bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes
Authors: Wang Kai , Wu Pingxian , Chen Dejuan , Zhou Jie , Yang Xidi , Shen Linyuan , Jiang Anan , Ma Jideng , Tang Qianzi , Xiao Weihang , Jiang Yanzhi , Zhu Li , Li Xuewei , Tang Guoqing 
Published: May 2020

Abstract
Background: DNA methylation is a key epigenetic mechanism. Most of epigenetic studies of pigs to date have focused on differential methylation analysis. However, few studies have conducted association study between DNA methylation and phenotypic traits. Thus, it is critical to link DNA methylation and phenotypic traits in order to understand the molecular mechanism on epigenomes. In this study, we aimed to identified CpG sites at which DNA methylation levels are associated with meat quality traits in 140 Yorkshire pigs, including pH at 45min (pH45min), pH at 24h (pH24h), drip loss (DL), meat redness value (a*), yellowness (b*) and lightness (L*).Results: Genome-wide methylation levels were measured in muscular tissue using reduced representation bisulfite sequencing (RRBS). Associations between DNA methylation levels and meat quality traits were examined using linear mixed-effect models that were adjusted for gender, year, month and body weight. A Bonferroni-corrected P value lower than was considered statistically significant threshold. Eight CpG sites were associated with DL, including CpG sites annotated to RBM14 gene (cpg301054, cpg301055, cpg301058, cpg301059, cpg301066, cpg301072 and cpg301073) and NCAM1 gene (cpg1802985). Two CpG sites were associated with b*, including RNFT1 and MED13 (cpg2272837) and TRIM37 gene (cpg2270611). Five CpG sites were associated with L*, including GSDMA and LRRC3C gene (cpg2252750) and ENSSSCG00000043539 and IRX1 gene (cpg2820178, cpg2820179, cpg2820181 and cpg2820182). No significant associations were observed with pH45min, pH24h or a*.Conclusion: We reported associations of meat quality traits with DNA methylation and identified some candidate genes associated with these traits, such as NCAM1, MED13 and TRIM37 gene. These results provide new insight into the epigenetic molecular mechanisms of meat quality traits in pigs.
The role of cyadox and recombinant growth hormone (rGH) on the promotion of growth through epigenetics
Authors: Liu Aimei , Zhu Feng , Zhu Xiaohui , Wang Yulian , Ihsan Awais , Liu Zhenli , Dai Menghong , Wang Xu 
Published: May 2020

Abstract
Background: Cyadox is an effective growth-promoting antibiotic, which is similar to the role of recombinant growth hormone (rGH). Current studies have shown that cyadox can promote animal growth through altering intestinal microflora, improving protein utilization and increasing protein synthesis. Increasing evidence suggests that epigenetics are also closely related to growth. However, the potential role of epigenetics in the cyadox for growth has not been explored. Results: Here, we used recombinant growth hormone (rGH) and cyadox to study the relationship between growth and changes in epigenetics including DNA methylation, histone modification and chromatin structure. Bisulfite DNA sequencing (BSP) assay suggested that cyadox and rGH treatments increased IGF-1 expression partially by hypomethylation at CpG sites within the promoter region of IGF-1, which was regulated by DNA methyltransferases (DNMTs). We also observed an enrichment of H3K4me3 and H3K27ac at the promoter regions of IGF-1 by ChIP-qPCR assay, which contributed to an increase in IGF-1 transcription. In addition, immunofluorometric assay displayed cellular accessible chromatin structure following the treatment of cyadox and rGH, facilitating the combination of transcription factors and DNA and thus enhancing gene transcription. Conclusions: Taken together, our findings indicated that cyadox and rGH promote cell growth partially through epigenetic changes, providing a prospect for the development of animal growth-promoting drugs in the future.
Dynamic alterations in rumen bacterial community and metabolome characteristics in response to feed nutrient levels of cashmere goats
Authors: Wang Yaoyue , Tang Peng , Xiao Yafei , Liu Jianming , Chen Yulin , Yang Yuxin 
Published: May 2020

Abstract
Background: Dietary energy and protein play important roles in rumen fermentation. However, the comprehensive impacts of dietary energy and protein on rumen bacterial composition and ruminal metabolites were largely unknown. Therefore, the objective of the current study was to investigate the changes in rumen bacterial community and metabolites in response to the diets with simultaneous changes of dietary energy and protein levels in Shaanbei white cashmere goats (SWCG). Methods: A total of 12 ruminal samples were collected from SWCG, which were divided into two groups, including high-energy and high-protein (Group H; crude protein, CP: 9.37% in dry matter; metabolic energy, ME: 9.24 MJ/kg) or control (Group C; CP: 8.73%; ME:8.60 MJ/kg) groups. The experiment lasted for 65 days, including 10 days for adaptation. 16S rRNA gene sequencing and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to identify the rumen bacterial community. Metabolomics analysis was done to investigate the rumen metabolites and the related metabolic pathways in Groups C and H. Results: The study observed 539 genera belonging to 30 phyla, which were distributed throughout the rumen samples. The high-energy and high-protein diets increased the relative abundance of phylum Bacteroidetes and genera Prevotella_1 and Succiniclasticum, while decreased the number of phylum Proteobacteria (p<0.05). Among the 24 differential metabolites (VIP>1.0, p<0.05) detected in this study, the dominant differential metabolites were amino acids, peptides and analogs. Tyrosine metabolism played an important role among the 9 main metabolic pathways. Correlation analysis revealed that Prevotella_1 showed strong positive correlation with 5-methoxyindole-3-acetic acid (r=0.601, p<0.05) and catechol (r=0.608, p<0.05). Succiniclasticum was positively correlated with 2-ketoadipate (r=0.741, p<0.01). Conclusions: Our findings revealed that the diets with high energy and protein in Group H significantly altered the composition of ruminal bacteria and metabolites, which could help to improve the dietary energy and protein use efficiency in goats.
Association of MTHFR C677T polymorphism with severity and localization of chronic atrophic gastritis: a case control study
Authors: Kong Siya , Ye Feng , Dang Yini , Hua Yifei , Zhang Guoxin 
Published: May 2020

Abstract
Background
Previous reports indicate that the methylenetetrahydrofolate reductase (MTHFR) 677C > T polymorphism plays a role in gastric cancer. However, whether it influences the development and progression of atrophic gastritis remains unclear. We aim to determine the possible association between the MTHFR 677C > T polymorphism and the severity of atrophic gastritis.
Methods
A total 128 patients with atrophic gastritis were included in the study. The presence and severity of gastric atrophy was assessed by histology using OLGA and OLGIM Gastritis Staging System. MTHFR 677C > T genotyping was performed by digital fluorescence molecular hybridization. Categorical variables were analyzed by percentages using the χ2 test.
Results
In this study, the TT genotype was significantly more frequent among patients aged ≤ 44 years (age ≤ 44 years vs. >44 years, P = 0.039). Patients with the TT genotype showed a higher ratio of incisura with atrophy or intestinal metaplasia (TT vs. CC + CT, P = 0.02). Furthermore, the TT genotype was associated with more severe lesions compared with the CC + CT genotypes (TT vs. CC + CT for atrophy: odds ratio [OR] = 2.18, P = 0.07; for intestinal metaplasia: OR = 3.39, P = 0.02; for moderate-to-severe lesions: OR = 3.84, P = 0.02). OLGA and OLGIM stages III-IV were observed more frequently in patients with the TT genotype compared with the CC + CT genotypes (for OLGA: OR = 3.98, P = 0.004; for OLGIM: OR = 2.45, P = 0.04).
Conclusions
The MTHFR 677C > T TT genotype showed an increased risk of moderate-to-severe lesions by OLGA and OLGIM stages, and these results suggest that the MTHFR C677T polymorphism may serve as a predictive marker for precancerous gastric lesions, especially in patients aged ≤ 44 years.
Signals of adverse drug reactions communicated by pharmacovigilance stakeholders: protocol for a scoping review of the global literature
Authors: Sartori Daniele , Aronson Jeffrey , Onakpoya Igho 
Published: May 2020

Abstract
Background: Signals of adverse drug reactions are the basis of some regulatory risk-minimization actions in pharmacovigilance, such as changes to the section of undesirable effects in Summaries of Products Characteristics (SmPCs). Reviews of the evidence of signals have highlighted that these are mostly supported by reports of adverse drug reactions or multiple types of evidence, but have so far been limited to specific medicinal products, time intervals, groups of adverse drug reactions and specific countries. The time that elapses between a report of a suspected adverse drug reaction and the communication of a signal has not been systematically investigated. Furthermore, difficulties in causally linking medicinal products to adverse events have been highlighted, but the elements of reports of suspected ADRs that authors used to support putative causal relationships have been rarely characterized.Methods: We plan a scoping review to chart the evidence underpinning signals in pharmacovigilance and the time that it takes to communicate a signal. We shall retrieve records from electronic databases, without language or publication restrictions; we shall apply backward and forward citation to adjust for variations in database indexing. We shall also hand-search the websites of 35 regulatory agencies/authorities, restricted publications from Uppsala Monitoring Centre, and drug bulletins in the list of International Society of Drug Bulletins. If websites do not report signals, signals will be requested from the competent stakeholder. We shall use the Oxford Centre for Evidence-Based Medicine Levels of Evidence to chart and summarize evidence. We shall use VigiBase, the World Health Organization’s Global Individual Case Safety Report database, to determine the date of reporting for reports of adverse drug reactions. Plots, or pictograms (if appropriate), will be used to represent the time from the first report of a suspected adverse drug reaction to a signal.Discussion: We expect that the findings from this exploratory investigation will be useful in better understanding global patterns of similarities or differences in regulatory decision-making in terms of evidence and timing of communications, and in identifying relevant research questions for future systematic reviews.Scoping review registration: osf.io/jtv38
The effectiveness of supplemental oxygen during exercise training in patients with chronic obstructive pulmonary disease who show sever exercise-induced desaturation: a protocol for a meta-regression analysis and systematic review
Authors: Kawachi Shohei , Yamamoto Shuhei , Nishie Kenichi , Yamaga Takayoshi , Shibuya Manaka , Sakai Yasunari , Fujimoto Keisaku 
Published: May 2020

Abstract
Background: Supplemental oxygen during exercise training has been used to prevent hypoxemia or allow toleration of higher intensity training in patients with chronic obstructive pulmonary disease (COPD) who show exercise-induced desaturation. Although some meta-analyses examined the efficacy of supplemental oxygen during exercise training, these studies concluded that it does not further improve exercise tolerance compared to exercise training alone. However, supplemental oxygen during exercise training may be effective to improve exercise tolerance in COPD patients with severe desaturation during exercise under breathing room air or compressed air. Therefore, this study will be performed to elucidate the efficacy of supplemental oxygen during exercise training and the relationship between its efficacy and severity of desaturation during exercise at baseline.Methods: We will first assess the effectiveness of supplemental oxygen during exercise training in COPD. The main outcome is the change in exercise tolerance before and after the intervention, indicated by 6-minute walking distance or shuttle walking distance, and analyzed as the standardized mean difference (SMD). The quality and risk of bias in individual studies will be assessed using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system and risk-of-bias tool (RoB ver.2). If statistical heterogeneity in effectiveness of exercise tolerance is shown, we will conduct meta-regression analyses to examine the association between efficacy of exercise training with supplemental oxygen and severity of desaturation at baseline.Discussion: One strength of this study is that it is a systematic review with meta-regression analysis to elucidate the effectiveness of supplemental oxygen during exercise training in patients with COPD who show sever exercise-induced desaturation. However, the quality and number of studies included meta-analysis may be low.Systematic review registration: Registration number, UMIN000039960.
Adipose-derived stem cells regulate fibrosis by altering CD4+ T-cell immune responses in fat grafting in a mouse model
Authors: Chen Xinyao , Chen Yunzi , Wang Zijue , Dong Ziqing , Yao Yao , Li Ye , Xia Jing , Guan Jingyan , Wang Xinhui , Sun Rongcun , Lu Feng , Hao Lijun , Luo Sai 
Published: May 2020

Abstract
Background

Autologous fat grafting is becoming increasingly common worldly. However, the long-term retention of fat grafting is still unpredictable due to the inevitable fibrosis that arises during tissue repair. Fibrosis may be regulated by T-cell immune responses that are influenced by adipose-derived stem cells (ASCs). Accordingly, we hypothesized that overly abundant ASCs might promote fibrosis by promoting T-cell immune responses to adipose tissue.
Methods

We performed 0.3 ml fat grafts with 104/ml, 106/ml and 108/ml ASCs and control group in C57 BL/6 mice in vivo. We observed retention, fibrosis, T-cell immunity, and macrophage infiltration over 12 weeks. In addition, CD4 + T-helper 1 (Th1) cells and T-helper 2 (Th2) cells were co-cultured with ASCs or ASCs conditioned media (CM) in vitro. We detected the ratio of Th2%/Th1% after 24 and 48 hours.
Results

In vivo, the retention rate was higher in the 104 group, while even lower in the 108 group with significantly increased inflammation and fibrosis than the control group at week 12. There was no significance between control group and the 106 group. Also, the 108 group increased infiltration of M2 macrophages, CD4 + T-cells and Th2/Th1 ratio. In vitro, the ratio of Th2%/Th1% induced by the ASCs-transwell group was higher than the ASCs-CM group and showed concentration-dependent.
Conclusions

High concentrations of ASCs in adipose tissue can promote Th1–Th2 shifting, and the excess of Th2 cells might promote the persistence of M2 macrophages and increase the level of fibrosis which lead to a decrease in the long-term retention of fat grafts. In addition, we found that ASCs promoted Th1–Th2 shifting in vitro.
Accelerated skeletal maturation is associated with overweight and obesity as early as preschool age: a cross-sectional study
Authors: Ke DanDan , Lu Dajiang , Cai Guang , Zhang Jing , Wang Xiaofei , Suzuki Koya 
Published: May 2020

Abstract
Background: Body mass index and skeletal age are important indicators of individual growth and maturation. The recognition of their association could contribute to the prevention of childhood obesity and accelerated skeletal maturation. This study aimed to examine the effects of overweight and obesity on accelerated skeletal maturation in preschool children. Methods: Participants included 1330 children aged 3.1-6.6 years. The main outcomes were skeletal age assessed by left hand-wrist radiograph, and body mass index classified as thinness, normal weight, overweight and obesity. Results: The percentage of accelerated skeletal maturation increased with body mass index ( x 2 = 89.442, df = 3, P <0.01) and age group ( x 2 = 43.417, df = 5, P <0.01). Logistic regression analysis showed a higher risk of accelerated skeletal maturation in children with overweight and obesity than children with normal weight after adjusting for gender and age (Overweight, OR = 3.27, 95% CI : 2.20-4.87; Obese, OR = 4.73, 95% CI : 2.99-7.48). Conclusions: Accelerated skeletal maturation was associated with overweight and obesity in preschool children, and its prevalence increased with age. These findings suggest that parents and child-health managers should be aware of an existing risk of accelerated skeletal maturation in preschool children with overweight and obesity.
P2X7R promotes angiogenesis and tumor-associated macrophage recruitment by regulating the NF-κB signaling pathway in colorectal cancer cells
Authors: Yang Chunhui , shi shuang , Su Ying , tong jingshan , Li Liangjun 
Published: May 2020

Abstract
Background

Overexpression of P2 × 7R has been observed in several tumors and is related to cancer advancement and metastasis. However, the role of P2 × 7R in colorectal cancer (CRC) patients is not well understood.
Methods

In the current study, overexpression of P2 × 7R and the effects at the molecular and functional levels in CRC were assessed in a mouse orthotopic model. Functional assays, such as the CCK-8 assay, wound healing and transwell assay, were used to determine the biological role of P2 × 7R in CRC cells. CSC-related genes and properties were detected via sphere formation and real-time PCR assays. The underlying mechanisms were explored by Western blotting, real-time PCR and Flow cytometry.
Results

In this study, we found that overexpression of P2 × 7R increase in the in vivo growth of tumors. P2 × 7R overexpression also increased CD31, VEGF and concurrent angiogenesis. P2 × 7R upregulates aldehyde dehydrogenase-1 (ALDH1) and CSC characteristics. Transplanted tumor cells with P2 × 7R overexpression stimulated cytokines to recruit TAMs to increase the growth of tumors. We also found that the NF-κB signaling pathway is involved in P2 × 7R-induced cytokine upregulation.
Conclusion

P2 × 7R promotes NF-κB-dependent cytokine induction, which leads to tumor-associated macrophage (TAM) recruitment to control tumor growth and advancement and remodeling of the stroma. Our findings demonstrate that P2 × 7R plays a key role in TAM recruitment, which may be a therapeutic target for CRC patients.
Impact Of Teacher-Student Writing Conferences On Frequency And Accuracy Of Using Cohesive Devices In Efl Students’ Writing
Authors: Alfalagg Abdullah Rajab 
Published: May 2020

Abstract
While the bulk of feedback studies have focused on written corrective feedback, oral feedback in teacher-student writing conferences in EFL context has been underexplored. This article investigated teacher oral feedback based on the tenets of sociocultural theory. It examined the impact of teacher-student writing conferences on students’ accuracy and frequency of cohesive devices employment. The study followed a quasi-experimental design with a pre-test, intervention and post-test. Data were collected from an intensive writing course for intermediate students at the college level. Based on guided-free writing prompts, the students had to write argumentative paragraphs of about 150-180 words followed by individual conference sessions to offer them oral feedback. The findings showed that oral feedback in writing conferences statistically impacted the students’ writing performance with huge effect size (Cohen’s d = 2.19). Moreover, the result demonstrated empirical evidence that writing conferences positively impacted the students’ frequency of employing referential markers (t value = -3.011; p= .006 < 0.05) and conjunctions (t value=-2.200; p= .039 < 0.05). Further, oral feedback statistically impacted the students’ accuracy of utilizing referential markers (t value= -6.874; p= .000. < 0.05) and conjunctions (t value= -7.253; p= .000 < 0.05). The oral feedback assisted the students to decrease the overuse of the first, second person pronouns and the definite article ‘the’ with generic meaning in their writing. Instead, they depended on noun phrases and the third person pronouns which contributed to the text overall cohesion by creating explicit chains of references to the antecedents within the textual environment. Also, oral feedback helped the students to use conjunctions appropriately and accurately, so their texts were written densely cohesive. Pedagogical implications were discussed at the end of the article.
Different hypothermic and cerebral perfusion strategies in extended arch replacement for acute type A aortic dissection: a retrospective comparative study
Authors: Dong Song-Bo , Xiong Jian-Xian , Zhang Kai , Zheng Jun , Xu Shang-Dong , Liu Yong-Min , Sun Li-Zhong , Pan Xu-Dong 
Published: May 2020

Abstract
Background: The optimal hypothermic level in total arch replacement with stented elephant trunk implantation for acute type A aortic dissection (aTAAD) was uncertain, and the superiority of unilateral or bilateral cerebral perfusion remained a controversial topic. We evaluated the application of moderate hypothermic circulatory arrest (MHCA) with a core temperature of 29℃ and bilateral selective antegrade cerebral perfusion in aTAAD treated by total arch replacement with stented elephant trunk implantation. Methods: From July 2019 to January 2020, 25 aTAAD patients underwent total arch replacement with stented elephant trunk implantation via MHCA (29℃) and bilateral selective antegrade cerebral perfusion (modified group). Thirty-six patients treated by the same procedure with MHCA (25℃) and unilateral selective antegrade cerebral perfusion during this period were selected as controls. Results: No difference existed among patients in both groups in terms of age, gender, incidence of hypertension, malperfusion, and pericardial effusion, except a higher incidence of cardiac tamponade in modified group (control 2.8%, modified 20%; P = 0.038). Lowest mean circulatory arrest temperature was 24.6±0.9℃ in control group, and 29±0.8℃ in modified group (p < 0.001). In-hospital mortality was 4.9% (3/61) for the entire cohort (control 8.3%, modified 0; P = 0.262). The incidence of permanent neurologic deficit was 4.9% (control 8.3%, modified 0; P = 0.262). There were no significant differences in the occurrence of temporary neurological deficit, renal failure, and paraplegia between groups. The rate of major adverse events in the modified group was lower (30.6% vs. 4%, P = 0.019). A shorter duration of ventilation and ICU stay was identified in the modified group, as well as a reduced volume of drainage within the first 48 h and red blood cell transfusion.Conclusions: The early results of MHCA (29℃) and bilateral selective antegrade cerebral perfusion applied in total arch replacement with stented elephant trunk implantation for aTAAD were acceptable, providing similar inferior cerebral and visceral protection compared with that of the conventional strategy. A higher core temperature may account for the shorter duration of ventilation and ICU stay, as well as a reduced volume of drainage and red blood cell transfusion.