bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Analysis of Amino-Terminal Domains of the Photoreceptor Phytochrome B
Authors: PalÁgyi Andrea , Terecskei Kata , ÁdÁm Éva , Kevei Éva , Kircher Stefan , Mérai Zsuzsanna , Schäfer Eberhard , Nagy Ferenc , Kozma-BognÁr LÁszló 
Published: June 2010

Abstract
At the core of the circadian network in Arabidopsis (Arabidopsis thaliana), clock genes/proteins form multiple transcriptional/translational negative feedback loops and generate a basic approximately 24-h oscillation, which provides daily regulation for a wide range of processes. This temporal organization enhances the fitness of plants only if it corresponds to the natural day/night cycles. Light, absorbed by photoreceptors, is the most effective signal in synchronizing the oscillator to environmental cycles. Phytochrome B (PHYB) is the major red/far-red light-absorbing phytochrome receptor in light-grown plants. Besides modulating the pace and phase of the circadian clock, PHYB controls photomorphogenesis and delays flowering. It has been demonstrated that the nuclear-localized amino-terminal domain of PHYB is capable of controlling photomorphogenesis and, partly, flowering. Here, we show (1) that PHYB derivatives containing 651 or 450 amino acid residues of the amino-terminal domains are functional in mediating red light signaling to the clock, (2) that circadian entrainment is a nuclear function of PHYB, and (3) that a 410-amino acid amino-terminal fragment does not possess any functions of PHYB due to impaired chromophore binding. However, we provide evidence that the carboxyl-terminal domain is required to mediate entrainment in white light, suggesting a role for this domain in integrating red and blue light signaling to the clock. Moreover, careful analysis of the circadian phenotype of phyB-9 indicates that PHYB provides light signaling for different regulatory loops of the circadian oscillator in a different manner, which results in an apparent decoupling of the loops in the absence of PHYB under specific light conditions.
Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data
Authors: He Fei , Zhou Yuan , Zhang Ziding 
Published: June 2010

Abstract
In a plant, the progression from vegetative growth to reproductive growth is called the floral transition. Over the past several decades, the floral transition has been shown to be determined not by a single gene but by a complicated gene network. This important biological process, however, has not been investigated at a genome-wide network level. We collected Arabidopsis (Arabidopsis thaliana) protein-protein interaction data from several public databases and compiled them into a genome-wide Arabidopsis interactome. Then, we integrated gene expression profiles during the Arabidopsis floral transition process into the established protein-protein interaction network to identify two types of anticorrelated modules associated with vegetative and reproductive growth. Generally, the vegetative modules are conserved in plants, while the reproductive modules are more specific to advanced plants. The existence of floral transition switches demonstrates that vegetative and reproductive processes might be coordinated by the interacting interface of these modules. Our work also provides many candidates for mediating the interactions between these modules, which may play important roles during the Arabidopsis vegetative/reproductive switch.
Plasma and cerebrospinal fluid pharmacokinetics of flurbiprofen in children
Authors: Kumpulainen Elina , Välitalo Pyry , Kokki Merja , Lehtonen Marko , Hooker Andrew , Ranta Veli‐Pekka , Kokki Hannu 
Published: June 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECTFlurbiprofen is a commonly used non‐steroidal anti‐inflammatory drug in children to treat pain and fever. There is limited information on the pharmacokinetics of flurbiprofen in children and no data on the cerebrospinal fluid permeation of flurbiprofen.WHAT THIS STUDY ADDSOur population pharmacokinetic model indicates that weight‐based dosing of flurbiprofen is appropriate in children older than 6 months. The bioavailability of oral flurbiprofen syrup is high, 71–91%, and thus, the oral syrup provides accurate dosing in paediatric patients. Cerebrospinal fluid concentrations of flurbiprofen are markedly higher than the unbound plasma concentrations.AIMSThis study was designed to characterize paediatric pharmacokinetics and central nervous system exposure of flurbiprofen.METHODSThe pharmacokinetics of flurbiprofen were studied in 64 healthy children aged 3 months to 13 years, undergoing surgery with spinal anaesthesia. Children were administered preoperatively a single dose of flurbiprofen intravenously as prodrug (n= 27) or by mouth as syrup (n= 37). A single cerebrospinal fluid (CSF) sample (n= 60) was collected at the induction of anaesthesia, and plasma samples (n= 304) before, during and after the operation (up to 20 h after administration). A population pharmacokinetic model was built using the NONMEM software package.RESULTSFlurbiprofen concentrations in plasma were well described by a three compartment model. The apparent bioavailability of oral flurbiprofen syrup was 81%. The estimated clearance (CL) was 0.96 l h−1 70 kg−1. Age did not affect the clearance after weight had been included as a covariate. The estimated volume of distribution at steady state (Vss) was 8.1 l 70 kg−1. Flurbiprofen permeated into the CSF, reaching concentrations that were seven‐fold higher compared with unbound plasma concentrations.CONCLUSIONSFlurbiprofen pharmacokinetics can be described using only weight as a covariate in children above 6 months, while more research is needed in neonates and in younger infants.
Relation of early antibiotic use to childhood asthma: confounding by indication?
Authors: Su Y. , Rothers J. , Stern D. A. , Halonen M. , Wright A. L. 
Published: June 2010

SummaryBackground
Findings from studies of the relation between early antibiotic use and subsequent asthma have been inconsistent, which may be attributable to methodologic issues.Objective
Our objective was to assess the impact of confounding by indication on the relation of early antibiotic use to childhood asthma through age 5 in a non‐selected birth cohort (n=424).Methods
Oral antibiotic use was assessed by frequent nurse interviews in the first 9 months of life. Physician‐diagnosed active asthma and eczema were assessed by questionnaire at 1, 2, 3, and 5 years, and were considered as ever asthma or ever eczema if positive at any age. Allergen‐specific IgE was assessed in plasma at 1, 2, 3, and 5 years. Confounding by indication was investigated by considering the relation of asthma to antibiotic use while controlling for the number of illness visits to a physician in early life.Results
There was no statistically significant relation of early antibiotic use with physician‐diagnosed eczema or allergen‐specific IgE. A dose–response relation was evident for antibiotic use with ever asthma (odds ratio [OR]=1.5, P=0.047). Ever asthma also increased significantly with the number of illness visits to a physician (P<0.001). After adjustment for number of illness visits, antibiotic use showed no relation with asthma.Conclusions
The relation of asthma to antibiotics in this cohort appears to be an artefact of the strong relation of number of physician visits for illness with both antibiotic use and risk for asthma. Cite this as: Y. Su, J. Rothers, D. A. Stern, M. Halonen and A. L. Wright, Clinical & Experimental Allergy, 2010 (40) 1222–1229.
Phenotypes of childhood asthma: are they real?
Authors: Spycher B. D. , Silverman M. , Kuehni C. E. 
Published: June 2010

SummaryIt has been suggested that there are several distinct phenotypes of childhood asthma or childhood wheezing. Here, we review the research relating to these phenotypes, with a focus on the methods used to define and validate them. Childhood wheezing disorders manifest themselves in a range of observable (phenotypic) features such as lung function, bronchial responsiveness, atopy and a highly variable time course (prognosis). The underlying causes are not sufficiently understood to define disease entities based on aetiology. Nevertheless, there is a need for a classification that would (i) facilitate research into aetiology and pathophysiology, (ii) allow targeted treatment and preventive measures and (iii) improve the prediction of long‐term outcome. Classical attempts to define phenotypes have been one‐dimensional, relying on few or single features such as triggers (exclusive viral wheeze vs. multiple trigger wheeze) or time course (early transient wheeze, persistent and late onset wheeze). These definitions are simple but essentially subjective. Recently, a multi‐dimensional approach has been adopted. This approach is based on a wide range of features and relies on multivariate methods such as cluster or latent class analysis. Phenotypes identified in this manner are more complex but arguably more objective. Although phenotypes have an undisputed standing in current research on childhood asthma and wheezing, there is confusion about the meaning of the term ‘phenotype’ causing much circular debate. If phenotypes are meant to represent ‘real’ underlying disease entities rather than superficial features, there is a need for validation and harmonization of definitions. The multi‐dimensional approach allows validation by replication across different populations and may contribute to a more reliable classification of childhood wheezing disorders and to improved precision of research relying on phenotype recognition, particularly in genetics. Ultimately, the underlying pathophysiology and aetiology will need to be understood to properly characterize the diseases causing recurrent wheeze in children. Cite this as: B. D. Spycher, M. Silverman and C. E. Kuehni, Clinical & Experimental Allergy, 2010 (40) 1130–1141.
Effect of intense swimming training on rhinitis in high‐level competitive swimmers
Authors: Bougault V. , Turmel J. , Boulet L. P. 
Published: June 2010

SummaryBackground
Rhinitis is commonly reported by swimmers. Seasonal allergic rhinitis may impair athletes' performance and quality of life (QOL). No data are currently available on the changes of nasal symptoms during and after a swimming season. We aimed to determine in competitive swimmers: (1) the prevalence of rhinitis and its impact on their QOL during an intense training programme, (2) the changes in nasal symptoms and QOL after a resting period and (3) the relationship between rhinitis and airway hyperresponsiveness (AHR).Methods
Thirty‐nine swimmers and 30 healthy controls answered the Rhinitis Quality of Life Questionnaire (RQLQ) and scored nasal symptoms on a seven‐point Likert scale during the week preceding their visit. Subjects had allergy skin prick tests and a methacholine challenge. Peak nasal inspiratory flows were also measured. The athletes performed these tests during an intense training period (V1), outside the pollen season and after at least 2 weeks without swimming (V2).Results
At V1, rhinitis symptoms were reported by 74% of swimmers and 40% of controls (P<0.01). Eighty‐four percent of swimmers and 72% of controls were atopic (NS). RQLQ score was higher in swimmers compared with controls at V1 (27.3 ± 28.5 vs. 9.5 ± 12.7, respectively, P<0.005). The presence of AHR during training did not correlate with the presence of rhinitis symptoms. At V2, the nasal symptoms and RQLQ scores were similar in swimmers and controls.Conclusion
Intense swimming training is associated with an increase in nasal symptoms and impairment in QOL in most competitive swimmers. Such an increase is not related to seasonal allergen exposure in atopic athletes and probably results from chlorine derivative exposure. Cite this as: V. Bougault, J. Turmel and L. P. Boulet, Clinical & Experimental Allergy, 2010 (40) 1238–1246.
Immunocytochemical detection of Ki‐67 in Diff‐Quik‐stained cytological smears of canine mammary gland tumours
Authors: Choi U. S. , Kim D. Y. 
Published: June 2010

U.S. Choi and D.Y. Kim Immunocytochemical detection of Ki‐67 in Diff‐Quik‐stained cytological smears of canine mammary gland tumours Objective:  To investigate whether Diff‐Quik stained fine needle aspirate smears can be used to evaluate Ki‐67 expression by immunocytochemistry.Methods:  Both cytological and histological samples were obtained from 24 dogs with spontaneously developed mammary gland tumours. The cytological and histological specimens were examined by Diff‐Quik and H&E stains, respectively. After examination, both samples were immunostained using the same Ki‐67 antibody. The % Ki‐67 values were calculated based on the percentage of positively stained tumour cells per 500 and 1000 tumour cells in cytology and histology specimens, respectively.Results:  Ki‐67 staining was successful in 17/24 smears (71%) and 19/23 sections (83%). The correlation coefficient between the percentage of Ki‐67‐positive cells in cytological smears and in the histological sections was 0.677 (P < 0.01). These values were significantly different between histologically benign and malignant tumour groups both in cytology and histology samples (P < 0.001). The threshold value of the percentage of Ki‐67‐positive cells for distinguishing benign from malignant tumours was set at 4.85% with 90.9% sensitivity and 92.3% specificity by Receiver Operating Characteristic (ROC) curve using histopathology as the gold standard.Conclusion:  Diff‐Quik‐stained cytology smears can be used to detect the presence of Ki‐67 antigen when histology sections are not available.
Comparison of SurePath® and ThinPrep® liquid‐based cervical cytology using positive predictive value, atypical predictive value and total predictive value as performance indicators
Authors: Wright P. K. , Marshall J. , Desai M. 
Published: June 2010

P. K. Wright, J. Marshall and M. Desai Comparison of SurePath
®
and ThinPrep
®
liquid‐based cervical cytology using positive predictive value, atypical predictive value and total predictive value as performance indicators Objective:  Two liquid‐based cytology (LBC) systems are in widespread use in the UK: ThinPrep® and SurePath®. A number of studies have now compared LBC with conventional cytology in cervical screening. However, to date, we are aware of no studies that have compared ThinPrep® with SurePath® LBC. As the selection and use of specific diagnostic systems in a laboratory has significant clinical and economic implications, there is a clear need to compare directly existing LBC technology. The objective of this study was to compare ThinPrep® with SurePath® LBC in a single cytology laboratory using performance indicators.Methods:  Data were collected for all cervical cytology samples processed at Manchester Cytology Centre over a 1‐year period. ThinPrep® LBC was compared with SurePath® LBC using positive predictive value (PPV), atypical predictive value (APV) and total predictive value (TPV), reflecting outcome of cervical intraepithelial neoplasia (CIN) grade 2 or worse for high‐grade dyskaryosis (PPV), low‐grade dyskaryosis or borderline (atypical) cytology (APV) and all (total) abnormal cytology (TPV).Results:  2287 (out of 56 467) (ThinPrep®) and 586 (out of 22 824) (SurePath®) samples showed borderline or worse cytology after exclusion criteria. PPV, APV and TPV were within acceptable ranges for both ThinPrep® and SurePath®.Conclusions:  ThinPrep® and SurePath® were equivalent based on three performance indicators. We suggest that APV and TPV should be used as an adjunct to PPV and other methods of quality assurance for cervical screening.
Immunoadsorption in dilated cardiomyopathy: long‐term reduction of cardiodepressant antibodies
Authors: Trimpert Christiane , Herda Lars R. , Eckerle Lars G. , Pohle Susanne , Müller Carina , Landsberger Martin , Felix Stephan B. , Staudt Alexander 
Published: June 2010

Eur J Clin Invest 2010; 40 (8): 685–691AbstractBackground  Disturbances of humoral immunity have been described in dilated cardiomyopathy (DCM), and a number of antibodies against cardiac cell proteins have been identified. Previous studies showed that immunoadsorption therapy with subsequent IgG substitution (IA/IgG) enhances cardiac function, and that removal of cardiodepressant antibodies may represent one essential mechanism of this therapy. The long‐term effect of IA/IgG on the level of cardiodepressant antibodies remains to be elucidated.Methods  A total of 17 patients with DCM were observed up to 12 months after IA/IgG. Echocardiographic measurements were performed at baseline, 3, 6 and 12 months after therapy. Cardiodepressant antibodies were detected by incubation of rat cardiomyocytes with purified patients’ IgG and recording of contractility and Ca2+ ratio.Results  In contrast to patients without cardiodepressant antibodies before IA/IgG, patients with negative inotropic antibodies showed an improvement of left ventricular ejection fraction (LVEF) from 33·8 ± 1·7% to 44·7 ± 2·7%; 44·5 ± 2·3% and 51·8 ± 1·7% after 3, 6 and 12 months (P < 0·001 vs. baseline, P < 0·05 vs. LVEF of non‐cardiodepressant group). Immediately after IA/IgG therapy, no cardiodepressant effects of patients’ IgG on isolated cardiomyocytes were detectable, and this effect remained diminished until 6 months after IA/IgG (P < 0·001 for contractility and Ca2+ ratio). Compared with the levels after 3 and 6 months, cardiodepressant antibodies reoccured after 12 months (P = 0·067 for contractility, P < 0·05 for Ca2+ ratio vs. 6 months after IA/IgG). However, the negative inotropic reaction is still diminished compared with the reaction before IA/IgG.Conclusion  IA/IgG therapy induces long‐term reduction of negative inotropic antibodies. After 12 months, however, re‐increase of negative inotropic antibodies cannot be excluded.
Relative influences of DOC flux and subterranean fauna on microbial abundance and activity in aquifer sediments: new insights from 13C‐tracer experiments
Authors: FOULQUIER ARNAUD , SIMON LAURENT , GILBERT FRANCK , FOUREL FRANCOIS , MALARD FLORIAN , MERMILLOD‐BLONDIN FLORIAN 
Published: June 2010

Summary1. Aquifers are considered to be controlled bottom‐up because of their dependence on organic matter supply from surface ecosystems. Microorganisms are generally assumed to form the base of the food web and to respond strongly to organic matter supply. Although the bottom‐up control of microorganisms by carbon sources has been well documented, the potential top‐down control of obligate groundwater invertebrates on microorganisms has never been addressed in alluvial aquifers.2. The main aims of the present study were (i) to quantify the relative influences of the activity of a subterranean amphipod (Niphargus rhenorhodanensis) and the flux of dissolved organic carbon (DOC) on organic matter processing and microbial activity, biomass and abundance in slow filtration columns mimicking an alluvial aquifer, and (ii) to determine the feeding rate of N. rhenorhodanensis on sedimentary microbes by tracing the flux of a 13C‐labelled source of DOC in batches (closed systems).3. Slow filtration column experiments showed that microbial abundance, biomass and activity were primarily controlled by DOC flux, whereas the activity of N. rhenorhodanensis had only a slight effect on the microbial compartment. Modelling of carbon fluxes in the 13C‐tracer experiments indicated that the feeding activity of the amphipod was too low to significantly modify microbial growth and activity.4. Our experiments supported the hypothesis that groundwater ecosystems are controlled bottom‐up. The small influence of N. rhenorhodanensis on the microbial compartment was probably linked to its slow metabolism. Our results highlight the need for further experiments to examine the relationship between metabolic rates of subterranean organisms and their role in ecosystem functioning.
Efficacy of ‘saltwater flushing’ in protecting the Great Lakes from biological invasions by invertebrate eggs in ships’ ballast sediment
Authors: BRISKI ELIZABETA , BAILEY SARAH A. , CRISTESCU MELANIA E. , MACISAAC HUGH J. 
Published: June 2010

Summary1. Mid‐ocean exchange and saltwater flushing were implemented as management practices to reduce the likelihood of new biological invasions in the Laurentian Great Lakes associated with ships’ ballast water and sediments. Despite this, there has been no formal assessment of the efficacy of these procedures. Here, we conduct a comparative analysis of community composition of dormant taxa transported by ballast sediment before and after regulations came into effect in 2006.2. Ballast sediment samples were collected from 17 ships during the post‐regulation interval of 2007 and 2008. Invertebrate eggs were counted, hatched and species identified in the laboratory. Results were compared to similar samples collected from 39 ships between 2000 and 2002, prior to implementation of saltwater flushing regulations.3. The estimated amount of residual ballast sediment transported by vessels was significantly lower during the post‐regulation period, ranging from <1 to 45 tonnes per ship, with an average of 5 tonnes. Mean density and number of dormant viable eggs per ship declined 91 and 81%, respectively.4. Community composition also changed through time, with Rotifera accounting for 78% of taxa transported prior to regulation, whereas Cladocera and Copepoda each accounted for 38% of abundance post‐regulation. Although the number of non‐indigenous species (NIS) declined 73% per ship after 2006, the reduction was not statistically significant; however, the number of freshwater NIS – which pose the greatest risk of invasion for the Great Lakes – was significantly lowered.5. Our comparative analysis suggests that ballast management regulations enacted in 2006 markedly reduced the probability of introduction of NIS via dormant eggs carried in ballast sediments.
Quantifying the effects of temperature and flow regime on the abundance of 0+ cyprinids in the upper River Rhone using Bayesian hierarchical modelling
Authors: PIFFADY JEREMY , SOUCHON YVES , CAPRA HERVE , PARENT ERIC 
Published: June 2010

Summary1. Assuming that recruitment variation is one of the main sources of fish population and assemblage changes, it is necessary to understand how natural variations in the environment influence 0+ fish abundance. Temperature regimes play an important role in enhancing both spawning activity and survival during early larval fish development. Flow regime variation, which is a powerful source of stream disturbance, is another factor to be taken into account.2. Responses to these variables need to be assessed using long‐term datasets, since standard statistical approaches fail to provide a causal structure or to quantify the different effects. We therefore used a 26‐year dataset to evaluate the respective effects of seven derived independent variables describing the effects of temperature and flow regimes on the 0+ juvenile abundance of eight fish species in the River Rhone.3. A clustering procedure using the Kendall tau rank correlation coefficient was implemented and identified three groups of fish according to their synchronic variations in juvenile abundance; i.e. varying with decreasing juvenile abundance, slightly increasing juvenile abundance and increasing juvenile abundance. These clusters provided the basis for building hierarchical log‐Poisson generalized linear models. The Bayesian paradigm gives a reliable framework for model selection, and the best model was determined using the Bayes Factor.4. The posterior distribution of the regression parameters was coherent with what was expected based on knowledge of the biology of the different species. It indicates that temperature regime drives 0+ juvenile abundance but that flow regime also plays an important regulating role. The models thus detected evidence of the consequences of specific flow events such as larval drift and an increase in available habitat during higher flow discharges.5. Our study illustrates the advantages of using a hierarchical modelling approach to quantify ecological effects by improving discrimination between the different sources of uncertainty, leading to better precision when estimating regression parameters.