bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequency and fate of microRNA editing in human brain
Authors: Kawahara Yukio , Megraw Molly , Kreider Edward , Iizasa Hisashi , Valente Louis , Hatzigeorgiou Artemis G. , Nishikura Kazuko 
Published: August 2008

Abstract
Primary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A→I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT-PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that ∼16% of human pri-miRNAs are subject to A→I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.
Genome-wide identification ofin vivoprotein-DNA binding sites from ChIP-Seq data
Authors: Jothi Raja , Cuddapah Suresh , Barski Artem , Cui Kairong , Zhao Keji 
Published: August 2008

AbstractChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein–DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to a reference genome for further analysis. Although genomic regions enriched with mapped reads could be inferred as approximate binding regions, short read lengths (∼25-50nt) pose challenges for determining the exact binding sites within these regions. Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. The sensitivity and specificity of SISSRs are demonstrated by applying it on ChIP-Seq data for three widely studied and well-characterized human transcription factors: CTCF (CCCTC-binding factor), NRSF (neuron-restrictive silencer factor) and STAT1 (signal transducer and activator of transcription protein 1). We identified 26814, 5813 and 73956 binding sites for CTCF, NRSF and STAT1 proteins, respectively, which is 32, 299 and 78% more than that inferred previously for the respective proteins. Motif analysis revealed that an overwhelming majority of the identified binding sites contained the previously established consensus binding sequence for the respective proteins, thus attesting for SISSRs’ accuracy. SISSRs’ sensitivity and precision facilitated further analyses of ChIP-Seq data revealing interesting insights, which we believe will serve as guidance for designing ChIP-Seq experiments to map in vivo protein–DNA interactions. We also show that tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites. Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding.
The RecU Holliday junction resolvase acts at early stages of homologous recombination
Authors: Cañas Cristina , Carrasco Begoña , Ayora Silvia , Alonso Juan C. 
Published: August 2008

Abstract
Homologous recombination is essential for DNA repair and generation of genetic diversity in all organisms. It occurs through a series of presynaptic steps where the substrate is presented to the recombinase (RecA in bacteria). Then, the recombinase nucleoprotein filament mediates synapsis by first promoting the formation of a D-loop and later of a Holliday junction (HJ) that is subsequently cleaved by the HJ resolvase. The coordination of the synaptic step with the late resolution step is poorly understood. Bacillus subtilis RecU catalyzes resolution of HJs, and biochemical evidence suggests that it might modulate RecA. We report here the isolation and characterization of two mutants of RecU (recU56 and recU71), which promote resolution of HJs, but do not promote RecA modulation. In vitro, the RecU mutant proteins (RecUK56A or RecUR71A) bind and cleave HJs and interact with RuvB. RecU interacts with RecA and inhibits its single-stranded DNA-dependent dATP hydrolysis, but RecUK56A and RecUR71A do not exert a negative effect on the RecA dATPase and fail to interact with it. Both activities are important in vivo since RecU mutants impaired only in RecA interaction are as sensitive to DNA damaging agents as a deletion mutant.
Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction
Authors: Dotson P. Patrick , Johnson Ashley K. , Testa Stephen M. 
Published: August 2008

Abstract
Group I intron-derived ribozymes can catalyze a variety of non-native reactions. For the trans-excision-splicing (TES) reaction, an intron-derived ribozyme from the opportunistic pathogen Pneumocystis carinii catalyzes the excision of a predefined region from within an RNA substrate with subsequent ligation of the flanking regions. To establish TES as a general ribozyme-mediated reaction, intron-derived ribozymes from Tetrahymena thermophila and Candida albicans, which are similar to but not the same as that from Pneumocystis, were investigated for their propensity to catalyze the TES reaction. We now report that the Tetrahymena and Candida ribozymes can catalyze the excision of a single nucleotide from within their ribozyme-specific substrates. Under the conditions studied, the Tetrahymena and Candida ribozymes, however, catalyze the TES reaction with lower yields and rates [Tetrahymena(kobs) = 0.14/min and Candida (kobs) = 0.34/min] than the Pneumocystis ribozyme (kobs = 3.2/min). The lower yields are likely partially due to the fact that the Tetrahymena and Candida catalyze additional reactions, separate from TES. The differences in rates are likely partially due to the individual ribozymes ability to effectively bind their 3’ terminal guanosines as intramolecular nucleophiles. Nevertheless, our results demonstrate that group I intron-derived ribozymes are inherently able to catalyze the TES reaction.
On the notion of ‘software independence’ in voting systems
Authors: Rivest Ronald L 
Published: August 2008

This paper defines and explores the notion of ‘software independence’ in voting systems: ‘A voting system issoftware independentif an (undetected) change or error in its software cannot cause an undetectable change or error in an election outcome’. For example, optical scan and some cryptographically based voting systems are software independent. Variations and implications of this definition are explored. It is proposed that software-independent voting systems should be preferred, andsoftware-dependentvoting systems should be avoided.An initial version of this paper was prepared for use by the Technical Guidelines Development Committee in their development of the Voluntary Voting System Guidelines, which will specify the requirements that the USA voting systems must meet to receive certification.
Peroxisomal Malate Dehydrogenase Is Not Essential for Photorespiration in Arabidopsis But Its Absence Causes an Increase in the Stoichiometry of Photorespiratory CO2 Release
Authors: Cousins Asaph B. , Pracharoenwattana Itsara , Zhou Wenxu , Smith Steven M. , Badger Murray R. 
Published: August 2008

Abstract
Peroxisomes are important for recycling carbon and nitrogen that would otherwise be lost during photorespiration. The reduction of hydroxypyruvate to glycerate catalyzed by hydroxypyruvate reductase (HPR) in the peroxisomes is thought to be facilitated by the production of NADH by peroxisomal malate dehydrogenase (PMDH). PMDH, which is encoded by two genes in Arabidopsis (Arabidopsis thaliana), reduces NAD+ to NADH via the oxidation of malate supplied from the cytoplasm to oxaloacetate. A double mutant lacking the expression of both PMDH genes was viable in air and had rates of photosynthesis only slightly lower than in the wild type. This is in contrast to other photorespiratory mutants, which have severely reduced rates of photosynthesis and require high CO2 to grow. The pmdh mutant had a higher O2-dependent CO2 compensation point than the wild type, implying that either Rubisco specificity had changed or that the rate of CO2 released per Rubisco oxygenation was increased in the pmdh plants. Rates of gross O2 evolution and uptake were similar in the pmdh and wild-type plants, indicating that chloroplast linear electron transport and photorespiratory O2 uptake were similar between genotypes. The CO2 postillumination burst and the rate of CO2 released during photorespiration were both greater in the pmdh mutant compared with the wild type, suggesting that the ratio of photorespiratory CO2 release to Rubisco oxygenation was altered in the pmdh mutant. Without PMDH in the peroxisome, the CO2 released per Rubisco oxygenation reaction can be increased by over 50%. In summary, PMDH is essential for maintaining optimal rates of photorespiration in air; however, in its absence, significant rates of photorespiration are still possible, indicating that there are additional mechanisms for supplying reductant to the peroxisomal HPR reaction or that the HPR reaction is altogether circumvented.
Molecules, morphology and fossils: a comprehensive approach to odonate phylogeny and the evolution of the odonate wing
Authors: Bybee Seth M. , Ogden T. Heath , Branham Marc A. , Whiting Michael F. 
Published: August 2008

AbstractWe undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher‐level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non‐monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta and Zygoptera were recovered as monophyletic. Ditaxinerua is supported as the sister lineage to Odonata, Epiophlebiidae and the lestid‐like damselflies are sister to the Epiprocta and Zygoptera, respectively. Austropetaliidae + Aeshnidae is the sister lineage to the remaining Anisoptera. Tarsophlebia's placement as sister to Epiprocta or as sister to Epiprocta + Zygoptera was not resolved. Refinements are made to the current classification. Fossil taxa did not seem to provide signals crucial to recovering a robust phylogeny, but were critical to understanding the evolution of key morphological features associated with flight. Characters associated with wing structure were optimized revealing two wing character complexes: the pterostigma–nodal brace complex and the costal wing base & costal–ScP junction complex. In turn, these two complexes appear to be associated; the pterostigma–nodal brace complex allowing for further modification of the wing characters comprised within the costal wing base & costal–ScP junction complex leading the modern odonate wing.© The Willi Hennig Society 2008.
Prognostic factor of adult patients with atopic dermatitis
Authors: KATOH Norito , HIRANO Shinya , KISHIMOTO Saburo 
Published: August 2008

ABSTRACTThe increased prevalence of atopic dermatitis (AD) in adults in recent decades suggests that dermatologists may be expected to estimate the prognosis of adult patients with AD when they visit as new patients. We therefore evaluated the change in the extent of involvement and analyzed the factors that contribute to the prognosis of adult AD. A retrospective chart review was performed for 65 adults patients (median age at first visit, 25 years) with AD who had been followed monthly for over 10 years. The median area of involvement at first visit was 19%. The area of the eruptions and peripheral eosinophil counts decreased significantly in the fifth and 10th years with standard treatment. The values of immunoglobulin (Ig)E were also reduced after 10 years. Patients with high values of serum total IgE and peripheral eosinophil count, and long duration of AD had wide areas of eruptions 10 years after the first visit. Total IgE had the highest correlation with area of involvement after 10 years. Although the prognosis of adult AD is not poor, patients with high IgE values are expected to have ongoing eczema with wide distribution after 10 years of follow up.
Pulsed dye laser treatment for viral warts: A study of 120 patients
Authors: PARK Hyun Su , CHOI Woo Seok 
Published: August 2008

ABSTRACTA prospective, non‐blinded, non‐randomized study on 120 wart patients treated with pulsed dye laser was performed to evaluate the efficacy and safety of pulsed dye laser treatment for viral warts and to demonstrate the proper application and effective technique of this method. The overall clearance rate was 49.5%. The clearance rates of flat warts, periungual warts, plantar warts and common warts were 67.6%, 51.1%, 47.6% and 44.3%, respectively. Overall, the response rates of pediatric warts, recalcitrant warts and old warts were superior to those of adult warts, simple warts and non‐old warts, respectively; however, those trends were not statistically significant. We concluded that pulsed dye laser treatment is a safe, tolerable and relatively effective treatment method for viral warts. Pulsed dye laser treatment may be a more efficacious method for flat warts and recalcitrant periungual warts, and it can be an effective modality for newly‐developed warts. The highest clearance rate was noted at a fluence of 9.5 J/cm2 (P ≤ 0.05) and it is recommended that practitioners perform pulsed dye laser treatments for viral warts at the fluences of 9.0–9.5 J/cm2. A replacement of pulsed dye laser treatment should be considered unless prominent improvement is observed after three treatment sessions.
Cutaneous and systemic plasmacytosis: A Chinese case
Authors: MA Hui‐Jun , LIU Wen , LI You , ZHAO Guang , MENG Ru‐Song , LI Dong‐Guang 
Published: August 2008

ABSTRACTCutaneous and systemic plasmacytosis (CSP) is an exceedingly rare condition arising primarily in patients of Japanese descent. Herein, we describe a patient of mainland Chinese origin suffering CSP. A 49‐year‐old Chinese male had asymptomatic brownish‐red plaques and papules of the face and trunk for 6 years. Physical examination revealed innumerable symmetric red‐brownish macules on face and trunk with fewer red‐brownish papules scattered among the macules. Chemical analysis revealed hypergammaglobulinemia. Computerized tomography scan discovered some lymphadenopathy in the axillary, paratracheal and pulmonary regions. Histological examination showed focal perivascular and periadnexal infiltrate of mainly plasma cells in the superficial and deep dermis. Immunohistochemical study showed that a great number of the infiltrating cells were CD20‐positive. The infiltrated polyclonal plasma cells expressed both κ and λ light chains. Topical therapy with tacrolimus 0.1% ointment for 2 months reduced the thickness and pigmentation of the facial skin lesions. The lesions resumed the original appearance 3 weeks after discontinuing the therapy. To the best of our knowledge, this is the first case of CSP from mainland China.
Effect of add‐on gabapentin on opioid withdrawal symptoms in opium‐dependent patients
Authors: Kheirabadi Gholam R. , Ranjkesh Mansour , Maracy Mohamad R. , Salehi Mehrdad 
Published: August 2008

ABSTRACTAims  Evaluation of the efficacy of gabapentin in patients undergoing out‐patient treatment for opiate withdrawal.Design  A 3‐week double‐blind, randomized, placebo‐controlled trial of adjunctive gabapentin in methadone‐assisted detoxification (MAD).Setting  Specialized Addictive Behaviors Unit, an out‐patient unit for the treatment of patients with an addictive disorder serving the city of Isfahan (Iran).Participants  Forty out‐patients, 37 males and three females, aged 21–61 years, who met DSM‐IV criteria for opiate dependence.Intervention  Random assignment of subjects to receive adjunctive treatment with either gabapentin (900 mg/day) or placebo under double‐blind conditions.Measurements  Severity of subjective withdrawal symptoms using the Subjective Opiate Withdrawal Scale at six stages.Findings  Despite the superiority of gabapentin on controlling some of withdrawal symptoms, no significant differences were reported between two groups.Conclusions  Dosage of 900 mg/day of gabapentin is not significantly superior to placebo in controlling opiate withdrawal symptoms.
Do graphic health warning labels have an impact on adolescents’ smoking‐related beliefs and behaviours?
Authors: White Victoria , Webster Bernice , Wakefield Melanie 
Published: August 2008

ABSTRACTAims To assess the impact of the introduction of graphic health warning labels on cigarette packets on adolescents at different smoking uptake stages.Design School‐based surveys conducted in the year prior to (2005) and approximately 6 months after (2006) the introduction of the graphic health warnings. The 2006 survey was conducted after a TV advertising campaign promoting two new health warnings.Setting Secondary schools in greater metropolitan Melbourne, Australia.Participants Students in year levels 8–12: 2432 students in 2005, and 2050 in 2006, participated.Measures Smoking uptake stage, intention to smoke, reported exposure to cigarette packs, knowledge of health effects of smoking, cognitive processing of warning labels and perceptions of cigarette pack image.Findings At baseline, 72% of students had seen cigarette packs in the previous 6 months, while at follow‐up 77% had seen packs and 88% of these had seen the new warning labels. Cognitive processing of warning labels increased, with students more frequently reading, attending to, thinking and talking about warning labels at follow‐up. Experimental and established smokers thought about quitting and forgoing cigarettes more at follow‐up. At follow‐up intention to smoke was lower among those students who had talked about the warning labels and had forgone cigarettes.Conclusions Graphic warning labels on cigarette packs are noticed by the majority of adolescents, increase adolescents’ cognitive processing of these messages and have the potential to lower smoking intentions. Our findings suggest that the introduction of graphic warning labels may help to reduce smoking among adolescents.
Assessing smoking status in children, adolescents and adults: cotinine cut‐points revisited
Authors: Jarvis Martin J. , Fidler Jennifer , Mindell Jennifer , Feyerabend Colin , West Robert 
Published: August 2008

ABSTRACTAims  To reassess saliva cotinine cut‐points to discriminate smoking status. Cotinine cut‐points that are in use were derived from relatively small samples of smokers and non‐smokers 20 or more years ago. It is possible that optimal cut‐points may have changed as prevalence and exposure to passive smoking have declined.Design  Cross‐sectional survey of the general population, with assessment of self‐reported smoking and saliva cotinine.Participants  A total of 58 791 respondents aged 4 years and older in the Health Survey for England for the years 1996–2004 who provided valid saliva cotinine specimens.Measures  Saliva cotinine concentrations, demographic variables, self‐reported smoking, presence or absence of smoking in the home, a composite index of social disadvantage derived from occupation, housing tenure and access to a car.Findings  A cut‐point of 12 ng/ml performed best overall, with specificity of 96.9% and sensitivity of 96.7% in discriminating confirmed cigarette smokers from never regular smokers. This cut‐point also identified correctly 95.8% of children aged 8–15 years smoking six or more cigarettes a week. There was evidence of substantial misreport in claimed ex‐smokers, especially adolescents (specificity 72.3%) and young adults aged 16–24 years (77.5%). Optimal cut‐points varied by presence (18 ng/ml) or absence (5 ng/ml) of smoking in the home, and there was a gradient from 8 ng/ml to 18 ng/ml with increasing social disadvantage.Conclusions  The extent of non‐smokers' exposure to other people's tobacco smoke is the principal factor driving optimal cotinine cut‐points. A cut‐point of 12 ng/ml can be recommended for general use across the whole age range, although different cut‐points may be appropriate for population subgroups and in societies with differing levels of exposure to secondhand smoke.
Old enough for a beer? Compliance with minimum legal age for alcohol purchases in monopoly and other off‐premise outlets in Finland and Norway
Authors: Rossow Ingeborg , Karlsson Thomas , Raitasalo Kirsimarja 
Published: August 2008

ABSTRACTAim To assess whether government monopoly outlets comply better with minimum legal age for purchase of alcohol compared to other off‐premise outlets for alcohol sales.Methods Under‐age‐appearing 18‐year‐olds attempted to purchase alcohol in off‐premise outlets applying identical procedures in Finland (n = 290) and Norway (n = 170). Outcomes were measured as whether or not the buyers were asked to present an identity (ID) card and whether or not they succeeded in purchasing alcohol.Results The buyers were asked to present an ID card in slightly more than half the attempts, and they succeeded in purchasing alcohol in 48% of the cases. The buyers were more likely to be requested to present an ID card and less likely to succeed in purchasing alcohol in monopoly outlets compared to other types of outlets, and also when other outcome predictors, such as age and gender of salesperson and crowdedness in the outlet, were taken into account.Conclusion Monopoly outlets may facilitate compliance with minimum legal age for purchase of alcohol.