bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative analysis of retrograde intrarenal surgery and modified Ultra-mini percutaneous nephrolithotomy in management of lower pole renal stones (1.5-3.5 cm)
Authors: Li Zhuohang , Lai Cong , Shah Arvind K. , Xie Weibin , Liu Cheng , Huang Li , Li Kuiqing , Yu Hao , Xu Kewei
Published: January 2020

Background：To compare the safety and efficacy of retrograde intrarenal surgery (RIRS) and modified Ultra-mini percutaneous nephrolithotomy (UMP) in semi-supine combined lithotomy position for the management of 1.5-3.5 cm lower pole renal stones (LPSs). Methods: A total of 63 patients with 1.5-3.5 cm LPSs who underwent RIRS (n= 33) or modified UMP (n= 30) in diameter between January 2017 and January 2019 were analyzed retrospectively. Modified UMP was performed in semi-supine combined lithotomy position and a 9.5/11.5 F ureteral access sheath (UAS) was inserted during the procedure in order to maintain low pelvic pressure and to facilitate the removal of stone fragments. Base-line parameters, stone characteristics, illness condition, operation time, postoperative hemoglobin (Hb) drop, postoperative creatinine (Cr) elevation, length of hospital stay, length of postoperative hospital stay, stone-free rate (SFR) and complications were compared between the two groups. Results: There were no significant differences between the two groups in base-line parameters, stone characteristics and illness condition. The mean operating time of RIRS group was longer than UMP group (95.61 ± 21.9 vs. 55.0 ± 16.1 min, p< 0.001). The mean postoperative Hb drop was less in RIRS group (7.42 ± 4.7 vs. 15.70 ± 9.8 g/L, p< 0.001). The length of hospital stay and postoperative hospital stay for RIRS were shorter than UMP (4.76 ± 1.1 vs. 5.83 ± 0.8 d, p< 0.001, 2.97 ± 0.9 vs. 4.07 ± 0.9 d, p< 0.001). The Early SFR was higher in UMP group (54.5 vs. 80.0%, p< 0.050) while SFR at 1-month and 3-months postoperatively was similar in both groups (p= 0.504, p= 0.675). There were no significant differences between the two groups in complications (p= 0.228). Conclusion：For patients with 1.5-3.5 cm LPSs, both modified UMP and RIRS are safe and viable. The modified UMP technique was used in this study, application semi-supine combined lithotomy position and the retention of UAS can improve the surgical efficiency and maintain low pressure perfusion in the kidney, which resulted in superior treatment efficacy. Therefore, we highly recommend this technique for LPSs with heavy stone burdens.
Reactivity and reproducibility of accelerometer-based sedentary behavior and physical activity in two measurement periods: Results of a feasibility randomized-controlled study
Authors: Ullrich Antje , Baumann Sophie , Voigt Lisa , John Ulrich , Ulbricht Sabina
Published: January 2020

Background: The aims of the study were to investigate measurement reactivity in sedentary behavior (SB), physical activity (PA), and accelerometer wear time in two measurement periods, to examine the reproducibility of these outcomes and to quantify measurement reactivity as a confounder for the reproducibility of SB and PA data.Methods: A total of 136 participants (65% women, mean age = 54.6 years, study period 02/2015 to 08/2016) received 7-day accelerometry at baseline and after 12 months. Latent growth models were used to identify measurement reactivity in each period. Intraclass correlations (ICC) were calculated to examine the reproducibility using two-level mixed-effects linear regression analyses. Results: At both measurement periods, participants increased time spent in SB (b=2.4 min/d; b=3.8 min/d), reduced time spent in light PA (b=2.0 min/day; b=3.2 min/d), but did not change moderate-to-vigorous PA. Participants reduced accelerometer wear time (b=5.2 min/d) only at baseline. The ICC coefficients ranged from 0.42 (95% CI=0.32-0.53) for accelerometer wear time to 0.74 (95% CI=0.68-0.79) for SB. In none of the regression models, a reactivity indicator was identified as a confounder for the reproducibility of SB and PA data.Conclusions: The results show that measurement reactivity differentially influences SB and PA in two measurement periods. Although 7-day accelerometry seems to be a reproducible measure of SB and PA, our findings highlight the importance of accelerometer wear time as a crucial confounder when using accelerometry in monitoring SB and PA, planning interventions, and analyzing SB and PA data.Clinical trial registration number: NCT02990039 (retrospectively registered); December 12, 2016
Library preparation and MiSeq sequencing for the genotyping-by-sequencing of the Huntington disease HTT exon one trinucleotide repeat and the quantification of somatic mosaicism
Authors: Ciosi Marc , Cumming Sarah A. , Alshammari Asma M. , Symeonidi Efthymia , Herzyk Pawel , McGuinness David , Galbraith Julie , Hamilton Graham , Monckton Darren G.
Published: January 2020

Huntington disease \(HD) is an autosomal dominant neurodegenerative disorder caused by the expansion of a CAG repeat in the first exon of the _HTT_ gene. Affected individuals inherit more than 40 repeats and the CAG repeat is genetically unstable in both the germline and soma. Molecular diagnosis and genotyping of the CAG repeat is traditionally performed by estimation of PCR fragment size. However, this approach is complicated by the presence of an adjacent polymorphic CCG repeat and provides no information on the presence of variant repeats, flanking sequence variants or on the degree of somatic mosaicism. To overcome these limitations, we have developed an amplicon-sequencing protocol that allows the sequencing of hundreds of samples in a single MiSeq run. The composition of the _HTT_ exon one trinucleotide repeat locus can be determined from the MiSeq sequencing reads generated. With sufficient sequencing depth, such MiSeq data can also be used to quantify the degree of somatic mosaicism of the _HTT_ CAG repeat in the tissue analysed.
Dilation of the Cystic Duct Confluence in Laparoscopic Common Bile Duct Exploration and stone extraction for Patients with Secondary Choledocholithiasis
Authors: Yang Xiao-Bin , Xu An-Shu , Li Jian-Gang , Xu Yong-Ping , Xu De-Song , Fu Chao-Chun , Deng Da-Bo , Li Jie , Zhang Ma-Zhong
Published: January 2020

Objectives: Many options exist in the management of cholelithiasis and secondary choledocholithiasis. Among them, laparoscopic common bile duct exploration (LCBDE) with the choledocotomy followed by laparoscopic cholecystectomy has gained popularity. However, efforts should be made for minimally invasive or non-invasive to the common bile duct (CBD). For this purpose, we modified the surgical modality of laparoscopic transcystic approach by dilating the cystic duct confluence in CBD exploration (LTD-CBDE). Based on our preliminary experience, the aim of this work was to assess the feasibility, safety and effectivity of LTD-CBDE.Patients and methods: Sixty-eight patients were arbitrarily offered new LTD-CBDE technique from December 2015 to April 2018. During the surgery, we dilated the cystic duct confluence with separation forceps and/or the columnar dilation balloon. Subsequently, the CBD exploration and stone extraction were performed with choledochoscope. The entrance of CBD was covered with cystic duct stump wall and primarily closed at the end of surgery.Results: 49 females and 19 males with cholelithiasis and secondary choledocholithiasis were included. The mean age was 53 years old (18 to 72 yr). Of which, 62 cases (91.2%) were performed with LTD-CBDE techniques successfully, bile leakage was observed in 3 cases (4.4%). The mean operation time was 106 minutes and the mean hospital stay was 5.9 days. As for the other 6 patients, 3 cases were converted to open cholecystectomy due to severe fibrosis, unclear anatomical structure at the Calot’s triangle (n=2) and Mirizze syndrome (n=1); LCBDE were performed in 3 patients due to cystic duct atresia (n=2) and low level of the gallbladder duct into CBD (n=1). These patients had smooth postoperative course. None of the patients presented radiological evidence of retained CBD stone on the postoperative follow-up in 43/68 (40 cases used LTD-CBDE) patients one year later.Conclusion: The current work suggests that LTD-CBDE for the management of cholelithiasis and secondary choledocholithiasis is a feasible, safe and effective technique with a low rate of complications. It offers another alternative for surgeons to treat patients in similar scenarios. However, additional randomized, controlled study is further needed to demonstrate its efficacy, safety, and impact on CBD stenosis.
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

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

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

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

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

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

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

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

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

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

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

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

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.
Economics of the Management of Craniospinal Chordoma and Chondrosarcoma and the Feasibility of the Bundled Payment Model
Authors: Aljuboori Zaid , Ugiliweneza Beatrice , Wang Dengzhi , Andaluz Norberto , Boakye Maxwell , Williams Brian
Published: January 2020

Background Healthcare expenditures are continuously rising in the United States. The Centers for Medicare and Medicaid Services (CMS) created a new reimbursement model called the “Bundled Payment for Care Improvement (BPCI)”. This model reimburses providers a predetermined payment in advance to cover all possible services delivered to patients within a certain time window. Chordoma and Chondrosarcoma are locally aggressive malignant primary bony tumors. Treatment includes surgical resection and radiotherapy with substantial risk for recurrence which necessitates monitoring and further treatment. We assess the BPCI model in complex neurosurgical diseases. Methods We obtained data from the United States MarketScan database. Patients were identified patients using the International Classification of Diseases 10 codes. Results A total of 2041 patients were included. 1412 patients had cranial, 343 patients had a mobile spine, and 286 patients had sacrococcygeal chordoma and chondrosarcoma. For Index hospitalization, the median length of stay (days) was 4, 6, and 7, mean total payments were ($58,130), ($84,854), and ($82,440), and complication rates were 30%, 35%, and 43% for groups 1, 2, and 3, respectively. The payments during the first 6 months after discharge were comparable to the amounts reimbursed during the index hospitalization for all groups. Conclusion The management of craniospinal chordoma and chondrosarcoma is costly and sustained over time. The success of BPCI requires a joint effort between insurers and hospitals. It should consider patients’ comorbidities, the complexity of the disease. Finally, adoption of quality improvement programs by hospitals can help with cost reduction.
Mapping Chronic Disease Prevalence based on Medication Use and Socio-demographic variables: an Application of LASSO in healthcare in the Netherlands
Authors: Füssenich Koen , Boshuizen Hendriek C. , Nielen Markus M.J. , Buskens Erik , Feenstra Talitha L.
Published: January 2020

Objectives Policymakers generally lack sufficiently detailed health information to develop localized health policy plans. Chronic disease prevalence mapping is difficult as accurate direct sources are often lacking. Improvement is possible by adding extra information such as medication use and demographic information to identify disease. The aim of the current study was to use a LASSO (Least Absolute Shrinkage and Selection) model on a wide set of variables including medication use to obtain small geographic area prevalence estimates for four common chronic diseases and investigate regional patterns of disease. Methods Administrative hospital records and general practitioner registry data were linked to medication use and socio-economic characteristics. The training set (n=707021) contained GP diagnosis and/or hospital admission diagnosis as the standard for disease prevalence. For the entire Dutch population (n = 16,777,888), all information except GP and hospital admission was available. A LASSO operator regression model for binary outcomes was used to select variables strongly associated with disease. Dutch municipality (non-)standardized prevalence estimates for stroke, CHD, COPD and diabetes were then based on the average of individual predicted probabilities. Results Adding medication use data as a predictor substantially improves model performance. Estimates at the municipality level are best for diabetes with a weighted percentage error (WPE) of 6.8%, and worst WPE for COPD, with 14.5%. Disease prevalence has clear regional patterns, also after standardization for age. Conclusion Adding medication use as an indicator of disease prevalence next to socio-economic variables substantially improved estimates at the municipality level. The resulting individual disease probabilities can be aggregated into any desired regional level and provide a useful tool to identify regional patterns and subsequently inform local policy.
Gut microbiota regulates autism-like behavior by mediating vitamin B6 metabolism in EphB6-deficient mice
Authors: Li Jian-Ming , Li Ying , Luo Zheng-Yi , Hu Yu-Ying , Bi Yue-Wei , Yang Jian-Ming , Zou Wen-Jun , Song Yun-Long , Li Shi , Shen Tong , Li Shu-Ji , Huang Lang , Zhou Ai-Jun , Gao Tian-Ming
Published: January 2020

Background Autism spectrum disorder (ASD) is a developmental disorder with limited effective pharmacological treatments for the core autistic symptoms so far. Increasing evidences, especially the clinical studies in ASD patients, suggest a functional link between gut microbiota and development of ASD. However, the mechanisms linking gut microbiota and brain dysfunctions (gut-brain axis) in ASD are still not well-established. With genetic mutations and down-regulated expression in patients with ASD, EPHB6, which is also important in homeostasis of gut, has been generally considered to be a candidate gene for ASD. Nonetheless, the role and mechanism of EPHB6 involved in regulating gut microbiota and development of ASD have been unclear. Results Here, we found deletion of EphB6 induced autism-like behavior and disturbed gut microbiota in mice. More importantly, transplanting fecal microbiota from EphB6-deficient mice resulted in autism-like behavior in antibiotics-treated C57BL/6J mice. Meanwhile, transplanting fecal microbiota from wild-type mice ameliorated autism-like behavior in EphB6-deficient mice. At the metabolic levels, disturbed gut microbiota led to vitamin B6 and dopamine defects in EphB6-deficient mice. At the cellular levels, excitation/inhibition (E/I) imbalance in medial prefrontal cortex was induced by gut microbiota-mediated defects of vitamin B6 metabolism in EphB6-deficient mice. Conclusions Our study uncovers a key role for gut microbiota in regulation of autism-like social behavior by mediating vitamin B6 metabolism, dopamine synthesis and E/I balance in EphB6-deficient mice, suggesting new strategies for understanding and treatment of ASD.
Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in antibiotic use, time to optimal antibiotics, and length of stay.
Authors: Torres-Miranda Daisy , Akselrod Hana , Karsner Ryan , Secco Alessandra , Silva-Cantillo Diana , Siegel Marc O. , Roberts Afsoon D. , Simon Gary L.
Published: January 2020

Rapid and accurate diagnostic tools are needed for appropriate management of infectious diarrhea. We evaluated the impact of the introduction of rapid multiplex PCR testing using the FilmArray gastrointestinal (GI) panel (BioFire Diagnostics, LLC, Salt Lake City, UT) at our institution, and compared the results to those of standard stool cultures. The most common pathogens detected by the FilmArray GI panel were Clostridium difficile (55.0%), Campylobacter species (20.9%), Salmonella species (12.4%), and Shigella/EIEC species (12.4%). Rates of reproducibility in stool culture for these pathogens ranged from 56.3% to 77.8%. Co-detection of two or more organisms was common (24.2%), most commonly involving EPEC, EAEC, ETEC, and STEC. The time from arrival in the Emergency Department to discharge or admission to the hospital was unchanged after the introduction of FilmArray GI panel, but length of hospital stay was shorter (3 vs. 7.5 days, p=0.0002) for the FilmArray group. The time to empiric antibiotics did not differ significantly, but optimal antibiotics were started earlier after introduction of the FilmArray GI panel (hospital day 1 vs. 2, p<0.0001). More patients were discharged without antibiotics after introduction of the FilmArray GI panel (14.0% vs. 4.5%; p<0.001). Our results demonstrate that the FilmArray GI panel is an important tool for improving both patient care and antibiotic stewardship, despite the tendency for positive results with multiple pathogens.
Number of remaining teeth and its association with educational level in Chilean adults: data from the National Health Survey 2016-2017
Authors: Margozzini Paula , Berrios Rodrigo , García-Huidobro Rosario , Véliz Claudia , Valle Carolina del , Vargas Juan Pablo , Padilla Oslando , Ortuno Duniel
Published: January 2020

Background: Several population studies have addressed oral health inequity-related issues. Edentulism, functional dentition and number of remaining teeth have been linked to different socioeconomic level measurements. The aim of this study was to evaluate the association between educational level (EL) and tooth loss in the Chilean population aged 15 years old and above, based on the recent data collected from the 2016-2017 National Health Survey (ENS 2016-2017). Methods: The sample for this cross-sectional study comprised 5473 subjects. The main independent variable in the study was educational level (LEL: low, MEL: medium, HEL: high). In order to measure tooth loss number of remaining teeth, edentulism and functional dentition were considered. Based on a multivariate logistic regression, it was possible to obtain odds ratios (OR) and, therefore, to assessing the condition of dentition according to the subject’s EL. As to the number of teeth variable, multiple linear regressions were conducted. The analyses were carried out in the SPSS 24.0 program considering the complex sampling design of ENS 2016-2017. Results: When comparing LEL subjects with HEL subjects, the adjusted difference in the number of remaining teeth was 3.11 for maxilla and 1.72 for mandible. An individual with a LEL had a 7.51 [3.50-16.10] and 6.06 [2.68-13.68] times higher risk of upper edentulism and lower edentulism than a HEL individual respectively. Regarding functional dentition, the adjusted OR in HEL subjects was 13.33 [8.02-22.15] and in MEL subjects was 2.81 [2.03-3.87], compared to LEL results. Conclusions: LEL was associated with a significant tooth loss in the Chilean population. Regardless of age, subjects with a LEL obtained a lower mean of number of remaining teeth, higher prevalence of edentulism and lower prevalence of functional dentition.
What might it cost to increase soil organic carbon using no-till on U.S. cropland
Authors: Sperow Mark
Published: January 2020

Background Existing research provides estimates of the biophysical potential for increasing soil organic carbon (SOC) stock, however additional research is needed to enhance our understanding of the economic potential for agricultural soils to offset or help reduce CO 2 emissions. This study derives the marginal cost to increase SOC sequestration by combining SOC sequestration potential estimates developed using the Intergovernmental Panel on Climate Change (IPCC) factors with an existing payment scheme that was designed to increase no-till (NT) adoption on U.S. cropland. The marginal costs of increasing SOC is a function of the amount of SOC that could be increased through NT and the expected cost to landowners of changing management to use NT. Results The variability in SOC sequestration rates due to different land-use, management histories, climate, and soils, combined with the 48 unique payment rates to adopt NT, yield over 5,000 unique marginal cost values for increasing SOC sequestration. Nearly 95 percent of the biophysical potential SOC sequestration increase on U.S. cropland (140.1 Tg CO 2 yr -1 ) could be captured for a cost less than $100 Mg -1 CO 2. An estimated 64 to 93 percent of the biophysical potential could be captured for less than the low and high estimated costs to capture CO 2 for geologic storage of $36.36 to $86.06 Mg -1 CO 2 , respectively. Conclusions Decreasing tillage intensity through adoption of no-till agricultural offers a cost-effective way to offset a portion of increasing global CO 2 emissions. This research demonstrates that increasing SOC stocks through NT adoption can offset CO 2 emissions at a lower cost than some other options for preventing CO 2 from entering the atmosphere.
Detection of Mycobacteria in Paraffin-Embedded Ziehl–Neelsen-Stained Tissues using Digital Pathology
Authors: Sua Luz Fernanda , Bolaños Jhon Edwar , Maya Juliana , Sanchez Aura , Medina Giovanna , Zúñiga-Restrepo Valeria , Fernández-Trujillo Liliana
Published: January 2020

BackgroundTuberculosis is the first infection-related cause of death worldwide. Early diagnosis of paucibacillary tuberculosis represents a challenge, even with direct tissue examination. Digital pathology allows the digital analysis of tissues to identify microorganisms. We aim to develop a program to detect and quantify typical and atypical mycobacteria in paraffin-embedded Ziehl–Neelsen-stained tissues.MethodsProgram development: The building of the program, named Pat-Scan, included pathology, systems engineering, and scientific applications. The iScan Coreo Au scanner® was used, and 9 variables were adjusted: Temp Directory Path, Output Directory Path, Server Path, Focus Approach, Focus Mode, AOI Detection Approach, Scan at, No. of Z Layers, and Z Delta. Software parameter settings: Brightness, contrast, sharpness, and red/green/blue. Control module scan and analysis: Ten Ziehl–Neelsen-stained samples were fragmented into 2,000 images and analyzed by a multidisciplinary team to validate the reproducibility of the bacilli images in the tissue, as detected by the software.ResultsPat-Scan included software and a scanner that were used to detect and quantify bacilli in paraffin-embedded Ziehl–Neelsen-stained tissues. HD quality image segmentation was performed, and nine planes of the Z-axis were scanned with a 1-micron distance between planes. Image magnification: 40x–80x. Scan time: 10–12 minutes. All samples containing mycobacteria were successfully analyzed by the scanner, and the bacilli could be detected; these results were validated by expert pathologists by microscopy examination, and the presence of bacilli was confirmed in all cases.ConclusionsPat-Scan allowed the identification and quantification of mycobacteria in paraffin-embedded Ziehl–Neelsen-stained tissues, offering a reproducible diagnostic method that reduces the time for diagnosis and does not affect precision. Further validation is needed for application in the clinical setting.