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Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework

BMC BIOINFORMATICS 2023年第1期24卷 1-18页

作者： Hu, shuwen Jing, Yi Li, Tao Wang, You-Gan Liu, Zhenyu Gao, Jing Tian, yu-Chu Queensland Univ Technol Sch Comp Sci Brisbane Qld 4001 Australia CSIRO Agr & Food St Lucia Qld 4067 Australia Univ New South Wales Fac Social Sci Sydney 2052 Australia Inner Mongolia Agr Univ Sch Life Sci Hohhot 010018 Peoples R China Australian Catholic Univ Inst Learning Sci & Teacher Educ Brisbane Qld 4000 Australia Inner Mongolia Agr Univ Sch Comp & Informat Engn Hohhot 010018 Peoples R China

BackgroundThe central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation. Understanding gene regulatory relationships is crucial for unravelling the mechanisms that underlie various cellular biological processes. While it is possible to infer circadian gene regulatory relationships from time-series gene expression data, relying solely on correlation-based inference may not provide sufficient information about causation. Moreover, gene expression data often have high dimensions but a limited number of observations, posing challenges in their *** this paper, we introduce a new hybrid framework, referred to as Circadian Gene Regulatory Framework (CGRF), to infer circadian gene regulatory relationships from gene expression data of rats. The framework addresses the challenges of high-dimensional data by combining the fuzzy C-means clustering algorithm with dynamic time warping distance. Through this approach, we efficiently identify the clusters of genes related to the target gene. To determine the significance of genes within a specific cluster, we employ the Wilcoxon signed-rank test. Subsequently, we use a dynamic vector autoregressive method to analyze the selected significant gene expression profiles and reveal directed causal regulatory relationships based on partial *** proposed CGRF framework offers a comprehensive and efficient solution for understanding circadian gene regulation. Circadian gene regulatory relationships are inferred from the gene expression data of rats based on the Aanat target gene. The results show that genes Pde10a, Atp7b, Prok2, Per1, Rhobtb3 and Dclk1 stand out, which have been known to be essential for the regulation of circadian activity. The potential relationships between genes Tspan15, Eprs, Eml5 and Fsbp with a circadian rhythm need further experimental research.

关键词： Circadian gene Gene regulatory relationships Gene expression data Fuzzy c-means clustering Dynamic time warping

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Clinical and gonadal transcriptome analysis of 38,XX disorder of sex development pigs

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BIOLOGY OF REPRODUCTION 2024年第1期111卷 212-226页

作者： Wu, Jinhua Tan, shuwen Zhou, Yi Zhao, Haiquan yu, Hui Zhong, Bingzhou yu, Congying Wang, Haoming Yang, Yin Li, Hua Li, yugu South China Agr Univ Coll Vet Med 483 Wushan Rd Guangzhou 510642 Peoples R China Foshan Univ Sch Life Sci & Engn Guangdong Prov Key Lab Anim Mol Design & Precise B 33 Guangyun Rd Foshan 528225 Peoples R China Zunyi Med Univ Coll Basic Med Zunyi Peoples R China

Pigs serve as a robust animal model for the study of human diseases, notably in the context of disorders of sex development (DSD). This study aims to investigate the phenotypic characteristics and molecular mechanisms underlying the reproductive and developmental abnormalities of 38,XX ovotestis-DSD (OT-DSD) and 38,XX testis-DSD (T-DSD) in pigs. Clinical and transcriptome sequencing analyses were performed on DSD and normal female pigs. Cytogenetic and SRY analyses confirmed that OT/T-DSD pigs exhibited a 38,XX karyotype and lacked the SRY gene. The DSD pigs had higher levels of follicle-stimulating hormone, luteinizing hormone, and progesterone, but lower testosterone levels when compared with normal male pigs. The reproductive organs of OT/T-DSD pigs exhibit abnormal development, displaying both male and female characteristics, with an absence of germ cells in the seminiferous tubules. Sex determination and development-related differentially expressed genes shared between DSD pigs were identified in the gonads, including WT1, DKK1, CTNNB1, WTN9B, SHOC, PTPN11, NRG1, and NXK3-1. DKK1 is proposed as a candidate gene for investigating the regulatory mechanisms underlying gonadal phenotypic differences between OT-DSD and T-DSD pigs. Consequently, our findings provide insights into the molecular pathogenesis of DSD pigs and present an animal model for studying into DSD in humans. Summary Sentence Clinical characterization of OT/T-DSD pigs and associated differentially expressed genes using clinical examination and transcriptomic approaches provide support for understanding the molecular pathogenesis of DSD pigs. [GRAPHICS] .

关键词： DSD pig phenotype sex hormone cytogenetic mRNA transcriptome

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Influence of color bagging on anthocyanin and sugar in bayberry fruit

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SCIENTIA HORTICULTURAE 2025年 345卷

作者： Li, Xiaobai Li, Sun yu, Zheping Zhang, Yang Yang, Han Wu, yuyong Ying, Zhengzheng Qi, Xingjiang Zhang, shuwen Zhejiang Acad Agr Sci Inst Hort State Key Lab Agr Prod Safety 298 Desheng Rd Hangzhou 310021 Zhejiang Peoples R China Xianghu Lab 168 Gengwen Rd Hangzhou 311231 Zhejiang Peoples R China Xianju Specialty Technol Promot Ctr Xianju 317300 Zhejiang Peoples R China

Fruit bagging is a prevalent technique in fruit production to enhance quality and protect fruits from various biotic and abiotic stresses. In this study, we employed bags of different colors (red, yellow, blue, green, and transparent as CK) to investigate their impacts on bayberry fruit quality. The red bag raised the most red light by 28.61 % and slightly elevated blue light by 7.55 %. Conversely, the blue bag filtered out nearly half (48.78 %) of photosynthetic irradiance, resulting in the lowest photosynthetic irradiance (1379.87 mW), despite increasing blue light by 24.71 %. As a result, the red bag led to the highest accumulation of anthocyanins and soluble sugars, while the blue bag resulted in the least accumulation of these compounds. Similarly, the red bag resulted in the highest level of gene expressions essential for anthocyanin biosynthesis, including MrCHS, MrCHI, MrF3H, MrDFR1, MrANS, MrUFGT, as well as the transcriptional factor, MrMYB1, along with genes crucial for sugar biosynthesis such as MrSPS1, MrSPS2, and MrINV1. In contrast, the blue bag resulted in the lowest expression levels of these genes. The results suggest that increased red light improves bayberry fruit quality, whereas low photosynthetic irradiance is detrimental. Therefore, red bagging could be adopted in bayberry production to improve fruit quality, while bags with poor light transmittance should be avoided.

关键词： Bayberry Color bagging Light quality Fruit quality

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Prefrontal cortex excitatory neurons show distinct response to heroin-associated cue and social stimulus after prolonged heroin abstinence in mice

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NEUROPSYCHOPHARMACOLOGY 2025年 1-14页

作者： Wang, yunwanbin Liu, Junting yue, shuwen Chen, Lu Singh, Archana yu, Tianshi Calipari, Erin S. Wang, Zi-Jun Univ Kansas Sch Pharm Dept Pharmacol & Toxicol Lawrence KS 66045 USA Vanderbilt Univ Dept Pharmacol Nashville TN USA Vanderbilt Univ Vanderbilt Brain Inst Nashville TN USA Vanderbilt Univ Vanderbilt Ctr Addict Res Nashville TN USA Univ Kansas Cofrin Logan Ctr Addict Res & Treatment Lawrence KS 66045 USA

Substance use disorder (SUD) has been linked with social impairments. The social cognitive dysfunctions can further increase the risk of the development of SUD or relapse. Therefore, understanding the neural mechanism of substance exposure-associated social impairments is beneficial for the development of novel prevention or treatment strategies for SUD. The prefrontal cortex (PFC) is a key brain region involved in both social cognition and drug addiction. Specifically, the prelimbic part of PFC (PrL) regulates social interaction and heroin-seeking behavior. Therefore, in this study, we explored how PFC excitatory neurons respond to social stimuli after prolonged abstinence from heroin self-administration (SA). Using fiber photometry calcium imaging, we monitored calcium-dependent fluorescent signals in PrL CaMKII-expressing neurons during drug seeking and social interaction tests following 14 days of abstinence from heroin SA. We found that GCaMP6f signals in PrL CaMKII-expressing neurons were increased when heroin-associated cues were presented during drug-seeking tests in both male and female mice after prolonged heroin abstinence, although the baseline neuronal activity in home cage is lower in the heroin group. Conversely, the calcium signals in PrL CaMKII-expressing neurons during social investigation were decreased after heroin abstinence in both sexes, along with reduced total social interaction time. In addition, drug-seeking behavior is partially negatively correlated with social investigation time. These findings provide direct evidence showing that opioid exposure impairs the PFC functional response to social stimuli, which may potentially increase the risk for opioid relapse.

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Pre-service student teachers' metacognition in an online learning community: An epistemic network analysis

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EDUCATION AND INFORMATION TECHNOLOGIES 2024年第11期29卷 14403-14429页

作者： Zhao, Li Wang, shuwen Su, yu-Sheng Nanjing Normal Univ Sch Educ Sci Nanjing Peoples R China Natl Chung Cheng Univ Dept Comp Sci & Informat Engn Chiayi Taiwan Natl Taiwan Ocean Univ Dept Comp Sci & Engn Keelung Taiwan

Pre-service student teachers (PSSTs) should improve their metacognition in order to support their long-term development in their future complex teaching and learning lives. Although previous studies have explored the role of metacognition in learners' learning effectiveness, the interrelationships pattern of metacognition elements in the process of metacognition and the metacognition characteristics of different genders and learning performance groups still remain unclear. This study clarified the intrinsic structure of metacognition, and gender and learning performance differences among PSSTs in an online learning community. We collected 33 PSSTs' self-reported reflection data on six learning topics. A total of 1,188 reflection paragraphs were coded and 2,335 metacognitive utterances were presented based on the metacognition model. Subsequently, this study identified metacognitive components among different groups of PSSTs by comparing epistemic networks of self-reported reflections via epistemic network analysis. Results show that metacognitive components of PSSTs in an online learning community were mainly metacognitive experiences (36.32%) and actions (or strategies) (28.01%). Female PSSTs used metacognitive knowledge (21.4%) and goals (or tasks) (15.8%) more frequently, and the relationship between their metacognitive knowledge and goals (or tasks) was closer compared with male PSSTs. Specifically, the ENA results showed that the associations between metacognitive knowledge and goals (or tasks) (connection coefficient: 0.24) of females were stronger than those of males. In addition, the high learning performance group used metacognitive knowledge (18.7%) and goals (or tasks) (15.9%) more frequently, and they also had a closer connection between metacognitive knowledge and goals (or tasks) compared with the high learning performance group. Specifically, the ENA results showed that compared with the low learning performance PSSTs, high learning performance PSSTs'

关键词： Epistemic network analysis Metacognition Online learning community Pre-service student teachers

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Oxidative degradation of p-chlorophenol by the persulfate-doped Fe-Mn bimetallic hydroxide, the parametrical significance, and systematical optimization

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ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH 2022年第1期29卷 1289-1300页

作者： Huang, Tao Du, Jing yu, Danni Deng, Shihan Zhang, shuwen Liu, Longfei Changshu Inst Technol Sch Mat Engn Changshu 215500 Jiangsu Peoples R China Univ South China Nucl Resources Engn Coll Hengyang 421001 Hunan Peoples R China

Aqueous Fe(II)-catalyzed activation commonly deteriorates the oxidation performance of persulfate (PS) to the treatment of organic contaminants. In this study, a PS-doped layered bimetallic hydroxide (Fe-Mn hydroxide) was synthesized to construct a heterogeneously catalytic system to solve the issue brought by homogeneity. The molar ratio of Fe(II) to Mn(II) and the mass ratio of PS to Fe-Mn hydroxide both had a significant impact on the catalytic degradation of p-CP. Reaction temperatures engaged in the most essential role in influencing the degradation and removal of p-chlorophenol (p-CP). The optimal combination of factors for the preparation of PS-hydroxide and the treatment of p-CP was finally determined by significance analysis. The degradation process was appropriately fitted by the pseudo-first-order kinetic model. The benzene ring in p-CP was broken by PS-hydroxide during the adsorption. The surface modification of PS-hydroxide caused by the valence transition of Mn was beneficial to the adsorption and catalytic degradation of p-CP.

关键词： Persulfate-doped Fe-Mn hydroxide P-chlorophenol degradation Optimization Degradation kinetics Systematical optimization

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Comparative Venous and Arterial Thromboembolism Profiles Associated with Different Cyclin-Dependent Kinase 4/6 Inhibitors: A Real-World Study

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BLOOD 2024年 144卷 5084-5085页

作者： Chiang, Cho Han Lin, shuwen Chang, yu-Cheng Song, Junmin Chi, Kuan-yu Xanthavanij, Nutchapon Chang, yu Chiang, Cho-Hung Xu, Xiaocao Haze Mt Auburn Hosp Dept Med Cambridge MA USA Montefiore Einstein Canc Ctr Montefiore Med Ctr Bronx NY USA Danbury Hosp Dept Med Danbury CT USA Albert Einstein Coll Med Jacobi Med Ctr Dept Med Bronx NY USA Mt Auburn Hosp Cambridge MA USA Natl Cheng Kung Univ Natl Cheng Kung Univ Hosp Coll Med Dept SurgSect Neurosurg Tainan Taiwan Natl Taiwan Univ Hosp Taipei Taiwan Univ Vermont Med Ctr Burlington VT USA

Introduction: Cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors are used in conjunction with endocrine therapy in hormone receptor-positive breast cancer. Recent data from clinical trials and real-world observational studies have reported an increased venous and arterial thromboembolism rates associated with CDK4/6 inhibitors. However, there has been limited data on the comparative thromboembolism rates among different types of CDK4/6 inhibitors. To address this knowledge gap, we leveraged a large global database to compare the thromboembolism profiles among different CDK4/6 inhibitors. Methods: We performed a retrospective, propensity score-matched cohort study using the TriNetX Analytics Network database, which includes de-identified electronic health records from over 70 healthcare organizations and 101 million individuals. We included adult female breast cancer patients who received an aromatase inhibitor (AI) and a CDK4/6 inhibitor from February 2015 to June 2023. We excluded patients with a prior history of venous thromboembolism (VTE), arterial thromboembolism (ATE), atrial fibrillation, and those who received oral anticoagulation. The index date was determined as the start date of AI and CDK4/6 inhibitor therapy. The primary outcomes were VTE, which was defined as a composite of pulmonary embolism (PE) and deep venous thrombosis (DVT), and ATE, which was defined as a composite of myocardial infarction and ischemic stroke. The secondary outcomes were individual components of VTE and ATE. All outcomes were captured within 1 year of the index date. Cohorts were matched using a propensity score that incorporated variables such as age, sex, race, underlying comorbidities, components of the Khorana score, and breast cancer-directed therapy. Results: We identified a total of 8912 patients eligible for inclusion, among which 6632 received palbociclib, 790 received ribociclib, and 1490 received abemaciclib. After propensity score matching, cohorts were well-balance

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Molecular-level transformations of biomass burning-derived water-soluble organic carbon during dark aqueous OH oxidation: Insights from absorption, fluorescence, high-performance size exclusion chromatography and high-resolution mass spectrometry analysis

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SCIENCE OF THE TOTAL ENVIRONMENT 2024年 912卷 169290页

作者： Fan, Xingjun Xie, shuwen yu, Xufang Cheng, Ao Chen, Dan Ji, Wenchao Liu, Xiaolong Song, Jianzhong Peng, Pingan Anhui Sci & Technol Univ Coll Resource & Environm Fengyang 233100 Peoples R China Chinese Acad Sci State Key Lab Organ Geochem Guangzhou Inst Geochem Guangzhou 510640 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

Biomass burning (BB) releases large amounts of water-soluble organic carbon (WSOC), which would undergo heterogenous oxidation processes that induce transformations in both molecular structures and compositions within BB WSOC. This study designed an aqueous oxidation initiated by OH radicals in the absence of light for WSOC extracted from smoke particles generated by burning of corn straw and fir wood. The BB WSOC was comprehensively characterized using a combination of UV-visible spectra, excitation-emission matrix fluorescence in conjunction with parallel factor analysis (EEM-PARAFAC), high-performance size exclusion chroma-tography (HPSEC), and high-resolution mass spectrometry (HRMS) analyses. Over the course of oxidation, both chromophores and fluorophores exhibited gradual decreases. Moreover, EEM-PARAFAC revealed a preferential degradation of larger-sized protein-like/phenol-like organic matters, accompanied by the accumulation and/or formation of humic-like substances in aged BB WSOC. HPSEC analysis showed notable changes in molecular weight (MW) distributions for both types of BB WSOC during oxidation. Specifically, high MW species (>1 kDa) displayed a tendency to form along with oxidation, possibly attributed to the formation of assemblies via intermolecular weak forces. After oxidation, evidence of CHO compound degradation and enrichment/formation of CHON compounds was observed for both types of BB WSOC. Remarkably, the resistant, degraded and produced molecules for BB WSOC were dominated by CHO (38-73 %) and lignin-like molecules (41-47 %), suggesting diverse responses to oxidation within these two groups. Furthermore, polyphenols experienced selective degradation, while CHON, aliphatic and poly-aromatic molecules tended to form during the oxidation process for both types of BB WSOC. In summary, this study provides a comprehensive understanding of the molecular-level transformations undergone by BB WSOC during dark aqueous OH oxidation. The findings sign

关键词： Water-soluble organic carbon Biomass burning Dark aqueous OH oxidation Optical properties

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Phase State Regulates Photochemical HONO Production from NaNO3/Dicarboxylic Acid Mixtures

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ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024年第17期58卷 7516-7528页

作者： Li, Qiong Ma, Shuaishuai Liu, yu Wu, Xinyuan Fu, Hongbo Tu, Xiang Yan, shuwen Zhang, Liwu George, Christian Chen, Jianmin Fudan Univ Dept Environm Sci & Engn Shanghai Key Lab Atmospher Particle Pollut Prevent Shanghai 200433 Peoples R China Nanjing Univ Informat Sci & Technol Collaborat Innovat Ctr Atmospher Environm & Equipm Nanjing 210044 Peoples R China Inst Ecochongming SIEC Shanghai 202162 Peoples R China Quzhou Univ Coll Chem & Mat Engn Quzhou 324000 Peoples R China Jiangxi Acad Ecoenvironm Sci & Planning Jiangxi Key Lab Environm Pollut Control Nanchang 330000 Peoples R China Univ Claude Bernard Lyon 1 Univ Lyon CNRS IRCELYON F-69626 Villeurbanne France

Field observations of daytime HONO source strengths have not been well explained by laboratory measurements and model predictions up until now. More efforts are urgently needed to fill the knowledge gaps concerning how environmental factors, especially relative humidity (RH), affect particulate nitrate photolysis. In this work, two critical attributes for atmospheric particles, i.e., phase state and bulk-phase acidity, both influenced by ambient RH, were focused to illuminate the key regulators for reactive nitrogen production from typical internally mixed systems, i.e., NaNO3 and dicarboxylic acid (DCA) mixtures. The dissolution of only few oxalic acid (OA) crystals resulted in a remarkable 50-fold increase in HONO production compared to pure nitrate photolysis at 85% RH. Furthermore, the HONO production rates (P HONO) increased by about 1 order of magnitude as RH rose from <5% to 95%, initially exhibiting an almost linear dependence on the amount of surface absorbed water and subsequently showing a substantial increase in P HONO once nitrate deliquescence occurred at approximately 75% RH. NaNO3/malonic acid (MA) and NaNO3/succinic acid (SA) mixtures exhibited similar phase state effects on the photochemical HONO production. These results offer a new perspective on how aerosol physicochemical properties influence particulate nitrate photolysis in the atmosphere.

关键词： nitrate photolysis HONO dicarboxylic acids phase state bulk-phase acidity atmosphericaerosols

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Field Evidence for Asian Outflow and Fast Depletion of Total Gaseous Mercury in the Polluted Coastal Atmosphere

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ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023年第10期57卷 4101-4112页

作者： Li, Tao Mao, Huiting Wang, Zhe yu, Jian Zhen Li, shuwen Nie, Xiaoling Herrmann, Hartmut Wang, Yan Shandong Univ Sch Environm Sci & Engn Shandong Key Lab Environm Proc & Hlth Qingdao 266237 Peoples R China SUNY Syracuse Coll Environm Sci & Forestry Dept Chem Syracuse NY 13210 USA Hong Kong Univ Sci & Technol Div Environm & Sustainabil Kowloon Hong Kong 999077 Peoples R China Chinese Acad Sci Inst Atmospher Phys Lab Cloud Precipitat Phys & Severe Storms LACS Beijing 100029 Peoples R China Leibniz Inst Tropospher Res TROPOS Atmospher Chem Dept ACD D-04318 Leipzig Germany

Atmospheric mercury (Hg) cycling in polluted coastal atmosphere is complicated and not fully understood. Here, we present measurements of total gaseous mercury (TGM) monitored at a coastal mountaintop in Hong Kong downwind of mainland China. Sharp TGM peaks during cold front passages were frequently observed due to Asian pollution outflow with typical TGM/CO slopes of 6.8 +/- 2.2 pg m-3 ppbv-1. Contrary to the daytime maximums of other air pollutants, TGM exhibited a distinct diurnal variation with a midday minimum. Moreover, we observed four cases of extremely fast TGM depletion after sunrise, during which TGM concentrations rapidly dipped to 0.3-0.6 ng m-3 accompanied by other pollutants on the rise. Simulated meteorological fields revealed that morning upslope flow trans-porting anthropogenically polluted but TGM-depleted air masses from the mixed layer caused morning TGM depletion at the mountaintop location. The TGM-depleted air masses were hypothesized to result mainly from fast photooxidation of Hg after sunrise with minor contributions from dry deposition (5.0%) and nocturnal oxidation (0.6%). A bromine-induced two-step oxidation mechanism involving abundant pollutants (NO2, O3, etc.) was estimated to play a dominant role, contributing 55%-60% of depleted TGM and requiring 0.20-0.26 pptv Br, an amount potentially available through sea salt aerosol debromination. Our findings suggest significant effects of the interaction between anthropogenic pollution and marine halogen chemistry on atmospheric Hg cycling in the coastal areas.

关键词： Mercury depletion Asian outflow anthropogenic pollution oxidation bromine

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