Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

Structural analysis of receptors and actin polarity in platelet protrusions.

During activation the platelet cytoskeleton is reorganized, inducing adhesion to the extracellular matrix and cell spreading. These processes are critical for wound healing and clot formation. Initially, this task relies on the formation of strong cellular-extracellular matrix interactions, exposed in subendothelial lesions. Despite the medical relevance of these processes, there is a lack of high-resolution structural information on the platelet cytoskeleton controlling cell spreading and adhesion. Here, we present in situ structural analysis of membrane receptors and the underlying cytoskeleton in platelet protrusions by applying cryoelectron tomography to intact platelets. We utilized three-dimensional averaging procedures to study receptors at the plasma membrane. Analysis of substrate interaction-free receptors yielded one main structural class resolved to 26 Å, resembling the αIIbß3 integrin folded conformation. Furthermore, structural analysis of the actin network in pseudopodia indicates a nonuniform polarity of filaments. This organization would allow generation of the contractile forces required for integrin-mediated cell adhesion.

Graphite to diamond transition induced by photoelectric absorption of ultraviolet photons.

The phase transition from graphite to diamond is an appealing object of study because of many fundamental and also, practical reasons. The out-of-plane distortions required for the transition are a good tool to understand the collective behaviour of layered materials (graphene, graphite) and the van der Waals forces. As today, two basic processes have been successfully tested to drive this transition: strong shocks and high energy femtolaser excitation. They induce it by increasing either pressure or temperature on graphite. In this work, we report a third method consisting in the irradiation of graphite with ultraviolet photons of energies above 4.4 eV. We show high resolution electron microscopy images of pyrolytic carbon evidencing the dislocation of the superficial graphitic layers after irradiation and the formation of crystallite islands within them. Electron energy loss spectroscopy of the islands show that the sp2 to sp3 hybridation transition is a surface effect. High sensitivity X-ray diffraction experiments and Raman spectroscopy confirm the formation of diamond within the islands.

Persistence of Breakage in Specific Chromosome Bands 6 Years after Acute Exposure to Oil.

BACKGROUND: The identification of breakpoints involved in chromosomal damage could help to detect genes involved in genetic disorders, most notably cancer. Until now, only one published study, carried out by our group, has identified chromosome bands affected by exposure to oil from an oil spill. In that study, which was performed two years after the initial oil exposure in individuals who had participated in clean-up tasks following the wreck of the Prestige, three chromosomal bands (2q21, 3q27, 5q31) were found to be especially prone to breakage. A recent follow-up study, performed on the same individuals, revealed that the genotoxic damage had persisted six years after oil exposure. OBJECTIVES: To determine whether there exist chromosome bands which are especially prone to breakages and to know if there is some correlation with those detected in the previous study. In addition, to investigate if the DNA repair problems detected previously persist in the present study. DESIGN: Follow-up study performed six years after the Prestige oil spill. SETTING: Fishermen cooperatives in coastal villages. PARTICIPANTS: Fishermen highly exposed to oil spill who participated in previous genotoxic study six years after the oil. MEASUREMENTS: Chromosome damage in peripheral lymphocytes. For accurate identification of the breakpoints involved in chromosome damage of circulating lymphocytes, a sequential stain/G-banding technique was employed. To determine the most break-prone chromosome bands, two statistical methods, the Fragile Site Multinomial and the chi-square tests (where the bands were corrected by their length) were used. To compare the chromosome lesions, structural chromosome alterations and gaps/breaks between two groups of individuals we used the GEE test which takes into account a possible within-individual correlation. Dysfunctions in DNA repair mechanisms, expressed as chromosome damage, were assessed in cultures with aphidicolin by the GEE test. RESULTS: Cytogenetic analyses were performed in 47 exposed individuals. A total of 251 breakpoints in exposed individuals) were identified, showing a non-uniform distribution in the human ideogram. Ten chromosome bands were found to be especially prone to breakage through both statistical methods. By comparing these bands with those observed in certain exposed individuals who had already participated the previous study, it was found in both studies that four bands (2q21, 3q27, 5q31 and 17p11.2) are particularly sensitive to breakage. Additionally, the dysfunction in DNA repair mechanisms was not significantly higher in oil-exposed individuals than in non-exposed individuals. LIMITATIONS: The sample size and the possibility of some kind of selection bias should be considered. Genotoxic results cannot be extrapolated to the high number of individuals who participated occasionally in clean-up tasks. CONCLUSION: Our findings show the existence of at least four target bands (2q21, 3q27, 5q31 and 17p11.2) with a greater propensity to break over time after an acute exposure to oil. The breaks in these bands, which are commonly involved in hematological cancer, may explain the increase of cancer risk reported in chronically benzene-exposed individuals. In addition, a more efficiency of the DNA repair mechanisms has been detected six years after in fishermen who were highly exposed to the oil spill. To date, only this study, performed by our group on the previous and present genotoxic effects, has analyzed the chromosomal regions affected by breakage after an acute oil exposure.

Follow-Up Genotoxic Study: Chromosome Damage Two and Six Years after Exposure to the Prestige Oil Spill.

BACKGROUND: The north-west coast of Spain was heavily contaminated by the Prestige oil spill, in 2002. Individuals who participated in the clean-up tasks showed increased chromosome damage two years after exposure. Long-term clinical implications of chromosome damage are still unknown. OBJECTIVE: To realize a follow-up genotoxic study to detect whether the chromosome damage persisted six years after exposure to the oil. DESIGN: Follow-up study. SETTING: Fishermen cooperatives in coastal villages. PARTICIPANTS: Local fishermen who were highly exposed (n = 52) and non-exposed (n = 23) to oil seven years after the spill. MEASUREMENTS: Chromosome damage in circulating lymphocytes. RESULTS: Chromosome damage in exposed individuals persists six years after oil exposure, with a similar incidence than those previously detected four years before. A surprising increase in chromosome damage in non-exposed individual was found six years after Prestige spill vs. those detected two years after the exposure. LIMITATIONS: The sample size and the possibility of some kind of selection bias should be considered. Genotoxic results cannot be extrapolated to the approximately 300,000 individuals who participated occasionally in clean-up tasks. CONCLUSION: The persistence of chromosome damage detected in exposed individuals six years after oil exposure seems to indicate that the cells of the bone marrow are affected. A surprising increase in chromosome damage in non-exposed individuals detected in the follow-up study suggests an indirect exposition of these individuals to some oil compounds or to other toxic agents during the last four years. More long-term studies are needed to confirm the presence of chromosome damage in exposed and non-exposed fishermen due to the association between increased chromosomal damage and increased risk of cancer. Understanding and detecting chromosome damage is important for detecting cancer in its early stages. The present work is the first follow-up cytogenetic study carried out in lymphocytes to determine genotoxic damage evolution between two and six years after oil exposure in same individuals.

Determinants of exercise capacity in obese and non-obese COPD patients.

BACKGROUND: The effects of obesity in combination with chronic obstructive pulmonary disease (COPD) on exercise capacity are receiving increased attention. But, a comprehensive analysis of factors associated with aerobic capacity in obese COPD patients has not been performed. METHODS: Six-min walking test (6MWT) was performed in 251 COPD patients, and 159 of those also carried out an incremental cardiopulmonary exercise test (CPET) to evaluate exercise capacity. In all patients, anthropometrics, dyspnea and anxiety-depression scores, lung function, daily physical activity, co-morbidities and circulating inflammatory biomarkers were also assessed. Six-min walking distance (6MWD) and peak oxygen uptake (VO2 peak) during CPET were two primary outcome variables. RESULTS: 57% of the patients showed body mass index (BMI) < 30 kg/m2 (COPDN) and the remaining 43% were obese with a BMI ≥ 30 kg/m2 (COPDO). In patients with COPDN, 6MWD showed independent negative associations with age, dyspnea score, sedentarism, depression scores and a positive relationship with arterial oxygenation; whereas in COPDO, 6MWD showed an inverse relationship with BMI. In COPDN, VO2 peak showed a negative association with age and positive relationships with both FEV1 and DLCO. However, in COPDO the dyspnea score was the strongest determinant of VO2 peak. CONCLUSIONS: Obese and non-obese COPD patients show different determinants of aerobic capacity, including pulmonary and non-pulmonary factors that are also dependent on the type of exercise protocol. These results could be considered in the evaluation of obese patients with COPD.

Hospital admissions and exercise capacity decline in patients with COPD.

Exercise capacity declines with time and is an important determinant of health status and prognosis in patients with chronic obstructive pulmonary disease (COPD). We hypothesised that hospital admissions are associated with exercise capacity decline in these patients. Clinical and functional variables were collected for 342 clinically stable COPD patients. The 6-min walk distance (6MWD) was determined at baseline and after a mean±sd of 1.7±0.3 years. Information on hospitalisations during follow-up was obtained from centralised administrative databases. Linear regression was used to model changes in exercise capacity. Patients were mostly male (92%), with mean±sd age 67.9±8.6 years, post-bronchodilator forced expiratory volume in 1 s 54±17% predicted and baseline 6MWD 433±93 m. During follow-up, 6MWD decreased by 21.9±51.0 m·year(-1) and 153 (45%) patients were hospitalised at least once. Among patients admitted only for COPD-related causes (50% of those ever admitted), the proportion presenting a clinically significant loss of 6MWD was higher than in patients admitted for only nonrespiratory conditions (53% versus 29%, p=0.040). After adjusting for confounders, annual 6MWD decline was greater (26 m·year(-1), 95% CI 13-38 m·year(-1); p<0.001) in patients with more than one all-cause hospitalisation per year, as compared with those with no hospitalisations. Hospitalisations are related to a greater decline in exercise capacity in COPD.

Evaluation of the persistence of functional and biological respiratory health effects in clean-up workers 6 years after the prestige oil spill.

Fishermen who had participated in clean-up activities of the Prestige oil spill showed increased bronchial responsiveness and higher levels of respiratory biomarkers 2 years later. We aimed to evaluate the persistence of these functional and biological respiratory health effects 6 years after clean-up work. In 2008/2009 a follow-up study was done in 230 never-smoking fishermen who had been exposed to clean-up work in 2002/2003 and 87 non-exposed fishermen. Lung function and bronchial responsiveness testing and the determination of respiratory biomarkers in exhaled breath condensate were done identically as in the baseline survey in 2004/2005. Associations between participation in clean-up work and respiratory health parameters were assessed using linear and logistic regression analyses adjusting for sex and age. Information from 158 exposed (69%) and 57 non-exposed (66%) fishermen was obtained. Loss to follow-up in the non-exposed was characterised by less respiratory symptoms at baseline. During the 4-year follow-up period lung function, bronchial hyperresponsiveness and the levels of respiratory biomarkers of oxidative stress and growth factors had deteriorated notably more among non-exposed than among exposed. At follow-up, respiratory health indices were similar or better in clean-up workers than in non-exposed. No clear differences between highly exposed and moderately exposed clean-up workers were found. In conclusion, we could not detect long-term respiratory health effects in clean-up workers 6 years after the Prestige oil spill. Methodological issues that need to be considered in this type of studies include the choice of a non-exposed control group and limitation of follow-up to subgroups such as never smokers.

Chromosomal bands affected by acute oil exposure and DNA repair errors.

BACKGROUND: In a previous study, we showed that individuals who had participated in oil clean-up tasks after the wreckage of the Prestige presented an increase of structural chromosomal alterations two years after the acute exposure had occurred. Other studies have also reported the presence of DNA damage during acute oil exposure, but little is known about the long term persistence of chromosomal alterations, which can be considered as a marker of cancer risk. OBJECTIVES: We analyzed whether the breakpoints involved in chromosomal damage can help to assess the risk of cancer as well as to investigate their possible association with DNA repair efficiency. METHODS: Cytogenetic analyses were carried out on the same individuals of our previous study and DNA repair errors were assessed in cultures with aphidicolin. RESULTS: Three chromosomal bands, 2q21, 3q27 and 5q31, were most affected by acute oil exposure. The dysfunction in DNA repair mechanisms, expressed as chromosomal damage, was significantly higher in exposed-oil participants than in those not exposed (p= 0.016). CONCLUSION: The present study shows that breaks in 2q21, 3q27 and 5q31 chromosomal bands, which are commonly involved in hematological cancer, could be considered useful genotoxic oil biomarkers. Moreover, breakages in these bands could induce chromosomal instability, which can explain the increased risk of cancer (leukemia and lymphomas) reported in chronically benzene-exposed individuals. In addition, it has been determined that the individuals who participated in clean-up of the oil spill presented an alteration of their DNA repair mechanisms two years after exposure.

Pulmonary vascular abnormalities in chronic obstructive pulmonary disease undergoing lung transplant.

BACKGROUND: Little is known about the structure and function relationships of pulmonary vessels in the most severe chronic obstructive pulmonary disease (COPD) spectrum. We investigated morphometric, cellular, and physiologic characteristics of pulmonary arteries from COPD patients undergoing bilateral lung transplant. METHODS: Seventeen patients with very severe COPD (forced expiratory volume in 1 second, 24% ± 7%) were assessed using inert gas exchange and pulmonary hemodynamics while breathing ambient air and 100% oxygen. Morphometry, in vitro reactivity to hypoxia, and inflammatory cell counts of pulmonary arteries were measured in explanted lungs. RESULTS: Patients had moderate ventilation-perfusion imbalance along with mild release of hypoxic pulmonary vasoconstriction. Mild pulmonary hypertension was observed in 7 patients. Explanted lungs had predominant emphysema with mild small airway involvement. In vitro reactivity was modestly altered, with relatively preserved endothelium-dependent relaxation, and vascular remodelling was discrete, with intense CD8+ T lymphocytes infiltrate. In vitro reactivity correlated with pulmonary vascular resistance (on ambient air) and oxygen-induced pulmonary artery pressure changes. Patients with pulmonary hypertension had more severe morphologic and physiologic emphysema. CONCLUSIONS: In end-stage COPD patients undergoing lung transplant, pulmonary vascular involvement is unexpectedly modest, with low-grade endothelial dysfunction. In this sub-set of COPD patients, pulmonary emphysema may constitute the major determinant of the presence of pulmonary hypertension.

Effect of nitric oxide inhalation on gas exchange in acute severe pneumonia.

Inhaled nitric oxide (NO) causes selective pulmonary vasodilatation and may improve gas exchange. The study was aimed to evaluate the acute effects of inhaled NO on pulmonary gas exchange in severe unilateral pneumonia, where hypoxemia results from increased intrapulmonary shunt. We studied 8 patients without preexisting lung disease (59±18 yr; 4M/4F) with early unilateral severe pneumonia and respiratory failure. Pulmonary and systemic hemodynamics and gas exchange, including ventilation-perfusion (V;A/Q;) distributions, were measured at baseline and while breathing 5 and 40 parts per million (ppm) of NO. Inhaled NO caused a dose-dependent fall in pulmonary vascular resistance (by 12% and 21%, with 5 and 40ppm, respectively; p<0.01, each) and improvement of PaO2 (by 25% and 23%; p<0.05, each), owing to the reduction of intrapulmonary shunt (by 23% and 27%; p<0.05, each), without changes in the amount of perfusion to low V;A/Q; ratio alveolar units. Patients with greater baseline intrapulmonary shunt exhibited greater improvement in arterial oxygenation (r(2)=0.55, p<0.05). We conclude that low doses of inhaled NO improve pulmonary gas exchange in acute severe pneumonia.

Echocardiographic abnormalities in patients with COPD at their first hospital admission.

Cardiovascular disease accounts for significant morbidity and mortality in chronic obstructive pulmonary disease (COPD). Its prevalence and mechanisms of association have not been elucidated. The study aimed to assess the prevalence of echocardiographic abnormalities and potential risk factors in patients with COPD at their first exacerbation requiring hospital admission. Transthoracic echocardiography was prospectively performed in 342 patients (forced expiratory volume in 1 s 52 ± 16% predicted) 3 months after discharge. Significant cardiac alterations were present in 64% of patients; 27% left- and 48% right-heart disorders. The most common were right ventricle enlargement (30%) and pulmonary hypertension (19%). Left ventricle enlargement was present in 6%, left ventricle systolic dysfunction in 13%, left ventricle diastolic impairment in 12% and left atrial dilatation in 29%. Echocardiographic abnormalities were unrelated to COPD severity and were more frequent in patients with self-reported cardiac disease. They were also observed in 63% of patients with no known cardiac disease or cardiovascular risk factors other than smoking. We conclude that cardiac abnormalities are highly prevalent in COPD patients at the time of their first severe exacerbation, even in the absence of established cardiac disease or cardiovascular risk factors. Considering the prognostic and therapeutic implications of cardiac comorbidity, echocardiography should be considered in the assessment of patients with clinically significant COPD.

Salbutamol but not ipratropium abolishes leukotriene D4-induced gas exchange abnormalities in asthma.

PURPOSE: Leukotriene D(4) (LTD(4)) is a central mediator in asthma inducing bronchoconstriction and profound disturbances in pulmonary gas exchange in asthmatic subjects. The aim of the study was to compare, for the first time, the influence of the bronchodilators salbutamol (400 µg) and ipratropium (80 µg) on lung function changes induced by inhaled LTD(4). METHODS: Treatments were evaluated in a randomized, three-period, double-blind, placebo-controlled, cross-over study where spirometric and pulmonary gas exchange indices were followed in 12 subjects with mild asthma before and after LTD(4) challenge. RESULTS: Compared with placebo, salbutamol provided significant protection against the fall in FEV(1) (forced expiratory volume in 1 s) after LTD(4) challenge. Salbutamol also abolished the LTD(4)-induced gas exchange disturbances [decreased arterial oxygen tension (PaO(2)) and increased alveolar-arterial oxygen tension difference (AaPO(2))]. Ipratropium provided significant but less marked attenuation of the changes in FEV(1) and arterial oxygenation induced by LTD(4). CONCLUSION: Despite the equal bronchodilatory effects of salbutamol and ipratropium before the challenge with LTD(4), salbutamol was superior to ipratropium in preventing spirometric and gas exchange abnormalities. This result indicates a broader action of salbutamol on several of the disturbances that contribute to airway obstruction including, for example, exudation of plasma in the airway mucosa. The clinical implication of this new finding is that in this model of acute asthmatic airway obstruction, salbutamol was more effective than ipratropium.

Association between Ω3 and Ω6 fatty acid intakes and serum inflammatory markers in COPD.

Dietary intake of polyunsaturated fatty acids, including omega-3 and omega-6, could modulate chronic obstructive pulmonary disease (COPD) persistent inflammation. We aimed to assess the relationship between dietary intake of omega-3 and omega-6 fatty acids and serum inflammatory markers in COPD. A total of 250 clinically stable COPD patients were included. Dietary data of the last 2 years were assessed using a validated food frequency questionnaire (122 items), which provided levels of three omega-3 fatty acids: docosahexaenoic acid, eicosapentaenoic acid and α-linolenic acid (ALA); and two omega-6 fatty acids: linoleic acid and arachidonic acid (AA). Inflammatory markers [C-reactive protein (CRP), interleukin (IL)-6, IL-8 and tumor necrosis factor alpha (TNFα)] were measured in serum. Fatty acids and inflammatory markers were dichotomised according to their median values, and their association was assessed using multivariate logistic regression. Higher intake of ALA (an anti-inflammatory omega-3 fatty acid) was associated with lower TNFα concentrations [adjusted odds ratio (OR)=0.46; P=.049]. Higher AA intake (a proinflammatory omega-6 fatty acid) was related to higher IL-6 (OR=1.96; P=.034) and CRP (OR=1.95; P=.039) concentrations. Therefore, this study provides the first evidence of an association between dietary intake of omega-3 and omega-6 fatty acids and serum inflammatory markers in COPD patients.

Cuál es el mejor FEV1 para detectar insuficiencia respiratoria crónica en la EPOC estable / Below what FEV1 Should Arterial Blood be Routinely Taken to Detect Chronic Respiratory Failure in COPD?

Introducción: La gasometría arterial es la medición de elección para el diagnóstico de insuficiencia respiratoria crónica en la enfermedad pulmonar obstructiva crónica (EPOC). Se ha sugerido que el FEV1 se sitúe entre el 30 y el 50% del valor teórico para su indicación, pero estas cifras nunca han sido validadas. Objetivo: Identificar los valores de FEV1 post-broncodilatador (BD) y saturación arterial de oxígeno (SaO2) que proporcionen la mejor sensibilidad, especificidad y coeficientes de probabilidad (CP) para el diagnóstico de insuficiencia respiratoria crónica hipoxémica y/o hipercápnica en la EPOC estable. Métodos: Se incluyeron 150 pacientes (39 con PaO2 < 60mmHg [8 kPa] y 14 de ellos con una PaCO2¡Ý50mmHg[6,7 kPa]). Se seleccionaron los mejores puntos de corte de FEV1 post-BD y SaO2 para predecirla insuficiencia respiratoria crónica empleando los CP y las curvas Receiver Operating Characteristic. Resultados: Un FEV1 post-BD igual al 36% y una SaO2 del 90% fueron los mejores valores predictivos de insuficiencia respiratoria hipoxémica y un FEV1 post-BD igual al 33% para la variante hipercápnica. Un FEV1 ¡Ý45% descartó la insuficiencia respiratoria hipoxémica. Conclusión: Un FEV1 post-BD igual al 36% se erige en el mejor punto de corte para predecir adecuadamentetanto la insuficiencia respiratoria hipoxémica como la hipercápnica en el paciente con EPOC estable. Por su parte, una SaO2 del 90% ofrece el mejor valor para la insuficiencia hipoxémica aislada. Estos valores podrían ser considerados para futuras recomendaciones/guías clínicas de la EPOC(AU)

Introduction: To diagnose and assess chronic respiratory failure in stable chronic obstructive pulmonarydisease (COPD) the measurement of arterial blood gases (ABG) is required. It has been suggested that ABGbe determined for this purpose when FEV1 ranges between 50% and 30% predicted, but these thresholdsare not evidence-based.Objective: To identify the post-bronchodilator (BD) FEV1 and arterial oxygen saturation (SaO2) valuesthat provide the best sensitivity, specificity, and likelihood ratio (LR) for the diagnosis of hypoxaemicand/or hypercapnic chronic respiratory failure in stable COPD.Methods: A total of 150 patients were included (39 with PaO2 < 60mmHg[8 kPa], 14 of them with a PaCO2¡Ý50mmHg[6.7 kPa]). The best post-BD FEV1 and SaO2 cut-off points to predict chronic respiratory failurewere selected using the PC and the Receiver Operating Characteristics (ROC) curves.Results: A post-BD FEV1 equal to 36% and an SaO2 of 90% were the best predictive values for hypoxaemicrespiratory failure and a post-BD FEV1 equal to 33% for the hypercapnic variant. An FEV1 ¡Ý45% ruled outhypoxaemic respiratory failure. Conclusion: A post-BD FEV1 of 36% is the best cut-off point to adequately predict both hypoxaemic andhypercapnic respiratory failure in the patient with stable COPD. For its part, an SaO2 of 90% is the bestvalue for isolated hypoxaemic failure. These values could be considered for future clinical recommendations/guidelines for COPD(AU)

Below what FEV1 should arterial blood be routinely taken to detect chronic respiratory failure in COPD?

INTRODUCTION: To diagnose and assess chronic respiratory failure in stable chronic obstructive pulmonary disease (COPD) the measurement of arterial blood gases (ABG) is required. It has been suggested that ABG be determined for this purpose when FEV1 ranges between 50% and 30% predicted, but these thresholds are not evidence-based. OBJECTIVE: To identify the post-bronchodilator (BD) FEV1 and arterial oxygen saturation (SaO(2)) values that provide the best sensitivity, specificity, and likelihood ratio (LR) for the diagnosis of hypoxaemic and/or hypercapnic chronic respiratory failure in stable COPD. METHODS: A total of 150 patients were included (39 with PaO2 < 60 mmHg [8 kPa], 14 of them with a PaCO2 ≥ 50 mmHg [6.7 kPa]). The best post-BD FEV(1) and SaO(2) cut-off points to predict chronic respiratory failure were selected using the PC and the Receiver Operating Characteristics (ROC) curves. RESULTS: A post-BD FEV(1) equal to 36% and an SaO(2) of 90% were the best predictive values for hypoxaemic respiratory failure and a post-BD FEV(1) equal to 33% for the hypercapnic variant. An FEV(1) ≥ 45% ruled out hypoxaemic respiratory failure. CONCLUSION: A post-BD FEV(1) of 36% is the best cut-off point to adequately predict both hypoxaemic and hypercapnic respiratory failure in the patient with stable COPD. For its part, an SaO(2) of 90% is the best value for isolated hypoxaemic failure. These values could be considered for future clinical recommendations/guidelines for COPD.

Identification and prospective validation of clinically relevant chronic obstructive pulmonary disease (COPD) subtypes.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is increasingly considered a heterogeneous condition. It was hypothesised that COPD, as currently defined, includes different clinically relevant subtypes. METHODS: To identify and validate COPD subtypes, 342 subjects hospitalised for the first time because of a COPD exacerbation were recruited. Three months after discharge, when clinically stable, symptoms and quality of life, lung function, exercise capacity, nutritional status, biomarkers of systemic and bronchial inflammation, sputum microbiology, CT of the thorax and echocardiography were assessed. COPD groups were identified by partitioning cluster analysis and validated prospectively against cause-specific hospitalisations and all-cause mortality during a 4 year follow-up. RESULTS: Three COPD groups were identified: group 1 (n=126, 67 years) was characterised by severe airflow limitation (postbronchodilator forced expiratory volume in 1 s (FEV(1)) 38% predicted) and worse performance in most of the respiratory domains of the disease; group 2 (n=125, 69 years) showed milder airflow limitation (FEV(1) 63% predicted); and group 3 (n=91, 67 years) combined a similarly milder airflow limitation (FEV(1) 58% predicted) with a high proportion of obesity, cardiovascular disorders, diabetes and systemic inflammation. During follow-up, group 1 had more frequent hospitalisations due to COPD (HR 3.28, p<0.001) and higher all-cause mortality (HR 2.36, p=0.018) than the other two groups, whereas group 3 had more admissions due to cardiovascular disease (HR 2.87, p=0.014). CONCLUSIONS: In patients with COPD recruited at their first hospitalisation, three different COPD subtypes were identified and prospectively validated: 'severe respiratory COPD', 'moderate respiratory COPD', and 'systemic COPD'.

Effects of inhaled nitric oxide at rest and during exercise in idiopathic pulmonary fibrosis.

Patients with idiopathic pulmonary fibrosis (IPF) usually develop hypoxemia and pulmonary hypertension when exercising. To what extent endothelium-derived vasodilating agents modify these changes is unknown. The study was aimed to investigate in patients with IPF whether exercise induces changes in plasma levels of endothelium-derived signaling mediators, and to assess the acute effects of inhaled nitric oxide (NO) on pulmonary hemodynamics and gas exchange, at rest and during exercise. We evaluated seven patients with IPF (6 men/1 woman; 57 ± 11 yr; forced vital capacity, 60 ± 13% predicted; carbon monoxide diffusing capacity, 52 ± 10% predicted). Levels of endothelin, 6-keto-prostaglandin-F(1α), thromboxane B(2), and nitrates were measured at rest and during submaximal exercise. Pulmonary hemodynamics and gas exchange, including ventilation-perfusion relationships, were assessed breathing ambient air and 40 ppm NO, both at rest and during submaximal exercise. The concentration of thromboxane B(2) increased during exercise (P = 0.046), whereas levels of other mediators did not change. The change in 6-keto-prostaglandin-F(1α) correlated with that of mean pulmonary arterial pressure (r = 0.94; P < 0.005). Inhaled NO reduced mean pulmonary arterial pressure at rest (-4.6 ± 2.1 mmHg) and during exercise (-11.7 ± 7.1 mmHg) (P = 0.001 and P = 0.004, respectively), without altering arterial oxygenation or ventilation-perfusion distributions in any of the study conditions. Alveolar-to-capillary oxygen diffusion limitation, which accounted for the decrease of arterial Po(2) during exercise, was not modified by NO administration. We conclude that, in IPF, some endothelium-derived signaling molecules may modulate the development of pulmonary hypertension during exercise, and that the administration of inhaled NO reduces pulmonary vascular resistance without disturbing gas exchange.

Anti-tissue antibodies are related to lung function in chronic obstructive pulmonary disease.

RATIONALE: Chronic obstructive pulmonary disease (COPD) is a multicomponent disease. Autoimmunity can contribute to the pathogenesis of COPD. OBJECTIVES: This study investigates the prevalence of circulating antinuclear antibodies (ANA) and anti-tissue (AT) antibodies, two common markers of autoimmunity, in COPD and their relationship with several components of the disease. METHODS: We determined lung function, the serum titers of ANA and AT by immunofluorescence, and the serum levels of C-reactive protein (CRP) by high sensitivity nephelometry in 328 patients with clinically stable COPD and in 67 healthy controls recruited in the PAC-COPD study. Multiple linear and logistic regression analysis was used to analyze results. MEASUREMENTS AND MAIN RESULTS: The prevalence of abnormal ANA and AT titers was 34% and 26% in patients and 3% and 6% in controls, respectively. Levels of AT greater than or equal to 1:320 were seen in 21% of patients with COPD and were independently associated with the severity of airflow limitation and gas transfer impairment (P < 0.05). Neither ANA or AT titers was related to body mass index, current smoking status, use of inhaled steroids, the Charlson index, or serum C-reactive protein values. CONCLUSIONS: Between a quarter and a third of patients with clinically stable COPD present abnormal titers of circulating ANA and AT. The observed relationship between AT and lung function supports a role for autoimmunity in the pathogenesis of COPD.

Short-term changes in respiratory biomarkers after swimming in a chlorinated pool.

BACKGROUND: Swimming in chlorinated pools involves exposure to disinfection by-products (DBPs) and has been associated with impaired respiratory health. OBJECTIVES: We evaluated short-term changes in several respiratory biomarkers to explore mechanisms of potential lung damage related to swimming pool exposure. METHODS: We measured lung function and biomarkers of airway inflammation [fractional exhaled nitric oxide (FeNO), eight cytokines, and vascular endothelial growth factor (VEGF) in exhaled breath condensate], oxidative stress (8-isoprostane in exhaled breath condensate), and lung permeability [surfactant protein D (SP-D) and the Clara cell secretory protein (CC16) in serum] in 48 healthy nonsmoking adults before and after they swam for 40 min in a chlorinated indoor swimming pool. We measured trihalomethanes in exhaled breath as a marker of individual exposure to DBPs. Energy expenditure during swimming, atopy, and CC16 genotype (rs3741240) were also determined. RESULTS: Median serum CC16 levels increased from 6.01 to 6.21 microg/L (average increase, 3.3%; paired Wilcoxon test p = 0.03), regardless of atopic status and CC16 genotype. This increase was explained both by energy expenditure and different markers of DBP exposure in multivariate models. FeNO was unchanged overall but tended to decrease among atopics. We found no significant changes in lung function, SP-D, 8-isoprostane, eight cytokines, or VEGF. CONCLUSIONS: We detected a slight increase in serum CC16, a marker of lung epithelium permeability, in healthy adults after they swam in an indoor chlorinated pool. Exercise and DBP exposure explained this association, without involving inflammatory mechanisms. Further research is needed to confirm the results, establish the clinical relevance of short-term serum CC16 changes, and evaluate the long-term health impacts.