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https://www.readbyqxmd.com/read/29241666/identification-of-human-circadian-genes-based-on-time-course-gene-expression-profiles-by-using-a-deep-learning-method
#1
Peng Cui, Tingyan Zhong, Zhuo Wang, Tao Wang, Hongyu Zhao, Chenglin Liu, Hui Lu
Circadian genes express periodically in an approximate 24-h period and the identification and study of these genes can provide deep understanding of the circadian control which plays significant roles in human health. Although many circadian gene identification algorithms have been developed, large numbers of false positives and low coverage are still major problems in this field. In this study we constructed a novel computational framework for circadian gene identification using deep neural networks (DNN) a deep learning algorithm which can represent the raw form of data patterns without imposing assumptions on the expression distribution...
December 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29237042/dual-antiplatelet-therapy-after-coronary-artery-bypass-surgery-is-there-an-increase-in-bleeding-risk-a-meta-analysis
#2
Yejing Zhao, Hongyu Peng, Xiaonan Li, Yujun Qin, Fangying Cao, Ding Peng, Jinghua Liu
OBJECTIVES: There is increasing evidence that dual antiplatelet therapy (DAPT) when compared with single antiplatelet therapy may improve venous graft patency after coronary artery bypass graft. However, it is not yet known whether postoperative administration of DAPT may increase the potential risk of bleeding, especially in the early postoperative period. METHODS: We searched studies on PubMed, Embase, Web of Science and the Cochrane Central Register of Controlled Trials...
December 8, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/29235839/room-temperature-processed-flexible-amorphous-ingazno-thin-film-transistor
#3
Xiang Xiao, Letao Zhang, Yang Shao, Xiaoliang Zhou, Hongyu He, Shengdong Zhang
A room-temperature flexible amorphous indium-gallium-zinc oxide thin film transistor (a-IGZO TFT) technology is developed on plastic substrates, in which both the gate dielectric and passivation layers of the TFTs are formed by an anodic oxidation (anodization) technique. While the gate dielectric Al2O3 is grown with a conventional anodization on an Al:Nd gate electrode, the channel passivation layer Al2O3 is formed using a localized anodization technique. The anodized Al2O3 passivation layer shows a superior passivation effect to that of PECVD SiO2...
December 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29232653/salicylic-acid-and-broad-spectrum-of-nbs-lrr-family-genes-are-involved-in-smv-soybean-interactions
#4
Qiqi Zhao, Haina Li, Hongyu Sun, Aoga Li, Shuxin Liu, Ruonan Yu, Xiuqi Cui, Dejian Zhang, Hada Wuriyanghan
Soybean mosaic virus (SMV) is a severe pathogen reducing crop yield and seed quality of soybean. Although several resistance gene loci including Rsv1, Rsv3 and Rsv4 are identified in some soybean varieties, most of the soybean genes related to SMV infection are still not characterized. In order to reveal genome-wide gene expression profiles in response to SMV infection, we used transcriptome analysis to determine SMV-responsive genes in susceptible variety Hefeng25. Time course RNA-seq analysis at 1, 5 and 10 dpi identified many deregulated pathways and gene families...
December 7, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29230364/complete-genome-sequence-and-comparative-genomics-of-the-golden-pompano-trachinotus-ovatus-pathogen-vibrio-harveyi-strain-qt520
#5
Zhigang Tu, Hongyue Li, Xiang Zhang, Yun Sun, Yongcan Zhou
Vibrio harveyi is a Gram-negative, halophilic bacterium that is an opportunistic pathogen of commercially farmed marine vertebrate species. To understand the pathogenicity of this species, the genome of V. harveyi QT520 was analyzed and compared to that of other strains. The results showed the genome of QT520 has two unique circular chromosomes and three endogenous plasmids, totaling 6,070,846 bp with a 45% GC content, 5,701 predicted ORFs, 134 tRNAs and 37 rRNAs. Common virulence factors, including ACF, IlpA, OmpU, Flagellin, Cya, Hemolysin and MARTX, were detected in the genome, which are likely responsible for the virulence of QT520...
2017: PeerJ
https://www.readbyqxmd.com/read/29228691/berberine-attenuated-pro-inflammatory-factors-and-protect-against-neuronal-damage-via-triggering-oligodendrocyte-autophagy-in-spinal-cord-injury
#6
Hongyu Wang, Chang Liu, Xifan Mei, Yang Cao, Zhanpeng Guo, Yajiang Yuan, Ziming Zhao, Changwei Song, Yue Guo, Zhaoliang Shen
Berberine exerts neuroprotective effect in neuroinflammation and neurodegeneration disease. However, berberine effect in acute spinal cord injury is yet to be elucidated. Herein, we investigated the neuroprotective effect of berberine in spinal cord injury (SCI). Sprague-Dawley rats were subjected to SCI by an intraperitoneal injection of berberine post-injury. The neurobehavioral recovery, cytokines of pro-inflammatory factors (TNF-α and IL-1β), autophagy-related proteins (LC3B, ATG16L, ATG7), and apoptosis-related protein cleaved caspase-3 were determined...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29227169/descriptive-study-of-the-relationship-between-the-subclinical-carotid-disease-and-biomarkers-carotid-femoral-pulse-wave-velocity-in-patients-with-hypertension
#7
XiaoXiao Zhao, Liujin Bo, Hongwei Zhao, Lihong Li, Yingyan Zhou, Hongyu Wang
BACKGROUND: Carotid intima-media thickness (cIMT) is a significant early prediction signal for preclinical atherosclerosis. Plasma homocysteine (Hcy) level is an independent risk factor for cardiovascular diseases. Pulse wave velocity (PWV), an index of arterial stiffness (AS), has showed its value in the evaluation of AS in vascular-related diseases. The data regarding the relationships between cIMT and other indices of vascular damage are limited and partly controversial. We aim to investigate the relationships between cIMT and other indices of vascular damage such as Hcy and carotid femoral PWV (CF-PWV)...
December 11, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/29226931/development-of-visible-light-responsive-and-mechanically-enhanced-smart-ucst-interpenetrating-network-hydrogels
#8
Yifei Xu, Onkar Ghag, Morgan Reimann, Philip Sitterle, Prithwish Chatterjee, Elizabeth Nofen, Hongyu Yu, Hanqing Jiang, Lenore L Dai
An interpenetrating polymer network (IPN), chlorophyllin-incorporated environmentally responsive hydrogel was synthesized and exhibited the following features: enhanced mechanical properties, upper critical solution temperature (UCST) swelling behavior, and promising visible-light responsiveness. Poor mechanical properties are known challenges for hydrogel-based materials. By forming an interpenetrating network between polyacrylamide (PAAm) and poly(acrylic acid) (PAAc) polymer networks, the mechanical properties of the synthesized IPN hydrogels were significantly improved compared to hydrogels made of a single network of each polymer...
December 11, 2017: Soft Matter
https://www.readbyqxmd.com/read/29220677/a-powerful-approach-to-estimating-annotation-stratified-genetic-covariance-via-gwas-summary-statistics
#9
Qiongshi Lu, Boyang Li, Derek Ou, Margret Erlendsdottir, Ryan L Powles, Tony Jiang, Yiming Hu, David Chang, Chentian Jin, Wei Dai, Qidu He, Zefeng Liu, Shubhabrata Mukherjee, Paul K Crane, Hongyu Zhao
Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics...
December 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29218243/elevated-hbxip-expression-is-associated-with-aggressive-phenotype-and-poor-prognosis-in-esophageal-squamous-cell-carcinoma
#10
Honggang Xia, Lan Ma, Jing Li, Hongyu Bai, Dongbin Wang
The oncoprotein hepatitis B virus X-interacting protein (HBXIP) has been suggested to play an essential role in several malignancies. However, the clinicopathological significance and prognostic value of HBXIP expression in esophageal squamous cell carcinoma (ESCC) is still unknown. Therefore the aim of this study was to characterize HBXIP expression and its prognostic value in ESCC. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to assess the mRNA and protein expression of HBXIP in ESCC tissues and cell lines...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/29212468/a-comparison-of-graph-and-kernel-based-omics-data-integration-algorithms-for-classifying-complex-traits
#11
Kang K Yan, Hongyu Zhao, Herbert Pang
BACKGROUND: High-throughput sequencing data are widely collected and analyzed in the study of complex diseases in quest of improving human health. Well-studied algorithms mostly deal with single data source, and cannot fully utilize the potential of these multi-omics data sources. In order to provide a holistic understanding of human health and diseases, it is necessary to integrate multiple data sources. Several algorithms have been proposed so far, however, a comprehensive comparison of data integration algorithms for classification of binary traits is currently lacking...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29212263/combination-of-betulinic-acid-and-chidamide-inhibits-acute-myeloid-leukemia-by-suppression-of-the-hif1%C3%AE-pathway-and-generation-of-reactive-oxygen-species
#12
Hongyu Zhang, Ling Li, Min Li, Xiaodong Huang, Weiguo Xie, Wei Xiang, Paul Yao
Acute myeloid leukemia (AML) is a heterogeneous disorder of the hematopoietic system with no common genetic "Achilles heel" that can be targeted. Most patients respond well to standard therapy, while a majority relapse, and development of an effective therapy for AML patients is still urgently needed. In this study, we demonstrated that betulinic acid (BA) significantly increased Aryl hydrocarbon receptor (AHR) expression through demethylation on the AHR promoter in AML cells, and the increased AHR expression interacts with and sequesters ARNT, subsequently suppressing hypoxia-inducible factor-1α (HIF1α) pathway...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29210663/dna-methylation-a-frontier-in-tooth-organogenesis-and-developmental-dental-defects
#13
Liwei Zheng, Hongyu Li, Zhou Yachuan, Wei Du, Xin Xu, Ling Ye, Xuedong Zhou, Mian Wan
Tooth development relies on interactions between epithelial and mesenchymal tissues, which is controlled by sophisticated networks of conserved signaling. The signaling networks regulating odontogenesis have been well characterized, but the mechanisms underlying remain to be elucidated. Researches on mammals have revealed that the genomic methylation, which occurs on cytosine residues, regulates certain genes transcription. Consequently, DNA methylation plays a crucial role in spatiotemporal organization of signaling pathways, and is essential for organogenesis...
December 6, 2017: Current Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29199250/ci-ambp-a-highly-conserved-member-of-the-microglobulin-superfamily-of-proteinase-inhibitors-in-grass-carp-ctenopharyngodon-idellus
#14
Jianming Su, Hongyu Lei, Tiaoyi Xiao, Shuliang Cui
A full-length cDNA clone encoding grass carp (Ctenopharyngodon idellus) α1-microglobulin/bikunin precursor (Ci-AMBP) was isolated by subtracted differential hybridization screening from a liver cDNA library. The deduced amino acid sequence shared approximately 50% sequence identity with its mammalian counterparts, but more than 90% identity with another fish species. AMBPs are the precursors of the plasma glycoproteins α1-microglobulin (α1m) and bikunin. Both peptide structures and their chromosomal organization were well conserved in Ci-AMBP...
December 4, 2017: Genes & Genetic Systems
https://www.readbyqxmd.com/read/29192714/2-2-hydroxyphenyl-imidazole-based-four-coordinate-organoboron-compounds-with-efficient-deep-blue-photoluminescence-and-electroluminescence
#15
Zhenyu Zhang, Zuolun Zhang, Hongyu Zhang, Yue Wang
Two new four-coordinate organoboron compounds with 2-(2-hydroxyphenyl)imidazole derivatives as the chelating ligands have been synthesized. They possess high thermal stability and are able to form an amorphous glass state. Crystallographic analyses indicate that the differences in ligand structure cause the change of ππ stacking character. The CH2Cl2 solutions and thin films of these compounds display bright blue emission, and these compounds have appropriate HOMO and LUMO energy levels for carrier injection in OLEDs...
December 1, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29191015/dynamics-sampling-in-transition-pathway-space
#16
Hongyu Zhou, Peng Tao
The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states, and should be identified to obtain a full view of the transitions...
November 30, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29178946/a-putative-causal-relationship-between-genetically-determined-female-body-shape-and-posttraumatic-stress-disorder
#17
Renato Polimanti, Ananda B Amstadter, Murray B Stein, Lynn M Almli, Dewleen G Baker, Laura J Bierut, Bekh Bradley, Lindsay A Farrer, Eric O Johnson, Anthony King, Henry R Kranzler, Adam X Maihofer, John P Rice, Andrea L Roberts, Nancy L Saccone, Hongyu Zhao, Israel Liberzon, Kerry J Ressler, Caroline M Nievergelt, Karestan C Koenen, Joel Gelernter
BACKGROUND: The nature and underlying mechanisms of the observed increased vulnerability to posttraumatic stress disorder (PTSD) in women are unclear. METHODS: We investigated the genetic overlap of PTSD with anthropometric traits and reproductive behaviors and functions in women. The analysis was conducted using female-specific summary statistics from large genome-wide association studies (GWAS) and a cohort of 3577 European American women (966 PTSD cases and 2611 trauma-exposed controls)...
November 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29169155/rho-kinase-regulates-aortic-vascular-smooth-muscle-cell-stiffness-via-actin-srf-myocardin-in-hypertension
#18
Ning Zhou, Jia-Jye Lee, Shaunrick Stoll, Ben Ma, Kevin D Costa, Hongyu Qiu
BACKGROUND/AIMS: Our previous studies demonstrated that intrinsic aortic smooth muscle cell (VSMC) stiffening plays a pivotal role in aortic stiffening in aging and hypertension. However, the underlying molecular mechanisms remain largely unknown. We here hypothesized that Rho kinase (ROCK) acts as a novel mediator that regulates intrinsic VSMC mechanical properties through the serum response factor (SRF) /myocardin pathway and consequently regulates aortic stiffness and blood pressure in hypertension...
November 23, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29168174/genetic-variants-in-the-platelet-derived-growth-factor-subunit-b-gene-associated-with-pancreatic-cancer-risk
#19
Bensong Duan, Jiangfeng Hu, Hongliang Liu, Yanru Wang, Hongyu Li, Shun Liu, Jichun Xie, Kouros Owzar, James Abbruzzese, Herbert Hurwitz, Hengjun Gao, Qingyi Wei
The platelet-derived growth factor (PDGF) signaling pathway plays important roles in development and progression of human cancers. In our study, we aimed to identify genetic variants of the PDGF pathway genes associated with pancreatic cancer (PC) risk in European populations using three published genome-wide association study datasets, which consisted of 9,381 cases and 7,719 controls. The expression quantitative trait loci (eQTL) analysis was also performed using data from the 1000 Genomes, TCGA and GTEx projects...
November 23, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29152099/s149r-a-novel-mutation-in-the-abcd1-gene-causing-x-linked-adrenoleukodystrophy
#20
Fang Yan, Wenbo Wang, Hui Ying, Hongyu Li, Jing Chen, Chao Xu
X-linked adrenoleukodystrophy (X-ALD) is the most common peroxisomal disorder. It is a heterogeneous disorder caused by mutations in the ATP-binding cassette protein subfamily D1 (ABCD1) gene, encoding the peroxisomal membrane protein ALDP, which is involved in the transmembrane transport of very long-chain fatty acids. For the first time, we report a case of olivopontocerebellar X-ALD on the Chinese mainland. In this study, a novel mutation (c.447T>A; p.S149R) in ABCD1 was detected in a patient diagnosed with X-ALD...
October 20, 2017: Oncotarget
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