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Article ; Online: Clinical treatment of cryptococcal meningitis: an evidence-based review on the emerging clinical data.

Liu, Mao-Zhu / Dai, Xin-Hua / Zeng, Ming-Tang / Chen, En-Qiang

2024

Abstract: Cryptococcal meningitis (CM) is a fatal fungal central nervous system (CNS) infection caused by Cryptococcus infecting the meninges and/or brain parenchyma, with fever, headache, neck stiffness, and visual disturbances as the primary clinical ... ...

Abstract	Cryptococcal meningitis (CM) is a fatal fungal central nervous system (CNS) infection caused by Cryptococcus infecting the meninges and/or brain parenchyma, with fever, headache, neck stiffness, and visual disturbances as the primary clinical manifestations. Immunocompromised individuals with human immunodeficiency virus (HIV) infection or who have undergone organ transplantation, as well as immunocompetent people can both be susceptible to CM. Without treatment, patients with CM may have a mortality rate of up to 100% after hospital admission. Even after receiving therapy, CM patients may still suffer from problems such as difficulty to cure, poor prognosis, and high mortality. Therefore, timely and effective treatment is essential to improve the mortality and prognosis of CM patients. Currently, the clinical outcomes of CM are frequently unsatisfactory due to limited drug choices, severe adverse reactions, drug resistance, etc. Here, we review the research progress of CM treatment strategies and discuss the suitable options for managing CM, hoping to provide a reference for physicians to select the most appropriate treatment regimens for CM patients.
Language	English
Publishing date	2024-01-30
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	187050-6
ISSN	1432-1459 ; 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
ISSN (online)	1432-1459
ISSN	0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
DOI	10.1007/s00415-024-12193-8
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Article ; Online: Absolute protein quantification based on calibrated particle counting using electrospray-differential mobility analysis.

Mi, Wei / Zhang, Xinyi / Wang, Bin / Sun, Ruixue / Ma, Shangying / Hu, Zhishang / Dai, Xinhua

Analytica chimica acta

2024 Volume 1304, Page(s) 342534

Abstract: The traceability of in vitro diagnostics or drug products is based on the accurate quantification of proteins. In this study, we developed an absolute quantification approach for proteins. This method is based on calibrated particle counting using ... ...

Abstract	The traceability of in vitro diagnostics or drug products is based on the accurate quantification of proteins. In this study, we developed an absolute quantification approach for proteins. This method is based on calibrated particle counting using electrospray-differential mobility analysis (ES-DMA) coupled with a condensation particle counter (CPC). The absolute concentration of proteins was quantified with the observed protein particle number measured with ES-DMA-CPC, and the detection efficiency was determined by calibrators. The measurement performance and quantitative level were verified using two certificated reference materials, BSA and NIMCmAb. The linear regression fit for the detection efficiency values of three reference materials and one highly purified protein (myoglobin, BSA, NIMCmAb and fibrinogen) indicated that the detection efficiency and the particle size distribution of these proteins exhibited a linear relationship. Moreover, to explore the suitability of the detection efficiency-particle size curve for protein quantification, the concentrations of three typical proteinaceous particles, including two high molecular weight proteins (NIST reference material 8671 and D-dimer) and one protein complex (glutathione S-transferase dimer), were determined. This work suggests that this calibrated particle counting method is an efficient approach for nondestructive, rapid and accurate quantification of proteins, especially for measuring proteinaceous particles with tremendous size and without reference standards.
MeSH term(s)	Ion Mobility Spectrometry ; Myoglobin ; Particle Size ; Glutathione Transferase ; Gold
Chemical Substances	Myoglobin ; Glutathione Transferase (EC 2.5.1.18) ; Gold (7440-57-5)
Language	English
Publishing date	2024-03-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2024.342534
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Article ; Online: Integrated Microwell Array-Based Microfluidic Chip with a Hand-Held Smartphone-Controlled Device for Nucleic Acid Detection.

Shen, Haiying / Dong, Lianhua / Gao, Yunhua / Wang, Xia / Dai, Xinhua

Analytical chemistry

2023 Volume 95, Issue 41, Page(s) 15394–15399

Abstract: In this study, we designed a highly integrated microfluidic chip for nucleic acid extraction, amplification, and detection. Magnetic beads, which are used to capture nucleic acids on the chip, are trapped in the microwell arrays in a one-well-one-bead ... ...

Abstract	In this study, we designed a highly integrated microfluidic chip for nucleic acid extraction, amplification, and detection. Magnetic beads, which are used to capture nucleic acids on the chip, are trapped in the microwell arrays in a one-well-one-bead manner after local surface modification of the inner faces of the microwells. On-chip liquid introduction, delivery, and mixing are all carried out manually with one syringe and no other equipment. A hand-held device with precise temperature control and high-quality imaging is developed, which is only 2.3 cubic decimeters in volume and 1.2 kg in weight. Via the use of the Internet for wireless communication, the experiment and data analysis after inserting the chip into the device can be conducted by a smartphone anywhere there is an Internet connection. We carried out reverse transcription loop-mediated isothermal amplification (RT-LAMP) on the chip with the hand-held device. SARS-CoV-2 pseudoviruses are extracted, reverse transcribed, amplified, and detected on the chip with the hand-held device with satisfactory results. Thus, a highly integrated, easy-to-operate, and rapid nucleic acid detection microfluidic chip with a hand-held smartphone-controlled device is proposed, and this new platform for nucleic acid detection shows great potential for mobile point-of-care testing (POCT).
MeSH term(s)	Microfluidics ; Smartphone ; Nucleic Acids/analysis ; Point-of-Care Testing ; Oligonucleotide Array Sequence Analysis ; Nucleic Acid Amplification Techniques/methods
Chemical Substances	Nucleic Acids
Language	English
Publishing date	2023-10-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c03525
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Article ; Online: Integrated Microwell Array-Based Microfluidic Chip with a Hand-Held Smartphone-Controlled Device for Nucleic Acid Detection

Shen, Haiying / Dong, Lianhua / Gao, Yunhua / Wang, Xia / Dai, Xinhua

Analytical Chemistry. 2023 Oct. 03, v. 95, no. 41 p.15394-15399

2023

Abstract	In this study, we designed a highly integrated microfluidic chip for nucleic acid extraction, amplification, and detection. Magnetic beads, which are used to capture nucleic acids on the chip, are trapped in the microwell arrays in a one-well-one-bead manner after local surface modification of the inner faces of the microwells. On-chip liquid introduction, delivery, and mixing are all carried out manually with one syringe and no other equipment. A hand-held device with precise temperature control and high-quality imaging is developed, which is only 2.3 cubic decimeters in volume and 1.2 kg in weight. Via the use of the Internet for wireless communication, the experiment and data analysis after inserting the chip into the device can be conducted by a smartphone anywhere there is an Internet connection. We carried out reverse transcription loop-mediated isothermal amplification (RT-LAMP) on the chip with the hand-held device. SARS-CoV-2 pseudoviruses are extracted, reverse transcribed, amplified, and detected on the chip with the hand-held device with satisfactory results. Thus, a highly integrated, easy-to-operate, and rapid nucleic acid detection microfluidic chip with a hand-held smartphone-controlled device is proposed, and this new platform for nucleic acid detection shows great potential for mobile point-of-care testing (POCT).
Keywords	Internet ; Pseudoviridae ; Severe acute respiratory syndrome coronavirus 2 ; analytical chemistry ; liquids ; magnetism ; mobile telephones ; nucleic acids ; organ-on-a-chip ; point-of-care systems ; reverse transcription loop-mediated isothermal amplification ; syringes ; temperature
Language	English
Dates of publication	2023-1003
Size	p. 15394-15399.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c03525
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Article: Generation, evolution, interfering factors, applications, and challenges of patient-derived xenograft models in immunodeficient mice.

Zeng, Mingtang / Ruan, Zijing / Tang, Jiaxi / Liu, Maozhu / Hu, Chengji / Fan, Ping / Dai, Xinhua

Cancer cell international

2023 Volume 23, Issue 1, Page(s) 120

Abstract: Establishing appropriate preclinical models is essential for cancer research. Evidence suggests that cancer is a highly heterogeneous disease. This follows the growing use of cancer models in cancer research to avoid these differences between xenograft ... ...

Abstract	Establishing appropriate preclinical models is essential for cancer research. Evidence suggests that cancer is a highly heterogeneous disease. This follows the growing use of cancer models in cancer research to avoid these differences between xenograft tumor models and patient tumors. In recent years, a patient-derived xenograft (PDX) tumor model has been actively generated and applied, which preserves both cell-cell interactions and the microenvironment of tumors by directly transplanting cancer tissue from tumors into immunodeficient mice. In addition to this, the advent of alternative hosts, such as zebrafish hosts, or in vitro models (organoids and microfluidics), has also facilitated the advancement of cancer research. However, they still have a long way to go before they become reliable models. The development of immunodeficient mice has enabled PDX to become more mature and radiate new vitality. As one of the most reliable and standard preclinical models, the PDX model in immunodeficient mice (PDX-IM) exerts important effects in drug screening, biomarker development, personalized medicine, co-clinical trials, and immunotherapy. Here, we focus on the development procedures and application of PDX-IM in detail, summarize the implications that the evolution of immunodeficient mice has brought to PDX-IM, and cover the key issues in developing PDX-IM in preclinical studies.
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2091573-1
ISSN	1475-2867
ISSN	1475-2867
DOI	10.1186/s12935-023-02953-3
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Article ; Online: Highly Sensitive and Quantitative Magnetic Nanoparticle-Based Lateral Flow Immunoassay with an Atomic Magnetometer.

Wang, Boyu / Peng, Tao / Jiang, Zhiyuan / Xu, Jinxin / Qu, Jifeng / Dai, Xinhua

ACS sensors

2023 Volume 8, Issue 12, Page(s) 4512–4520

Abstract: Lateral flow immunoassay (LFIA) is a simple point-of-care method for detecting various analytes. However, the lack of test result precision and poor quantification are the main bottlenecks of LFIA. Although magnetic nanoparticles (MNPs) have gained ... ...

Abstract	Lateral flow immunoassay (LFIA) is a simple point-of-care method for detecting various analytes. However, the lack of test result precision and poor quantification are the main bottlenecks of LFIA. Although magnetic nanoparticles (MNPs) have gained prominence as potent labels in LIFA, the quantitative detection method for trace biomarkers remains to be improved. Here, we propose a promising real-time biosensing platform based on a highly sensitive atomic magnetometer to fulfill the quantitative detection of MNP-based lateral flow immunochromatographic assays. The strategy entails obtaining the residual flux density component spectrum by continuously and linearly scanning the trace MNP label and then resolving the magnetization and quantity from the spectrum. Moreover, we exploit the theoretical model of the magnetic dipole to verify the method's reliability. Regarding carcinoembryonic antigen detection, the atomic magnetometer exhibits a low detection limit of ∼0.01 ng mL
MeSH term(s)	Magnetite Nanoparticles/chemistry ; Reproducibility of Results ; Limit of Detection ; Magnetics ; Immunoassay/methods
Chemical Substances	Magnetite Nanoparticles
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ISSN	2379-3694
ISSN (online)	2379-3694
DOI	10.1021/acssensors.3c01028
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Article ; Online: Suppression of

Mudgett, Michael / Shen, Zhouxin / Dai, Xinhua / Briggs, Steven P / Zhao, Yunde

Proceedings of the National Academy of Sciences of the United States of America

2023 Volume 120, Issue 48, Page(s) e2312918120

Abstract: Disruption of either the auxin transporter PIN-FORMED 1 (PIN1) or the protein kinase PINOID (PID) leads to the development of pin-like inflorescences. Previous studies have shown that phosphoregulation of PIN1 by AGC kinases including PID directs auxin ... ...

Abstract	Disruption of either the auxin transporter PIN-FORMED 1 (PIN1) or the protein kinase PINOID (PID) leads to the development of pin-like inflorescences. Previous studies have shown that phosphoregulation of PIN1 by AGC kinases including PID directs auxin flux to drive organ initiation. Here, we report unexpected findings on the genetic interactions between these two genes. We deleted the first 2/3 of the
MeSH term(s)	Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Arabidopsis/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Indoleacetic Acids/metabolism ; Mutation ; Phenotype ; Gene Expression Regulation, Plant ; Membrane Transport Proteins/metabolism
Chemical Substances	Arabidopsis Proteins ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Green Fluorescent Proteins (147336-22-9) ; Indoleacetic Acids ; PIN1 protein, Arabidopsis ; Membrane Transport Proteins
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2312918120
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Article: High-throughput single-cell mass spectrometry enables metabolic network analysis by resolving phospholipid C[double bond, length as m-dash]C isomers.

Cheng, Simin / Cao, Chenxi / Qian, Yao / Yao, Huan / Gong, Xiaoyun / Dai, Xinhua / Ouyang, Zheng / Ma, Xiaoxiao

Chemical science

2024 Volume 15, Issue 17, Page(s) 6314–6320

Abstract: Single-cell mass spectrometry (MS) is an essential technology for sensitive and multiplexed analysis of metabolites and lipids for cell phenotyping and pathway studies. However, the structural elucidation of lipids from single cells remains a challenge, ... ...

Abstract	Single-cell mass spectrometry (MS) is an essential technology for sensitive and multiplexed analysis of metabolites and lipids for cell phenotyping and pathway studies. However, the structural elucidation of lipids from single cells remains a challenge, especially in the high-throughput scenario. Technically, there is a contradiction between the inadequate sample amount (
Language	English
Publishing date	2024-04-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d3sc06573a
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Article ; Online: SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data.

Huang, Jinze / Zhao, Yang / Meng, Bo / Lu, Ao / Wei, Yaoguang / Dong, Lianhua / Fang, Xiang / An, Dong / Dai, Xinhua

Briefings in bioinformatics

2024 Volume 25, Issue 3

Abstract: Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without ...

Abstract	Quality control in quantitative proteomics is a persistent challenge, particularly in identifying and managing outliers. Unsupervised learning models, which rely on data structure rather than predefined labels, offer potential solutions. However, without clear labels, their effectiveness might be compromised. Single models are susceptible to the randomness of parameters and initialization, which can result in a high rate of false positives. Ensemble models, on the other hand, have shown capabilities in effectively mitigating the impacts of such randomness and assisting in accurately detecting true outliers. Therefore, we introduced SEAOP, a Python toolbox that utilizes an ensemble mechanism by integrating multi-round data management and a statistics-based decision pipeline with multiple models. Specifically, SEAOP uses multi-round resampling to create diverse sub-data spaces and employs outlier detection methods to identify candidate outliers in each space. Candidates are then aggregated as confirmed outliers via a chi-square test, adhering to a 95% confidence level, to ensure the precision of the unsupervised approaches. Additionally, SEAOP introduces a visualization strategy, specifically designed to intuitively and effectively display the distribution of both outlier and non-outlier samples. Optimal hyperparameter models of SEAOP for outlier detection were identified by using a gradient-simulated standard dataset and Mann-Kendall trend test. The performance of the SEAOP toolbox was evaluated using three experimental datasets, confirming its reliability and accuracy in handling quantitative proteomics.
MeSH term(s)	Proteomics ; Reproducibility of Results ; Quality Control ; Data Interpretation, Statistical ; Data Management
Language	English
Publishing date	2024-04-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbae129
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Article ; Online: Simultaneous determination of diquat, paraquat, glufosinate, and glyphosate in plasma by liquid chromatography/tandem mass spectrometry: from method development to clinical application.

Liu, Maozhu / Fan, Fei / Zhang, Jing / Fang, Shiyong / Bai, Yangjuan / Li, Yamei / Zou, Yuangao / An, Yunfei / Dai, Xinhua

Analytical and bioanalytical chemistry

2024 Volume 416, Issue 12, Page(s) 3073–3083

Abstract: Diquat (DQ), paraquat (PQ), glufosinate (GLU), and glyphosate (GLYP) are commonly used herbicides that have been confirmed to be toxic to humans. Rapid and accurate measurements of these toxicants in clinical practice are beneficial for the correct ... ...

Abstract	Diquat (DQ), paraquat (PQ), glufosinate (GLU), and glyphosate (GLYP) are commonly used herbicides that have been confirmed to be toxic to humans. Rapid and accurate measurements of these toxicants in clinical practice are beneficial for the correct diagnosis and timely treatment of herbicide-poisoned patients. The present study aimed to establish an efficient, convenient, and reliable method to achieve the simultaneous quantification of DQ, PQ, GLU, and GLYP in human plasma using liquid chromatography-tandem mass spectrometry (LC-MS/MS) without using derivatization or ion-pairing reagents. DQ, PQ, GLU, and GLYP were extracted by the rapid protein precipitation and liquid-liquid extraction method and then separated and detected by LC-MS/MS. Subsequently, linearity, limit of detection (LOD), limit of quantification (LOQ), precision, accuracy, extraction recovery, matrix effect, dilution integrity, and stability were evaluated to validate the method based on the FDA criteria. Finally, the validated method was applied to real plasma samples collected from 166 Chinese patients with herbicide poisoning. The results showed satisfactory linearity with low LOD (1 ng/mL for DQ and PQ, 5 ng/mL for GLU, and 10 ng/mL for GLYP, respectively) and low LOQ (5 ng/mL for DQ and PQ, 25 ng/mL for GLU and GLYP, respectively). In addition, the precision, accuracy, extraction recovery, and stability of the method were acceptable. The matrix effect was not observed in the analyzed samples. Moreover, the developed method was successfully applied to determine the target compounds in real plasma samples. These data provided reliable evidence for the application of this LC-MS/MS method for clinical poisoning detection.
MeSH term(s)	Humans ; Tandem Mass Spectrometry/methods ; Glycine/analogs & derivatives ; Glycine/blood ; Glyphosate ; Aminobutyrates/blood ; Diquat/blood ; Diquat/poisoning ; Paraquat/blood ; Paraquat/poisoning ; Herbicides/blood ; Herbicides/poisoning ; Limit of Detection ; Chromatography, Liquid/methods ; Reproducibility of Results
Chemical Substances	Glycine (TE7660XO1C) ; phosphinothricin (51276-47-2) ; Glyphosate (4632WW1X5A) ; Aminobutyrates ; Diquat (A9A615U4MP) ; Paraquat (PLG39H7695) ; Herbicides
Language	English
Publishing date	2024-03-22
Publishing country	Germany
Document type	Journal Article ; Validation Study
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-024-05257-1
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