bluuebunny/crossref_metadata_2025_split huggingface dataset:
Induction of an incomplete autophagic response by cancer-preventive geranylgeranoic acid (GGA) in a human hepatoma-derived cell line
Authors: Okamoto Kyoko , Sakimoto Yoko , Imai Katsuyuki , Senoo Haruki , Shidoji Yoshihiro 
Published: July 2011

GGA (geranylgeranoic acid) is a natural polyprenoic acid, derivatives of which has been shown to prevent second primary hepatoma. GGA induces mitochondria-mediated PCD (programmed cell death), which may be relevant to cancer prevention. To gain further insights into GGA-induced PCD, autophagy processes were examined in human hepatoma-derived HuH-7 cells. Treatment of HuH-7/GFP (green fluorescent protein)–LC3 cells with GGA induced green fluorescent puncta in the cytoplasm within 30 min and their massive accumulation at 24 h. After 15 min of GGA treatment, a burst of mitochondrial superoxide production occurred and LC3β-I was appreciably converted into LC3β-II. GGA-induced early stages of autophagy were unequivocally confirmed by electron-microscopic observation of early/initial autophagic vacuoles. On the other hand, LC3β-II as well as p62/SQSTM1 (sequestosome 1) continuously accumulated and co-localized in the cytoplasmic puncta after GGA treatment. Furthermore, GGA treatment of HuH-7/mRFP (monomeric red fluorescent protein)–GFP–LC3 cells showed yellow fluorescent puncta, whereas glucose deprivation of the cells gave red fluorescent puncta. These results strongly suggest that GGA induces the initial phase of autophagy, but blocks the maturation process of autolysosomes or late stages of autophagy, insomuch that GGA provides substantial accumulation of autophagosomes under serum-starvation conditions in human hepatoma cells.
RseqFlow: workflows for RNA-Seq data analysis
Authors: Wang Ying , Mehta Gaurang , Mayani Rajiv , Lu Jingxi , Souaiaia Tade , Chen Yangho , Clark Andrew , Yoon Hee Jae , Wan Lin , Evgrafov Oleg V. , Knowles James A. , Deelman Ewa , Chen Ting 
Published: July 2011

Abstract
Summary: We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps.
Availability and implementation: http://genomics.isi.edu/rnaseq
Contact: wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Sevoflurane Protects Ventricular Myocytes from Ca2+Paradox-mediated Ca2+Overload by Blocking the Activation of Transient Receptor Potential Canonical Channels
Authors: Kojima Akiko , Kitagawa Hirotoshi , Omatsu-Kanbe Mariko , Matsuura Hiroshi , Nosaka Shuichi 
Published: July 2011

Background
Volatile anesthetics produce cardioprotective action by attenuating cellular Ca2+ overload. The Ca2+ paradox is an important model for studying the mechanisms associated with Ca2+ overload-mediated myocardial injury, and was recently found to be mediated by Ca2+ entry through the transient receptor potential canonical channels upon Ca2+ repletion. This study investigated the effect of sevoflurane on cellular mechanisms underlying the Ca2+ paradox.

Methods
The Ca2+ paradox was examined in fluo-3 or mag-fluo-4-loaded mouse ventricular myocytes using confocal laser scanning microscope, upon Ca2+ repletion after 15 min of Ca2+ depletion in the absence and presence of sevoflurane.

Results
The Ca2+ paradox was evoked in approximately 65% of myocytes upon Ca2+ repletion, as determined by an abrupt elevation of cytosolic Ca2+ accompanied by hypercontracture. The Ca2+ paradox was significantly suppressed by sevoflurane administered for 3 min before and during Ca2+ repletion (Post) or during Ca2+ depletion and repletion (Postlong), and Postlong was more beneficial than Post application. The sarcoplasmic reticulum Ca2+ levels gradually decreased during Ca2+ depletion, and the Ca2+ paradox was readily evoked in myocytes with reduced sarcoplasmic reticulum Ca2+ levels. Postlong but not Post application of sevoflurane prevented decrease in sarcoplasmic reticulum Ca2+ levels by blocking Ca2+ leak through ryanodine receptors. Whole cell patch-clamp recordings revealed that sevoflurane rapidly blocked thapsigargin-induced transient receptor potential canonical currents.

Conclusions
Sevoflurane protects ventricular myocytes from Ca2+ paradox-mediated Ca2+ overload by blocking transient receptor potential canonical channels and by preventing the decrease in sarcoplasmic reticulum Ca2+ levels, which is associated with less activation of transient receptor potential canonical channels.
Enhancing Arabidopsis Leaf Growth by Engineering the BRASSINOSTEROID INSENSITIVE1 Receptor Kinase
Authors: Oh Man-Ho , Sun Jindong , Oh Dong Ha , Zielinski Raymond E. , Clouse Steven D. , Huber Steven C. 
Published: July 2011

Abstract
The BRASSINOSTEROID INSENSITIVE1 (BRI1) receptor kinase has recently been shown to possess tyrosine kinase activity, and preventing autophosphorylation of the tyrosine-831 regulatory site by site-directed mutagenesis enhances shoot growth. In this study, we characterized the increased leaf growth of Arabidopsis (Arabidopsis thaliana) plants expressing BRI1(Y831F)-Flag compared with BRI1-Flag (both driven by the native promoter and expressed in the bri1-5 weak allele background) and provide insights into the possible mechanisms involved. On average, relative leaf growth rate was increased 16% in the Y831F plants (in the bri1-5 background), and the gain of function of the Y831F-directed mutant was dominant in the wild-type background. Leaves were larger as a result of increased cell numbers and had substantially increased vascularization. Transcriptome analysis indicated that genes associated with brassinolide biosynthesis, secondary cell wall biosynthesis and vascular development, and regulation of growth were altered in expression and may contribute to the observed changes in leaf architecture and whole plant growth. Analysis of gas exchange and chlorophyll fluorescence indicated that Y831F mutant plants had higher rates of photosynthesis, and metabolite analysis documented enhanced accumulation of starch, sucrose, and several amino acids, most prominently glycine and proline. These results demonstrate that mutation of BRI1 can enhance photosynthesis and leaf growth/vascularization and may suggest new approaches to increase whole plant carbon assimilation and growth.
Predictors of caregiver burden in caregivers of individuals with dementia
Authors: Kim Heejung , Chang Mido , Rose Karen , Kim Sunha 
Published: July 2011

kim h., chang m., rose k. & kim s. (2011) Predictors of caregiver burden in caregivers of individuals with dementia. Journal of Advanced Nursing 68(4), 846–855.AbstractAims.  This article is a report on a study of the multidimensional predictors of caregiver burden in caregivers of individuals with dementia using nationally representative data.Background.  Caregiver burden affects the health of both caregivers and their care‐recipients. Although previous studies identified various predictors of caregiver burden, these predictors have not been confirmed in nationally representative population.Methods.  Data for this secondary analysis was provided by the National Alliance for Caregiving, American Association of Retired Persons. The data were collected through a telephone survey of randomly selected adults in seven states in 2003 (weight adjusted n = 302). Descriptive statistics, inter‐correlation analysis and a hierarchical multiple regression analysis were performed.Results/findings.  Disease‐related factors were the most significant predictors, explaining 16% of caregiver burden; these were followed by caregiver socio‐demographical factors and caregiving‐related factors (F = 21·28, P < 0·01). Significant individual predictors were impairment of activities of daily living or instrumental activities of daily living, the number of hours of caregiving, use of coping strategies, co‐residence, spousal status and caregiver gender (P < 0·05).Conclusion.  Impaired function in care‐recipients predicts caregiver burden, and also interacts with demographical‐ and caregiving‐related factors. Thus, it will be beneficial to both care‐recipients and caregivers to target nursing interventions and community services to improve the functional abilities of individuals with dementia.
Stillbirth Collaborative Research Network: design, methods and recruitment experience
Authors: Parker Corette B. , Hogue Carol J. R. , Koch Matthew A. , Willinger Marian , Reddy Uma M. , Thorsten Vanessa R. , Dudley Donald J. , Silver Robert M. , Coustan Donald , Saade George R. , Conway Deborah , Varner Michael W. , Stoll Barbara , Pinar Halit , Bukowski Radek , Carpenter Marshall , Goldenberg Robert ,   for the Stillbirth Collaborative Research Network
Published: July 2011

SummaryParker CB, Hogue CJR, Koch MA, Willinger M, Reddy UM, Thorsten VR, Dudley DJ, Silver RM, Coustan D, Saade GR, Conway D, Varner MW, Stoll B, Pinar H, Bukowski R, Carpenter M, Goldenberg R for the Stillbirth Collaborative Research Network. Stillbirth Collaborative Research Network: design, methods and recruitment experience. Paediatric and Perinatal Epidemiology 2011; 25: 425–435.The Stillbirth Collaborative Research Network (SCRN) has conducted a multisite, population‐based, case–control study, with prospective enrolment of stillbirths and livebirths at the time of delivery. This paper describes the general design, methods and recruitment experience. The SCRN attempted to enrol all stillbirths and a representative sample of livebirths occurring to residents of pre‐defined geographical catchment areas delivering at 59 hospitals associated with five clinical sites. Livebirths <32 weeks gestation and women of African descent were oversampled. The recruitment hospitals were chosen to ensure access to at least 90% of all stillbirths and livebirths to residents of the catchment areas. Participants underwent a standardised protocol including maternal interview, medical record abstraction, placental pathology, biospecimen testing and, in stillbirths, post‐mortem examination. Recruitment began in March 2006 and was completed in September 2008 with 663 women with a stillbirth and 1932 women with a livebirth enrolled, representing 69% and 63%, respectively, of the women identified. Additional surveillance for stillbirths continued until June 2009 and a follow‐up of the case–control study participants was completed in December 2009.Among consenting women, there were high consent rates for the various study components. For the women with stillbirths, 95% agreed to a maternal interview, chart abstraction and a placental pathological examination; 91% of the women with a livebirth agreed to all of these components. Additionally, 84% of the women with stillbirths agreed to a fetal post‐mortem examination. This comprehensive study is poised to systematically study a wide range of potential causes of, and risk factors for, stillbirths and to better understand the scope and incidence of the problem.
Hypothalamic–pituitary–adrenal axis suppression in asthmatic children on inhaled and nasal corticosteroids: is the early‐morning serum adrenocorticotropic hormone (ACTH) a useful screening test?
Authors: Zöllner Ekkehard W. , Lombard Carl , Galal Ushma , Hough Stephen , Irusen Elvis , Weinberg Eugene 
Published: July 2011

To cite this article: Zöllner EW, Lombard C, Galal U, Hough S, Irusen E, Weinberg E. Hypothalamic–pituitary–adrenal axis suppression in asthmatic children on inhaled and nasal corticosteroids: is the early‐morning serum adrenocorticotropic hormone (ACTH) a useful screening test? Pediatr Allergy Immunol 2011; 22: 614–620.AbstractBackground:  Hypothalamic–pituitary–adrenal axis suppression (HPAS) in asthmatic children treated with inhaled corticosteroids (ICS), with or without nasal steroids (NS), may be more common than previously thought. Only dynamic testing will identify children at risk of adrenal crisis. It is impractical to test all asthmatic children for HPAS with a gold standard adrenal function test, i.e. the metyrapone or insulin tolerance test.Objective:  To determine which clinical or biochemical parameter is the most useful screening test for HPAS in asthmatic children.Methods:  Twenty‐six asthmatic children, 5–18 yr old, on ICS ± NS, not treated with oral or topical steroids in the preceding year were recruited. Height, weight, height velocity, weight velocity and a change in systolic blood pressure from the recumbent to the standing position (ΔSBP) were recorded. Early‐morning urine for urinary free cortisol (UFC) and urinary cortisol metabolites (UCM) was collected. UFC was analysed by both a chemiluminescent assay and gas chromatography/mass spectrometry (GC‐MS). Morning serum cortisol and adrenocorticotropic hormone (ACTH) levels were measured. The overnight metyrapone test was performed if the fasting morning serum cortisol was >83 nmol/l. HPAS was diagnosed if the ACTH failed to rise >100 pg/ml after metyrapone. Spearman correlation coefficients (r) were calculated between the post‐metyrapone ACTH and each variable. A receiver‐operating characteristics (ROC) curve was drawn for the most promising test, and the diagnostic performance was calculated.Results:  All clinical and biochemical parameters investigated were weakly and non‐significantly correlated with the post‐metyrapone ACTH, except for the morning serum ACTH (r = 0.68; p <0.001). The best discrimination between those who have and those who do not have HPAS is a morning serum ACTH level of 11.7 pg/ml. This corresponds to a sensitivity of 0.89 (0.57–0.98), a specificity of 0.77 (0.53–0.90), a positive predictive value of 0.67 (0.39–0.87), a negative predictive value of 0.93 (0.69–0.99), an accuracy of 0.81 (0.61–0.94), a positive likelihood ratio of 3.78 (1.68–9.49) and a negative likelihood ratio of 0.15 (0.03–0.60).Conclusions:  The morning serum ACTH level was found to be the most useful screening test to detect HPAS in this sample of children receiving ICS ± NS. A larger study should be undertaken to refine the diagnostic precision of the morning serum ACTH level.
Safety of pre‐engraftment prophylactic foscarnet administration after allogeneic stem cell transplantation
Authors: Ishiyama K. , Katagiri T. , Ohata K. , Hosokawa K. , Kondo Y. , Yamazaki H. , Takami A. , Nakao S. 
Published: July 2011

K. Ishiyama, T. Katagiri, K. Ohata, K. Hosokawa, Y. Kondo, H. Yamazaki, A. Takami, S. Nakao. Safety of pre‐engraftment prophylactic foscarnet administration after allogeneic stem cell transplantation. Transpl Infect Dis 2011. All rights reserved
Abstract: Human herpesvirus‐6 (HHV‐6) is a major cause of limbic encephalitis with a dismal prognosis after allogeneic hematopoietic stem cell transplantation (SCT). Because our previous trial of preemptive therapy with foscarnet sodium (phosphonoformic acid; PFA) failed to prevent HHV‐6 encephalitis, we conducted a prospective study to examine the safety of prophylactic PFA administration and elucidate the changes in the plasma HHV‐6 DNA levels in the early post‐SCT period. Plasma HHV‐6 DNA was measured thrice weekly from day 6. PFA, 90 mg/kg/day, was administered from days 7 to 21 after bone marrow or peripheral blood SCT and to day 25 after umbilical cord blood transplantation. Of the 10 patients enrolled, 2 dropped out of the study, 1 because of early death, and 1 with a low glomerular filtration rate. Grade 3 or greater adverse events occurred in 9 of the 10 prophylactic PFA patients and in 7 of the 10 control patients who had clinical backgrounds similar to the study subjects and underwent SCT during the same period. Neurological disorders developed in none of the study subjects but in 4 of the 10 control patients, including 2 with HHV‐6 encephalitis. HHV‐6 reactivation occurred in 3 of the 10 study subjects. The prophylactic PFA regimen was thus safe and it may reduce the risk of limbic encephalitis, but is not considered to be potent enough to prevent HHV‐6 reactivation.
Endoscopic papillary large balloon dilation in Billroth II gastrectomy patients with bile duct stones
Authors: Choi Cheol Woong , Choi Jung Sik , Kang Dae Hwan , Kim Bong Gap , Kim Hyung Wook , Park Su Bum , Yoon Ki Tae , Cho Mong 
Published: July 2011

AbstractBackground and Aims:  Patients with Billroth II (B‐II) gastrectomy present technical difficulties during endoscopic stone removal due to altered anatomy. Although endoscopic sphincterotomy alone or endoscopic balloon dilation alone has been used for removal of bile duct stones in patients with B‐II gastrectomy, the results are not satisfactory. The aim of this study was to evaluate the efficacy and safety of endoscopic papillary large balloon dilation (EPLBD) for removal of bile duct stones in patients with B‐II gastrectomy.Methods:  Twenty‐six patients (20 men and six women; median age 72 years) with bile duct stones and a history of B‐II gastrectomy were enrolled. After cannulation, limited endoscopic sphincterotomy was performed. Then, balloon dilation (balloon size, 10–15 mm) was performed and stones were removed conventionally or via mechanical lithotripsy. Successful stone removal and complications were evaluated.Results:  In all cases, stones were successfully removed. The median number of sessions for complete stone removal was one (range 1–3). Stone removal by mechanical lithotripsy was achieved in three patients (11.5%). There were no significant complications, such as bleeding, pancreatitis, or perforation.Conclusions:  Endoscopic papillary large balloon dilation is an effective and safe method for removal of bile duct stones. We suggest consideration of this technique for removal of bile duct stones in patients with B‐II gastrectomy.
Transition from hepatic steatosis to steatohepatitis: Unique microRNA patterns and potential downstream functions and pathways
Authors: Jin Xi , Chen Yi‐peng , Kong Mei , Zheng Lin , Yang Yi‐da , Li You‐ming 
Published: July 2011

AbstractBackground and Aim:  This study aimed to explore the unique miRNA responsible for transition from hepatic steatosis to steatohepatitis and to investigate the functions and pathways of their downstream targets.Methods:  Microarray and stem‐loop reverse transcription‐polymerase chain reaction were utilized to detect dysregulated miRNA in a rat model. SAM, PAM and clustering analysis were jointly applied to calculate significantly changed miRNA. The targets of miRNA were predicted through web server “microrna.” The functions and pathways of those predicted genes were analyzed using databases of Gene Ontology and KEGG by the web server “DAVID.”Results:  Fourteen upregulated and six downregulated miRNA were selected as an accurate molecular signature in distinguishing hepatic steatohepatitis from steatosis. Through Gene ontology, 499 and 287 enriched functional categories were found for the target genes of upregulated and downregulated miRNA, including ion homeostasis, protein transport and so on. Through KEGG, 46 and 41 enriched pathways were collected for the target genes of upregulated and downregulated miRNA, including apoptosis, fatty acid metabolism and so on. Analysis of common target genes of all downregulated miRNA revealed potential involvement of ion transport and the membrane structure in steatohepatitis.Conclusion:  We reported the dysregulated miRNA in transition from hepatic steatosis to steatohepatitis and showed potential clinical application in disease differentiation. This study provided data reservoir for miRNA exploration and revealed novel disease‐specific Gene Ontology functions and KEGG pathways such as uncoupling‐protein‐guided membrane change. Our data contributes to further researches on the pathogenesis and treatment of non‐alcoholic steatohepatitis.
Use of thiopurines in the treatment of inflammatory bowel disease is associated with an increased risk of non‐melanoma skin cancer in an at‐risk population: A cohort study
Authors: Setshedi Mashiko , Epstein David , Winter Trevor A , Myer Landon , Watermeyer Gillian , Hift Richard 
Published: July 2011

AbstractBackground and Aim:  The thiopurines azathioprine and 6‐mercaptopurine are effective in the management of patients with inflammatory bowel disease (IBD) in whom aminosalicylates, antibiotics and corticosteroids have failed to induce or maintain remission. Long‐term use of these agents has been linked to a greatly increased risk of non‐melanoma skin cancer and lymphatic cancer in organ transplant recipients. There is some evidence to suggest that IBD patients receiving thiopurines might be at increased risk of cancer. Our aim was to determine the incidence of cancer in a cohort of patients with IBD managed in our clinic, and to relate this to thiopurine exposure.Methods:  We conducted a retrospective study based on the clinical and pathology records of patients attending a specialist IBD clinic at Groote Schuur Hospital, Cape Town, South Africa between 1960 and 2007.Results:  We analyzed the records of 1084 patients. A total of 123 subjects (11.5%) had received thiopurine therapy. Cancer was identified in 51 patients (4.7%), including colorectal cancer (15 patients), melanoma (two patients), non‐melanoma skin cancer (seven patients) and non‐Hodgkin's lymphoma (five patients). A diagnosis of non‐melanoma skin cancer was significantly associated with thiopurine exposure (odds ratio 5.0, 95% confidence interval 1.1–22.8). Six of seven non‐melanoma skin cancers occurred in Caucasian patients, with a highly significant association with thiopurine use (odds ratio 12.4, 95% confidence interval 2.3–67.4).Conclusions:  Patients with IBD who receive thiopurines are at increased risk of non‐melanoma skin cancer. The risk is highest in Caucasian patients, and is negligible in other groups.
Comparison of patients of chronic laryngitis with and without troublesome reflux symptoms
Authors: Wang An Jiang , Liang Mao Jin , Jiang Ai Yun , Lin Jin Kun , Xiao Ying Lian , Peng Sui , Chen Jie , Wen Wei Ping , Chen Min Hu 
Published: July 2011

AbstractBackground and Aim:  Little is known about the difference between patients of chronic laryngitis with and without troublesome reflux symptoms. The aim of this study was to compare the clinical characteristics and response to acid suppression between patients of chronic laryngitis with and without troublesome reflux symptoms.Methods:  Consecutive patients with chronic laryngitis were enrolled. The frequency and severity of reflux and laryngeal symptoms were scored. All the patients underwent laryngoscopy, esophagogastroduodenoscopy and 24‐h multichannel intraluminal impedance and pH monitoring before receiving rabeprazole 10 mg b.i.d. for 3 months. Mild typical reflux symptoms (heartburn or regurgitation) occurring ≥ 2 days/week or moderate/severe symptoms occurring ≥ 1 day/week were defined as troublesome reflux symptoms.Results:  Compared to patients without troublesome reflux symptoms, those with troublesome reflux symptoms were older and had more episodes of acid and liquid gastroesophageal reflux (GER) and acid and weakly acidic laryngopharyngeal reflux (LPR). They also had higher percentages of both bolus exposure time and acid exposure time of GER and LPR. Patients with troublesome reflux symptoms responded to acid suppression more often at 12 weeks (67.3% vs 20.9%, P < 0.001) and more rapidly (40.8% vs 14.0%, 3 weeks after the start of acid suppression; P = 0.004) compared to those without.Conclusion:  Difference in reflux profile of GER and LPR between patients with and without troublesome reflux symptoms could partly explain the discrepancy of response to acid suppression among patients with chronic laryngitis. Acid suppression therapy may provide limited therapeutic benefits to patients of chronic laryngitis without troublesome reflux symptoms.