bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of reactance to estimate transpulmonary resistance
Authors: Johnson M. K. , Birch M. , Carter R. , Kinsella J. , Stevenson R. D. 
Published: June 2005

This study examines the relationship of respiratory system resistance (Rrs) and reactance (Xrs) measured by forced oscillometry with transpulmonary resistance (RL) measured by oesophageal manometry.Simultaneous forced oscillometry using a single frequency of 5 Hz and oesophageal manometry were performed on five asthmatics during bronchoprovocation. The data obtained were used to derive prediction equations forRLfrom oscillometric parameters, which were tested on a further six asthmatics and 35 nonasthmatic subjects.In the first five asthmatic subjects,RLcorrelated more strongly withXrsthan withRrs. In the second set of asthmatics,RLranged 0.0005–4.57 kPa·s·L−1, with a median of 0.21 kPa·s·L−1. TheRLvalues predicted fromXrsshowed a mean±sddifference of −0.067±0.25 kPa·s·L−1compared with the values measured in this set of patients.Xrsin subjects with other respiratory conditions appeared to follow the same relationship withRLas in asthmatics. Lumped element modelling suggested that the linear relationship betweenXrsandRLwas a consequence of the increasing contribution of central and upper airway wall shunts as peripheral airway resistance rose, and that this effect was much larger than that due to changes in static elastance.In conclusion, the reactance of the respiratory system can predict transpulmonary resistance more accurately than can the resistance of the respiratory system.
Altered protein tyrosine phosphorylation in asthmatic bronchial epithelium
Authors: Hamilton L. M. , Puddicombe S. M. , Dearman R. J. , Kimber I. , Sandström T. , Wallin A. , Howarth P. H. , Holgate S. T. , Wilson S. J. , Davies D. E. 
Published: June 2005

A disease-related, corticosteroid-insensitive increase in the expression of epidermal growth factor (EGF) receptor (EGFR) tyrosine kinase in asthmatic bronchial epithelium has been shown previously by the current authors. To determine whether this is associated with enhanced intracellular signalling, the aim of this study was to evaluate epithelial tyrosine phosphorylation.Bronchial biopsies were analysed for the presence of phosphotyrosine by immunohistochemistry. Bronchial epithelial cells were exposed to EGF, hydrogen peroxide or tumour necrosis factor-αin vitrofor measurement of tyrosine phosphorylated signalling intermediates and interleukin (IL)-8 release.Phosphotyrosine was increased significantly in the epithelium of severe asthmatics when compared with controls or mild asthmatics; however, in mild asthma, phosphotyrosine levels were significantly decreased when compared with controls. There was no significant difference between phosphotyrosine levels before or after 8 weeks of treatment with budesonide. Stimulation of bronchial epithelial cells resulted in tyrosine phosphorylation of several proteins, including EGFR, Shc and p42/p44 mitogen-activated protein kinase. In the presence of salbutamol, a transient partial suppression of EGFR phosphorylation occurred, whereas dexamethasone was without effect. Neither salbutamol nor dexamethasone inhibited EGF-stimulated IL-8 release.These data indicate that regulation of protein tyrosine kinase activity is abnormal in severe asthma. The epidermal growth factor receptor and/or other tyrosine kinase pathways may contribute to persistent, corticosteroid-unresponsive inflammation in severe asthma.
Acoustic analysis of snoring before and after palatal surgery
Authors: Jones T. M. , Swift A. C. , Calverley P. M. A. , Ho M. S. , Earis J. E. 
Published: June 2005

To investigate the effectiveness of palatal surgery for nonapnoeic snoring, 35 patients were block randomised to undergo one of two different palatoplasty procedures. Patients were admitted pre-operatively for audio recording of snoring sound and video recording of sleeping position, and between 1.0 and 4.1 months (mean 2.5) and between 5.9 and 17.5 months (mean 9.7) post-operatively. Sound files, comprising the inspiratory sound of the first 100 snores whilst sleeping in a supine position, were analysed using specifically designed software.Snore duration (s), loudness (dBA), periodicity (%) and energy ratios for the frequency bands 0–200 Hz, 0–250 Hz and 0–400 Hz were calculated. Subjective outcomes were noted. Operation type, body mass index, age, peak nasal inspiratory flow rate, Epworth sleep score and alcohol intake were considered as confounding variables.No patient was cured from snoring. Paired t-test analysis demonstrated statistically significant changes between pre- and early post-operative recordings for snore periodicity and energy ratios in the frequency ranges 0–200 Hz, 0–250 Hz and 0–400 Hz.In conclusion, only the 0–250-Hz energy ratio measurements maintained a statistically significant improvement at the time of the late post-operative recording, despite an obvious drift back to pre-operative levels. No confounding variables were identified. The subjective and objective results correlated poorly. Post-operative changes in the acoustic parameters of snoring sound, following palatal surgery, are demonstrable but short-lived.
Involvement of retinoic acid-inducible gene-I in the IFN-γ/STAT1 signalling pathway in BEAS-2B cells
Authors: Imaizumi T. , Kumagai M. , Taima K. , Fujita T. , Yoshida H. , Satoh K. 
Published: June 2005

Bronchial epithelial cells play an important role in airway host defence, and interferon (IFN)-γ controls immune reactions by regulating the expression of various genes in bronchial epithelial cells. Signal transducer and activator of transcription 1 (STAT1) is the key transcriptional factor in IFN-γ signalling. Retinoic acid-inducible gene-I (RIG-I) is a member of the DExH box family of proteins and designated a putative RNA helicase. RNA helicases play diverse roles in regulation of gene expression and cellular functions, and RIG-I is implicated in antiviral responses.The aim of the present study was to investigate the effect of IFN-γ on RIG-I expression in a cell line derived from human bronchial epithelial cells, BEAS-2B.Induction of RIG-I in response to IFN-γ was found in BEAS-2B cells. Induction of RIG-I by IFN-γ was also demonstrated in another pulmonary epithelial cell line, NCI-H292. Transfection of BEAS-2B cells with RIG-I complementary DNA resulted in the upregulation of STAT1. Induction of IFN-γ-inducible protein 10 by IFN-γ was enhanced in the cells overexpressing RIG-I.It is concluded that retinoic acid-inducible gene-I may play an important role in the regulation of immunological reactions in bronchial epithelial cells elicited by interferon-γ.
Patient stratification in the management of acute bacterial exacerbation of chronic bronchitis: the role of levofloxacin 750 mg
Authors: Martinez F. J. , Grossman R. F. , Zadeikis N. , Fisher A. C. , Walker K. , Ambruzs M. E. , Tennenberg A. M. 
Published: June 2005

This is the first prospective clinical trial in which patients with acute bacterial exacerbation of chronic bronchitis have been stratified by degree of underlying illness.Uncomplicated patients were randomised to levofloxacin 750 mg once daily (q.d.) for 3 days or azithromycinq.d.for 5 days. Complicated patients were randomised to levofloxacin 750 mgq.d.for 5 days or amoxicillin 875 mg/clavulanate 125 mg twice daily for 10 days.Regardless of therapy, complicated patients demonstrated lower clinical and microbiological success than uncomplicated patients. Clinical success for clinically evaluable patients was similar for levofloxacin and azithromycin (93.0versus90.1%, respectively), and levofloxacin and amoxicillin/clavulanate (79.2versus81.7%, respectively). For microbiologically evaluable patients, clinical response to levofloxacin for 3 days was superior to azithromycin for 5 days (96.3versus87.4%, respectively), and levofloxacin for 5 days was similar to amoxicillin/clavulanate for 10 days (81.4versus80.9%, respectively). Microbiological eradication was superior for levofloxacin for 3 days compared with azithromycin for 5 days (93.8versus82.8%, respectively), and similar for levofloxacin and amoxicillin/clavulanate for 10 days (81.4versus79.8%, respectively).In conclusion, levofloxacin 750 mg for 3 days was comparable to azithromycin for 5 days for uncomplicated patients with acute bacterial exacerbation of chronic bronchitis, while 5 days of 750 mg levofloxacin was comparable to 10 days of amoxicillin/clavulanate for complicated acute bacterial exacerbation of chronic bronchitis.
Randomised trial of ambulatory oxygen in oxygen-dependent COPD
Authors: Lacasse Y. , Lecours R. , Pelletier C. , Bégin R. , Maltais F. 
Published: June 2005

Long-term oxygen therapy may limit a patient's ability to remain active and may be detrimental to the rehabilitation process. This study aimed to determine the effect of ambulatory oxygen on quality of life and exercise capacity in patients with chronic obstructive pulmonary disease fulfilling the usual criteria of long-term oxygen therapy.In a 1-yr, randomised, three-period, crossover trial, 24 patients (mean age 68 yrs; mean arterial partial pressure of oxygen at rest 7.1 kPa (53 mmHg)) were allocated to one of the six possible sequences generated by three interventions: 1) standard therapy (home oxygen therapy with an oxygen concentrator only); 2) standard therapy plus as-needed ambulatory oxygen; and 3) standard therapy plus ambulatory compressed air. The comparison of ambulatory oxygenversusambulatory compressed air was double blind. The main outcomes were quality of life (Chronic Respiratory Questionnaire), exercise tolerance (6-min walk test) and daily duration of exposure to oxygen therapy.The trial was stopped prematurely after an interim analysis. On average, the patients used few ambulatory cylinders (7.5 oxygen cylindersversus7.4 compressed air cylinders over a 3-month study period). Ambulatory oxygen had no effect on any of the outcomes.In conclusion, the current results do not support the widespread provision of ambulatory oxygen to patients with oxygen-dependent chronic obstructive pulmonary disease.
Predictive value of image cytometry for diagnosis of lung cancer in heavy smokers
Authors: Xing S. , Khanavkar B. , Nakhosteen J. A. , Atay Z. , Jöckel K-H. , Marek W. 
Published: June 2005

The Research Institute for Diagnosis and Treatment of Early Lung Cancer (RIDTELC) Lung Study was initiated to determine whether lung cancer screening by automated sputum cytometry combined with conventional sputum cytology and auto-fluorescence in addition to white light bronchoscopy could enhance the detection rate of early lung cancer. The present study analyses the initial findings to evaluate the efficiency of automated sputum cytology in predicting the diagnosis of lung cancer.In this study, malignancy grade was used as a predictive parameter for lung cancer. In total, 2,480 heavy smokers (>30 pack-yrs), aged 50–74 yrs, with no previous cancer in the last 5 yrs, received chest radiology, conventional sputum cytology and sputum cytometry screening.In total, twenty-seven lung cancers were diagnosed, representing a prevalence of 1.1%, 25 of which provided sputum samples. Positive automated sputum cytology results were seen in 176 smokers (7.2%), 10 (0.4%) of whom had severe dysplasia or higher lesions (positive results) by conventional sputum cytology examination. Out of 25 tumour cases, 20 had suspicious results using automated sputum cytology, representing 80% sensitivity. One patient out of 24 with tumours had positive results on conventional sputum cytology, representing a sensitivity of 4.2%. For all stages of squamous cell lung cancer and later stage adenocarcinoma the sensitivity of automated sputum cytology was 100%. For adenocarcinoma stage I sensitivity was 25%.In conclusion, DNA analysis of sputum slides by automated sputum cytology may be a suitable tool for the detection of early lung cancer and the characterisation of a high-risk group with pre-invasive lesions for follow-up.
Endobronchial pseudo-tumour caused by herpes simplex
Authors: Upadya A. , Tilluckdharry L. , Nagy C. D. , Ravichandran P. , Manthous C. 
Published: June 2005

Herpes simplex virus (HSV) causes tracheobronchitis and pneumonitis; however, to date, there has only been one report of an endobronchial mass caused by HSV type II.This case study describes a 68-yr-old female with severe kyphoscoliosis who was intubated for acute on chronic hypercapnic respiratory failure and developed blood-tinged endotracheal secretions.Fibreoptic bronchoscopy demonstrated an endobronchial mass in the right middle lobe. Cultures grew HSV type I and biopsy specimens demonstrated cytopathological changes consistent with HSV infection.This is the first reported case of HSV type I presenting as an endobronchial tumour.
Alveolar nitric oxide in adults with asthma: evidence of distal lung inflammation in refractory asthma
Authors: Berry M. , Hargadon B. , Morgan A. , Shelley M. , Richter J. , Shaw D. , Green R. H. , Brightling C. , Wardlaw A. J. , Pavord I. D. 
Published: June 2005

Recent studies have suggested that alveolar nitric oxide (NO) concentration is a noninvasive test of distal lung inflammation.The current study determined whether alveolar NO concentration can be measured in patients with asthma of varying severity, tested the hypothesis that there is an association between alveolar NO and bronchoalveolar lavage (BAL) eosinophil count and determined whether refractory asthma is characterised by a raised alveolar NO concentration. Finally, the present authors assessed the effect of 2 weeks of prednisolone (30 mgq.d.) on alveolar NO concentration.Alveolar NO concentration was both measurable and repeatable in patients with refractory asthma. A positive correlation was found between alveolar NO concentration and BAL eosinophil count but not with bronchial wash or sputum eosinophil count. Alveolar NO concentration was increased in patients with refractory asthma (7.1 ppb) compared with mild-to-moderate asthma (3.4 ppb) and normal controls (3.4 ppb) and reduced by treatment with prednisolone.In conclusion, these findings support the hypothesis that alveolar nitric oxide is a measure of distal airway inflammation and suggest that distal lung inflammation is present in refractory asthma.
The six-minute walk test in healthy children: reliability and validity
Authors: Li A. M. , Yin J. , Yu C. C. W. , Tsang T. , So H. K. , Wong E. , Chan D. , Hon E. K. L. , Sung R. 
Published: June 2005

The aim of this study was to assess the reliability and validity of the 6-min walk test (6MWT) in healthy children.Chinese secondary school students were randomly recruited. They attended the current authors' unit on two occasions, separated by 2 weeks. Physical examination and standardised maximum incremental exercise testing on a treadmill were performed on the first visit. Spirometry and 6MWT were carried out on the second visit. A randomly selected subgroup was invited to return for repeat 6MWT at an interval of 2–4 weeks.Seventy-eight subjects were recruited; however, four failed to achieve maximal effort on exercise test. The final group included 43 young females and the mean±sdage of the subjects was 14.2±1.2 yrs. Physical examination was unremarkable in all cases. The mean±sdper cent predicted forced expiratory volume in one second was 91.4±10.2%. Concurrent validity was demonstrated by good correlation between the 6-min walking distance and maximum oxygen uptake determined on the exercise treadmill. Test–retest reliability was undertaken in 52 subjects, and the intraclass correlation coefficient (95% confidence interval) was calculated as 0.94 (0.89–0.96). In addition, Bland and Altman plots demonstrated a high degree of repeatability.In healthy children, the 6-min walk test is a reliable and valid functional test for assessing exercise tolerance and endurance.
Bacterial activity in cystic fibrosis lung infections
Authors: Rogers Geraint B , Carroll Mary P , Serisier David J , Hockey Peter M , Kehagia Valia , Jones Graeme R , Bruce Kenneth D 
Published: June 2005

Abstract
Background
Chronic lung infections are the primary cause of morbidity and mortality in Cystic Fibrosis (CF) patients. Recent molecular biological based studies have identified a surprisingly wide range of hitherto unreported bacterial species in the lungs of CF patients. The aim of this study was to determine whether the species present were active and, as such, worthy of further investigation as potential pathogens.

Methods
Terminal Restriction Fragment Length Polymorphism (T-RFLP) profiles were generated from PCR products amplified from 16S rDNA and Reverse Transcription Terminal Restriction Fragment Length Polymorphism (RT-T-RFLP) profiles, a marker of metabolic activity, were generated from PCR products amplified from 16S rRNA, both extracted from the same CF sputum sample. To test the level of activity of these bacteria, T-RFLP profiles were compared to RT-T-RFLP profiles.

Results
Samples from 17 individuals were studied. Parallel analyses identified a total of 706 individual T-RF and RT-T-RF bands in this sample set. 323 bands were detected by T-RFLP and 383 bands were detected by RT-T-RFLP (statistically significant; P ≤ 0.001). For the group as a whole, 145 bands were detected in a T-RFLP profile alone, suggesting metabolically inactive bacteria. 205 bands were detected in an RT-T-RFLP profile alone and 178 bands were detected in both, suggesting a significant degree of metabolic activity. Although Pseudomonas aeruginosa was present and active in many patients, a low occurrence of other species traditionally considered to be key CF pathogens was detected. T-RFLP profiles obtained for induced sputum samples provided by healthy individuals without CF formed a separate cluster indicating a low level of similarity to those from CF patients.

Conclusion
These results indicate that a high proportion of the bacterial species detected in the sputum from all of the CF patients in the study are active. The widespread activity of bacterial species in these samples emphasizes the potential importance of these previously unrecognized species within the CF lung.
Empirical codon substitution matrix
Authors: Schneider Adrian , Cannarozzi Gina M , Gonnet Gaston H 
Published: June 2005

Abstract
Background
Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution.

Results
A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons.

Conclusion
The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.
YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities
Authors: Schwarz Roland , Musch Patrick , von Kamp Axel , Engels Bernd , Schirmer Heiner , Schuster Stefan , Dandekar Thomas 
Published: June 2005

Abstract
Background
A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has been improved by an editor and analyzer of metabolic flux modes. Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest.

Results
YANA features a platform-independent, dedicated toolbox for metabolic networks with a graphical user interface to calculate (integrating METATOOL), edit (including support for the SBML format), visualize, centralize, and compare elementary flux modes. Further, YANA calculates expected flux distributions for a given Elementary Mode (EM) activity pattern and vice versa. Moreover, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomics or gene expression data give a rough indication of some individual enzyme activities, whereas the complete flux distribution in the network is often not known. As such data are noisy, YANA features a fast evolutionary algorithm (EA) for the prediction of EM activities with minimum error, including alerts for inconsistent experimental data. We offer the possibility to include further known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as an illustration example. All software and documentation are available for download at http://yana.bioapps.biozentrum.uni-wuerzburg.de.

Conclusion
A graphical toolbox and an editor for METATOOL as well as a series of additional routines for metabolic network analyses constitute a new user-friendly software for such efforts.