment, Stress, Physiological, Transcription Factors chemistry, DNA-Binding Proteins genetics, Evolution, Molecular, Heat-Shock Proteins genetics, Plant Proteins genetics, Poaceae genetics, Transcription Factors genetics
- Abstract
Background: Heat stress transcription factors (Hsfs) regulate gene expression in response to heat and many other environmental stresses in plants. Understanding the adaptive evolution of Hsf genes in the grass family will provide potentially useful information for the genetic improvement of modern crops to handle increasing global temperatures., Results: In this work, we performed a genome-wide survey of Hsf genes in 5 grass species, including rice, maize, sorghum, Setaria, and Brachypodium, by describing their phylogenetic relationships, adaptive evolution, and expression patterns under abiotic stresses. The Hsf genes in grasses were divided into 24 orthologous gene clusters (OGCs) based on phylogeneitc relationship and synteny, suggesting that 24 Hsf genes were present in the ancestral grass genome. However, 9 duplication and 4 gene-loss events were identified in the tested genomes. A maximum-likelihood analysis revealed the effects of positive selection in the evolution of 11 OGCs and suggested that OGCs with duplicated or lost genes were more readily influenced by positive selection than other OGCs. Further investigation revealed that positive selection acted on only one of the duplicated genes in 8 of 9 paralogous pairs, suggesting that neofunctionalization contributed to the evolution of these duplicated pairs. We also investigated the expression patterns of rice and maize Hsf genes under heat, salt, drought, and cold stresses. The results revealed divergent expression patterns between the duplicated genes., Conclusions: This study demonstrates that neofunctionalization by changes in expression pattern and function following gene duplication has been an important factor in the maintenance and divergence of grass Hsf genes.
- Published
- 2014
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30. Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines.
- Author
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Yang Z, Zhang E, Li J, Jiang Y, Wang Y, Hu Y, and Xu C
- Subjects
- Asian People, Genome, Plant, Haplotypes, Humans, Linkage Disequilibrium, Phenotype, Polymorphism, Single Nucleotide, Genetic Variation, Plant Proteins genetics, Polymorphism, Genetic, Zea mays genetics
- Abstract
Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes Zfl1 and Zfl2, duplicate orthologs of Arabidopsis LEAFY, are key regulators in plant branching, inflorescence and flower development, and reproduction. In this study, the full gene sequences of Zfl1 and Zfl2 from 62 Chinese elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of 254 and 192 variants that included SNPs and indels were identified from the full sequences of Zfl1 and Zfl2, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorphisms of CDS sequences classified Zfl1 into 16 haplotypes encoding 16 different proteins and Zfl2 into 18 haplotypes encoding eight different proteins. The population of Huangzaosi and its derived lines showed statistically significant signals of post-domestication selection on the Zfl1 CDS sequences, as well as lower nucleotide polymorphism and haplotype diversity than the whole set. However, the Zfl2 locus was only selected for in the heterotic group Reid. Further evidence revealed that at least 17 recombination events contributed to the genetic and haplotype diversities at the Zfl1 locus and 16 recombination events at the Zfl2 locus.
- Published
- 2014
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31. Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection.
- Author
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Yang Z, Wang Y, Zhou Y, Gao Q, Zhang E, Zhu L, Hu Y, and Xu C
- Subjects
- Bryophyta genetics, Exons genetics, Introns genetics, Magnoliopsida genetics, Phylogeny, Evolution, Molecular, Gene Transfer, Horizontal genetics, Racemases and Epimerases genetics
- Abstract
Background: The L-Ala-D/L-Glu epimerases (AEEs), a subgroup of the enolase superfamily, catalyze the epimerization of L-Ala-D/L-Glu and other dipeptides in bacteria and contribute to the metabolism of the murein peptide of peptidoglycan. Although lacking in peptidoglycan, land plants possess AEE genes that show high similarity to those in bacteria., Results: Similarity searches revealed that the AEE gene is ubiquitous in land plants, from bryophytas to angiosperms. However, other eukaryotes, including green and red algae, do not contain genes encoding proteins with an L-Ala-D/L-Glu_epimerase domain. Homologs of land plant AEE genes were found to only be present in prokaryotes, especially in bacteria. Phylogenetic analysis revealed that the land plant AEE genes formed a monophyletic group with some bacterial homologs. In addition, land plant AEE proteins showed the highest similarity with these bacterial homologs and shared motifs only conserved in land plant and these bacterial AEEs. Integrated information on the taxonomic distribution, phylogenetic relationships and sequence similarity of the AEE proteins revealed that the land plant AEE genes were acquired from bacteria through an ancient horizontal gene transfer (HGT) event. Further evidence revealed that land plant AEE genes had undergone positive selection and formed the main characteristics of exon/intron structures through gaining some introns during the initially evolutionary period in the ancestor of land plants., Conclusions: The results of this study clearly demonstrated that the ancestor of land plants acquired an AEE gene from bacteria via an ancient HGT event. Other findings illustrated that adaptive evolution through positive selection has contributed to the functional adaptation and fixation of this gene in land plants.
- Published
- 2013
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32. Nucleotide polymorphisms and haplotype diversity of RTCS gene in China elite maize inbred lines.
- Author
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Zhang E, Yang Z, Wang Y, Hu Y, Song X, and Xu C
- Subjects
- Arabidopsis Proteins genetics, Breeding, Genetic Variation, Introns genetics, Linkage Disequilibrium, Protein Structure, Tertiary, Untranslated Regions genetics, Haplotypes, Plant Proteins genetics, Polymorphism, Single Nucleotide genetics, Transcription Factors genetics, Zea mays genetics
- Abstract
The maize RTCS gene, encoding a LOB domain transcription factor, plays important roles in the initiation of embryonic seminal and postembryonic shoot-borne root. In this study, the genomic sequences of this gene in 73 China elite inbred lines, including 63 lines from 5 temperate heteroric groups and 10 tropic germplasms, were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. A total of 63 sequence variants, including 44 SNPs and 19 indels, were identified at this locus, and most of them were found to be located in the regions of UTR and intron. The coding region of this gene in all tested inbred lines carried 14 haplotypes, which encoding 7 deferring RTCS proteins. Analysis of the polymorphism sites revealed that at least 6 recombination events have occurred. Among all 6 groups tested, only the P heterotic group had a much lower nucleotide diversity than the whole set, and selection analysis also revealed that only this group was under strong negative selection. However, the set of Huangzaosi and its derived lines possessed a higher nucleotide diversity than the whole set, and no selection signal were identified.
- Published
- 2013
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33. The feasibility study of US-MRI virtual navigation in the shoulder.
- Author
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Liu J, Zhan W, Zhou M, Zhang X, Hu Y, and Zhu Y
- Subjects
- Equipment Design, Equipment Failure Analysis, Feasibility Studies, Fiducial Markers, Humans, Muscle, Skeletal diagnostic imaging, Muscle, Skeletal pathology, Reproducibility of Results, Sensitivity and Specificity, Magnetic Resonance Imaging instrumentation, Shoulder diagnostic imaging, Shoulder pathology, Subtraction Technique instrumentation, Tendinopathy diagnosis, Ultrasonography instrumentation, User-Computer Interface
- Abstract
Purpose: The aim of this study was to evaluate the feasibility of ultrasound sonography (US)-magnetic resonance imaging (MRI) virtual navigation in the shoulder., Methods: We selected 10 healthy volunteers and 10 patients with supraspinatus tendinitis to fuse in the shoulder with a Virtual Navigator System. We selected five internal marks as follows: (1) ① acromion, ② the point of junction between the supraspinatus muscle and the tendon, ③ the point of the middle in the surface of the head of humerus in the plane of ②, ④ the point of attachment of the supraspinatus tendon in the great tuberosity of humerus, and ⑤ the point of the middle in the surface of the head of humerus in the plane of ④. To make three, four, and five marks in different combinations in the process of image fusion successively, it should be based on these points. The observed targets included coincidence, stability, and accuracy in the sonography and magnetic resonance images by two radiologists., Results: The supraspinatus tendon of the 10 volunteers and the lesions of 10 patients with supraspinatus tendinitis could be fused between the sonography image and the magnetic resonance image. The effect of the combination of ②+③+④+⑤ in the group with four-point internal marks was most satisfactory (P<.05)., Conclusion: The process of the combination of ②+③+④+⑤ in the group with four-point internal marks is considered the best method, and the application of US-MRI virtual navigation is regarded feasible in the shoulder., (Copyright © 2012 Elsevier Inc. All rights reserved.)
- Published
- 2012
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34. [Effect of allergy on outcomes after endoscopic sinus surgery in patients with chronic rhinosinusitis].
- Author
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Shangguan C, Wang S, Cai C, and Hu Y
- Subjects
- Adolescent, Adult, Aged, Cation Transport Proteins blood, Chronic Disease, Endoscopy, Humans, Middle Aged, Postoperative Period, Quality of Life, Sinusitis surgery, Treatment Outcome, Young Adult, Allergens blood, Eosinophil Cationic Protein blood, Immunoglobulin E blood, Sinusitis blood
- Abstract
Objective: To explore correlation of allergy and outcomes after endoscopic sinus surgery (ESS) in patients with chronic rhinosinusitis., Method: Before ESS, 115 cases were arranged to detect allergic serum relative index: the concentration of serum TIgE, specific IgE semi-quantitative test and the concentration of serum ECP; to survey QOL status: VAS, SNOT-20 and SF-36; as well as inquire medical record, Lund-Mackay CT system scoring, clinical classification of chronic rhinosinusitis. After ESS (>1 year), 74 cases were followed up. The subjective and objective assessment were achieved by means of VAS, SNOT-20, SF-36 and Lund-Kennedy endoscopic scores., Result: The improvements of VAS scores of the cases with increased serum TIgE were significantly lower than those without increased serum TIgE (P<0.05). In cases of II, III types, the objective outcomes of the cases with increased serum TIgE were significantly worse than those without increased serum TIgE (P<0.05). The objective outcomes of the cases with positive allergen (> or = 3) were significantly worse than those with positive allergen (<3) (P<0.05). The objective outcomes of the cases with strong positive allergen were significantly worse than those without strong positive allergen (P<0.05). VAS scores and SNOT-20 scores after endoscopic sinus surgery of the cases with strong positive allergen were significantly worse than those without strong positive allergen (P<0.05). The concentration of serum ECP of the invalid cases was significantly higher than effective cases (P<0.05). The concentration of serum ECP was positive correlated with Lund-Kennedy endoscopic scores (r=0.49, P<0.05). In cases of II, III types, the objective outcomes of the cases with increased serum ECP were significantly worse than those without increased serum ECP (P<0.05), VAS scores and SNOT-20 scores after endoscopic sinus surgery of the cases with increased serum ECP were significantly worse than those without incre- ased serum ECP (P<0.05), the improvements of VAS scores of the cases with increased serum ECP were significantly lower than those without increased serum ECP (P<0.05)., Conclusion: Those allergic serum relative indexes make some negative effect on subjective and objective outcomes. Especially, in cases with polyps, the increase of serum TIgE and serum ECP has more negative effect. Our results might help to choose immunotherapy to combine with endoscopic sinus surgery for those selected patients to improve the outcomes of chronic rhinosinusitis.
- Published
- 2009
35. [Effect of allergic factors on chronic rhinosinusitis].
- Author
-
Hu Y, Wang S, and Cai C
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Case-Control Studies, Chronic Disease, Female, Humans, Male, Middle Aged, Sinusitis blood, Sinusitis immunology, Young Adult, Allergens blood, Eosinophil Cationic Protein blood, Immunoglobulin E blood, Sinusitis pathology
- Abstract
Objective: To explore the correlation between allergic factors and chronic rhinosinusitis, and discuss its effects on the development of illness., Method: One hundred and one cases were selected to detect allergic serum relative index: the concentration of serum TIgE, specific IgE semi-quantitative test, the concentration of serum ECP as well as inquiring medical record, Lund-Mackay CT system scoring., Result: The concentration of serum TIgE and serum ECP in CRS was higher than those in control (P < 0.01). The increased proportion of serum TIgE and serum ECP was significantly different among clinical stages (P < 0.05) and between the cases with and without prior sinus surgery (P < 0.05). CT scores of the cases with serum TIgE and serum ECP increased were significantly higher than those without serum TIgE and serum ECP increased. The strong positive rate in CRS was significantly different among clinical stages (P < 0.05). The strong positive rate increased significantly in the cases with prior sinus surgery (P < 0.05). CT scores in the cases with strong positive allergen were significantly higher than that in the cases without positive allergen (P < 0.05)., Conclusion: These results suggest that allergic factors make some negative effect on the severity of CRS and are the index for the severity and worse prognosis of illness.
- Published
- 2008
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