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Article ; Online: Causal relationships between atopic dermatitis and psychiatric disorders: a bidirectional two-sample Mendelian randomization study.

Cao, Suqi / Zhang, Zicheng / Liu, Lei / Li, Yin / Li, Wei / Li, Yunling / Wu, Dingfeng

2024 Volume 24, Issue 1, Page(s) 16

Abstract: Background: Observational studies have suggested the potential associations between atopic dermatitis (AD) and psychiatric disorders. However, the causal relationship between them remains uncertain. This study aimed to evaluate the potential ... ...

Abstract	Background: Observational studies have suggested the potential associations between atopic dermatitis (AD) and psychiatric disorders. However, the causal relationship between them remains uncertain. This study aimed to evaluate the potential bidirectional causal relationship between AD and psychiatric disorders, including autism spectrum disorder (ASD), major depressive disorder (MDD), attention deficit hyperactivity disorder (ADHD), bipolar disorder (BD), anorexia nervosa (AN), Tourette syndrome (TS), schizophrenia, and anxiety. Methods: Bidirectional two-sample Mendelian randomization (MR) was employed to elucidate the causality between AD and psychiatric disorders, using summary statistics from the most comprehensive genome-wide association studies conducted on AD (N Results: Bidirectional two-sample MR analysis uncovered significant causal associations between AD and severe psychiatric disorders. Specifically, liability to AD was associated with increased risk of ADHD (OR = 1.116; 95% CI: [1.009, 1.234]; P = 0.033) and ASD (OR = 1.131; 95% CI: [1.023, 1.251]; P = 0.016). Additionally, evidence suggested that liability to ADHD (OR = 1.112; 95% CI: [1.094, 1.130]; P = 9.20e-40), liability to AN (OR = 1.1; 95% CI: [1.068, 1.134]; P = 4.45e-10) and liability to BD (OR = 1.067; 95% CI: [1.009, 1.128]; P = 0.023) were associated with an increased risk of AD. Only the causal association between AD and ASD was independent of the reverse effect bias. These causal associations were robust and not affected by biases of heterogeneity and horizontal pleiotropy. Conclusions: Our study emphasizes the significant causal association between AD and an increased risk of ASD, and also identifying BD and AN as risk factors for AD.
MeSH term(s)	Humans ; Autism Spectrum Disorder/complications ; Autism Spectrum Disorder/genetics ; Depressive Disorder, Major ; Dermatitis, Atopic/complications ; Dermatitis, Atopic/genetics ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Anorexia Nervosa
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2050438-X
ISSN	1471-244X ; 1471-244X
ISSN (online)	1471-244X
ISSN	1471-244X
DOI	10.1186/s12888-023-05478-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides.

Liu, Lei / Yang, Liu / Cao, Suqi / Gao, Zhigang / Yang, Bin / Zhang, Guoqing / Zhu, Ruixin / Wu, Dingfeng

Briefings in bioinformatics

2024 Volume 25, Issue 3

Abstract: Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a ... ...

Abstract	Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a comprehensive database that consolidates both synthetically derived and naturally occurring cyclic peptides is conspicuously absent. To address this void, we introduce CyclicPepedia (https://www.biosino.org/iMAC/cyclicpepedia/), a pioneering database that encompasses 8744 known cyclic peptides. This repository, structured as a composite knowledge network, offers a wealth of information encompassing various aspects of cyclic peptides, such as cyclic peptides' sources, categorizations, structural characteristics, pharmacokinetic profiles, physicochemical properties, patented drug applications, and a collection of crucial publications. Supported by a user-friendly knowledge retrieval system and calculation tools specifically designed for cyclic peptides, CyclicPepedia will be able to facilitate advancements in cyclic peptide drug development.
MeSH term(s)	Peptides, Cyclic/chemistry ; Knowledge Bases ; Databases, Protein
Chemical Substances	Peptides, Cyclic
Language	English
Publishing date	2024-04-27
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/bbae190
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Article ; Online: Evaluation of Chinese healthcare organizations' innovative performance in the digital health era.

Gu, Wenjun / Shu, Luchengchen / Chen, Wanning / Wang, Jinhua / Wu, Dingfeng / Ai, Zisheng / Li, Jiyu

Frontiers in public health

2023 Volume 11, Page(s) 1141757

Abstract: Background: Healthcare workers' relationship with industry is not merely an agent mediating between consumer and vendor, but they are also inventors of the interventions they exist to deliver. Driven by the background of the digital health era, ... ...

Abstract	Background: Healthcare workers' relationship with industry is not merely an agent mediating between consumer and vendor, but they are also inventors of the interventions they exist to deliver. Driven by the background of the digital health era, scientific research and technological (Sci-tech) innovation in the medical field are becoming more and more closely integrated. However, scholars shed little light on Sci-tech relevance to evaluate the innovation performance of healthcare organizations, a distinctive feature of healthcare organizations' innovation in the digital health era. Methods: Academic publications and patents are the manifestations of scientific research outputs and technological innovation outcomes, respectively. The study extracted data from publications and patents of 159 hospitals in China to evaluate their innovation performance. A total of 18 indicators were constructed, four of which were based on text similarity match and represented the Sci-tech relevance. We then applied factor analyses, analytical hierarchy process, and logistic regression to construct an evaluation model. We also examined the relationship between hospitals' innovation performance and their geographical locations. Finally, we implemented a mediation analysis to show the influence of digital health on hospital innovation performance. Results: A total of 16 indicators were involved, four of which represented the Sci-tech including the number of articles matched per patent (NAMP), the number of patents matched per article (NPMA), the proportion of highly matched patents (HMP), and the proportion of highly matched articles (HMA). Indicators of HMP ( Conclusion: This study constructed an assessment model with four invented indicators focusing on Sci-tech relevance to provide a novel tool for researchers to evaluate the innovation performance of healthcare organizations in the digital health era. The regions with high RIP were concentrated on the eastern coastal areas with a higher level of economic development. Therefore, the promotion of scientific and technological innovation policies could be carried out in advance in areas with better economic development. The innovations in the digital health field by healthcare workers enhance the Sci-tech relevance in hospitals and boost their innovation performance. The development of digital health in hospitals depends on the input of medical personnel.
MeSH term(s)	China ; Delivery of Health Care ; Digital Technology ; Hospitals ; Inventions ; Technology
Language	English
Publishing date	2023-07-06
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2711781-9
ISSN	2296-2565 ; 2296-2565
ISSN (online)	2296-2565
ISSN	2296-2565
DOI	10.3389/fpubh.2023.1141757
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Article ; Online: Applications of Dynamic Trust Management Model in Agricultural Scientific Data Security

WU Dingfeng, LIU Tingting, WANG Jian, HU Lin

Nongye tushu qingbao xuebao, Vol 32, Iss 10, Pp 16-

2020 Volume 24

Abstract: Purpose/Significance] In order to meet the needs of intensive agricultural data research, the security protection of agricultural data needs to be developed in a dynamic and adaptive direction. Trust management is one of the core means to ensure data ... ...

Abstract	[Purpose/Significance] In order to meet the needs of intensive agricultural data research, the security protection of agricultural data needs to be developed in a dynamic and adaptive direction. Trust management is one of the core means to ensure data security, the dynamic research and application exploration of its management model is of great significance. [Method/Process] This paper reviews the development process and theoretical framework of dynamic trust management model, analyzes the characteristics of the whole life cycle of agricultural data, summarizes the practical needs of trust management of agricultural data, and expounds the rationality and feasibility of practicing the dynamic trust management model in the field of agricultural data security. On the basis of the above research, combined with the business characteristics of agricultural research itself, this paper explores the application methods and key points of dynamic trust management model in the field of agricultural data security from the aspects of user trust, equipment trust and application trust. [Results/Conclusions] At the end of this paper, the application prospect and future development direction of dynamic trust management model are prospected. The possibility and necessity of expansion and development of a dynamic trust management model to dynamic traffic management and dynamic authorization management, as well as combining with SDP, are discussed.
Keywords	dynamic trust management\|data security\|agricultural\|scientific data ; Bibliography. Library science. Information resources ; Z ; Agriculture ; S
Subject code	650
Language	Chinese
Publishing date	2020-10-01T00:00:00Z
Publisher	Editorial Department of Journal of Library and Information Science in Agriculture
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.

Gao, Wenxing / Gao, Xiang / Zhu, Lixin / Gao, Sheng / Sun, Ruicong / Feng, Zhongsheng / Wu, Dingfeng / Liu, Zhanju / Zhu, Ruixin / Jiao, Na

Gut microbes

2023 Volume 15, Issue 2, Page(s) 2245562

Abstract: Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for ... ...

Abstract	Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.
MeSH term(s)	Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/microbiology ; Polymorphism, Single Nucleotide ; Early Detection of Cancer/methods ; Metagenomics ; Precancerous Conditions/diagnosis ; Precancerous Conditions/microbiology ; Adenoma/diagnosis ; Adenoma/microbiology ; Metagenome ; Gastrointestinal Microbiome/genetics ; Genetic Markers ; Feces/microbiology ; Humans ; Fungi/genetics ; Fungi/isolation & purification ; Bacteria/genetics ; Bacteria/isolation & purification ; Archaea/genetics ; Archaea/isolation & purification ; Viruses/genetics ; Viruses/isolation & purification ; Cohort Studies
Chemical Substances	Genetic Markers
Language	English
Publishing date	2023-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2575755-6
ISSN	1949-0984 ; 1949-0984
ISSN (online)	1949-0984
ISSN	1949-0984
DOI	10.1080/19490976.2023.2245562
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Article ; Online: Host-microbiota interactions contributing to the heterogeneous tumor microenvironment in colorectal cancer.

Li, Xiaoyi / Wu, Dingfeng / Li, Qiuyu / Gu, Jinglan / Gao, Wenxing / Zhu, Xinyue / Yin, Wenjing / Zhu, Ruixin / Zhu, Lixin / Jiao, Na

Physiological genomics

2023 Volume 56, Issue 2, Page(s) 221–234

Abstract: Colorectal cancer (CRC) exhibits pronounced heterogeneity and is categorized into four widely accepted consensus molecular subtypes (CMSs) with unique tumor microenvironments (TMEs). However, the intricate landscape of the microbiota and host-microbiota ... ...

Abstract	Colorectal cancer (CRC) exhibits pronounced heterogeneity and is categorized into four widely accepted consensus molecular subtypes (CMSs) with unique tumor microenvironments (TMEs). However, the intricate landscape of the microbiota and host-microbiota interactions within these TMEs remains elusive. Using RNA-sequencing data from The Cancer Genome Atlas, we analyzed the host transcriptomes and intratumoral microbiome profiles of CRC samples. Distinct host genes and microbial genera were identified among the CMSs. Immune microenvironments were evaluated using CIBERSORTx and ESTIMATE, and microbial coabundance patterns were assessed with FastSpar. Through LASSO penalized regression, we explored host-microbiota associations for each CMS. Our analysis revealed distinct host gene signatures within the CMSs, which encompassed ferroptosis-related genes and specific immune microenvironments. Moreover, we identified 293, 153, 66, and 109 intratumoral microbial genera with differential abundance, and host-microbiota associations contributed to distinct TMEs, characterized by 829, 1,270, 634, and 1,882 robust gene-microbe associations for each CMS in CMS1-CMS4, respectively. CMS1 featured inflammation-related HSF1 activation and gene interactions within the endothelin pathway and
MeSH term(s)	Humans ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/pathology ; Gene Expression Profiling ; Tumor Microenvironment/genetics ; Transcriptome
Language	English
Publishing date	2023-12-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2038823-8
ISSN	1531-2267 ; 1094-8341
ISSN (online)	1531-2267
ISSN	1094-8341
DOI	10.1152/physiolgenomics.00103.2023
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Article: Finding the molecular scaffold of nuclear receptor inhibitors through high-throughput screening based on proteochemometric modelling.

Qiu, Tianyi / Wu, Dingfeng / Qiu, Jingxuan / Cao, Zhiwei

Journal of cheminformatics

2018 Volume 10, Issue 1, Page(s) 21

Abstract: Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specific genes and associated with various diseases, ...

Abstract	Nuclear receptors (NR) are a class of proteins that are responsible for sensing steroid and thyroid hormones and certain other molecules. In that case, NR have the ability to regulate the expression of specific genes and associated with various diseases, which make it essential drug targets. Approaches which can predict the inhibition ability of compounds for different NR target should be particularly helpful for drug development. In this study, proteochemometric modelling was introduced to analysis the bioactivity between chemical compounds and NR targets. Results illustrated the ability of our PCM model for high-throughput NR-inhibitor screening after evaluated on both internal (AUC > 0.870) and external (AUC > 0.746) validation set. Moreover, in-silico predicted bioactive compounds were clustered according to structure similarity and a series of representative molecular scaffolds can be derived for five major NR targets. Through scaffolds analysis, those essential bioactive scaffolds of different NR target can be detected and compared. Generally, the methods and molecular scaffolds proposed in this article can not only help the screening of potential therapeutic NR-inhibitors but also able to guide the future NR-related drug discovery.
Language	English
Publishing date	2018-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2486539-4
ISSN	1758-2946
ISSN	1758-2946
DOI	10.1186/s13321-018-0275-x
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Article ; Online: Reply to: Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact.

Fan, Lu / Wu, Dingfeng / Goremykin, Vadim / Trost, Katharina / Knopp, Michael / Zhang, Chuanlun / Martin, William F / Zhu, Ruixin

Nature ecology & evolution

2022 Volume 6, Issue 12, Page(s) 1832–1835

MeSH term(s)	Rickettsiales ; Phylogeny ; Artifacts ; Mitochondria
Language	English
Publishing date	2022-10-24
Publishing country	England
Document type	Letter ; Comment
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-022-01896-8
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Article ; Online: Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence.

Gao, Sheng / Gao, Xiang / Zhu, Ruixin / Wu, Dingfeng / Feng, Zhongsheng / Jiao, Na / Sun, Ruicong / Gao, Wenxing / He, Qing / Liu, Zhanju / Zhu, Lixin

Gut microbes

2023 Volume 15, Issue 1, Page(s) 2221428

Abstract: Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a ... ...

Abstract	Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. We collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. Microbial alterations in CD patients were assessed at multidimensional levels including species, gene, and SNV level, and then diagnostic models were constructed using artificial intelligence algorithm. A total of 227 species, 1047 microbial genes, and 21,877 microbial SNVs were identified that differed between CD and controls. The species, gene, and SNV models achieved an average AUC of 0.97, 0.95, and 0.77, respectively. Notably, the gene model exhibited superior diagnostic capability, achieving an average AUC of 0.89 and 0.91 for internal and external validations, respectively. Moreover, the gene model was specific for CD against other microbiome-related diseases. Furthermore, we found that phosphotransferase system (PTS) contributed substantially to the diagnostic capability of the gene model. The outstanding performance of PTS was mainly explained by genes celB and manY, which demonstrated high predictabilities for CD with metagenomic datasets and was validated in an independent cohort by qRT-PCR analysis. Our global metagenomic analysis unravels the multidimensional alterations of the microbial communities in CD and identifies microbial genes as robust diagnostic biomarkers across geographically and culturally distinct cohorts.
MeSH term(s)	Humans ; Crohn Disease/diagnosis ; Crohn Disease/genetics ; Metagenome ; Artificial Intelligence ; Gastrointestinal Microbiome/genetics ; Feces ; Genes, Microbial ; Dysbiosis/diagnosis ; Dysbiosis/genetics
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2575755-6
ISSN	1949-0984 ; 1949-0984
ISSN (online)	1949-0984
ISSN	1949-0984
DOI	10.1080/19490976.2023.2221428
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Article ; Online: NAFLDkb: A Knowledge Base and Platform for Drug Development against Nonalcoholic Fatty Liver Disease.

Xu, Tingjun / Gao, Wenxing / Zhu, Lixin / Chen, Wanning / Niu, Chaoqun / Yin, Wenjing / Ma, Liangxiao / Zhu, Xinyue / Ling, Yunchao / Gao, Sheng / Liu, Lei / Jiao, Na / Chen, Weiming / Zhang, Guoqing / Zhu, Ruixin / Wu, Dingfeng

Journal of chemical information and modeling

2023 Volume 64, Issue 7, Page(s) 2817–2828

Abstract: Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with a broad spectrum of histologic manifestations. The rapidly growing prevalence and the complex pathologic mechanisms of NAFLD pose great challenges for treatment ... ...

Abstract	Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease with a broad spectrum of histologic manifestations. The rapidly growing prevalence and the complex pathologic mechanisms of NAFLD pose great challenges for treatment development. Despite tremendous efforts devoted to drug development, there are no FDA-approved medicines yet. Here, we present NAFLDkb, a specialized knowledge base and platform for computer-aided drug design against NAFLD. With multiperspective information curated from diverse source materials and public databases, NAFLDkb presents the associations of drug-related entities as individual knowledge graphs. Practical drug discovery tools that facilitate the utilization and expansion of NAFLDkb have also been implemented in the web interface, including chemical structure search, drug-likeness screening, knowledge-based repositioning, and research article annotation. Moreover, case studies of a knowledge graph repositioning model and a generative neural network model are presented herein, where three repositioning drug candidates and 137 novel lead-like compounds were newly established as NAFLD pharmacotherapy options reusing data records and machine learning tools in NAFLDkb, suggesting its clinical reliability and great potential in identifying novel drug-disease associations of NAFLD and generating new insights to accelerate NAFLD drug development. NAFLDkb is freely accessible at https://www.biosino.org/nafldkb and will be updated periodically with the latest findings.
MeSH term(s)	Humans ; Non-alcoholic Fatty Liver Disease/drug therapy ; Non-alcoholic Fatty Liver Disease/epidemiology ; Non-alcoholic Fatty Liver Disease/pathology ; Reproducibility of Results ; Drug Development
Language	English
Publishing date	2023-05-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c00395
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