Publications by authors named "Yun Yu"

356 Publications

Visceral adiposity index is associated with arterial stiffness in hypertensive adults with normal-weight: the china H-type hypertension registry study.

Nutr Metab (Lond) 2021 Oct 9;18(1):90. Epub 2021 Oct 9.

Department of Cardiology, Nanchang University Second Affiliated Hospital, No. 1 Minde Road, Nanchang, 330006, Jiangxi, China.

Background: Limited information is available on arterial stiffness risk among hypertensive patients with metabolically abnormal but normal weight. Visceral adiposity index (VAI) is a novel indicator for visceral fat mass and metabolism, however, whether can be used to assessed arterial stiffness in a normal-weight population remains unclear. The goal of this study was to examine the independent association of VAI with arterial stiffness in normal-weight hypertensive patients.

Methods: 3258 participants recruited from the China H-type Hypertension Registry Study. VAI value was calculated using sex-specific equations. High arterial stiffness was defined as baPWV ≥ 18 m/s. Multivariable regression analysis was used to identify the association of VAI with baPWV and high arterial stiffness.

Results: Of participants, 50.5% (1644) were males, the mean age was 65.5 (SD, 9.1) years. Mean VAI and baPWV were 2.0 (SD, 2.3) and 18.2 (SD, 3.9) m/s, respectively. For each unit increase of lg VAI in multivariable regression analysis, there was a 1.05 m/s increase in baPWV (95% CI 0.67, 1.43) and a 2.13-fold increase in the risk of high arterial stiffness (95% CI 1.59, 2.86). In all models, the VAI was consistently and significantly associated with baPWV after adjustment for different confounders. High VAI levels were stably associated with baPWV in all subgroups.

Conclusions: We found positive association of VAI with baPWV and high arterial stiffness in normal-weight adults with hypertension. The establishment of this association could help the arterial stiffness risk stratification in normal-weight hypertensive populations, who are frequently overlooked in preventing cardiovascular disease.
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http://dx.doi.org/10.1186/s12986-021-00617-5DOI Listing
October 2021

Continuation versus discontinuation of aspirin-based antiplatelet therapy for perioperative bleeding and ischaemic events in adults undergoing neurosurgery: protocol for a systematic review and meta-analysis.

BMJ Open 2021 Sep 30;11(9):e046741. Epub 2021 Sep 30.

Department of Anesthesiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China

Introduction: Antiplatelet therapy is commonly used in primary or secondary prevention of atherosclerotic and thrombotic diseases, such as coronary artery disease, transient ischaemic attack or stroke. Recent studies noted that antiplatelet therapy should be continued perioperatively in patients at high risk of thrombosis and low bleeding risk in orthopaedic, spinal or urological surgery. However, evidence in neurosurgery is lacking. Thus, we aim to conduct a systematic review and meta-analysis to assess whether the continuous use of antiplatelet drugs in neurosurgery increases the risk of perioperative bleeding.

Methods And Analysis: We will search PubMed, Cochrane Central Register of Controlled Trials and Embase using a strategy that combines the terms aspirin, bleeding/ischaemic and neurosurgery. Two reviewers will independently screen all identified abstracts for eligibility and evaluate the risk of bias of the included studies using the Cochrane risk of bias tool for randomised controlled studies and the Newcastle-Ottawa Scale for observational studies (including cohort studies, case-control studies, case series). Discrepancies will be resolved by consultation with a third researcher. We will conduct a systematic review and meta-analysis. If evidence suggests moderate statistical or clinical heterogeneity, we plan to investigate this heterogeneity by performing subgroup analyses and sensitivity analysis.

Ethics And Dissemination: No ethics approval will be sought as no original data will be collected for this review. Findings will be disseminated through peer-reviewed publication and conference presentations.

Prospero Registration Number: CRD42020202590.
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http://dx.doi.org/10.1136/bmjopen-2020-046741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8487199PMC
September 2021

Quantitative detection of crystal violet using a surface-enhanced Raman scattering based on a flower-like HAp/Ag nanocomposite.

Anal Methods 2021 Sep 23;13(36):4143-4149. Epub 2021 Sep 23.

MOE Key Laboratory of OptoElectronic Science and Technology for Medicine, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China.

Herein, we proposed a simple one-pot sol-thermal strategy to prepare a highly sensitive and reproducible SERS substrate. The silver-doped hydroxyapatite nanocomposite (HAp/Ag) could suppress the oxidation of silver nanoparticles, which endow the SERS substrate with good stability and reproducibility. Due to the strong interaction between the HAp/Ag substrate and the analytes, a stronger Raman signal generated during the process of SERS detection. In particular, the HAp/Ag substrate enabled the determination of rhodamine 6G (R6G) and crystal violet (CV), and the limits of detection (LOD) were low at 10 M and 10 M, respectively. In addition, the HAp/Ag substrate could be used for the quantitative analysis of CV in wastewater with a good linear relationship between 10 and 10 M. In this context, the HAp/Ag substrate combines the superior properties of both Ag NPs and HAp particles, providing a potential method for monitoring the environment and building a convenient SERS platform to detect pollutants in wastewater.
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http://dx.doi.org/10.1039/d1ay01107cDOI Listing
September 2021

Predictive value of early amplitude integrated electroencephalogram (aEEG) in sleep related problems in children with perinatal hypoxic-ischemia (HIE).

BMC Pediatr 2021 Sep 18;21(1):410. Epub 2021 Sep 18.

Soochow Key Laboratory of Prevention and Treatment of Child Brain Injury, Children's Hospital of Soochow University, No.92 Zhongnanjie Road, Suzhou, 215025, P.R. China.

Background: While great attention has been paid to motor and cognitive impairments in children with neonatal Hypoxic-Ischemic Encephalopathy (HIE), sleep related circadian rhythm problems, although commonly present, are often neglected. Subsequently, no early clinical indicators have been reported to correlate with sleep-related circadian dysfunction during development.

Methods: In this study, we first analyzed patterns of the amplitude integrated electroencephalogram (aEEG) in a cohort of newborns with various degrees of HIE. Next, during follow-ups, we collected information of sleep and circadian related problems in these patients and performed correlation analysis between aEEG parameters and different sleep/circadian disorders.

Results: A total of 101 neonates were included. Our results demonstrated that abnormal aEEG background pattern is significantly correlated with circadian rhythmic (r = 0.289, P = 0.01) and breathing issues during sleep (r = 0.237, P = 0.037). In contrast, the establishment of sleep-wake cycle (SWC) showed no correlation with sleep/circadian problems. Detailed analysis showed that summation of aEEG score, along with low base voltage (r = 0.272, P = 0.017 and r = -0.228, P = 0.048, respectively), correlates with sleep circadian problems. In contrast, background pattern (BP) score highly correlates with sleep breathing problem (r = 0.319, P = 0.004).

Conclusion: Abnormal neonatal aEEG pattern is correlated with circadian related sleep problems. Our study thus provides novel insights into predictive values of aEEG in sleep-related circadian problems in children with HIE.
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http://dx.doi.org/10.1186/s12887-021-02796-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8449491PMC
September 2021

Study on degranulation of mast cells under C48/80 treatment by electroporation-assisted and ultrasound-assisted surface-enhanced Raman spectrascopy.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Aug 27;265:120331. Epub 2021 Aug 27.

MOE Key Laboratory of Optoelectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China; School of opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, Fujian, China. Electronic address:

Both electroporation-assisted and ultrasound-assisted delivery methods can rapidly deliver nanoparticles into living cells for surface-enhanced Raman scattering (SERS) detection, but these two methods have never been compared. In this study, electroporation-assisted SERS and ultrasound-assisted SERS were employed to detect the biochemical changes of degranulated mast cells induced by mast cell stimulator (C48/80). The results showed that the cell damage of electroporation based on controllable electric pulse was smaller than that of ultrasound based on cavitation. Transmission electron microscope images of cells indicated that the nanoparticles delivered by electroporation were mainly distributed in the cytoplasm, while ultrasound could transport nanoparticles to the cytoplasm and nucleus. Therefore, electroporation-assisted SERS mainly detects the biochemical information of cytoplasm, while ultrasound-assisted SERS gets more spectral signals of nucleic acid. Both methods can obtain high quality SERS signal of cells. With drug treatment, the SERS peak intensity of 733 cm attributed to phosphatidylserine decreased significantly, which may be due to the activation of mast cell degranulation pathway stimulated by C48/80 agonist, resulting in a large amount of intracellular serine being used to synthesize tryptase, while the production of phosphatidylserine decreased. Further, based on principal component analysis and linear discriminant analysis (PCA-LDA approach), ultrasound-assisted SERS could achieve better sensitivity, specificity and accuracy in the discrimination and identification of drug-treated degranulated mast cells than electroporation assisted SERS. This exploratory work is helpful to realize the real-time dynamic SERS detection of intracellular biochemical components, and it also has great potential in intracellular SERS analysis, such as the cytotoxicity assay of anti-tumor drugs or cancer cell screening.
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http://dx.doi.org/10.1016/j.saa.2021.120331DOI Listing
August 2021

Familial follicular cell thyroid carcinomas in a large number of Dutch German longhaired pointers.

Vet Comp Oncol 2021 Aug 31. Epub 2021 Aug 31.

Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.

Thyroid carcinomas (TCs) originating from follicular cells of the thyroid gland occur in both humans and dogs, and they have highly similar histomorphologic patterns. In dogs, TCs have not been extensively investigated, especially concerning the familial origin of TCs. Here, we report familial thyroid follicular cell carcinomas (FCCs) confirmed by histology in 54 Dutch origin German longhaired pointers. From the pedigree, 45 of 54 histopathologically confirmed cases are closely related to a pair of first-half cousins in the past, indicating a familial disease. In addition, genetics contributed more to the thyroid FCC than other factors by an estimated heritability of 0.62 based on pedigree. The age of diagnosis ranged between 4.5 and 13.5 years, and 76% of cases were diagnosed before 10 years of age, implying an early onset of disease. We observed a significant higher pedigree-based inbreeding coefficient in the affected dogs (mean F, 0.23) compared to unaffected dogs (mean F, 0.14), suggesting the contribution of inbreeding to tumour development. The unique occurrence of familial thyroid FCC in this dog population and the large number of affected dogs make this population an important model to identify the genetic basis of familial thyroid FCC in this breed and may contribute to the research into pathogenesis, prevention and treatment in humans.
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http://dx.doi.org/10.1111/vco.12769DOI Listing
August 2021

Effect of Collagen Peptide-Chelated Zinc Nanoparticles From Pufferfish Skin on Zinc Bioavailability in Rats.

J Med Food 2021 Sep 26;24(9):987-996. Epub 2021 Aug 26.

Technology Innovation Center for Exploitation of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen City, China.

Small-molecular-weight collagen peptides (CPs) with high zinc-chelating ability were extracted from pufferfish skin. Chelation of CPs with zinc was performed to prepare novel CP-chelated zinc (CP-Zn) nanoparticles. CP-Zn nanoparticles were spherical, regular, and well dispersed with an average size of ∼100 nm. The zeta potential assay was used to explore the stability of CP-Zn nanoparticles. CP-Zn nanoparticles were much more stable in the pH range of 3-8. The structural properties of CP-Zn nanoparticles were characterized by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry, Fourier transform infrared spectroscopy, and H nuclear magnetic resonance spectroscopy. The results indicated that CPs were chelated with Zn ions through the amino nitrogen and oxygen atoms from the carboxyl groups. Furthermore, the animal experiment results showed that CP-Zn nanoparticles were more effective in improving zinc bioavailability of Zn-deficient rats than zinc gluconate and zinc sulfate. The study demonstrated that CP-Zn nanoparticles were ideal for zinc supplementation.
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http://dx.doi.org/10.1089/jmf.2021.K.0038DOI Listing
September 2021

Uricase deficiency causes mild and multiple organ injuries in rats.

PLoS One 2021 26;16(8):e0256594. Epub 2021 Aug 26.

Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, Yunnan Province, China.

Uricase-deficient rats could be one of the optimal model animals to study hyperuricemia. The present study aimed to find the biological differences between uricase-deficient (Kunming-DY rats) and wild-type male rats. Uricase-deficient rats and wild-type rats were commonly bred. Their body weight, water and food consumption, 24-h urine and feces, uric acid in serum and organs, and serum indexes were recorded or assayed. Organs, including the heart, liver, spleen, lung, kidney, thymus, stomach, duodenum, and ileum, were examined using a routine hematoxylin-eosin staining assay. We found that the growth of male uricase-deficient rats was retarded. These rats excreted more urine than the wild-type rats. Their organ indexes (organ weight body weight ratio), of the heart, liver, kidney, and thymus significantly increased, while those of the stomach and small intestine significantly decreased. The uricase-deficient rats had a significantly higher level of serum uric acid and excreted more uric acid via urine at a higher concentration. Except for the liver, uric acid increased in organs and intestinal juice of uricase-deficient rats. Histological examination of the uricase-deficient rats showed mild injuries to the heart, liver, spleen, lung, kidney, thymus, stomach, duodenum, and ileum. Our results suggest that uricase-deficient rats have a different biological pattern from the wild-type rats. Uricase deficiency causes growth retardation of young male rats and the subsequent increase in serum uric acid results in mild organs injuries, especially in the kidney and liver.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0256594PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8389383PMC
August 2021

Parental Self-Efficacy and Behavioral Problems in Children with Autism During COVID-19: A Moderated Mediation Model of Parenting Stress and Perceived Social Support.

Psychol Res Behav Manag 2021 14;14:1291-1301. Epub 2021 Aug 14.

School of Education, Guangzhou University, Guangzhou, People's Republic of China.

Purpose: COVID-19 pandemic has been verified as a public health emergency of international concern. During the special period, the health of vulnerable groups, such as children with autism, should be concerned. Some studies have been carried out to investigate the behavioral problems of children with autism during the COVID-19, but underlying mechanisms behind it is not clear. This study examines the role of parenting stress as a mediator in the relationship between parental self-efficacy and behavioral problems in Chinese children as well as the role of perceived social support as a moderator for this mediation effect.

Methods: A total of 439 parents of children with autism (mean age=40.17, SD=5.26) were surveyed and completed five questionnaires (Conners Parent Symptom Questionnaire, Parental Self-Efficacy Questionnaire, Parenting Stress Index-Short Form 15, Perceived Social Support Questionnaire, and Neuroticism Extraversion Openness Five Factor Inventory). The statistical analyses were conducted by SPSS 26.0 and SPSS PROCESS macro.

Results: Controlling for neuroticism, which is highly associated with psychological changes in parents, the study found that parental self-efficacy was significantly and negatively correlated with behavioral problems in children with autism. In addition, the relationship between parental self-efficacy and behavioral problems was mediated by parenting stress. Furthermore, parenting stress moderated the indirect relationship between parental self-efficacy and behavioral problems via perceived social support.

Conclusion: These results provide direct evidences for the inextricable relationship between family, social factors and behavioral problems of children with autism. It suggest that improving perceived social support to enhance parental self-efficacy is critical to buffering against parenting stress and stabilizing children with autism during the COVID-19 pandemic.
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http://dx.doi.org/10.2147/PRBM.S327377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8374842PMC
August 2021

Mutual regulation between chicken telomerase reverse transcriptase and the Wnt/β-catenin signalling pathway inhibits apoptosis and promotes the replication of ALV-J in LMH cells.

Vet Res 2021 Aug 19;52(1):110. Epub 2021 Aug 19.

College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.

This study aimed to explore the mutual regulation between chicken telomerase reverse transcriptase (chTERT) and the Wnt/β-catenin signalling pathway and its effects on cell growth and avian leukosis virus subgroup J (ALV-J) replication in LMH cells. First, LMH cells stably overexpressing the chTERT gene (LMH-chTERT cells) and corresponding control cells (LMH-NC cells) were successfully constructed with a lentiviral vector expression system. The results showed that chTERT upregulated the expression of β-catenin, Cyclin D1, TCF4 and c-Myc. chTERT expression level and telomerase activity were increased when cells were treated with LiCl. When the cells were treated with ICG001 or IWP-2, the activity of the Wnt/β-catenin signalling pathway was significantly inhibited, and chTERT expression and telomerase activity were also inhibited. However, when the β-catenin gene was knocked down by small interfering RNA (siRNA), the changes in chTERT expression and telomerase activity were consistent with those in cells treated with ICG001 or IWP-2. These results indicated that chTERT and the Wnt/β-catenin signalling pathway can be mutually regulated. Subsequently, we found that chTERT not only shortened the cell cycle to promote proliferation but also inhibited apoptosis by downregulating the expression of Caspase 3, Caspase 9 and BAX; upregulating BCL-2 and BCL-X expression; and promoting autophagy. Moreover, chTERT significantly enhanced the migration ability of LMH cells, upregulated the protein and mRNA expression of ALV-J and increased the virus titre. ALV-J replication promoted chTERT expression and telomerase activity.
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http://dx.doi.org/10.1186/s13567-021-00979-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8375160PMC
August 2021

extract attenuates staurosporine induced neurotoxicity by restoring the FGF2-PI3K/Akt signaling axis and Dnmt3.

Heliyon 2021 Jul 7;7(7):e07503. Epub 2021 Jul 7.

Key Laboratory of Ecology and Environment in Minority Areas, National Ethnic Affairs Commission, Center on Translational Neuroscience, College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.

We previously demonstrated the antioxidant activity of extract (CE) in rat cortical neurons and in mice with chemically induced cognitive impairment. In this work, we established a staurosporine (STS)-induced toxicity model to decipher the neuroprotective mechanisms of CE. We found that CE protected cell viability and neurite integrity in STS-induced toxicity by restoring the levels of FGF2 and its associated PI3K/Akt signaling axis. LY294002, a pan-inhibitor of PI3K, antagonized the activity of CE, although its-mediated restoration of FGF2 was unaffected. In addition, CE restored levels of Bcl-2/Caspase-3, PKCα/CaM pathway, and Dnmt3a and Dnmt3b, two methyltransferases that contribute to DNA methylation. The Dnmts inhibitor 5-azacytidine impaired CE-mediated restoration of Dnmt3 or CaM, as well as the transition of DNA methylation status on the Dnmt3 promoter. These results reveal potential mechanisms that could facilitate the study and application of CE as a neuroprotective agent.
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http://dx.doi.org/10.1016/j.heliyon.2021.e07503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8353313PMC
July 2021

Label-free determination of liver cancer stages using surface-enhanced Raman scattering coupled with preferential adsorption of hydroxyapatite microspheres.

Anal Methods 2021 Sep 16;13(35):3885-3893. Epub 2021 Sep 16.

MOE Key Laboratory of OptoElectronic Science and Technology for Medicine, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China.

Here, we explored a label-free albumin targeted analysis method by utilizing hydroxyapatite (HAp) to adsorb-release serum albumin, in conjunction with surface-enhanced Raman scattering (SERS) for screening liver cancer (LC) at different tumor (T) stages. Excitingly, albumin can be preferentially adsorbed by HAp as compared with other serum proteins. Moreover, we developed a novel strategy using a high concentration of PO solution as the albumin-release agent. This method overcomes the shortcomings of the traditional purification technology of serum albumin, which requires acid to release protein, and ensures that the structure and properties of albumin are not damaged. The SERS spectra of serum albumin obtained from three sample groups were analyzed to verify the feasibility of this new method: healthy volunteers ( = 35), LC patients with T1 stage ( = 25) and LC patients with T2-T4 stage ( = 23). Furthermore, principal component analysis (PCA) combined with linear discriminant analysis (LDA) was employed to classify the early T (T1) stage LC normal group and advanced T (T2-T4) stage LC normal group, yielding high diagnostic accuracies of 90.00% and 96.55%, respectively, which showed a 10% improvement in diagnostic accuracy for the early stage detection of cancer as compared with previous studies. The results of this exploratory work demonstrated that HAp-adsorbed-released serum albumin combined with SERS analysis has great potential for label-free, noninvasive and sensitive detection of different T stages of liver cancer.
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http://dx.doi.org/10.1039/d1ay00946jDOI Listing
September 2021

ANP32B-mediated repression of p53 contributes to maintenance of normal and CML stem cells.

Blood 2021 Aug 6. Epub 2021 Aug 6.

Rui-Jin hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Proper regulation of p53 signaling is critical for the maintenance of hematopoietic stem cells (HSCs) and leukemic stem cells (LSCs). The hematopoietic cell-specific mechanisms regulating p53 activity remain largely unknown. Here, we demonstrate that conditional deletion of acidic leucine-rich nuclear phosphoprotein 32B (ANP32B) in hematopoietic cells impairs repopulation capacity and post-injury regeneration of HSCs. Mechanistically, ANP32B forms a repressive complex with and thus inhibits the transcriptional activity of p53 in hematopoietic cells, and p53 deletion rescues the functional defect in Anp32b-deficient HSCs. Of great interest, ANP32B is highly expressed in leukemic cells from chronic myelogenous leukemia (CML) patients. Anp32b deletion enhances p53 transcriptional activity to impair LSCs function in a murine CML model, and exhibits synergistic therapeutic effects with tyrosine kinase inhibitors in inhibiting CML propagation. In summary, our findings provide a novel strategy to enhance p53 activity in LSCs by inhibiting ANP32B, and identify ANP32B as a potential therapeutic target in treating CML.
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http://dx.doi.org/10.1182/blood.2020010400DOI Listing
August 2021

Corrigendum to "Anti-arthritis effect of berberine associated with regulating energy metabolism of macrophages through AMPK/HIF-1α pathway". [Int. Immunopharmacol. 87 (2020) 106830].

Int Immunopharmacol 2021 Oct 2;99:107911. Epub 2021 Aug 2.

School of Pharmacy, Bengbu Medical College, No.2600, Donghai Avenue, Bengbu 233000, Anhui, China; Anhui BBCA Pharmaceuticals Co, Ltd, No.6288, Donghai Avenue, Bengbu 233000, Anhui, China; School of Chemistry and Chemical Engineering, Anhui University, No.3, Feixi Rode, Hefei 230039, Anhui, China. Electronic address:

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http://dx.doi.org/10.1016/j.intimp.2021.107911DOI Listing
October 2021

Label-free diagnosis of breast cancer based on serum protein purification assisted surface-enhanced Raman spectroscopy.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Dec 28;263:120234. Epub 2021 Jul 28.

Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China; School of opto-electronic and Communication Engineering, Xiamen University of Technology, Xiamen, Fujian, China. Electronic address:

Serum protein is generally used to assess the severity of disease, as well as cancer progression and prognosis. Herein, a simple and rapid serum proteins analysis method combined with surface-enhanced Raman spectroscopy (SERS) technology was applied for breast cancer detection. The cellulose acetate membrane (CA) was employed to extract human serum proteins from 30 breast cancer patients and 45 healthy volunteers and then extracted proteins were mixed with silver nanoparticles for SERS measurement. Additionally, we also mainly assessed the use of different ratios of proteins-silver nanoparticles (Ag NPs) mixture to generate maximum SERS signal for clinical samples detection. Two multivariate statistical analyses, principal component analysis-linear discriminate analysis (PCA-LDA) and partial least square-support vector machines (PLS-SVM) were used to analyze the obtained serum protein SERS spectra and establish the diagnostic model. The results demonstrate that the PLS-SVM model provides superior performance in the classification of breast cancer diagnosis compared with PCA-LDA. This exploratory work demonstrates that the label-free SERS analysis technique combined with CA membrane purified serum proteins has great potential for breast cancer diagnosis.
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http://dx.doi.org/10.1016/j.saa.2021.120234DOI Listing
December 2021

Decrease in abundance of bacteria of the genus in gut microbiota may be related to pre-eclampsia progression in women from East China.

Food Nutr Res 2021 28;65. Epub 2021 Jun 28.

Department of Obstetrics and Gynecology, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, China.

Background: Pre-eclampsia (PE) can result in severe damage to maternal and fetal health. It has been reported that gut microbiota (GM) had important roles in regulating the metabolic and inflammatory responses of the mother. However, investigations on GM in PE are rare.

Objective: The objective of the present study was to investigate the changes of GM in PE and how to alter the GM composition in PE by dietary or dietary supplements.

Design: We analyzed the composition changes in GM as well as the relationship between bacteria of different genera and clinical indices by amplifying the V4 region of the 16S ribosomal RNA gene in 12 PE patients and eight healthy pregnant women in East China.

Results: In the PE group, the Observed Species Index was lower than that in the control group, indicating that the α-diversity of the microbiome in the PE group decreased. At phylum, family, and genus levels, the relative abundance of different bacteria in PE patients displayed substantial differences to those from healthy women. We noted a decreased abundance of bacteria of the phylum Actinobacteria ( = 0.042), decreased abundance of bacteria of the family Bifidobacteriaceae ( = 0.039), increased abundance of bacteria of the genus ( = 0.026) and ( = 0.048), and decreased abundance of bacteria of the genus ( = 0.038) Among three enriched genera, bacteria of the genus showed a negative correlation with the systolic blood pressure (SBP), diastolic blood pressure (DBP), and dyslipidemia, which involved glucose metabolism, lipid metabolism, and the oxidative-phosphorylation pathway. The increased abundance of bacteria of the genera and was positively correlated with obesity and dyslipidemia, which involved lipid metabolism, glycosyltransferases, biotin metabolism, and the oxidative-phosphorylation pathways. Moreover, women in the PE group ate more than women in the control group, so fetuses were more prone to overnutrition in the PE group.

Conclusion: There is a potential for GM dysbiosis in PE patients, and they could be prone to suffer from metabolic syndrome. We speculate that alterations in the abundance of bacteria of certain genera (e.g. increased abundance of and , and decreased abundance of ) were associated with PE development to some degree. Our data could help to monitor the health of pregnant women and may be helpful for preventing and assisting treatment of PE by increasing dietary fiber or probiotics supplement.
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http://dx.doi.org/10.29219/fnr.v65.5781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254465PMC
June 2021

Levenshtein Distance, Sequence Comparison and Biological Database Search.

IEEE Trans Inf Theory 2021 Jun 21;67(6):3287-3294. Epub 2020 May 21.

Department of Mathematics, University of Toronto, Toronto, ON M5S 2E4, Canada, and also with the Department of Computer and Mathematical Sciences, University of Toronto at Scarborough, Toronto, ON M1C 1A4, Canada.

Levenshtein edit distance has played a central role-both past and present-in sequence alignment in particular and biological database similarity search in general. We start our review with a history of dynamic programming algorithms for computing Levenshtein distance and sequence alignments. Following, we describe how those algorithms led to heuristics employed in the most widely used software in bioinformatics, BLAST, a program to search DNA and protein databases for evolutionarily relevant similarities. More recently, the advent of modern genomic sequencing and the volume of data it generates has resulted in a return to the problem of local alignment. We conclude with how the mathematical formulation of Levenshtein distance as a metric made possible additional optimizations to similarity search in biological contexts. These modern optimizations are built around the low metric entropy and fractional dimensionality of biological databases, enabling orders of magnitude acceleration of biological similarity search.
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http://dx.doi.org/10.1109/tit.2020.2996543DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8274556PMC
June 2021

Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories.

Bioinformatics 2021 07;37(Suppl_1):i151-i160

Department of Mathematics, University of Toronto, Toronto, ON M5S 1A1, Canada.

Motivation: The rapid growth in of electronic medical records provide immense potential to researchers, but are often silo-ed at separate hospitals. As a result, federated networks have arisen, which allow simultaneously querying medical databases at a group of connected institutions. The most basic such query is the aggregate count-e.g. How many patients have diabetes? However, depending on the protocol used to estimate that total, there is always a tradeoff in the accuracy of the estimate against the risk of leaking confidential data. Prior work has shown that it is possible to empirically control that tradeoff by using the HyperLogLog (HLL) probabilistic sketch.

Results: In this article, we prove complementary theoretical bounds on the k-anonymity privacy risk of using HLL sketches, as well as exhibit code to efficiently compute those bounds.

Availability And Implementation: https://github.com/tzyRachel/K-anonymity-Expectation.
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http://dx.doi.org/10.1093/bioinformatics/btab292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275349PMC
July 2021

BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from Bacillus thuringiensis.

Bioinformatics 2021 Jul 9. Epub 2021 Jul 9.

State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.

Summary: Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of GM crops against pests. We previously developed a web-based insecticidal gene mining tool BtToxin_scanner. It has been frequently used by many researchers worldwide. However, it can only handle the genome one by one online. To facilitate efficiently mining toxin genes from large-scale sequence data, we re-designed this tool with a new workflow and the novel bacterial pesticidal protein database. Here we present BtToxin_Digger, a comprehensive and high-throughput Bt toxin mining tool. It can be used to predict Bt toxin genes from thousands of raw genome and metagenome data, and provides accurate results for downstream analysis and experiment testing. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the replacement of the database.

Availability And Implementation: The BtToxin_Digger codes and web services are freely available at https://github.com/BMBGenomics/BtToxin_Digger and https://bcam.hzau.edu.cn/BtToxin_Digger, respectively.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btab506DOI Listing
July 2021

Deleterious Mutations in the TPO Gene Associated with Familial Thyroid Follicular Cell Carcinoma in Dutch German Longhaired Pointers.

Genes (Basel) 2021 06 29;12(7). Epub 2021 Jun 29.

Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

Familial thyroid cancer originating from follicular cells accounts for 5-15% of all the thyroid carcinoma cases in humans. Previously, we described thyroid follicular cell carcinomas in a large number of the Dutch German longhaired pointers (GLPs) with a likely autosomal recessive inheritance pattern. Here, we investigated the genetic causes of the disease using a combined approach of genome-wide association study and runs of homozygosity (ROH) analysis based on 170k SNP array genotype data and whole-genome sequences. A region 0-5 Mb on chromosome 17 was identified to be associated with the disease. Whole-genome sequencing revealed many mutations fitting the recessive inheritance pattern in this region including two deleterious mutations in the TPO gene, chr17:800788G>A (686F>V) and chr17:805276C>T (845T>M). These two SNP were subsequently genotyped in 186 GLPs (59 affected and 127 unaffected) and confirmed to be highly associated with the disease. The recessive genotypes had higher relative risks of 16.94 and 16.64 compared to homozygous genotypes for the reference alleles, respectively. This study provides novel insight into the genetic causes leading to the familial thyroid follicular cell carcinoma, and we were able to develop a genetic test to screen susceptible dogs.
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http://dx.doi.org/10.3390/genes12070997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8306087PMC
June 2021

Potential therapeutic target genes for systemic lupus erythematosus: a bioinformatics analysis.

Bioengineered 2021 12;12(1):2810-2819

Department of Cardiovascular Medicine, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease involving multiple organs. However, the underlying etiology and mechanisms remain unclear. This study was performed to identify potential therapeutic targets for SLE using bioinformatics methods. First, 584 differentially expressed genes were identified based on the GSE61635 dataset. Tissue-specific analyses, enrichment analyses, and Protein-Protein interaction network were successively conducted. Furthermore, ELISA was performed to confirm the expression levels of key genes in the control and SLE blood samples. The findings revealed that tissue-specific expression of markers of the hematological system (25.5%, 28/110) varied significantly. , and expression was markedly increased in the SLE samples compared with controls. In conclusion, the identified key genes (, and ) may act as possible therapeutic targets for the treatment of SLE.
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http://dx.doi.org/10.1080/21655979.2021.1939637DOI Listing
December 2021

Single cell detection using intracellularly-grown-Au-nanoparticle based surface-enhanced Raman scattering spectroscopy for nasopharyngeal cell line classification.

Anal Methods 2021 07 23;13(28):3147-3153. Epub 2021 Jun 23.

College of Integrated Traditional Chinese and Western Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China.

The aim of this study was to evaluate the feasibility of applying intracellularly-grown-Au-nanoparticle (IGAuNP)-based surface-enhanced Raman scattering (SERS) technology to classify two types of nasopharyngeal cancer (NPC) cell lines (CNE2 and CNE1). The IGAuNP technology provides excellent delivery efficiency of Au NPs to the cytoplasm and nucleus, thus leading to an extraordinary enhancement of the Raman signals of cells. Compared with normal Raman scattering (NRS) spectra of cells, IGAuNP-based SERS spectra not only have a high signal-to-noise ratio, but also can detect more characteristic Raman peaks, which can be used to explore more differences when comparing the biochemical components of different nasopharyngeal carcinoma cell lines. Based on the linear discriminant analysis (LDA) and support vector machine (SVM) analysis of SERS spectral data, an exciting result with a diagnostic sensitivity of 100%, specificity of 100%, and accuracy of 100%, could be achieved to differentiate CNE2 and CNE1 cells, which is better than the result obtained by NRS spectroscopy. This exploratory study indicated that the SERS technology based on IGAuNPs in conjunction with multivariate statistical analysis methods has great potential in the identification of nasopharyngeal carcinoma cell lines.
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http://dx.doi.org/10.1039/d1ay00554eDOI Listing
July 2021

Characterizing Brain Tumor Regions Using Texture Analysis in Magnetic Resonance Imaging.

Front Neurosci 2021 3;15:634926. Epub 2021 Jun 3.

School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China.

Purpose: To extract texture features from magnetic resonance imaging (MRI) scans of patients with brain tumors and use them to train a classification model for supporting an early diagnosis.

Methods: Two groups of regions (control and tumor) were selected from MRI scans of 40 patients with meningioma or glioma. These regions were analyzed to obtain texture features. Statistical analysis was conducted using SPSS (version 20.0), including the Shapiro-Wilk test and Wilcoxon signed-rank test, which were used to test significant differences in each feature between the tumor and healthy regions. T-distributed stochastic neighbor embedding (t-SNE) was used to visualize the data distribution so as to avoid tumor selection bias. The Gini impurity index in random forests (RFs) was used to select the top five out of all features. Based on the five features, three classification models were built respectively with three machine learning classifiers: RF, support vector machine (SVM), and back propagation (BP) neural network.

Results: Sixteen of the 25 features were significantly different between the tumor and healthy areas. Through the Gini impurity index in RFs, standard deviation, first-order moment, variance, third-order absolute moment, and third-order central moment were selected to build the classification model. The classification model trained using the SVM classifier achieved the best performance, with sensitivity, specificity, and area under the curve of 94.04%, 92.3%, and 0.932, respectively.

Conclusion: Texture analysis with an SVM classifier can help differentiate between brain tumor and healthy areas with high speed and accuracy, which would facilitate its clinical application.
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http://dx.doi.org/10.3389/fnins.2021.634926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8209330PMC
June 2021

A microsphere nanoparticle based-serum albumin targeted adsorption coupled with surface-enhanced Raman scattering for breast cancer detection.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Nov 1;261:120039. Epub 2021 Jun 1.

MOE Key Laboratory of OptoElectronic Science and Technology for Medicine and Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China. Electronic address:

The serum albumin level is inseparable associated with survival in patients with breast cancer, and simultaneously serve as a good indicator of prognosis of cancer. Here, we proposed a novel extraction-isolation analysis method of albumin for breast cancer detection utilizing hydroxyapatite particles (HAp) to targeted adsorb albumin from serum relying on its specific adsorption capacity. An ideal protein-release reagent was used for isolating albumin from the surface of HAp, and meanwhile ensuring that the structure and property of albumin was not suffered damage. The surface-enhanced Raman scattering (SERS) signal of extracted albumin was obtained, and partial least squares (PLS) and linear discriminant analysis (LDA) analysis approach were employed to analyze SERS spectra data, with the aim to assess the capability of HAp method for identifying breast cancer, yielding an ideal diagnostic accuracy of 98.6%, demonstrating promising potential as a non-invasive and sensitive nanotechnology for breast cancer screening.
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http://dx.doi.org/10.1016/j.saa.2021.120039DOI Listing
November 2021

Erratum: Assessment of radiotherapy effect for nasopharyngeal cancer using plasma surface-enhanced Raman spectroscopy technology: errata.

Biomed Opt Express 2021 May 2;12(5):2557-2558. Epub 2021 Apr 2.

Fujian Normal University, Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fuzhou, 350007, China.

[This corrects the article on p. 3413 in vol. 9, PMID: 29984106.].
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http://dx.doi.org/10.1364/BOE.426301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176798PMC
May 2021

Prehospital Airway Management: A Systematic Review.

Prehosp Emerg Care 2021 Jul 20:1-12. Epub 2021 Jul 20.

To assess comparative benefits and harms across three airway management approaches (bag valve mask [BVM], supraglottic airway [SGA], and endotracheal intubation [ETI]) used by prehospital emergency medical services (EMS) to treat patients with trauma, cardiac arrest, or medical emergencies, and how they differ based on techniques and devices, EMS personnel and patient characteristics. We searched electronic citation databases (Ovid® MEDLINE, CINAHL, the Cochrane Central Register of Controlled Trials, the Cochrane Database of Systematic Reviews, and Scopus) from 1990 to September 2020. We followed Agency for Healthcare Research and Quality Effective Health Care Program Methods guidance. Outcomes included mortality, neurological function, return of spontaneous circulation (ROSC), and successful advanced airway insertion. Meta-analyses using profile-likelihood random effects models were conducted, with analyses stratified by study design, emergency type, and age. We included 99 studies involving 630,397 patients. We found few differences in primary outcomes across airway management approaches. For survival, there was no difference for BVM versus ETI or SGA in adult and pediatric patients with cardiac arrest or trauma. For neurological function, there was no difference for BVM versus ETI and SGA versus ETI in pediatric patients with cardiac arrest. There was no difference in BVM versus ETI in adults with cardiac arrest, but improved neurological function with BVM or ETI versus SGA. There was no difference in ROSC for patients with cardiac arrest for BVM versus ETI or SGA in adults and pediatrics, or SGA versus ETI in pediatrics. There was higher frequency of ROSC in adults with SGA versus ETI. For successful advanced airway insertion, there was higher first-pass success with SGA versus ETI for all patients except adult medical patients (no difference), and no difference in overall success using SGA versus ETI in adults. The currently available evidence does not indicate benefits of more invasive airway approaches based on survival, neurological function, ROSC, or successful airway insertion. Strength of evidence was low or moderate; most included studies were observational. This supports the need for high-quality randomized controlled trials to advance clinical practice and EMS education and policy, and improve patient-centered outcomes.
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http://dx.doi.org/10.1080/10903127.2021.1940400DOI Listing
July 2021

Aboriginal Bacterial Flora in the Uricase-Deficient Rat Gut is Not the Main Factor Affecting Serum Uric Acid.

Evid Based Complement Alternat Med 2021 18;2021:5587642. Epub 2021 May 18.

Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming 650500, Yunnan, China.

The relationship between intestinal bacteria and hyperuricemia is a hot research topic. To better understand this relationship, uricase-deficient Sprague-Dawley rats (Kunming-DY rats) were used. The wild-type rats and Kunming-DY rats were used as controls. Kunming-DY rats were treated with ampicillin (90 mg/kg) and ciprofloxacin (150 mg/kg) for 5 days. Bacterial 16S rDNA in the fresh stool was sequenced, and the abundance was calculated. The rats' serum uric acid (SUA) level was assayed, and the rats' intake and output in 24 h were recorded. The bacterial diversity in three groups' fresh stool was analyzed. The gut bacterial diversity and abundance changed in the Kunming-DY rats. More than 99% of bacteria were inhibited or killed by the combination of antibiotics. In contrast to each of the antibiotics alone, the combination of antibiotics lowered the Kunming-DY rats' SUA level; it also caused mild diarrhea, which increased uric acid excretion through stool. These results suggested that the aboriginal gut bacteria in uricase-deficient rats play a minor role in determining the SUA levels. It is too early to conclude that aboriginal gut bacteria are a tempting target for lowering SUA levels.
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http://dx.doi.org/10.1155/2021/5587642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8154307PMC
May 2021

Contributions of meat waste decomposition to the abundance and diversity of pathogens and antibiotic-resistance genes in the atmosphere.

Sci Total Environ 2021 Aug 16;784:147128. Epub 2021 Apr 16.

Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green development, Department of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China. Electronic address:

Airborne transmission of antibiotic-resistance genes (ARGs) in landfill and acquisition of antibiotic resistance by pathogenic bacteria are posing potential threat to human and environmental health. However, little is known about contribution of waste decomposition to airborne ARGs and pathogens during landfilling of household waste. Herein, the dynamic changes of microbial communities and ARGs were comparatively investigated in leachate and bioaerosol during the decomposition of chicken, fish, and pork wastes. Results found that chicken and pork decomposition could result in emitting high abundance of bioaerosol and pathogen, while fish fermentation will lead to high airborne microbial activity. The main pathogens were Bacilli, Burkholderia-Paraburkholderia and Mycobacterium in bioaerosols, but were Wohlfahrtiimonas, Peptoniphilus and Fusobacterium in leachate, suggesting that the ability of aerosolization of bacteria in leachate was independent of their abundance and diversity. Whereas, diversity and relative abundance of ARGs in leachate were significantly higher than bioaerosol. Moreover, the relative abundance of ARGs in leachate and bioaerosols was not completely relevant. The changes of pathogenic community contributed significantly to the prevalence of ARGs in bioaerosol and leachate. The results will define the contribution of household waste decomposition to airborne pathogen and ARG distribution and provide foundation for airborne bacterial exposure risk and control in landfill.
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http://dx.doi.org/10.1016/j.scitotenv.2021.147128DOI Listing
August 2021

Contributions of meat waste decomposition to the abundance and diversity of pathogens and antibiotic-resistance genes in the atmosphere.

Sci Total Environ 2021 Aug 16;784:147128. Epub 2021 Apr 16.

Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green development, Department of Education, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China. Electronic address:

Airborne transmission of antibiotic-resistance genes (ARGs) in landfill and acquisition of antibiotic resistance by pathogenic bacteria are posing potential threat to human and environmental health. However, little is known about contribution of waste decomposition to airborne ARGs and pathogens during landfilling of household waste. Herein, the dynamic changes of microbial communities and ARGs were comparatively investigated in leachate and bioaerosol during the decomposition of chicken, fish, and pork wastes. Results found that chicken and pork decomposition could result in emitting high abundance of bioaerosol and pathogen, while fish fermentation will lead to high airborne microbial activity. The main pathogens were Bacilli, Burkholderia-Paraburkholderia and Mycobacterium in bioaerosols, but were Wohlfahrtiimonas, Peptoniphilus and Fusobacterium in leachate, suggesting that the ability of aerosolization of bacteria in leachate was independent of their abundance and diversity. Whereas, diversity and relative abundance of ARGs in leachate were significantly higher than bioaerosol. Moreover, the relative abundance of ARGs in leachate and bioaerosols was not completely relevant. The changes of pathogenic community contributed significantly to the prevalence of ARGs in bioaerosol and leachate. The results will define the contribution of household waste decomposition to airborne pathogen and ARG distribution and provide foundation for airborne bacterial exposure risk and control in landfill.
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http://dx.doi.org/10.1016/j.scitotenv.2021.147128DOI Listing
August 2021
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