Publications by authors named "Qingyun Li"

143 Publications

A hybrid learning pedagogy for surmounting the challenges of the COVID-19 pandemic in the performing arts education.

Educ Inf Technol (Dordr) 2021 Jun 28:1-21. Epub 2021 Jun 28.

The Open University of Hong Kong, Hong Kong SAR, China.

For performing arts education, Sage on the stage and Learn from the Masters were halted by the COVID-19 pandemic, and so did everything else. All lectures, tutorials and other face-to-face skill-based training sections were cancelled and were replaced by the online model. Such a model was only seen as one of the supplementary components for performing arts education in the past. From January 2020, this online pedagogy was inevitably placed to surmount the challenges caused by the COVID-19 pandemic. The social distancing measures demanded the blended pedagogy into a new online approach, in which the traditional face-to-face teaching to be replaced by synchronous online learning (facilitated by technologies such as Zoom, Cisco Webex, Google Class, Panopto etc.). Meanwhile, to offer opportunities for cognitive participation which allows students to process the learning and be reflective, webinar and innovative performance projects were launched from the concept of 'flipped classroom and outcome-based education.' This mixed approach (blended learning, flipped classroom, and outcome-based education) is described as 'hybrid learning' in this study. The 'hybrid learning' pedagogy is implemented at the Hong Kong Academy for Performing Arts (HKAPA) for all teaching activities in the 2nd semester 2020/2021 to overcome the challenges caused by the COVID-19 pandemic. A questionnaire survey about how it affected the performing arts education, and how the new pedagogy was implemented took place in July 2020. The survey results from both the teachers (76) and students (163) share lessons, insights, and new understandings on teaching and learning online. Hybrid learning has been widely investigated and researched, yet study on hybrid learning in performing arts such as creative art, theatre art and music, remains insufficient. This study fills the research gap.
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http://dx.doi.org/10.1007/s10639-021-10612-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8236386PMC
June 2021

Systematic Review and Meta-Analysis of Fear of COVID-19.

Front Psychol 2021 11;12:661078. Epub 2021 Jun 11.

Women's Ward of Department of Psychosomatics, Third People's Hospital of Yichun, Yichun, China.

Due to lack of preparedness of health systems, fast spread of the new virus, high mortality rates, and lack of a definite treatment, the outbreak of Coronavirus disease (COVID-19) led to high levels of fear and anxiety in different populations. In addition, isolation, mental disorders, and limitations in social interactions as a result of lockdown and travel ban increased the fear of the new coronavirus. International databases, including Scopus, PubMed, Web of Science, and Google scholar, were searched without any time limitation, and all observational studies published in English reporting the mean of fear of COVID-19 based on the Fear of COVID-19 scale (FCV-19S) were included in the analysis. Methodological quality was assessed using the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines. Random effects model, subgroup analysis, and meta-regression analysis were used to analyze the data. Heterogeneity across studies was examined using Cochran's test and statistic. All the statistical analyses were conducted using R software v4.0.3. A total of 44 articles with a sample size of 52,462 were reviewed. A pooled mean of 18.57 was found for fear of COVID-19. The mean of fear of COVID-19 was higher in women than in men (20.67 vs. 18.21). The highest and lowest means of fear of COVID-19 had been found in Asia (18.36) and Australia (17.43) based on continent, and in hospital staff (19.51) and college students (17.95) based on target population, respectively. In addition, the highest and lowest means of fear of COVID-19 were related to items #1 and #3 of the scale, respectively. According to the results of meta-regression analysis, there was no significant association between the mean of fear of COVID-19 and sample size and participants' age. In addition, publication error was not significant ( = 0.721). The mean of fear of COVID-19 was high around the world; therefore, it seems necessary to pay more attention to the negative effects of the COVID-19 pandemic on mental health.
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http://dx.doi.org/10.3389/fpsyg.2021.661078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8231929PMC
June 2021

Identification of tumor-infiltrating lymphocyte subpopulations correlated with patient prognosis in esophageal squamous cell carcinoma.

J Int Med Res 2021 May;49(5):3000605211016206

Department of Thoracic Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.

Objective: To identify biomarkers related to esophageal squamous cell carcinoma (ESCC) prognosis by analyzing genetic variations and the infiltration levels of tumor-infiltrating lymphocytes (TILs) in patients.

Methods: The clinical features of 61 patients with ESCC were collected. DNA panel sequencing was performed to screen differentially expressed genes (DEGs). Transcriptome sequencing was performed to identify gene expression profiles, and subsequent enrichment analysis of DEGs was conducted using Metascape.

Results: We identified 488 DEGs between patients with ESCC with distinct prognoses that were mainly enriched in the human immune response, fibrinogen complex, and protein activation cascade pathways. Among patients with ESCC treated with postoperative chemotherapy, those with a high infiltration level of myeloid-derived suppressor cells (MDSCs) had longer overall survival (OS), and OS was positively correlated with the infiltration level of T helper type 2 (Th2) cells among patients treated without chemotherapy after surgery. Additionally, in the case of MDSCs >0.7059 or Th2 cells <0.6290, patients receiving postoperative chemotherapy had a longer OS than those treated without chemotherapy following surgery.

Conclusion: The level of MDSCs or Th2 cells can be used as a biomarker for assessing the prognosis of patients with ESCC treated with or without postoperative chemotherapy, respectively.
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http://dx.doi.org/10.1177/03000605211016206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168053PMC
May 2021

Whole genome re-sequencing identifies unique adaption of single nucleotide polymorphism, insertion/deletion and structure variation related to hypoxia in Tibetan chickens.

Gene Expr Patterns 2021 Jun 15;40:119181. Epub 2021 May 15.

Sichuan Animal Science Academy, Chengdu, Sichuan, 610066, China; Animal Breeding and Genetics key Laboratory of Sichuan Province, Chengdu, Sichuan, 610066, China. Electronic address:

Background: The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a biological model to search for genetic diversity of hypoxia adaption.

Methods: The whole genome re-sequencing technology was conducted to investigate the genetic diversity.

Results: In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including HIF1A, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF signaling pathway, MAPK signaling pathway, PPAR signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs.

Conclusions: This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands.
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http://dx.doi.org/10.1016/j.gep.2021.119181DOI Listing
June 2021

Protein-Protein Interaction Inhibitor of SRPKs Alters the Splicing Isoforms of VEGF and Inhibits Angiogenesis.

iScience 2021 May 20;24(5):102423. Epub 2021 Apr 20.

School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.

Serine-arginine (SR) protein kinases (SRPKs) regulate the functions of the SR-rich splicing factors by phosphorylating multiple serines within their C-terminal arginine-serine-rich domains. Dysregulation of these phosphorylation events has been implicated in many diseases, suggesting SRPKs are potential therapeutic targets. In particular, aberrant SRPK1 expression alters the balances of proangiogenic (VEGF) and antiangiogenic (VEGFb) splicing isoforms of the key angiogenesis factor, vascular endothelial growth factor (VEGF), through the phosphorylation of prototypic SR protein SRSF1. Here, we report a protein-protein interaction (PPI) inhibitor of SRPKs, docking blocker of SRPK1 (DBS1), that specifically blocks a conserved substrate docking groove unique to SRPKs. DBS1 is a cell-permeable inhibitor that effectively inhibits the binding and phosphorylation of SRSF1 and subsequently switches VEGF splicing from the proangiogenic to the antiangiogenic isoform. Our findings thus provide a new direction for the development of SRPK inhibitors through targeting a unique PPI site to combat angiogenic diseases.
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http://dx.doi.org/10.1016/j.isci.2021.102423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8102418PMC
May 2021

Determinants of mortality of patients with COVID-19 in Wuhan, China: a case-control study.

Ann Palliat Med 2021 Apr 15;10(4):3937-3950. Epub 2021 Apr 15.

Emergency Department, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Background: Coronavirus disease 2019 (COVID-19) has resulted in an overwhelmed challenge to the healthcare system worldwide.

Methods: A case-control study of COVID-19 patients in Wuhan Third Hospital was conducted. 96 deceased COVID-19 patients and 230 discharged patients were included as the case group and control group, respectively. Demographic, epidemiological, clinical and laboratory variables on admission were collected from electronic medical records. Univariate and multivariate logistic regression were adopted to investigate the independent predictors of mortality. A nomogram was formed for predicting the mortality risk.

Results: The multivariate stepwise logistic model demonstrated that age of 60+ years (OR =4.426, 95% CI: 1.955-10.019), comorbidity of cerebrovascular disease (OR =7.084, 95% CI: 1.545-32.471), white blood cell (WBC) count >9.5×109/L (OR =7.308, 95% CI: 1.650-32.358), platelet count <125×109/L (OR =5.128, 95% CI: 2.157-12.191), aspartate aminotransferase (AST) >40 U/L (OR =2.554, 95% CI: 1.253-5.206), cystatin C >1.1 mg/L (OR =4.132, 95% CI: 2.118-8.059), C reactive protein (CRP) ≥100 mg/L (OR =2.830, 95% CI: 1.311-6.109), creatine kinase isoenzymes (CK-MB) >24 U/L (OR =6.015, 95% CI: 2.119-17.07) and D-dimer >5 µg/L (OR =4.917, 95% CI: 1.619-14.933) were independent predictors of mortality of COVID-19 patients. The nomogram demonstrated a well discriminatory accuracy for mortality prediction with a C-index of 0.903.

Conclusions: The determinants identified may help to determine patients at high risk of death at an early stage and guide the optimal treatment.
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http://dx.doi.org/10.21037/apm-20-2107DOI Listing
April 2021

Assessment of an Exhaled Breath Test Using High-Pressure Photon Ionization Time-of-Flight Mass Spectrometry to Detect Lung Cancer.

JAMA Netw Open 2021 03 1;4(3):e213486. Epub 2021 Mar 1.

Department of Thoracic Surgery, Peking University People's Hospital, Beijing, China.

Importance: Exhaled breath is an attractive option for cancer detection. A sensitive and reliable breath test has the potential to greatly facilitate diagnoses and therapeutic monitoring of lung cancer.

Objective: To investigate whether the breath test is able to detect lung cancer using the highly sensitive high-pressure photon ionization time-of-flight mass spectrometry (HPPI-TOFMS).

Design, Setting, And Participants: This diagnostic study was conducted with a prospective-specimen collection, retrospective-blinded evaluation design. Exhaled breath samples were collected before surgery and detected by HPPI-TOFMS. The detection model was constructed by support vector machine (SVM) algorithm. Patients with pathologically confirmed lung cancer were recruited from Peking University People's Hospital, and healthy adults without pulmonary noncalcified nodules were recruited from Aerospace 731 Hospital. Data analysis was performed from August to October 2020.

Exposures: Breath testing and SVM algorithm.

Main Outcomes And Measures: The detection performance of the breath test was measured by sensitivity, specificity, accuracy, and area under the receiver-operating characteristic curve (AUC).

Results: Exhaled breath samples were from 139 patients with lung cancer and 289 healthy adults, and all breath samples were collected and tested. Of all participants, 228 (53.27%) were women and the mean (SD) age was 57.0 (11.4) years. After clinical outcomes were ascertained, all participants were randomly assigned into the discovery data set (381 participants) and the blinded validation data set (47 participants). The discovery data set was further broken into a training set (286 participants) and a test set (95 participants) to construct and test the detection model. The detection model reached a mean (SD) of 92.97% (4.64%) for sensitivity, 96.68% (2.21%) for specificity, and 95.51% (1.93%) for accuracy in the test set after 500 iterations. In the blinded validation data set (47 participants), the model revealed a sensitivity of 100%, a specificity of 92.86%, an accuracy of 95.74%, and an AUC of 0.9586.

Conclusions And Relevance: This diagnostic study's results suggest that a breath test with HPPI-TOFMS is feasible and accurate for lung cancer detection, which may be useful for future lung cancer screenings.
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http://dx.doi.org/10.1001/jamanetworkopen.2021.3486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8010591PMC
March 2021

Transcriptome sequencing reveals genes involved in cadmium-triggered oxidative stress in the chicken heart.

Poult Sci 2021 Mar 23;100(3):100932. Epub 2021 Jan 23.

Sichuan Animal Science Academy, Chengdu, Sichuan 610066 China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu, Sichuan 610066 China. Electronic address:

As a ubiquitous heavy metal, cadmium (Cd) is highly toxic to various organs. However, the effects and molecular mechanism of Cd toxicity in the chicken heart remain largely unknown. The goal of our study was to investigate the cardiac injury in chickens' exposure to Cd. We detected the levels of oxidative stress-related molecules in the Cd-induced chicken heart, and assessed the histopathological changes by hematoxylin and eosin staining. RNA sequencing was performed to identify differentially expressed mRNAs between the Cd-induced group and control group. The expression of candidate genes involved in oxidative stress was certified by quantitative reverse transcription PCR. Our results showed that the expression of glutathione, peroxidase, and superoxide dismutase was significantly decreased and malondialdehyde was increased in the heart of chickens by Cd induction. The disorderly arranged cardiomyocytes, swelled and enlarged cells, partial cardiomyocyte necrosis, blurred morphological structure, and notable inflammatory cell infiltration were observed in the Cd-induced chicken heart. RNA sequencing identified 23 upregulated and 11 downregulated mRNAs in the heart tissues of the chicken in the Cd-induced group, and functional pathways indicated that they were associated with oxidative stress. Moreover, CREM, DUSP8, and ITGA11 expressions were significantly reduced, whereas LAMA1 expression was induced in heart tissue of chickens by Cd treatment. Overall, our findings revealed that oxidative stress and pathological changes in the chicken heart could be triggered by Cd. The mRNA transcriptional profiles identified differentially expressed genes in the chicken heart by Cd induction, revealing oxidative stress-related key genes and enhancing our understanding of Cd toxicity in the chicken heart.
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http://dx.doi.org/10.1016/j.psj.2020.12.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936198PMC
March 2021

Distribution and source of microplastics in China's second largest reservoir - Danjiangkou Reservoir.

J Environ Sci (China) 2021 Apr 28;102:74-84. Epub 2020 Sep 28.

Brook Byers Institute of Sustainable Systems, School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Fresh water microplastic pollution is of pressing concern globally, but its distribution and sources in reservoirs are poorly documented. Danjiangkou Reservoir is the second largest reservoir in China and is divided into the Han Reservoir and Dan Reservoir. In this work, microplastic abundances and morphological characteristics of the reservoir were investigated. The microplastic abundance of 15 main tributaries of the reservoir was also measured. The vertical distribution (in water column and sediment), horizontal distribution (in Han Reservoir and Dan Reservoir) and source of microplastics were analyzed. Microplastics accumulated in the middle layer of the reservoir, and the size and color of the microplastic particles changed from the surface to the bottom, which implies that surveys of surface water are not enough to determine the microplastic contamination for deep water reservoirs. In the surface water, the microplastic abundance in the Han Reservoir was lower than that in the Dan Reservoir (p < 0.05), but microplastic abundance did not differ significantly in the intermediate and bottom water. Tributaries were one of the main sources of microplastics for Han Reservoir but not for Dan Reservoir. Agricultural cultivation in the hydro-fluctuation belt might be an important source of microplastics in the Dan Reservoir, which should be given additional attention. The results of this study can provide valuable information for developing microplastic sampling strategies in deep water reservoirs. Further studies are recommended to investigate the process through which microplastics in the hydro-fluctuation belt enter the reservoir and the sinking behavior of microplastics in the reservoir.
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http://dx.doi.org/10.1016/j.jes.2020.09.018DOI Listing
April 2021

The predictors and prognosis for unexpected reocclusion after mechanical thrombectomy: a meta-analysis.

Ann Transl Med 2020 Dec;8(23):1566

Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China.

Background: Mechanical thrombectomy (MT) is the cornerstone for treating acute ischemic stroke (AIS) in emergency cases. However, 3-9% of patients display reocclusion in the recanalized vessels within 24 hours after performing MT. This meta-analysis aimed to further identify the predictors and prognosis of unexpected reocclusion after MT.

Methods: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement, we searched several literature databases, including PubMed, Embase, and Cochrane, for publications related to the subject term "thrombectomy" that were published prior to March 2020. Pooled analysis was performed with the fixed-effects model using the Mantel-Haenszel method if the heterogeneity was expected to be available (I≤50%). Otherwise, the random-effects model computed by the DerSimonian-Laird method was used (I>50%). R software (http://www.r-project.org) was used for analysis in this study.

Results: A total of five articles comprising 1,883 patients (126 patients with reocclusion, 1,757 patients without reocclusion) who were confirmed to have AIS and who underwent emergency MT were finally included in this study. The pooled analysis (reocclusion versus non-reocclusion) showed that atrial fibrillation [odds ratio (OR), 0.36; 95% confidence interval (CI), 0.20-0.63], cardiogenic embolism (OR, 0.35; 95% CI, 0.20-0.63), long-term statin use (OR, 0.39; 95% CI, 0.21-0.75), long-term antiplatelet use (OR, 0.53; 95% CI, 0.31-0.92), and target occlusion at middle cerebral artery-M1 (MCA-M1) (OR, 0.39; 95% CI, 0.19-0.77) might prevent reocclusion and longer onset-to-reperfusion time (mean difference, 66.51; 95% CI, 36.66-96.35) might promote reocclusion after MT performance. Furthermore, the clinical outcomes including early neurological deterioration (OR, 4.87; 95% CI, 2.08-11.40), 90-day modified Rankin Scale score ≤2 (OR, 0.28; 95% CI, 0.18-0.45), and 90-day death rate (OR, 1.85; 95% CI, 1.04-3.29) were also associated with reocclusion after MT performance.

Conclusions: Atrial fibrillation, cardiogenic embolism, long-term statin use, long-term antiplatelet use, and target occlusion at MCA-M1 might prevent reocclusion, and longer onset-to-reperfusion time seemed to promote reocclusion after MT. Reocclusion after MT results in a high risk of poor prognosis.
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http://dx.doi.org/10.21037/atm-20-3465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7791239PMC
December 2020

Whole-genome resequencing reveals aberrant autosomal SNPs affect chicken feathering rate.

Anim Biotechnol 2020 Dec 21:1-13. Epub 2020 Dec 21.

Sichuan Animal Science Academy, Chengdu, Sichuan, China.

Previous studies have shown that the feather growth rate of chicks is determined by two alleles located on the sex chromosome Z; however, in chicken production, feathering is usually not consistently controlled by the sex chromosome. To identify whether the feathering rate is related to autosomal inheritance, whole-genome resequencing was performed in eight chickens with slow- and fast-feathering rate. A total of 54,984 autosomal single nucleotide polymorphisms (SNPs) were identified, including 393 and 376 exonic SNPs in slow-feathering and fast-feathering chickens, respectively. Mutated genes were mainly involved in response to stimuli and growth and reproduction processes. Mutated genes related to slow-feathering rate were mainly involved in wingless-type MMTV integration site signaling pathway and mitogen-activated protein kinase signaling pathway, whereas mutated genes associated with fast-feathering rate were primarily enriched in autophagy, calcium signaling pathway, extracellular matrix-receptor interaction, and Focal adhesion processes. Importantly, two SNPs, involved in feather development, were found in the exonic regions of Wnt signaling genes. These results shed new light on the relationship between genetic mutation and feather growth rate from the perspective of autosomal inheritance and may have economic significance in chicken breeding.
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http://dx.doi.org/10.1080/10495398.2020.1846545DOI Listing
December 2020

Impacts of red mud on lignin depolymerization and humic substance formation mediated by laccase-producing bacterial community during composting.

J Hazard Mater 2021 05 18;410:124557. Epub 2020 Nov 18.

School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China; Key Laboratory of Guangxi Biorefinery, Guangxi University, Nanning 530004, China. Electronic address:

The aim of this study was to investigate the impacts of red mud on lignin degradation, humic substance formation and laccase-producing bacterial community in composting to better improve composting performances. The results indicated that the organic matter contents of final compost products in the treatment group with red mud (T) decreased by 25.74%, which was more than the control group without red mud (CK) (12.09%). The final lignin degradation ratio and humic substance concentration of the T were 18.67% and 22.80% higher than that of the CK, respectively. The final C/N values of compost in the CK and T were 11.32 and 10.66, respectively, which were both less than 15, suggesting that compost reached maturity. Redundancy analysis showed that temperature was the main factors driving the variation of laccase-producing bacterial community. Pearson analysis suggested that Pseudomonas, Phenylobacterium, and Caulobacter were the most significantly correlated with lignin degradation and humification in the T.
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http://dx.doi.org/10.1016/j.jhazmat.2020.124557DOI Listing
May 2021

Cognitive frailty as a predictor of adverse outcomes among older adults: A systematic review and meta-analysis.

Brain Behav 2021 01 6;11(1):e01926. Epub 2020 Nov 6.

Nursing School, Nanjing University of Chinese Medicine, Nanjing, China.

Objective: A systematic review and meta-analysis basing on the prospective cohort studies were conducted to explore the risk of all-cause mortality and dementia in cognitively frail older adults compared to robust older adults and to determine whether it was a predictor of adverse outcomes.

Methods: Pubmed, Web of Science, The Cochrane Library, EMBASE, and CINAHL databases were searched to retrieve studies on adverse outcomes of cognitive frailty. Two reviewers independently screened the literature, extracted data, and assessed the risk of bias of the included studies. Stata 15.0 Software was used to perform the meta-analysis. The all-cause mortality and dementia were observed to be the primary outcomes, while the other data were considered as the secondary outcome.

Results: A total of 14 studies were included in qualitative analysis and 12 studies were included in the meta-analysis, with low risk of bias and moderate to good methodological quality. The results showed that cognitive frailty in older people had a higher risk of all-cause mortality [HR = 1.93, 95%CI (1.67, 2.23), p < .001] and dementia [HR = 3.66, 95%CI (2.86, 4.70) as compared with robust. The subgroup analysis showed that the assessment tools were the main source of heterogeneity.

Conclusion: In older adults living in communities, the cognitive frailty was found to be a significant predictor of all-cause mortality and dementia. Nonetheless, cognitive frailty was found to be a better predictor of all-cause mortality and dementia than just frailty.
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http://dx.doi.org/10.1002/brb3.1926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821586PMC
January 2021

Hydrochemical composition, distribution, and sources of typical organic pollutants and metals in Lake Bangong Co, Tibet.

Environ Sci Pollut Res Int 2021 Feb 6;28(8):9877-9888. Epub 2020 Nov 6.

Brook Byers Institute of Sustainable Systems, School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.

Lake Bangong Co is a special lake in western Tibet, with characteristics of increased salinity from the eastern area to the western area. Due to its remote location and poor environmental conditions, there are few background data on the water environment of this lake. In this study, the water chemical composition of Lake Bangong Co was studied, and the concentration levels, distribution characteristics, and pollution sources of polycyclic aromatic hydrocarbons (PAHs), phthalic acid esters (PAEs), and metals (As, Pb, Cr, Mn, Cu, Cd, Ni, and Zn) were investigated. The hydrochemical characteristics of the lake showed significant spatial differences. Conductivity, salinity, degree of mineralization, total hardness, Cl, and SO generally increased from the eastern part to the western part. Most water quality parameters met the class III standards of the Chinese surface water standards; however, the Cl and SO concentrations in the western part exceeded the surface water standard limits. ΣPAH and ΣPAE concentrations in lake water have no significant relationship with hydrochemical parameters. Among the 16 target PAHs, 4 PAH monomers with a (5 + 6)-ring were not detected in the lake water. The main sources of PAHs included emissions from biomass combustion, petroleum volatilization, and automobile exhaust. Six PAE monomers were detected at all sampling sites with relatively low concentrations, and di-2-ethylhexyl phthalate (DEHP) and di-n-butyl phthalate (DBP) were the main pollutants. The main source of PAEs was domestic waste, which might be related to increasing human activities in this area recently. In general, the concentrations of metals in the water of Lake Bangong Co were lower than those in the regions affected by anthropogenic activities except As. The results of PCA showed that As, Cu, and Cr mainly originated from natural sources; Pb, Mn, and Cr came from both natural and anthropogenic sources; and Cd was highly likely from anthropogenic sources.
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http://dx.doi.org/10.1007/s11356-020-11449-wDOI Listing
February 2021

PendoTMBase: A Database for Plant Endogenous Target Mimics.

Interdiscip Sci 2020 Dec 30;12(4):526-529. Epub 2020 Sep 30.

College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.

With fast-evolving next-generation sequencing technology, a great amount of plant genome and transcriptome data are becoming available. Due to the availability of mature microRNA (miRNA) sequence information from the miRBase (release 21) database, it is possible to predict endogenous target mimics (eTMs) in plant by searching seed-matched target sites. We identified a total of 2669 non-redundant eTM records in 43 plant species to create a specialized web-based database platform. The platform is named PendoTMBase, which can provide details of the eTMs. Predicted pairing structure between eTMs and their target miRNA, expression levels of eTMs pairs and associated GO annotations are also stored in the database. With evaluations performed in silico, we have found that the eTMs are representative and fit for genetic studies and high value-added plants breeding. The platform also provides a function of predicting novel eTMs based on the miRNA sequences submitted by users.
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http://dx.doi.org/10.1007/s12539-020-00396-2DOI Listing
December 2020

Influence of tissue fixation on depth-resolved birefringence of oral cavity tissue samples.

J Biomed Opt 2020 09;25(9)

University of Surrey, Surrey Biophotonics, School of Physics, Guilford, United Kingdom.

Significance: To advance our understanding of the contrast observed when imaging with polarization-sensitive optical coherence tomography (PS-OCT) and its correlation with oral cancerous pathologies, a detailed comparison with histology provided via ex vivo fixed tissue is required. The effects of tissue fixation, however, on such polarization-based contrast have not yet been investigated.

Aim: A study was performed to assess the impact of tissue fixation on depth-resolved (i.e., local) birefringence measured with PS-OCT.

Approach: A PS-OCT system based on depth-encoded polarization multiplexing and polarization-diverse detection was used to measure the Jones matrix of a sample. A wide variety of ex vivo samples were measured freshly after excision and 24 h after fixation, consistent with standard pathology. Some samples were also measured 48 h after fixation.

Results: The tissue fixation does not diminish the birefringence contrast. Statistically significant changes were observed in 11 out of 12 samples; these changes represented an increase in contrast, overall, by 11% on average.

Conclusions: We conclude that the fixed samples are suitable for studies seeking a deeper understanding of birefringence contrast in oral tissue pathology. The enhancement of contrast removes the need to image immediately postexcision and will facilitate future investigations with PS-OCT and other advanced polarization-sensitive microscopy methods, such as mapping of the local optic axis with PS-OCT and PS-optical coherence microscopy.
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http://dx.doi.org/10.1117/1.JBO.25.9.096003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7481436PMC
September 2020

In vivo imaging of the depth-resolved optic axis of birefringence in human skin.

Opt Lett 2020 Sep;45(17):4919-4922

Recent progress has enabled the reconstruction of the local (i.e., depth-resolved) optic axis (OAx) of biological tissue from measurements made with polarization-sensitive optical coherence tomography (PS-OCT). Here we demonstrate local OAx imaging in healthy human skin in vivo. The images reveal dense, weaving patterns that are imperceptible in OCT intensity tomograms or conventional PS-OCT metrics and that suggest a mesh-like tissue organization, consistent with the morphology of dermal collagen. Using co-registered polarization-sensitive optical coherence microscopy, we furthermore investigated the impact of spatial resolution on the recovered OAx patterns and confirmed their consistency. OAx orientation as a contrast mechanism merits further exploration for applications in dermatology.
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http://dx.doi.org/10.1364/OL.400855DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7535952PMC
September 2020

Simultaneous leaching of multiple heavy metals from a soil column by extracellular polymeric substances of Aspergillus tubingensis F12.

Chemosphere 2021 Jan 5;263:127883. Epub 2020 Aug 5.

College of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China; Key Laboratory of Guangxi Biorefinery, Guangxi University, Nanning, 530003, China. Electronic address:

The use of the biological agents for leaching heavy metals from contaminated soils is a very promising method that is both efficient and eco-friendly. In this study, a fungus Aspergillus tubingensis F12 was reported to possess a strong adsorption capacity for various heavy metal ions and shown to adsorb 90.8% Pb, 68.4% Zn, 64.5% Cr, 13.1% Cu, 12.9% Ni, and 6.9% Cd in aqueous solution. As extracellular polymeric substance (EPS) was found to play a leading role in the adsorption of metal ions, we applied EPS as a leaching agent to simultaneously remove six metals from soil in a column leaching experiment. The flow rate, initial solution pH, initial EPS concentration, and ionic strength were investigated using response surface methodology. The minimum and maximum metal leaching capacities were determined to be 0.089 mg/g and 3.703 mg/g, respectively. Verified by Fourier transform infrared spectroscopy, scanning electron microscope energy dispersive X-ray spectroscopy, and X-ray photoelectron spectroscopy, we made the preliminary deductions that ion exchange determines the leaching capacity limit and that biosorption plays a large role in reaching that limit. Additionally, the redox behaviour of Cu produced more carboxyl groups, which increased the adsorption of heavy metals. The ecological impact of this method was also examined; we found that the influences of leaching with EPS on soil properties and microbial community structure were slight. Therefore, the reported leaching process might have application prospects for metal removal from soil.
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http://dx.doi.org/10.1016/j.chemosphere.2020.127883DOI Listing
January 2021

Lab in hydrogel portable kit: On-site monitoring of oxalate.

Biosens Bioelectron 2020 Nov 9;167:112457. Epub 2020 Aug 9.

State Key Laboratory of Integrated Optoelectronics, Jilin Key Laboratory on Advanced Gas Sensor, College of Electronic Science and Engineering, Jilin University, Changchun 130012, People's Republic of China.

Oxalate is commonly employed as adjuvant of pesticide agent, causing renal injury of human even in trace residues. Despite the great achievements of the existing point-of-care testing (POCT) technology, accurate on-site screening of oxalate remains a tricky issue. To this aim, we proposed a "lab in a tube" platform which integrated portable hydrogel kit with smartphone for real-time monitoring of oxalate to achieve quantitatively precise analysis. In this work, a stimuli-responsive hydrogel-based kit was constructed via embedding manganese dioxide (MnO) nanosheets into sodium alginate hydrogel system. Based on the intrinsic oxidase-like activity, MnO nanosheets-based nanozyme triggered color reaction by introducing a common sensing probe 3,3',5,5'-tetramethylbenzidine. Meanwhile, the presence of oxalate would decompose MnO nanosheets, inducing the decrease of nanozyme activity, which resulted in the color response of portable kit. Coupling with ImageJ software, the image information of kit captured via smartphone could be transduced into the hue intensity, which provided a directly quantitative tool to detect oxalate with a detection limit of 8.0 μmol L. This portable smartphone biosensor was successfully applied for screening urine sample within 10 min for high-throughput analysis (twelve samples) without the need for any advanced analytical instruments. Based on the merits of simple operation, cost-efficiency, and good selectivity, the availability of the miniaturized biosensor platform for POCT will achieve the requirements of routine screening and disease prevention.
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http://dx.doi.org/10.1016/j.bios.2020.112457DOI Listing
November 2020

Preparation of PVDF/CdS/BiWO/ZnO hybrid membrane with enhanced visible-light photocatalytic activity for degrading nitrite in water.

Environ Res 2020 12 15;191:110036. Epub 2020 Aug 15.

School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi Province, 530004, China; Key Laboratory of Guangxi Biorefinery, Guangxi University, Nanning, GuangxiProvince, 530003, China. Electronic address:

In this work, a visible light-driven ternary heterojunction photocatalyst, CdS/BiWO/ZnO, was synthesized using hydrothermal, ultrasonic dispersion, and deposition precipitation methods. The results show that photocatalysts with flower-like heterostructures were obtained, which could efficiently separate electron-hole pairs, and the photocatalytic activity was thereby significantly enhanced. Furthermore, CdS/BiWO/ZnO and polyvinylidene fluoride (PVDF) were used to fabricate hybrid membranes via a phase-conversion method. The samples were characterized using SEM, TEM, EDX, XRD, DRS, XPS, PL, and N adsorption-desorption isotherms, and the transient photocurrent response. The photocatalytic activity of the hybrid membrane was evaluated, and 92.58% of the nitrite was converted into non-toxic substances within 4 h under simulated sunlight irradiation. This result indicated that the photocatalyst exhibited a good photocatalytic activity after immobilization. The possible mechanism was elucidated by studying the product during the photocatalytic degradation, and the effects of different pH values, electron scavengers, and hole scavengers on the photocatalytic performance were further investigated.
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http://dx.doi.org/10.1016/j.envres.2020.110036DOI Listing
December 2020

TumorGAN: A Multi-Modal Data Augmentation Framework for Brain Tumor Segmentation.

Sensors (Basel) 2020 Jul 28;20(15). Epub 2020 Jul 28.

College of Information Science and Engineering, Ocean University of China, Qingdao 266100, China.

The high human labor demand involved in collecting paired medical imaging data severely impedes the application of deep learning methods to medical image processing tasks such as tumor segmentation. The situation is further worsened when collecting multi-modal image pairs. However, this issue can be resolved through the help of generative adversarial networks, which can be used to generate realistic images. In this work, we propose a novel framework, named TumorGAN, to generate image segmentation pairs based on unpaired adversarial training. To improve the quality of the generated images, we introduce a regional perceptual loss to enhance the performance of the discriminator. We also develop a regional L1 loss to constrain the color of the imaged brain tissue. Finally, we verify the performance of TumorGAN on a public brain tumor data set, BraTS 2017. The experimental results demonstrate that the synthetic data pairs generated by our proposed method can practically improve tumor segmentation performance when applied to segmentation network training.
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http://dx.doi.org/10.3390/s20154203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7435374PMC
July 2020

Bioavailability of l-lysine sulfate relative to l-lysine HCl for growing-finishing pigs.

Transl Anim Sci 2019 Jul 27;3(4):1254-1262. Epub 2019 Jun 27.

Department of Animal Science, Iowa State University, Ames, IA.

The objective of this study was to evaluate the relative bioavailability (RBV) of l-Lys sulfate in comparison to l-Lys HCl based on the growth performance response from approximately 26 to 48 kg and from approximately 68 to 114 kg. The effect of Lys source on blood urea nitrogen (BUN), digestibility of dry matter (DM) and sulfur (S), as well as carcass characteristics was determined. A total of 280 growing pigs (25.9 ± 0.25 kg BW) were randomly assigned to one of seven dietary treatments in 56 pens, with five pigs per pen. The diets included a Lys-deficient basal diet (65% of requirement) and the basal diet supplemented with three graded levels of Lys (75%, 85%, and 95% of requirement), as either l-Lys HCl (78.8% Lys purity) or l-Lys sulfate (54.6% Lys purity). The experiment lasted for 112 d, with four dietary phases: Phase 1 lasted for 4 wk (BW: 25.9 to 47.5 kg), Phase 2 lasted for 3 wk (common commercial diet as washout period), Phase 3 lasted for 5 wk (BW: 67.5 to 98.2 kg), and Phase 4 lasted for 3 or 4 wk to reach an average market weight of 114.2 kg. Fresh fecal samples of pigs fed the highest levels of Lys (both Lys sources) were collected on 7 to 10 days after the beginning of Phase 3 for digestibility assay. Blood samples were collected on day 21 and day 81 to determine BUN. Carcass data were collected at a commercial packing plant. Data were analyzed using PROC GLM of SAS (9.4) according to a completely randomized design with pen as the experimental unit. The RBV of l-Lys sulfate was determined using the multiple regression slope-ratio method. Increasing levels of Lys, independent of source, increased ( < 0.05) BW, ADG, and feed efficiency during Phases 1, 3, and 4; market BW increased linearly ( < 0.01) and backfat and BUN decreased linearly ( < 0.01). Lysine source had no impact on growth performance, carcass characteristics, BUN, or digestibility of S and DM. The RBV of l-Lys sulfate compared with l-Lys HCl was also not different based upon ADG or G:F during Phase 1, 3, or 4. These data suggest that the bioavailability of Lys in l-Lys sulfate and l-Lys HCl is at least equivalent for growing-finishing pigs.
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http://dx.doi.org/10.1093/tas/txz094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7200400PMC
July 2019

The role of glia in protein aggregation.

Neurobiol Dis 2020 09 12;143:105015. Epub 2020 Jul 12.

Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:

Protein aggregation diseases involve intracellular accumulation or extracellular deposition of certain protein species in neuronal or glial cells, leading to neurodegeneration and shortened lifespan. Prime examples include Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and Huntington's disease (HD), which are affected by overlapping or specific aggregation-prone proteins. Mounting evidence suggests that dysfunctional glial cells may be major drivers for some diseases, and when they are not causal factors, they could still significantly exacerbate or alleviate disease progression by playing a plethora of detrimental or beneficial roles. Here we review the diverse functions performed by glial cells in a variety of protein aggregation diseases, highlighting the complexity of the issue and the interconnected relationships between these multifaceted effects.
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http://dx.doi.org/10.1016/j.nbd.2020.105015DOI Listing
September 2020

Overseeing Memory Circuits by NFIA: New Face In Astrocytes.

Authors:
Qingyun Li

Neuron 2020 06;106(6):878-880

Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA. Electronic address:

Astrocytes are heterogeneous controlling numerous aspects of brain function. In this issue of Neuron, Huang et al. (2020) uncover a novel role of NFIA, which regulates unique properties of adult hippocampal astrocytes via region-specific DNA binding, thereby modulating the plasticity of local circuits.
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http://dx.doi.org/10.1016/j.neuron.2020.05.027DOI Listing
June 2020

Dietary Soluble and Insoluble Fiber With or Without Enzymes Altered the Intestinal Microbiota in Weaned Pigs Challenged With Enterotoxigenic F18.

Front Microbiol 2020 27;11:1110. Epub 2020 May 27.

Department of Animal Science, Iowa State University, Ames, IA, United States.

Post-weaning diarrhea caused by enterotoxigenic (ETEC) causes significant economic losses for pig producers. This study was to test the hypotheses that an ETEC challenge disrupts intestinal microbial homeostasis and the inclusion of dietary soluble (10% sugar beet pulp) or insoluble fiber (15% corn distillers dried grains with solubles) with or without exogenous carbohydrases will protect or restore the gut microbial homeostasis in weaned pigs. Sixty crossbred piglets (6.9 ± 0.1 kg) were blocked by body weight and randomly assigned to one of six treatments ( = 10), including a non-challenged control (NC), ETEC F18-challenged positive control (PC), ETEC-challenged soluble fiber without (SF-) or with carbohydrases (SF+), and ETEC-challenged insoluble fiber without (IF-) or with carbohydrases (IF+). Pigs were housed individually and orally received either ETEC inoculum or PBS-sham inoculum on day 7 post-weaning. Intestinal contents were collected on day 14 or 15. The V4 region of the bacterial 16S rRNA was amplified and sequenced. High-quality reads (total 6,671,739) were selected and clustered into 3,330 OTUs. No differences were observed in α-diversity among treatments. The ileal microbiota in NC and PC had modest separation in the weighted PCoA plot; the microbial structures were slightly altered by SF+ and IF- compared with PC. The PC increased ileal ( < 0.01) and numerically decreased compared to NC. Predicted functional pathways enriched in the ileal microbiota of PC pigs indicated enhanced activity of Gram-negative bacteria, in agreement with increased . The SF+ tended to decrease ( < 0.10) ileal compared to PC. Greater abundance of ileal , , and and colonic were observed in SF- and SF+ than PC ( < 0.05). Pigs fed IF + had greater and than PC pigs ( < 0.05). The ETEC challenge reduced total volatile fatty acid (VFA) compared with NC ( < 0.05). The SF+ tended to increase ( < 0.10) and SF- significantly increased ( < 0.05) colonic total VFA compared with PC. Collectively, ETEC challenge disrupted gut microbial homeostasis and impaired microbial fermentation capacity. Soluble fiber improved VFA production. Dietary fiber and carbohydrases altered microbiota composition to maintain or restore microbial homeostasis.
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http://dx.doi.org/10.3389/fmicb.2020.01110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267687PMC
May 2020

How Support of Early Career Researchers Can Reset Science in the Post-COVID19 World.

Cell 2020 06 12;181(7):1445-1449. Epub 2020 Jun 12.

Department of Neurosurgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA.

The COVID19 crisis has magnified the issues plaguing academic science, but it has also provided the scientific establishment with an unprecedented opportunity to reset. Shoring up the foundation of academic science will require a concerted effort between funding agencies, universities, and the public to rethink how we support scientists, with a special emphasis on early career researchers.
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http://dx.doi.org/10.1016/j.cell.2020.05.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291965PMC
June 2020

Identification of long noncoding RNAs involved in adaptability to chronic hypoxic by whole transcriptome sequencing.

3 Biotech 2020 Jun 27;10(6):269. Epub 2020 May 27.

Sichuan Animal Science Academy, 7# Niusha Road, Chengdu, 610066 Sichuan China.

Hypoxia affects the physiology of cells and organisms; however, the mechanisms associated with hypoxia adaptation remain unknown in Tibetan chickens. In this study, we aimed to identify long noncoding RNAs (lncRNAs) involved in hypoxia adaptation in Tibetan chickens and Daheng broilers, to provide insights into the mechanisms underlying hypoxia induction. RNA sequencing results revealed that a total of 5504 lncRNAs and 16,779 microRNAs were differentially expressed in four Tibetan chickens and four Daheng broilers; 70 lncRNAs were up-regulated and 113 lncRNAs were down-regulated in the Tibetan chickens compared to the expression levels in the Daheng broilers. The differentially expressed lncRNAs (DElncRNAs) were enriched in the following Gene ontology terms: protein complex localization, small-molecule metabolic process, and RNA splicing. Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DElncRNAs were mainly enriched in pathways that regulate cell junctions and intercellular spaces and oxygen or energy metabolism, mainly involved in hypoxic adaption. Moreover, a predicted ceRNA network with five DElncRNAs interacted with three miRNAs that acted on 42 pathways through 19 target genes. Quantitative real-time polymerase chain reaction was used to verify that the expression levels of ENSGALG00000008047, ENSGALG00000050044, and ENSGALG00000053982 were significantly lower in Tibetan chickens than in the Daheng broilers, consistent with the RNA sequencing results. We obtained lncRNA expression profiles for the heart tissue of Tibetan chickens for the first time and have provided novel data that may aid research on biological adaptation to hypoxic stress.
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http://dx.doi.org/10.1007/s13205-020-02272-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253556PMC
June 2020

Jones matrix-based speckle-decorrelation angiography using polarization-sensitive optical coherence tomography.

J Biophotonics 2020 09 23;13(9):e202000007. Epub 2020 Jun 23.

Surrey Biophotonics, Advanced Technology Institute and School of Biosciences and Medicine, University of Surrey, Surrey, UK.

We show that polarization-sensitive optical coherence tomography angiography (PS-OCTA) based on full Jones matrix assessment of speckle decorrelation offers improved contrast and depth of vessel imaging over conventional OCTA. We determine how best to combine the individual Jones matrix elements and compare the resulting image quality to that of a conventional OCT scanner by co-locating and imaging the same skin locations with closely matched scanning setups. Vessel projection images from finger and forearm skin demonstrate the benefits of Jones matrix-based PS-OCTA. Our study provides a promising starting point and a useful reference for future pre-clinical and clinical applications of Jones matrix-based PS-OCTA.
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http://dx.doi.org/10.1002/jbio.202000007DOI Listing
September 2020

Highly selective and sensitive online measurement of trace exhaled HCN by acetone-assisted negative photoionization time-of-flight mass spectrometry with in-source CID.

Anal Chim Acta 2020 May 18;1111:31-39. Epub 2020 Mar 18.

Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning, 116023, People's Republic of China. Electronic address:

Exhaled hydrogen cyanide (HCN) has been extensively investigated as a promising biomarker of the presence of Pseudomonas aeruginosa in the airways of patients with cystic fibrosis (CF) disease. Its concentration profile for exhalation can provide useful information for medical disease diagnosis and therapeutic procedures. However, the complexity of breath gas, like high humidity, carbon dioxide (CO) and trace organic compounds, usually leads to quantitative error, poor selectivity and sensitivity for HCN with some of existing analytical techniques. In this work, acetone-assisted negative photoionization (AANP) based on a vacuum ultraviolet (VUV) lamp with a time-of- flight mass spectrometer (AANP-TOFMS) was firstly proposed for online measurement of trace HCN in human breath. In-source collision-induced dissociation (CID) was adopted for sensitivity improvement and the signal response of the characteristic ion CN (m/z 26) was improved by about 24-fold. For accurate and reliable analysis of the exhaled HCN, matrix influences in the human breath including humidity and CO were investigated, respectively. A Nafion tube was used for online dehumidification of breath samples. Matrix-adapted calibration in the concentration range of 0.5-50 ppbv with satisfactory dynamic linearity and repeatability was obtained. The limit of quantitation (LOQ) for HCN at 0.5 ppbv was achieved in the presence of 100% relative humidity and 4% CO. Finally, the method was successfully applied for online determination of human mouth- and nose-exhaled HCN, and the nose-exhaled HCN were proved to be reliable for assessing systemic HCN levels for individuals. The results are encouraging and highlight the potential of AANP-TOFMS with in-source CID as a selective, accurate, sensitive and noninvasive technique for determination of the exhaled HCN for CF clinical diagnosis and HCN poisoning assessment.
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http://dx.doi.org/10.1016/j.aca.2020.03.035DOI Listing
May 2020
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