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Decision implication is an important form of knowledge representation and acquisition in Formal Concept Analysis. Decision implication reduces the redundancy of knowledge extracted from data. However, decision implication cannot extract negative information from data, so there is information loss in decision implication. This paper introduces negative attributes to decision implication and proposes mixed decision implication, enabling decision implication to extract negative knowledge from data and to represent richer decision knowledge. This paper studies the logical systems of mixed decision implications. The semantical system of mixed decision implications is constructed to represent and deduce sound mixed decision implications and avoid contradictory mixed decision implications. In the syntactical system, Mixed Augmentation and Mixed Combination are introduced and the soundness, completeness and non-redundancy of these two inference rules are proved.

Abstract Background The transcriptional changes around zygotic genome activation (ZGA) in preimplantation embryos are critical for studying mechanisms of embryonic developmental arrest and searching for key transcription factors. However, studies on the transcription profile of porcine ZGA are limited. Results In this study, we performed RNA sequencing in porcine in vivo developed (IVV) and somatic cell nuclear transfer (SCNT) embryo at different stages and compared the transcriptional activity of porcine embryos with mouse, bovine and human embryos. The results showed that the transcriptome map of the early porcine embryos was significantly changed at the 4-cell stage, and 5821 differentially expressed genes (DEGs) in SCNT embryos failed to be reprogrammed or activated during ZGA, which mainly enrichment to metabolic pathways. c-MYC was identified as the highest expressed transcription factor during ZGA. By treating with 10,058-F4, an inhibitor of c-MYC, the cleavage rate (38.33 ± 3.4%) and blastocyst rate (23.33 ± 4.3%) of porcine embryos were significantly lower than those of the control group (50.82 ± 2.7% and 34.43 ± 1.9%). Cross-species analysis of transcriptome during ZGA showed that pigs and bovines had the highest similarity coefficient in biological processes. KEGG pathway analysis indicated that there were 10 co-shared pathways in the four species. Conclusions Our results reveal that embryos with impaired developmental competence may be arrested at an early stage of development. c-MYC helps promote ZGA and preimplantation embryonic development in pigs. Pigs and bovines have the highest coefficient of similarity in biological processes during ZGA. This study provides an important reference for further studying the reprogramming regulatory mechanism of porcine embryos during ZGA.

Resveratrol is a polyphenol with antiaging and anticancer effects. Most previous studies used a single analysis to determine the key functions of resveratrol in inhibiting cancer progression. However, most of the signal transmission pathways in biological processes are multilevel. We used bioinformatics to elucidate the mechanism of resveratrol inhibition of breast cancer development. The mRNA expression profile of GSE25412 from the National Center for Biotechnology Information (NCBI) and the microRNA (miRNA) expression profile of PubMed identifier (PMID) 26890143 were integrated. De novo motifs were used to obtain predicted transcription factor (TF) motifs for differentially expressed genes. The regulatory effect of resveratrol on key nodes in the comprehensive analysis results was verified. The TF–miRNA–mRNA interaction network based on the STITCH and miRDB databases showed that resveratrol exerted a dual inhibitory effect by activating inhibitory TFs to block the cell cycle and inhibit miRNAs from upregulating apoptosis. However, these two processes did not work completely independently. TP53 is the dominant hub gene associated with the cell cycle and apoptosis throughout the TF–miRNA network. Kaplan–Meier plotter analysis found that resveratrol‐induced expression changes in key RNAs, such as E2F2, JUN, FOS, BRCA1, CDK1, CDKN1A, TNF, and hsa‐miR‐34a‐5p, significantly improved the prognosis of breast cancer patients, which was further verified using real‐time quantitative PCR (qPCR) and western blotting. This study constructed a TF–miRNA regulatory network with TP53 and E2F as the main central genes to elucidate the molecular mechanism of resveratrol in the treatment of breast cancer.

Oocyte senescence alters the shape and function, thereby weakening the fertilization potential. Nicotinamide mononucleotide (NMN) reverses age-related dysfunctions in various organs. Studies had shown long-term administration of NMN reduced the physiological decline associated in aged mice and reversed the aging of the ovaries. However, the protective effect of NMN on aged porcine oocytes is still unclear. In this study, we investigated the effects of NMN on aging porcine oocytes and subsequent embryonic development. We established a model of senescence of porcine oocytes after ovulation by extending the culture time in vitro. NMN supplementation significantly reduced reactive oxygen species (ROS) levels in senescence oocytes and increased the mRNA levels of antioxidant genes SOD1 and Cat. The mitochondrial membrane potential of aged oocytes treated with NMN was increased compared with that of untreated oocytes. In addition, the mRNA level of apoptosis-related gene Bax was significantly decreased in senescence oocytes treated with NMN, while the mRNA level of anti-apoptosis-related gene BCL-2 was significantly increased. Furthermore, NMN supplementation enhanced the subsequent development ability of senescent oocytes during in vitro aging. Compared with untreated senescent oocytes, the blastocyst formation rate and pluripotent genes of senescent oocytes treated with NMN were significantly increased. Taken together, these results suggest that NMN is beneficial for delaying the aging process in porcine oocytes.

The study of preimplantation development is of great significance to reproductive biology and regenerative medicine. With the development of high-throughput deep sequencing technology, it has been found that lncRNAs play a very important role in the regulation of embryonic development. In this study, key lncRNAs that regulate embryonic development were screened by analyzing the expression pattern of lncRNAs in porcine in vivo fertilization (IVV) embryos. By knocking down lncRNA expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development. The results showed that the expression pattern of lncRNA was consistent with the time of gene activation. The lncRNAs were highly expressed in the 4-cell to blastocyst stage but barely expressed in the oocytes and 2-cell stage. So we speculated this part of lncRNAs may regulate gene expression. The lncRNA LOC102165808 (named lncT because the gene near this lncRNA is TFAP2C) was one of them. The knockdown (KD) of lncT inhibited embryonic development, resulting in decreased H3K4me3, H3K4me2, and H3K9me3, and increased DNA methylation. Meanwhile, RNAseq showed SIN3A was the top decreased gene in lncT-KD embryos. There was a severe blastocyst formation defect in SIN3A-KD embryos. Both lncT and SIN3A could affect NANOG and induce more cell apoptosis. In conclusion, the knockdown of lncT inhibits embryonic development by regulating H3K4me3, H3K4me2, DNA methylation, pluripotency gene, and apoptosis, and SIN3A is one of the downstream genes of lncT in regulating embryonic development.

Zygotic gene activation (ZGA) and epigenetic reprogramming are critical in early embryonic development in mammals, and transcription factors are involved in regulating these events. However, the effects of ELF4 on porcine embryonic development remain unclear. In this study, the expression of ELF4 was detected in early porcine embryos and different tissues. By knocking down ELF4, the changes of H3K9me3 modification, DNA methylation and ZGA-related genes were analyzed. Our results showed that ELF4 was expressed at all stages of early porcine embryos fertilized in vitro (IVF), with the highest expression level at the 8-cell stage. The embryonic developmental competency and blastocyst quality decreased after ELF4 knockdown (20.70% control vs. 17.49% si-scramble vs. 2.40% si-ELF4; p < 0.001). Knockdown of ELF4 induced DNA damage at the 4-cell stage. Interfering with ELF4 resulted in abnormal increases in H3K9me3 and DNA methylation levels at the 4-cell stage and inhibited the expression of genes related to ZGA. These results suggest that ELF4 affects ZGA and embryonic development competency in porcine embryos by maintaining genome integrity and regulating dynamic changes of H3K9me3 and DNA methylation, and correctly activating ZGA-related genes to promote epigenetic reprogramming. These results provide a theoretical basis for further studies on the regulatory mechanisms of ELF4 in porcine embryos.

In recent decades, the increasing incidence of depression has contributed to an increase in the use of serotonergic drugs, such as antidepressants, which predisposes humans to serotonin syndrome. Serotonin syndrome is caused by elevated serotonin levels in the central and peripheral nervous systems. It has been well documented that the development of offspring can be affected by maternal exposure to environmental challenges, such as stress, diseases, or an unhealthy diet during pregnancy. Serotonin, also called 5-hydroxytryptamine (5-HT), is widely expressed in the female reproductive system and plays an important role in the development of follicles and embryos. However, whether the suffering of the mother from serotonin syndrome before pregnancy affects fetal development is still uncertain. In the present study, to explore the effect of maternal prepregnancy 5-HT exposure on the fetus, intraperitoneal injection of 5-HT was used to change maternal prepregnancy 5-HT levels. It was found that maternal prepregnancy 5-HT exposure significantly reduced the body weight and liver weight and the levels of estrogen and progesterone in female mice. Although there was no significant difference in the cleavage rate and blastocyst rate between the 5-HT and control groups, maternal prepregnancy 5-HT exposure increased the percentage of embryo resorption, decreased placental weight, and led to placental inflammation at E13.5. Notably, 5-HT exposure caused weight loss in the offspring at 2 weeks. These results suggested that maternal prepregnancy 5-HT exposure could affect the development of the offspring, which was partly caused by reduced hormonal secretion and placental inflammation.

Abstract Background Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, animal development, metabolism, and adipogenesis. In this study, to assess the functional roles of circRNAs in adipogenesis and tissue-specific fat deposition, we comprehensively analyzed the Ribo-Zero RNA-Seq and miRNAs data during chicken intramuscular and abdominal adipogenic differentiation. Results circRNAs and miRNAs profiles during chicken adipogenic differentiation were found in adipocytes derived from various adipose tissues. It was also discovered that high levels of downregulated miRNAs potentially promote adipogenesis by activating their target genes which are associated with fatty acid metabolism and adipogenic differentiation. Through analysis of the correlation between the expression levels of circRNAs and adipogenic genes, as well as the dynamic expression patterns of circRNAs during adipogenic differentiation, several candidate circRNAs were identified. Moreover, competing endogenous RNA (ceRNAs) networks were constructed during chicken intramuscular and abdominal adipogenesis by combining miRNAs with mRNAs data. Several candidate circRNAs potentially influence adipogenesis by regulating miRNAs via PPAR and fatty acid metabolism-related pathways were identified, such as circLCLAT1, circFNDC3AL, circCLEC19A and circARMH1. Conclusion In conclusion, our findings reveal that circRNAs and the circRNA-miRNAs-mRNAs-ceRNAs network may play important roles in chicken adipocytes differentiation and tissue-specific fat deposition.

N6-methyladenosine (m6A) is one of the most abundant internal mRNA modifications, and it affects multiple biological processes related to eukaryotic mRNA. The majority of m6A sites are located in stop codons and 3′UTR regions of mRNAs. m6A regulates RNA metabolism, including alternative splicing (AS), alternative polyadenylation (APA), mRNA export, decay, stabilization, and translation. The m6A metabolic pathway is regulated by a series of m6A writers, erasers and readers. Recent studies indicate that m6A is essential for the regulation of gene expression, tumor formation, stem cell fate, gametogenesis, and animal development. In this systematic review, we summarized the recent advances in newly identified m6A effectors and the effects of m6A on RNA metabolism. Subsequently, we reviewed the functional roles of RNA m6A modification in diverse cellular bioprocesses, such as stem cell fate decisions, cell reprogramming and early embryonic development, and we discussed the potential of m6A modification to be applied to regenerative medicine, disease treatment, organ transplantation, and animal reproduction.

Intramuscular fat (IMF), which regulated by genetics, nutrition and environment is an important factor that influencing meat quality. Up to now, the epigenetic regulation mechanism underlying poultry IMF deposition remains poorly understood. Here, we focused on the DNA methylation, which usually regulate genes in transcription level. To look into the essential role of DNA methylation on the IMF deposition, chicken intramuscular preadipocytes were isolated and cultured in vitro, and a model of intramuscular adipocyte differentiation was constructed. Combined the whole genome bisulfite sequencing (WGBS) and RNA-Seq technologies, we identified several methylated genes, which mainly affecting fatty acid metabolism and muscle development. Furthermore, we reported that DNA methylation regulate intramuscular adipogenesis by regulating the genes, such as collagen, type VI, alpha 1 (COL6A1) thus affecting IMF deposition. Overexpression of COL6A1 increases the lipid droplet and inhibits cell proliferation by regulating CHAD and CAMK2 in intramuscular adipocytes, while knockdown of COL6A1 shows the opposite effect. Taken together, our results reveal that DNA methylation plays an important role in poultry IMF deposition.

Background/Aims: DNA methylation and histone modifications are essential epigenetic marks that can significantly affect the mammalian somatic cell nuclear transfer (SCNT) embryo development. However, the mechanisms by which the DNA methylation affects the epigenetic reprogramming have not been fully elucidated. Methods: In our study, we used quantitative polymerase chain reaction (qPCR), Western blotting, immunofluorescence staining (IF) and sodium bisulfite genomic sequencing to examine the effects of RG108, a DNA methyltransferase inhibitor (DNMTi), on the dynamic pattern of DNA methylation and histone modifications in porcine SCNT embryos and investigate the mechanism by which the epigenome status of donor cells’ affects SCNT embryos development and the crosstalk between epigenetic signals. Results: Our results showed that active DNA demethylation was enhanced by the significantly improving expression levels of TET1, TET2, TET3 and 5hmC, and passive DNA demethylation was promoted by the remarkably inhibitory expression levels of DNMT1, DNMT3A and 5mC in embryos constructed from the fetal fibroblasts (FFs) treated with RG108 (RG-SCNT embryos) compared to the levels in embryos from control FFs (FF-SCNT embryos). The signal intensity of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 9 acetylation (H3K9Ac) was significantly increased and the expression levels of H3K4 methyltransferases were more than 2-fold higher expression in RG-SCNT embryos. RG-SCNT embryos had significantly higher cleavage and blastocyst rates (69.3±1.4%, and 24.72±2.3%, respectively) than FF-SCNT embryos (60.1±2.4% and 18.38±1.9%, respectively). Conclusion: Dynamic changes in DNA methylation caused by RG108 result in dynamic alterations in the patterns of H3K4me3, H3K9Ac and histone H3 lysine 9 trimethylation (H3K9me3), which leads to the activation of embryonic genome and epigenetic modification enzymes associated with H3K4 methylation, and contributes to reconstructing normal epigenetic modifications and improving the developmental efficiency of porcine SCNT embryos.

Background/Aims: Aberrantly high levels of H3K4me3, caused by incomplete epigenetic reprogramming, likely cause a low efficiency of somatic cell nuclear transfer (SCNT). Smal molecule inhibitors aimed at epigenetic modification can be used to improve porcine SCNT embryo development. In this study, we examined the effects of MM-102, an H3K4 histone methyltransferase inhibitor, on porcine SCNT preimplantation embryos to investigate the mechanism by which H3K4 methylation regulated global epigenetic reprograming during SCNT. Methods: MM-102 was added to the SCNT embryos culture system and the global levels of various epigenetic modifications were measured by immunofluorescence (IF) staining and were quantified by Image J software. Relative genes expression levels were detected by quantitative real-time PCR. Results: MM-102 (75 μM) treatment reduced global H3K4, H3K9 methylation and 5mC levels especially at the zygotic gene activation (ZGA) and blastocyst stages. MM-102 treatment mainly down-regulated a series of DNA and histone methyltransferases, and up-regulated a number of hitone acetyltransferases and transcriptional activators. Furthermore, MM-102 treatment positively regulated the mRNA expression of genes related to pluripotency (OCT4, NANOG, CDX2) and apoptosis (BCL2). Conclusion: Down-regulation of H3K4me3 with MM-102 rescued aberrant gene expression patterns of a series of epigenetic chromatin modification enzymes, pluripotent and apoptotic genes at the ZGA and blastocyst stages, thereby greatly improving porcine SCNT efficiency and blastocyst quality, making them more similar to in vivo embryos (IVV).

Fuzzy decision implication is an extension of decision implication in the fuzzy setting, serving to uncover the dependencies of fuzzy attributes. This study presents the interpretation of fuzzy decision implication in the fuzzy decision context. Specially, they will show that from fuzzy decision contexts one can obtain a closed fuzzy set of fuzzy decision implications, and the semantical characteristic of the obtained fuzzy set can be interpreted by fuzzy decision context and can be represented by some operators of fuzzy decision context. Conversely, starting from a fuzzy set of fuzzy decision implications, they can form a fuzzy decision context, from which the given fuzzy set can be derived. The result actually implies that they have constructed a correspondence between closed fuzzy sets of fuzzy decision implications and fuzzy decision contexts, and thus shows the equivalence of two interpretations of fuzzy decision implications.

DNA demethylation catalysed by the ten-eleven translocation (TET) protein is an important step during extensive global epigenetic reprogramming in mammals. However, whether TET proteins play a key role in DNA demethylation during the development of bovine pre-implanted embryos is still unclear. In this study, we utilized dimethyloxallyl glycine (DMOG), a small-molecule inhibitor of the TET protein, to impede the enzymatic activity of TET and explore subsequent effects on bovine parthenogenetic embryo development. We first detected the expression of the TET family, consisting of TET1, TET2 and TET3, in bovine MII stage oocytes and found that TET3 is more highly expressed than TET1 and TET2. Treatment with 1 mM DMOG increased 5mC levels (30.4% vs 79.8% at the 8-cell stage for satellite I, 25.3% vs 40.6% at the 8-cell stage for α-satellite, 20.5% vs 73.5% at the blastocyst stage for satellite I and 16.6% vs 30.0% at the blastocyst stage for α-satellite) at every bovine parthenogenetic embryo developmental stage. At the same time, DNA methylation level of satellite DNA and pluripotency gene promoters increased significantly. Real-time PCR analysis results indicated that the transcription levels of NANOG and OCT-4 decreased in the DMOG-treated group. Furthermore, TET inhibition negatively affected blastocyst formation, resulting in a decline in the blastocyst rate (17.1 ± 1.3% vs 24.1 ± 0.6%); however, the percentage of apoptotic cells was significantly increased according to the results of a TUNEL assay. Additionally, expression levels of the apoptosis-related gene BAX were up-regulated, while the expression of BCL-2 was down-regulated. In conclusion, these results support that TET plays important roles in bovine parthenogenetic embryo development by influencing DNA methylation reprogramming, gene expression and apoptosis.

Background and objective The deletion of allele located at 3p21.3 region is found in 50%-80% of nonsmall cell lung cancer (NSCLC), suggesting that this region might harbor some tumor suppressor genes (TSGs). It is anticipated that some TSGs closely related to NSCLC carcinogenesis might be found by screening the expression of genes, located at the commonly deleted region 3p21.3, in NSCLC. Methods Semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) and related statistical analysis were applied to examine the expression status of 11 genes closely related to tumor selected from 3p21.3 by bioinformatics in 16 NSCLC biopsies. Results No expression or down-regulation of RASSF1A, GNAT1, SEMA3B, SEMA3F, Blu were observed in 43.8% (7/16), 37.5% (6/16), 62.5% (10/16), 50% (8/16), 56.3% (9/16) respectively, in NSCLC tissues (P

The paper investigated an avian influenza virus propagation model with nonlinear incidence rate and delay based on SIR epidemic model. We regard delay as bifurcating parameter to study the dynamical behaviors. At first, local asymptotical stability and existence of Hopf bifurcation are studied; Hopf bifurcation occurs when time delay passes through a sequence of critical values. An explicit algorithm for determining the direction of the Hopf bifurcations and stability of the bifurcation periodic solutions is derived by applying the normal form theory and center manifold theorem. What is more, the global existence of periodic solutions is established by using a global Hopf bifurcation result.

Owing to the high dimensionality of multilabel data, feature selection in multilabel learning will be necessary in order to reduce the redundant features and improve the performance of multilabel classification. Rough set theory, as a valid mathematical tool for data analysis, has been widely applied to feature selection (also called attribute reduction). In this study, we propose a variable precision attribute reduct for multilabel data based on rough set theory, called δ-confidence reduct, which can correctly capture the uncertainty implied among labels. Furthermore, judgement theory and discernibility matrix associated with δ-confidence reduct are also introduced, from which we can obtain the approach to knowledge reduction in multilabel decision tables.

The paper investigates the behavior of price differential equation model based on economic theory with two delays. The primary aim of this thesis is to provide a research method to explore the undeveloped areas of the price model with two delays. Firstly, we modify the traditional price model by considering demand function as a downward opening quadratic function, and supply and demand functions both depending on the price of the past and the present. Then the price model with two delays is established. Secondly, by considering the price model with one delay, we get the stable interval. Regarding another delay as a parameter, we studied the linear stability and local Hopf bifurcation. In addition, we pay attention to the direction and stability of the bifurcating periodic solutions which are derived by using the normal form theory and center manifold method. Afterwards, the study turns to simulate the results through numerical analysis, which shows that the provided method is valid.

We research the dynamics of the chemostat model with time delay. The conclusion confirms that a Hopf bifurcation occurs due to the existence of stability switches when the delay varies. By using the normal form theory and center manifold method, we derive the explicit formulas determining the stability and direction of bifurcating periodic solutions. Finally, some numerical simulations are given to illustrate the effectiveness of our results.

This paper mainly modifies and further develops the Reyleigh price model. By modifying the basic Reyleigh model, we can more accurately illustrate the economic phenomena with price varying. First, we research the dynamics of the modified Reyleigh model with time delay. By employing the normal form theory and center manifold theory, we obtain some testable results on these issues. The conclusion confirms that a Hopf bifurcation occurs due to the existence of stability switches when the delay varies. Finally, some numerical simulations are given to illustrate the effectiveness of our results.

Decision implication is a form of decision knowledge representation, which is able to avoid generating attribute implications that occur between condition attributes and between decision attributes. Compared with other forms of decision knowledge representation, decision implication has a stronger knowledge representation capability. Attribute granularization may facilitate the knowledge extraction of different attribute granularity layers and thus is of application significance. Decision implication canonical basis (DICB) is the most compact set of decision implications, which can efficiently represent all knowledge in the decision context. In order to mine all decision information on decision context under attribute granulating, this paper proposes an updated method of DICB. To this end, the paper reduces the update of DICB to the updates of decision premises after deleting an attribute and after adding granulation attributes of some attributes. Based on this, the paper analyzes the changes of decision premises, examines the properties of decision premises, designs an algorithm for incrementally generating DICB, and verifies its effectiveness through experiments. In real life, by using the updated algorithm of DICB, users may obtain all decision knowledge on decision context after attribute granularization. [ABSTRACT FROM AUTHOR]