bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana
Authors: Chen Peng , Jäger Gunilla , Zheng Bo 
Published: September 2010

Abstract

Background
In all domains of life, transfer RNA (tRNA) molecules contain modified nucleosides. Modifications to tRNAs affect their coding capacity and influence codon-anticodon interactions. Nucleoside modification deficiencies have a diverse range of effects, from decreased virulence in bacteria, neural system disease in human, and gene expression and stress response changes in plants. The purpose of this study was to identify genes involved in tRNA modification in the model plant Arabidopsis thaliana, to understand the function of nucleoside modifications in plant growth and development.

Results
In this study, we established a method for analyzing modified nucleosides in tRNAs from the model plant species, Arabidopsis thaliana and hybrid aspen (Populus tremula × tremuloides). 21 modified nucleosides in tRNAs were identified in both species. To identify the genes responsible for the plant tRNA modifications, we performed global analysis of the Arabidopsis genome for candidate genes. Based on the conserved domains of homologs in Sacccharomyces cerevisiae and Escherichia coli, more than 90 genes were predicted to encode tRNA modifying enzymes in the Arabidopsis genome. Transcript accumulation patterns for the genes in Arabidopsis and the phylogenetic distribution of the genes among different plant species were investigated. Transcripts for the majority of the Arabidopsis candidate genes were found to be most abundant in rosette leaves and shoot apices. Whereas most of the tRNA modifying gene families identified in the Arabidopsis genome was found to be present in other plant species, there was a big variation in the number of genes present for each family.
Through a loss of function mutagenesis study, we identified five tRNA modification genes (AtTRM10, AtTRM11, AtTRM82, AtKTI12 and AtELP1) responsible for four specific modified nucleosides (m1G, m2G, m7G and ncm5U), respectively (two genes: AtKTI12 and AtELP1 identified for ncm5U modification). The AtTRM11 mutant exhibited an early-flowering phenotype, and the AtELP1 mutant had narrow leaves, reduced root growth, an aberrant silique shape and defects in the generation of secondary shoots.

Conclusions
Using a reverse genetics approach, we successfully isolated and identified five tRNA modification genes in Arabidopsis thaliana. We conclude that the method established in this study will facilitate the identification of tRNA modification genes in a wide variety of plant species.
Developing criteria for Cesarean Section using the RAND appropriateness method
Authors: Ostovar Rahim , Rashidian Arash , Pourreza Abolghasem , Rashidi Batool Hossein , Hantooshzadeh Sedigheh , Ardebili Hassan Eftekhar , Mahmoudi Mahmood ,   The members of the panel of the Cesarean Section RAM Study
Published: September 2010

Abstract

Background
Cesarean section rates are increasing worldwide, and a rapid increase has been observed in Iran. Disagreement exists between clinicians about when to use cesarean section. We aimed to identify the appropriateness criteria for the use of cesarean section in Iran.

Method
A consensus development study using a modified version of the RAND Appropriateness Method (RAM). We generated scenarios from valid clinical guidelines and expert opinions. A panel of experts participated in consensus development: first round via mail (12 members), second round face-to-face (9 members). We followed the RAM recommendations for the development of the scenario lists, rating scales, and statistical analyses.

Results
294 scenarios relevant to cesarean section were identified. 191 scenarios were considered appropriate, of which 125 scenarios were agreed upon. The panel found cesarean inappropriate for 21% of scenarios, and 'equivocal' for 14% of scenarios.

Conclusion
RAM is useful for identifying stakeholder views in settings with limited resources. The participants' views on appropriateness of certain indications differed with available evidence. A large number of scenarios without agreement may partly explain why it has been difficult to curb the growth in cesarean section rate.
Dose escalation improves therapeutic outcome: post hoc analysis of data from a 12-week, multicentre, double-blind, parallel-group trial of trospium chloride in patients with urinary urge incontinence
Authors: Bödeker Rolf-Hasso , Madersbacher Helmut , Neumeister Claudia , Zellner Michael 
Published: September 2010

AbstractBackgroundFlexible dosing of anticholinergics used for overactive bladder (OAB) treatment is a useful strategy in clinical practice for achieving a maximum effective and maximum tolerated level of therapeutic benefit. In this post hoc analysis we evaluated the efficacy and tolerability of trospium chloride treatment for urinary urge incontinence (UUI) with focus on flexible dosing.MethodsThe data came from a 12-week, randomised, double-blind, phase IIIb study in which 1658 patients with urinary frequency plus urge incontinence received trospium chloride 15 mg TID (n = 828) or 2.5 mg oxybutynin hydrochloride TID (n = 830). After four weeks, daily doses were doubled and not readjusted in 29.2% (242/828) of patients in the trospium group, and in 23.3% (193/830) in the oxybuytnin group, until the end of treatment. We assessed the absolute reduction in weekly UUI episodes and the change in intensity of dry mouth, recorded in patients' micturition diaries. Adverse events were also evaluated. Statistics were descriptive.ResultsDose escalation of either trospium or oxybutynin increased reduction in UUI episodes in the population studied. At study end, there were no relevant differences between the "dose adjustment" subgroups and the respective "no dose adjustment" subgroups (trospium:P= 0.249; oxybutynin:P= 0.349). After dose escalation, worsening of dry mouth was higher in both dose adjusted subgroups compared to the respective "no dose adjustment" subgroups (P< 0.001). Worsening of dry mouth was lower in the trospium groups than in the oxybutynin groups (P< 0.001). Adverse events were increased in the dose adjusted subgroups.ConclusionsFlexible dosing of trospium was proven to be as effective, but better tolerated as the officially approved adjusted dose of oxybutynin.Trial registration (parent study)The study was registered with the German Federal Institute for Drugs and Medical Devices (BfArM, Berlin, Germany), registration number 4022383, as required at the time point of planning this study.
Chicken model of steroid-induced bone marrow adipogenesis using proteome analysis: a preliminary study
Authors: Li Sing Chung , Lin Ching Yu , Kuo Tzong Fu , Lin Yun Ho , Chen Chia Chun , Lin Way Neng , Chan Wing P 
Published: September 2010

AbstractBackgroundSteroid-induced adipogenesis increases fat-cell volume and pressure in bone marrow. This may be a contributing factor in some forms of osteonecrosis. In this observational study, we aimed to determine the protein expression relating to steroid-induced adipogenesis of femoral bone marrow with use of a chicken model. We compared the histologic features of the femoral marrow of eight methylprednisolone (MP)-treated chickens with those of three control chickens and assessed differential proteins with 2-dimensional gel electrophoresis and differential proteins were identified by MALDI-TOF MS.ResultsOne MP-induced chicken died of overdose anesthesia. Methylprednisolone-induced proliferation of adipose tissue and new bone formation were found on histologic examination. In our study, 13 proteins in the control and MP-induced groups were differently expressed and nine protein spots showed marked threefold downregulation after 19 weeks of MP treatment. These were serum amyloid P-component precursor, zinc finger protein 28, endothelial zinc finger protein 71, T-box transcription factor 3, cyclin-dependent kinase inhibitor 1, myosin 1D, dimethylaniline monooxygenase, and two uncharacterized proteins.ConclusionsProteomic profiling can be a useful dynamic approach for detecting protein expression in MP-induced adipogenesis of the femur in chickens.
Pathological axes of wound repair: Gastrulation revisited
Authors: Aller Maria-Angeles , Arias Jose-Ignacio , Arias Jaime 
Published: September 2010

Abstract
Post-traumatic inflammation is formed by molecular and cellular complex mechanisms whose final goal seems to be injured tissue regeneration.
In the skin -an exterior organ of the body- mechanical or thermal injury induces the expression of different inflammatory phenotypes that resemble similar phenotypes expressed during embryo development. Particularly, molecular and cellular mechanisms involved in gastrulation return. This is a developmental phase that delineates the three embryonic germ layers: ectoderm, endoderm and mesoderm. Consequently, in the post-natal wounded skin, primitive functions related with the embryonic mesoderm, i.e. amniotic and yolk sac-derived, are expressed. Neurogenesis and hematogenesis stand out among the primitive function mechanisms involved.
Interestingly, in these phases of the inflammatory response, whose molecular and cellular mechanisms are considered as traces of the early phases of the embryonic development, the mast cell, a cell that is supposedly inflammatory, plays a key role.
The correlation that can be established between the embryonic and the inflammatory events suggests that the results obtained from the research regarding both great fields of knowledge must be interchangeable to obtain the maximum advantage.
Amino acid substitutions in the E2 glycoprotein of Sindbis-like virus XJ-160 confer the ability to undergo heparan sulfate-dependent infection of mouse embryonic fibroblasts
Authors: Zhu Wuyang , Fu Shihong , He Ying , Li Jinping , Liang Guodong 
Published: September 2010

Abstract
We have recently demonstrated an essential role of the domain of 145-150 amino acid in the E2 glycoprotein of Sindbis virus in the interaction with cellular heparan sulfate (HS) and in the infection of mouse embryonic fibroblasts (MEF) cells. In this study, we constructed and characterized the mutants of Sindbis-like virus XJ-160 in which Tyr-146 and/or Asn-149 in the E2 glycoprotein had been substituted with His and Arg, respectively. Unlike parental virus XJ-160, mutants with either or both substitutions were able to infect wild-type mouse embryonic fibroblasts (MEF-wt) or MEF-Epi

-/-
cells which produce mutant HS. Significantly more infectious particles were released from MEF-wt than from MEF-Epi

-/-
cells. The mutant virus with both substitutions release was inhibited by pre-incubation of virus with heparin or pre-treatment of BHK-21 cells with HS-degrading enzyme. Both XJ-160 and the mutant viruses retained substantial neurovirulence in suckling mice. Our findings provide further support to the importance of positively charged residues in the HS-binding site of E2 in mediating Sindbis virus infection of MEF cells.
Long-Term Efficacy of Methylphenidate in Enhancing Attention Regulation, Social Skills, and Academic Abilities of Childhood Cancer Survivors
Authors: Conklin Heather M. , Reddick Wilburn E. , Ashford Jason , Ogg Susan , Howard Scott C. , Morris E. Brannon , Brown Ronald , Bonner Melanie , Christensen Robbin , Wu Shengjie , Xiong Xiaoping , Khan Raja B. 
Published: September 2010

Purpose Methylphenidate (MPH) ameliorates attention problems experienced by some cancer survivors in the short term, but its long-term efficacy is unproven. Patients and Methods This study investigates the long-term effectiveness of maintenance doses of MPH in survivors of childhood brain tumors (n = 35) and acute lymphoblastic leukemia (n = 33) participating in a 12-month MPH trial. Measures of attention (Conners' Continuous Performance Test [CPT], Conners' Rating Scales [CRS]), academic abilities (Wechsler Individual Achievement Test [WIAT]), social skills (Social Skills Rating System [SSRS]), and behavioral problems (Child Behavior Checklist [CBCL]) were administered at premedication baseline and at the end of the MPH trial while on medication. A cancer control group composed of patients who were not administered MPH (brain tumor = 31 and acute lymphoblastic leukemia = 23) was assessed on the same measures 2 months apart. Results For the MPH group, repeated measures analysis of variance revealed significant improvement in performance on a measure of sustained attention (CPT indices, P < .05); parent, teacher, and self-report ratings of attention (CRS indices, P < .05), and parent ratings of social skills or behavioral problems (SSRS and CBCL indices; P < .05). In contrast, the cancer control group only showed improvement on parent ratings of attention (Conners' Parent Rating Scale indices; P < .05) and social skills (SSRS and CBCL indices; P < .05). There was no significant improvement on the academic measure (WIAT) in either group. Conclusion Attention and behavioral benefits of MPH for childhood cancer survivors are maintained across settings over the course of a year. Although academic gains were not identified, MPH may offer benefits in academic areas not assessed.
Phase III Randomized Trial Assessing Rofecoxib in the Adjuvant Setting of Colorectal Cancer: Final Results of the VICTOR Trial
Authors: Midgley Rachel S. , McConkey Christopher C. , Johnstone Elaine C. , Dunn Janet A. , Smith Justine L. , Grumett Simon A. , Julier Patrick , Iveson Claire , Yanagisawa Yoko , Warren Bryan , Langman Michael J. , Kerr David J. 
Published: September 2010

Purpose Laboratory and case-control studies suggest a pivotal role for the cyclooxygenase-2 (COX-2) pathway in colorectal carcinogenesis. The purpose of this study was to test whether the COX-2 inhibitor rofecoxib could reduce recurrence and improve survival when administered in the adjuvant setting of colorectal cancer (CRC). Patients and Methods Patients who had undergone potentially curative surgery and completion of adjuvant therapy for stage II and III CRC were randomly assigned to receive rofecoxib (20 mg daily) or placebo. The primary end point was overall survival (OS). Where formalin-fixed paraffin-embedded tumor tissue samples were available, COX-2 expression was evaluated by immunohistochemistry and correlated with clinical outcome. Results Two thousand four hundred thirty-four patients were entered onto the study. The trial was terminated early because of the worldwide withdrawal of rofecoxib. At this point, 1,167 patients had received rofecoxib and 1,160 patients had received placebo for median treatment durations of 7.4 and 8.2 months, respectively. For the rofecoxib and placebo arms, median follow-up times were 4.84 and 4.85 years, with 241 and 246 deaths and 297 and 329 recurrences, respectively. No difference was demonstrated in OS (hazard ratio [HR] = 0.97; 95% CI, 0.81 to 1.16; P = .75) or recurrence (HR = 0.89; 95% CI, 0.76 to 1.04; P = .15) comparing the two groups. Tumor COX-2 expression by immunohistochemistry was assessed for 871 patients, but neither prognostic nor predictive effects were observed. Conclusion In this study of abbreviated therapy in the adjuvant setting of CRC, rofecoxib did not improve OS or protect from recurrence in unselected patients. In addition, COX-2 expression did not correlate with prognosis overall or predict effectiveness of COX-2 inhibitors.
New mechanisms involved in paternal 20q disomy associated with pseudohypoparathyroidism
Authors: Fernández-Rebollo Eduardo , Lecumberri Beatriz , Garin Intza , Arroyo Javier , Bernal-Chico Ana , Goñi Fernando , Orduña Rosa , _ _ , Castaño Luis , Pérez de Nanclares Guiomar 
Published: September 2010

PurposeType I pseudohypoparathyroidism (PHP-I) can be subclassified into Ia and Ib, depending on the presence or absence of Albright's hereditary osteodystrophy's phenotype, diminished α-subunit of the stimulatory G protein (Gsα) activity and multihormonal resistance. Whereas PHP-Ia is mainly associated with heterozygous inactivating mutations in Gsα-coding exons ofGNAS, PHP-Ib is caused by imprinting defects ofGNAS. To date, just one patient with PHP and complete paternal uniparental disomy (UPD) has been described.We sought to identify the underlining molecular defect in twenty patients with parathyroid hormone resistance, hypocalcemia and hyperphosphatemia, and abnormal methylation pattern at GNAS locus.MethodsMicrosatellite typing and comparative genome hybridization were performed for proband and parents.ResultsWe describe four patients with partial paternal UPD of chromosome 20 involving pat20qUPD in one case, from 20q13.13-qter in two cases, and pat20p heterodisomy plus interstitial 20q isodisomy in one patient.ConclusionsThese observations demonstrate that mitotic recombination of chromosome 20 can also give rise to UPD and PHP, a situation similar to other imprinting disorders, such as Beckwith–Wiedemann syndrome or neonatal diabetes.
Helmet Versus Active Repositioning for Plagiocephaly: A Three-Dimensional Analysis
Authors: Lipira Angelo B. , Gordon Shayna , Darvann Tron A. , Hermann Nuno V. , Van Pelt Andrea E. , Naidoo Sybill D. , Govier Daniel , Kane Alex A. 
Published: September 2010

BACKGROUND AND PURPOSE:
Orthotic helmets and active repositioning are the most common treatments for deformational plagiocephaly (DP). Existing evidence is not sufficient to objectively inform decisions between these options. A three-dimensional (3D), whole-head asymmetry analysis was used to rigorously compare outcomes of these 2 treatment methods.

PATIENTS AND METHODS:
Whole-head 3D surface scans of 70 infants with DP were captured before and after treatment by using stereophotogrammetric imaging technology. Helmeted (n = 35) and nonhelmeted/actively repositioned (n = 35) infants were matched for severity of initial deformity. Surfaces were spatially registered to a symmetric template, which was deformed to achieve detailed right-to-left point correspondence for every point on the head surface. A ratiometric asymmetry value was calculated for each point relative to its contralateral counterpart. Maximum and mean asymmetry values were determined. Change in mean and maximum asymmetry with treatment was the basis for group comparison.

RESULTS:
The helmeted group had a larger reduction than the repositioned group in both maximum (4.0% vs 2.5%; P = .02) and mean asymmetry (0.9% vs 0.5%; P = .02). The greatest difference was localized to the occipital region.

CONCLUSIONS:
Whole-head 3D asymmetry analysis is capable of rigorously quantifying the relative efficacy of the 2 common treatments of DP. Orthotic helmets provide statistically superior improvement in head symmetry compared with active repositioning immediately after therapy. Additional studies are needed to (1) establish the clinical significance of these quantitative differences in outcome, (2) define what constitutes pathologic head asymmetry, and (3) determine whether superiority of orthotic treatment lasts as the child matures.
Stimulant-Responsive and Stimulant-Refractory Aggressive Behavior Among Children With ADHD
Authors: Blader Joseph C. , Pliszka Steven R. , Jensen Peter S. , Schooler Nina R. , Kafantaris Vivian 
Published: September 2010

OBJECTIVES:The objective of this study was to examine factors that are associated with aggression that is responsive versus refractory to individualized optimization of stimulant monotherapy among children with attention-deficit/hyperactivity disorder (ADHD).METHODS:Children who were aged 6 to 13 years and had ADHD, either oppositional defiant disorder or conduct disorder, significant aggressive behavior, and a history of insufficient response to stimulants completed an open stimulant monotherapy optimization protocol. Stimulant titration with weekly assessments of behavior and tolerability identified an optimal regimen for each child. Families also received behavioral therapy. Parents completed the Retrospective-Modified Overt Aggression Scale (R-MOAS) at each visit. Children were classified as having stimulant-refractory aggression on the basis of R-MOAS ratings and clinician judgment. Differences that pertained to treatment, demographic, and psychopathology between groups with stimulant monotherapy–responsive and –refractory aggression were evaluated.RESULTS:Aggression among 32 (49.3%) of 65 children was reduced sufficiently after stimulant dosage adjustment and behavioral therapy to preclude adjunctive medication. Those who responded to stimulant monotherapy were more likely to benefit from the protocol's methylphenidate preparation (once-daily, triphasic release), showed a trend for lower average dosages, and received fewer behavioral therapy sessions than did children with stimulant-refractory aggression. Boys, especially those with higher ratings of baseline aggression and of depressive and manic symptoms, more often exhibited stimulant-refractory aggression.CONCLUSIONS:Among children whose aggressive behavior develops in the context of ADHD and of oppositional defiant disorder or conduct disorder, and who had insufficient response to previous stimulant treatment in routine clinical care, systematic, well-monitored titration of stimulant monotherapy often culminates in reduced aggression that averts the need for additional agents.
X-ray and neutron imaging – Complementary techniques for materials science and engineering
Authors: Banhart John , Borbély András , Dzieciol Krzysztof , Garcia-Moreno Francisco , Manke Ingo , Kardjilov Nikolay , Kaysser-Pyzalla Anke Rita , Strobl Markus , Treimer Wolfgang 
Published: September 2010

AbstractUsing X-ray and neutron radiography and tomography, images of material and component inhomogeneities and their development with time can be obtained. Due to their non-destructiveness and non-invasive nature both methods give insight into the function of devices and their decay processes. Fundamentals of X-ray and neutron radiography and tomography are briefly outlined, examples for both techniques are given, their complementarities are highlighted and emerging techniques and frontiers are discussed.
Fast in-situ X-ray micro tomography characterisation of microstructural evolution and strain-induced damage in alloys at various temperatures
Authors: Suéry Michel , Adrien Jérôme , Landron Caroline , Terzi Sofiane , Maire Eric , Salvo Luc , Blandin Jean-Jacques 
Published: September 2010

AbstractFast in-situ X-ray tomography has been used at ESRF Grenoble to characterise the microstructural evolution and the formation of strain-induced damage in various materials during different thermomechanical treatments. Materials are both light alloys (Al and Mg based alloys) and steels. The thermomechanical treatments include tensile deformation both in the solid state at room and high temperatures and in the semi-solid state together with thermal treatments above the solidus temperature. Melting and solidification of Al-alloys are also considered in this paper.
Synthesis and characterization of nanostructured Cu/ZnO/Al2O3 from lyotropic liquid crystalline templates
Authors: Wang Xiaodong , Guo Ruijie , Sun Yuan 
Published: September 2010

Abstract
The hexagonal lyotropic liquid crystalline phases of nonionic surfactants AEO-9 were used to template directly the fabrication of nanostructured Cu/ZnO/Al2O3 oxides. The reaction between metal precursors and alkaline reacting substance dissolved within the aqueous domains of the liquid crystalline templates generated nanostructured oxides. Low-angle X-ray diffraction and transmission election microscopy characterization reveals the product as a hexagonal array of cylindrical pores with pore-to-pore separation of ca. 6.3 nm. Possessing ordered nanochannels, Cu/ZnO/Al2O3 oxides could find more potential application in catalysis.