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Article ; Online: Transcriptome Analysis Reveals the Important Role of Vitamin B

Wang, Qi / Wang, Zhiwei / Guan, Jiaqi / Song, Jinzhu

International journal of molecular sciences

2024 Volume 25, Issue 8

Abstract: Natronorubrum ... ...

Abstract	Natronorubrum daqingense
MeSH term(s)	Vitamin B 12/metabolism ; Salt Stress ; Gene Expression Profiling ; Sodium Chloride/pharmacology ; Transcriptome ; Salt Tolerance/genetics ; Gene Expression Regulation, Archaeal
Chemical Substances	Vitamin B 12 (P6YC3EG204) ; Sodium Chloride (451W47IQ8X)
Language	English
Publishing date	2024-04-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25084168
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sanmiao wan alleviates inflammation and exhibits hypouricemic effect in an acute gouty arthritis rat model.

Wang, Xiaoqian / Sheng, Yunjie / Guan, Jiaqi / Zhang, Fengling / Lou, Chenghua

Journal of ethnopharmacology

2024 Volume 324, Page(s) 117764

Abstract: Ethnopharmacological relevance: Sanmiao wan (SMW), a classical traditional Chinese medicine (TCM) formula, has been employed to treat gouty diseases in clinic as early as Yuan dynasty. It shows remarkably therapeutic effects in acute gouty arthritis (GA) ...

Abstract	Ethnopharmacological relevance: Sanmiao wan (SMW), a classical traditional Chinese medicine (TCM) formula, has been employed to treat gouty diseases in clinic as early as Yuan dynasty. It shows remarkably therapeutic effects in acute gouty arthritis (GA). However, the potential mechanisms of SMW are still not fully revealed. Aim of the study: The objective of this project is to evaluate the pharmacological effects and possible mechanisms of SMW in a rat model of acute GA. Materials and methods: Monosodium urate (MSU) suspension was injected into the ankle joint of rats to establish acute GA model. The inflammation was evaluated by measuring the posterior ankle diameter. The pathological status of synovial tissue was assessed by hematoxylin eosin (HE), Masson, and picrosirius red staining. The level of IL-6 was measured using ELISA kit. The levels of blood urea nitrogen (BUN), creatinine (CR), UA (uric acid), and xanthine oxidase (XOD) in the serum were measured using standard diagnostic kits. The percentage of Th17 cells in blood samples was performed using flow cytometry. Moreover, RT-qPCR was performed to examine the mRNA level of RANK, RORγt, RANKL, and STAT3 in the synovial tissue. Furthermore, immunofluorescence was carried out to assess the expression of STAT3 in the synovial tissue. Results: SMW effectively alleviated the inflammation and improved the pathological status of the ankle joint in rats with acute GA. It significantly suppressed the release of proinflammatory cytokine (IL-6). Meanwhile, the levels of UA, BUN, and CR were markedly reduced after SMW treatment. A remarkable reduction of XOD activity was observed in the study. Importantly, SMW treatment significantly reduced the frequency of Th17 cells, decreased the mRNA levels of RANK, RORγt, RANKL, and STAT3 in the synovial tissue. Furthermore, the suppression of STAT3 was also demonstrated using immunofluorescence in SMW-treated group. Conclusion: SMW showed significant anti-inflammatory and hypouricemic effects in a rat model of GA. It is an effective TCM formula for GA therapy.
MeSH term(s)	Rats ; Animals ; Arthritis, Gouty/metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Interleukin-6 ; Inflammation/drug therapy ; Uric Acid ; RNA, Messenger
Chemical Substances	Nuclear Receptor Subfamily 1, Group F, Member 3 ; Interleukin-6 ; Uric Acid (268B43MJ25) ; RNA, Messenger
Language	English
Publishing date	2024-01-12
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	134511-4
ISSN	1872-7573 ; 0378-8741
ISSN (online)	1872-7573
ISSN	0378-8741
DOI	10.1016/j.jep.2024.117764
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Zs.A 1494: Show issues

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Article ; Online: Baizhu-Baishao herb pair ameliorates functional constipation and intestinal microflora disorder in rats.

Li, Xiaojun / Wang, Xiaoting / Wang, Ziyan / Guan, Jiaqi

Animal models and experimental medicine

2023 Volume 6, Issue 6, Page(s) 598–608

Abstract: Background: In China, Rhizoma atractylodis macrocephalae-Paeonia lactiflora Pall (Biazhu-Baishao, BZBS) is a classic herb pair used to treat intestinal stress syndrome, ulcerative colitis and other diseases. However, the mechanism of BZBS in the ... ...

Abstract	Background: In China, Rhizoma atractylodis macrocephalae-Paeonia lactiflora Pall (Biazhu-Baishao, BZBS) is a classic herb pair used to treat intestinal stress syndrome, ulcerative colitis and other diseases. However, the mechanism of BZBS in the treatment of functional constipation (FC) has been little studied and remains unclear. In this study, a behavioral investigation, colon tissue morphology, enzyme-linked immunosorbent assay (Elisa) and intestinal microflora analysis have been used to illuminate the potential mechanism of the effects of BZBS on FC in a rat model. Methods: A FC rat model was constructed and BZBS was given as treatment. Observations and recordings were made of the fecal moisture content, the defecation time of the first black stool, and the rate of intestinal propulsion. Elisa was used to detect the expression levels of substance P (SP), vasoactive intestinal peptide (VIP), 5-hydroxytryptamine (5-HT) in the colon. To ascertain the composition of the microbial community, a high throughput 16S ribosomal RNA (16S rRNA) gene sequencing technique was employed. Results: Oral administration of BZBS significantly ameliorated several key excretion parameters, including the time to first black stool defecation, stool water content, and the propulsion rate in the small intestine in FC rats. It increased the expression of SP, VIP and 5-HT in the colon. 16S rRNA gene sequencing results showed that BZBS changed the microbial community structure, decreased the Bacteroidetes/Firmicutes ratio, increased the relative abundance of Blautia and Fusicatenibacter, and decreased the relative abundance of Ruminococcus and Roseburia. Conclusions: BZBS effectively alleviates FC and improves dysbacteriosis.
MeSH term(s)	Rats ; Animals ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Serotonin ; Constipation/drug therapy ; Constipation/genetics ; Vasoactive Intestinal Peptide/pharmacology ; Vasoactive Intestinal Peptide/genetics ; Substance P
Chemical Substances	Baizhu ; RNA, Ribosomal, 16S ; Serotonin (333DO1RDJY) ; Vasoactive Intestinal Peptide (37221-79-7) ; Substance P (33507-63-0)
Language	English
Publishing date	2023-10-20
Publishing country	United States
Document type	Journal Article
ISSN	2576-2095
ISSN (online)	2576-2095
DOI	10.1002/ame2.12351
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Article ; Online: A Child with Posterior Ectopic Cilia.

Guan, Jiaqi / Ye, Huijing / Yang, Huasheng

Ophthalmology

2023

Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	392083-5
ISSN	1549-4713 ; 0161-6420
ISSN (online)	1549-4713
ISSN	0161-6420
DOI	10.1016/j.ophtha.2023.11.005
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Ul II Zs.83: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MO 533: Show issues

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Article ; Online: A Chinese Patient with Eyelid Trichofolliculoma.

Guan, Jiaqi / Ye, Huijing / Yang, Huasheng

Ophthalmology

2023

Language	English
Publishing date	2023-11-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	392083-5
ISSN	1549-4713 ; 0161-6420
ISSN (online)	1549-4713
ISSN	0161-6420
DOI	10.1016/j.ophtha.2023.10.003
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Ul II Zs.83: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MO 533: Show issues

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Book ; Online: MolDiff

Peng, Xingang / Guan, Jiaqi / Liu, Qiang / Ma, Jianzhu

Addressing the Atom-Bond Inconsistency Problem in 3D Molecule Diffusion Generation

2023

Abstract: Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding ...

Abstract	Deep generative models have recently achieved superior performance in 3D molecule generation. Most of them first generate atoms and then add chemical bonds based on the generated atoms in a post-processing manner. However, there might be no corresponding bond solution for the temporally generated atoms as their locations are generated without considering potential bonds. We define this problem as the atom-bond inconsistency problem and claim it is the main reason for current approaches to generating unrealistic 3D molecules. To overcome this problem, we propose a new diffusion model called MolDiff which can generate atoms and bonds simultaneously while still maintaining their consistency by explicitly modeling the dependence between their relationships. We evaluated the generation ability of our proposed model and the quality of the generated molecules using criteria related to both geometry and chemical properties. The empirical studies showed that our model outperforms previous approaches, achieving a three-fold improvement in success rate and generating molecules with significantly better quality.
Keywords	Quantitative Biology - Biomolecules ; Computer Science - Machine Learning ; Quantitative Biology - Quantitative Methods
Subject code	541
Publishing date	2023-05-11
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Network-based pharmacology to predict the mechanism of

Meng, Yuxiao / Li, Xiaojun / Guan, Jiaqi

International journal of clinical and experimental pathology

2021 Volume 14, Issue 9, Page(s) 964–971

Abstract: Background: Viral pneumonia (VP) is a common inflammatory disease caused by a virus in the upper respiratory tract. However, current treatment options for pneumonia are limited because of the strong infectivity and lack of research.: Method: Based on ...

Abstract	Background: Viral pneumonia (VP) is a common inflammatory disease caused by a virus in the upper respiratory tract. However, current treatment options for pneumonia are limited because of the strong infectivity and lack of research. Method: Based on various databases, the mechanisms of Results: Twenty-eight active ingredients of Conclusion: We successfully predicted the active components and targets of
Language	English
Publishing date	2021-09-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2418306-4
ISSN	1936-2625 ; 1936-2625
ISSN (online)	1936-2625
ISSN	1936-2625
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Article ; Online: A Method for Generating Synthetic Electronic Medical Record Text.

Guan, Jiaqi / Li, Runzhe / Yu, Sheng / Zhang, Xuegong

IEEE/ACM transactions on computational biology and bioinformatics

2021 Volume 18, Issue 1, Page(s) 173–182

Abstract: Machine learning (ML) and Natural Language Processing (NLP) have achieved remarkable success in many fields and have brought new opportunities and high expectation in the analyses of medical data, of which the most common type is the massive free-text ... ...

Abstract	Machine learning (ML) and Natural Language Processing (NLP) have achieved remarkable success in many fields and have brought new opportunities and high expectation in the analyses of medical data, of which the most common type is the massive free-text electronic medical records (EMR). However, the free EMR texts are lacking consistent standards, rich of private information, and limited in availability. Also, it is often hard to have a balanced number of samples for the types of diseases under study. These problems hinder the development of ML and NLP methods for EMR data analysis. To tackle these problems, we developed a model called Medical Text Generative Adversarial Network or mtGAN, to generate synthetic EMR text. It is based on the GAN framework and is trained by the REINFORCE algorithm. It takes disease tags as inputs and generates synthetic texts as EMRs for the corresponding diseases. We evaluate the model from micro-level, macro-level and application-level on a Chinese EMR text dataset. The results show that the method has a good capacity to fit real data and can generate realistic and diverse EMR samples. This provides a novel way to avoid potential leakage of patient privacy while still supply sufficient well-controlled cohort data for developing downstream ML and NLP methods.
MeSH term(s)	Algorithms ; Electronic Health Records ; Humans ; Machine Learning ; Medical Informatics/methods ; Natural Language Processing
Language	English
Publishing date	2021-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-9964
ISSN (online)	1557-9964
DOI	10.1109/TCBB.2019.2948985
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Network pharmacological prediction and molecular docking analysis of the combination of Atractylodes macrocephala Koidz. and Paeonia lactiflora Pall. in the treatment of functional constipation and its verification.

Meng, Yuxiao / Li, Xiaojun / Wang, Xiaoting / Zhang, Lu / Guan, Jiaqi

Animal models and experimental medicine

2022 Volume 5, Issue 2, Page(s) 120–132

Abstract: Background: We aimed to reveal the mechanism of functional constipation in the treatment of Atractylodes macrocephala Koidz. (AMK) and Paeonia lactiflora Pall. (PLP).: Methods: The main active ingredients of AMK and PLP were screened by the ... ...

Abstract	Background: We aimed to reveal the mechanism of functional constipation in the treatment of Atractylodes macrocephala Koidz. (AMK) and Paeonia lactiflora Pall. (PLP). Methods: The main active ingredients of AMK and PLP were screened by the Traditional Chinese Medicine Systems Pharmacology (TCMSP) platform. A database of functional constipation targets was established by GeneCard and OMIM. An "ingredient-target" network map was constructed with Cytoscape software (version 3.7.1), and molecular docking analysis was performed on the components and genes with the highest scores. The rats in the normal group were given saline, and those in the other groups were given 10 mg/kg diphenoxylate once a day for 14 days. The serum and intestinal tissue levels of adenosine monophosphate (cAMP), protein kinase A (PKA), and adenylyl cyclase (AC) of the rats and aquaporin (AQP)1, AQP3, and AQP8 were measured. Results: AMK and PLP had a significant role in the regulation of targets in the treatment of functional constipation. After treatment with AMK, PLP, or mosapride, the serum and intestinal tissue levels of AC, cAMP, and PKA were significantly downregulated. Groups receiving AMK and PLP or mosapride exhibited a reduction in the level of AQP1, AQP3, and AQP8 to varying degrees. Conclusion: Molecular docking analysis revealed that AMK and PLP had a significant role in the regulation of targets in the treatment of functional constipation. Studies have confirmed that AMK and PLP can also affect AC, cAMP, and PKA. AC, cAMP, and PKA in model rats were significantly downregulated. AQP expression is closely related to AC, cAMP, and PKA. AMK and PLP can reduce the expression of AQP1, AQP3, and AQP9 in the colon of constipated rats.
MeSH term(s)	Animals ; Aquaporins ; Atractylodes ; Constipation/drug therapy ; Cyclic AMP-Dependent Protein Kinases/therapeutic use ; Medicine, Chinese Traditional ; Molecular Docking Simulation ; Paeonia ; Rats
Chemical Substances	Aqp9 protein, rat ; Aquaporins ; Cyclic AMP-Dependent Protein Kinases (EC 2.7.11.11)
Language	English
Publishing date	2022-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2576-2095
ISSN (online)	2576-2095
DOI	10.1002/ame2.12226
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mechanisms of Ferritinophagy and Ferroptosis in Diseases.

Li, Siqi / Huang, Ping / Lai, Feifan / Zhang, Ting / Guan, Jiaqi / Wan, Haitong / He, Yu

Molecular neurobiology

2023 Volume 61, Issue 3, Page(s) 1605–1626

Abstract: The discovery of the role of autophagy, particularly the selective form like ferritinophagy, in promoting cells to undergo ferroptosis has inspired us to investigate functional connections between diseases and cell death. Ferroptosis is a novel model of ... ...

Abstract	The discovery of the role of autophagy, particularly the selective form like ferritinophagy, in promoting cells to undergo ferroptosis has inspired us to investigate functional connections between diseases and cell death. Ferroptosis is a novel model of procedural cell death characterized by the accumulation of iron-dependent reactive oxygen species (ROS), mitochondrial dysfunction, and neuroinflammatory response. Based on ferroptosis, the study of ferritinophagy is particularly important. In recent years, extensive research has elucidated the role of ferroptosis and ferritinophagy in neurological diseases and anemia, suggesting their potential as therapeutic targets. Besides, the global emergence and rapid transmission of COVID-19, which is caused by SARS-CoV-2, represents a considerable risk to public health worldwide. The potential involvement of ferroptosis in the pathophysiology of brain injury associated with COVID-19 is still unclear. This review summarizes the pathophysiological changes of ferroptosis and ferritinophagy in neurological diseases, anemia, and COVID-19, and hypothesizes that ferritinophagy may be a potential mechanism of ferroptosis. Advancements in these fields will enhance our comprehension of methods to prevent and address neurological disorders, anemia, and COVID-19.
MeSH term(s)	Humans ; Ferroptosis ; Autophagy ; Brain Injuries ; COVID-19 ; Anemia
Language	English
Publishing date	2023-09-22
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-023-03640-0
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