An Approach to Robot Commonsense Reasoning

Kejun Wang,Tongchun Du,Xiaofei Yang 보안공학연구지원센터 2015 International Journal of Multimedia and Ubiquitous Vol.10 No.4

To perform missions assigned by people, the mobile robot needs to learn both itself and the world it is in, to use the learned knowledge to reason and make decisions to resolve problems, and to guide further learning, and to establish its knowledge base which contains huge amounts of common sense. During the process of executing missions by reasoning and learning, it is critical to enable domain-specific robots be more tolerant rather than puzzled when encountering perturbations. In this paper, active logic is improved to deal with contradicted beliefs, metacognitive loop is incorporated to supervise and guide the whole reasoning process. Finally, route crack experiments state that this metacognitive loop and improved active logic based method can handle robot commonsense reasoning in an efficient way and be comparatively robust with perturbations.

Comparative transcriptome analysis of salt-sensitive and salt-tolerant maize reveals potential mechanisms to enhance salt resistance

Mingquan Wang,Yufeng Wang,Yifei Zhang,Chunxia Li,Shichen Gong,Shuqin Yan,Guoliang Li,Guanghui Hu,Honglei Ren,Jianfei Yang,Tao Yu,Kejun Yang 한국유전학회 2019 Genes & Genomics Vol.41 No.7

Background Salt stress is a devastating environmental stress that causes plant growth inhibition and yield reduction. Objective The identification of salt-tolerant genes brings hope for the generation of salinity-tolerant crop plants through molecular breeding. Methods In this study, one salt-sensitive and one salt-tolerant maize inbred line were screened from 242 maize inbred lines. Reactive oxygen species (ROS)-related enzyme activities were detected and salt-responsive comparative transcriptome analysis was performed for control and 220 mM NaCl treated maize leaves. Results Salt-tolerant maize inbred line (L87) showed higher ROS-related enzyme (SOD, POD, APX and CAT) activities and accumulated relatively lower levels of ROS under salt stress. Of the total DEGs, 1856 upregulated DEGs were specific to L87, including stress tolerance-related members of the 70kDa family of heat shock proteins (Hsp70s) and aquaporins. The DEGs involved in the abscisic acid (ABA), ethylene, jasmonic acid (JA) and salicylic acid (SA) signal transduction pathways may determine the difference in salt tolerance between the two varieties, especially one central component SnRK2, that positively regulates ABA signaling and was only upregulated in L87. Analysis of DEGs related to ROS scavenging showed that some peroxidase (POD), glutathione S-transferase (GST), catalase (CAT) and superoxide dismutase (SOD) genes specific to L87 probably enhanced its salt tolerance. The analysis of differentially expressed transcription factors (TFs) suggested that WRKY TFs could contribute to the difference in salt tolerance between the two maize lines. Conclusion Compared with Salt-sensitive maize inbred line (L29), L87 exhibits specific regulatory mechanisms related to salt tolerance, including plant hormone interactions, ROS scavenging and the regulation of TFs. Our study identifies new candidate genes that may regulate maize tolerance to salt stress and provides useful information for breeding maize with high salt resistance.

Integrated analysis of transcriptomic and proteomic analyses reveals different metabolic patterns in the livers of Tibetan and Yorkshire pigs

Duan, Mengqi,Wang, Zhenmei,Guo, Xinying,Wang, Kejun,Liu, Siyuan,Zhang, Bo,Shang, Peng Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.5

Objective: Tibetan pigs, predominantly originating from the Tibetan Plateau, have been subjected to long-term natural selection in an extreme environment. To characterize the metabolic adaptations to hypoxic conditions, transcriptomic and proteomic expression patterns in the livers of Tibetan and Yorkshire pigs were compared. Methods: RNA and protein were extracted from liver tissue of Tibetan and Yorkshire pigs (n = 3, each). Differentially expressed genes and proteins were subjected to gene ontology and Kyoto encyclopedia of genes and genomes functional enrichment analyses. Results: In the RNA-Seq and isobaric tags for relative and absolute quantitation analyses, a total of 18,791 genes and 3,390 proteins were detected and compared. Of these, 273 and 257 differentially expressed genes and proteins were identified. Evidence from functional enrichment analysis showed that many genes were involved in metabolic processes. The combined transcriptomic and proteomic analyses revealed that small molecular biosynthesis, metabolic processes, and organic hydroxyl compound metabolic processes were the major processes operating differently in the two breeds. The important genes include retinol dehydrogenase 16, adenine phosphoribosyltransferase, prenylcysteine oxidase 1, sorbin and SH3 domain containing 2, ENSSSCG00000036224, perilipin 2, ladinin 1, kynurenine aminotransferase 1, and dimethylarginine dimethylaminohydrolase 1. Conclusion: The findings of this study provide novel insight into the high-altitude metabolic adaptation of Tibetan pigs.

Administration of antibiotics contributes to cholestasis in pediatric patients with intestinal failure via the alteration of FXR signaling

Yongtao Xiao,Kejun Zhou,Ying Lu,Weihui Yan,Wei Cai,Ying Wang 생화학분자생물학회 2018 Experimental and molecular medicine Vol.50 No.-

The link between antibiotic treatment and IF-associated liver disease (IFALD) is unclear. Here, we study the effect of antibiotic treatment on bile acid (BA) metabolism and investigate the involved mechanisms. The results showed that pediatric IF patients with cholestasis had a significantly lower abundance of BA-biotransforming bacteria than patients without cholestasis. In addition, the BA composition was altered in the serum, feces, and liver of pediatric IF patients with cholestasis, as reflected by the increased proportion of primary BAs. In the ileum, farnesoid X receptor (FXR) expression was reduced in patients with cholestasis. Correspondingly, the serum FGF19 levels decreased significantly in patients with cholestasis. In the liver, the expression of the rate-limiting enzyme in bile salt synthesis, cytochrome P450 7a1 (CYP7A1), increased noticeably in IF patients with cholestasis. In mice, we showed that oral antibiotics (gentamicin, GM or vancomycin, VCM) reduced colonic microbial diversity, with a decrease in both Gram-negative bacteria (GM affected Eubacterium and Bacteroides) and Gram-positive bacteria (VCM affected Clostridium, Bifidobacterium and Lactobacillus). Concomitantly, treatment with GM or VCM decreased secondary BAs in the colonic contents, with a simultaneous increase in primary BAs in plasma. Moreover, the changes in the colonic BA profile especially that of tauro-beta-muricholic acid (TβMCA), were predominantly associated with the inhibition of the FXR and further altered BA synthesis and transport. In conclusion, the administration of antibiotics significantly decreased the intestinal microbiota diversity and subsequently altered the BA composition. The alterations in BA composition contributed to cholestasis in IF patients by regulating FXR signaling.

Identification of growth trait related genes in a Yorkshire purebred pig population by genome-wide association studies

Qingli Meng,Kejun Wang,Xiallei Liu,Haishen Zhou,Li Xu,Zhaojun Wang,Meiying Fang 아세아·태평양축산학회 2017 Animal Bioscience Vol.30 No.4

Objective: The aim of this study is to identify genomic regions or genes controlling growth traits in pigs. Methods: Using a panel of 54,148 single nucleotide polymorphisms (SNPs), we performed a genome-wide Association (GWA) study in 562 pure Yorshire pigs with four growth traits: average daily gain from 30 kg to 100 kg or 115 kg, and days to 100 kg or 115 kg. Fixed and random model Circulating Probability Unification method was used to identify the associations between 54,148 SNPs and these four traits. SNP annotations were performed through the Sus scrofa data set from Ensembl. Bioinformatics analysis, including gene ontology analysis, pathway analysis and network analysis, was used to identify the candidate genes. Results: We detected 6 significant and 12 suggestive SNPs, and identified 9 candidate genes in close proximity to them (suppressor of glucose by autophagy [SOGA1], R-Spondin 2 [RSPO2], mitogen activated protein kinase kinase 6 [MAP2K6], phospholipase C beta 1 [PLCB1], rho GTPASE activating protein 24 [ARHGAP24], cytoplasmic polyadenylation element binding protein 4 [CPEB4], GLI family zinc finger 2 [GLI2], neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2 [NYAP2], and zinc finger protein multitype 2 [ZFPM2]). Gene ontology analysis and literature mining indicated that the candidate genes are involved in bone, muscle, fat, and lung development. Pathway analysis revealed that PLCB1 and MAP2K6 participate in the gonadotropin signaling pathway and suggests that these two genes contribute to growth at the onset of puberty. Conclusion: Our results provide new clues for understanding the genetic mechanisms underlying growth traits, and may help improve these traits in future breeding programs.

A double-labeling marker-based method for estimating inbreeding and parental genomic components in a population under conservation

Li, Wenting,Zhang, Mengmeng,Wang, Kejun,Lu, Yunfeng,Tang, Hui,Wu, Keliang Asian Australasian Association of Animal Productio 2020 Animal Bioscience Vol.33 No.1

Objective: The objective of a conservation program is to maintain maximum genetic diversity and preserve the viability of a breed. However, the efficiency of a program is influenced by the ability to accurately measure and predict genetic diversity. Methods: To examine this question, we conducted a simulation in which common measures (i.e. heterozygosity) and novel measures (identity-by-descent probabilities and parental genomic components) were used to estimate genetic diversity within a conserved population using double-labeled single nucleotide polymorphism markers. Results: The results showed that the accuracy and sensitivity of identity-by-state probabilities and heterozygosity were close to identity by descent (IBD) probabilities, which reflect the true genetic diversity. Expected heterozygosity most closely aligned with IBD. All common measures suggested that practices used in the current Chinese pig conservation program result in a ~5% loss in genetic diversity every 10 generations. Parental genomic components were also analyzed to monitor real-time changes in genomic components for each male and female ancestor. The analysis showed that ~7.5% of male families and ~30% of female families were lost every 5 generations. After 50 generations of simulated conservation, 4 male families lost ~50% of their initial genomic components, and the genomic components for 24.8% of the female families were lost entirely. Conclusion: In summary, compared with the true genetic diversity value obtained using double-labeled markers, expected heterozygosity appears to be the optimal indicator. Parental genomic components analysis provides a more detailed picture of genetic diversity and can be used to guide conservation management practices.

Correlation between fat accumulation and fecal microbiota in crossbred pigs

Li Xin,Li Mengyu,Han Jinyi,Liu Chuang,Han Xuelei,Wang Kejun,Qiao Ruimin,Li Xiu-Ling,Li Xin-Jian 한국미생물학회 2022 The journal of microbiology Vol.60 No.11

Backfat thickness (BF) is an important indicator of fat deposition capacity and lean meat rate in pigs and is very important in porcine genetics and breeding. Intestinal microbiota plays a key role in nutrient digestion and utilization with a profound impact on fat deposition of livestock animals. To investigate the relationship between the pig gut microbiome and BF, 20 low-BF (L-BF) and 20 high-BF (H-BF) pigs were selected as two groups from Yunong Black pigs in the present study. Fecal samples from pigs were analyzed for microbial diversity, composition, and predicted functionality using 16S rRNA gene sequencing. The results showed that there were significant differences in microbial β diversity between the two groups. LEfSe analysis revealed a number of bacterial features being differentially enriched in either L-BF or H-BF pigs. Spearman correlation analysis identified the abundance of Oscillospira, Peptococcus, and Bulleidia were significantly positive correlations with BF (P < 0.05), while Sutterella and Bifidobacterium were significantly negatively correlated with BF (P < 0.05). Importantly, the bacteria significantly positively correlated with BF mainly belong to Clostridium, which can ferment host-indigestible plant polysaccharides into shortchain fatty acid (SCFA) and promote fat synthesis and deposition. Predictive functional analysis indicated that the pathway abundance of cell motility and glycan biosynthesis were significantly widespread in the microbiota of the H-BF group. The results of this study will be useful for the development of microbial biomarkers for predicting and improving porcine BF, as well as for the investigation of targets for dietary strategies.

Insights into the genetic diversity of indigenous goats and their conservation priorities

Gang Liu,Qian Jun Zhao,Jian Lu,Feizhou Sun,Xu Han,Junjin Zhao,Haiyong Feng,Kejun Wang,Chousheng Liu 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.10

Objective: An experiment was conducted to evaluate genetic diversity of 26 Chinese indigenous goats by 30 microsatellite markers, and then to define conservation priorities to set up the protection programs according to the weight given to within- and between-breed genetic diversity. Methods: Twenty-six representative populations of Chinese indigenous goats, 1,351 total, were sampled from different geographic regions of China. Within-breed genetic diversity and marker polymorphism were estimated calculating the mean number of alleles, observed heterozygosities, expected heterozygosities, fixation index, effective number of alleles and allelic richness. Conservation priorities were analyzed by statistical methods. Results: A relatively high level of genetic diversity was found in twenty-four population; the exceptions were in the Daiyun and Fuqing goat populations. Within-breed kinship coefficient matrices identified seven highly inbred breeds which should be of concern. Of these, six breeds receive a negative contribution to heterozygosity when the method was based on proportional contribution to heterozygosity. Based on Weitzman or Piyasatian and Kinghorn methods, the breeds distant from others i.e. Inner Mongolia Cashmere goat, Chengdu Brown goat and Leizhou goat obtain a high ranking. Evidence from Caballero and Toro and Fabuel et al method prioritized Jining Gray goat, Liaoning Cashmere goat, and Inner Mongolia Cashmere goat, which agree with results from Kinship-based methods. Conclusion: Conservation priorities were determined according to multiple methods. Our results suggest Inner Mongolia Cashmere goat (most methods), Jining Gray goat and Liaoning Cashmere goat (high contribution to heterozygosity and total diversity) should be prioritized based on most methods. Furthermore, Daiyun goat and Shannan White goat also should be prioritized based on consideration of effective population size. However, if one breed can continually survive under changing conditions, the straightforward approach would be to increase its utilization and attraction for production via mining breed germplasm characteristics.