bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence, Distribution, and Risk Factor Correlates of High Pericardial and Intrathoracic Fat Depots in the Framingham Heart Study
Authors: Thanassoulis George , Massaro Joseph M. , Hoffmann Udo , Mahabadi Amir A. , Vasan Ramachandran S. , O'Donnell Christopher J. , Fox Caroline S. 
Published: June 2010

Background—
Pericardial and intrathoracic fat depots may represent novel risk factors for obesity-related cardiovascular disease. We sought to determine the prevalence, distribution, and risk factor correlates of high pericardial and intrathoracic fat deposits.

Methods and Results—

Participants from the Framingham Heart Study (n=3312; mean age, 52 years; 48% women) underwent multidetector CT imaging in 2002 to 2005; high pericardial and high intrathoracic fat were defined on the basis of the sex-specific 90th percentile for these fat depots in a healthy reference sample. For men and women, the prevalence of high pericardial fat was 29.3% and 26.3%, respectively, and high intrathoracic fat was 31.4% and 35.3%, respectively. Overall, 22.1% of the sample was discordant for pericardial and intrathoracic fat depots: 8.3% had high pericardial but normal intrathoracic fat and 13.8% had high intrathoracic but normal pericardial fat. Higher body mass index, higher waist circumference, and increased prevalence of metabolic syndrome were more prevalent in participants with high intrathoracic fat depots than with high pericardial fat (
P
<0.05 for all comparisons). High abdominal visceral adipose tissue was more frequent in participants with high intrathoracic adipose tissue compared with those with high pericardial fat (
P
<0.001). Intrathoracic fat but not waist circumference was more highly correlated with visceral adipose tissue (
r
=0.76 and 0.78 in men and women, respectively;
P
<0.0001) than with subcutaneous adipose tissue (SAT) (
r
=0.46 and 0.54 in men and women, respectively;
P
<0.0001).

Conclusions—
Although prevalence of pericardial fat and intrathoracic fat were comparable at 30%, intrathoracic fat correlated more closely with metabolic risk and visceral fat. Intrathoracic fat may be a potential marker of metabolic risk and visceral fat on thoracic imaging.
Materials on the Bandari Dialect
Authors: Pelevin Mikhail 
Published: June 2010

AbstractIn this paper, a short description of the main phonological and morphological features of Bandari, a dialect spoken in Bandar 'Abbās (Hormozgān province in Iran), is supplemented with new materials recorded by the author, including a Glossary (about 400 items) with parallels from closely related South-Iranian dialects, and texts of three popular songs.
Pregnancy and fetal outcomes of symptoms of sleep-disordered breathing
Authors: Bourjeily G. , Raker C.A. , Chalhoub M. , Miller M.A. 
Published: June 2010

The physiological changes of pregnancy may predispose females to develop sleep-disordered breathing (SDB) or protect against it. Studies evaluating outcomes of SDB symptoms in pregnancy are scarce. The goal of this study was to evaluate the prevalence of SDB symptoms in pregnancy and their relationship with pregnancy and neonatal outcomes.A cross-sectional survey of randomly selected immediate postpartum females was performed using the multivariable apnoea prediction index. Record review, including demographics and medical history, was performed. Main outcome measures included pregnancy and neonatal outcomes.1,000 subjects were recruited. Mean±sdage was 29.1±6.1 yrs. Factors used in the regression analysis included age, body mass index, diabetes, chronic hypertension, multifetal gestations, smoking and renal disease. Snoring was present in 35.1% of subjects. Symptoms of SDB were associated with a higher likelihood of pregnancy-induced hypertension and pre-eclampsia (adjusted OR 2.3, 95% CI 1.4–4.0), gestational diabetes (adjusted OR 2.1, 95% CI 1.3–3.4) and unplanned Caesarean deliveries (adjusted OR 2.1, 95% CI 1.4–3.2) after multivariable regression analysis. Gasping may have been associated with a higher likelihood of preterm delivery, after adjusting for age and multifetal pregnancies (adjusted OR 1.8, 95% CI 1.1–3.2) but this association appeared to be mediated by pre-eclampsia.Symptoms of SDB are common in pregnancy and associated with a higher likelihood of gestational hypertensive disorders, gestational diabetes and unplanned Caesarean deliveries.
Inhaled drugs as risk factors for community-acquired pneumonia
Authors: Almirall J. , Bolíbar I. , Serra-Prat M. , Palomera E. , Roig J. , Hospital I. , Carandell E. , Agustí M. , Ayuso P. , Estela A. , Torres A. 
Published: June 2010

The effect of inhaled drugs in community-acquired pneumonia (CAP) is unclear. This case–control study was designed to determine whether inhaled drugs were risk factors for CAP.All incident cases of confirmed CAP that occurred over 1 yr in patients with chronic bronchitis (CB), chronic obstructive pulmonary disease (COPD) or asthma were included, as well as CB, COPD and asthma controls. Risk factors for CAP and inhaled treatment were recorded during a personal interview.An effect of inhaled drugs on the risk of CAP was observed in COPD and asthma patients after adjusting for the effect of other respiratory diseases and their concomitant treatments. In COPD patients, inhaled steroids had a risk OR of 3.26 (95% CI 1.07–9.98) and in asthma patients inhaled anticholinergics had a risk OR of 8.80 (95% CI 1.02–75.7). In CB patients, no association with CAP was observed for any inhaler. These effects were independent of adjusting variables related to severity and other respiratory and non-respiratory risk factors for CAP, including vaccines. Inhaled β2-adrenergic agonists did not show a significant effect on the risk of CAP in any of the respiratory diseases.Inhaled steroids may favour CAP in COPD patients, whereas anticholinergics may favour CAP in asthma patients. It is difficult to differentiate the effect of inhaled therapy from the effect of COPD or asthma severity on the risk of CAP, and these relationships may not be causal, but could call attention to inhaled therapy in COPD and asthma patients.
Treprostinil inhibits the recruitment of bone marrow-derived circulating fibrocytes in chronic hypoxic pulmonary hypertension
Authors: Nikam V.S. , Schermuly R.T. , Dumitrascu R. , Weissmann N. , Kwapiszewska G. , Morrell N. , Klepetko W. , Fink L. , Seeger W. , Voswinckel R. 
Published: June 2010

A unique subpopulation of peripheral blood mononuclear cells that exhibit a parallel expression of haematopoietic and mesenchymal markers has been described as “circulating fibrocytes”. These cells were demonstrated to obtain a fibroblastic phenotype in tissues or cell culture and contribute to pulmonary fibrotic disorders and tissue remodelling processes.The aim of our study was to characterise the recruitment of circulating fibrocytesin vivoin the model of chronic hypoxic pulmonary hypertension in mice and to analyse the therapeutic effect of the stable prostacyclin analogue trepostinil with respect to this cell population.To track circulating fibrocytesin vivo, we transplanted wild-type mice with bone marrow from ubiquitously eGFP expressing mice and subjected them to chronic hypoxia. We observed significantly increased recruitment of circulating fibrocytes to the remodelled pulmonary resistance arteries in response to hypoxia. Treatment with treprostinil significantly reduced the recruitment of these cells compared to normoxic mice. Treprostinil also reduced right ventricular systolic pressure and slightly reduced the vascular remodelling but failed to reverse the right ventricular hypertrophy.In summary, we show that circulating fibrocytes contribute to hypoxic pulmonary vascular remodelling and may be specifically targeted by a prostacyclin analogue. Further investigations of cellular and paracrine mechanisms are warranted to decipher their role in pulmonary hypertension.
Trimodality therapy for malignant pleural mesothelioma: results from an EORTC phase II multicentre trial
Authors: Van Schil P.E. , Baas P. , Gaafar R. , Maat A.P. , Van de Pol M. , Hasan B. , Klomp H.M. , Abdelrahman A.M. , Welch J. , van Meerbeeck J.P. 
Published: June 2010

The European Organisation for Research and Treatment of Cancer (EORTC; protocol 08031) phase II trial investigated the feasibility of trimodality therapy consisting of induction chemotherapy followed by extrapleural pneumonectomy and post-operative radiotherapy in patients with malignant pleural mesothelioma (with a severity of cT3N1M0 or less).Induction chemotherapy consisted of three courses of cisplatin 75 mg·m−2and pemetrexed 500 mg·m−2. Nonprogressing patients underwent extrapleural pneumonectomy followed by post-operative radiotherapy (54 Gy, 30 fractions). Our primary end-point was “success of treatment” and our secondary end-points were toxicity, and overall and progression-free survival.59 patients were registered, one of whom was ineligible. Subjects’ median age was 57 yrs. The subjects’ TNM scores were as follows: cT1, T2 and T3, 36, 16 and six patients, respectively; cN0 and N1, 57 and one patient, respectively. 55 (93%) patients received three cycles of chemotherapy with only mild toxicity. 46 (79%) patients received surgery and 42 (74%) had extrapleural pneumonectomy with a 90-day mortality of 6.5%. Post-operative radiotherapy was completed in 37 (65%) patients. Grade 3–4 toxicity persisted after 90 days in three (5.3%) patients. Median overall survival time was 18.4 months (95% CI 15.6–32.9) and median progression-free survival was 13.9 months (95% CI 10.9–17.2). Only 24 (42%) patients met the definition of success (one-sided 90% CI 0.36–1.00).Although feasible, trimodality therapy in patients with mesothelioma was not completed within the strictly defined timelines of this protocol and adjustments are necessary.
TB or not TB: update from the ERS Respiratory Infection Assembly 10
Authors: Miravitlles M. , Ferrara G. , Lange C. , Dimopoulos G. , Rohde G. , Blasi F. , Migliori G.B. 
Published: June 2010

Lower respiratory tract infections and tuberculosis represent some of the top health priorities in Europe. In the present report, the most recent advances in the field of disease control, clinical research and basic science of lower respiratory tract infections and tuberculosis are presented through analysis of some of the best abstracts presented at the 19th European Respiratory Society Congress in Vienna (Austria).Pathogenesis, diagnosis, treatment, prognostic factors and novel diagnostic techniques relevant for bacterial and viral infections, as well as new tools for the diagnosis of latent and active tuberculosis in different sub-groups of patients, are discussed. The growing epidemiological threat represented by multidrug-resistant and extensively drug-resistant tuberculosis cases is presented and its impact analysed.
Association of COPD candidate genes with computed tomography emphysema and airway phenotypes in severe COPD
Authors: Kim W.J. , Hoffman E. , Reilly J. , Hersh C. , DeMeo D. , Washko G. , Silverman E.K. 
Published: June 2010

The principal determining factors influencing the development of the airway disease and emphysema components of chronic obstructive pulmonary disease (COPD) have not been clearly defined. Genetic variability in COPD patients might influence the varying degrees of involvement of airway disease and emphysema. Therefore, we investigated the genetic association of single nucleotide polymorphisms (SNPs) in COPD candidate genes for association with emphysema severity and airway wall thickness phenotypes.Polymorphisms in six candidate genes were analysed in 379 subjects of the National Emphysema Treatment Trial (NETT) Genetics Ancillary Study with quantitative chest computed tomography (CT) data. Genetic association with per cent of lung area below -950 HU (LAA950), airway wall thickness, and derived square root wall area (SRWA) of 10-mm internal perimeter airways were investigated.Three SNPs inEPHX1, five SNPs inSERPINE2and one SNP inGSTP1were significantly associated with LAA950. Five SNPs inTGFB1, two SNPs inEPHX1, one SNP inSERPINE2and two SNPs inADRB2were associated with airway wall phenotypes in NETT.In conclusion, several COPD candidate genes showed evidence for association with airway wall thickness and emphysema severity using CT in a severe COPD population. Further investigation will be required to replicate these genetic associations for emphysema and airway wall phenotypes.
Aclidinium inhibits cholinergic and tobacco smoke-induced MUC5AC in human airways
Authors: Cortijo J. , Mata M. , Milara J. , Donet E. , Gavaldà A. , Miralpeix M. , Morcillo E.J. 
Published: June 2010

Mucus hypersecretion and mucin MUC5AC overexpression are pathological features of chronic obstructive pulmonary disease (COPD). This study examines the inhibitory effect of aclidinium, a new long-acting muscarinic antagonist, on MUC5AC expression in human airway epithelial cells.MUC5AC mRNA (RT-PCR) and protein expression (ELISA and immunohistochemistry) were studied in human bronchial tissue and differentiated human airway epithelial cells activated with carbachol (100 μM) or cigarette smoke extract in the absence or presence of aclidinium.Carbachol increased MUC5AC mRNA and protein expression in human bronchus and cultured epithelial cells. Aclidinium inhibited the carbachol-induced MUC5AC mRNA and protein expression with potency (half maximal inhibitory concentration) ∼1 nM in human bronchus and cultured airway epithelial cells. AG1478, a selective inhibitor of epidermal growth factor receptor (EGFR) tyrosine kinase, inhibited carbachol-induced MUC5AC responses, indicating EGFR transactivation. Aclidinium inhibited carbachol-induced phospho-EGFR and phospho-p44/42 MAPK expression. In cultured airway epithelial cells transfected with small interfering (si)RNA against muscarinic receptor subtypes, siRNA-M3 but not siRNA-M2 blocked carbachol-induced MUC5AC expression. Cigarette smoke-induced MUC5AC upregulation in cultured airway epithelial cells was suppressed by aclidinium.In conclusion, aclidinium decreases carbachol and tobacco smoke-induced MUC5AC overexpression in human airway epithelial cells. This effect may contribute to the clinical efficacy of aclidinium in mucus hypersecretory diseases including COPD.
Significant increase of CD57+cells in pulmonary lymphoid follicles of COPD patients
Authors: Olloquequi J. , Montes J.F. , Prats A. , Rodríguez E. , Montero M.A. , García-Valero J. , Ferrer J. 
Published: June 2010

Although the presence of pulmonary lymphoid follicles (LFs) has been associated with the progression of chronic obstructive pulmonary disease (COPD), there is no information regarding the pattern of vascularisation, expression of addressins or inflammatory cell densities within these structures in COPD.Histological and immunohistochemical techniques were used to assess the prevalence, structure, localisation, vascularisation and cell proliferation/apoptosis of LFs, as well as the follicular density of B- and T-lymphocytes, macrophages, dendritic cells and CD57+cells, in lung tissue of nine nonsmokers, 18 smokers without COPD, 16 smokers with moderate COPD and 16 patients with very severe COPD.The density of CD57+cells within LFs of COPD patients was significantly increased compared to that of nonsmokers and smokers without COPD (p<0.05). Moreover, the percentage of LF profiles with cell apoptosis was also significantly higher in COPD patients (p = 0.03). By contrast, no significant differences among groups were observed in the follicular densities of other inflammatory cells, nor in the distribution of blood and lymphatic vessels within LFs.Since CD57+cells are important effectors of cytotoxicity and immune regulation, an increase in their follicular density supports the hypothesis of local immune dysfunction in COPD.
14 nights of intermittent hypoxia elevate daytime blood pressure and sympathetic activity in healthy humans
Authors: Tamisier R. , Pépin J.L. , Rémy J. , Baguet J.P. , Taylor J.A. , Weiss J.W. , Lévy P. 
Published: June 2010

Obstructive sleep apnoea syndrome (OSAS) causes nocturnal chronic intermittent hypoxia (IH) that contributes to excess cardiovascular morbidity. To explore the consequences of IH, we used our recently developed model of nocturnal IH in healthy humans to characterise the profile of this blood pressure increase, to determine if it is sustained and to explore potential physiological mechanisms.We performed 24-h ambulatory monitoring of blood pressure in 12 healthy subjects before and after 2 weeks of IH exposure. We also assessed systemic haemodynamics, muscle sympathetic nerve activity (MSNA), ischaemic calf blood flow responses and baroreflex gain. We obtained blood samples for inflammatory markers before, during and after exposure. IH significantly increased daytime ambulatory blood pressure after a single night of exposure (3 mmHg for mean and diastolic) and further increased daytime pressures after 2 weeks of exposure (8 mmHg systolic and 5 mmHg diastolic). Mean±sdMSNA increased across the exposure (17.2±5.1versus21.7±7.3 bursts·min−1; p<0.01) and baroreflex control of sympathetic outflow declined from -965.3±375.1 to -598.4±162.6 AIU·min−1·mmHg−1(p<0.01). There were no evident changes in either vascular reactivity or systemic inflammatory markers.These data are the first to show that the arterial pressure rise is sustained throughout the waking hours beyond the acute phase immediately after exposure. Moreover, they may suggest that sympathoactivation induced by IH likely contributes to blood pressure elevation and may derive from reduced baroreflex inhibition. These mechanisms may reflect those underlying the blood pressure elevation associated with OSAS.
Beyond rotamers: a generative, probabilistic model of side chains in proteins
Authors: Harder Tim , Boomsma Wouter , Paluszewski Martin , Frellsen Jes , Johansson Kristoffer E , Hamelryck Thomas 
Published: June 2010

Abstract

Background
Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common way to capture this conformational space is through rotamer libraries - discrete collections of side chain conformations derived from experimentally determined protein structures. The discretization can be exploited to efficiently search the conformational space. However, discretizing this naturally continuous space comes at the cost of losing detailed information that is crucial for certain applications. For example, rigorously combining rotamers with physical force fields is associated with numerous problems.

Results
In this work we present BASILISK: a generative, probabilistic model of the conformational space of side chains that makes it possible to sample in continuous space. In addition, sampling can be conditional upon the protein's detailed backbone conformation, again in continuous space - without involving discretization.

Conclusions
A careful analysis of the model and a comparison with various rotamer libraries indicates that the model forms an excellent, fully continuous model of side chain conformational space. We also illustrate how the model can be used for rigorous, unbiased sampling with a physical force field, and how it improves side chain prediction when used as a pseudo-energy term. In conclusion, BASILISK is an important step forward on the way to a rigorous probabilistic description of protein structure in continuous space and in atomic detail.
FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases
Authors: Goodswen Stephen J , Gondro Cedric , Watson-Haigh Nathan S , Kadarmideen Haja N 
Published: June 2010

Abstract

Background
Whole genome association studies using highly dense single nucleotide polymorphisms (SNPs) are a set of methods to identify DNA markers associated with variation in a particular complex trait of interest. One of the main outcomes from these studies is a subset of statistically significant SNPs. Finding the potential biological functions of such SNPs can be an important step towards further use in human and agricultural populations (e.g., for identifying genes related to susceptibility to complex diseases or genes playing key roles in development or performance). The current challenge is that the information holding the clues to SNP functions is distributed across many different databases. Efficient bioinformatics tools are therefore needed to seamlessly integrate up-to-date functional information on SNPs. Many web services have arisen to meet the challenge but most work only within the framework of human medical research. Although we acknowledge the importance of human research, we identify there is a need for SNP annotation tools for other organisms.

Description
We introduce an R package called FunctSNP, which is the user interface to custom built species-specific databases. The local relational databases contain SNP data together with functional annotations extracted from online resources. FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies). We also introduce dbAutoMaker, a suite of Perl scripts, which can be scheduled to run periodically to automatically create/update the customised SNP databases. We illustrate the use of FunctSNP with a livestock example, but the approach and software tools presented here can be applied also to human and other organisms.

Conclusions
Finding the potential functional significance of SNPs is important when further using the outcomes from whole genome association studies. FunctSNP is unique in that it is the only R package that links SNPs to functional annotation. FunctSNP interfaces to local SNP customised databases which can be built for any species contained in the National Center for Biotechnology Information dbSNP database.