bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genetic discontinuity in root‐nodulating bacteria of cultivated pea in the Indian trans‐Himalayas
Authors: RAHI PRAVEEN , KAPOOR RITI , YOUNG J. P. W. , GULATI ARVIND 
Published: November 2011

AbstractEvolutionary relationships of 120 root‐nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans‐Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR‐RFLP, ERIC‐PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon‐source utilization pattern (BIOLOG™), and whole‐cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates from the two valleys were clearly separated on the basis of ERIC fingerprints, carbon‐source utilization pattern, and whole‐cell fatty acid methyl esters. Phylogenetic analysis of atpD, recA, nodC and nifH genes revealed a common Rlv sublineage in Spiti valley. Lahaul valley isolates were represented by three sequence types of atpD and recA genes, and four sequence types of nodC and nifH genes. Genotypes from the two valleys were completely distinct, except for two Lahaul isolates that shared nodC and nifH sequences with Spiti isolates but were otherwise more similar to other Lahaul isolates. Isolates from the two highest Spiti valley sites (above 4000 m) had a distinctive whole‐cell fatty acid profile. Spiti valley isolates are closely related to Rlv sublineages from Xinjiang and Shanxi provinces in China, while Lahaul valley isolates resemble cosmopolitan strains of the western world. The high mountain pass between these valleys represents a boundary between two distinct microbial populations.
Reflections on a sticky situation: how surface contact pulls the trigger for bacterial adhesion
Authors: Kirkpatrick Clare L. , Viollier Patrick H. 
Published: November 2011

SummaryAdhesion of bacterial cells to surfaces can be mediated by a wide variety of extracellular structures, which can either recognize specific molecular motifs or adhere in non‐specific ways to multiple types of surfaces. The attachment is thought to be highly regulated, but the underlying sensory mechanism(s) are poorly understood. In the α‐proteobacterium Caulobacter crescentus, the formation of adhesive organelles is ‘hardwired’ into the cell cycle regulatory circuitry. In this issue of Molecular Microbiology, Li et al. (2011) employed this model organism to examine the adhesion process and the transition from temporary to permanent attachment using total internal reflection fluorescence (TIRF) microscopy. Surprisingly, they observed that adhesin production was not only under developmental control, but was also stimulated by surface contact. Initial reversible contact of the pili with the surface was followed by flagellum rotation arrest and subsequent induction of the holdfast to allow irreversible surface adhesion. These findings demonstrate that Caulobacter produces its holdfast only at the appropriate time for surface attachment, preventing premature export of the adhesin, which could then be inactivated by ‘curing’ or be masked by occluding particles. Importantly, their results support the notion that the flagellum serves as a mechanosensor for adhesion.
Systematic knockdown of morphine pathway enzymes in opium poppy using virus‐induced gene silencing
Authors: Wijekoon Champa P. , Facchini Peter J. 
Published: November 2011

SummaryOpium poppy (Papaver somniferum) remains the sole commercial source for several pharmaceutical alkaloids including the narcotic analgesics codeine and morphine, and the semi‐synthetic drugs oxycodone, buprenorphine and naltrexone. Although most of the biosynthetic genes have been identified, the post‐transcriptional regulation of the morphinan alkaloid pathway has not been determined. We have used virus‐induced gene silencing (VIGS) as a functional genomics tool to investigate the regulation of morphine biosynthesis via a systematic reduction in enzyme levels responsible for the final six steps in the pathway. Specific gene silencing was confirmed at the transcript level by real‐time quantitative PCR (polymerase chain reaction), and at the protein level by immunoblot analysis using antibodies raised against salutaridine synthase (SalSyn), salutaridine reductase (SalR), salutaridine 7‐O‐acetyltransferase (SalAT), thebaine 6‐O‐demethylase (T6ODM), codeinone reductase (COR), and codeine O‐demethylase (CODM). In some cases, silencing a specific biosynthetic gene resulted in a predictable accumulation of the substrate for the corresponding enzyme. Reduced SalSyn, SalR, T6ODM and CODM protein levels correlated with lower morphine levels and a substantial increase in the accumulation of reticuline, salutaridine, thebaine and codeine, respectively. In contrast, the silencing of genes encoding SalAT and COR resulted in the accumulation of salutaridine and reticuline, respectively, which are not the corresponding enzymatic substrates. The silencing of alkaloid biosynthetic genes using VIGS confirms the physiological function of enzymes previously characterized in vitro, provides insight into the biochemical regulation of morphine biosynthesis, and demonstrates the immense potential for metabolic engineering in opium poppy.
Critical review of the Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA): suggestions for harmonization, implementation and improvement
Authors: Datema Tjeerd A. M. , Oskam Linda , van Beers Stella M. , Klatser Paul R. 
Published: November 2011

AbstractObjective  Clinical laboratories in low‐ and middle‐income countries (LMIC) need fundamental improvement because quality laboratory services are essential for the decision‐making capacity of clinicians, health workers and public health authorities. To this end, a tiered accreditation scheme Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA) was developed by WHO‐AFRO, CDC and others for clinical laboratories in LMIC. One to five stars are accredited to laboratories based on the level of compliance with a checklist. Our aim was to evaluate the quality and applicability of this accreditation scheme compared with international quality standards.Methods  We performed a critical review of this scheme to formulate recommendations for implementation, harmonization and improvement. Two analyses were performed: one assessing its coverage of the ISO 15189:2007 standard and one to identify and evaluate priorities of the accreditation checklist.Results  Although the content of the checklist covers all aspects of total quality management, it strongly prioritizes resource management activities. We recommend identifying critical requirements for each tier of accreditation to assure a certain level of quality for each tier or instead using a pass/fail approach towards accreditation. In addition, the checklist should include more questions for assessing proper management, ethics and continuous improvement to meet ISO 15189.Conclusion  Launching accreditation schemes for laboratories in LMIC should be encouraged. After further optimization of SLIPTA, clinical laboratories may certainly benefit, leading to more correctly diagnosed patients and less waste of resources.
A multi‐allergen standard for the calibration of immunoassays: CREATE principles applied to eight purified allergens
Authors: Filep S. , Tsay A. , Vailes L. , Gadermaier G. , Ferreira F. , Matsui E. , King E. M. , Chapman M. D. 
Published: November 2011

To cite this article: Filep S, Tsay A, Vailes L, Gadermaier G, Ferreira F, Matsui E, King EM, Chapman MD. A multi‐allergen standard for the calibration of immunoassays: CREATE principles applied to eight purified allergens. Allergy 2012; 67: 235–241.Abstract
Background:  Allergen measurements are widely used for environmental exposure assessments and for determining the potency of allergen vaccines, yet few purified allergen standards have been developed. The aim of the study was to develop a single standard containing multiple purified allergens that could be used in enzyme immunoassays and in multiplex arrays for the standardization of allergen measurements.
Methods:  Eight purified allergens were formulated into a single multi‐allergen, or ‘universal’, standard based on amino acid analysis. Dose–response curves were compared with previous individual ELISA standards and allergen measurements of house dust extracts to obtain correction factors. Measured allergen concentrations were also modeled using linear regression, and the predictive accuracy was determined.
Results:  Parallel dose–response curves were obtained between the universal allergen standard and the individual ELISA standards, with close agreement between curves for 5/8 allergens. Quantitative differences of greater than twofold were observed for Fel d 1, Can f 1, and Der f 1, which were confirmed by the analysis of house dust extracts. Correction factors were developed that allowed ELISA data to be expressed in terms of the universal standard. Linear regression data confirmed the predictive accuracy of the universal standard.
Conclusion:  This study shows that a single standard of eight purified allergens can be used to compare allergen measurements by immunoassay. This approach will improve the continuity of environmental exposure assessments and provide improved standardization of allergy diagnostics and vaccines used for immunotherapy.
Quantitation of human herpesvirus‐6 (HHV‐6) DNA in a cord blood transplant recipient with chromosomal integration of HHV‐6
Authors: Kobayashi D. , Kogawa K. , Imai K. , Tanaka T. , Hiroi S. , Satoh H. , Tanaka‐Taya K. , Nonoyama S. 
Published: November 2011

AbstractChromosomal integration of the human herpesvirus‐6 (HHV‐6) genome (CIHHV‐6) is an important consideration if HHV‐6 DNA is detected during the course of transplantation. A 4‐year‐old girl with refractory anemia with excess blasts type‐2 was diagnosed with CIHHV‐6 before a cord blood transplantation. HHV‐6 DNA was serially quantitated by polymerase chain reaction assay in the transplant period. The possibility of HHV‐6 reactivation in a transplant recipient with CIHHV‐6 was suspected in our case.
Evaluation of the hemostatic potential including thrombin generation of three different therapeutic pathogen‐reduced plasmas
Authors: Hacquard M. , Lecompte T. , Belcour B. , Geschier C. , Jacquot C. , Jacquot E. , Schneider T. 
Published: November 2011

Background and Objectives  Several pathogen inactivation methods currently applied to therapeutic plasma may result in products with different hemostatic properties. This study aims at evaluating and comparing the hemostatic potential of different therapeutic plasma preparations currently available in France.Materials and methods  We studied three types of pathogen‐reduced plasma for transfusion (MB/light, Amotosalen/UVA, industrial S/D plasma). Quarantine, non‐pathogen‐reduced plasma, was used as a control. This study compared more specifically the content in FVIII, fibrinogen (clottable and antigen assays) and ADAMTS‐13 and evaluated the intrinsic hemostatic properties using a thrombin generation test [Calibrated Automated Thrombogram (CAT)] at high and low concentrations of tissue factor to assess the maximum quantity of thrombin generated or the contribution of FVIII and FIX in the amplification phase of thrombin generation, respectively.Results  The median FVIII concentration was >70 IU/dl for each preparation. Endogenous thrombin potential values were significantly different among the methods of plasma preparation (P < 0·001) but were all in the range of the values measured in donors’ plasma. Control by the thrombomodulin‐activated protein C system was preserved in all preparations (>50% inhibition of endogenous thrombin potential). Fibrinogen concentrations were all within normal range but fibrinogen levels were lower in the plasmas treated with photochemical methods. ADAMTS‐13 levels were preserved.Conclusion  The hemostatic potential appears well preserved in all therapeutic plasmas tested but there are some differences between preparations, the clinical relevance of which remains to be elucidated.
High‐dose esomeprazole is required for intraesophageal acid control in gastroesophageal reflux disease patients with hiatus hernia
Authors: Peng Sui , Xiao Ying‐Lian , Cui Yi , Lin Jin‐Kun , Zhang Ning , Hu Pin‐Jin , Chen Min‐Hu 
Published: November 2011

AbstractBackground and Aim:  The aim of this study was to assess whether the efficacy of proton pump inhibitors (PPI) therapy at a standard dose in esophageal acid control is affected by the presence of hiatus hernia in Chinese gastroesophageal reflux disease patients, and whether a higher dose of PPI is required for acid control.Methods:  Consecutive gastroesophageal reflux disease patients who had typical reflux symptoms and abnormal baseline 24‐h esophageal pH and underwent upper endoscopy were enrolled to receive esomeprazole at 40 mg once daily for 4 weeks. Patients underwent the dual‐channel 24‐h pH test at the end of 4‐week therapy. If the 24‐h esophageal pH was still abnormal at the end of 4‐week therapy, then esomeprazole at 40 mg twice daily was given for another 4 weeks after a washout interval of 1 week, and a 24‐h pH test was repeated at the end of the therapy.Results:  Overall, 76 patients were included, 13 with hiatus hernia. Of the 76 patients treated with a 40 mg of esomeprazole daily, esophageal acid exposure was normalized in 64 (84.2%). Normalization of acid exposure was achieved by standard PPI therapy in 53.2% (7/13) of patients with hiatus hernia and 90.5% (57/63) of those without (P = 0.004). A double dose of esomeprazole was successful in normalizing the esophageal pH in all 12 non‐responders to the standard dose of esomeprazole, including the six patients with hiatus hernia and six patients without.Conclusions:  The standard‐dose of esomeprazole fails to normalize the esophageal pH in almost 50% of patients with hiatus hernia, in whom the “double‐dose” esomeprazole therapy is required.
Expression profile of genes involved in pathogenesis of pediatric Crohn's disease
Authors: Sim Winnie H , Wagner Josef , Cameron Donald J , Catto‐Smith Anthony G , Bishop Ruth F , Kirkwood Carl D 
Published: November 2011

AbstractBackground and Aim:  Expression profiling of genes specific to pediatric Crohn's Disease (CD) patients was performed to elucidate the molecular mechanisms underlying disease cause and pathogenesis at disease onset.Methods:  We used suppressive subtractive hybridization (SSH) and differential screening analysis to profile the mRNA expression patterns of children with CD and age‐ and sex‐matched controls without inflammatory bowel disease (IBD).Results:  Sequence analysis of 1000 clones enriched by SSH identified 75 functionally annotated human genes, represented by 430 clones. The 75 genes have potential involvement in gene networks, such as antigen presentation, inflammation, infection mechanism, connective tissue development, cell cycle and cancer. Twenty‐eight genes were previously described in association with CD, while 47 were new genes not previously reported in the context of IBD. Additionally, 29 of the 75 genes have been previously implicated in bacterial and viral infections. Quantitative real‐time reverse transcription polymerase chain reaction performed on ileal‐derived RNA from 13 CD and nine non‐IBD patients confirmed the upregulation of extracellular matrix gene MMP2 (P = 0.001), and cell proliferation gene REG1A (P = 0.063) in our pediatric CD cohort.Conclusion:  The retrieval of 28 genes previously reported in association with adult CD emphasizes the importance of these genes in the pediatric setting. The observed upregulation of REG1A and MMP2, and their known impact on cell proliferation and extracellular matrix remodeling, agrees with the clinical behavior of the disease. Moreover, the expressions of bacterial‐ and virus‐related genes in our CD‐patient tissues support the concept that microbial agents are important in the etiopathogenesis of CD.
Clinical impact of HFE mutations in Japanese patients with chronic hepatitis C
Authors: Ishizu Yoji , Katano Yoshiaki , Honda Takashi , Hayashi Kazuhiko , Ishigami Masatoshi , Itoh Akihiro , Hirooka Yoshiki , Nakano Isao , Goto Hidemi 
Published: November 2011

AbstractBackground and Aim:  HFE mutations, a common cause of hereditary hemochromatosis (HH), are reportedly associated with hepatic iron overload, severe liver fibrosis, and good response to interferon treatment in European patients with chronic hepatitis C (CHC). HH shows ethnicity‐based differences and little is known about the effects of HH mutations on CHC in the Japanese. Thus, the aim of this study was to clarify the clinical influence of HFE mutations in Japanese CHC patients.Methods:  In a total of 251 patients with CHC, we analyzed the frequencies of H63D and S65C mutations in the HFE gene, and the influence of these mutations on clinical parameters and response to pegylated‐interferon‐alpha 2b (PEG‐IFN) plus ribavirin therapy.Results:  Fourteen patients (5.6%) carried the H63D mutation; all were heterozygotes. No S65C mutations were found. Only hemoglobin levels in the H63D heterozygotes were higher than in wild‐type patients. Eleven of 14 H63D heterozygotes achieved sustained virological response (SVR). On univariate analysis, factors associated with SVR were interleukin 28B (IL28B) polymorphism, age, hepatitis C virus (HCV) genotype, HCV viral load, white blood cell count, stage of fibrosis and H63D mutation. All patients with both TT genotype in IL28B (rs8099917) and H63D mutation in HFE (n = 10) achieved SVR.Conclusions:  The H63D mutation has little impact on the clinical characteristics of CHC, but is related to favorable response to PEG‐IFN plus ribavirin therapy, particularly in patients with the TT allele in IL28B.
Clinical outcomes of endoscopic submucosal dissection and endoscopic mucosal resection for laterally spreading tumors larger than 20 mm
Authors: Terasaki Motomi , Tanaka Shinji , Oka Shiro , Nakadoi Koichi , Takata Sayaka , Kanao Hiroyuki , Yoshida Shigeto , Chayama Kazuaki 
Published: November 2011

AbstractBackground and Aims:  Colorectal laterally spreading tumors (LST) > 20 mm are usually treated by endoscopic submucosal dissection (ESD) or endoscopic mucosal resection (EMR). Endoscopic piecemeal mucosal resection (EPMR) is sometimes required. The aim of our study was to compare the outcomes of ESD and EMR, including EPMR, for such LST.Methods:  A total of 269 consecutive patients with a colorectal LST > 20 mm were treated endoscopically at our hospital from April 2006 to December 2009. We retrospectively evaluated the complications and local recurrence rates associated with ESD, hybrid ESD (ESD with EMR), EMR, and EPMR.Results:  ESD and EMR were performed successfully for 89 and 178 LST, respectively: 61 by ESD; 28 by hybrid ESD; 70 by EMR; and 108 by EPMR. Between‐group differences in perforation rates were not significant. Local recurrence rates in cases with curative resection were as follows: 0% (0/56) in ESD; 0% (0/27) in hybrid ESD; 1.4% (1/69) in EMR; and 12.1% (13/107) in EPMR; that is, significantly higher in EPMR. No metastasis was seen at follow up. The recurrence rate for EPMR yielding ≥ three pieces was significantly high (P < 0.001). All 14 local recurrent lesions were adenomas that were cured endoscopically.Conclusions:  As for safety, ESD/hybrid ESD is equivalent to EMR/EPMR. ESD/hybrid ESD is a feasible technique for en bloc resection and showed no local recurrence. Although local recurrences associated with EMR/EPMR were seen, which were conducted based on our indication criteria, all local recurrences could obtain complete cure by additional endoscopic treatment.
Association of tumor necrosis factor‐α gene promoter polymorphism at sites ‐308 and ‐238 with non‐alcoholic fatty liver disease: A meta‐analysis
Authors: Wang Ji‐kai , Feng Zhe‐wei , Li Ying‐chun , Li Qing‐yan , Tao Xing‐yong 
Published: November 2011

AbstractBackground and Aim:  Environmental and genetic factors play a role in the pathogenesis and natural history of non‐alcoholic fatty liver disease (NAFLD). The objective of this study was to quantitatively evaluate the association between tumor necrosis factor (TNF)‐α gene promoter polymorphism at sites ‐308 and ‐238 and NAFLD susceptibility.Methods:  We performed an extensive search of relevant studies and made a meta‐analysis, including eight studies with 837 NAFLD cases and 990 controls in the association between TNF‐α ‐308 polymorphism and NAFLD; and seven studies with 771 cases and 787 controls in TNF‐α ‐238 polymorphism.Results:  The combined results showed that there was a significant difference in TNF‐α‐238 genotype distribution between NAFLD and control based on all studies (GA/AA vs GG [odds ratio = 2.06, 95% confidence interval = 1.58–2.69, P < 0.000 01]). However, the combined results based on all studies showed there was no evidence of association of TNF‐α‐308 genotype distribution between NAFLD cases and controls (GA/AA vs GG [odds ratio = 1.08, 95% confidence interval = 0.82–1.42, P = 0.60]). When stratifying for race, the significant results did not change materially compared with whole populations.Conclusion:  This meta‐analysis suggested that TNF‐α gene promoter polymorphism at position ‐238 but not ‐308 might be a risk factor for NAFLD.
Characterization of microRNA expression profiles associated with hepatitis B virus replication and clearance in vivo and in vitro
Authors: Pan Xiao‐Ben , Ma Hui , Jin Qian , Wei Lai 
Published: November 2011

AbstractBackground and Aim:  Alpha interferon (IFN‐α) is an approved treatment for chronic hepatitis B (CHB). MicroRNA (miRNA) are currently known as a part of IFN‐mediated antiviral defense. We aimed at characterizing the miRNA expression associated with hepatitis B virus (HBV) replication and IFN‐mediated HBV clearance.Methods:  We investigated the expression patterns of cellular miRNA induced by HBV replication and/or IFN‐α treatment in HepG2 cells, and also analyzed the miRNA response in peripheral blood mononuclear cells in CHB patients on IFN‐α treatment. The differentially expressed miRNA were verified using quantitative real‐time polymerase chain reaction and an miRNA expression pattern was classified based on the final virological response.Results:  A total of 223 miRNA were differentially expressed (> 1.5 folds) between the HepG2.2.15 and HepG2 cells, including 24 highly differentially expressed miRNA (> 5 folds). With 12 h of IFN‐α treatment, 23 totally differentially expressed miRNA were identified in HepG2 cells; whereas only five miRNA were identified in HepG2.2.15 cells. Similar amounts of the miRNA were regulated in patients with HBeAg or non‐HBeAg seroconversion; whereas levels of eight miRNA were significantly differentially expressed between the two groups.Conclusions:  HBV replication alters miRNA expression profiles and impairs IFN‐inducible miRNA response in HepG2 cells. The miRNA expression pattern of peripheral blood mononuclear cells in CHB patients with IFN therapy can be associated with their therapeutic outcome.