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Chen Y, Wang Y, Tao Q, Lu P, Meng F, Zhuang L, Qiao S, Zhang Y, Luo B, Liu Y, Peng G. Diagnostic value of isolated plasma biomarkers and its combination in neurodegenerative dementias: A multicenter cohort study. Clin Chim Acta 2024; 558:118784. [PMID: 38588788 DOI: 10.1016/j.cca.2024.118784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Plasma amyloid-β (Aβ), phosphorylated tau-181 (p-tau181), neurofilament light (NfL) and glial fibrillary acidic protein (GFAP) potentially aid in the diagnosis of neurodegenerative dementias. We aim to conduct a comprehensive comparison between different biomarkers and their combination, which is lacking, in a multicenter Chinese dementia cohort consisting of Alzheimer's disease (AD), frontotemporal dementia (FTD), and progressive supranuclear palsy (PSP). METHODS We enrolled 92 demented patients [64 AD, 16 FTD, and 12 PSP with dementia] and 20 healthy controls (HC). Their plasma Αβ, p-tau181, NfL, and GFAP were detected by highly sensitive-single molecule immunoassays. Αβ pathology in patients was measured by cerebrospinal fluid or/and amyloid positron emission tomography. RESULTS All plasma biomarkers tested were significantly altered in dementia patients compared with HC, especially Aβ42/Aβ40 and NfL showed significant performance in distinguishing AD from HC. A combination of plasma Aβ42/Aβ40, p-tau181, NfL, and GFAP could discriminate FTD or PSP well from HC and was able to distinguish AD and non-AD (FTD/PSP). CONCLUSIONS Our results confirmed the diagnostic performance of individual plasma biomarkers Aβ42/Aβ40, p-tau181, NfL, and GFAP in Chinese dementia patients and noted that a combination of these biomarkers may be more accurate in identifying FTD/PSP patients and distinguishing AD from non-AD dementia.
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Affiliation(s)
- Yi Chen
- Department of Neurology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunyun Wang
- Department of Neurology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; Department of Neurology, Shengzhou People's Hospital, Shaoxing, China
| | - Qingqing Tao
- Department of Neurology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peilin Lu
- Department of Neurology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fanxia Meng
- Department of Neurology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liying Zhuang
- Department of Neurology, the Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Song Qiao
- Department of Neurology, the Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Zhang
- Department of Geriatrics, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Benyan Luo
- Department of Neurology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yang Liu
- Department of Neurology, Saarland University, KirrbergerstraBe Geb., 90D-66421 Homburg/Sarr, German.
| | - Guoping Peng
- Department of Neurology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Kujawska A, Bromage S, Simoes JA, Zupkauskienė J, McMahon N, Zalewski P, Kujawski S. The impact of dietary supplements on blood pressure in older adults: A network meta-analysis of randomized controlled trials. Heliyon 2024; 10:e25615. [PMID: 38380006 PMCID: PMC10877265 DOI: 10.1016/j.heliyon.2024.e25615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/27/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
Purpose The prevalence of hypertension (HTN) increases with age and there is a need for effective, evidence-based treatments for HTN among older adults. The objective of this study was to perform a network meta-analysis to evaluate the effectiveness of different forms of nutritional supplementation on reducing blood pressure in older adults. Methods A systematic review using PubMed and Clinical Key was performed to identify randomized controlled trials (RCTs) evaluating the effects of dietary supplements on blood pressure in adults older than 65 years of age. Network meta-analysis (NMA) was used to compare and rank the effects of different supplements on systolic (sBP), diastolic (dBP), and mean (mBP) blood pressure. Supplements were ranked according to P score. Meta-regressions were conducted to examine whether treatment effects were moderated by baseline BP and supplementation duration. Findings We identified 144 relevant studies in the literature, twelve of which met criteria for inclusion in NMA. The included studies were published between 2003 and 2022. In reducing sBP, docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), inorganic nitrates, tart cherry juice, and vitamin D supplementation were more effective than placebo, and the effect of tart cherry juice outranked that of vitamin D, vitamin E, and vitamin K2. In reducing dBP, inorganic nitrates, DHA and EPA, protein, resveratrol, and vitamin D supplementation were more effective than placebo, and the effect of resveratrol outranked that of tart cherry juice, vitamin D, vitamin E, and vitamin K2. However, the effects of tart cherry juice on sBP and resveratrol on dPB were smaller than the pooled effect of placebo, and none of the pairwise differences between the effects of examined supplements were statistically significant. Caution is needed when interpreting these results given concerns about the risk of bias assessed in seven of the twelve studies included in this analysis.
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Affiliation(s)
- Agnieszka Kujawska
- Department of Exercise Physiology and Functional Anatomy, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Toruń, Świętojańska 20, 85-077, Bydgoszcz, Poland
| | - Sabri Bromage
- Institute of Nutrition, Mahidol University, Salaya, Thailand
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Jose Augusto Simoes
- Department of Medical Sciences, University of Beira Interior, 6200-506, Covilha, Portugal
| | - Jūratė Zupkauskienė
- Clinic of Cardiac and Vascular Diseases, Vilnius University, 08661, Vilnius, Lithuania
| | - Nicholas McMahon
- School of Human Movement and Nutrition Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - Paweł Zalewski
- Department of Exercise Physiology and Functional Anatomy, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Toruń, Świętojańska 20, 85-077, Bydgoszcz, Poland
- Department of Experimental and Clinical Physiology, Laboratory of Centre for Preclinical Research, Warsaw Medical University, 1b Banacha Street, 02-097, Warsaw, Poland
| | - Sławomir Kujawski
- Department of Exercise Physiology and Functional Anatomy, Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Toruń, Świętojańska 20, 85-077, Bydgoszcz, Poland
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3
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Zhou Y, Liu Z. Saliva biomarkers in oral disease. Clin Chim Acta 2023; 548:117503. [PMID: 37536520 DOI: 10.1016/j.cca.2023.117503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Saliva is a versatile biofluid that contains a wide variety of biomarkers reflecting both physiologic and pathophysiologic states. Saliva collection is noninvasive and highly applicable for tests requiring serial sampling. Furthermore, advances in test accuracy, sensitivity and precision for saliva has improved diagnostic performance as well as the identification of novel markers especially in oral disease processes. These include dental caries, periodontitis, oral squamous cell carcinoma (OSCC) and Sjögren's syndrome (SS). Numerous growth factors, enzymes, interleukins and cytokines have been identified and are the subject of much research investigation. This review highlights current procedures for successful determination of saliva biomarkers including preanalytical factors associated with sampling, storage and pretreatment as well as subsequent analysis. Moreover, it provides an overview of the diagnostic applications of these salivary biomarkers in common oral diseases.
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Affiliation(s)
- Yuehong Zhou
- Wenzhou Medical University Renji College, Wenzhou, China
| | - Zhenqi Liu
- Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Berska J, Bugajska J, Sztefko K. The accuracy of serum osmolarity calculation in small children. J Med Biochem 2023; 42:67-77. [PMID: 36819138 PMCID: PMC9920940 DOI: 10.5937/jomb0-37490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/18/2022] [Indexed: 11/02/2022] Open
Abstract
Background Serum osmolality can be measured (Omeas) or calculated (Ocal). Many formulas for Ocal have been already published, but data regarding the most accurate equation in small babies is not available. Thus, we aim to compare Omeas and Ocal obtained by different formulas in newborns and small children. Methods The study included 280 serum samples taken from children, from the first day of life to 2 years (mean age 8.2 ± 7.6 months) treated in the University Children's Hospital in Krakow. The serum osmolality was measured by osmometer and calculated by 8 common formulas. Results The mean value of Omeas (2 8 5 .8 ± 5 .1 mOsm/kgH2O) was significantly different as compared to the mean values of Ocal (p< 0.01) for all formulas, except Ocal obtained by the formula: 1.86*(N a + K) +1.15*Glu + Urea + 14. According to Bland-Altman analysis, this formula showed the best performance for estimating osmolality. In children under 3 months of life Passing-Bablok regression indicated both systematic and proportional error for results obtained by each formula compared to the measured values. Conclusions To calculate osmolarity in children aged between 3 months and 2 years old the following equation: 1 .86*(N a + K) + 1.1 5*G lu+ U rea+ 14 might be used, whereas serum osmolality in children up to 3 month of life should be measured.
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Affiliation(s)
- Joanna Berska
- Jagiellonian University College of Medicine, Institute of Pediatrics, Clinical Biochemistry Department, Krakow, Poland
| | - Jolanta Bugajska
- Jagiellonian University College of Medicine, Institute of Pediatrics, Clinical Biochemistry Department, Krakow, Poland
| | - Krystyna Sztefko
- Jagiellonian University College of Medicine, Institute of Pediatrics, Clinical Biochemistry Department, Krakow, Poland
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Sen Ding S, Xiao Li M, Xiang Y, Tang J, Zhang Q, Huang M, Hui Zhao X, Wang J, Mei Li C. Synergistic effect-mediated fluorescence switching of nitrogen-doped carbon dots for visual detection of alkaline phosphatase. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Hatipoğlu Ö, Önsüren AS, Hatipoğlu FP, Kurt A. Caries-related salivary parameters and oral microbial flora in patients with type 1 diabetes: A meta-analysis. Diabetes Metab Res Rev 2022; 38:e3527. [PMID: 35289060 DOI: 10.1002/dmrr.3527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/01/2022] [Accepted: 02/24/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVES This study aimed to conduct a meta-analysis by synthesising the outcomes of studies that investigated the relationship between type 1 diabetes (T1D) and salivary flow rate (SFR), salivary pH (SpH), salivary buffer capacity (SBC), streptococcus Mutans (SM), and lactobacillus (LB) counts. MATERIAL AND METHODS The PRISMA statement guide was followed for the meta-analysis. Electronic databases were searched, and study selection and data collection processes were performed. The risks of bias in individual studies and across studies were assessed. Mean differences (MD) and Odds Ratio (OR) were used to measure the effect estimates in the comparisons. RESULTS 29 studies were included in the qualitative and quantitative syntheses. Significantly higher SFR (MD = -0.22, CI: -0.26, -0.18; p < 0.001) and SpH (MD = -0.59, CI: -0.81, -0.36; p < 0.001) were observed in the healthy individuals than T1D individuals. No significant difference was observed among groups in terms of SBC (MD = 0.10, CI: -0.46,0.66; p = 0.73). An increased odds ratio of SM counts were observed regarding the T1D (OR = 3.09, 95% CI: 1.16, 8.20; p = 0.02). No association was found between LB counts and T1D (OR = 2.15, 95% CI: 0.38, 11.98; p = 0.38). CONCLUSIONS Subjects with T1D have a significantly lesser SFR and SpH than healthy individuals. But no significant difference is available in terms of SBC. Lower SM counts were observed in individuals with T1D, while no association was observed regarding LB counts. The tendency to dental caries is more likely in subjects with T1D due to lower SFR, SpH, and higher SM.
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Affiliation(s)
- Ömer Hatipoğlu
- Department of Restorative Dentistry, Niğde Ömer Halisdemir University, Niğde, Turkey
| | | | | | - Ayça Kurt
- Department of Pediatric Dentistry, Recep Tayyip Erdoğan University, Rize, Turkey
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Almofti N, Ballesteros-Gómez A, Rubio S, Girela-López E. Analysis of conventional and nonconventional forensic specimens in drug-facilitated sexual assault by liquid chromatography and tandem mass spectrometry. Talanta 2022; 250:123713. [PMID: 35779361 DOI: 10.1016/j.talanta.2022.123713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/22/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
The incidence of drug-facilitated sexual assault (DFSA) has dramatically increased in the last decades. Forensic analytical scientists continuously seek new methods and specimens to prove the incidence of intoxication for the judiciary system. Factors influencing sample selection include the ease of obtaining the samples and the window of detection of the drugs, among others. Both conventional (blood, urine) and non-conventional specimens (hair, nails, fluids) have been proposed as suitable in DFSA cases. Reported sample treatments include a variety of liquid-liquid and solid-phase extraction as well as dilute-and-shoot procedures and microextraction techniques. Regarding analysis, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) has emerged as the preferred confirmatory technique, due to its sensitivity, selectivity, and wide-scope applicability. In this review, we critically discuss the most common specimens and sample treatments/analysis procedures (related to LC-MS/MS) that have been reported during the last ten years. As a final goal, we intend to provide a critical overview and suggest analytical recommendations for the establishment of suitable analytical strategies in DFSA cases.
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Affiliation(s)
- N Almofti
- Department of Analytical Chemistry, Institute of Fine Chemistry and Nanochemistry, Marie Curie Annex Building, Campus of Rabanales, University of Córdoba, 14071, Córdoba, Spain; Section of Forensic and Legal Medicine, Department of Morphological and Sociosanitary Sciences, Faculty of Medicine and Nursing, University of Córdoba, 14071, Córdoba, Spain
| | - A Ballesteros-Gómez
- Department of Analytical Chemistry, Institute of Fine Chemistry and Nanochemistry, Marie Curie Annex Building, Campus of Rabanales, University of Córdoba, 14071, Córdoba, Spain.
| | - S Rubio
- Department of Analytical Chemistry, Institute of Fine Chemistry and Nanochemistry, Marie Curie Annex Building, Campus of Rabanales, University of Córdoba, 14071, Córdoba, Spain
| | - E Girela-López
- Section of Forensic and Legal Medicine, Department of Morphological and Sociosanitary Sciences, Faculty of Medicine and Nursing, University of Córdoba, 14071, Córdoba, Spain
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8
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Empirical Analysis of Forest Penalizing Attribute and Its Enhanced Variations for Android Malware Detection. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
As a result of the rapid advancement of mobile and internet technology, a plethora of new mobile security risks has recently emerged. Many techniques have been developed to address the risks associated with Android malware. The most extensively used method for identifying Android malware is signature-based detection. The drawback of this method, however, is that it is unable to detect unknown malware. As a consequence of this problem, machine learning (ML) methods for detecting and classifying malware applications were developed. The goal of conventional ML approaches is to improve classification accuracy. However, owing to imbalanced real-world datasets, the traditional classification algorithms perform poorly in detecting malicious apps. As a result, in this study, we developed a meta-learning approach based on the forest penalizing attribute (FPA) classification algorithm for detecting malware applications. In other words, with this research, we investigated how to improve Android malware detection by applying empirical analysis of FPA and its enhanced variants (Cas_FPA and RoF_FPA). The proposed FPA and its enhanced variants were tested using the Malgenome and Drebin Android malware datasets, which contain features gathered from both static and dynamic Android malware analysis. Furthermore, the findings obtained using the proposed technique were compared with baseline classifiers and existing malware detection methods to validate their effectiveness in detecting malware application families. Based on the findings, FPA outperforms the baseline classifiers and existing ML-based Android malware detection models in dealing with the unbalanced family categorization of Android malware apps, with an accuracy of 98.94% and an area under curve (AUC) value of 0.999. Hence, further development and deployment of FPA-based meta-learners for Android malware detection and other cybersecurity threats is recommended.
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Improving the phishing website detection using empirical analysis of Function Tree and its variants. Heliyon 2021; 7:e07437. [PMID: 34278030 PMCID: PMC8264617 DOI: 10.1016/j.heliyon.2021.e07437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/30/2021] [Accepted: 06/25/2021] [Indexed: 11/22/2022] Open
Abstract
The phishing attack is one of the most complex threats that have put internet users and legitimate web resource owners at risk. The recent rise in the number of phishing attacks has instilled distrust in legitimate internet users, making them feel less safe even in the presence of powerful antivirus apps. Reports of a rise in financial damages as a result of phishing website attacks have caused grave concern. Several methods, including blacklists and machine learning-based models, have been proposed to combat phishing website attacks. The blacklist anti-phishing method has been faulted for failure to detect new phishing URLs due to its reliance on compiled blacklisted phishing URLs. Many ML methods for detecting phishing websites have been reported with relatively low detection accuracy and high false alarm. Hence, this research proposed a Functional Tree (FT) based meta-learning models for detecting phishing websites. That is, this study investigated improving the phishing website detection using empirical analysis of FT and its variants. The proposed models outperformed baseline classifiers, meta-learners and hybrid models that are used for phishing websites detection in existing studies. Besides, the proposed FT based meta-learners are effective for detecting legitimate and phishing websites with accuracy as high as 98.51% and a false positive rate as low as 0.015. Hence, the deployment and adoption of FT and its meta-learner variants for phishing website detection and applicable cybersecurity attacks are recommended.
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Zhu LN, Cheng R, Kang KW, Chen MY, Zhan T, Wang J. Size-dependent light scattering of CoOOH nanoflakes for convenient and sensitive detection of alkaline phosphatase in human serum. LUMINESCENCE 2021; 36:1317-1326. [PMID: 33870595 DOI: 10.1002/bio.4059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 01/05/2023]
Abstract
As a natural enzyme, alkaline phosphatase (ALP) plays an essential role in clinicopathological examinations and biomedical research, and is capable of hydrolyzing the phosphate group of l-ascorbic acid-2-phosphate (AAP) to yield l-ascorbic acid (L-AA). L-AA reduced cobalt oxyhydroxide (CoOOH) nanoflakes to Co2+ , leading to a smaller size and weaker light scattering, which could be monitored by electron microscopic images and optical spectra. The indirect detection of ALP was achieved by the reduced light scattering signal of CoOOH nanoflakes. Under optimal conditions, the decrease in scattering intensity was proportional to the ALP concentration over the range 0.1-160 U/L and the detection limit was 0.034 U/L (3σ/k). Compared with other assays, this proposed light scattering method was more convenient and economic for ALP sensing. The method was successfully applied to ALP analysis in human serum samples, and was similar to the results obtained by commercial kits.
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Affiliation(s)
- Lu Ning Zhu
- Ministry of Education, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Chongqing, China.,Chongqing Science and Technology Bureau, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Ru Cheng
- Ministry of Education, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Chongqing, China.,Chongqing Science and Technology Bureau, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Kai Wen Kang
- Ministry of Education, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Chongqing, China.,Chongqing Science and Technology Bureau, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Ming Yun Chen
- Ministry of Education, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Chongqing, China.,Chongqing Science and Technology Bureau, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Tianrong Zhan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Qingdao University of Science and Technology, Qingdao, China
| | - Jian Wang
- Ministry of Education, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Chongqing, China.,Chongqing Science and Technology Bureau, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing, China.,College of Pharmaceutical Sciences, Southwest University, Chongqing, China
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Jia E, Zhou Y, Shi H, Pan M, Zhao X, Ge Q. Effects of brain tissue section processing and storage time on gene expression. Anal Chim Acta 2021; 1142:38-47. [PMID: 33280702 DOI: 10.1016/j.aca.2020.10.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022]
Abstract
The pre-processing of samples is important factors that affect the results of the RNA-sequencing (RNA-seq) data. However, the effects of frozen sections storage conditions on the integrity of RNA and sequencing results haven't been reported. The study of frozen section protection schemes can provide reliable experimental results for single-cell and spatial transcriptome sequencing. In this study, RNA was isolated to be studied for RNA from brain section at different temperatures (RT: room temperature, -20 °C) and storage time (0 h, 2 h, 4 h, 8 h, 12 h, 16 h, 24 h, 7day, 3week, 6month). The stability of reference genes was validated using reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that the storage at room temperature significantly affected RNA integrity number (RIN), and the RIN value was lower with the prolongation of storage, while the storage at -20 °C exerted less effect on the RIN value. Cresyl violet staining for brain tissue sections had little effect on RNA integrity. 1925, 899 and 3390 differential expression genes (DEGs) were screened at 2 h, 4 h and 8 h at room temperature, respectively. A total of 892, 478 and 619 genes were shown to be differentially expressed at -20 °C for 7d, 3w and 6 m, respectively. Among them, the expression of glycoprotein m6a (Gpm6a), calmodulin 1 (Calm1), calmodulin 1 (Calm2), thymosin, beta 4, X chromosome (Tmsb4x), ribosomal protein S21 (Rps21) and so on were correlated with RNA quality. According to the expression stability of 4 reference genes (Actb: beta-actin; Gapdh: glyceraldehyde-3-phosphate dehydrogenase; 18S: 18S ribosomal; Hprt1: hypoxanthine phosphoribosyltransferase 1), 18S is the most stable reference gene in the brain. In conclusion, the storage temperature and time of frozen sections have significant effects on RNA integrity and sequencing results. But there are still some genes that are stable and not affected by worsening of overall RNA integrity ie the decrease of RIN value. In addition, 1% cresyl violet staining can protect RNA.
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Affiliation(s)
- Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing, 210097, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.
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Mona M, Kobeissy F, Park YJ, Miller R, Saleh W, Koh J, Yoo MJ, Chen S, Cha S. Secretome Analysis of Inductive Signals for BM-MSC Transdifferentiation into Salivary Gland Progenitors. Int J Mol Sci 2020; 21:E9055. [PMID: 33260559 PMCID: PMC7730006 DOI: 10.3390/ijms21239055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Severe dry mouth in patients with Sjögren's Syndrome, or radiation therapy for patients with head and neck cancer, significantly compromises their oral health and quality of life. The current clinical management of xerostomia is limited to palliative care as there are no clinically-proven treatments available. Previously, our studies demonstrated that mouse bone marrow-derived mesenchymal stem cells (mMSCs) can differentiate into salivary progenitors when co-cultured with primary salivary epithelial cells. Transcription factors that were upregulated in co-cultured mMSCs were identified concomitantly with morphological changes and the expression of acinar cell markers, such as α-amylase (AMY1), muscarinic-type-3-receptor(M3R), aquaporin-5(AQP5), and a ductal cell marker known as cytokeratin 19(CK19). In the present study, we further explored inductive molecules in the conditioned media that led to mMSC reprogramming by high-throughput liquid chromatography with tandem mass spectrometry and systems biology. Our approach identified ten differentially expressed proteins based on their putative roles in salivary gland embryogenesis and development. Additionally, systems biology analysis revealed six candidate proteins, namely insulin-like growth factor binding protein-7 (IGFBP7), cysteine-rich, angiogenetic inducer, 61(CYR61), agrin(AGRN), laminin, beta 2 (LAMB2), follistatin-like 1(FSTL1), and fibronectin 1(FN1), for their potential contribution to mMSC transdifferentiation during co-culture. To our knowledge, our study is the first in the field to identify soluble inductive molecules that drive mMSC into salivary progenitors, which crosses lineage boundaries.
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Affiliation(s)
- Mahmoud Mona
- Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL 32610, USA; (M.M.); (R.M.)
- Oral Biology, University of Florida College of Dentistry, Gainesville, FL 32610, USA
| | - Firas Kobeissy
- Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA;
| | - Yun-Jong Park
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Rehae Miller
- Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL 32610, USA; (M.M.); (R.M.)
| | - Wafaa Saleh
- Oral Medicine and Periodontology Department, Faculty of Dentistry, Mansoura University, Mansoura 35516, Egypt;
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA; (J.K.); (S.C.)
| | - Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA;
| | - Sixue Chen
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA; (J.K.); (S.C.)
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Seunghee Cha
- Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL 32610, USA; (M.M.); (R.M.)
- Oral Biology, University of Florida College of Dentistry, Gainesville, FL 32610, USA
- Center for Orphaned Autoimmune Disorders, University of Florida College of Dentistry, Gainesville, FL 32610, USA
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Arul P, John SA. Organic solvent free in situ growth of flower like Co-ZIF microstructures on nickel foam for glucose sensing and supercapacitor applications. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.03.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Chang YJ, Yang SS, Yu X, Zhang H, Shang W, Gu ZY. Ultrahigh efficient laser desorption ionization of saccharides by Ti-based metal-organic frameworks nanosheets. Anal Chim Acta 2018; 1032:91-98. [DOI: 10.1016/j.aca.2018.06.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 11/29/2022]
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Characterization and validation of candidate reference methods for the determination of calcium and magnesium in biological fluids. Microchem J 2017. [DOI: 10.1016/j.microc.2017.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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