Publications by authors named "Xiaolong Wang"

587 Publications

Iron metabolism protein transferrin receptor 1 involves in cervical cancer progression by affecting gene expression and alternative splicing in HeLa cells.

Genes Genomics 2022 Jan 23. Epub 2022 Jan 23.

Department of Allergy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China.

Background: Transferrin receptor 1 (TfR1), encoded by TFRC, is a key regulator of iron homeostasis and plays important roles in many diseases, including cancers.

Objective: To decipher the underlying molecular functions of TfR1 based on its influence on transcriptome profile in cancer cells.

Methods: In this study, we first identified the expression pattern and prognostic influence of TFRC in cervical cancer patients from TCGA database. To explore the regulatory outcomes of TfR1 from the view of whole transcriptome profile, we generated TFRC knockdown (TFRC-KD) HeLa cells and negative control (NC) cells using short hairpin RNA (shRNA) method. Unbiased transcriptome sequencing (RNA-seq) experiment was used to analyze the global expression level and alternative splicing (AS) changes between TFRC-KD and NC cells.

Results: We found TFRC was consistently elevated in cervical cancer samples and tightly associated with prognosis of patients. Differential expression analysis revealed that 629 differentially expressed genes (DEGs) were identified between TFRC-KD and NC. Functional enrichment analysis of these DEGs revealed that TFRC-KD extensively disturbed cell physiology related pathways, including immunity, cell metabolism and gene expression. Moreover, dysregulated AS profile also indicated that TfR1 has important roles in the AS regulation. Hundreds of TfR1-regulated AS genes were involved in DNA repair, cell death, transcription and viral reproduction pathways, which were tightly associated with cancer cell progression.

Conclusions: In summary, we for the first time explored the molecular functions of TfR1 at transcriptional and post-transcriptional levels. These results demonstrate TfR1 participates in the progression of cervical cancer by affecting the expression and AS levels of genes in cancer associated pathways, which greatly extends our understanding of TfR1 functions besides iron homeostasis and provide novel options in cancer treatment by targeting TfR1.
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http://dx.doi.org/10.1007/s13258-021-01205-wDOI Listing
January 2022

Augmentation and heterogeneous graph neural network for AAAI2021-COVID-19 fake news detection.

Int J Mach Learn Cybern 2022 Jan 8:1-11. Epub 2022 Jan 8.

School of Computer Science and Technology, Harbin Institute of Technology, Harbin, 150001 China.

Misinformation has become a frightening specter of society, especially fake news that concerning Covid-19. It massively spreads on the Internet, and then induces misunderstandings of information to the national and global communities during the pandemic. Detecting massive misinformation on the Internet is crucial and challenging because humans have struggled against this phenomenon for a long time. Our research concerns detecting fake news related to covid-19 using augmentation [random deletion (RD), random insertion (RI), random swap (RS), synonym replacement (SR)] and several graph neural network [graph convolutional network (GCN), graph attention network (GAT), and GraphSAGE (SAmple and aggreGatE)] model. We constructed nodes and edges in the graph, word-word node, and word-document node to graph neural network. Then, we tested those models in different amounts of sample training data to obtain accuracy for each model and compared them. For our fake news detection task, we found training accuracy steadily increasing for GCN, GAT, and SAGE models from the beginning to the end of the epochs. This result proved that the performance of GNN, whether GCN, GAT, or SAGE gained an entirely insignificant difference precision result.
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http://dx.doi.org/10.1007/s13042-021-01503-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8742573PMC
January 2022

miR-1 Regulates Differentiation and Proliferation of Goat Hair Follicle Stem Cells by Targeting and Genes.

DNA Cell Biol 2022 Jan 10. Epub 2022 Jan 10.

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.

Hair follicle stem cells (HFSCs) play a significant role in hair development. miR-1 has been reported as an important regulatory factor that affects hair follicle growth and development, but its regulatory mechanism on HFSC development remains unknown. In this study, the molecular mechanism of miR-1 in regulating HFSC proliferation and differentiation was investigated. High-throughput RNA-seq and integrated analysis were performed to identify differentially transcribed mRNAs and microRNAs (miRNAs) in HFSCs co-cultured with dermal papilla cells (named dHFSCs) and control HFSCs. We then determined the molecular function of miR-1 in HFSCs. Compared with HFSCs, 13 differentially transcribed miRNAs were identified in dHFSCs. The results indicated that the overtranscription of miR-1 inhibited HFSC proliferation, but enhanced HFSC differentiation by targeting and genes. This study provides new insights into the molecular mechanisms of HFSC development. Approval ID (2014ZX08008-002).
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http://dx.doi.org/10.1089/dna.2021.0288DOI Listing
January 2022

Implementation of novel boolean logic gates for IMPLICATION and XOR functions using riboregulators.

Bioengineered 2022 01;13(1):1235-1248

The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China.

To date, several different types of synthetic genetic switches, including riboregulators, riboswitches, and toehold switches, have been developed to construct AND, OR, NOT, NAND, NOR, and NOT IMPLICATION (NIMP) gates. The logic gate can integrate multiple input signals following a set of algorithms and generate a response only if strictly defined conditions are met. However, there are still some logic gates that have not been implemented but are necessary to build complex genetic circuits. Here, based on the toehold switches and three-way-junction (3WJ) repressors, we designed two novel biological Boolean logic gates of IMPLICATION (IMP) and XOR. Subsequently, the outputs of these two logic gates were characterized by fluorescence analysis, indicating that they can achieve the truth tables of logical gates. Furthermore, the fluorescence intensity under the logical TRUE condition was significantly higher than under the logical FALSE condition, suggesting the high dynamic range of the ON/OFF ratios. Because of the programmability of synthetic RNA switches, the constructed RNA logic gates could serve as elementary units to build a versatile and powerful platform for translational regulation and RNA-based biological computation.
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http://dx.doi.org/10.1080/21655979.2021.2020493DOI Listing
January 2022

Document-level medical relation extraction via edge-oriented graph neural network based on document structure and external knowledge.

BMC Med Inform Decis Mak 2021 12 30;21(Suppl 7):368. Epub 2021 Dec 30.

Harbin Institute of Technology, Shenzhen, China.

Objective: Relation extraction (RE) is a fundamental task of natural language processing, which always draws plenty of attention from researchers, especially RE at the document-level. We aim to explore an effective novel method for document-level medical relation extraction.

Methods: We propose a novel edge-oriented graph neural network based on document structure and external knowledge for document-level medical RE, called SKEoG. This network has the ability to take full advantage of document structure and external knowledge.

Results: We evaluate SKEoG on two public datasets, that is, Chemical-Disease Relation (CDR) dataset and Chemical Reactions dataset (CHR) dataset, by comparing it with other state-of-the-art methods. SKEoG achieves the highest F1-score of 70.7 on the CDR dataset and F1-score of 91.4 on the CHR dataset.

Conclusion: The proposed SKEoG method achieves new state-of-the-art performance. Both document structure and external knowledge can bring performance improvement in the EoG framework. Selecting proper methods for knowledge node representation is also very important.
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http://dx.doi.org/10.1186/s12911-021-01733-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8717642PMC
December 2021

Fast ORB-SLAM without Keypoint Descriptors.

IEEE Trans Image Process 2021 Dec 24;PP. Epub 2021 Dec 24.

Indirect methods for visual SLAM are gaining popularity due to their robustness to environmental variations. ORB-SLAM2 [1] is a benchmark method in this domain, however, it consumes significant time for computing descriptors that never get reused unless a frame is selected as a keyframe. To overcome these problems, we present FastORB-SLAM which is light-weight and efficient as it tracks keypoints between adjacent frames without computing descriptors. To achieve this, a two stage descriptor-independent keypoint matching method is proposed based on sparse optical flow. In the first stage, we predict initial keypoint correspondences via a simple but effective motion model and then robustly establish the correspondences via pyramid-based sparse optical flow tracking. In the second stage, we leverage the constraints of the motion smoothness and epipolar geometry to refine the correspondences. In particular, our method computes descriptors only for keyframes. We test FastORB-SLAM on TUM and ICL-NUIM RGB-D datasets and compare its accuracy and efficiency to nine existing RGB-D SLAM methods. Qualitative and quantitative results show that our method achieves state-of-the-art accuracy and is about twice as fast as the ORB-SLAM2.
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http://dx.doi.org/10.1109/TIP.2021.3136710DOI Listing
December 2021

Improving deep learning method for biomedical named entity recognition by using entity definition information.

BMC Bioinformatics 2021 Dec 17;22(Suppl 1):600. Epub 2021 Dec 17.

Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.

Background: Biomedical named entity recognition (NER) is a fundamental task of biomedical text mining that finds the boundaries of entity mentions in biomedical text and determines their entity type. To accelerate the development of biomedical NER techniques in Spanish, the PharmaCoNER organizers launched a competition to recognize pharmacological substances, compounds, and proteins. Biomedical NER is usually recognized as a sequence labeling task, and almost all state-of-the-art sequence labeling methods ignore the meaning of different entity types. In this paper, we investigate some methods to introduce the meaning of entity types in deep learning methods for biomedical NER and apply them to the PharmaCoNER 2019 challenge. The meaning of each entity type is represented by its definition information.

Material And Method: We investigate how to use entity definition information in the following two methods: (1) SQuad-style machine reading comprehension (MRC) methods that treat entity definition information as query and biomedical text as context and predict answer spans as entities. (2) Span-level one-pass (SOne) methods that predict entity spans of one type by one type and introduce entity type meaning, which is represented by entity definition information. All models are trained and tested on the PharmaCoNER 2019 corpus, and their performance is evaluated by strict micro-average precision, recall, and F1-score.

Results: Entity definition information brings improvements to both SQuad-style MRC and SOne methods by about 0.003 in micro-averaged F1-score. The SQuad-style MRC model using entity definition information as query achieves the best performance with a micro-averaged precision of 0.9225, a recall of 0.9050, and an F1-score of 0.9137, respectively. It outperforms the best model of the PharmaCoNER 2019 challenge by 0.0032 in F1-score. Compared with the state-of-the-art model without using manually-crafted features, our model obtains a 1% improvement in F1-score, which is significant. These results indicate that entity definition information is useful for deep learning methods on biomedical NER.

Conclusion: Our entity definition information enhanced models achieve the state-of-the-art micro-average F1 score of 0.9137, which implies that entity definition information has a positive impact on biomedical NER detection. In the future, we will explore more entity definition information from knowledge graph.
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http://dx.doi.org/10.1186/s12859-021-04236-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8680061PMC
December 2021

Identification of the Immune Cell Infiltration Landscape in Hepatocellular Carcinoma to Predict Prognosis and Guide Immunotherapy.

Front Genet 2021 25;12:777931. Epub 2021 Nov 25.

Department of Integrated TCM and Western Medicine, Nanjing Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, China.

Globally, hepatocellular carcinoma (HCC) is the sixth most frequent malignancy with a high incidence and a poor prognosis. Immune cell infiltration (ICI) underlies both the carcinogenesis and immunogenicity of tumors. However, a comprehensive classification system based on the immune features for HCC remains unknown. The HCC dataset from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) cohorts was used in this study. The ICI patterns of 571 patients were characterized using two algorithms: the patterns were determined based on the ICI using the ConsensusClusterPlus package, and principal component analysis (PCA) established the ICI scores. Differences in the immune landscape, biological function, and somatic mutations across ICI scores were evaluated and compared, followed by a predictive efficacy evaluation of ICI scores for immunotherapy by the two algorithms and validation using an external immunotherapy cohort. Based on the ICI profile of the HCC patients, three ICI patterns were identified, including three subtypes having different immunological features. Individual ICI scores were determined; the high ICI score subtype was characterized by enhanced activation of immune-related signaling pathways and a significantly high tumor mutation burden (TMB); concomitantly, diminished immunocompetence and enrichment of pathways associated with cell cycle and RNA degradation were found in the low ICI score subtype. Taken together, our results contribute to a better understanding of an active tumor and plausible reasons for its poor prognosis. The present study reveals that ICI scores may serve as valid prognostic biomarkers for immunotherapy in HCC.
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http://dx.doi.org/10.3389/fgene.2021.777931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8657761PMC
November 2021

A BERT-Based Generation Model to Transform Medical Texts to SQL Queries for Electronic Medical Records: Model Development and Validation.

JMIR Med Inform 2021 Dec 8;9(12):e32698. Epub 2021 Dec 8.

University of Texas Health Science Center at Houston, Houston, TX, United States.

Background: Electronic medical records (EMRs) are usually stored in relational databases that require SQL queries to retrieve information of interest. Effectively completing such queries can be a challenging task for medical experts due to the barriers in expertise. Existing text-to-SQL generation studies have not been fully embraced in the medical domain.

Objective: The objective of this study was to propose a neural generation model that can jointly consider the characteristics of medical text and the SQL structure to automatically transform medical texts to SQL queries for EMRs.

Methods: We proposed a medical text-to-SQL model (MedTS), which employed a pretrained Bidirectional Encoder Representations From Transformers model as the encoder and leveraged a grammar-based long short-term memory network as the decoder to predict the intermediate representation that can easily be transformed into the final SQL query. We adopted the syntax tree as the intermediate representation rather than directly regarding the SQL query as an ordinary word sequence, which is more in line with the tree-structure nature of SQL and can also effectively reduce the search space during generation. Experiments were conducted on the MIMICSQL dataset, and 5 competitor methods were compared.

Results: Experimental results demonstrated that MedTS achieved the accuracy of 0.784 and 0.899 on the test set in terms of logic form and execution, respectively, which significantly outperformed the existing state-of-the-art methods. Further analyses proved that the performance on each component of the generated SQL was relatively balanced and offered substantial improvements.

Conclusions: The proposed MedTS was effective and robust for improving the performance of medical text-to-SQL generation, indicating strong potential to be applied in the real medical scenario.
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http://dx.doi.org/10.2196/32698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8701710PMC
December 2021

Exosomal non-coding RNAs: Emerging roles in bilateral communication between cancer cells and macrophages.

Mol Ther 2021 Dec 2. Epub 2021 Dec 2.

Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology Tissue Bank, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Research Institute of Breast Cancer, Shandong University, Jinan, Shandong 250012, China. Electronic address:

The tumor microenvironment (TME) is a dynamic network of cellular organization that comprises diverse cell types and significantly contributes to cancer development. As pivotal immune stromal cells in the TME, macrophages are extensively heterogeneous and exert both antitumor and protumor functions. Exosomes are nanosized extracellular membranous vesicles with diameters between 30 and 150 nm. By transferring multiple bioactive substances such as proteins, lipids, and nucleic acids, exosomes play an important role in the communication between cells. Recently, growing evidence has demonstrated that non-coding RNAs (ncRNAs) are enriched in exosomes and that exosomal ncRNAs are involved in the crosstalk between cancer cells and macrophages. Furthermore, circulating exosomal ncRNAs can be detected in biofluids, serving as promising noninvasive biomarkers for the early diagnosis and prognostic prediction of cancer. Exosome-based therapies are emerging as potent strategies that can be utilized to alleviate tumor progression. Herein, the present knowledge of exosomal ncRNAs and their vital roles in regulating the interplay between cancer cells and macrophages, as well as their clinical applications are summarized.
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http://dx.doi.org/10.1016/j.ymthe.2021.12.002DOI Listing
December 2021

Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets.

J Hazard Mater 2022 02 14;423(Pt B):127220. Epub 2021 Sep 14.

College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China. Electronic address:

The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.
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http://dx.doi.org/10.1016/j.jhazmat.2021.127220DOI Listing
February 2022

Comparison of MicroRNA Profiles in Extracellular Vesicles from Small and Large Goat Follicular Fluid.

Animals (Basel) 2021 Nov 8;11(11). Epub 2021 Nov 8.

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China.

Extracellular vesicles (EVs), which exist in the follicular fluid of ruminant ovaries, are considered as cargo carriers for the transfer of biomolecules to recipient cells. However, the functions and changes in EVs in antral follicles remain ambiguous. In the present study, we isolated and characterized EVs from goat follicular fluid by means of differential ultracentrifugation and Western blotting of marker proteins. Bioinformatics tools were used to detect miRNA expression levels in EVs. Different miRNA expression patterns of EVs exist in small to large follicles. Thirteen differentially expressed miRNAs (seven upregulated and six downregulated) were identified and used for analysis. A total of 1948 predicted target genes of 13 miRNAs were mapped to signaling pathways, and three significantly enriched pathways (FoxO, MAPK, and PI3K-AKT signaling pathways) were involved in follicular development, as revealed by KEGG enrichment analysis. Our findings suggest that EVs in follicular fluid play biofunctional roles during follicular development in goats.
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http://dx.doi.org/10.3390/ani11113190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8614480PMC
November 2021

Optimized ratoon rice system to sustain cleaner food production in Jianghan Plain, China: a comprehensive emergy assessment.

Environ Sci Pollut Res Int 2021 Nov 25. Epub 2021 Nov 25.

College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wet Land, Ministry of Education, Yangtze University, No.88-2 Jingmi Road, Jingzhou District, Jingzhou, 434025, Hubei, China.

Ratoon rice (RR) is regarded as a labor-saving and efficient approach to rice cultivation; however, sub-optimal production techniques (fertilization, irrigation, harvesting) may lead to serious environmental problems and unsustainable agriculture. In this study, emergy analysis was combined with indicators of soil fertility, global warming potential (GWP), and profitability to comprehensively assess the sustainability performance of three cultivation modes: (i) traditional farm practice (TRA), (ii) optimized mode (OPT), and (iii) OPT plus green manure planting (OPTM). Over 2 years, compared with the TRA mode, OPT and OPTM modes increased total rice yield by 10% and 19% on average and improved profit by 233.7 and 456.5 Yuan ha, respectively. Single emergy analysis results showed that, compared with the TRA mode, OPT and OPTM (2-year average value) modes increased production efficiency by 10% and 8%, reduced renewable fraction and emergy sustainability index by 14-19% and 18-23%, respectively, and increased environmental loading ratio by 31% and 22%. Multiple EMA analysis results showed that, compared with the TRA mode, OPT and OPTM (2-year average value) modes reduced UEV by 23% and 21% and increased UEV 32% and 51%, respectively. The UEV and UEV of OPT and OPTM increased by 8-29% and 4-37%, respectively, compared with TRA mode. The comprehensive assessment indicated that, despite OPT and OPTM modes have a range of improvements and dis-improvements versus the TRA mode, OPTM was the more sustainable mode of RR production overall. However, some sustainability indicators remained poor, and there remains scope for further optimization via, e.g., precision application of enhanced-efficiency fertilizers, application of a straw-decomposing inoculant to improve soil fertility, and use of new improved rice varieties with high regenerative ability to improve the yield of ratoon crops.
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http://dx.doi.org/10.1007/s11356-021-17747-1DOI Listing
November 2021

Clinical epidemiological characteristics of nitrous oxide abusers: A single-center experience in a hospital in China.

Brain Behav 2021 Dec 13;11(12):e2416. Epub 2021 Nov 13.

Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.

Purpose: This study investigated the clinical epidemiological characteristics of nitrous oxide (N O) abusers in a hospital in China, which have not been systematically reported.

Methods: The characteristics of patients abusing N O who were examined and treated at the Affiliated Hospital of Xuzhou Medical University from January 2017 to December 2020 were analyzed.

Results: A total of 61 patients (average age: 21.7 ± 3.2 years; 42 male and 19 female) were enrolled; 60.7% of the patients had an education level of high school or lower, and most (59.0%) had no stable occupation. The mean exposure time was 8.5 ± 7.7 months (range: 1-36 months). Only 52.5% of the abusers reported the physician of the relevant exposure history at the first time of visiting the doctor. The main clinical type was mixed (49.2%). The most common clinical manifestation was distal limb numbness (80.3%). The most frequent outcome was peripheral neuropathy (59%) and subacute combined degeneration (36%). Serum homocysteine level was elevated in 67.5% (27/40) of the patients, while 44.4% (20/45) showed reduced vitamin B12. Note that 61% (22/36) showed abnormal signals in the posterior or lateral funiculus of the spinal cord, and 97% (31/32) of the patients showed peripheral nerve damage by electromyography. In all cases, symptoms were alleviated after halting N O intake and receiving nutritional neurotherapy.

Conclusions: N O abuse can lead to nervous system damage, especially peripheral nerve and spinal cord damage. A full understanding of its clinical epidemiological characteristics is helpful for clinicians to make a timely and clear diagnosis.
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http://dx.doi.org/10.1002/brb3.2416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8671768PMC
December 2021

Statistical analysis of the community lockdown for COVID-19 pandemic.

Appl Intell (Dordr) 2021 Jul 7:1-18. Epub 2021 Jul 7.

School of Computer Science and Technology, Harbin Institute of Technology, Shenzhen, 518055 China.

As the global pandemic of the COVID-19 continues, the statistical modeling and analysis of the spreading process of COVID-19 have attracted widespread attention. Various propagation simulation models have been proposed to predict the spread of the epidemic and the effectiveness of related control measures. These models play an indispensable role in understanding the complex dynamic situation of the epidemic. Most existing work studies the spread of epidemic at two levels including population and agent. However, there is no comprehensive statistical analysis of community lockdown measures and corresponding control effects. This paper performs a statistical analysis of the effectiveness of community lockdown based on the Agent-Level Pandemic Simulation (ALPS) model. We propose a statistical model to analyze multiple variables affecting the COVID-19 pandemic, which include the timings of implementing and lifting lockdown, the crowd mobility, and other factors. Specifically, a motion model followed by ALPS and related basic assumptions is discussed first. Then the model has been evaluated using the real data of COVID-19. The simulation study and comparison with real data have validated the effectiveness of our model.
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http://dx.doi.org/10.1007/s10489-021-02615-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261037PMC
July 2021

High-efficiency diffraction gratings for EUV and soft x-rays using spin-on-carbon underlayers.

Nanotechnology 2021 Nov 15;33(6). Epub 2021 Nov 15.

Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute, 5232 Villigen, Switzerland.

We report on the fabrication and characterization of high-resolution gratings with high efficiency in the extreme ultraviolet (EUV) and soft x-ray ranges using spin-on-carbon (SOC) underlayers. We demonstrate the fabrication of diffraction gratings down to 20 nm half-pitch (HP) on SiNmembranes with a bilayer of hydrogen silsesquioxane (HSQ) and spin-on-carbon and show their performance as a grating mask for extreme ultraviolet interference lithography (EUV-IL). High-resolution patterning of HSQ is possible only for thin films due to pattern collapse. The combination of this high-resolution resist with SOC circumvents this problem and enables the fabrication of high aspect ratio nanostructures. Rigorous coupled-wave analysis shows that the bilayer gratings exhibit higher diffraction efficiency than what is feasible with a grating made of HSQ. We also demonstrate a simple and accurate method to experimentally measure the diffraction efficiency of high-resolution gratings by measuring the relative ratio of the dose-to-clear curves of the photoresist. The measured diffraction efficiencies are in good agreement with the theoretically predicted values. Furthermore, we verify our calculations and measurements by printing line/space patterns in chemically amplified resists down to 10 nm HP with both HSQ and bilayer grating masks using EUV-IL. The improved diffraction efficiency of the bilayers is expected to have applications not only in gratings for interference lithography, but also in Fresnel zone plates and gratings for spectroscopy in the EUV and soft x-ray ranges.
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http://dx.doi.org/10.1088/1361-6528/ac328bDOI Listing
November 2021

Two-dimensional numerical studies of particle motion and deposition in the channel of diesel particulate filters.

R Soc Open Sci 2021 Oct 13;8(10):211162. Epub 2021 Oct 13.

Marine Engineering College, Dalian Maritime University, Dalian 116026, Liaoning, People's Republic of China.

A numerical investigation on the soot laden flow of gas in a partial diesel particulate filter (PDPF) is presented based on solving the momentum equations for a continuous phase in the Euler frame and the motion equations for the dispersed phase in the Lagrangian frame. The interaction between the gas phase and the particles is considered as a one-way coupling for dilute particle concentration, while the interaction between particles and porous wall is implemented through user-definedsubroutines. To accurately track motion of nanoscale particles, the Brownian excitation and drag force as well as partial slip are taken into account in the particulate motion equation. Two methods are used to verify the gas flow model and reasonable agreements for both comparisons are observed. The effects of inlet velocity, wall permeability and particle size on the filtration efficiency and deposition distribution of the particles along with wall surface of inlet channel are quantitatively studied. The results show that (i) wall permeability plays the primary role in determining the filtration efficiency of PDPF, (ii) both upstream velocity and particle size have an effect on the initial deposition position of particles and (iii) filtration efficiency of PDPF is not markedly proportional to gas flow into inlet channels at a low wall permeability.
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http://dx.doi.org/10.1098/rsos.211162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8511759PMC
October 2021

Evaluation of environmental factors affecting the genetic diversity, genetic structure, and the potential distribution of Georgi under changing climate.

Ecol Evol 2021 Sep 25;11(18):12294-12306. Epub 2021 Aug 25.

National & Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation Jilin University Changchun China.

Understanding genetic variation and structure, adaptive genetic variation, and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic differentiation of (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors, and (Ⅳ) exactly calculate the development trend of population of , as it is confronted with severe climate change and to provide information for designing effective conservation and management strategies. We found high genetic variation ( = 0.584) and differentiation among populations (  = 0.703) and moderate levels of genetic diversity within populations of . A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of different populations was caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci are identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of to the environment. Species distribution models (SDMs) showed that climate warming will cause a significant reduction in suitable areas for , especially under the RCP 85 scenario. Our results help to understand the potential response of to climatic changes and provide new perspectives for resource management and conservation strategies.
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http://dx.doi.org/10.1002/ece3.7803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8462154PMC
September 2021

Integrated analysis identifies a novel lncRNA prognostic signature associated with aerobic glycolysis and hub pathways in breast cancer.

Cancer Med 2021 11 27;10(21):7877-7892. Epub 2021 Sep 27.

Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.

Long noncoding RNAs (lncRNAs) play a crucial role in cancer aerobic glycolysis. However, glycolysis-related lncRNAs are still underexplored in breast cancer. In this study, we identified the five most glycolysis-related lncRNAs in breast cancer to construct a prognostic signature, which could distinguish between patients with unfavorable and favorable prognoses. To investigate the role of signature lncRNAs in breast cancer, we profiled their expression levels in breast cancer progression cell line model. Real-time PCR revealed that the five lncRNAs could contribute to breast cancer initiation or progression. Furthermore, we observed that the levels of four lncRNAs expression had a significant trend of gradient upregulation with the addition of glycolysis inhibitor in breast cancer cells. Afterward, random forest and logistic regression were conducted to assess the model's performance in stratifying glycolysis status. Finally, a nomogram including the lncRNA signature and clinical features was developed, and its efficacy in predicting the survival time and clinical utility was evaluated using a calibration curve, concordance index, and decision curve analysis. In this study, gene set enrichment analysis showed that the mTOR pathway, a central pathway in tumor initiation and progression, was significantly enriched in the high-risk group. In addition, gene set variation analysis was performed to validate our findings in two independent datasets. Subsequent weighted gene co-expression network analysis, followed by enrichment analysis, indicated that downstream cell growth-related signaling was strikingly activated in the high-risk group, and may directly promote tumor progression and escalate mortality risk in patients with high-risk scores. Overall, our findings may provide novel insight into lncRNA-related metabolic regulation, and help to develop promising prognostic indicators and therapeutic targets for breast cancer patients.
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http://dx.doi.org/10.1002/cam4.4291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559482PMC
November 2021

Transboundary spread of peste des petits ruminants virus in western China: A prediction model.

PLoS One 2021 23;16(9):e0257898. Epub 2021 Sep 23.

College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang province, P. R. China.

In pan Pamir Plateau countries, Peste des petits ruminants (PPR) has brought huge losses to the livestock industry and threaten the endangered wildlife. In unknown regions, revealing PPRV transmission among countries is the premise of effective prevention and control, therefore calls for quantified monitoring on disease communication among countries. In this paper, a MaxEnt model was built for the first time to predict the PPR risk within the research area. The least cost path (LCP) for PPR transboundary communication were calculated and referred to as the maximum available paths (MAP). The results show that there are many places with high-risk in the research area, and the domestic risk in China is lower than that in foreign countries and is mainly determined by human activities. Five LCPs representing corridors among Kazakhstan, Tajikistan, Pakistan, India and China were obtained. This study proves for the first time that there is the possibility of cross-border transmission of diseases by wild and domestic animals. In the future, it will play an important role in monitoring the PPR epidemic and blocking-up its cross-border transmission.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0257898PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459964PMC
November 2021

Identification and Validation of a Five-Gene Signature Associated With Overall Survival in Breast Cancer Patients.

Front Oncol 2021 26;11:660242. Epub 2021 Aug 26.

Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan, China.

Background: Recent years, the global prevalence of breast cancer (BC) was still high and the underlying molecular mechanisms remained largely unknown. The investigation of prognosis-related biomarkers had become an urgent demand.

Results: In this study, gene expression profiles and clinical information of breast cancer patients were downloaded from the TCGA database. The differentially expressed genes (DEGs) were estimated by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A risk score formula involving five novel prognostic associated biomarkers (EDN2, CLEC3B, SV2C, WT1, and MUC2) were then constructed by LASSO. The prognostic value of the risk model was further confirmed in the TCGA entire cohort and an independent external validation cohort. To explore the biological functions of the selected genes, assays were performed, indicating that these novel biomarkers could markedly influence breast cancer progression.

Conclusions: We established a predictive five-gene signature, which could be helpful for a personalized management in breast cancer patients.
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http://dx.doi.org/10.3389/fonc.2021.660242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428534PMC
August 2021

Long-term ketamine administration induces bladder damage and upregulates autophagy-associated proteins in bladder smooth muscle tissue.

Environ Toxicol 2021 Dec 6;36(12):2521-2529. Epub 2021 Sep 6.

School of Forensic Medicine, China Medical University, Shenyang, China.

Long-term ketamine abuse can cause significant lower urinary tract symptoms in humans, termed ketamine-associated cystitis (KC). Here, we established a model of long-term (6 months) ketamine administration in wild-type (C57BL/6) mice. We elucidated the pathological effects of ketamine in the bladder and investigated changes in autophagy-associated protein expression (i.e., LC3, Beclin-1, and P62) and inflammatory cytokines (i.e., IL-6 and IL-1β) in the bladder smooth muscle tissue. Long-term ketamine administration reduced the number of layers in the bladder mucosal epithelial cells (4-5 layers in the saline group vs. 2-3 layers in the ketamine groups), but increased the number of mast cells and collagen fibers. LC3-II/LC3-I, Beclin-1, IL-6, and IL-1β protein expression in the bladder smooth muscle tissues of ketamine-treated mice was significantly increased. The mRNA and protein levels of P62 in the Ket-60 mg/kg group were also significantly increased, but not the Ket-30 mg/kg group. Our results reveal that long-term ketamine administration can cause cystitis-like pathological changes in mice, and the disordered autophagy in the bladder tissue may be involved in the persistent bladder damage following long-term administration of ketamine at 60 mg/kg.
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http://dx.doi.org/10.1002/tox.23365DOI Listing
December 2021

Plasma-induced destruction of Candida albicans cell wall components: A reactive molecular dynamics simulation.

Biochem Biophys Res Commun 2021 10 31;576:53-58. Epub 2021 Aug 31.

School of Electrical Engineering, Shandong University, Jinan, 250061, People's Republic of China. Electronic address:

Cold atmospheric plasma (CAP) has attracted significant attention and has been widely used to inactivate pathogens based on its excellent effect; however, the mechanisms underlying the interactions between plasma-generated species and organisms have not yet been fully elucidated. In this paper, the interactions of reactive oxygen plasma species (O, OH and HO) with chitin polymer (the skeletal component of the Candida albicans cell wall) were investigated by means of reactive molecular dynamics simulations from a microscopic point of view. Our simulations show that O and OH species can break important structural bonds (e.g., N-H bonds, O-H bonds and C-H bonds) of chitin. This is followed by a cascade of bond cleavage and double bond formation events. This simulation study aimed to improve the understanding of the micromechanism of plasma-inactivated Candida albicans at the atomic level.
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http://dx.doi.org/10.1016/j.bbrc.2021.08.093DOI Listing
October 2021

circ-EIF6 encodes EIF6-224aa to promote TNBC progression via stabilizing MYH9 and activating the Wnt/beta-catenin pathway.

Mol Ther 2022 Jan 25;30(1):415-430. Epub 2021 Aug 25.

Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong, China; Pathology Tissue Bank, Qilu Hospital of Shandong University, Ji'nan, Shandong, China; Research Institute of Breast Cancer, Shandong University, Ji'nan, Shandong, China. Electronic address:

The protein-coding ability of circular RNAs (circRNAs) has recently been a hot topic, but the expression and roles of protein-coding circRNAs in triple-negative breast cancer (TNBC) remain uncertain. By intersecting circRNA sequencing data from clinical samples and cell lines, we identified a circRNA, termed circ-EIF6, which predicted a poorer prognosis and correlated with clinicopathological characteristics in a cohort of TNBC patients. Functionally, we showed that circ-EIF6 promoted the proliferation and metastasis of TNBC cells in vitro and in vivo. Mechanistically, we found that circ-EIF6 contains a 675-nucleotide (nt) open reading frame (ORF) and that the -150-bp sequence from ATG functioned as an internal ribosome entry site (IRES), which is required for translation initiation in 5' cap-independent coding RNAs. circ-EIF6 encodes a novel peptide, termed EIF6-224 amino acid (aa), which is responsible for the oncogenic effects of circ-EIF6. The endogenous expression of EIF6-224aa was further examined in TNBC cells and tissues by specific antibody. Moreover, EIF6-224aa directly interacted with MYH9, an oncogene in breast cancer, and decreased MYH9 degradation by inhibiting the ubiquitin-proteasome pathway and subsequently activating the Wnt/beta-catenin pathway. Our study provided novel insights into the roles of protein-coding circRNAs and supported circ-EIF6/EIF6-224aa as a novel promising prognostic and therapeutic target for tailored therapy in TNBC patients.
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http://dx.doi.org/10.1016/j.ymthe.2021.08.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8753373PMC
January 2022

PFC: A Novel Perceptual Features-Based Framework for Time Series Classification.

Entropy (Basel) 2021 Aug 17;23(8). Epub 2021 Aug 17.

College of Computer Science and Technology, Harbin Institute of Technology, Shenzhen 518055, China.

Time series classification (TSC) is a significant problem in data mining with several applications in different domains. Mining different distinguishing features is the primary method. One promising method is algorithms based on the morphological structure of time series, which are interpretable and accurate. However, existing structural feature-based algorithms, such as time series forest (TSF) and shapelet traverse, all features through many random combinations, which means that a lot of training time and computing resources are required to filter meaningless features, important distinguishing information will be ignored. To overcome this problem, in this paper, we propose a perceptual features-based framework for TSC. We are inspired by how humans observe time series and realize that there are usually only a few essential points that need to be remembered for a time series. Although the complex time series has a lot of details, a small number of data points is enough to describe the shape of the entire sample. First, we use the improved perceptually important points (PIPs) to extract key points and use them as the basis for time series segmentation to obtain a combination of interval-level and point-level features. Secondly, we propose a framework to explore the effects of perceptual structural features combined with decision trees (DT), random forests (RF), and gradient boosting decision trees (GBDT) on TSC. The experimental results on the UCR datasets show that our work has achieved leading accuracy, which is instructive for follow-up research.
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http://dx.doi.org/10.3390/e23081059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8391677PMC
August 2021

More abundant and healthier meat: will the MSTN editing epitome empower the commercialization of gene editing in livestock?

Sci China Life Sci 2021 Aug 20. Epub 2021 Aug 20.

Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, 31535, Germany.

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http://dx.doi.org/10.1007/s11427-021-1980-4DOI Listing
August 2021

Corrigendum to "Changing of haemostatic system in a pig model during different types of hypothermic circulatory arrest" [95, 2021, 102817].

J Therm Biol 2021 Jul 13;99:102974. Epub 2021 May 13.

Department of Cardiac Surgery, Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Aortic Disease Center, Cardiovascular Surgery Center, Beijing, China; Beijing Engineering Research Center for Vascular Prostheses, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/j.jtherbio.2021.102974DOI Listing
July 2021

Inhibition of LIM kinase reduces contraction and proliferation in bladder smooth muscle.

Acta Pharm Sin B 2021 Jul 7;11(7):1914-1930. Epub 2021 Jan 7.

Department of Urology and Guangdong Key Laboratory of Urology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510230, China.

Overactive bladder (OAB) is the most bothersome symptom in lower urinary tract symptoms (LUTS). Current pharmacologic treatment aims to inhibit detrusor contraction; however, shows unsatisfied efficacy and high discontinuation rate. LIM kinases (LIMKs) promote smooth muscle contraction in the prostate; however, their function in the bladder smooth muscle remains unclear. Here, we studied effects of the LIMK inhibitors on bladder smooth muscle contraction and proliferation both and experiments. Bladder expressions of LIMKs are elevated in OAB rat detrusor tissues. Two LIMK inhibitors, SR7826 and LIMKi3, inhibit contraction of human detrusor strip, and cause actin filament breakdown, as well as cell proliferation reduction in cultured human bladder smooth muscle cells (HBSMCs), paralleled by reduced cofilin phosphorylation. Silencing of and in HBSMCs resulted in breakdown of actin filaments and decreased cell proliferation. Treatment with SR7826 or LIMKi3 decreased micturition frequency and bladder detrusor hypertrophy in rats with bladder outlet obstruction. Our study suggests that LIMKs may promote contraction and proliferation in the bladder smooth muscle, which could be inhibited by small molecule LIMK inhibitors. LIMK inhibitors could be a potential therapeutic strategy for OAB- related LUTS.
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http://dx.doi.org/10.1016/j.apsb.2021.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8343115PMC
July 2021

Expression of FcεRIα and tryptase in human lung tissue during drug-induced anaphylactic death.

Forensic Sci Med Pathol 2021 12 12;17(4):547-552. Epub 2021 Aug 12.

School of Forensic Medicine, China Medical University, Shenyang, 110122, P.R. China.

The diagnosis of drug-induced anaphylactic death is an important component of forensic medicine. The purpose of this study was to explore the expression of FcεRIα and tryptase in human lung tissue during drug-induced anaphylactic death and its value for forensic medicine. The expression of FcεRIα and tryptase in lung tissues of the drug-induced anaphylactic death group (n = 30) and control group (who died due to sudden cardiac death, falling from a height, or traffic accidents, n = 30) was detected by immunohistochemistry and immunofluorescence staining. The difference in FcεRIα and tryptase expression in the lung tissue between the drug-induced anaphylactic death group and the control group was statistically significant (p < 0.05). The levels of FcεRIα and tryptase expression greatly increased in the lung tissue of the drug-induced anaphylactic death group, which may provide morphological evidence and a reference for the diagnosis of drug-induced anaphylactic death in forensic medicine.
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http://dx.doi.org/10.1007/s12024-021-00405-wDOI Listing
December 2021

Physicochemical and in vitro digestibility properties on complexes of fermented wheat starches with konjac gum.

Int J Biol Macromol 2021 Oct 3;188:197-206. Epub 2021 Aug 3.

College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.

In this study, the wheat starch with natural fermentation for 72 h was combined with konjac gum (KGM) at different concentrations (0, 0.1, 0.3, 0.5%, w/w), and the changes in physicochemical and digestible characteristics of the complexes were investigated. The results showed that KGM clumped fermented starch (FS) granules together and caused the FS gels to form a close network structure. The addition of KGM significantly decreased the amylose content and swelling power, and reduced peak viscosity, final viscosity, and setback value (SB), which indicated that FS-KGM complexes possessed soft gel structure and could resist the short-term retrogradation. KGM impeded the increase of relative crystallinity, retrogradation enthalpy and gel firmness of FS during storage, suggesting the long-term retrogradation of FS was retarded by KGM. All starch pastes had a weak gel-like structure, and higher storage modulus (G') and loss tangent (tan δ) values obtained after the addition of KGM. In vitro digestion results showed that KGM could slow the hydrolysis of FS, resulting in the increase of slowly digested starch (SDS) and resistant starch (RS). In particularly, the FS-0.3KGM showed the ideal structure, the best anti-retrogradation effected, and slowest the hydrolysis.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.08.005DOI Listing
October 2021
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