bluuebunny/crossref_metadata_2025_split huggingface dataset:
The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the microbiota
Authors: Feye Kristina , Swaggerty Christina L. , Kogut Michael H. , Ricke Steven C. , Piva Andrea , Grilli Ester 
Published: March 2020

Abstract
Background: Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry. A blend of vanillin, thymol, sorbic, and citric acids (AviPlus®P) has previously been shown to reduce Salmonella and other foodborne pathogens in chickens; however, changes to the microbiota of the jejunum and ileum have not been evaluated. Microbiota diversity is linked to, but not correlated with, the efficacy of natural products including organic acids and natural compounds; therefore, understanding the effects of these products on the microbiota is a necessary first step into evaluating the potential for wide-spread use within the poultry industry as an alternative to antibiotics. Results: Day-of-hatch by-product breeder chicks (n=30) were placed into either the control (0 g/MT AviPlus®P; n=5) or one of two experimental groups (300 g/MT; n=5; 500 g/MT AviPlus®P; n=5). The experiment was conducted using two replicate pens therefore 10 chicks/treatment were used for all analysis. Chickens were sacrificed 15d post-hatch and total jejunum and ileum contents were individually collected and snap frozen until further processing and analysis. The DNA was extracted and sequenced using the Illumina 16S rDNA MiSeq V3 platform and the samples analyzed in QIIME2.2019.1. Samples were filtered for quality and chimeras using DADA2, with OTU frequencies less than three removed from the study. Alpha and beta diversity analytics indicated compartmentalization within the poultry gastrointestinal tract (GIT). Additionally, LEfSE and ANCOM analysis showed a reduction in Enterobacteriaceae with increased inclusion rate and an increase in Clostridia, both of which are associated with optimal GIT health. Conclusion: The addition of a blend of organic acids and botanicals to the diet of chickens does not adversely impact the microbiota, and in fact, is associated with microbial changes within the ileum and jejunum that are largely thought of as beneficial. Promotion of a healthy GIT has the potential to limit colonization by Salmonella and other foodborne pathogens. The inclusion of the microencapsulated blend of organic acids and botanicals may be a viable antibiotic alternative for use in the poultry industry.
MiR-4792 regulates inflammatory responses in Cryptococcus neoformans infected microglia
Authors: Chen Jianghan , Yao Guotai , Wang Xiaoli , Hou Qing , Gao Rui , Wang Yilin , Teng Liang , Lin Wenting , Wang Yan , Wang Zhongzhi , Jin Yi 
Published: March 2020

Abstract
Background: Investigating the factors that influence inflammatory response of microglial cells is important to understand the pathogenesis of cryptococcal meningitis (CM). MicroRNA (miRNA) have been shown to play an important role in inducing host defenses and activating immune response in the process of microbial infection; however, the regulatory mechanisms of miRNAs in cryptococcal meningitis are poorly defined. In our previous analysis, we assessed the miRNA profiles of BV2 cells following Cryptococcus neoformans (C. neoformans) infection. In this study, we characterized the expression of miR-4792 in CM patients to further our understanding of the host response to pathogen infections.Results: miR-4792 was downregulated in BV2 cells infected with C. neoformans while its target gene EGFR was upregulated. Infected cells with up-regulated miR-4792 exhibited decreased EGFR expression, reduced MAPK signaling and a decreased secretion of inflammatory cytokines. Following antifungal treatment in cryptococcal meningitis patients, the levels of miR-4792 in the CSF significantly increased, while the expression of EGFR significantly decreased.Conclusion: This study identified that miR-4792 and its target EGFR regulate the secretion of inflammatory cytokines in C. neoformans infected BV2 cells. This furthers our knowledge of the host immune responses to fungal infections in the CNS.
Genome-wide scan for runs of homozygosity identifies potential candidate regions associated with growth traits in beef cattle
Authors: Zhao Guoyao , Zhang Tianliu , Liu Yuqiang , Wang Zezhao , Xu Lei , Zhu Bo , Gao Xue , Zhang Lupei , Gao Huijiang , Li Junya , Xu Lingyang 
Published: March 2020

Abstract
Background: Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of regions of the genome lead to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with growth traits in a commercial beef cattle population.Results: We identified a total of 29,271 ROH segments with an average number of 63.36 and an average length of 0.98 Mb in this commercial beef cattle population, representing ~2.53% (~63.36Mb) of the genome. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events identified across all individuals. Of these, nine regions were significantly associated with six growth phenotype traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, carcass length; P<0.01), which contain 187 candidate genes. Furthermore, we found 26 consensus ROH regions with frequencies exceeding 10%, and several of these consensus overlapped with QTLs which are associated with weight gain, calving difficulty and stillbirth. To precisely locate locus within each ROH for every studied trait, we further utilized loci-based methods for association analysis among these identified regions. Totally, we obtained 9,360 loci within ROH, and 1,631 loci displaying significant association (P<0.01) for eight traits. In addition, we found that 67 genes embedded with homozygous loci. Several identified candidate genes, including EBF2, SLC20A2, SH3BGRL2, HMGA1 and ACSL1, were related to growth traits.Conclusions: This study assessed genome-wide autozygosity pattern and inbreeding level in a commercial beef cattle population. Our study identified many candidate regions and genes with ROH for growth traits in beef cattle, which can provide important insights into investigating homozygosity across genome in other farm animals. Our findings may further be unitized to assist the design of selection mating strategy.
WITHDRAWN: Deep expression scrutiny provides genetic basis of aluminium tolerance in wild (Lens nigrican) and cultivated lentil (Lens culinaris Medik.)
Authors: Singh Dharmendra , Singh Chandan Kumar , Taunk Jyoti , Sharma Shristi , Tomar RamSewak Singh , Pal Madan , Konjengbam Noren Singh , Singh M. Premjit , Sharma Ph Ranjit , Sengar Rakesh Singh 
Published: March 2020

Abstract
Background: Aluminium (Al) stress hinders crop productivity in acidic soils. Lentil contains rich source of protein and micronutrients and cultivated in different parts of world. To enhance knowledge about Al toxicity tolerance, present study emphasizes on mechanistic analysis of genes associated with Al stress through de novo transcriptomic analysis of tolerant (L-4602), wild (ILWL-15) and sensitive (BM-4) genotypes. Result: Illumina HiSeq 2500 platform evaluated contigs ranging from 15,305 to 18,861 for all the samples with N50 values of 1795 bp. Four annotation softwares revealed differential regulation of several genes where 30,158 genes were specifically up-regulated for combinations under Al stress conditions alone. Top up-regulated Differentially Expressed Genes (DEGs) in tolerant cultivar when compared to the sensitive one were found to be involved in protein transport as well as degradation, defences, cell growth and development. Wild v/s cultivar comparison revealed upregulation of wild DEGs that are involved in regulation of transcription in differentiating cells, pre-mRNA splicing, catalysis and protein ubiquitination. Based on assembled Unigenes, 89,722 high-quality SNPs and 39,874 SSRs were detected. Twelve selected genes were validated using qRT-PCR. KEGG pathway analysis extracted 8,757 GO annotation terms within molecular, cellular and biological processes. Pathway analysis indicated that organic acid synthesis and their transportation along with detoxification of ROS, an alternate pathway involving metacaspase-1,4,9 for programmed cell death were also significantly induced due to Al stress.Conclusion: Present study unveils the characterization of differential transcripts generated under Al stress indicating Al tolerance as a multiplex phenomenon which will directly widen crop improvement programmes for Al toxicity utilizing molecular approaches.
Analysis of Regulation Networks in the Formation of Green Pigment in Garlic
Authors: Li Ningyang , Lu Xiaoming , Sun Xiudong , Qiao Xuguang 
Published: March 2020

Abstract
Background: Garlic (Allium sativum L.) has high medical and edible value, but is prone to producing green pigment during storage, which seriously affects product quality. Herein, we found multiple metabolic pathways involved in green pigment formation by analyzing the transcriptome and proteome changes of garlic stored at 4 °C for 0 day (DS0), 10 days (DS1), 15 days (DS2) and 40 days (DS3). Results: In this work, we found that porphobilinogen is a precursor of garlic green pigment and the citrate cycle (TCA cycle) can promote the formation of garlic green pigment by increasing the content of porphobilinogen. The salicylic acid (SA) inhibits garlic greening, whereas the lignin synthesis pathway positively correlates with greening. In addition to the above metabolic pathways, other pathways may be associated with the formation of garlic’s green pigment, such as glycolysis/gluconeogenesis, pyruvate metabolism and fatty acid metabolism. It has been reported that pyruvate and amino acids play a role in garlic greening, which were also demonstrated in this study. Conclusion: our results have important implications for understanding the mechanism of green pigment formation in garlic.
Structural variants in Mongolian originated ruminant: role in adaptation of extreme-environment
Authors: Xing Yanping , Qi Yu , Purev Chimgee , Wang Shengyuan , Wang Hongbing , Wu Kaifeng , Cao Junwei , Liu Chunxia , Liu Yiyi , Li Lu , Zhang Yanru , Zhou Huanmin 
Published: March 2020

Abstract
Background: Mongolian cattle (MC) is one of an ancient livestock breeds with good economic traits such as adaptation to Mongolian Plateau extreme low temperature in winter, resistant to pathogenic organisms infection and high quality meat. To reveal the molecular mechanism underlying these, the whole genome sequencing and comparative transcriptome sequencing of MC were performed.Results：By genome sequencing and structure variation analysis, 8 genes related to pathogenic organisms infection, including 4 members of bata-defensins gene family (LAP, DEFB1, DEFB2, and DEFB5), 2 members of interferon (IFN) gene family (IFNW1 and IFNT2) and 2 genes coding for BoLA proteins(Mongolian_cattle_21532 and Mongolian_cattle_19448) were found in MC genome inversion region. By transcriptome-sequencing, it was elucidated that 8 genes (FATP, FABP, PEPCK, SCP-X, ADIPO, FABP1, SCD-1, APO) related to PPARα pathway, 23 genes involved in oxidative phosphorylation and 10 P450 genes (CYP7B1, CYP4V2, CYP3A5, CYP11A1, CYP2C18, CYP2B6, CYP7A1, CYP2R1, CYP2E1, CYP27B1) were significantly up-regulated in winter MC transcriptomes, comparative to summer MC transcriptomes.Conclusions: Here, we characterized 41 genes implicated in fatty acid metabolism were up-regulated in winter MC transcriptomes. These genes probably account for the MC adaptation to extreme low temperature. At the same time, 8 genes in MC genome inversion region were discovered. And these genes gave clue to the MC resistant to pathogenic organisms infection. In sum, our revealed genes are of important for us to understand the molecular mechanisms of MC to adapt to their environments and valuable for cattle breeding.
Immunoregulation of PD-1/PD-L1 Inhibitory Pathway on Fetomaternal Tolerance in abortion Triggered by thyroid autoimmunity
Authors: Liu Haixia , Chen Mengya , Shan Zhongyan , Teng Weiping 
Published: March 2020

Abstract
Background: TAI in euthyroid pregnant women is associated with miscarriage. Studies have shown that the PD-1/PD-L1 signaling pathway plays an important role in maternal-fetal tolerance by promoting Treg cells development and inhibition of Th17 cells responses, whereby it is essential for normal pregnancy maintenance. However, whether the PD-1/PD-L1 pathway leads to a Treg/Th17 imbalance has not been fully investigated in TAI.Methods: TAI fetal loss model was established by thyroglobulin (mTg) immunized CBA/J female mice. The frequencies of splenic Th17, Treg, PD-1 and PD-L1 were tested by flow cytometry. IL-17, Foxp3, RORγt, PD-1 and PD-L1 mRNA levels were tested by real-time PCR.Results: Compared with the control group, the number of CD4 + CD25 + Foxp3 + T lymphocyte in the placenta and spleen were significantly reduced (P<0.05) in the experimental group (mTg group), CD4 + IL-17 + T-cell subsets and expression of RORγt and IL-17 mRNA in the placenta were increased (P<0.05), the ratio of Treg/IL-17 in the placenta and spleen was decreased (P<0.05). The expression of PD-1 and PD-L1 in mice immunized with mTg in CD4 + T group decreased the subsetof cells in the placenta and spleen including Tregs.Conclusions: The role of PD-1/PD-L1 pathway in an isolated thyroglobulin antibodies (TgAb) positive mouse abortion model is that it may lead to a peripheral Treg/Th17 imbalance and the maternal-fetal tolerance balance breakdown, which may ultimately result in fetal loss.
An analysis of the negative asymmetry in the coronal body shape of the old people in South Korea
Authors: Chen Lin , Lee Soo-Min , Nam Yunja , Park Jinhee 
Published: March 2020

Abstract
Background Existing positive shape models are based on values for the right side of the body. To the best of our knowledge, this is the first comparative study to analyze both left- and right-side data to explore asymmetrical body characteristics, considering that most older people are not able to maintain a healthy spinal vertical tilt presentation. In this study, 3D scanning and 3D measurement were used to analyze and study the asymmetry of the elderly in South Korea to provide more complete basic size data for the development of clothing patterns for the elderly.Methods The calculated values were analyzed by ANOVA and correlation analysis, and the paired sample t-test was performed to find asymmetrical characteristics of the older adult body. Finally, we used the independent t-test to analyze sex differences. Geomagic Design X software was used to record the coordinates of the measured points to reconstruct 3D models of the older adult body. We present a new method based on analysis of the vertex-anterior neck plane, the anterior neck-omphalion plane, and the omphalion-crotch point plane as benchmarks for the center of the head, the upper torso and the lower torso, respectively, to determine lateral asymmetry.Results The Kolmogorov-Smirnov normality test indicated the tendency of the torso to tilt to the right in older men and women. Compared with the inclination of the head, the inclination of the lower torso is more obvious. The correlation analysis results show that the tilt of the head does not affect the asymmetrical characteristics of the trunk.Conclusions This study did not use the traditional median sagittal plane as a central datum plane, instead separating the model according to the structure of the human body into the head, upper body, and lower body, with three independent central datum planes. Therefore, this study contributes an analysis of human asymmetry, thus providing more complete basic size data for the development of clothing patterns for the elderly in South Korea.
Serum Iron for Prognosis of Acute Ischemic Stroke by Endovascular Treatment
Authors: Liu Mingli , Hao Zhongfei , Li Ruiyan , Cai Jinquan , Li Yongli , Jiang Chuanlu 
Published: March 2020

Abstract
Background Iron, as an import micronutrient, is related to many diseases in a human body. Although the function of iron in acute ischemic stroke is yet debatable, there are few reports from clinical data on serum iron for the prognosis of acute ischemic stroke by endovascular treatment. The current retrospective study aimed to investigate the correlation between serum iron and acute ischemic stroke prognosis by endovascular treatment.Methods This study was carried out retrospectively and 84 patients participated from March 2016 to April 2019 who suffered acute ischemic stroke and were treated by endovascular treatment at this stroke center. The laboratory test and clinical data were assessed for the prognosis of acute ischemic stroke by endovascular treatment. An independent relationship was analyzed through binary logistic analysis and receiver operating characteristic curves for the accuracy of the test.Results This retrospective study was carried out at Harbin Medical University’s Second Affiliated Hospital, and enrolled 84 patients from March 2018 to September 2019, including 32 patients in whom the outcomes were clinically favorable and 52 patients with unfavorable clinical outcomes. The groin puncture to recanalization time significantly varied between patients with favorable as well as unfavorable clinical outcomes (45.0 min vs 72.5 min, p = 0.001), serum iron (10.87 μmol/L vs 4.07 μmol/L, p < 0.001) and thrombin time (13.40 s vs 14.25 s, p = 0.034) from univariable analysis. Serum iron (p < 0.001; adjusted OR [95% CI]:70.765 [9.904 - 505.636]) was associated independently with acute ischemic stroke prognosis by endovascular treatment, and receiver operating characteristic showed area under the curve of 0.926 (p < 0.001, 95% CI: 0.872 - 0.979).Conclusions The outcomes of this study reveal that serum iron level was associated independently with acute ischemic stroke prognosis, and high serum iron level could predict favorable clinical outcomes with a significantly accurate ability. Thus, serum iron could be a marker for acute ischemic stroke prognosis through endovascular treatment.
Midterm follow-up with modular fluted tapered stem in the management of Vancouver B3 femoral periprosthetic fracture
Authors: Cheng Qi , Zheng Li , Ding Yunzhi , Zhao Fengchao 
Published: March 2020

Abstract
BackgroundTo evaluate the technique and clinical results of the uncemented fluted, tapered, modular stems in treating Vancouver B3 periprosthetic femoral fractures. MethodsA retrospective study was carried out on 56 patients (56 hips) with the use of the modular femoral stem in revision of total hip arthroplasty between August 2007 and January 2009. The mean patient age was 73.4±6.6 years(rang, 62-82years). Bone defect was categorised as Paprosky types：32 Type IIIA , 20 Type IIIB, 4 Type Ⅳ. 28 hips had allograft struts placed around the fracture. 44 patients had concomitant revision of the acetabular component. The mean duration of follow-up was 102.1±12.2 months (rang, 84-120 months). Hip function and treatment outcome were assessed using Harris Hip Score System and Beals and Tower 's standard. Radiography were used to evaluate the implant stability, bone stock restoration, fracture healing, stem subsidence and complications. ResultsThe mean HHS improved from 45.6 ±5.4 points (range, 32-53 points) preoperatively to 86.3±8.4 points (range, 81-92 points) at the most recent follow-up. Radiographic review showed all fractures of patients united, with maintenance or improvement of bone stock in 96% of patients. The average value of the stem subsidence 4.9±1.5mm (rang, 0-9mm), happening mainly within the first six months after the operation. No implant had been revised because of aseptic loosening or dislocation. 8 of all the 28 allografts united to the host bone. In the last follow-up, 20 cases of treatment results were excellent, 36 cases were good. There were four patients occuring complications such as deep vein thrombosis of lower limbs or subcutaneous haematomas after surgery, all cured during hospitalization. There were no patients occurring the dislocation of hips after revision. Conclusion﻿The uncemented fluted, tapered, modular prosthesis is a good choice with a high rate of fracture union and implant osteointegration when the treatment of the Vancouver B3 femoral periprosthetic fracture.
Analysis of 5 Rare Cases of Esophageal Fistula after Anterior Cervical Decompression, Bone Graft Fusion and Internal Fixation Surgeries
Authors: Huang Yu , Lin Jin , Zhou Lihan , Lin Jianhua , Chen Xuanwei 
Published: March 2020

Abstract
Objective: To retrospectively analyze and discuss the characteristics of the pathogenesis, diagnosis and treatment of esophageal fistula after anterior cervical surgery. Methods: A retrospective analysis of the clinical data of 5 patients complicated with esophageal fistula after anterior cervical surgery in our hospital from January 2003 to December 2018 was performed. Results: Of the 5 patients, 3 died of severe pulmonary infection and sepsis after conservative treatment, and 2 patients healed after surgery performed for debridement and internal fixator removal. Conclusion: Esophageal fistula after anterior cervical spine surgery is a rare and serious complication with a high mortality rate. Surgical debridement and removal of the internal fixator accompanied by other active treatment measures can achieve good curative effects and significantly improve the outcomes of patients.
Analysis on the MRI Results of Neonatal Brain with Different Levels of Bilirubin
Authors: ZHONGXING LU , DING SHOULING , WANG FEN , Lv Haitao 
Published: March 2020

Abstract
Numerous studies have focused on abnormal changes in craniocerebral MRI in neonates at severe bilirubin levels, and no abnormal changes have been reported at moderate and low levels, and the abnormal changes are related to gestational age, birth weight and bilirubin levels And other factors. Here, by analyzing the neonatal craniocerebral MRI manifestations at different levels of bilirubin, it is found that at moderate and low levels of bilirubin, the neonatal cranial MRI has abnormal changes, and the craniocerebras at severe bilirubin levels MRI abnormal changes were not statistically significant, and were not significantly related to gestational age, birth weight, and bilirubin levels. This suggests that neurotoxicity may occur at low and medium levels of bilirubin.