bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypereosinophilic obliterative bronchiolitis: a distinct, unrecognised syndrome
Authors: Cordier Jean-François , Cottin Vincent , Khouatra Chahéra , Revel Didier , Proust Clément , Freymond Nathalie , Thivolet-Béjui Françoise , Glérant Jean-Charles 
Published: December 2012

Biopsy-proven cases of eosinophilic bronchiolitis have only been reported in isolation, and all come from Japan.We present six patients with hypereosinophilic obliterative bronchiolitis (HOB), defined by the following criteria: 1) blood eosinophil cell count >1 G·L−1and/or bronchoalveolar lavage eosinophil count >25%; 2) persistent airflow obstruction despite high-dose inhaled bronchodilators and corticosteroids; and 3) eosinophilic bronchiolitis at lung biopsy (n=1) and/or direct signs of bronchiolitis (centrilobular nodules and branching opacities) on computed tomography (n=6).Chronic dyspnoea and cough which was often severe, without the characteristic features of asthma, were the main clinical manifestations. Atopy and asthma were present in the history of three and two patients, respectively. One patient met biological criteria of the lymphoid variant of idiopathic hypereosinophilic syndrome. Mean blood eosinophil cell count was 2.7 G·L−1and mean eosinophil differential percentage at bronchoalveolar lavage was 63%. Mean initial forced expiratory volume in 1 s/forced vital capacity ratio was 50%, normalising with oral corticosteroid therapy in all patients. HOB manifestations recurred when oral prednisone was decreased to 10–20 mg·day−1, but higher doses controlled the disease.HOB is a characteristic entity deserving to be individualised among the eosinophilic respiratory disorders. Thorough analysis is needed to determine whether unrecognised and/or smouldering HOB may further be a cause of irreversible airflow obstruction in chronic eosinophilic respiratory diseases.
Respiratory muscle function in interstitial lung disease
Authors: Walterspacher Stephan , Schlager Daniel , Walker David J. , Müller-Quernheim Joachim , Windisch Wolfram , Kabitz Hans-Joachim 
Published: December 2012

Interstitial lung diseases limit daily activities, impair quality of life and result in (exertional) dyspnoea. This has mainly been attributed to a decline in lung function and impaired gas exchange. However, the contribution of respiratory muscle dysfunction to these limitations remains to be conclusively investigated.Interstitial lung disease patients and matched controls performed body plethysmography, a standardised 6-min walk test, volitional tests (respiratory drive (P0.1), global maximal inspiratory mouth occlusion pressure (PImax), sniff nasal pressure (SnPna) and inspiratory muscle load) and nonvolitional tests on respiratory muscle function and strength (twitch mouth and transdiaphragmatic pressure during bilateral magnetic phrenic nerve stimulation (TwPmoand TwPdi)).25 patients and 24 controls were included in the study.PImaxand SnPnaremained unaltered (both p>0.05), whereasP0.1and the load on the inspiratory muscles were higher (both p<0.05) in interstitial lung disease patients compared with controls. TwPmoand TwPdiwere lower in interstitial lung disease patients (mean±sdTwPmo0.86±0.4versus1.32±0.4, p<0.001; TwPdi1.34±0.6versus1.88±0.5, p=0.022).Diaphragmatic force generation seems to be impaired in this cohort of interstitial lung disease patients while global respiratory muscle strength remains preserved. Central respiratory drive and the load imposed on the inspiratory muscles are increased. Whether impaired respiratory muscle function impacts morbidity and mortality in interstitial lung disease patients needs to be investigated in future studies.
Comparisons of health status scores with MRC grades in COPD: implications for the GOLD 2011 classification
Authors: Jones Paul W. , Adamek Lukasz , Nadeau Gilbert , Banik Norbert 
Published: December 2012

The 2011 Global Initiative for Chronic Obstructive Lung Disease (GOLD) strategy document recommends assessment of chronic obstructive pulmonary disease (COPD) using symptoms and future exacerbation risk, employing two score cut-points: COPD Assessment Test (CAT) score ≥10 or modified Medical Research Council dyspnoea scale (mMRC) grade ≥2. To explore the equivalence of these two symptom cut-points, the relationship between the CAT and the mMRC and St George's Respiratory Questionnaire (SGRQ), the Short-form Health Survey and the Functional Assessment of Chronic Illness Therapy Fatigue scores were retrospectively analysed using a primary care dataset.Data from 1817 patients (mean±sdforced expiratory volume in 1 s 1.6±0.6 L) showed a significant association between mMRC grades and all health status scores (ANOVA p<0.0001). mMRC grade 1 was associated with significant levels of health status impairment (SGRQ 39.4±15.5 and CAT 15.7±7.0); even patients with mMRC grade 0 had modestly elevated scores (SGRQ 28.5±15.1 and CAT 11.7±6.8). An mMRC grading ≥2 categorised 57.2% patients with low symptom (groups A and C)versus17.2% with the CAT. Using the mMRC cut-point (≥1) resulted in similar GOLD group categorisations as the CAT (18.9%).The mMRC showed a clear relationship with health status scores; even low mMRC grades were associated with health status impairment. Cut-points of mMRC grade ≥1 and CAT score ≥10 were approximately equivalent in determining low-symptom patients. The GOLD assessment framework may require refinement.
Sniff nasal inspiratory pressure in the longitudinal assessment of young Duchenne muscular dystrophy children
Authors: Nève Véronique , Cuisset Jean-Marie , Edmé Jean-Louis , Carpentier Alain , Howsam Mike , Leclerc Olivier , Matran Régis 
Published: December 2012

Traditional measures of respiratory function in children with Duchenne muscular dystrophy (DMD) are based on maximal inspiratory pressure (PImax) and vital capacity (VC). Sniff nasal inspiratory pressure (SNIP) measurements are easily performed by young children with neuromuscular disorders. The clinical value of SNIP in the longitudinal assessment of respiratory weakness remains to be assessed. The objective of the present study was to assess longitudinally the changes in SNIP,PImaxand VC with age in DMD children. We hypothesised that their longitudinal assessment would show an earlier decline in SNIP than VC.A 3-year, prospective follow-up, at 6-month intervals of, 33 steroid-naïve, 5–20-year-old DMD patients was analysed using a linear mixed model.SNIP measurements were reliable (within-session coefficient of variation 8%). SNIP and VC increased until 10.5 and 12.5 years of age, respectively, and declined thereafter, whilePImaxdid not change with age.SNIP was an earlier marker of decline in respiratory muscle strength (at 10.5 years) than VC (at 12.5 years) in young DMD patients. SNIP longitudinal assessment is useful in the detection of inspiratory strength decline in young DMD patients when VC values remain within normal values and as an outcome measure in clinical trials for emerging therapeutics in young DMD patients from the age of 5 years.
Effects of obstructive sleep apnoea on heart rhythm
Authors: Rossi Valentina A. , Stradling John R. , Kohler Malcolm 
Published: December 2012

Symptomatic obstructive sleep apnoea (OSA) has been proven to be a risk factor for hypertension and vascular dysfunction, and has been proposed to be causally related with cardiac arrhythmias and sudden cardiac death.Searches of bibliographical databases revealed that several mechanisms seem to underpin the association between OSA and cardiac arrhythmias: intermittent hypoxia associated with autonomic nervous system activation and increased oxidative stress, which may lead to cardiac cellular damage and alteration in myocardial excitability; recurrent arousals, resulting in sympathetic activation and coronary vasoconstriction; and increased negative intrathoracic pressure which may mechanically stretch the myocardial walls and, thus, promote acute changes in myocardial excitability as well as structural remodelling of the myocardium.Findings from cross-sectional studies suggest a high prevalence of cardiac arrhythmias in patients with OSA and a high prevalence of OSA in those with cardiac arrhythmias. Preliminary evidence from uncontrolled interventional studies suggests that treatment of OSA may prevent cardiac arrhythmias.In conclusion, there is preliminary evidence that OSA is associated with the development of cardiac arrhythmias. Data from randomised controlled studies are needed to definitively clarify the role of OSA in arrhythmogenesis.
Pulmonary function and sputum characteristics predict computed tomography phenotype and severity of COPD
Authors: Camiciottoli Gianna , Bigazzi Francesca , Paoletti Matteo , Cestelli Lucia , Lavorini Federico , Pistolesi Massimo 
Published: December 2012

Airway obstruction and parenchymal destruction underlie phenotype and severity in chronic obstructive pulmonary disease (COPD). We aimed to predict, by clinical and pulmonary function data, the predominant type and severity of pathological changes quantitatively assessed by computed tomography (CT).Airway wall thickness (AWT-Pi10) and percentage of lung area with X-ray attenuation values <-950 HU (%LAA-950) were measured in 100 (learning set) out of 473 COPD outpatients undergoing clinical and functional evaluation. Original CT measurements were translated by principal component analysis onto a plane with the novel coordinates CT1 and CT2, depending on the difference (prevalent mechanism of airflow limitation) and on the sum (severity) of AWT-Pi10 and %LAA-950, respectively. CT1 and CT2, estimated in the learning set by cross-validated models of clinical and functional variables, were used to classify 373 patients in the testing set.A model based on diffusing capacity of the lung for carbon monoxide, total lung capacity and purulent sputum predicted CT1 (r = 0.64; p<0.01). A model based on forced expiratory volume in 1 s/vital capacity, functional residual capacity and purulent sputum predicted CT2 (r = 0.77; p<0.01). Classification of patients in the testing set obtained by model-predicted CT1 and CT2 reflected, according to correlations with clinical and functional variables, both COPD phenotype and severity.Multivariate models based on pulmonary function variables and sputum purulence classify patients according to overall severity and predominant phenotype of COPD as assessed quantitatively by CT.
Opioids for chronic refractory breathlessness: patient predictors of beneficial response
Authors: Johnson Miriam J. , Bland J. Martin , Oxberry Stephen G. , Abernethy Amy P. , Currow David C. 
Published: December 2012

Chronic refractory breathlessness is common and distressing in advanced disease. Despite level I evidence to support the use of opioids for this symptom, not all patients benefit. This study aimed to discover which patient characteristics predict those most likely to gain improvement in breathlessness.This is an international, multicentre, retrospective analysis of 213 individual pooled datasets from four clinical trials of an opioid for chronic refractory breathlessness. “Response to opioid” was defined as 1) an absolute value of ≥10 mm improvement on the visual analogue scale (VAS) and 2) a relative value of ≥10% improvement from baseline VAS. We investigated baseline predictors using logistic regression.In the final model, higher baseline breathlessness intensity scores strongly predicted absolute and relative response (p<0.001). Younger age also predicted relative response (p = 0.025); functional status and dominant cause of breathlessness did not. Some evidence supported the descriptor “not enough air”, but was not statistically significant (p = 0.052).A therapeutic trial of opioids is appropriate, irrespective of the cause of the breathlessness or functional status. Younger people or those with worse breathlessness are more likely to benefit. Opioids have a role in the management of chronic refractory breathlessness, but net benefit for individuals must be optimised.
Serotypes associated with the development of pneumococcal para-pneumonic effusion in adults
Authors: Bewick Thomas , Sheppard Carmen , Greenwood Sonia , Slack Mary , Trotter Caroline , George Robert , Lim Wei Shen 
Published: December 2012

Serotypes 1, 3, 7F and 19A are implicated in childhood pneumococcal para-pneumonic effusion (PPE). It is not known whether the same is true for adult PPE.A prospective cohort study was conducted over a 2-year period. Consecutive adults admitted with community-acquired pneumonia (CAP) were studied. Pneumococcal serotype was identified from urine samples using a multiplex immunoassay.Of 920 patients recruited, 366 had pneumococcal CAP; 100 of these had PPE and a serotype was determined in 73 patients. Factors associated with PPE were age, pneumonia severity index score and serotype. Serotypes most associated with PPE were 1 (18 (45%) out of 40), 19A (9 (45%) out of 20) and 3 (8 (40%) out of 20). Serotypes common in childhood PPE were independently associated with adult PPE (adjusted OR 2.3; p = 0.003). Serotypes not included in the 7-valent pneumococcal conjugate vaccine (PCV) were more likely to be associated with PPE (OR 2.1; p = 0.024) compared with those in the vaccine. Serotypes included in PCV-13 were as likely to be associated with PPE as those that are not (OR 0.8; p = 0.301).Serotypes 1, 3, 7F and 19A are independently associated with adult PPE, a similar finding to childhood PPE. Serotype replacement following pneumococcal vaccine implementation may influence the spectrum of clinical disease.
Xpert MTB/RIF for diagnosis of tuberculosis and drug-resistant tuberculosis: a cost and affordability analysis
Authors: Pantoja Andrea , Fitzpatrick Christopher , Vassall Anna , Weyer Karin , Floyd Katherine 
Published: December 2012

Xpert MTB/RIF is a rapid test to diagnose tuberculosis (TB) and rifampicin-resistant TB. Cost and affordability will influence its uptake.We assessed the cost, globally and in 36 high-burden countries, of two strategies for diagnosing TB and multidrug-resistant (MDR)-TB: Xpert with follow-on diagnostics, and conventional diagnostics. Costs were compared with funding available for TB care and control, and donor investments in HIV prevention and care.Using Xpert to diagnose MDR-TB would cost US$70–90 million per year globally and be lower cost than conventional diagnostics globally and in all high-burden countries. Diagnosing TB in HIV-positive people using Xpert would also cost US$90–101 million per year and be lower cost than conventional diagnostics globally and in 33 out of 36 high-burden countries. Testing everyone with TB signs and symptoms would cost US$434–468 million per year globally, much more than conventional diagnostics. However, in European countries, Brazil and South Africa, the cost would represent <10% of TB funding.Introducing Xpert to diagnose MDR-TB and to diagnose TB in HIV-positive people is warranted in many countries. Using it to test everyone with TB signs and symptoms is affordable in several middle-income countries, but financial viability in low-income countries requires large increases in TB funding and/or further price reductions.
COPD and air travel: does hypoxia-altitude simulation testing predict in-flight respiratory symptoms?
Authors: Edvardsen Anne , Ryg Morten , Akerø Aina , Christensen Carl Christian , Skjønsberg Ole H. 
Published: December 2012

The reduced pressure in an aircraft cabin may cause significant hypoxaemia and respiratory symptoms in patients with chronic obstructive pulmonary disease (COPD). The current study evaluated whether there is a relationship between hypoxaemia obtained during hypoxia-altitude simulation testing (HAST), simulating an altitude of 2438 m, and the reporting of respiratory symptoms during air travel.82 patients with moderate to very severe COPD answered an air travel questionnaire. Arterial oxygen tensions during HAST (PaO2HAST) in subjects with and without in-flight respiratory symptoms were compared. The same questionnaire was answered within 1 year after the HAST.Mean±sdPaO2HASTwas 6.3±0.6 kPa and 62 (76%) of the patients hadPaO2HAST<6.6 kPa. 38 (46%) patients had experienced respiratory symptoms during air travel. There was no difference inPaO2HASTin those with and those without in-flight respiratory symptoms (6.3±0.7 kPaversus6.3±0.6 kPa, respectively; p=0.926). 54 (66%) patients travelled by air after the HAST, and patients equipped with supplemental oxygen (n=23, 43%) reported less respiratory symptoms when flying with than those without such treatment (four (17%)versus11 (48%) patients; p=0.039).In conclusion, no difference inPaO2HASTwas found between COPD patients with and without respiratory symptoms during air travel.
Cluster analysis application identifies muscle characteristics of importance for beef tenderness
Authors: Chriki Sghaier , Gardner Graham E , Jurie Catherine , Picard Brigitte , Micol Didier , Brun Jean-Paul , Journaux Laurent , Hocquette Jean-Francois 
Published: December 2012

AbstractBackgroundAn important controversy in the relationship between beef tenderness and muscle characteristics including biochemical traits exists among meat researchers. The aim of this study is to explain variability in meat tenderness using muscle characteristics and biochemical traits available in the Integrated and Functional Biology of Beef (BIF-Beef) database. The BIF-Beef data warehouse contains characteristic measurements from animal, muscle, carcass, and meat quality derived from numerous experiments. We created three classes for tenderness (high, medium, and low) based on trained taste panel tenderness scores of all meat samples consumed (4,366 observations from 40 different experiments). For each tenderness class, the corresponding means for the mechanical characteristics, muscle fibre type, collagen content, and biochemical traits which may influence tenderness of the muscles were calculated.ResultsOur results indicated that lower shear force values were associated with more tender meat. In addition, muscles in the highest tenderness cluster had the lowest total and insoluble collagen contents, the highest mitochondrial enzyme activity (isocitrate dehydrogenase), the highest proportion of slow oxidative muscle fibres, the lowest proportion of fast-glycolytic muscle fibres, and the lowest average muscle fibre cross-sectional area. Results were confirmed by correlation analyses, and differences between muscle types in terms of biochemical characteristics and tenderness score were evidenced by Principal Component Analysis (PCA). When the cluster analysis was repeated using only muscle samples fromm. Longissimus thoracis(LT), the results were similar; only contrasting previous results by maintaining a relatively constant fibre-type composition between all three tenderness classes.ConclusionOur results show that increased meat tenderness is related to lower shear forces, lower insoluble collagen and total collagen content, lower cross-sectional area of fibres, and an overall fibre type composition displaying more oxidative fibres than glycolytic fibres.
RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures
Authors: Pietal Michal J , Szostak Natalia , Rother Kristian M , Bujnicki Janusz M 
Published: December 2012

Abstract

Background
The structures of biological macromolecules provide a framework for studying their biological functions. Three-dimensional structures of proteins, nucleic acids, or their complexes, are difficult to visualize in detail on flat surfaces, and algorithms for their spatial superposition and comparison are computationally costly. Molecular structures, however, can be represented as 2D maps of interactions between the individual residues, which are easier to visualize and compare, and which can be reconverted to 3D structures with reasonable precision. There are many visualization tools for maps of protein structures, but few for nucleic acids.

Results
We developed RNAmap2D, a platform-independent software tool for calculation, visualization and analysis of contact and distance maps for nucleic acid molecules and their complexes with proteins or ligands. The program addresses the problem of paucity of bioinformatics tools dedicated to analyzing RNA 2D maps, given the growing number of experimentally solved RNA structures in the Protein Data Bank (PDB) repository, as well as the growing number of tools for RNA 2D and 3D structure prediction. RNAmap2D allows for calculation and analysis of contacts and distances between various classes of atoms in nucleic acid, protein, and small ligand molecules. It also discriminates between different types of base pairing and stacking.

Conclusions
RNAmap2D is an easy to use method to visualize, analyze and compare structures of nucleic acid molecules and their complexes with other molecules, such as proteins or ligands and metal ions. Its special features make it a very useful tool for analysis of tertiary structures of RNAs. RNAmap2D for Windows/Linux/MacOSX is freely available for academic users at http://iimcb.genesilico.pl/rnamap2d.html
Abundance, distribution and potential impact of transposable elements in the genome of Mycosphaerella fijiensis
Authors: Santana Mateus F , Silva José CF , Batista Aline D , Ribeiro Lílian E , da Silva Gilvan F , de Araújo Elza F , de Queiroz Marisa V 
Published: December 2012

Abstract

Background

Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed repetitive DNA sequences found in a host genome. These elements have the ability to move from one location to another within the genome, and their insertion can cause a wide spectrum of mutations in their hosts. Some of the deleterious effects of TEs may be due to ectopic recombination among TEs of the same family. In addition, some transposons are physically linked to genes and can control their expression. To prevent possible damage caused by the presence of TEs in the genome, some fungi possess TE-silencing mechanisms, such as RIP (Repeat Induced Point mutation). In this study, the abundance, distribution and potential impact of TEs in the genome of M. fijiensis were investigated.

Results
A total of 613 LTR-Gypsy and 27 LTR-Copia complete elements of the class I were detected. Among the class II elements, a total of 28 Mariner, five Mutator and one Harbinger complete elements were identified. The results of this study indicate that transposons were and are important ectopic recombination sites. A distribution analysis of a transposable element from each class of the M. fijiensis isolates revealed variable hybridization profiles, indicating the activity of these elements. Several genes encoding proteins involved in important metabolic pathways and with potential correlation to pathogenicity systems were identified upstream and downstream of transposable elements. A comparison of the sequences from different transposon groups suggested the action of the RIP silencing mechanism in the genome of this microorganism.

Conclusions
The analysis of TEs in M. fijiensis suggests that TEs play an important role in the evolution of this organism because the activity of these elements, as well as the rearrangements caused by ectopic recombination, can result in deletion, duplication, inversion and translocation. Some of these changes can potentially modify gene structure or expression and, thus, facilitate the emergence of new strains of this pathogen.