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Article ; Online: A systematic review and meta-analysis on the correlation between HIV infection and multidrug-resistance tuberculosis

Yulong Song / Qian Jin / Jihai Qiu / Dan Ye

Heliyon, Vol 9, Iss 11, Pp e21956- (2023)

2023

Abstract: Background: The emergence of multidrug-resistant tuberculosis (MDR-TB) in HIV-positive people poses a significant challenge to international efforts to eradicate tuberculosis (TB). Many studies found conflicting results when examining the correlation ... ...

Abstract	Background: The emergence of multidrug-resistant tuberculosis (MDR-TB) in HIV-positive people poses a significant challenge to international efforts to eradicate tuberculosis (TB). Many studies found conflicting results when examining the correlation between HIV and MDR-TB. The purpose of the present investigation was to comprehensively review the literature on the association between HIV infection and MDR-TB in order to evaluate the impact of HIV on MDR-TB worldwide. Methods: Utilizing the databases PubMed, Scopus, Google Scholar, and ScienceDirect, studies published between January 2000 and March 2023 that are eligible for meta-analysis were selected. Using the random-effects model, the aggregated odds ratio of the empirical relationship between HIV and MDR-TB was calculated, along with a confidence interval ranging from 0 to 95 %. Examining the asymmetry of the funnel plot and utilizing Egger's and Begg's test, the possibility of publication bias was investigated. The extent of heterogeneity was determined using the I2 statistics. Results: Through a database search, we identified 1214 studies, from which we ultimately selected 15 studies involving 9667 patients. The odds ratio of 2.78 (95 % confidence interval: 1.07–7.20) between HIV/AIDS and MDR-TB indicates a significant positive correlation. Tau 2 = 3.46, chi 2 = 1440.46, df = 14, I2 = 99.0 %, z = 2.10, and p 0.05 indicate that there is substantial heterogeneity among pooled studies. Since I2 is 99 % (>50 %), a random effect model was employed. The percentage of multidrug-resistant HIV-positive patients across all included studies follows a normal distribution, as shown by a Box and whisker plot with a symmetric skewness and a mesokurtic tail and a scatter plot with a significant R2 value below 1 [R2 = 0.2476] showed the positive correlation between multidrug resistance and HIV infection. Conclusion: HIV infection increases MDR-TB risk, and the preceding pooled analysis showed an increased risk trend. Thus, MDR-TB, especially in HIV-positive patients, ...
Keywords	Multidrug resistant ; Tuberculosis ; MDR-TB ; HIV ; Meta-analysis ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	310 ; 306
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: A Multi-Level Auto-Adaptive Noise-Filtering Algorithm for Land ICESat-2 Photon-Counting Data

Jun Liu / Jingyun Liu / Huan Xie / Dan Ye / Peinan Li

Remote Sensing, Vol 15, Iss 21, p

2023 Volume 5176

Abstract: Due to atmospheric scattering, solar radiation, and other factors, the Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) product data suffer from a substantial amount of background noise. This poses a significant challenge when attempting to directly ...

Abstract	Due to atmospheric scattering, solar radiation, and other factors, the Ice, Cloud, and land Elevation Satellite-2 (ICESat-2) product data suffer from a substantial amount of background noise. This poses a significant challenge when attempting to directly utilize the raw data. Consequently, data denoising becomes an indispensable preprocessing step for its subsequent applications, such as the extraction of forest structure parameters and ground elevation data. While the Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm is currently the most widely used method, it remains susceptible to complexities arising from terrain, low signal-to-noise ratio (SNR), and input parameter variations. This paper proposes an efficient Multi-Level Auto-Adaptive Noise Filter (MLANF) algorithm based on photon spatial density. Its purpose is to extract signal photons from ICESat-2 terrestrial data of different ground cover types. The algorithm follows a two-step process. Firstly, random noise photons are removed from the upper and lower regions of the signal photons through a coarse denoising process. Secondly, in the fine denoising step, the K-Nearest Neighbor (KNN) algorithm selects the K photons to calculate the slope along the track. The calculated slope is then used to rotate the direction of the searching neighborhood in the DBSCAN algorithm. The proposed algorithm was tested in eight datasets of four surface types: forest, grassland, desert, and urban, and the extraction results were compared with those from the ATL08 datasets and the DBSCAN algorithm. Based on the ground-truth signal photons obtained by visual inspection, the classification precision, recall, and F-score of our algorithm, as well as two other algorithms, were calculated. The MLANF could achieve a good balance between classification precision (97.48% averaged) and recall (97.96% averaged). Its F-score (97.69% averaged) was higher than that of the other two methods. This demonstrates that the MLANF algorithm successfully obtained a ...
Keywords	ICESat-2 ; photon-counting LiDAR ; noise removal algorithm ; DBSCAN ; Science ; Q
Subject code	006
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: NIK-mediated reactivation of SIX2 enhanced the CSC-like traits of hepatocellular carcinoma cells through suppressing ubiquitin-proteasome system.

Daren, Liu / Dan, Ye / Jinhong, Wu / Chao, Li

Environmental toxicology

2023 Volume 39, Issue 2, Page(s) 583–591

Abstract: The critical roles of NF-κB Inducing Kinase (NIK) in tumor progression have been elucidated in various tumors; however, its effects on hepatocellular carcinoma (HCC) progression are still confusing. Here, we found that NIK level was upregulated in HCC ... ...

Abstract	The critical roles of NF-κB Inducing Kinase (NIK) in tumor progression have been elucidated in various tumors; however, its effects on hepatocellular carcinoma (HCC) progression are still confusing. Here, we found that NIK level was upregulated in HCC tissues compared to that of normal tissues, and positively correlated with the levels of cancer stem cell (CSC) markers. Then we established HCC cells with NIK-stable knockdown and found that NIK knockdown suppressed the CSC-like traits of HCC cells through in vivo and in vitro experiments. Mechanistically, we revealed that SIX2 protein level, but not its mRNA level, was significantly reduced in HCC cells with NIK knockdown, which was rescued by MG132 treatment. Furthermore, NIK knockdown promoted the ubiquitination level of SIX2 and decreased its protein stability. Moreover, Six2 overexpression partially reversed the inhibition of NIK knockdown on the CSC-like traits of HCC cells. This study identified a novel NIK/SIX2 axis conferring HCC stemness.
MeSH term(s)	Humans ; Carcinoma, Hepatocellular/pathology ; Cell Line, Tumor ; Homeodomain Proteins/genetics ; Liver Neoplasms/pathology ; Nerve Tissue Proteins/genetics ; NF-kappaB-Inducing Kinase ; Proteasome Endopeptidase Complex ; Ubiquitin
Chemical Substances	Homeodomain Proteins ; Nerve Tissue Proteins ; NF-kappaB-Inducing Kinase (EC 2.7.11.25) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; SIX2 protein, human ; Ubiquitin ; MAP3K14 protein, human
Language	English
Publishing date	2023-07-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	1463449-1
ISSN	1522-7278 ; 1520-4081
ISSN (online)	1522-7278
ISSN	1520-4081
DOI	10.1002/tox.23892
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Article ; Online: Research on the rapid combustion process of butane under microwave discharge

Qiang Tang / Zhibin Hu / Zechao Tao / Dan Ye / Jau Tang

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 7

Abstract: Abstract To study the combustion process of fuel in the microwave plasma torch, we designed a butane microwave plasma device exploiting a tungsten rod as an electrode. Through analysis of the image record by high-speed camera, we found that the discharge ...

Abstract	Abstract To study the combustion process of fuel in the microwave plasma torch, we designed a butane microwave plasma device exploiting a tungsten rod as an electrode. Through analysis of the image record by high-speed camera, we found that the discharge of butane microwave plasma torch is a cyclic process at atmospheric pressure at a frequency of around 100 Hz. During the discharge, the active particles continuously diffuse from the electrode to the outside like the bloom of the flower. Then, the variation of plasma torch of jet height and temperature with microwave power is obtained. In addition, we studied the effects of different butane flow rates on the plasma torch. The results illustrate that excessive butane will lead to carbon deposition on the electrode. All in all, this work provides a new understanding of the combustion of the microwave plasma torch, which is conducive to the further development of microwave plasma in the fields of waste gas treatment, fuel combustion, and plasma engine.
Keywords	Medicine ; R ; Science ; Q
Subject code	660
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Constituents, Pharmacokinetics, and Pharmacology of Gegen-Qinlian Decoction

Jing-Ze Lu / Dan Ye / Bing-Liang Ma

Frontiers in Pharmacology, Vol

2021 Volume 12

Abstract: Gegen-Qinlian decoction (GQD) is a classic traditional Chinese medicine (TCM) formula. It is composed of four TCMs, including Puerariae Lobatae Radix, Scutellariae Radix, Coptidis Rhizoma, and Glycyrrhizae Radix et Rhizoma Praeparata cum Melle. GQD is ... ...

Abstract	Gegen-Qinlian decoction (GQD) is a classic traditional Chinese medicine (TCM) formula. It is composed of four TCMs, including Puerariae Lobatae Radix, Scutellariae Radix, Coptidis Rhizoma, and Glycyrrhizae Radix et Rhizoma Praeparata cum Melle. GQD is traditionally and clinically used to treat both the “external and internal symptoms” of diarrhea with fever. In this review, key words related to GQD were searched in the Web of Science, PubMed, China National Knowledge Infrastructure (CNKI), and other databases. Literature published mainly from 2000 to 2020 was screened and summarized. The main constituents of GQD could be classified into eight groups according to their structures: flavonoid C-glycosides, flavonoid O-glucuronides, benzylisoquinoline alkaloids, free flavonoids, flavonoid O-glycosides, coumarins, triterpenoid saponins, and others. The parent constituents of GQD that enter circulation mainly include puerarin and daidzein from Puerariae Lobatae Radix, baicalin and wogonoside from Scutellariae Radix, berberine and magnoflorine from Coptidis Rhizoma, as well as glycyrrhetinic acid and glycyrrhizic acid from Glycyrrhizae Radix et Rhizoma Praeparata cum Melle. GQD is effective against inflammatory intestinal diseases, including diarrhea, ulcerative colitis, and intestinal adverse reactions caused by chemotherapeutic agents. Moreover, GQD has significant effects on metabolic diseases, such as nonalcoholic fatty liver and type 2 diabetes. Furthermore, GQD can be used to treat lung injury. In brief, the main constituents, the pharmacokinetic and pharmacological profiles of GQD were summarized in this review. In addition, several issues of GQD including effective constituents, interactions between the constituents, pharmacokinetics, interaction potential with drugs and pharmacological effects were discussed, and related future researches were prospected in this review.
Keywords	Gegen-Qinlian decoction ; traditional Chinese medicine ; quality control ; material basis ; pharmacokinetics ; pharmacological effects ; Therapeutics. Pharmacology ; RM1-950
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Seismic Analysis Method for Underground Structure in Loess Area Based on the Modified Displacement-Based Method

Ruijie Zhang / Dan Ye / Jianting Zhou / Dengzhou Quan

Applied Sciences, Vol 11, Iss 11245, p

2021 Volume 11245

Abstract: At present, the seismic design research of underground structures in loess areas is lagging behind compared with practical engineering requirements. The selection of seismic calculation methods and parameters does not consider the influences of the ... ...

Abstract	At present, the seismic design research of underground structures in loess areas is lagging behind compared with practical engineering requirements. The selection of seismic calculation methods and parameters does not consider the influences of the special geological conditions in various regions, so their usefulness is limited. Based on the above problems, a modified displacement-based method (DBM) was proposed and its application was compared with the most commonly used methods of analysis (force-based design method, displacement-based design method, detailed equivalent static analysis numerical method, and the full dynamic time-history method). The results were also validated by considering data from shaking table tests conducted on a case study involving the underground Feitian Road subway station in Xi’an. The results show that compared with DBM, the average accuracy of the modified DBM technique is improved by 41.65%. The modified DBM offers good accuracy, simplicity in its model, a rapid analysis time, and easy convergence.
Keywords	traffic engineering ; seismic calculation ; loess area ; DBM ; DESANM ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	670
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Automated Testing Framework for ODBC Driver

Dan Ye

Journal of Software Engineering and Applications, Vol 04, Iss 12, Pp 688-

2011 Volume 699

Abstract: At first, the core ideology, advantage and principle of Software Testing Automation Framework (STAF) are presented in this paper. Several automated testing frameworks are summarized and analyzed. In addition, date driven automation test framework is ... ...

Abstract	At first, the core ideology, advantage and principle of Software Testing Automation Framework (STAF) are presented in this paper. Several automated testing frameworks are summarized and analyzed. In addition, date driven automation test framework is given more attention. Test script is the important composing part of software test automation. Then this paper introduces several technologies of script along with their characteristics. Every technology applies to different places. Moreover, an automated test system with an automated test script language XML which is implemented to solve the problems in current automatic testing solutions. The design and implantation of the test script automation framework based on apache ant is put forward. The proposed key technology details of framework are also introduced. We take the automation test methodology of database connectivity operations by ODBC data source as example for validation, using auto test script as the key technology. Finally, the results demonstrate that it can best increase software test effectiveness and reduce workloads as well as save more efforts.
Keywords	Software Automation Testing ; Universal Test Script ; XML ; Data-Driven ; Apache Ant ; Electronic computers. Computer science ; QA75.5-76.95 ; Instruments and machines ; QA71-90 ; Mathematics ; QA1-939 ; Science ; Q ; DOAJ:Computer Science ; DOAJ:Technology and Engineering
Subject code	501
Language	English
Publishing date	2011-12-01T00:00:00Z
Publisher	Scientific Research Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Photoactivatable CRISPR/Cas12a Sensors for Biomarkers Imaging and Point-of-Care Diagnostics.

Li, Qing-Nan / Wang, Dong-Xia / Chen, Dan-Ye / Lyu, Jia-Ao / Wang, Ya-Xin / Wu, Shun-Li / Jiang, Hong-Xin / Kong, De-Ming

Analytical chemistry

2024 Volume 96, Issue 6, Page(s) 2692–2701

Abstract: In recent years, the CRISPR/Cas12a-based sensing strategy has shown significant potential for specific target detection due to its rapid and sensitive characteristics. However, the "always active" biosensors are often insufficient to manipulate nucleic ... ...

Abstract	In recent years, the CRISPR/Cas12a-based sensing strategy has shown significant potential for specific target detection due to its rapid and sensitive characteristics. However, the "always active" biosensors are often insufficient to manipulate nucleic acid sensing with high spatiotemporal control. It remains crucial to develop nucleic acid sensing devices that can be activated at the desired time and space by a remotely applied stimulus. Here, we integrated photoactivation with the CRISPR/Cas12a system for DNA and RNA detection, aiming to provide high spatiotemporal control for nucleic acid sensing. By rationally designing the target recognition sequence, this photoactivation CRISPR/Cas12a system could recognize HPV16 and
MeSH term(s)	CRISPR-Cas Systems/genetics ; Survivin/genetics ; Biomarkers ; Point-of-Care Testing ; Nucleic Acids ; Biosensing Techniques
Chemical Substances	Survivin ; Biomarkers ; Nucleic Acids
Language	English
Publishing date	2024-02-02
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.3c05497
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Article ; Online: Rapid syntheses of N-fused heterocycles via acyl-transfer in heteroaryl ketones

Dan Ye / Hong Lu / Yi He / Zhaojing Zheng / Jinghao Wu / Hao Wei

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 9

Abstract: Heteroaryl ketones are ubiquitous molecular scaffolds but seldom used as synthetic precusors. Here, the authors develop an acyl transfer-annulation to convert heteroaryl ketones to N-fused heterocycles, which are prevalent in bioactive molecules. ...

Abstract	Heteroaryl ketones are ubiquitous molecular scaffolds but seldom used as synthetic precusors. Here, the authors develop an acyl transfer-annulation to convert heteroaryl ketones to N-fused heterocycles, which are prevalent in bioactive molecules.
Keywords	Science ; Q
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Sin3a drives mesenchymal-to-epithelial transition through cooperating with Tet1 in somatic cell reprogramming

Jiabao Feng / Fugui Zhu / Dan Ye / Qingquan Zhang / Xudong Guo / Changsheng Du / Jiuhong Kang

Stem Cell Research & Therapy, Vol 13, Iss 1, Pp 1-

2022 Volume 16

Abstract: Abstract Background Identifying novel regulatory factors and uncovered mechanisms of somatic cell reprogramming will be helpful for basic research and clinical application of induced pluripotent stem cells (iPSCs). Sin3a, a multifunctional transcription ... ...

Abstract	Abstract Background Identifying novel regulatory factors and uncovered mechanisms of somatic cell reprogramming will be helpful for basic research and clinical application of induced pluripotent stem cells (iPSCs). Sin3a, a multifunctional transcription regulator, has been proven to be involved in the maintenance of pluripotency in embryonic stem cells (ESCs), but the role of Sin3a in somatic cell reprogramming remains unclear. Methods RNA interference of Sin3a during somatic cell reprogramming was realized by short hairpin RNAs. Reprogramming efficiency was evaluated by the number of alkaline phosphatase (AP)-positive colonies and Oct4-GFP-positive colonies. RNA sequencing was performed to identify the influenced biological processes after Sin3a knockdown and further confirmed by quantitative RT-PCR (qRT-PCR), western blotting and flow cytometry. The interaction between Sin3a and Tet1 was detected by coimmunoprecipitation. The enrichment of Sin3a and Tet1 at the epithelial gene promoters was measured by chromatin immunoprecipitation. Furthermore, DNA methylation patterns at the gene loci were investigated by hydroxymethylated DNA immunoprecipitation. Finally, Sin3a mutants that disrupt the interaction of Sin3a and Tet1 were also introduced to assess the importance of the Sin3a–Tet1 interaction during the mesenchymal-to-epithelial transition (MET) process. Results We found that Sin3a was gradually increased during OSKM-induced reprogramming and that knockdown of Sin3a significantly impaired MET at the early stage of reprogramming and iPSC generation. Mechanistic studies showed that Sin3a recruited Tet1 to facilitate the hydroxymethylation of epithelial gene promoters. Moreover, disrupting the interaction of Sin3a and Tet1 significantly blocked MET and iPSC generation. Conclusions Our studies revealed that Sin3a was a novel mediator of MET during early reprogramming, where Sin3a functioned as an epigenetic coactivator, cooperating with Tet1 to activate the epithelial program and promote the initiation of somatic ...
Keywords	Reprogramming ; Sin3a ; Mesenchymal-to-epithelial transition ; Tet1 ; Hydroxymethylation ; Medicine (General) ; R5-920 ; Biochemistry ; QD415-436
Subject code	571
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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