bluuebunny/crossref_metadata_2025_split huggingface dataset:
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: July 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.
COL4A1 promotes the growth and metastasis of hepatocellular carcinoma cells by activating FAK-Src signaling
Authors: Wang Ting , Jin Haojie , Hu Jingying , Li Xi , Ruan Haoyu , Xu Huili , Wei Lin , Dong Weihua , Teng Fei , Gu Jianren , Qin Wenxin , Luo Xiaoying , Hao Yujun 
Published: July 2020

Abstract
Background: Collagens are the most abundant proteins in extra cellular matrix and important components of tumor microenvironment. Recent studies have showed that aberrant expression of collagens can influence tumor cell behaviors. However, their roles in hepatocellular carcinoma (HCC) are poorly understood. Methods: In this study, we screened all 44 collagen members in HCC using whole transcriptome sequencing data from the public datasets, and collagen type IV alpha1 chain (COL4A1) was identified as most significantly differential expressed gene. Expression of COL4A1 was detected in HCC samples by quantitative real-time polymerase chain reaction (qRT-PCR), western blot and immunohistochemistry (IHC). Finally, functions and potential mechanisms of COL4A1 were explored in HCC progression.Results: COL4A1 is the most significantly overexpressed collagen gene in HCC. Upregulation of COL4A1 facilitates the proliferation, migration and invasion of HCC cells through FAK-Src signaling. Expression of COL4A1 is upregulated by RUNX1 in HCC. HCC cells with high COL4A1 expression are sensitive to the treatment with FAK or Src inhibitor. Conclusion: COL4A1 facilitates growth and metastasis in HCC via activation of FAK-Src signaling. High level of COL4A1 may be a potential biomarker for diagnosis and treatment with FAK or Src inhibitor for HCC.
Diagnostic ability of OCT parameters and retinal ganglion cells count in identification of glaucoma in myopic preperimetric eyes
Authors: Rolle Teresa , Bonetti Beatrice , Mazzucco Alberto , Dallorto Laura 
Published: July 2020

Abstract
BACKGROUND: The aim of the study is to evaluate the diagnostic ability of OCT parameters and retinal ganglion cells (RGCs) count in identify glaucomatous disease in myopic preperimetric eyes. METHODS: This was a cross-sectional observational study. The study group consisted of 154 eyes: 36 controls, 64 preperimetric (PPG), and 54 primary openangle glaucoma (POAG) eyes. Each group was divided into three subgroups based on axial length: emmetropic, myopic with axial length (AL) <25 mm, and myopic with AL>25 mm, to analyze the effect of myopia. The RGCs count was obtained using a model described later. As regard the influence of myopia on OCT parameters and RGC count, we performed Pearson’s correlation. The Area Under Receiver Operator Characteristics Curves (AUROC curves) evaluated which parameter had the best sensitivity and specificity in identifying glaucoma in myopic eyes. RESULTS: In Pearson’s test, all Ganglion Cell Complex (GCC) thicknesses showed the weakest and less significant correlation with AL in all groups. All the AUROCs were statistically significant, and above 0.5. Inferior GCC and Global Loss Volume (GLV) showed the highest AUCs in all myopic group and the best diagnostic ability in distinguishing control from glaucomatous eyes. RGCcount showed good AUROC in all groups, with sensitivities of about 83% in myopic eyes, and specificity over 91% in all groups.CONCLUSIONS: GCC is the parameter less influenced by the AL, and the inferior GCC and the GLV have the best diagnostic performance. The RGCcount has good sensitivity and specificity, so it can be used as a complementary test in the diagnosis of glaucoma in myopic preperimetric eyes.
Integrated Genomic and Transcriptomic Analysis Revealed Mutation Patterns of De-differentiated Liposarcoma and Leiomyosarcoma
Authors: Liu Wenshuai , Tong Hanxing , Zhang Chenlu , Zhuang Rongyuan , Guo He , Chentao Lv , Yang Hua , Lin Qiaowei , Guo Xi , Wang Zhiming , Wang Yan , Shen Feng , Wang Shengzhou , Wang Guan , Liu Jun , Dai Chun , Lu Weiqi , Zhang Yong , Zhou Yuhong 
Published: July 2020

Abstract
Background Treating patients with advanced sarcomas is challenging due to great histologic diversity among its subtypes. Leiomyosarcoma (LMS) and de-differentiated liposarcoma (DDLPS) are two common and aggressive subtypes of soft tissue sarcoma (STS). They differ significantly in histology and clinical behaviors. However, the molecular driving force behind the difference is unclear.Methods We collected 20 LMS and 12 DDLPS samples and performed whole exome sequencing (WES) to obtain their somatic mutation profiles. We also performed RNA-Seq to analyze the transcriptomes of 8 each of the LMS and DDLPS samples and obtained information about differential gene expression, pathway enrichment, immune cell infiltration in tumor microenvironment, and chromosomal rearrangement including gene fusions. Selected gene fusion events from the RNA-seq prediction were checked by RT-PCR in tandem with Sanger sequencing.Results We detected loss of function mutation and deletion of tumor suppressors mostly in LMS, and oncogene amplification mostly in DDLPS. A focal amplification affecting chromosome 12q13–15 region which encodes MDM2, CDK4 and HMGA2 is notable in DDLPS. Mutations in TP53, ATRX, PTEN, and RB1 are identified in LMS but not DDLPS, while mutation of HERC2 is only identified in DDLPS but not LMS. RNA-seq revealed overexpression of MDM2, CDK4 and HMGA2 in DDLPS and down-regulation of TP53 and RB1 in LMS. It also detected more fusion events in DDLPS than LMS (4.5 vs. 1, p=0.0195), and the ones involving chromosome 12 in DDLPS stand out. RT-PCR and Sanger sequencing verified the majority of the fusion events in DDLPS but only one event in LMS selected to be tested. The tumor microenvironmental signatures are highly correlated with histologic types. DDLPS has more endothelial cells and fibroblasts content than LMS. Conclusions Our analysis revealed different recurrent genetic variations in LMS and DDLPS including simultaneous upregulation of gene expression and gene copy number amplification of MDM2 and CDK4. Up-regulation of tumor related genes is favored in DDLPS, while loss of suppressor function is favored in LMS. DDLPS harbors more frequent fusion events which can generate neoepitopes and potentially targeted by personalized immune treatment.
Authorship diversity among systematic reviews in eyes and vision
Authors: Qureshi Riaz , Han Genie , Fapohunda Kolade , Abariga Samuel , Wilson Renee , Li Tianjing 
Published: July 2020

Abstract
Importance: The inclusion of authors from diverse backgrounds and with different lived experiences is critical to ensuring the questions addressed in systematic reviews (SRs), as well as the subsequent conclusions and recommendations made, are representative of the global community.Objective: To assess the gender and geographic diversity of authors among all Cochrane SRs in eyes and vision as compared with a random sample of non-Cochrane SRs of interventions in the field of eyes and vision.Design: The Cochrane Eyes and Vision United States Satellite maintains a database of SRs in the field of eyes and vision. We selected all (n = 313) eyes and vision intervention SRs published in The Cochrane Library and a random sample of 313 eyes and vision intervention SRs published elsewhere for this study. We determined gender of the first and corresponding authors (‘woman,’ ‘man,’ or ‘unknown’) using a previously developed algorithm and their location based on institution country and the World Health Organization region. Results: From the 626 reviews included in our sample, we identified 751 unique authors who comprised 887 author positions (i.e., first and/or corresponding authors). We were able to ascertain the gender of 647/751 (86%) authors: 276 women, and 371 men. Among Cochrane eyes and vision SRs, the proportions of women in first and/or corresponding author positions were consistent and approximately equal to men. Among non-Cochrane eyes and vision SRs, the representation of women was markedly lower as corresponding authors than other positions. Most authors of Cochrane eyes and vision SRs were from the United Kingdom (31%) and United States of America (26%), whereas most authors of non-Cochrane SRs were from China (34%). Conclusions and relevance: Compared with authors of non-Cochrane SRs in eyes and vision, authors of Cochrane SRs appear to have approximately equal representation of women and men among perceived important author positions and be located in European and North American countries, possibly due to the locations of the Cochrane editorial teams. Cochrane Eyes and Vision should continue to recruit authors from around the world in locations that reflect the global burden of eye disease.
Implementation and adherence to the Bedside Paediatric Early Warning System (BedsidePEWS) in a pediatric tertiary care hospital
Authors: Gawronski Orsola , Ferro Federico , Cecchetti Corrado , Atti Marta Luisa Ciofi Degli , Dall'oglio Immacolata , Tiozzo Emanuela , Raponi Massimiliano 
Published: July 2020

Abstract
Background Escalation of care in deteriorating children admitted to hospital wards in relation to pediatric early warning scores has been rarely reported. The aim of this study is to examine adherence to the vital signs and BedsidePEWS escalation protocol at a large tertiary care children’s hospital.Methods This is a prospective observational study. A 6-month audit on adherence to BedsidePEWS was performed on the wards in 2018. Data on the frequency and accuracy of BedsidePEWS score calculations, escalation of patient observations, monitoring and medical reviews were recorded.Two research nurses performed weekly visits to the hospital wards to collect data on BedsidePEWS scores, medical reviews, type of monitoring and vital signs recorded. Data were described through means or medians according to the distribution. Inferences were calculated either with Chi-square, Student’s t test or Wilcoxon-Mann–Whitney test, as appropriate (P <0.05 considered as significant).Results A total of 522 Vital Signs (VS) and score calculations on 177 patient clinical records were observed from 13 hospital inpatient wards. Frequency of VS and score documentation occurred <3 times per day in 33% of the observations. Adherence to the VS documentation frequency according to the hospital protocol was observed in 54% for all patients; for children with chronic health conditions (CHC) it was significantly lower than children admitted for acute medical conditions (47%, P=0.006). The BedsidePEWS score was correctly calculated and documented in 84%, systolic blood pressure was recorded in 79% and temperature in 91% of the VS recording events. Patients within a 0-2 BedsidePEWS score range were all reviewed at least once a day by a physician. Only 50% of the patients in the 5-6 score range were reviewed within 4 hours and 42% of the patients with a score ≥7 within 2 hours. Transcutaneous Oxygen Saturation continuous monitoring was applied to 60% of the children at higher risk (BedsidePEWS ≥5).Conclusions Escalation of patient observations, monitoring and medical reviews matching the BedsidePEWS is still suboptimal. Children with CHC are at higher risk of lower compliance. Impact of adherence to predefined response algorithms on patient outcomes should be further explored.
Illuminating the dark side of the human transcriptome with long read transcript sequencing
Authors: Kuo Richard , Cheng Yuanyuan , Zhang Runxuan , Brown John W.S. , Smith Jacqueline , Archibald Alan L. , Burt Dave W. 
Published: July 2020

Abstract
Background: The human transcriptome annotation is regarded as one of the most complete of any eukaryotic species. However, limitations in sequencing technologies have biased the annotation toward multi-exonic protein coding genes. Accurate high-throughput long read transcript sequencing can now provide stronger evidence for rare transcripts and genes such as mono-exonic and non-coding genes that were previously either undetectable or impossible to differentiate from sequencing noise. Results: We developed the Transcriptome Annotation by Modular Algorithms (TAMA) software to leverage the power of long read transcript sequencing and address the issues with current data processing pipelines. TAMA achieved high sensitivity and precision for gene and transcript model predictions in both reference guided and unguided approaches in our benchmark tests using simulated Pacific Biosciences (PacBio) and Nanopore sequencing data and real PacBio datasets. By analyzing PacBio Sequel II Iso-Seq sequencing data of the Universal Human Reference RNA (UHRR) using TAMA and other commonly used pipelines, we found that the convention of using mapping identity to measure error correction performance does not reflect actual gain in accuracy of predicted transcript models. In addition, inter-read error correction can cause major changes to read mapping, resulting in potentially over 6K erroneous gene model predictions in the Iso-Seq based human genome annotation. Using TAMA’s genome assembly based error correction and gene feature evidence, we identified 2,566 putative novel non-coding genes and 1,557 putative novel protein coding gene models.Conclusions: Long read transcript sequencing data has the power to identify novel genes within the highly annotated human genome. The use of parameter tuning and extensive output information of the TAMA software package allows for in depth exploration of eukaryotic transcriptomes. We have found long read data based evidence for thousands of unannotated genes within the human genome. More development in sequencing library preparation and data processing are required for differentiating sequencing noise from real genes in long read RNA sequencing data.
Improving the production of AHL lactonase AiiO-AIO6 from Ochrobactrum sp. M231 in intracellular protease-deficientBacillus subtilis
Authors: Xia Rui , Yang Yalin , Pan Xingliang , Gao Chenchen , Yao Yuanyuan , Liu Xuewei , Teame Tsegay , Zhang Fengli , Hu Juan , Ran Chao , Zhang Zhen , Liu-Clarke Jihong , Zhou Zhigang 
Published: July 2020

Abstract
Quorum quenching (QQ) blocks bacterial cell-to-cell communication (i.e., quorum sensing), and is a promising antipathogenic strategy to control bacterial infection via inhibition of virulence factor expression and biofilm formation. QQ enzyme AiiO-AIO6 from Ochrobactrum sp. M231 has several excellent properties and shows biotherapeutic potential against important bacterial pathogens of aquatic species. AiiO-AIO6 can be secretory expressed in Bacillus subtilis via a non-classical secretion pathway.To improve AiiO-AIO6 production, four intracellular protease-deletion mutants of B. subtilis1A751 were constructed by individually knocking out the intracellular protease-encoding genes (tepA, ymfH, yrrNandywpE). The AiiO-AIO6 expression plasmid pWB-AIO6BS was transformed into the B. subtilis 1A751 and its four intracellular protease-deletion derivatives. Results showed that all recombinant intracellular protease-deletion derivatives (BSΔtepA, BSΔymfH, BSΔyrrNand BSΔywpE) had a positive impact on AiiO-AIO6 production. The highest amount of AiiO-AIO6 extracellular production of BSΔywpE in shake flask reached 1416.47 U/mL/OD600, which was about 121% higher than that of the wild-type strain. Furthermore, LC-MS/MS analysis of the degrading products of 3-oxo-C8-HSL by purification of AiiO-AIO6 indicated that AiiO-AIO6 was an AHL-lactonase which hydrolyzes the lactone ring of AHLs. Phylogenetic analysis showed that AiiO-AIO6was classified as a member of the α/β hydrolase family with a conserved “nucleophile-acid-histidine” catalytic triad. In summary, this study showed that intracellular proteases were responsible for the reduced yields of heterologous proteins and provided an efficient strategy to enhance the extracellular production of AHL lactonase AiiO-AIO6.
Efficacy of Acupuncture for Sciatica: Study Protocol for A Randomized Controlled Pilot Trial.
Authors: Yu Fang-Ting , Ni Guang-Xia , Liu Zhi-Shun , Meng Xiu-Li , Li Jin-Ling , Tu Jian-Feng , Wang Li-Qiong , Yang Jing-Wen , Fu Hai-Yang , Zhang Xin-Chang , Zhang Xiao-Hui , Zhang Hao-Lin , Shi Guang-Xia , Liu Cun-Zhi 
Published: July 2020

Abstract
Background: Acupuncture is widely used for pain diseases while evidence of its efficacy for sciatica is insufficient. This pilot study aims to investigate the feasibility and efficacy of acupuncture for sciatica induced by lumbar disc herniation. Methods: This is a multicenter, three-arm, patient-assessor-blinded randomized controlled pilot trial. 90 patients will be assigned randomly into 3 groups including disease-affected meridians (DAM) group, non-affected meridians (NAM) group, and sham acupuncture (SA) group in a 1:1:1 ratio. The trial involves a 4-week treatment along with follow-up for 22 weeks. The primary outcome is the change of leg pain intensity measured by the Visual-Analogue Scale (VAS) from baseline to week 4 after randomization. Secondary outcomes include functional status, back pain intensity, and quality of life. Adverse events will also be recorded.Discussion: This pilot study will investigate the feasibility and efficacy of acupuncture for patients with sciatica. The results of the study will help improve a better design and establish a power calculation for a full-scale study.Trial registration: ChiCTR2000030680 (Chinese Clinical Trial Registry, http://www.chictr.org.cn, registered on 9th March 2020).
Examining the effector mechanisms of Xuebijing Injection on COVID-19 based on network pharmacology.
Authors: Zheng Wenjiang , Yan Qian , Ni Yongshi , Zhan Shaofeng , Yang Liuliu , Zhuang Hongfa , Liu Xiaohong , Jiang Yong 
Published: July 2020

Abstract
Objective: To examine the potential effector mechanisms of Xuebijing (XBJ) on coronavirus disease 2019 (COVID-19) based on network pharmacology.Methods: We searched Chinese and international papers to obtain the active ingredients of XBJ. Then, we compiled COVID-19 disease targets from the GeneCards gene database and via literature searches. Next, we used the SwissTargetPrediction database to predict XBJ’s effector targets and map them to the abovementioned COVID-19 disease targets in order to obtain potential therapeutic targets of XBJ. Cytoscape software version 3.7.0 was used to construct a “XBJ active-compound-potential-effector target” network and protein-protein interaction (PPI) network, and then to carry out network topology analysis of potential targets. We used the ClueGO and CluePedia plugins in Cytoscape to conduct gene ontology (GO) biological process (BP) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analysis of XBJ’s effector targets. Results: We obtained 144 potential COVID-19 effector targets of XBJ. Fourteen of these targets—glyceraldehyde 3-phosphate dehydrogenase (GAPDH), albumin (ALB), tumor necrosis factor (TNF), epidermal growth factor receptor (EGFR), mitogen-activated protein kinase 1 (MAPK1), Caspase-3 (CASP3), signal transducer and activator of transcription 3 (STAT3), MAPK8, prostaglandin-endoperoxide synthase 2 (PTGS2), JUN, interleukin-2 (IL-2), estrogen receptor 1 (ESR1), and MAPK14—had degree values >40 and therefore could be considered key targets. They participated in extracellular signal–regulated kinase 1 and 2 (ERK1, ERK2) cascade, the T-cell receptor signaling pathway, activation of MAPK activity, cellular response to lipopolysaccharide, and other inflammation- and immune-related BPs. XBJ exerted its therapeutic effects through the renin–angiotensin system (RAS), nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB), MAPK, phosphatidylinositol-4, 5-bisphosphate 3-kinase (PI3K)–protein kinase B (Akt)–vascular endothelial growth factor (VEGF), toll-like receptor (TLR), TNF, and inflammatory-mediator regulation of transient receptor potential (TRP) signaling pathways to ultimately construct a “ingredient-target-pathway” effector network. Conclusion: The active ingredients of XBJ regulated different genes, acted on different pathways, and synergistically produced anti-inflammatory and immune-regulatory effects, which fully demonstrated the synergistic effects of different components on multiple targets and pathways. Our study demonstrated that existing studies on the pharmacological mechanisms of XBJ in the treatment of sepsis and severe pneumonia, could explain the effector mechanism of XBJ in COVID-19 treatment, and those provided a preliminary examination of the potential effector mechanism in this disease.
Value of artificial ascites to assist thermal ablation of liver cancer adjacent to the gastrointestinal tract in patients with previous abdominal surgery
Authors: Huang Qiannan , Li Jianguo , Zeng Qingjing , Tan Lei , Zheng Rongqin , He Xuqi , Li Kai 
Published: July 2020

Abstract
Background

To evaluate the feasibility and effectiveness of artificial ascites to assist thermal ablation of liver cancer adjacent to the gastrointestinal tract in patients with previous abdominal surgery.

Methods

Thirty-nine patients with a total of 40 liver malignant tumors were enrolled between January 2016 and June 2019. All had histories of hepatectomy, splenectomy, cholecystectomy, and intestinal surgery. The distance between the tumor and the gastrointestinal tract was < 5 mm. Normal saline was used as artificial ascites to protect the gastrointestinal tract during thermal ablation. The success rate of the procedure, incidence of major complications, and the technical efficacy of ablation were recorded. Patients were followed for local tumor progression (LTP), and overall survival (OS).

Results

The use of artificial ascites was successful in 38 of the 40 procedures (95%). Major complications occurred in two of the 39 patients (5.1%) following the procedure. One was an intestinal fistula that occurred in a failed case and was associated with an infection. The other was a liver abscess that occurred in a successful case. The technical efficacy of ablation was 100% (40/40 procedures). The median follow-up was 20 months. The 1-, 2-, and 3-year LTP rates were 2.9%, 5.7% and 5.7%. The 1-, 2-, and 3-year OS rates were 97.1%, 86.8% and 69.5%.

Conclusion

In patients with previous abdominal surgery, artificial ascites is feasible and effective for assisting thermal ablation of liver cancer adjacent to the gastrointestinal tract.