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372 results on '"Xu, Xinran"'

103. Cdc42 activity is essential for the interplay between cAMP/PKA pathway and CatSper function

Author

Luque, Guillermina M., primary, Xu, Xinran, additional, Romarowski, Ana, additional, Gervasi, María G., additional, Orta, Gerardo, additional, De la Vega-Beltrán, José L., additional, Stival, Cintia, additional, Gilio, Nicolás, additional, Dalotto-Moreno, Tomás, additional, Krapf, Dario, additional, Visconti, Pablo E., additional, Krapf, Diego, additional, Darszon, Alberto, additional, and Buffone, Mariano G., additional

Published
2020
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107. EPIHC: Improving Enhancer-Promoter Interaction Prediction by Using Hybrid Features and Communicative Learning

Author

Liu, Shuai, Xu, Xinran, Yang, Zhihao, Zhao, Xiaohan, Liu, Shichao, and Zhang, Wen

Abstract

Enhancer-promoter interactions (EPIs) regulate the expression of specific genes in cells, which help facilitate understanding of gene regulation, cell differentiation and disease mechanisms. EPI identification approaches through wet experiments are often costly and time-consuming, leading to the design of high-efficiency computational methods is in demand. In this paper, we propose a deep neural network-based method named EPIHC to predict Enhancer-Promoter Interactions with Hybrid features and Communicative learning. EPIHC extracts enhancer and promoter sequence-derived features using convolutional neural networks (CNN), and then we design a communicative learning module to capture the communicative information between enhancer and promoter sequences. Besides, EPIHC takes the genomic features of enhancers and promoters into account, incorporating with the sequence-derived features to predict EPIs. The computational experiments show that EPIHC outperforms the existing state-of-the-art EPI prediction methods on the benchmark datasets and chromosome-split datasets, and the study reveals that the communicative learning module can bring explicit information about EPIs, which is ignored by CNN, and provide explainability about EPIs to some degree. Moreover, we consider two strategies to improve the performances of EPIHC in the cross-cell line prediction, and experimental results show that EPIHC constructed on some cell lines can exhibit good performances for other cell lines. The codes and data are available at https://github.com/BioMedicalBigDataMiningLab/EPIHC.

Published
2022
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109. META-DDIE: predicting drug–drug interaction events with few-shot learning.

Author

Deng, Yifan, Qiu, Yang, Xu, Xinran, Liu, Shichao, Zhang, Zhongfei, Zhu, Shanfeng, and Zhang, Wen

Subjects
DRUG interactions, CHEMICAL structure, FORECASTING
Abstract

Drug–drug interactions (DDIs) are one of the major concerns in pharmaceutical research, and a number of computational methods have been developed to predict whether two drugs interact or not. Recently, more attention has been paid to events caused by the DDIs, which is more useful for investigating the mechanism hidden behind the combined drug usage or adverse reactions. However, some rare events may only have few examples, hindering them from being precisely predicted. To address the above issues, we present a few-shot computational method named META-DDIE, which consists of a representation module and a comparing module, to predict DDI events. We collect drug chemical structures and DDIs from DrugBank, and categorize DDI events into hundreds of types using a standard pipeline. META-DDIE uses the structures of drugs as input and learns the interpretable representations of DDIs through the representation module. Then, the model uses the comparing module to predict whether two representations are similar, and finally predicts DDI events with few labeled examples. In the computational experiments, META-DDIE outperforms several baseline methods and especially enhances the predictive capability for rare events. Moreover, META-DDIE helps to identify the key factors that may cause DDI events and reveal the relationship among different events. [ABSTRACT FROM AUTHOR]

Published
2022
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110. SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations.

Author

Zhang, Guangzhan, Li, Menglu, Deng, Huan, Xu, Xinran, Liu, Xuan, and Zhang, Wen

Subjects
BIPARTITE graphs, LINCRNA, DEREGULATION, NON-coding RNA, PREDICTION models, MICRORNA, DRUG development
Abstract

MiRNAs are a class of small non-coding RNA molecules that play an important role in many biological processes, and determining miRNA-disease associations can benefit drug development and clinical diagnosis. Although great efforts have been made to develop miRNA-disease association prediction methods, few attention has been paid to in-depth classification of miRNA-disease associations, e.g. up/down-regulation of miRNAs in diseases. In this paper, we regard known miRNA-disease associations as a signed bipartite network, which has miRNA nodes, disease nodes and two types of edges representing up/down-regulation of miRNAs in diseases, and propose a s igned g raph n eural n etwork method (SGNNMD) for predicting deregulation types of m iRNA- d isease associations. SGNNMD extracts subgraphs around miRNA-disease pairs from the signed bipartite network and learns structural features of subgraphs via a labeling algorithm and a neural network, and then combines them with biological features (i.e. miRNA–miRNA functional similarity and disease–disease semantic similarity) to build the prediction model. In the computational experiments, SGNNMD achieves highly competitive performance when compared with several baselines, including the signed graph link prediction methods, multi-relation prediction methods and one existing deregulation type prediction method. Moreover, SGNNMD has good inductive capability and can generalize to miRNAs/diseases unseen during the training. [ABSTRACT FROM AUTHOR]

Published
2022
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111. Power spectral density of a single Brownian trajectory

Author

Krapf, Diego, Marinari, Enzo, Metzler, Ralf (Prof. Dr.), Oshanin, Gleb, Xu, Xinran, and Squarcini, Alessio

Subjects
Institut für Physik und Astronomie, ddc:530, Mathematisch-Naturwissenschaftliche Fakultät
Abstract

The power spectral density (PSD) of any time-dependent stochastic processX (t) is ameaningful feature of its spectral content. In its text-book definition, the PSD is the Fourier transform of the covariance function of X-t over an infinitely large observation timeT, that is, it is defined as an ensemble-averaged property taken in the limitT -> infinity. Alegitimate question is what information on the PSD can be reliably obtained from single-trajectory experiments, if one goes beyond the standard definition and analyzes the PSD of a single trajectory recorded for a finite observation timeT. In quest for this answer, for a d-dimensional Brownian motion (BM) we calculate the probability density function of a single-trajectory PSD for arbitrary frequency f, finite observation time T and arbitrary number k of projections of the trajectory on different axes. We show analytically that the scaling exponent for the frequency-dependence of the PSD specific to an ensemble of BM trajectories can be already obtained from a single trajectory, while the numerical amplitude in the relation between the ensemble-averaged and single-trajectory PSDs is afluctuating property which varies from realization to realization. The distribution of this amplitude is calculated exactly and is discussed in detail. Our results are confirmed by numerical simulations and single-particle tracking experiments, with remarkably good agreement. In addition we consider a truncated Wiener representation of BM, and the case of a discrete-time lattice random walk. We highlight some differences in the behavior of a single-trajectory PSD for BM and for the two latter situations. The framework developed herein will allow for meaningful physical analysis of experimental stochastic trajectories.

Published
2019

112. The Method of Eliminating the Receiving Response Fluctuation of Planar PVDF Hydrophone at Low Frequency

Author

Yan Guo, Zheng Zhenyu, and Xu Xinran

Subjects
Materials science, Hydrophone, Acoustics, 02 engineering and technology, Bending, Low frequency, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Noise (electronics), 0104 chemical sciences, Transducer, Planar, 0210 nano-technology, Acoustic impedance, Sensitivity (electronics)
Abstract

Due to its high piezoelectric constant, strong noise and impact resistance, good hydrostatic resistance, good flexibility, low acoustic impedance, planar PVDF hydrophone is widely used in submarine side array. However, due to the existence of low frequency bending mode of hydrophone, the sensitivity response of hydrophone fluctuates at low frequency. In this paper, COMSOL finite element software is used to analyze the bending mode and sensitivity response of plane PVDF hydrophone. By researching the principle of sensitivity fluctuation, four methods are proposed to eliminate low frequency sensitivity fluctuation. The four cases have their own different effects and disadvantages. According to the actual operating frequency band and the requirements of hydrophone area, weight and cost, these four methods can be considered synthetically to eliminate the sensitivity fluctuation.

Published
2019
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116. Association between Take-Out Food Consumption and Obesity among Chinese University Students: A Cross-Sectional Study

Author

Jiang, Yuhe, primary, Wang, Junbo, additional, Wu, Shaowei, additional, Li, Nan, additional, Wang, Yiming, additional, Liu, Jiarui, additional, Xu, Xinran, additional, He, Zonghan, additional, Cheng, Yawen, additional, Zeng, Xueqing, additional, Wang, Bingwei, additional, Zhang, Chenyu, additional, Zhao, Miao, additional, Su, Zhijie, additional, Guo, Bingbing, additional, Yang, Wenzhong, additional, and Zheng, Ruimao, additional

Published
2019
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117. Reproductive characteristics modify the association between global DNA methylation and breast cancer risk in a population-based sample of women

Author

Collin, Lindsay J., primary, McCullough, Lauren E., additional, Conway, Kathleen, additional, White, Alexandra J., additional, Xu, Xinran, additional, Cho, Yoon Hee, additional, Shantakumar, Sumitra, additional, Teitelbaum, Susan L., additional, Neugut, Alfred I., additional, Santella, Regina M., additional, Chen, Jia, additional, and Gammon, Marilie D., additional

Published
2019
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118. Spectral Content of a Single Non-Brownian Trajectory

Author

Krapf, Diego, primary, Lukat, Nils, additional, Marinari, Enzo, additional, Metzler, Ralf, additional, Oshanin, Gleb, additional, Selhuber-Unkel, Christine, additional, Squarcini, Alessio, additional, Stadler, Lorenz, additional, Weiss, Matthias, additional, and Xu, Xinran, additional

Published
2019
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119. Inhibition of microRNA‐149 protects against recurrent miscarriage through upregulating RUNX2 and activation of the PTEN/Akt signaling pathway.

Author

Wang, Peng, Chen, Xu, Chang, Ying, Wang, Yanping, Xu, Xinran, Guo, Yuling, and Cui, Hongyan

Subjects
APOPTOSIS, BLASTOCYST, CELL physiology, CELLULAR signal transduction, STATISTICAL correlation, GENE expression, MISCARRIAGE, PHOSPHATASES, PHOSPHORYLATION, PREGNANT women, TRANSCRIPTION factors, TRANSFERASES, WESTERN immunoblotting, MICRORNA
Abstract

Aim: Recently, microRNA‐149 (miR‐149) has been indicated to act as an oncogene or a tumor suppressor in various malignant tumors, while its inner mechanisms in recurrent miscarriage (RM) are still in infancy. Therein, this study intends to decode the mechanism of miR‐149 in RM. Methods: miR‐149 and RUNX2 expression in the chorionic tissues of normal pregnant women and RM patients were first examined, and the correlation between miR‐149 and RUNX2 was analyzed. Subsequently, miR‐149 was upregulated in HTR‐8 cells or downregulated in BEWO cells, and then the changes in biological functions of trophoblasts in RM were detected. Furthermore, the expression of PTEN/Akt signaling pathway‐related factors in trophoblasts was detected by western blot analysis. Results: miR‐149 expression was increased while RUNX2 expression was suppressed in RM patients, and miR‐149 was negatively correlated with RUNX2. Overexpressed miR‐149 induced cell apoptosis and inhibited cell activity, while reduced miR‐149 in trophoblasts contributed to opposite experimental results. Moreover, miR‐149 promoted the expression of PTEN and inhibited Akt phosphorylation by targeting RUNX2, thereby inhibiting trophoblast activity and promoting their apoptosis. Conclusion: Our study demonstrates that miR‐149 knockdown halted the RM development through upregulating RUNX2 and activation of the PTEN/Akt signaling pathway. [ABSTRACT FROM AUTHOR]

Published
2020
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123. Super-resolution imaging of live sperm reveals dynamic changes of the actin cytoskeleton during acrosomal exocytosis

Author

Romarowski, Ana, primary, Velasco Félix, Ángel G., additional, Torres Rodríguez, Paulina, additional, Gervasi, María G., additional, Xu, Xinran, additional, Luque, Guillermina M., additional, Contreras-Jiménez, Gastón, additional, Sánchez-Cárdenas, Claudia, additional, Ramírez-Gómez, Héctor V., additional, Krapf, Diego, additional, Visconti, Pablo E., additional, Krapf, Dario, additional, Guerrero, Adán, additional, Darszon, Alberto, additional, and Buffone, Mariano G., additional

Published
2018
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126. Leveraging Functional Annotations in Genetic Risk Prediction for Human Complex Diseases

Author

Hu, Yiming, Lu, Qiongshi, Powles, Ryan, Yao, Xinwei, Yang, Can, Fang, Fang, Xu, Xinran, Zhao, Hongyu, Hu, Yiming, Lu, Qiongshi, Powles, Ryan, Yao, Xinwei, Yang, Can, Fang, Fang, Xu, Xinran, and Zhao, Hongyu

Abstract

Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome wide association studies (GWAS), genetic risk prediction accuracy remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes in the presence of linkage disequilibrium. In this paper, we introduce AnnoPred, a principled framework that leverages diverse types of genomic and epigenomic functional annotations in genetic risk prediction for complex diseases. AnnoPred is trained using GWAS summary statistics in a Bayesian framework in which we explicitly model various functional annotations and allow for linkage disequilibrium estimated from reference genotype data. Compared with state-of-the-art risk prediction methods, AnnoPred achieves consistently improved prediction accuracy in both extensive simulations and real data. © 2017 Hu et al.

Published
2017

129. Interventions to reduce Salmonellaand Campylobacterduring chilling and post-chilling stages of poultry processing: a systematic review and meta-analysis

Author

Leone, Cortney, Xu, Xinran, Mishra, Abhinav, Thippareddi, Harshavardhan, and Singh, Manpreet

Abstract

Salmonellaand Campylobacterare common bacterial hazards causing foodborne illnesses worldwide. A large proportion of Salmonellaand Campylobacterillnesses are attributed to contaminated poultry products that are mishandled or under cooked. Processing interventions such as chilling and post-chill dip are critical to reducing microbial contamination of poultry. A comprehensive search of the literature published between 2000 and 2021 was conducted in the databases Web of Science, Academic Search Complete, and Academic OneFile. Studies were included if they were in English and investigated the effects of interventions against Salmonellaand/or Campylobacteron whole carcasses and/or parts during the chilling or post-chill stages of poultry processing. Random-effects meta-analyses were performed using the “meta” package in the R programming language. Subgroup analyses were assessed according to outcome measure reported, microorganism tested, processing stage assessed, and chemical treatment used. The results included 41 eligible studies. Eighteen studies reported results of 28 separate interventions against Salmonellaand 31 reported results of 50 separate interventions against Campylobacter.No significant difference (P> 0.05) was observed when comparing the combined mean difference of all interventions targeting Salmonellato the combined mean difference of all interventions targeting Campylobacteror when comparing chilling times within each pathogen subgroup. For analyses examining antimicrobial additives, peroxyacetic acid (PAA) had the largest reduction against Salmonellapopulation regardless of chilling time (P< 0.05). PAA also had the largest reduction against Campylobacterpopulation and prevalence during primary chilling (P< 0.01). Air chilling showed a lower reduction for Campylobacterthan any immersion chilling intervention (P< 0.05). Chilling time and antimicrobial used during poultry processing had varying effects depending on the pathogen and outcome measure investigated (concentration or prevalence). High heterogeneity and low sample numbers in most analyses suggest that more high-quality research that is well-designed and has transparent reporting of methodology and results is needed to corroborate the results.

Published
2024
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130. The tyrosine kinase FER is responsible for the capacitation-associated increase in tyrosine phosphorylation in murine sperm

Author

Alvau, Antonio, primary, Battistone, Maria Agustina, additional, Gervasi, Maria Gracia, additional, Navarrete, Felipe A., additional, Xu, Xinran, additional, Sánchez-Cárdenas, Claudia, additional, De la Vega-Beltran, Jose Luis, additional, Da Ros, Vanina G., additional, Greer, Peter, additional, Darszon, Alberto, additional, Krapf, Diego, additional, Salicioni, Ana Maria, additional, Cuasnicu, Patricia, additional, and Visconti, Pablo E., additional

Published
2016
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133. Cloning and analysis of the Glwc-1 and Glwc-2 genes encoding putative blue light photoreceptor from Ganoderma lucidum.

Author

Xu, Xinran, Chen, Xiangdong, Yu, Wumengxiao, Liu, Yu, Zhang, Weiwei, and Lan, Jin

Subjects
CLONING, BLUE light, GANODERMA lucidum, MACROFUNGI, FUNGAL growth, PHYSIOLOGICAL effects of blue light, PHOTORECEPTORS
Abstract

Blue light plays an important role during the growth of Ganoderma lucidum, one of the best-known medicinal macrofungi in China. In the present study, we cloned Glwc-1 and Glwc-2, the homologue of the blue light photoreceptors Ncwc-1 and Ncwc-2 of Neurospora crassa, from G. lucidum. The deduced amino acid sequence of Glwc-1 contained the similar function domains as NcWC-1 including LOV, PAS B, PAS C, and PAC domains. The deduced amino acid sequence of Glwc-2 contained PAS domain and GATA-type zinc finger (Znf) domain as well as NcWC-2. Phylogenetic analysis based on fungal WC-1 and WC-2 supported GlWC-1 and GlWC-2 were blue light receptors. The expression of Glwc-1 and Glwc-2 indicated that they might play an important role during the primordium differentiation process of G. lucidum, and the external blue light stimulation increased the expression of Glwc-1 and Glwc-2. [ABSTRACT FROM AUTHOR]

Published
2017
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134. Promoter Hypermethylation in White Blood Cell DNA and Breast Cancer Risk

Author

Cho, Yoon Hee, primary, McCullough, Lauren E., additional, Gammon, Marilie D., additional, Wu, Hui-Chen, additional, Zhang, Yu-Jing, additional, Wang, Qiao, additional, Xu, Xinran, additional, Teitelbaum, Susan L., additional, Neugut, Alfred I., additional, Chen, Jia, additional, and Santella, Regina M., additional

Published
2015
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135. Global DNA Methylation, Measured by the Luminometric Methylation Assay (LUMA), Associates with Postmenopausal Breast Cancer in Non-Obese and Physically Active Women

Author

McCullough, Lauren E., primary, Chen, Jia, additional, White, Alexandra J., additional, Xu, Xinran, additional, Cho, Yoon Hee, additional, Bradshaw, Patrick T., additional, Eng, Sybil M., additional, Teitelbaum, Susan L., additional, Terry, Mary Beth, additional, Garbowski, Gail, additional, Neugut, Alfred I., additional, Hibshoosh, Hanina, additional, Santella, Regina M., additional, and Gammon, Marilie D., additional

Published
2015
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137. Abstract LB-290: The influence of body size and weight gain on global and gene promoter methylation in a population-based breast cancer study

Author

McCullough, Lauren E., primary, Chen, Jia, additional, White, Alexandra J., additional, Xu, Xinran, additional, Cho, Yoon Hee, additional, Bradshaw, Patrick T., additional, Eng, Sybil M., additional, Teitelbaum, Susan L., additional, Terry, Mary Beth, additional, Garbowski, Gail, additional, Neugut, Alfred I., additional, Hibshoosh, Hanina, additional, Santella, Regina M., additional, and Gammon, Marilie D., additional

Published
2014
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138. FEMA

Author

Jiang, Meng, primary, Cui, Peng, additional, Wang, Fei, additional, Xu, Xinran, additional, Zhu, Wenwu, additional, and Yang, Shiqiang, additional

Published
2014
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139. Tom70 serves as a molecular switch to determine pathological cardiac hypertrophy

Author

Li, Jun, primary, Qi, Man, additional, Li, Changming, additional, Shi, Dan, additional, Zhang, Dasheng, additional, Xie, Duanyang, additional, Yuan, Tianyou, additional, Feng, Jing, additional, Liu, Yi, additional, Liang, Dandan, additional, Xu, Xinran, additional, Chen, Jinjin, additional, Xu, Liang, additional, Zhang, Hong, additional, Ye, Jiangchuan, additional, Lv, Fei, additional, Huang, Jian, additional, Peng, Luying, additional, and Chen, Yi-Han, additional

Published
2014
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140. mi RNA ‐940 reduction contributes to human Tetralogy of Fallot development

Author

Liang, Dandan, primary, Xu, Xinran, additional, Deng, Fangfei, additional, Feng, Jing, additional, Zhang, Hong, additional, Liu, Ying, additional, Zhang, Yangyang, additional, Pan, Lei, additional, Liu, Yi, additional, Zhang, Dasheng, additional, Li, Jun, additional, Liang, Xingqun, additional, Sun, Yunfu, additional, Xiao, Junjie, additional, and Chen, Yi‐Han, additional

Published
2014
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141. Genetic variation in multiple biologic pathways, flavonoid intake, and breast cancer

Author

Khankari, Nikhil K., primary, Bradshaw, Patrick T., additional, McCullough, Lauren E., additional, Teitelbaum, Susan L., additional, Steck, Susan E., additional, Fink, Brian N., additional, Xu, Xinran, additional, Ahn, Jiyoung, additional, Ambrosone, Christine B., additional, Crew, Katherine D., additional, Terry, Mary Beth, additional, Neugut, Alfred I., additional, Chen, Jia, additional, Santella, Regina M., additional, and Gammon, Marilie D., additional

Published
2013
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142. Aberrant dynamin 2‐dependent Na+/H+exchanger‐1 trafficking contributes to cardiomyocyte apoptosis

Author

Li, Jun, primary, Xu, Liang, additional, Ye, Jiangchuan, additional, Li, Xiang, additional, Zhang, Dasheng, additional, Liang, Dandan, additional, Xu, Xinran, additional, Qi, Man, additional, Li, Changming, additional, Zhang, Hong, additional, Wang, Jing, additional, Liu, Yi, additional, Zhang, Yuzhen, additional, Zhou, Zhaonian, additional, Liang, Xingqun, additional, Li, Jue, additional, Peng, Luying, additional, Zhu, Weidong, additional, and Chen, Yi‐Han, additional

Published
2013
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145. The influence of one-carbon metabolism on gene promoter methylation in a population-based breast cancer study

Author

Xu, Xinran, primary, Gammon, Marilie D., additional, Jefferson, Elizabeth, additional, Zhang, Yujing, additional, Cho, Yoon Hee, additional, Wetmur, James G., additional, Teitelbaum, Susan L., additional, Bradshaw, Patrick T., additional, Terry, Mary Beth, additional, Garbowski, Gail, additional, Hibshoosh, Hanina, additional, Neugut, Alfred I., additional, Santella, Regina M., additional, and Chen, Jia, additional

Published
2011
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146. Prognostic significance of gene-specific promoter hypermethylation in breast cancer patients

Author

Cho, Yoon Hee, primary, Shen, Jing, additional, Gammon, Marilie D., additional, Zhang, Yu-Jing, additional, Wang, Qiao, additional, Gonzalez, Karina, additional, Xu, Xinran, additional, Bradshaw, Patrick T., additional, Teitelbaum, Susan L., additional, Garbowski, Gail, additional, Hibshoosh, Hanina, additional, Neugut, Alfred I., additional, Chen, Jia, additional, and Santella, Regina M., additional

Published
2011
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150. Gene promoter methylation is associated with increased mortality among women with breast cancer

Author

Xu, Xinran, primary, Gammon, Marilie D., additional, Zhang, Yujing, additional, Cho, Yoon Hee, additional, Wetmur, James G., additional, Bradshaw, Patrick T., additional, Garbowski, Gail, additional, Hibshoosh, Hanina, additional, Teitelbaum, Susan L., additional, Neugut, Alfred I., additional, Santella, Regina M., additional, and Chen, Jia, additional

Published
2009
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