First-principles study of oxygen vacancy defects in orthorhombic Hf0.5_{0.5}Zr0.5_{0.5}O2_2/SiO2_2/Si gate stack

The gate defect of the ferroelectric HfO$_2$-based Si field-effect transistor (Si FeFET) plays a dominant role in its reliability issue. The first-principles calculations are an effective method for the atomic-scale understanding of gate defects. However, the first-principles study on the defects of FeFET gate stacks, i.e., metal/orthorhombic-Hf$_{0.5}$Zr$_{0.5}$O$_2$/SiO$_2$/Si structure, has not been reported so far. The key challenge is the construction of metal/orthorhombic-Hf$_{0.5}$Zr$_{0.5}$O$_2$/SiO$_2$/Si gate stack models. Here, we use the Hf$_{0.5}$Zr$_{0.5}$O$_2$(130) high-index crystal face as the orthorhombic ferroelectric layer and construct a robust atomic structure of the orthorhombic-Hf$_{0.5}$Zr$_{0.5}$O$_2$/SiO$_2$/Si gate stack without any gap states. Its high structural stability is ascribed to the insulated interface. The calculated band offsets show that this gate structure is of the type-I band alignment. Furthermore, the formation energies and charge transition levels (CTLs) of defects reveal that the oxygen vacancy defects are more favorable to form compared with other defects such as oxygen interstitial and Hf/Zr vacancy, and their CTLs are mainly localized near the Si conduction band minimum and valence band maximum, in agreement with the reported experimental results. The oxygen vacancy defects are responsible for charge trapping/de-trapping behavior in Si FeFET. This work provides an insight into gate defects and paves the way to carry out the first-principles study of ferroelectric HfO$_2$-based Si FeFET.Comment: 18 pages, 5 figure

Effect of Different Arbuscular Mycorrhizal Fungi on Growth and Physiology of Maize at Ambient and Low Temperature Regimes

The effect of four different arbuscular mycorrhizal fungi (AMF) on the growth and lipid peroxidation, soluble sugar, proline contents, and antioxidant enzymes activities of Zea mays L. was studied in pot culture subjected to two temperature regimes. Maize plants were grown in pots filled with a mixture of sandy and black soil for 5 weeks, and then half of the plants were exposed to low temperature for 1 week while the rest of the plants were grown under ambient temperature and severed as control. Different AMF resulted in different root colonization and low temperature significantly decreased AM colonization. Low temperature remarkably decreased plant height and total dry weight but increased root dry weight and root-shoot ratio. The AM plants had higher proline content compared with the non-AM plants. The maize plants inoculated with Glomus etunicatum and G. intraradices had higher malondialdehyde and soluble sugar contents under low temperature condition. The activities of catalase (CAT) and peroxidase of AM inoculated maize were higher than those of non-AM ones. Low temperature noticeably decreased the activities of CAT. The results suggest that low temperature adversely affects maize physiology and AM symbiosis can improve maize seedlings tolerance to low temperature stress

Association Between the Methylation Statuses at CpG Sites in the Promoter Region of the SLCO1B3, RNA Expression and Color Change in Blue Eggshells in Lushi Chickens

The formation mechanism underlying the blue eggshell characteristic has been discovered in birds, and SLCO1B3 is the key gene that regulates the blue eggshell color. Insertion of an endogenous retrovirus, EAV-HP, in the SLCO1B3 5′ flanking region promotes SLCO1B3 expression in the chicken shell gland, and this expression causes bile salts to enter the shell gland, where biliverdin is secreted into the eggshell, forming a blue shell. However, at different laying stages of the same group of chickens, the color of the eggshell can vary widely, and the molecular mechanism underlying the eggshell color change remains unknown. Therefore, to reveal the molecular mechanism of the blue eggshell color variations, we analyzed the change in the eggshell color during the laying period. The results indicated that the eggshell color in Lushi chickens can be divided into three stages: 20–25 weeks for dark blue, 26–45 weeks for medium blue, and 46–60 weeks for light blue. We further investigated the expression and methylation levels of the SLCO1B3 gene at eight different weeks, finding that the relative expression of SLCO1B3 was significantly higher at 25 and 30 weeks than at other laying weeks. Furthermore, the overall methylation rate of the SLCO1B3 gene in Lushi chickens increased gradually with increasing weeks of egg production, as shown by bisulfite sequencing PCR. Pearson correlation analysis showed that methylation of the promoter region of SLCO1B3 was significantly negatively correlated with both SLCO1B3 expression in the shell gland tissue and eggshell color. In addition, we predicted that CpG5 and CpG8 may be key sites for regulating SLCO1B3 gene transcription. Our findings show that as the level of methylation increases, methylation of the CpG5 and CpG8 sites hinders the binding of transcription factors to the promoter, reducing SLCO1B3 expression during the late period and resulting in a lighter eggshell color

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A System Dynamics Model to Evaluate Effects of Retailer-Led Recycling Based on Dual Chains Competition: A Case of e-Waste in China

China, as the largest electronic waste producer in the world, is facing a critical challenge to manage its negative impacts on the environment. Hence, e-waste management is crucial for sustainable Chinese economic development. In this paper, a system dynamics model is adopted to identify the effects of retailer-led recycling based on closed-loop dual chains competition. The influence of contracts made by manufacturers on different retail modes is also discussed. From the aspects of total revenue (TR), market share (MS) and market competitiveness (MC), this paper analyzes the impact of e-waste recycling coefficient (ERC) on supply chain and analyzes the equilibrium solution of total supply chain return. The research results show that the contract incentive mechanism can improve the retailer’s recycling enthusiasm, and the effect on the retail mode of executive shop is more obvious. When the ERC is adjusted to 44.3%, the TR of supply chain is optimal, and the MS and MC occupy an obvious advantage

Transcriptomic Analysis of Spleen Revealed Mechanism of Dexamethasone-Induced Immune Suppression in Chicks

Stress-induced immunosuppression is a common problem in the poultry industry, but the specific mechanism of its effect on the immune function of chicken has not been clarified. In this study, 7-day-old Gushi cocks were selected as subjects, and a stress-induced immunosuppression model was successfully established via daily injection of 2.0 mg/kg (body weight) dexamethasone. We characterized the spleen transcriptome in the control (B_S) and model (D_S) groups, and 515 significant differentially expressed genes (SDEGs) (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) > 1, adjusted p-value (padj) < 0.05 and Fold change (|FC|) ≥ 2) were identified. The cytokine-cytokine receptor interaction signaling pathway was identified as being highly activated during stress-induced immunosuppression, including the following SDEGs—CXCL13L2, CSF3R, CSF2RB, CCR9, CCR10, IL1R1, IL8L1, IL8L2, GHR, KIT, OSMR, TNFRSF13B, TNFSF13B, and TGFBR2L. At the same time, immune-related SDEGs including CCR9, CCR10, DMB1, TNFRSF13B, TNFRSF13C and TNFSF13B were significantly enriched in the intestinal immune network for the IgA production signaling pathway. The SDEG protein-protein interaction module analysis showed that CXCR5, CCR8L, CCR9, CCR10, IL8L2, IL8L1, TNFSF13B, TNFRSF13B and TNFRSF13C may play an important role in stress-induced immunosuppression. These findings provide a background for further research on stress-induced immunosuppression. Thus, we can better understand the molecular genetic mechanism of chicken stress-induced immunosuppression

MicroRNA-101-2-5p targets the ApoB gene in liver of chicken (Gallus Gallus)

Apolipoprotein B (ApoB) is a major protein component of plasma lipoproteins, which have been involved in many important biological processes such as lipid transportation, enzyme activity regulation and receptor recognition. Extensive studies have showed that the expression of the ApoB was regulated at multiple levels. However, the regulation of ApoB expression by microRNAs (miRNAs) still remains unknown. In present studies, miRNAs that interact with ApoB have been predicted in chicken. The targeted relationship between the predicated miRNAs and ApoB was verified through dual luciferase reporter assay in chicken DF1 cells, and the effect of miRNAs on ApoB expression was analyzed in chicken embryo hepatocytes stimulated by 17β-estradiol. The results showed that miR-101-2-5p was predicted to interact with ApoB. Dual luciferase reporter assay together with the miR-101-2-5p mimics study demonstrate that ApoB is the target of miR-101-2-5p that suppresses the expression of ApoB through binding with the 3’UTR of ApoB. Our experiments suggested that miR-101-2-5p might be involved in lipid metabolism through binding with the 3’UTR of ApoB gene in liver of egg-laying chickens.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens

Abstract Background Estrogen plays an essential role in female development and reproductive function. In chickens, estrogen is critical for lipid metabolism in the liver. The regulatory molecular network of estrogen in chicken liver is poorly understood. To identify estrogen-responsive genes and estrogen functional sites on a genome-wide scale, we determined expression profiles of mRNAs, lncRNAs, and miRNAs in estrogen-treated ((17β-estradiol)) and control chicken livers using RNA-Sequencing (RNA-Seq) and studied the estrogen receptor α binding sites by ChIP-Sequencing (ChIP-Seq). Results We identified a total of 990 estrogen-responsive genes, including 962 protein-coding genes, 11 miRNAs, and 17 lncRNAs. Functional enrichment analyses showed that the estrogen-responsive genes were highly enriched in lipid metabolism and biological processes. Integrated analysis of the data of RNA-Seq and ChIP-Seq, identified 191 genes directly targeted by estrogen, including 185 protein-coding genes, 4 miRNAs, and 2 lncRNAs. In vivo and in vitro experiments showed that estrogen decreased the mRNA expression of PPARGC1B, which had been reported to be linked with lipid metabolism, by directly increasing the expression of miR-144-3p. Conclusions These results increase our understanding of the functional network of estrogen in chicken liver and also reveal aspects of the molecular mechanism of estrogen-related lipid metabolism