bluuebunny/crossref_metadata_2025_split huggingface dataset:
Management of patients with early stage lung cancer – why do some patients not receive treatment with curative intent?
Authors: Lawrenson Ross , Lao Chunhuan , Brown Leonie , Moosa Lucia , Chepulis Lynne , Keenan Rawiri , Kidd Jacquie , Middleton Karen , Conaglen Paul , de Groot Charles , Aitken Denise , Wong Janice 
Published: January 2020

Abstract
Backgrounds This study aims to understand the factors that influence whether patients receive potentially curative treatment for early stage lung cancer. A key question was whether indigenous Māori patients were less likely to receive treatment. Methods Patients included those diagnosed with early stage lung cancer in 2011-2018 and resident in the New Zealand Midland Cancer Network region. Logistic regression model was used to estimate the odds ratios of having curative surgery/ treatment. The Kaplan Meier method was used to examine the all-cause survival and Cox proportional hazard model was used to estimate the hazard ratio of death. Results In total 419/583 (71.9%) of patients with Stage I and II disease were treated with curative intent - 272 (46.7%) patients had curative surgery. Patients not receiving potentially curative treatment were older, were less likely to have non-small cell lung cancer (NSCLC), had poorer lung function and were more likely to have an ECOG performance status of 2+. Current smokers were less likely to be treated with surgery and more likely to receive treatment with radiotherapy and chemotherapy. Those who were treated with surgery had a 2-year survival of 87.8% (95% CI: 83.8%-91.8%) and 5-year survival of 69.6% (95% CI: 63.2%-76.0%). Stereotactic ablative body radiotherapy (SABR) has equivalent effect on survival compared to curative surgery (hazard ratio: 0.77, 95% CI: 0.37-1.61). After adjustment we could find no difference in treatment and survival between Māori and non-Māori. Conclusions The majority of patients with stage I and II lung cancer are managed with potentially curative treatment – mainly surgery and increasingly with SABR. The outcomes of those being diagnosed with stage I and II disease and receiving treatment is positive with 70% surviving 5 years.
Analysis of transcriptomic changes in bovine endometrial stromal cells treated with lipopolysaccharide
Authors: Ding Xuefen , Lv Haimiao , Deng Lixin , Hu Wenju , Peng Zhan , Yan Chenbo , Yang Dexin , Tong Chao , wang Xinzhuang 
Published: January 2020

Abstract
Background: Endometritis adversely affects the ability of cattle to reproduce, and significantly reduces milk production. Consequently, it has great influence on the economic value of dairy cows. The endometrium is mainly composed of epithelial and stromal cells and they produce the first immune response to invading pathogens. Epithelial cells are the first cellular barrier through which bacteria enter the uterine endometrium. However, most of the epithelial cells are disrupted and stromal cells are exposed to an inflammatory environment when endometritis occurs, especially postpartum. A loss of the protective epithelium allows bacteria or toxins to access the underlying stromal cells. The activation of Toll-like receptor（TLRs）on stromal cells induces increased production of cytokines and chemokines. Understanding the genome-wide characterization of the bovine endometritis will be beneficial for prevention and treatment of endometritis. In this study, whole-transcriptomic gene changes in bovine stromal cells treated with LPS were compared with those treated with PBS (control group) and were analyzed by RNA sequencing (RNA-seq). Results: Compared with the control group, a total of 366 differentially expressed genes (DEGs) were identified in LPS-induced group (234 upregulated and 132 downregulated genes), with an adjusted P-value＜0.05 by DESeq. Gene ontology (GO) enrichment analysis revealed DEGs were most enriched in lymphocyte activation, interleukin-1 receptor binding, regulation of cell activation, and lymphocyte-activated interleukin-12 production. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed DEGs were most enriched in TNF signaling pathway, Toll-like receptor signaling pathway, cytokine-cytokine receptor interaction, nucleotide-binding oligomerization domain-like (NOD-like) receptor signaling pathway, NF-κB signaling pathway, and chemokine signaling pathway.Conclusion: The results of this study unraveled endometrial stromal cells transcriptome profile alterations in bovine affected by LPS which may have a significant effect on the eliminating or reducing inflammation by comprehending molecular mechanisms and authenticating unique genes related to endometritis.
Classification of Andrographis paniculata extracts according to solvent extraction by HPLC fingerprint analysis and chemometrics
Authors: Rafi Mohamad , Devi Anggun Fenika , Syafitri Utami Dyah , Heryanto Rudi , Suparto Irma Herawati , Amran Muhammad Bachri , Rohman Abdul , Prajogo Bambang , Lim Lee Wah 
Published: January 2020

Abstract
Objective: Andrographis paniculata, widely used as an antidiabetic in Indonesian traditional medicines (jamu), contains chemical compounds whose concentration is related to its therapeutic effects. The concentration of solvents used for extraction will also affect the number of compounds extracted. Therefore, a quality control method is needed to ensure consistency in quantifying these compounds in A. paniculata to improve its therapeutic application. High-performance liquid chromatography fingerprint analysis combined with chemometrics was used to evaluate extracts from different solvent extraction treatments. The content of andrographolide, the main bioactive compound in A. paniculata, and the level of α-glucosidase inhibition activity, an indicator of its antidiabetic activity, were also determined. Results: Fingerprint chromatograms of A. paniculata extracts from different treatments exhibited a similar pattern with several peaks in common, only differing in area and intensity value. The A. paniculata extracts were classified using HPLC fingerprint and principal component analysis to allow grouping according to their respective solvent extraction treatments. The highest andrographolide content and α-glucosidase inhibition activity occurred in the 50% ethanol extract and the lowest in the water extract. HPLC fingerprint analysis could be used for identifying A. paniculata extracts based on solvent extraction, thus improving quality control for their therapeutic application.
High copy number and highly stable Escherichia coli-Bacillus subtilis shuttle plasmids based on pWB980
Authors: Zhao XingYa , Xu JianYong , Tan Ming , Zhen Jie , Shu WenJu , Yang ShiBin , Ma YanHe , Zheng Hongchen , Song Hui 
Published: January 2020

Abstract
Background: pWB980 derived from pUB110 is a promising expression vector in Bacillus for its high copy number and high stability. However, the low transformation rate of recombinant plasmids to the wild cells limited the application of it. On the basis of pWB980, constructing an E. coli-B. subtilis shuttle plasmid could facilitate the transformation rate to Bacillus cells. Because the insertion site for E. coli replication origin sequence (ori) is not unique in pWB980, in order to investigate the best insertion site, eight shuttle plasmids (pUC980-1~pUC980-8) containing all possible insertion sites and directions were constructed. Results: The results showed that all the selected insertion sites could be used to construct shuttle plasmid but some sites required a specific direction. And different insertion sites led to different properties of the shuttle plasmids. The best shuttle plasmids pUC980-1 and pUC980-2, which showed copies more than 450 per cell and segregational stabilities up to 98%, were selected for heterologous expressions of an alkaline pectate lyase gene pelN, an alkaline protease spro1 and a pullulanase gene pulA11, respectively. The highest extracellular activities of PelN, Spro1 and PulA11 were upto 5200 U/mL, 21537 U/mL and 504 U/mL correspondingly after 54 h, 60 h and 48 h fermentation in a 10 L fermentor. Notably, PelN and Spro1 showed remarkably higher yields in Bacillus than previous reports. Conclusion: The optimum ori insertion site was the upstream region of BA3-1 in pWB980 which resulted in shuttle plasmids with higher copy numbers and higher stabilities. The novel shuttle plasmids pUC980-1 and pUC980-2 will be promising expression vectors in B. subtilis. Moreover, the ori insertion mechanism revealed in this work could provide theoretical guidance for further studies of pWB980 and constructions of other shuttle plasmids. Keywords: Expression vectors; pUC980; Bacillus subtilis; Alkaline pectate lyase; Alkaline protease; Pullulanase.
Axitinib as a third or further line of treatment in renal cancer. A single institution experience
Authors: Tsironis Giorgos , Liontos Michalis , KYRIAZOGLOU ANASTASIOS , Koutsoukos Konstantinos , Tsiara Anna , Kaparelou Maria , Zakopoulou Roubini , Cohen Abis , Skafida Efi , Fontara Sofia , Zagouri Flora , Bamias Aristotelis , Dimopoulos Meletios Athanasios 
Published: January 2020

Abstract
Kidney cancer is a lethal neoplasm that affects several thousands of people every year. Renal cell carcinoma (RCC) is the most common histologic type. Recent developments in the therapeutic approach include antiangiogenic targeted approaches and Immunotherapy. Thus, the therapeutic algorithm of RCC patients and the survival outcomes have changed dramatically. Herein we present a retrospective study of the patients treated in our Department with an antiangiogenic agent -Axitinib, a tyrosine kinase inhibitor- as a third or further line treatment. Our real world data reflect that axitinib is a safe and effective option, even beyond the second line.
Functional comaparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs Lymphoprep Tubes
Authors: Chen Han , Schürch Christian M , Noble Kevin , Kim Kenneth , Krutzik Peter , O'Donnell Erika , Tuig Jason V , Nolan Garry P , McIlwain David Robert 
Published: January 2020

Abstract
Background : Cryopreserved human peripheral blood mononuclear cells (PBMCs) are a commonly used sample type for a variety of immunological assays. Many factors can affect the quality of PBMCs, and careful consideration and validation of an appropriate PBMC isolation and cryopreservation method is important for well-designed clinical studies. A major point of divergence in PBMC isolation protocols is the collection of blood, either directly into vacutainers pre-filled with density gradient medium or the use of conical tubes containing a porous barrier to separate the density gradient medium from blood. Results : To address potential differences in sample outcome, we isolated, cryopreserved, and compared frequency and functionality of PBMCs using parallel protocols differing only in the use of one of two common tube types for isolation. Whole blood was processed in parallel using both Cell Preparation Tubesä (CPT, BD Biosciences) and Lymphoprepä Tubes (Axis-Shield) and assessed for yield and viability prior to cryopreservation. After thawing, samples were further examined by flow cytometry for cell yield, cell viability, frequency of ten cell subsets, and capacity for stimulation-dependent CD4+ and CD8+ T cell intracellular cytokine production. Cell recovery, viability, frequency of immune cell subsets, and T cell functionality between PBMC samples isolated using CPT or Lymphoprep tubes were comparable. Conclusion : CPT and Lymphoprep tubes are both effective for PBMC isolation and may be used interchangeably for immunological studies involving T cell activation.
Anti-inflammatory effect of HGF responses to traumatic oral ulcers using an HGF-Tg mouse model
Authors: Wang Xinhong , Yan Liting , Tang Yinghua , He Xiaoxi , luo gang 
Published: January 2020

Abstract
Background: Hepatocyte growth factor (HGF) has been implicated in inhibiting diverse types of inflammation and promoting wound healing. In this study, we demonstrate the anti-inflammatory effect of HGF on traumatic ulcer of oral mucosa using HGF overexpression transgenic C57BL/6 (HGF-Tg) mice. In total, 29 C57BL/6 (WT) and 29 HGF-Tg mice were used in this study. Traumatic ulcer of left mucosa was performed by abrasion using a n 15 surgery knife. Ulcer tissues and serum samples were collected on 5 th day, histological score, expression of inflammatory cells and serum cytokines expression were measured and analyzed. Results: There existed statistical significant difference in connective Ly6G positive cells and NF-кB positive expression, HGF-Tg mice showed lower number of positive cells ( p =0.048, p =0.020 ). Eotaxin ( t -test, p =0.002), MIP-1gamma ( t -test, p =0.011), BLC ( t -test, p =0.03),Eotaxin-2 ( t -test, p =0.027), RANTES ( t -test, p =0.038), Lix ( t -test, p =0.04) and IL-3 ( t -test, p =0.047) had statistical significance higher expression in HGF-Tg mice. No significant difference of blood T cells ( p =0.998), Neutrophils ( p =0.331),Macrophages ( p =0.470) and CD4+/CD8+ ratio ( p =0.451) between HGF-Tg and WT group. Conclusions: We observed that HGF-Tg animals presented less Ly6G-positive neutrophil infiltration, higher levels of circulating cytokines and less NF- к B expression in connective tissue, with a positive effect on the healing of oral traumatic ulcers. Key words: HGF, oral ulcer, cytokine, inflammation
MYB transcription factor CiMYB42 regulates limonoids biosynthesis in citrus
Authors: zhang pan , Liu Xiaofeng , Xu Xin , Wang Fusheng , Long Junhong , Shen Wanxia , Jiang Dong , Zhao Xiaochun 
Published: January 2020

Abstract
Backgrounds Limonoids, a major bioactive components, are produced by triterpenoids metabolic pathway. So far, the detailed biochemical reactions regarding to limonoid biosynthesis and their molecular regulation remain elusive. The identification of transcription factors that regulate limonoids biosynthetic pathways is not only necessary for understanding the regulatory mechanisms but also as a tool for manipulating biosynthetic genes for biotechnological applications.Results In this study, CiMYB42 transcription factor was isolated and identified. Multiple alignment analysis and phylogenetic analysis demonstrated that CiMYB42 is a typical R2R3MYB transcription factor and its amino acid is similar to that of AtMYB42 . The limonoids content was higher in the citrus sinensis and citrus grandis than other species. The diverse accumulation patterns also showed in different leaf developmental stages. Expression of CiMYB42 was significantly related to limonoids content and the expression of CiOSC in some of citrus varieties. CiMYB42 transgenic sweet orange resulted significantly change on limonoids contents. Noticeably, CiMYB42 -RNAi induced dwarf phenotype and mainly decreased nomilin accumulation. Overexpressing CiMYB42 mainly increased limonin content. Yeast one hybrid assay results indicated that CiMYB42 exclusively bind to the promoter of CiOSC. In brief, CiMYB42 involved in the limonoids biosynthesis through binding the promoter of CiOSC in citrus.Conclusions These results indicated that CiMYB42 is an important transcription activator involved in limonoids biosynthesis by regulating the expression of CiOSC . This is the first report elucidating the role of transcription factor in citrus limonoids biosynthesis. Our contributions will provide a reference to understanding regulatory mechanisms of R2R3MYB TFs in the triterpenoids biosynthetic pathway.
Spaceflight Induces Novel Regulatory Responses in Arabidopsis Seedling as Revealed by Combined Proteomic and Transcriptomic Analyses
Authors: Kruse Colin Peter Singer , Meyers Alexander D , Basu Proma , Hutchinson Sarahann , Luesse Darron R , Wyatt Sarah E. 
Published: January 2020

Abstract
Background: Understanding of gravity sensing and response is critical to long-term human habitation in space and can provide new advantages for terrestrial agriculture. To this end, the altered gene expression profile induced by microgravity has been repeatedly queried by microarray and RNA-seq experiments to understand gravitropism. However, the quantification of altered protein abundance in space has been minimally investigated.Results: Proteomic (iTRAQ-labelled LC-MS/MS) and transcriptomic (RNA-seq) analyses simultaneously quantified protein and transcript differential expression of three-day old, etiolated Arabidopsis thaliana seedlings grown aboard the International Space Station along with their ground control counterparts. Protein extracts were fractionated to isolate soluble and membrane proteins and analyzed to detect differentially phosphorylated peptides. In total, 968 RNAs, 107 soluble proteins, and 103 membrane proteins were identified as differentially expressed. In addition, the proteomic analyses identified 16 differential phosphorylation events. Proteomic data delivered novel insights and simultaneously provided new context to previously made observations of gene expression in microgravity. There is a sweeping shift in post-transcriptional mechanisms of gene regulation including RNA-decapping protein DCP5, the splicing factors GRP7 and GRP8, and AGO4. These data also indicate AHA2 and FERONIA as well as CESA1 and SHOU4 as central to the cell wall adaptations seen in spaceflight. Patterns of tubulin-a 1, 3,4 and 6 phosphorylation further reveal an interaction of microtubule and redox homeostasis that mirrors osmotic response signaling elements. The absence of gravity also results in a seemingly wasteful dysregulation of plastid gene transcription. Conclusions: The datasets gathered from Arabidopsis seedlings exposed to microgravity revealed marked impacts on post-transcriptional regulation, cell wall synthesis, redox/microtubule dynamics, and plastid gene transcription. The impact of post-transcriptional regulatory alterations represents an unstudied element of the plant microgravity response with the potential to significantly impact plant growth efficiency and beyond. What’s more, addressing the effects of microgravity on AHA2, CESA1, and alpha tubulins has the potential to enhance cytoskeletal organization and cell wall composition, thereby enhancing biomass production and growth in microgravity. Finally, understanding and manipulating the dysregulation of plastid gene transcription has further potential to address the goal of enhancing plant growth in the stressful conditions of microgravity.
Comparative transcriptome profiling reveals the cold stress responsiveness in two contrasting Chinese jujube cultivars
Authors: Author) Heying Zhou(Former Corresponding , Author) Xiaoming Pang(New Corresponding , He Ying , Zhu Yongsheng , Li Meiyu , Song Shuang , Bo Wenhao , Li Yingyue 
Published: January 2020

Abstract
Background Low temperature is a major factor influences the growth and development of Chinese jujube ( Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms for coping with different freezing stress conditions in jujube. To gain insight into the freezing-related molecular changes, we conducted comparative transcriptome analyses from the cold-sensitive cultivar ‘Dongzao’ and cold-tolerant cultivar ‘Jinsixiaozao’ using RNA-Seq. Results In our study, more than 20,000 genes were detected at chilling (4°C) and freezing (-10°C, -20°C, -30°C and -40°C) stress between two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars was 1831, 2030, 1993, 1845 and 2137 under the five treatments, respectively. Functional enrichment analysis suggested that metabolic pathway, response to stimulus and catalytic activity were significantly enriched at stronger freezing stress. Among them, nine DEGs participated in the pathway of Ca 2+ signal, thirty-two DEGs were identified to take part in sucrose metabolism, and other DEGs were identified to participate in the regulation of ROS, plant hormones and antifreeze protein. In addition, important transcription factors ( WRKY , AP2 / ERF , NAC and bZIP ) participating in the freezing stress were activated under different degrees of freezing stress. Conclusions Our research provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome levels in Z. jujuba , especially two cultivars with different cold tolerance. These results expanding our understanding on the complex molecular mechanism of jujube, which also provide new insights and candidate genes for genetic improvement of jujube tolerance to freezing stress.
Two Nucleoporin 98 homologous genes jointly participate in the regulation of starch degradation to enhance growth in Arabidopsis
Authors: Xiao Long , Jiang Shanshan , Huang Penghui , Chen Fulu , Wang Xu , Cheng Zhiyuan , Miao Yuchen , Liu Liangyu , Searle Iain , Liu Chunyan , Wu Xiaoxia , Fu Yong-Fu , Chen Qingshan , Zhang Xiaomei 
Published: January 2020

Abstract
Background: Starch is synthesized during the day for temporary storage in leaves and then degraded during the subsequent night to support plant growth and development. Impairment of starch degradation leads to stunted growth, even senescence and death. The nuclear pore complex is involved in many cellular processes, but its relationship with starch degradation is unclear until now. We previously identified two Nucleoporin98 ( Nup98 ) genes ( Nup98a and Nup98b ) redundantly regulated flowering through CONSTANS ( CO ) independent pathway. in Arabidopsis thaliana. The nup98a nup98b double mutant also showed severe senescence phenotypes. Results: We found that Nucleoporin 98 ( Nup98 ) participated in the regulation of sugar metabolism in leaves and in turn is involved in senescence regulation in Arabidopsis . We show that Nup98a and Nup98b redundantly function in the different steps of starch degradation, the nup98a nup98b double mutant accumulates more starch than wild type and has a severe early senescence phenotype compared to wild type. The expression of marker genes related to starch degradation was impaired in the nup98a nup98b double mutant, and indicator genes of carbon starvation and senescence expressed earlier in the nup98a nup98b double mutant than that in wild type plants, suggesting abnormality of energy metabolism was the cause of senescence of the nup98a nup98b double mutant. Addition of sucrose to the growth medium can rescue early senescence phenotype of the nup98a nup98b mutant. Conclusions: Our results provided a line of evidence on a novel role of the nuclear pore complex in energy metabolism related to growth and development, whereas Nup98 functioned in starch degradation conferring growth regulation in Arabidopsis .
Small Auxin Up RNAs influence the distribution of indole-3-acetic acid and play a potential role in increasing seed size in Euryale ferox Salisb.
Authors: Huang Zhiheng , Bao Ke , Jin Zonghui , Wang Qian , Duan Huifang , Zhu Yayin , Zhang Sen , Wu Qinan 
Published: January 2020

Abstract
Background: Aquatic Euryale ferox Salisb. is an economically important crop in China and India. Unfortunately, low yield limitations seriously hinder market growth. Here, we generated a new hybrid line (HL) by crossing South Gordon Euryale and North Gordon Euryale (WT). The hybrid showed significant heterosis, including a non-prickly, thin-coated, large seed. However, the growth mechanism in HL is unclear.Results: Both concentration and localization of indole-3-acetic acid (IAA) at two growth stages of fruits of WT and HL were detected by LC-MS and immunofluorescence. Although IAA content between the two lines did not differ, IAA distribution was significantly different. To elucidate the mechanism underlying this difference, RNA-Seq was performed on young fruits at the two selected growth stages, and differentially expressed genes related to the auxin transduction pathway were selected for further analysis. Conclusion: hybrid Euryale ferox Salisb. expressed significant heterosis, resulting in non-prickly, thin-coated, large seeds, which accounted for the significantly larger yield of HL than that of WT. Our study indicated that Small Auxin Up RNAs-mediated localization of IAA regulates seed size in Euryale ferox Salisb. We found that some SAURs may act as a positive mediator of the auxin transduction pathway, thereby contributing to the observed heterosis.