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Article ; Online: Cauchy combination methods for the detection of gene-environment interactions for rare variants related to quantitative phenotypes.

Jin, Xiaoqin / Shi, Gang

2023 Volume 131, Issue 4, Page(s) 241–252

Abstract: The characterization of gene-environment interactions (GEIs) can provide detailed insights into the biological mechanisms underlying complex diseases. Despite recent interest in GEIs for rare variants, published GEI tests are underpowered for an ... ...

Abstract	The characterization of gene-environment interactions (GEIs) can provide detailed insights into the biological mechanisms underlying complex diseases. Despite recent interest in GEIs for rare variants, published GEI tests are underpowered for an extremely small proportion of causal rare variants in a gene or a region. By extending the aggregated Cauchy association test (ACAT), we propose three GEI tests to address this issue: a Cauchy combination GEI test with fixed main effects (CCGEI-F), a Cauchy combination GEI test with random main effects (CCGEI-R), and an omnibus Cauchy combination GEI test (CCGEI-O). ACAT was applied to combine p values of single-variant GEI analyses to obtain CCGEI-F and CCGEI-R and p values of multiple GEI tests were combined in CCGEI-O. Through numerical simulations, for small numbers of causal variants, CCGEI-F, CCGEI-R and CCGEI-O provided approximately 5% higher power than the existing GEI tests INT-FIX and INT-RAN; however, they had slightly higher power than the existing GEI test TOW-GE. For large numbers of causal variants, although CCGEI-F and CCGEI-R exhibited comparable or slightly lower power values than the competing tests, the results were still satisfactory. Among all simulation conditions evaluated, CCGEI-O provided significantly higher power than that of competing GEI tests. We further applied our GEI tests in genome-wide analyses of systolic blood pressure or diastolic blood pressure to detect gene-body mass index (BMI) interactions, using whole-exome sequencing data from UK Biobank. At a suggestive significance level of 1.0 × 10
Language	English
Publishing date	2023-07-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2423-5
ISSN	1365-2540 ; 0018-067X
ISSN (online)	1365-2540
ISSN	0018-067X
DOI	10.1038/s41437-023-00640-7
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Article ; Online: Effect of promoting the concept of rapid rehabilitation surgery on perioperative pain management in patients undergoing orthopedic trauma surgery.

Xu, Feng / Shi, Jiaping / Huang, Xiaoqin / Wang, Keqian

Minerva pediatrics

2023 Volume 75, Issue 6, Page(s) 914–916

MeSH term(s)	Humans ; Pain Management ; Orthopedic Procedures ; Pain, Postoperative/etiology ; Orthopedics ; Medicine
Language	English
Publishing date	2023-05-08
Publishing country	Italy
Document type	Journal Article
ZDB-ID	3062664-X
ISSN	2724-5780
ISSN (online)	2724-5780
DOI	10.23736/S2724-5276.23.07160-4
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Article ; Online: Research progress of traditional Chinese medicine monomer in treating diabetic peripheral neuropathy: A review.

Xiaoqin, Shi / Yi, Tian / Xiaoyu, Liu / Ya, Bu / Jingwen, Shui / Yin, Liping

Medicine

2024 Volume 103, Issue 13, Page(s) e37767

Abstract: Diabetes peripheral neuropathy is one of the most common complications of diabetes. Early symptoms are insidious, while late symptoms mainly include numbness, pain, swelling, and loss of sensation in the limbs, which can lead to disability, foot ulcers, ... ...

Abstract	Diabetes peripheral neuropathy is one of the most common complications of diabetes. Early symptoms are insidious, while late symptoms mainly include numbness, pain, swelling, and loss of sensation in the limbs, which can lead to disability, foot ulcers, amputation, and so on. At present, the pathogenesis is also complex and diverse, and it is not yet clear. Western medicine treatment mainly focuses on controlling blood sugar and nourishing nerves, but the effect is not ideal. In recent years, it has been found that many drug monomers have shown good therapeutic and prognostic effects in the prevention and treatment of diabetes peripheral neuropathy, and related research has become a hot topic. To understand the specific mechanism of action of traditional Chinese medicine monomers in treatment, this article provides a review of their mechanism research and key roles. It mainly includes flavonoids, phenols, terpenes, saponins, alkaloids, polysaccharides, etc. By nuclear factor-κB (NF-κB), the signaling pathways of adenosine monophosphate-activated protein kinase (AMPK), Nrf2/ARE, SIRT1/p53, etc, can play a role in lowering blood sugar, antioxidant, anti-inflammatory, inhibiting cell apoptosis, and autophagy, promoting sciatic nerve regeneration, and have great potential in the prevention and treatment of this disease. A systematic summary of its related mechanisms of action was conducted, providing ideas for in-depth research and exploration of richer traditional Chinese medicine components, and also providing a relatively complete theoretical reference for clinical research on diabetes peripheral neuropathy treatment.
MeSH term(s)	Humans ; Medicine, Chinese Traditional ; Diabetic Neuropathies/drug therapy ; Blood Glucose ; Drugs, Chinese Herbal/therapeutic use ; Drugs, Chinese Herbal/pharmacology ; Sciatic Nerve/pathology ; Diabetes Mellitus
Chemical Substances	Blood Glucose ; Drugs, Chinese Herbal
Language	English
Publishing date	2024-03-29
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.0000000000037767
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Article: Summary of the best evidence for the prevention of nasal injury in preterm infants with nasal noninvasive ventilation.

Fu, Yali / Li, Xiaoqin / Yu, Youxia / Li, Renfeng / Shi, Tian

Translational pediatrics

2024 Volume 13, Issue 2, Page(s) 224–235

Abstract: Background: Due to immaturity, the nose of preterm infants can easily be injured, by even a short application of a nasal device. However, 20% to 60% of preterm infants suffer nasal damage while using nasal continuous positive airway pressure (NCPAP) due ...

Abstract	Background: Due to immaturity, the nose of preterm infants can easily be injured, by even a short application of a nasal device. However, 20% to 60% of preterm infants suffer nasal damage while using nasal continuous positive airway pressure (NCPAP) due to weak skin tissue, prolonged use of nasal device, and improper nursing practices, leading to increased risk of infection and decreased compliance and tolerance. In this study, we retrieved, obtained and integrated the related evidences of prevention of nasal injury in premature infants with nasal noninvasive ventilation to provide reference for clinical practice. Methods: We searched the relevant guidelines, expert consensus, evidence summaries and systematic reviews in the databases and guideline websites of the National Institute for Health and Care Excellence (NICE), Scottish Intercollegiate Guidelines Network (SIGN), the Agency for Health care Research and Quality (AHRQ), Guidelines International Network (GIN), the World Health Organization (WHO) guideline websites, Registered Nurses' Association of Ontario (RANO), Association of Women's Health, Obstetric and Neonatal Nurses (AWHONN), European Pressure Ulcer Advisory Panel (EPUAP), Yi Maitong, British Medical Journal best-practice, Cochrane Library, UpToDate, Embase, PubMed, China National Knowledge Infrastructure (CNKI), Wanfang. The search was limited to the time of library establishment to February 2023. Results: In total, 16 articles were included, including six guidelines, three expert consensuses, two evidence summaries and five systematic reviews. Twenty-eight pieces of evidence were summarized from six aspects: risk assessment, ventilation and connection, skin protection, skin assessment, training and support, and continuous quality improvement. Conclusions: This study summarized the best evidence for the prevention of nasal injury in premature infants through nasal noninvasive ventilation. It is suggested that nurses should consider the actual clinical situation when applying the suggestions from the evidence, formulate corresponding nursing measures, and reduce the occurrence of nasal injury in premature infants.
Language	English
Publishing date	2024-02-26
Publishing country	China
Document type	Journal Article
ZDB-ID	2901309-4
ISSN	2224-4344 ; 2224-4344 ; 2224-4336
ISSN (online)	2224-4344
ISSN	2224-4344 ; 2224-4336
DOI	10.21037/tp-23-465
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Article ; Online: Kernel-based gene-environment interaction tests for rare variants with multiple quantitative phenotypes.

Xiaoqin Jin / Gang Shi

PLoS ONE, Vol 17, Iss 10, p e

2022 Volume 0275929

Abstract: Previous studies have suggested that gene-environment interactions (GEIs) between a common variant and an environmental factor can influence multiple correlated phenotypes simultaneously, that is, GEI pleiotropy, and that analyzing multiple phenotypes ... ...

Abstract	Previous studies have suggested that gene-environment interactions (GEIs) between a common variant and an environmental factor can influence multiple correlated phenotypes simultaneously, that is, GEI pleiotropy, and that analyzing multiple phenotypes jointly is more powerful than analyzing phenotypes separately by using single-phenotype GEI tests. Methods to test the GEI for rare variants with multiple phenotypes are, however, lacking. In our work, we model the correlation among the GEI effects of a variant on multiple quantitative phenotypes through four kernels and propose four multiphenotype GEI tests for rare variants, which are a test with a homogeneous kernel (Hom-GEI), a test with a heterogeneous kernel (Het-GEI), a test with a projection phenotype kernel (PPK-GEI) and a test with a linear phenotype kernel (LPK-GEI). Through numerical simulations, we show that correlation among phenotypes can enhance the statistical power except for LPK-GEI, which simply combines statistics from single-phenotype GEI tests and ignores the phenotypic correlations. Among almost all considered scenarios, Het-GEI and PPK-GEI are more powerful than Hom-GEI and LPK-GEI. We apply Het-GEI and PPK-GEI in the genome-wide GEI analysis of systolic blood pressure (SBP) and diastolic blood pressure (DBP) in the UK Biobank. We analyze 18,101 genes and find that LEUTX is associated with SBP and DBP (p = 2.20×10-6) through its interaction with hemoglobin. The single-phenotype GEI test and our multiphenotype GEI tests Het-GEI and PPK-GEI are also used to evaluate the gene-hemoglobin interactions for 22 genes that were previously reported to be associated with SBP or DBP in a meta-analysis of genetic main effects. MYO1C shows nominal significance (p < 0.05) by the Het-GEI test. NOS3 shows nominal significance in DBP and MYO1C in both SBP and DBP by the single-phenotype GEI test.
Keywords	Medicine ; R ; Science ; Q
Subject code	310
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: Kernel-based gene-environment interaction tests for rare variants with multiple quantitative phenotypes.

Jin, Xiaoqin / Shi, Gang

PloS one

2022 Volume 17, Issue 10, Page(s) e0275929

Abstract	Previous studies have suggested that gene-environment interactions (GEIs) between a common variant and an environmental factor can influence multiple correlated phenotypes simultaneously, that is, GEI pleiotropy, and that analyzing multiple phenotypes jointly is more powerful than analyzing phenotypes separately by using single-phenotype GEI tests. Methods to test the GEI for rare variants with multiple phenotypes are, however, lacking. In our work, we model the correlation among the GEI effects of a variant on multiple quantitative phenotypes through four kernels and propose four multiphenotype GEI tests for rare variants, which are a test with a homogeneous kernel (Hom-GEI), a test with a heterogeneous kernel (Het-GEI), a test with a projection phenotype kernel (PPK-GEI) and a test with a linear phenotype kernel (LPK-GEI). Through numerical simulations, we show that correlation among phenotypes can enhance the statistical power except for LPK-GEI, which simply combines statistics from single-phenotype GEI tests and ignores the phenotypic correlations. Among almost all considered scenarios, Het-GEI and PPK-GEI are more powerful than Hom-GEI and LPK-GEI. We apply Het-GEI and PPK-GEI in the genome-wide GEI analysis of systolic blood pressure (SBP) and diastolic blood pressure (DBP) in the UK Biobank. We analyze 18,101 genes and find that LEUTX is associated with SBP and DBP (p = 2.20×10-6) through its interaction with hemoglobin. The single-phenotype GEI test and our multiphenotype GEI tests Het-GEI and PPK-GEI are also used to evaluate the gene-hemoglobin interactions for 22 genes that were previously reported to be associated with SBP or DBP in a meta-analysis of genetic main effects. MYO1C shows nominal significance (p < 0.05) by the Het-GEI test. NOS3 shows nominal significance in DBP and MYO1C in both SBP and DBP by the single-phenotype GEI test.
MeSH term(s)	Epistasis, Genetic ; Gene-Environment Interaction ; Models, Genetic ; Phenotype
Language	English
Publishing date	2022-10-12
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0275929
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Article ; Online: Clinical and Pathological Characteristics of Patients With Papillary Thyroid Carcinoma Coexisting With Hashimoto's Thyroiditis: A Retrospective Cohort Study.

Yang, Ye / Liu, Jun / Shi, Xiaoqin / Wang, Min

Cancer control : journal of the Moffitt Cancer Center

2023 Volume 30, Page(s) 10732748231199647

Abstract: Background: Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid carcinoma, and Hashimoto's thyroiditis (HT) has been postulated to have a relationship with PTC. This study aims to assess clinical and pathological characteristics of ... ...

Abstract	Background: Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid carcinoma, and Hashimoto's thyroiditis (HT) has been postulated to have a relationship with PTC. This study aims to assess clinical and pathological characteristics of patients with papillary thyroid carcinoma coexisting with Hashimoto's thyroiditis. Methods: A retrospective study was conducted in a cohort of patients with thyroid carcinoma at the Department of Surgery, Shanghai General Hospital from January 2017 to December 2018. Medical records of patients who had PTC with or without HT were reviewed and clinical and histopathological characteristics of these patients were analyzed. Results: A total of 632 patients with thyroid carcinoma were identified. Among them, 614 (97.15%) had PTC and 120/614 (19.0%) harbored PTC together with HT. PTC was significantly associated with HT, as compared with other histological subtypes ( Conclusions: Our study revealed that patients with coexisting PTC and HT were younger, had smaller tumor diameters, a better prognosis, and higher positive rates and expression intensity of Ki67, than did patients with PTC alone.
MeSH term(s)	Humans ; Female ; Thyroid Cancer, Papillary/complications ; Retrospective Studies ; Carcinoma/pathology ; Carcinoma, Papillary/complications ; Carcinoma, Papillary/pathology ; Ki-67 Antigen ; China ; Hashimoto Disease/complications ; Hashimoto Disease/metabolism ; Hashimoto Disease/pathology ; Thyroid Neoplasms/surgery
Chemical Substances	Ki-67 Antigen
Language	English
Publishing date	2023-08-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	1328503-8
ISSN	1526-2359 ; 1073-2748
ISSN (online)	1526-2359
ISSN	1073-2748
DOI	10.1177/10732748231199647
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Article ; Online: What else should hemostatic materials do beyond hemostasis: A review.

Yang, Xinran / Wang, Xiudan / Gao, Xing / Guo, Xiaoqin / Hou, Shike / Shi, Jie / Lv, Qi

Materials today. Bio

2024 Volume 25, Page(s) 101008

Abstract: Massive blood loss due to injury is the leading cause of prehospital deaths in disasters and emergencies. Hemostatic materials are used to realize rapid hemostasis and protect patients from death. Researchers have designed and developed a variety of ... ...

Abstract	Massive blood loss due to injury is the leading cause of prehospital deaths in disasters and emergencies. Hemostatic materials are used to realize rapid hemostasis and protect patients from death. Researchers have designed and developed a variety of hemostatic materials. However, in addition to their hemostatic effect, hemostatic materials must be endowed with additional functions to meet the practical application requirements in different scenarios. Here, strategies for modifications of hemostatic materials for use in different application scenarios are listed: effective positioning at the site of deep and narrow wounds to stop bleeding, resistance to high blood pressure and wound movement to maintain wound formation, rapid and easy removal from the wound without affecting further treatment after hemostasis is completed, and continued function when retained in the wound as a dressing (such as antibacterial, antiadhesion, tissue repair, etc.). The problems encountered in the practical use of hemostatic materials and the strategies and progress of researchers will be further discussed in this review. We hope to provide valuable references for the design of more comprehensive and practical hemostatic materials.
Language	English
Publishing date	2024-03-02
Publishing country	England
Document type	Journal Article ; Review
ISSN	2590-0064
ISSN (online)	2590-0064
DOI	10.1016/j.mtbio.2024.101008
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Article ; Online: Peanut origin traceability: A hybrid neural network combining an electronic nose system and a hyperspectral system.

Wang, Zi / Yu, Yang / Liu, Junqi / Zhang, Qinglun / Guo, Xiaoqin / Yang, Yixin / Shi, Yan

Food chemistry

2024 Volume 447, Page(s) 138915

Abstract: Peanuts, sourced from various regions, exhibit noticeable differences in quality owing to the impact of their natural environments. This study proposes a fast and nondestructive detection method to identify peanut quality by combining an electronic nose ... ...

Abstract	Peanuts, sourced from various regions, exhibit noticeable differences in quality owing to the impact of their natural environments. This study proposes a fast and nondestructive detection method to identify peanut quality by combining an electronic nose system with a hyperspectral system. First, the electronic nose and hyperspectral systems are used to gather gas and spectral information from peanuts. Second, a module for extracting gas and spectral information is designed, combining the lightweight multi-head transposed attention mechanism (LMTA) and convolutional computation. The fusion of gas and spectral information is achieved through matrix combination and lightweight convolution. A hybrid neural network, named UnitFormer, is designed based on the information extraction and fusion processes. UnitFormer demonstrates an accuracy of 99.06 %, a precision of 99.12 %, and a recall of 99.05 %. In conclusion, UnitFormer effectively distinguishes quality differences among peanuts from various regions, offering an effective technological solution for quality supervision in the food market.
MeSH term(s)	Arachis ; Electronic Nose ; Environment ; Food ; Neural Networks, Computer
Language	English
Publishing date	2024-03-02
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2024.138915
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Article ; Online: Theoretical study of Mo

Lin, Long / Long, Xiaoqin / Yang, Xinyu / Shi, Pei / Su, Linlin

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 36, Page(s) 24721–24732

Abstract: The rational design and development of an efficient bifunctional catalyst for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is the key to developing new renewable energy storage and conversion technologies. Transition metal ... ...

Abstract	The rational design and development of an efficient bifunctional catalyst for the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is the key to developing new renewable energy storage and conversion technologies. Transition metal nitrides (TMNs) have shown excellent energy storage and electrochemistry potential due to their unique electronic structure and physicochemical properties. In this paper, based on the first-principles method of density functional theory (DFT), a series of efficient and stable bifunctional single-atom catalysts (SACs) were designed on Mo
Language	English
Publishing date	2023-09-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp02565a
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