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Book ; Online ; E-Book: Traditional Chinese medicine and diseases

Ning, Kang

an omics big-data mining perspective

(Translational bioinformatics)

2022

Author's details	Kang Ning, editor
Series title	Translational bioinformatics
Keywords	Medicine, Chinese ; Bioinformatics ; Big data
Subject code	610.951
Language	English
Size	1 online resource (144 pages)
Publisher	Springer
Publishing place	Gateway East, Singapore
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
ISBN	9789811947711 ; 9789811947704 ; 9811947716 ; 9811947708
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Book ; Online ; E-Book: Methodologies of multi-omics data integration and data mining

Ning, Kang

techniques and applications

(Translational Bioinformatics, ; 19)

2023

Abstract: This book features multi-omics big-data integration and data-mining techniques. In the omics age, paramount of multi-omics data from various sources is the new challenge we are facing, but it also provides clues for several biomedical or clinical ... ...

Author's details	Kang Ning
Series title	Translational Bioinformatics, ; 19
Abstract	This book features multi-omics big-data integration and data-mining techniques. In the omics age, paramount of multi-omics data from various sources is the new challenge we are facing, but it also provides clues for several biomedical or clinical applications. This book focuses on data integration and data mining methods for multi-omics research, which explains in detail and with supportive examples the “What”, “Why” and “How” of the topic. The contents are organized into eight chapters, out of which one is for the introduction, followed by four chapters dedicated for omics integration techniques focusing on several omics data resources and data-mining methods, and three chapters dedicated for applications of multi-omics analyses with application being demonstrated by several data mining methods. This book is an attempt to bridge the gap between the biomedical multi-omics big data and the data-mining techniques for the best practice of contemporary bioinformatics and the in-depth insights for the biomedical questions. It would be of interests for the researchers and practitioners who want to conduct the multi-omics studies in cancer, inflammation disease, and microbiome researches.
Keywords	Data integration (Computer science) ; Data mining/Methodology
Subject code	005.73
Language	English
Size	1 online resource (173 pages)
Edition	1st ed. 2023.
Publisher	Springer
Publishing place	Singapore
Document type	Book ; Online ; E-Book
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
ISBN	9789811982101 ; 9789811982095 ; 9811982104 ; 9811982090
DOI	10.1007/978-981-19-8210-1
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: How does severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) achieve immune evasion?: A narrative review.

Bai, Yahu / Ning, Kang

Medicine

2024 Volume 103, Issue 16, Page(s) e37780

Abstract: COVID-19 caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is a highly contagious disease known for its significant lung damage. Although the impact of the COVID-19 pandemic on our daily lives has been limited, ...

Abstract	COVID-19 caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2, (SARS-CoV-2) is a highly contagious disease known for its significant lung damage. Although the impact of the COVID-19 pandemic on our daily lives has been limited, the virus has not vanished entirely and continues to undergo mutations. This calls for a concentrated focus on the matter of SARS-CoV-2 immune evasion. Drawing on observations of immune escape mechanisms in other viruses, some scholars have proposed that liquid-liquid phase separation might play a crucial role in SARS-CoV-2's ability to evade the immune system. Within the structure of SARS-CoV-2, the nucleocapsid protein plays a pivotal role in RNA replication and transcription. Concurrently, this protein can engage in phase separation with RNA. A thorough examination of the phase separation related to the nucleocapsid protein may unveil the mechanism by which SARS-CoV-2 accomplishes immune evasion. Moreover, this analysis may provide valuable insights for future development of innovative antiviral drugs or vaccines.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Immune Evasion ; Pandemics/prevention & control ; Nucleocapsid Proteins
Chemical Substances	Nucleocapsid Proteins
Language	English
Publishing date	2024-04-19
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	80184-7
ISSN	1536-5964 ; 0025-7974
ISSN (online)	1536-5964
ISSN	0025-7974
DOI	10.1097/MD.0000000000037780
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Article ; Online: Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera

Ning Kang / Hongying Hu

PLoS ONE, Vol 18, Iss 11, p e

Chalcidoidea).

2023 Volume 0294687

Abstract: Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses ... ...

Abstract	Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses responsible for energy production via oxidative phosphorylation, are sensitive to various environmental factors such as extreme cold, hypoxia, and intense ultraviolet radiation characteristic of alpine regions. Whether the molecular evolution of mitochondrial genes in these parasitoids corresponds to changes in the energy requirements and alpine environmental adaptations remains unknown. In this study, we performed a comparative analysis of mitochondrial protein-coding genes from 11 alpine species of Pteromalidae and Eulophidae, along with 18 lowland relatives, including 16 newly sequenced species. We further examined the codon usage preferences (RSCU, ENC-GC3s, neutrality, and PR2 bias plot) in these mitochondrial protein-coding sequences and conducted positive selection analysis based on their Bayesian phylogenetic relationships, and identified positive selection sites in the ATP6, ATP8, COX1, COX3, and CYTB genes, emphasizing the crucial role of mitochondrial gene adaptive evolution in the adaptation of Pteromalidae and Eulophidae to alpine environments. The phylogenetically independent contrast (PIC) analysis results verified the ω ratio of 13 PCGs from Pteromalidae and Eulophidae increased with elevation, and results from generalized linear model confirm that ATP6, ATP8, COX3, and ND1 are closely correlated with temperature-related environmental factors. This research not only enriched the molecular data of endemic alpine species but also underscores the significance of mitochondrial genes in facilitating the adaptation of these minor parasitoids to plateau habitats.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Highly accurate diagnosis of pancreatic cancer by integrative modeling using gut microbiome and exposome data.

Zhang, Yuli / Zhang, Haohong / Liu, Bingqiang / Ning, Kang

iScience

2024 Volume 27, Issue 3, Page(s) 109294

Abstract: The noninvasive detection of pancreatic ductal adenocarcinoma (PDAC) remains an immense challenge. In this study, we proposed a robust, accurate, and noninvasive classifier, namely Multi-Omics Co-training Graph Convolutional Networks (MOCO-GCN). It ... ...

Abstract	The noninvasive detection of pancreatic ductal adenocarcinoma (PDAC) remains an immense challenge. In this study, we proposed a robust, accurate, and noninvasive classifier, namely Multi-Omics Co-training Graph Convolutional Networks (MOCO-GCN). It achieved high accuracy (0.9
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2024.109294
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assessment of Society’s Perceptions on Cultural Ecosystem Services in a Cultural Landscape in Nanchang, China

Ning Kang / Guanhong Xie / Chunqing Liu

Sustainability, Vol 15, Iss 10308, p

2023 Volume 10308

Abstract: Ancient villages are a unique landscape of cultural heritage with both tangible and intangible culture, which provide rich ecosystem services for human beings. Assessment of society’s perceptions on cultural heritage landscapes can improve the ... ...

Abstract	Ancient villages are a unique landscape of cultural heritage with both tangible and intangible culture, which provide rich ecosystem services for human beings. Assessment of society’s perceptions on cultural heritage landscapes can improve the integration of cultural heritage values into decision-making processes that affect landscapes, thereby contributing to maximizing the benefits people receive from cultural ecosystem services. Based on this premise, a new sense-based hierarchical assessment framework for a cultural landscape of ancient villages in China from the perspectives of experts and the public was developed in this study. Field research was conducted by the experts to preliminarily extract the evaluation indicators by identifying and refining the characteristics of the landscape perception units based on the classification of village’s landscape resources. The public indicators as supplements were determined by the semantic and social networks generated with ROSTCM tool post-processing, which followed crawling public comments on the tourism platforms with Python. The findings indicated that visual stimulation (57.36%) is the strongest, while touch perception is the weakest (3.56%). The proportion of hearing, smell, and taste was 21.52%, 12.05%, and 5.53%, respectively. Furthermore, people consider variety, historicity, culture, and localism as the core themes of perception in their landscape experiences. The value and usefulness of the sensory experiences for cultural landscape assessment and for decision-making in the context of cultural ecosystem services are discussed.
Keywords	landscape experience ; landscape assessment ; cultural landscape ; ecosystem services ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	710
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ontology-aware neural network: a general framework for pattern mining from microbiome data.

Zha, Yuguo / Ning, Kang

Briefings in bioinformatics

2022 Volume 23, Issue 2

Abstract: With the rapid accumulation of microbiome data around the world, numerous computational bioinformatics methods have been developed for pattern mining from such paramount microbiome data. Current microbiome data mining methods, such as gene and species ... ...

Abstract	With the rapid accumulation of microbiome data around the world, numerous computational bioinformatics methods have been developed for pattern mining from such paramount microbiome data. Current microbiome data mining methods, such as gene and species mining, rely heavily on sequence comparison. Most of these methods, however, have a clear trade-off, particularly, when it comes to big-data analytical efficiency and accuracy. Microbiome entities are usually organized in ontology structures, and pattern mining methods that have considered ontology structures could offer advantages in mining efficiency and accuracy. Here, we have summarized the ontology-aware neural network (ONN) as a novel framework for microbiome data mining. We have discussed the applications of ONN in multiple contexts, including gene mining, species mining and microbial community dynamic pattern mining. We have then highlighted one of the most important characteristics of ONN, namely, novel knowledge discovery, which makes ONN a standout among all microbiome data mining methods. Finally, we have provided several applications to showcase the advantage of ONN over other methods in microbiome data mining. In summary, ONN represents a paradigm shift for pattern mining from microbiome data: from traditional machine learning approach to ontology-aware and model-based approach, which has found its broad application scenarios in microbiome data mining.
MeSH term(s)	Computational Biology ; Data Mining/methods ; Machine Learning ; Microbiota ; Neural Networks, Computer
Language	English
Publishing date	2022-01-28
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/bbac005
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Article ; Online: Myopia and Rate of Peripapillary Retinal Nerve Fiber Layer Thickness in Diabetic Patients Without Retinopathy: A 2-Year Longitudinal Study.

Wu, Yi / Ning, Kang / He, Mingguang / Huang, Wenyong / Wang, Wei

Current eye research

2024 , Page(s) 1–8

Abstract: Purpose: The aim of this study was to investigate the association between myopia and longitudinal changes in peripapillary retinal nerve fiber layer (pRNFL) thickness in type 2 diabetic patients without diabetic retinopathy (DR).: Methods: A total of ...

Abstract	Purpose: The aim of this study was to investigate the association between myopia and longitudinal changes in peripapillary retinal nerve fiber layer (pRNFL) thickness in type 2 diabetic patients without diabetic retinopathy (DR). Methods: A total of 1069 participants with a median follow-up time of 1.9 years were included in this study. The participants were categorized into four groups based on the presence of myopia (≤ -0.5 diopter [D]) and diabetes without DR, including a control group ( Results: The baseline estimated pRNFL thickness after adjustment for covariates was 113.7 μm, 116.2 μm, 108.0 μm, and 105.6 μm in the control, diabetes, myopia, and diabetes + myopia group, respectively (diabetes > control > myopia = diabetes + myopia, Conclusions: The diabetes group showed a faster rate of average pRNFL thickness reduction compared to healthy controls, regardless of the presence of myopia. The average pRNFL thickness decreased more rapidly when diabetes and myopia were present simultaneously than in the individual diabetes or myopia group. Both diabetes and myopia were associated with accelerated pRNFL loss.
Language	English
Publishing date	2024-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	82079-9
ISSN	1460-2202 ; 0271-3683
ISSN (online)	1460-2202
ISSN	0271-3683
DOI	10.1080/02713683.2024.2327087
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Article ; Online: Investigating the causal associations between metabolic biomarkers and the risk of kidney cancer.

Lin, Lede / Tang, Yaxiong / Ning, Kang / Li, Xiang / Hu, Xu

Communications biology

2024 Volume 7, Issue 1, Page(s) 398

Abstract: Metabolic reprogramming plays an important role in kidney cancer. We aim to investigate the causal effect of 249 metabolic biomarkers on kidney cancer from population-based data. This study extracts data from previous genome wide association studies with ...

Abstract	Metabolic reprogramming plays an important role in kidney cancer. We aim to investigate the causal effect of 249 metabolic biomarkers on kidney cancer from population-based data. This study extracts data from previous genome wide association studies with large sample size. The primary endpoint is random-effect inverse variance weighted (IVW). After completing 249 times of two-sample Mendelian randomization analysis, those significant metabolites are included for further sensitivity analysis. According to a strict Bonferrion-corrected level (P < 2e-04), we only find two metabolites that are causally associated with renal cancer. They are lactate (OR:3.25, 95% CI: 1.84-5.76, P = 5.08e-05) and phospholipids to total lipids ratio in large LDL (low density lipoprotein) (OR: 0.63, 95% CI: 0.50-0.80, P = 1.39e-04). The results are stable through all the sensitivity analysis. The results emphasize the central role of lactate in kidney tumorigenesis and provide novel insights into possible mechanism how phospholipids could affect kidney tumorigenesis.
MeSH term(s)	Humans ; Genome-Wide Association Study ; Carcinoma, Renal Cell/genetics ; Kidney Neoplasms/genetics ; Carcinogenesis ; Lactic Acid ; Mendelian Randomization Analysis ; Phospholipids ; Biomarkers
Chemical Substances	Lactic Acid (33X04XA5AT) ; Phospholipids ; Biomarkers
Language	English
Publishing date	2024-04-01
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06114-8
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Article ; Online: Retrospective assessment of neoadjuvant camrelizumab combined with induction chemotherapy: efficacy in laryngeal preservation for advanced hypopharyngeal and laryngeal squamous cell carcinoma.

Peng, Jin / Luo, Guangfeng / Yu, Yongchao / Ning, Kang / Liu, Xuekui

Cancer immunology, immunotherapy : CII

2024 Volume 73, Issue 3, Page(s) 54

Abstract: Background: Hypopharyngeal and laryngeal squamous cell carcinoma (SCC) account for 25-30% of head and neck SCC. Total laryngectomy, while effective, compromises the quality of life. Immune checkpoint inhibitors such as Camrelizumab offer potential in ... ...

Abstract	Background: Hypopharyngeal and laryngeal squamous cell carcinoma (SCC) account for 25-30% of head and neck SCC. Total laryngectomy, while effective, compromises the quality of life. Immune checkpoint inhibitors such as Camrelizumab offer potential in laryngeal preservation. The study investigated Camrelizumab combined with TP regimen as a neoadjuvant therapy for laryngeal preservation in advanced hypopharyngeal and laryngeal SCC. Methods: A retrospective study was conducted at Sun Yat-sen University Cancer Center on patients diagnosed with locally advanced SCC of the hypopharynx and larynx from October 1, 2019, to October 25, 2022. The efficacy of a first-line treatment combining Camrelizumab (200 mg) and TP regimen (Albumin-bound paclitaxel at 260 mg/m Results: Of the 71 included patients, the median age was 60.7 years. Post the first-line treatment, 90.1% demonstrated an overall response. The one-year and two-year OS rates were 91.5% and 84.3%, respectively. One-year and two-year PFS rates were 92.9% and 83.9%, respectively, with LFS at 85.6% and 73.2%. The initial T4 stage as significantly associated with reduced OS and LFS. Skin reaction was the predominant adverse event. Conclusion: The Camrelizumab-TP regimen demonstrated promising results for advanced hypopharyngeal/laryngeal SCC patients, exhibiting high response rates, OS, and LFS, positioning it as a potential primary option for laryngeal preservation. Further comprehensive, randomized controlled studies are imperative to validate these initial observations and elucidate the regimen's full clinical efficacy in optimizing laryngeal outcomes.
MeSH term(s)	Humans ; Middle Aged ; Neoadjuvant Therapy ; Retrospective Studies ; Hypopharynx ; Quality of Life ; Squamous Cell Carcinoma of Head and Neck/drug therapy ; Larynx ; Head and Neck Neoplasms ; Antibodies, Monoclonal, Humanized
Chemical Substances	camrelizumab (73096E137E) ; Antibodies, Monoclonal, Humanized
Language	English
Publishing date	2024-02-15
Publishing country	Germany
Document type	Journal Article
ZDB-ID	195342-4
ISSN	1432-0851 ; 0340-7004
ISSN (online)	1432-0851
ISSN	0340-7004
DOI	10.1007/s00262-023-03579-0
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