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  1. Article: Correlation of vitamin D receptor gene (ApaI) polymorphism with periodontitis: A meta‐analysis of Chinese population

    Pan, Jian

    Food Science & Nutrition, 7(11):3607-3612

    2019  

    Abstract: Many studies have tried to elucidate the connection between vitamin D receptor (VDR) gene (ApaI) polymorphism and periodontitis; however, so far there is no consensus. To further assess the impact of ApaI polymorphism on periodontitis risk, we have ... ...

    Abstract Many studies have tried to elucidate the connection between vitamin D receptor (VDR) gene (ApaI) polymorphism and periodontitis; however, so far there is no consensus. To further assess the impact of ApaI polymorphism on periodontitis risk, we have conducted a meta‐analysis of Chinese population. Relevant literatures were searched according to PubMed and Chinese database in January 2019. The strength of correlation was evaluated by combining odds ratio (ORs) and 95% confidence interval (CIs). Six case–control studies were identified with inclusion criteria, including 734 cases of periodontitis and 687 controls. Based on the overall analysis, the VDR ApaI polymorphism was not due to the risk of periodontitis in all models. Subgroup analysis showed that the risk of periodontitis in North China was significantly reduced. To sum up, the study shows that VDR‐ApaI polymorphism may be connected with a lower risk of periodontitis in northern China. It is suggested that inferential studies should be conducted in other ethnic groups.
    Keywords VDR ApaI ; meta‐analysis ; polymorphism ; periodontitis
    Language English
    Document type Article
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  2. Book ; Thesis: The role of Tiam1 in cardiac fibroblast activation

    Pan, Jianyuan / Wieland, Thomas

    2020  

    Institution Universität Heidelberg
    Author's details vorgelegt von Jianyuan Pan ; Referent: Prof. Dr. rer. nat. Thomas Wieland
    Language English
    Size 87 Blätter, Illustrationen, Diagramme, 30 cm
    Publishing place Heidelberg
    Publishing country Germany
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Dissertation, Ruprecht-Karls-Universität zu Heidelberg, 2022
    HBZ-ID HT030073238
    Database Catalogue ZB MED Medicine, Health

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    2023 E 1032 order for loan Magazin

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  3. Article ; Online: SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks.

    Pan, Jian-Hua / Du, Pu-Feng

    Briefings in bioinformatics

    2024  Volume 25, Issue 1

    Abstract: Silencers are repressive cis-regulatory elements that play crucial roles in transcriptional regulation. Experimental methods for identifying silencers are always costly and time-consuming. Computational methods, which relies on genomic sequence features, ...

    Abstract Silencers are repressive cis-regulatory elements that play crucial roles in transcriptional regulation. Experimental methods for identifying silencers are always costly and time-consuming. Computational methods, which relies on genomic sequence features, have been introduced as alternative approaches. However, silencers do not have significant epigenomic signature. Therefore, we explore a new way to computationally identify silencers, by incorporating chromatin structural information. We propose the SilenceREIN method, which focuses on finding silencers on anchors of chromatin loops. By using graph neural networks, we extracted chromatin structural information from a regulatory element interaction network. SilenceREIN integrated the chromatin structural information with linear genomic signatures to find silencers. The predictive performance of SilenceREIN is comparable or better than other states-of-the-art methods. We performed a genome-wide scanning to systematically find silencers in human genome. Results suggest that silencers are widespread on anchors of chromatin loops. In addition, enrichment analysis of transcription factor binding motif support our prediction results. As far as we can tell, this is the first attempt to incorporate chromatin structural information in finding silencers. All datasets and source codes of SilenceREIN have been deposited in a GitHub repository (https://github.com/JianHPan/SilenceREIN).
    MeSH term(s) Humans ; Chromatin/genetics ; Silencer Elements, Transcriptional ; Regulatory Sequences, Nucleic Acid ; Genome, Human ; Neural Networks, Computer
    Chemical Substances Chromatin
    Language English
    Publishing date 2024-01-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbad494
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  4. Article: Extracellular vesicles: Emerged as a promising strategy for regenerative medicine.

    Wang, Dian-Ri / Pan, Jian

    World journal of stem cells

    2023  Volume 15, Issue 4, Page(s) 165–181

    Abstract: Cell transplantation therapy has certain limitations including immune rejection and limited cell viability, which seriously hinder the transformation of stem cell-based tissue regeneration into clinical practice. Extracellular vesicles (EVs) not only ... ...

    Abstract Cell transplantation therapy has certain limitations including immune rejection and limited cell viability, which seriously hinder the transformation of stem cell-based tissue regeneration into clinical practice. Extracellular vesicles (EVs) not only possess the advantages of its derived cells, but also can avoid the risks of cell transplantation. EVs are intelligent and controllable biomaterials that can participate in a variety of physiological and pathological activities, tissue repair and regeneration by transmitting a variety of biological signals, showing great potential in cell-free tissue regeneration. In this review, we summarized the origins and characteristics of EVs, introduced the pivotal role of EVs in diverse tissues regeneration, discussed the underlying mechanisms, prospects, and challenges of EVs. We also pointed out the problems that need to be solved, application directions, and prospects of EVs in the future and shed new light on the novel cell-free strategy for using EVs in the field of regenerative medicine.
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2583482-4
    ISSN 1948-0210
    ISSN 1948-0210
    DOI 10.4252/wjsc.v15.i4.165
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  5. Article ; Online: Quantum control of reactions and collisions at ultralow temperatures.

    Zhao, Bo / Pan, Jian-Wei

    Chemical Society reviews

    2022  Volume 51, Issue 5, Page(s) 1685–1701

    Abstract: At temperatures close to absolute zero, the molecular reactions and collisions are dominantly governed by quantum mechanics. Remarkable quantum phenomena such as quantum tunneling, quantum threshold behavior, quantum resonances, quantum interference, and ...

    Abstract At temperatures close to absolute zero, the molecular reactions and collisions are dominantly governed by quantum mechanics. Remarkable quantum phenomena such as quantum tunneling, quantum threshold behavior, quantum resonances, quantum interference, and quantum statistics are expected to be the main features in ultracold reactions and collisions. Ultracold molecules offer great opportunities and challenges in the study of these intriguing quantum phenomena in molecular processes. In this article, we review the recent progress in the preparation of ultracold molecules and the study of ultracold reactions and collisions using ultracold molecules. We focus on the controlled ultracold chemistry and the scattering resonances at ultralow temperatures. The challenges in understanding the complex ultracold reactions and collisions are also discussed.
    Language English
    Publishing date 2022-03-07
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1472875-8
    ISSN 1460-4744 ; 0306-0012
    ISSN (online) 1460-4744
    ISSN 0306-0012
    DOI 10.1039/d1cs01040a
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  6. Article ; Online: Rare Simultaneous Left and Right-Sided Native Valve Infective Endocarditis Caused by Rare Bacterium.

    Pan, Jian-Hong

    International heart journal

    2019  Volume 60, Issue 2, Page(s) 474–476

    Abstract: Simultaneous left and right-sided native valve infective endocarditis (IE) is rare. Staphylococcus aureus was the predominant organism for bilateral IE. Shunt diseases are common risk factors of both-sided IE. Streptococcus anginosus (S. anginosus) is ... ...

    Abstract Simultaneous left and right-sided native valve infective endocarditis (IE) is rare. Staphylococcus aureus was the predominant organism for bilateral IE. Shunt diseases are common risk factors of both-sided IE. Streptococcus anginosus (S. anginosus) is usually associated with pyogenic infections, but rarely a cause of IE. Here we present an extremely rare case of simultaneous left and right-sided native valve IE affecting the mitral and tricuspid valves caused by S. anginosus in an adult patient that has not been reported in the literature previously, particularly without the most frequent predisposing factors of IE. A 66-year-old man was admitted due to generalized fatigue, chills, malaise, and intermittent fevers for 1 year. A grade III-IV/VI systolic murmur at the mitral area and a III/VI systolic murmur at the tricuspid area were noted on physical examination. Laboratory evaluation revealed an elevated erythrocyte sedimentation rate and C-reactive protein level, and high fasting blood glucose. Blood culture was positive for S. anginosus. Echocardiography revealed vegetations in both sides of the heart: a large mitral valve vegetation with severe mitral regurgitation, as well as another vegetation on the tricuspid valve with moderate regurgitation. The case highlights a rare pathogen of both-sided IE, a rare presentation of S. anginosus infection, and several points worthy of note in echocardiography of IE.
    MeSH term(s) Adult ; Aged ; Anti-Infective Agents/administration & dosage ; Blood Culture/methods ; Blood Sedimentation ; C-Reactive Protein/analysis ; Cardiac Valve Annuloplasty/methods ; Echocardiography/methods ; Echocardiography, Transesophageal/methods ; Endocarditis, Bacterial/blood ; Endocarditis, Bacterial/microbiology ; Endocarditis, Bacterial/physiopathology ; Endocarditis, Bacterial/therapy ; Heart Valve Prosthesis Implantation/methods ; Humans ; Male ; Mitral Valve/diagnostic imaging ; Mitral Valve/microbiology ; Mitral Valve/surgery ; Mitral Valve Insufficiency/diagnosis ; Mitral Valve Insufficiency/etiology ; Mitral Valve Insufficiency/surgery ; Physical Examination/methods ; Streptococcal Infections/blood ; Streptococcal Infections/diagnosis ; Streptococcal Infections/physiopathology ; Streptococcal Infections/therapy ; Streptococcus anginosus/isolation & purification ; Tomography, X-Ray Computed/methods ; Treatment Outcome ; Tricuspid Valve/diagnostic imaging ; Tricuspid Valve/microbiology ; Tricuspid Valve/surgery ; Tricuspid Valve Insufficiency/diagnosis ; Tricuspid Valve Insufficiency/etiology ; Tricuspid Valve Insufficiency/surgery
    Chemical Substances Anti-Infective Agents ; C-Reactive Protein (9007-41-4)
    Language English
    Publishing date 2019-01-10
    Publishing country Japan
    Document type Case Reports ; Journal Article
    ZDB-ID 2187806-7
    ISSN 1349-3299 ; 1349-2365
    ISSN (online) 1349-3299
    ISSN 1349-2365
    DOI 10.1536/ihj.18-347
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  7. Article ; Online: Role of epigenetic regulatory mechanisms in age-related bone homeostasis imbalance.

    Zhong, Yunyu / Zhou, Xueer / Pan, Zijian / Zhang, Jiankang / Pan, Jian

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2024  Volume 38, Issue 9, Page(s) e23642

    Abstract: Alterations to the human organism that are brought about by aging are comprehensive and detrimental. Of these, an imbalance in bone homeostasis is a major outward manifestation of aging. In older adults, the decreased osteogenic activity of bone marrow ... ...

    Abstract Alterations to the human organism that are brought about by aging are comprehensive and detrimental. Of these, an imbalance in bone homeostasis is a major outward manifestation of aging. In older adults, the decreased osteogenic activity of bone marrow mesenchymal stem cells and the inhibition of bone marrow mesenchymal stem cell differentiation lead to decreased bone mass, increased risk of fracture, and impaired bone injury healing. In the past decades, numerous studies have reported the epigenetic alterations that occur during aging, such as decreased core histones, altered DNA methylation patterns, and abnormalities in noncoding RNAs, which ultimately lead to genomic abnormalities and affect the expression of downstream signaling osteoporosis treatment and promoter of fracture healing in older adults. The current review summarizes the impact of epigenetic regulation mechanisms on age-related bone homeostasis imbalance.
    MeSH term(s) Humans ; Epigenesis, Genetic ; Homeostasis ; Aging/genetics ; Aging/physiology ; Animals ; Bone and Bones/metabolism ; DNA Methylation ; Osteoporosis/genetics ; Osteoporosis/metabolism ; Mesenchymal Stem Cells/metabolism ; Osteogenesis/genetics ; Osteogenesis/physiology ; Histones/metabolism
    Chemical Substances Histones
    Language English
    Publishing date 2024-05-01
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.202302665R
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    Zs.MO 296: Show issues

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  8. Article: RUNX1在骨发育及骨相关疾病中的作用研究进展.

    Pan, Zijian / Zhou, Xue'er / Cao, Zhiwei / Pan, Jian

    Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition

    2024  Volume 55, Issue 2, Page(s) 256–262

    Abstract: Runt-related transcription factor (RUNX1) is a transcription factor closely involved in hematopoiesis. ...

    Title translation Latest Findings on the Role of RUNX1 in Bone Development and Disorders.
    Abstract Runt-related transcription factor (RUNX1) is a transcription factor closely involved in hematopoiesis.
    MeSH term(s) Core Binding Factor Alpha 2 Subunit/genetics ; Core Binding Factor Alpha 2 Subunit/metabolism ; Humans ; Animals ; Cell Differentiation ; Bone Development/physiology ; Bone Development/genetics ; Chondrocytes/metabolism ; Osteoblasts/metabolism ; Osteoblasts/cytology ; Osteoclasts/metabolism ; Osteoclasts/cytology ; Mesenchymal Stem Cells/metabolism ; Mesenchymal Stem Cells/cytology ; Mice ; Bone Diseases/genetics ; Bone Diseases/metabolism ; Osteoporosis/genetics ; Osteoporosis/metabolism ; Osteoarthritis/metabolism ; Osteoarthritis/genetics ; Osteoarthritis/etiology
    Chemical Substances Core Binding Factor Alpha 2 Subunit ; RUNX1 protein, human
    Language Chinese
    Publishing date 2024-04-19
    Publishing country China
    Document type Review ; English Abstract ; Journal Article
    ZDB-ID 2106840-9
    ISSN 1672-173X
    ISSN 1672-173X
    DOI 10.12182/20240360103
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  9. Article: Quantum control of reactions and collisions at ultralow temperatures

    Zhao, Bo / Pan, Jian-Wei

    Chemical Society reviews. 2022 Mar. 7, v. 51, no. 5

    2022  

    Abstract: At temperatures close to absolute zero, the molecular reactions and collisions are dominantly governed by quantum mechanics. Remarkable quantum phenomena such as quantum tunneling, quantum threshold behavior, quantum resonances, quantum interference, and ...

    Abstract At temperatures close to absolute zero, the molecular reactions and collisions are dominantly governed by quantum mechanics. Remarkable quantum phenomena such as quantum tunneling, quantum threshold behavior, quantum resonances, quantum interference, and quantum statistics are expected to be the main features in ultracold reactions and collisions. Ultracold molecules offer great opportunities and challenges in the study of these intriguing quantum phenomena in molecular processes. In this article, we review the recent progress in the preparation of ultracold molecules and the study of ultracold reactions and collisions using ultracold molecules. We focus on the controlled ultracold chemistry and the scattering resonances at ultralow temperatures. The challenges in understanding the complex ultracold reactions and collisions are also discussed.
    Keywords chemistry ; quantum mechanics ; statistics
    Language English
    Dates of publication 2022-0307
    Size p. 1685-1701.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ZDB-ID 1472875-8
    ISSN 1460-4744 ; 0306-0012
    ISSN (online) 1460-4744
    ISSN 0306-0012
    DOI 10.1039/d1cs01040a
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: ScInfoVAE: interpretable dimensional reduction of single cell transcription data with variational autoencoders and extended mutual information regularization.

    Pan, Weiquan / Long, Faning / Pan, Jian

    BioData mining

    2023  Volume 16, Issue 1, Page(s) 17

    Abstract: Single-cell RNA-sequencing (scRNA-seq) data can serve as a good indicator of cell-to-cell heterogeneity and can aid in the study of cell growth by identifying cell types. Recently, advances in Variational Autoencoder (VAE) have demonstrated their ability ...

    Abstract Single-cell RNA-sequencing (scRNA-seq) data can serve as a good indicator of cell-to-cell heterogeneity and can aid in the study of cell growth by identifying cell types. Recently, advances in Variational Autoencoder (VAE) have demonstrated their ability to learn robust feature representations for scRNA-seq. However, it has been observed that VAEs tend to ignore the latent variables when combined with a decoding distribution that is too flexible. In this paper, we introduce ScInfoVAE, a dimensional reduction method based on the mutual information variational autoencoder (InfoVAE), which can more effectively identify various cell types in scRNA-seq data of complex tissues. A joint InfoVAE deep model and zero-inflated negative binomial distributed model design based on ScInfoVAE reconstructs the objective function to noise scRNA-seq data and learn an efficient low-dimensional representation of it. We use ScInfoVAE to analyze the clustering performance of 15 real scRNA-seq datasets and demonstrate that our method provides high clustering performance. In addition, we use simulated data to investigate the interpretability of feature extraction, and visualization results show that the low-dimensional representation learned by ScInfoVAE retains local and global neighborhood structure data well. In addition, our model can significantly improve the quality of the variational posterior.
    Language English
    Publishing date 2023-06-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2438773-3
    ISSN 1756-0381
    ISSN 1756-0381
    DOI 10.1186/s13040-023-00333-1
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