bluuebunny/crossref_metadata_2025_split huggingface dataset:
The underlying mechanism of partial anterior cruciate ligament injuries to the meniscus degeneration of knee joint in rabbit models
Authors: Wang Dalin , Wang Zhe , Li Mingcheng , Xu Songbao 
Published: September 2020

Abstract
Background: The diagnosis, treatment and efficacy evaluation of anterior cruciate ligament (ACL) partial rupture remains controversial. This research aims to investigate the underlying mechanism of partial ACL injuries to the meniscus degeneration in the rabbit knee.Methods: Sixty New Zealand, white rabbits were randomly divided into three groups including an experimental group, a sham group (n=6) and and a blank control group (n=6). The experimental group is composed of an anteromedial bundle (AMB) rupture group (n=24), a posterolateral bundle (PLB) rupture group (n=24). Rabbits in the experimental group were subjected to right hind limbs knee surgery to induce ACL part injury under the arthroscopy. Finally, eight rabbits including 6 in the model group and 2 in the control group were sampled randomly on the second, fourth and eighth weeks respectively. We observed the typical form of the meniscus through HE staining. Expressions of inflammatory factors including interleukin-1β (IL-1β) and IL-17 in the knee joint fluid were determined by means of an ELISA. Analysis of the mRNA expressions of matrix metalloproteinases-13(MMP-13) was performed to evaluate the inflammatory mediators in the pathogenesis of the meniscus.Results: HE staining results showed that the surface was rough and the tissues were loose displaying collagen fibers of varying thickness. Both IL-1β and IL-17 in the synovial fluid, and the positive rate of MMP-13 in addition to MMP-13 mRNA showed a demonstrable increase treads from the 2nd to the 8th week. The significant difference was found (P<0.05) compared to the control group.Conclusion: We conclude that the elevated levels of IL-1β and IL-17, along with increased MMP13 expression, resulted in meniscus degradation in the rabbit knee joint model with partial ACL injury.
Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep
Authors: Han Fuhui , Li Jing , Liu Nan , Zhao Ranran , Liu Lirong , Li Lanlan , Li Qian , He Jianning 
Published: September 2020

Abstract
Background: Intramuscular fat (IMF) content has become one of the most important indicators for measuring meat quality, and levels of IMF are affected by various genes. Long non-coding RNAs (lncRNAs) are widely expressed non-coding RNAs that play an important regulatory role in a variety of biological processes; however, research on the lncRNAs involved in sheep IMF deposition is still in its infancy. Aohan fine-wool sheep (AFWS), one of China's most important meat-hair, dual-purpose sheep breed, provides a great model for studying the role of lncRNAs in the regulation of IMF deposition. We identified lncRNAs by RNA sequencing in Longissimus thoracis et lumborum (LTL) samples of sheep at two ages: 2 months (Mth-2) and 12 months (Mth-12). Results: We identified a total of 26,247 genes and 6,935 novel lncRNAs in LTL samples of sheep. Among these, 199 mRNAs and 61 lncRNAs were differentially expressed. We then compared the structural characteristics of lncRNAs and mRNAs. We obtained target genes of differentially expressed lncRNAs (DELs) and performed enrichment analyses using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). We found that target mRNAs were enriched in metabolic processes and developmental pathways. Three pathways were significantly enriched, namely tight junction, glycosaminoglycan biosynthesis-heparan sulfate/heparin and lysosome. Based on the analysis of critical target genes, we obtained seven candidate lncRNAs that potentially regulated lipid deposition and constructed an lncRNA-mRNA co-expression network that included MSTRG.4051.3-FZD4,MSTRG.16157.3-ULK1, MSTRG.21053.3-PAQR3, MSTRG.19941.2-TPI1, MSTRG.12864.1-FHL1,MSTRG.2469.2-EXOC6 and MSTRG.21381.1-NCOA1. We speculated that these candidate lncRNAs might play a role by regulating the expression of target genes. We randomly selected five mRNAs and five lncRNAs to verify the accuracy of the sequencing data by qRT-PCR. Conclusions: Our study provided a list of the lncRNAs and mRNAs related to intramuscular lipid deposition in sheep and laid a foundation for future research on regulatory mechanisms.
Deep Factor Analysis for Weather Varied Sense-through-foliage Target Detection
Authors: Xue Wenling , Jiang Ting , Sun Xuebin , Zheng Xiaokun , Ding Xue 
Published: September 2020

Abstract
In this paper, the influence of seasonal variation on target detection accuracy and the effectiveness of deep factor analysis(DFA) in signal denoising are studied. To extensively verify the universality of the proposed DFA approach, a variety of target objects, including no target, human, wood board and iron cabinet targets, are measured in foliage environment under four different weather conditions. Then, after removing background noise from the collected data, deep factor analysis is carried out to further reduce the impact of noise. The experimental results show that the influence of weather variation on target detection can be effectively eliminated by the presented DFA, which can improve the average classification accuracy in all seasons. At the end of the paper, it is verified by cross validation that the DFA method can be stabilized at around 93% even in hazy day and snowy day which has stability and universality in any weather conditions, even in snowy and haze days.
Diet-induced Changes in Bacterial Communities in the Jejunum and Their Associations with Bile Acids in Angus Beef Cattle
Authors: Liu Jianan , Liu Fang , Cai Wentao , Jia Cunling , Bai Ying , He Yanghua , Zhu Weiyun , Li Robert W. , Song Jiuzhou 
Published: September 2020

Abstract
Background: The small intestine, while serving as the main absorption organ, also possesses a unique bacterial environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able to regulate bacterial composition and promote the growth of bacteria that convert primary bile acids to secondary bile acids. However, in beef cattle, few studies have explored the influence of diets on jejunal bacterial communities and examined its relationships with bile acids. Here, we examined the impact of grain- and grass-based diets on jejunal and fecal bacterial communities’ composition and investigated possible association of bacterial features with bile acids.Results: We demonstrated that the influences of diets on intestinal bacteria can be observed in young beef cattle after weaning. A significantly higher level of microbial diversity was documented in feces of grass-fed cattle comparing to grain-fed cattle. Top 20 important genera identified with random forest analysis on fecal bacterial community can be good candidates for microbial biomarkers. Moreover, the jejunal bacteria of adult Angus beef cattle exhibited significant differences in microbial composition and metabolic potential under different diets. Global balances and bacteria signatures predictive of bile acids were identified, indicative of the potential association of bacterial features with bile acids.Conclusions: The findings from this study provided novel insights into the relationships between jejunal bacteria and bile acids under different diets in Angus beef cattle. Our results should help us gain a better understanding of potential health benefits of grass-fed beef.
Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence
Authors: Zhu Chen , Xiaoyu Lu , Junlan Gao , Yun Xuan , Ren Jie 
Published: September 2020

Abstract
Background: To fully elucidate the roles and mechanisms of plant hormones in leaf senescence, we adopted an integrated analysis of both non-senescing and senescing leaves from red maple with transcriptome and metabolome data. Results: Transcription and metabolite profiles were generated through a combination of deep sequencing, third-generation sequencing data analysis, and ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS), respectively. We investigated the accumulation of compounds and the expression of biosynthesis and signaling genes for eight hormones. The results revealed that ethylene and abscisic acid concentrations increased during the leaf senescence process, while the contents of cytokinin, auxin, jasmonic acid, and salicylic acid continued to decrease. Correlation tests between the hormone content and transcriptional changes were analyzed, and in six pathways, genes closely linked with leaf senescence were identified. Conclusions: These results will enrich our understanding of the mechanisms of plant hormones that regulate leaf senescence in red maple, while establishing a foundation for the genetic modification of Acer in the future.
Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa Oblata
Authors: Yang Yunyao , He Ruiqing , Zheng Jian , Hu Zenghui , Wu Jing , Leng Pingsheng 
Published: September 2020

Abstract
Background: Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata.Results: In this study, a total of 10,988 SSRs were obtained from 9,864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3,611). A set of 2,042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. 234 alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait.Conclusion: The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of ﬂoral traits for lilac.
Estimation of the Reproduction Number of Influenza A(H1N1)pdm2009 in South Korea Using Heterogeneous Models
Authors: Lee Yunjeong , Lee Dong Han , Kwon Hee-Dae , Kim Changsoo , Lee Jeehyun 
Published: September 2020

Abstract
Background: The reproduction number is one of the most crucial parameters in determining disease dynamics, providing a summary measure of the transmission potential. However, estimating this value is particularly challenging owing to the characteristics of epidemic data, including non-reproducibility and incompleteness.Methods: In this study, we propose mathematical models with different population structures; each of these models can produce data on the number of cases of the influenza A(H1N1)pdm09 epidemic in South Korea. These structured models incorporating the heterogeneity of age and region are used to estimate the reproduction numbers at various terminal times. Subsequently, the age- and region-specific reproduction numbers are also computed to analyze the differences illustrated in the incidence data.Results: The basic SIR fails to provide a reasonable estimation of the reproduction numbers. The estimated values demonstrate a large variation and remains outside of the feasible range for the influenza, regardless of the time period for data. Real-time estimation using age- and region-structured models demonstrated that the effective reproduction number rose sharply during mid-October when the ㅜumber of patients increased dramatically. The reproduction number fell below unity at the end of October and stayed lower than unity indicating that the epidemic starts decreasing, which is consistent with the incidence data.Conclusions: Numerical results reveal that the introduction of heterogeneity into the population to represent the general characteristics of dynamics is essential for the robust estimation of parameters. Keywords: Influenza; Reproduction number; Antiviral agents
Long non-coding RNA MIR4300HG polymorphisms are associated with postoperative nausea and vomiting: a genome-wide association study
Authors: Sugino Shigekazu , Konno Daisuke , Kawai Yosuke , Nagasaki Masao , Endo Yasuhiro , Hayase Tomo , Yamazaki-Higuchi Misako , Kumeta Yukihiro , Tachibana Shunsuke , Saito Katsuhiko , Suzuki Jun , Kido Kanta , Kurosawa Nahoko , Namiki Akiyoshi , Yamauchi Masanori 
Published: September 2020

Abstract
Background: Genetic factors such as single nucleotide polymorphisms (SNPs) play a key role in the development of postoperative nausea and vomiting (PONV). However, previous findings are not widely applicable to different populations because of population-specific genetic variation. We developed a Japanese-specific DNA microarray for high-throughput genotyping. The aim of the current study was to identify SNPs associated with PONV on a genome-wide scale using this microarray in a sample of Japanese surgical patients.

Methods: Associations between 659,636 SNPs and the incidence of PONV 24 h after surgery in a limited sample of 24 female patients were assessed using the microarray. After imputation of genotypes at 24,330,529 SNPs, 78 SNPs were found to be associated with the incidence of PONV. We chose 4 of the 78 SNPs to focus on by in silico functional annotation. Finally, we genotyped these 4 candidate SNPs in 255 patients using real-time PCR to verify association with the incidence of PONV.

Results: The T > C variant of rs11232965 in the long non-coding RNA MIR4300HG was significantly associated with reduced incidence of PONV among genotypes and between alleles (p = 0.01 and 0.007).

Conclusions: We identified a novel SNP (rs11232965) in the long non-coding RNA MIR4300HG that is associated with PONV. The rs11232965-SNP variant (T > C) is protective against the incidence of PONV.

Trial registration: This study was registered at the UMIN Clinical Trials Registry (Identifier: UMIN000022903, date of registration: June 27th, 2016, retrospectively registered, https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000026392).
Acute hospital staff’s attitudes towards dementia and perceived dementia knowledge: a cross-sectional survey in Ireland
Authors: Keogh Brian , To Wing Ting , Daly Louise , Hynes Geralyn , Kennelly Siobhan , Lawlor Brian , Timmons Suzanne , O’Reilly Susan , Bracken-Scally Mairead , Ciblis Aurelia , Cole Natalie , Drury Amanda , Pittalis Chiara , Kennelly Brendan , McCarron Mary , Brady Anne-Marie 
Published: September 2020

Abstract
Background: Little is known about staff’s attitudes in Irish acute hospital settings towards people living with dementia and their perceived dementia knowledge. The aim of this study was to understand the general level of dementia knowledge and attitudes towards dementia in different types of hospital staff, as well as to explore the potential influence of previous dementia training and experience (having a family member with dementia) and the potential moderating effects of personal characteristics. This data was required to plan and deliver general and targeted educational interventions to raise awareness of dementia throughout the acute services. Methods: A cross-sectional survey was carried out among a diverse range of hospital staff (n = 1795) in three urban acute general hospitals in Ireland, including doctors, nurses, healthcare attendants, allied professionals, and general support staff. Participants’ perceived dementia knowledge and attitudes were assessed as well as their previous dementia training and experience. To measure participant’s attitude towards dementia, the validated Approaches to Dementia Questionnaire (ADQ) was used. Results: Hospital staff demonstrated positive attitudes towards people living with dementia, and believed they had a fair to moderate understanding of dementia. Both ‘having previous dementia training’ and ‘having a relative living with dementia’ predicted attitude towards dementia and perceived dementia knowledge. Interestingly, certain personal staff characteristics did impact dementia training in predicting attitude towards dementia and perceived dementia knowledge. Conclusion: This study provides a baseline of data regarding the attitudes towards dementia and perceived dementia knowledge for hospital staff in Irish acute hospitals. The results can inform educational initiatives that target different hospital staff, in order to increase awareness and knowledge to improve quality of dementia care in Irish hospitals.
CXCL1 contributes to IL-6 expression in osteoarthritis and rheumatoid arthritis synovial fibroblasts by CXCR2, c-Raf, MAPK and AP-1 pathway
Authors: Hou Sheng-Mou , Chen PoChun , Lin Chieh-Mo , Fang Mei-Ling , Chi Miao-Ching , Liu Ju-Fang 
Published: September 2020

Abstract
Background: Osteoarthritis (OA) and rheumatoid arthritis (RA) are common joint disorders that are considered to be different diseases due to their unique molecular mechanisms and pathogenesis. Chemokines and their corresponding receptors have been well-characterized in RA progression, but less so in OA pathogenesis. Methods: The human primary synovial fibroblasts (SFs) were obtained from human OA and RA tissue samples. The Western blot and qPCR were performed to analyze expression levels of CXCL1, as well as CXCL-promoted IL-6 expression in both OASFs and RASFs. The signal cascades that mediate the CXCL1-promoted IL-6 expression were identified by using chemical inhibitors, siRNAs and shRNAs. Results: Here, we found that both diseases feature elevated levels of CXCL1 and interleukin (IL)-6, an important proinflammatory cytokine that participates in OA and RA pathogenesis. In OASFs and RASFs, CXCL1 promoted IL-6 expression in a dose- and time-dependent manner. In OASFs and RASFs overexpressing CXCL1 or transduced with shRNA plasmid, IL-6 expression was markedly upregulated. CXCR2, c-Raf and MAPKs was found to regulate CXCL1-induced IL-6 expression in OASFs and RASFs. Finally, CXCL1 triggered the transcriptional activities of c-Jun (which regulates the expression of proinflammatory proteins) in OASFs and RASFs. Conclusions: Our present work suggests that the CXCL1/CXCR2 axis helps to orchestrate inflammatory responses in OA and RA SFs.
Evaluation of right ventricle pulmonary artery coupling on right ventricular function in post operative Tetralogy of Fallot patients underwent for pulmonary valve replacement
Authors: Bhushan Sandeep , Xin Huang , Yuan Li , Xiaowei Wang , Long Mao , Yue Kan , Dan Xiong , Ke Gao , Xiao Zongwei 
Published: September 2020

Abstract
Background: To evaluate RV-PA coupling in post operative TOF patients with ventricular dilatation underwent for PVR and investigate the correlation between ventricular functions measuring Ea/Emax ratio using cardio magnetic resonance and the effect of surgical type at primary repair of TOF on coupling.Method: RV-PA coupling was measured noninvasively by Ea/Emax ratio from CMRI and ECHO. From CMRI results the patients were divided in two groups, RV-PA coupling and RV-PA uncoupling. Ea/Emax ≤1 was considered for coupling patients and Ea/Emax >1 for uncoupling patients.Results : 90 patients were uncoupled (Ea/Emax: 1.55±0.46) and 45 were coupled (Ea/Emax: 0.81±0.15). Out of 75 TAP repaired patients 60 were uncoupled RV-PV. In addition, higher pro-BNP is an important factor for uncoupled RV-PV ( P =0.001). CMR evaluation for right ventricular function between uncoupling and coupling were RVEDVi (196.65±63.57 vs. 154.28±50.07, P =0.001), RVESVi (121.19±51.47 vs. 83.94±20.43, P =0.001), RVSVi (67.19±19.87 vs. 106.31±33.44, P =0.001), and RVEF (40.90±8.73 vs. 54.63±4.76, P =0.001). The increased RVEDVi, RVESVi and RVSVi and decreased RVEF have significant correlation with Ea/Emax. Ea/Emax was also found positively correlated with RVEDVi ( P=< 0.05, r =0.35), RVESVi ( P=< 0.001, r =0.41) and negatively correlated with RVSVi ( P=< 0.05, r =0.22) and RVEF ( P=< 0.05, r =0.78).Conclusions: Unfavorable RV-PA coupling is present in post operative TOF patients and it is affected by several factors. Our results explain a new concept of RV-PA interactions as a contributing mechanism for the observed decline in RV function.
Survival analysis of patients with stage T2a and T2b perihilar cholangiocarcinoma treated with radical resection
Authors: Zhao Jian , Zhang Wei , Zhang Jun , Zhang Yi , Ma Wenjie , Liu Siyun , Li Fuyu , Song Bin 
Published: September 2020

Abstract
Background: Both the 7th and 8th editions of the American Joint Committee on Cancer (AJCC) staging system for perihilar cholangiocarcinoma (pCCA) had the same definition for T2a and T2b. But the value of this classification as prognostic factor remains unclear. Methods: 178 patients with stage T2a or T2b who underwent curative intent resection for pCCA between Jan 2010 and Dec 2018 were enrolled. Relationships between survival and clinicopathological factors including patient demographics and tumor characteristics were evaluated using univariate and multivariate Cox regression analysis. The overall survival (OS) were calculated by Kaplan-Meier method.Results: There was no significant difference in OS between T2a and T2b groups，and the median OS duration were 37 and 31 months (P=0.354). Both the 7th and 8th edition of the AJCC TNM staging demonstrated a poor prognostic predictive performance. High level of preoperative AST (≥85.0IU/L) and CA19-9 (≥1000 U/mL), vascular resection and lower pathological differentiation of the tumor were the independent predictors for poor survival after resection.Conclusion: The newly released 8th edition of AJCC staging system demonstrated a poor ability to discriminate the prognosis of patients with stage T2a and T2b pCCA after resection.