bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patients’ experience of identifying and managing exacerbations in COPD: a qualitative study
Authors: Williams Veronika , Hardinge Maxine , Ryan Sara , Farmer Andrew 
Published: November 2014

Abstract
Background:
Effective self-management in chronic obstructive pulmonary disease (COPD) is crucial to reduce hospital admissions and improve outcomes for patients. This includes early detection and treatment of exacerbations by patients themselves.

Aims:
To explore patients’ current understanding and experience of managing and identifying COPD exacerbations at home.

Methods:
A qualitative, interview-based study was carried out in patients’ homes. Interviews were audio-recorded, transcribed and analysed using a grounded theory approach. Forty-four patients (17 women, 27 men; age range 55–85 years), with moderate-to-very-severe COPD, were recruited to the interview study from primary and secondary care settings in Oxford, UK, during 2012–2013.

Results:
Patients identified exacerbations on the basis of measurable, ‘visible’ symptoms, such as cough and sputum and ‘invisible’ symptoms, such as chest sensations and bodily knowledge. Most patients seemed to use a combination of these approaches when identifying exacerbations, according to the symptoms that had the most impact on their well-being. Patients used additional self-management strategies during an exacerbation, such as self-medication (antibiotics and steroids) and monitored their recovery. Contact with health-care professionals usually occurred when patients felt no longer able to manage themselves.

Conclusions:
Patients use both assessment of objective biomarkers, which are aligned with medical knowledge, and subjective symptoms based on their experience, to identify and manage exacerbations of COPD. Health-care professionals and clinicians should acknowledge this ‘expert patient’ knowledge and integrate this into patients’ care plans to facilitate early recognition and treatment of exacerbations.
Quantum magnetic phase transition in square-octagon lattice
Authors: Bao An , Tao Hong-Shuai , Liu Hai-Di , Zhang XiaoZhong , Liu Wu-Ming 
Published: November 2014

AbstractQuantum magnetic phase transition in square-octagon lattice was investigated by cellular dynamical mean field theory combining with continuous time quantum Monte Carlo algorithm. Based on the systematic calculation on the density of states, the double occupancy and the Fermi surface evolution of square-octagon lattice, we presented the phase diagrams of this splendid many particle system. The competition between the temperature and the on-site repulsive interaction in the isotropic square-octagon lattice has shown that both antiferromagnetic and paramagnetic order can be found not only in the metal phase, but also in the insulating phase. Antiferromagnetic metal phase disappeared in the phase diagram that consists of the anisotropic parameter λ and the on-site repulsive interaction U while the other phases still can be detected at T = 0.17. The results found in this work may contribute to understand well the properties of some consuming systems that have square-octagon structure, quasi square-octagon structure, such as ZnO.
Altered profile of circulating microparticles in rheumatoid arthritis patients
Authors: Rodríguez-Carrio Javier , Alperi-López Mercedes , López Patricia , Alonso-Castro Sara , Carro-Esteban Santiago R. , Ballina-García Francisco J. , Suárez Ana 
Published: November 2014

Microparticles (MPs) could be considered biomarkers of cell damage and activation as well as novel signalling structures. Since rheumatoid arthritis (RA) is characterized by immune and endothelial activation, the main aim of the present study was to analyse MP counts in RA patients. Citrated-blood samples were obtained from 114 RA patients, 33 healthy controls (HC) and 72 individuals with marked cardiovascular (CV) risk without autoimmune manifestations (CVR). MPs were analysed in platelet-poor plasma (PPP) and different subsets were identified by their surface markers: platelet- (CD41+), endothelial- (CD146+), granulocyte- (CD66+), monocyte- (CD14+) and Tang- (CD3+CD31+) derived. Disease activity score (DAS28), clinical and immunological parameters as well as traditional CV risk factors (diabetes, hypertension, dyslipidaemia and obesity) were registered from clinical records and all data were integrated using Principal Component Analysis (PCA). Absolute MP number was increased in RA patients compared with HC and positively correlated with traditional CV risk factors, similar to that of CVR subjects. In addition, frequency of the different MP subsets was different in RA patients and significantly associated with disease features. Moreover, in vitro assays revealed that MPs isolated from RA patients were able to promote endothelial activation and exhibited detrimental effects on human microvascular endothelial cells (HMEC-I) endothelial cell functionality. Circulating MPs from RA patients displayed quantitative and qualitative alterations that are the result of both disease-specific and traditional CV risk factors. Accordingly, this MP pool exhibited in vitro detrimental effects on endothelial cells, thus supporting their role as biomarkers of vascular damage.
Favorable Effects of Vitamin D Supplementation on Pregnancy Outcomes in Gestational Diabetes: A Double Blind Randomized Controlled Clinical Trial
Authors: Asemi Z. , Karamali M. , Esmaillzadeh A. 
Published: November 2014

AbstractGestational diabetes mellitus (GDM) has been recognized as a significant risk factor for unfavorable pregnancy outcomes. Prevalence of vitamin D deficiency is highly prevalent among women with GDM. This study was designed to assess the effect of vitamin D supplementation on pregnancy outcomes of pregnant women with GDM who were not on oral hypoglycemic agents. This randomized controlled clinical trial was performed among 45 pregnant women diagnosed with GDM at 24–28 weeks’ gestation. Subjects were randomly assigned to consume either vitamin D supplements (cholecalciferol) or placebo. Individuals in the vitamin D group (n=22) received 50 000 IU vitamin D3 pearl 2 times during the study: at study baseline and day 21 of intervention and those in placebo group (n=23) received 2 placebos at the mentioned times. Fasting blood samples were taken at baseline to measure fasting plasma glucose. Participants underwent a 3-h oral glucose tolerance tests (OGTT) and the blood samples were collected at time 60, 120, and 180 min to measure plasma glucose levels. Newborn’s weight, height, head circumference, Apgar score, and hyperbilirubinemia were determined. Taking vitamin D supplements, compared with placebo, resulted in improved pregnancy outcomes; such that those in the vitamin D group had no case of polyhydramnios, while 17.4% of subjects in placebo group had this condition (p=0.04). In addition, newborn’s hyperbilirubinemia was significantly lower in vitamin D group than that in placebo group (27.3% vs. 60.9%, p=0.02). In conclusion, vitamin D supplementation for 6 weeks among pregnant women with GDM resulted in decreased maternal polyhydramnios and infant hyperbilirubinemia compared with placebo.
Clinical trial registration number www.irct.ir:IRCT201305115623N7.
Maresin 1 biosynthesis during platelet–neutrophil interactions is organ-protective
Authors: Abdulnour Raja-Elie E. , Dalli Jesmond , Colby Jennifer K. , Krishnamoorthy Nandini , Timmons Jack Y. , Tan Sook Hwa , Colas Romain A. , Petasis Nicos A. , Serhan Charles N. , Levy Bruce D. 
Published: November 2014

Significance
Neutrophil accumulation is fundamental to acute inflammation. In response to tissue injury, circulating neutrophil–platelet aggregates (N-PAs) form for secondary capture. Counterregulation of acute inflammatory processes by specialized proresolving mediators is essential to mitigate collateral injury to healthy bystander tissue. Here, we identified a biosynthetic route in human platelets for the proresolving mediator maresin 1 (MaR1) that is amplified during platelet–neutrophil interactions. In a self-resolving murine model of acute lung injury, N-PAs rapidly formed and a MaR1 counterregulatory circuit was engaged to restrain N-PAs and acute inflammation and restore homeostasis of the injured lung.
Cerebral small vessel disease-related protease HtrA1 processes latent TGF-β binding protein 1 and facilitates TGF-β signaling
Authors: Beaufort Nathalie , Scharrer Eva , Kremmer Elisabeth , Lux Vanda , Ehrmann Michael , Huber Robert , Houlden Henry , Werring David , Haffner Christof , Dichgans Martin 
Published: November 2014

Significance
Cerebral small vessel disease (SVD) is a major cause of stroke and dementia. Hereditary forms, such as cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL), may provide insights into key molecular mechanisms and pathways. The serine protease HtrA1, whose activity is impaired in CARASIL, has been proposed to attenuate TGF-β signaling leading to increased pathway activity in diseased arteries. We analyzed HtrA1-deficient mouse brain tissue and mouse and CARASIL patient fibroblasts and found a reduction in signaling activity on various pathway levels suggesting a facilitating role of HtrA1. Moreover, we identified LTBP-1 as a novel HtrA1 substrate and provide evidence for its functional modulation by HtrA1-dependent proteolysis. Our data suggest down-regulation of TGF-β signaling as a key mechanism underlying CARASIL pathogenesis.
JAMSS: proteomics mass spectrometry simulation in Java
Authors: Smith Rob , Prince John T. 
Published: November 2014

Abstract
Summary: Countless proteomics data processing algorithms have been proposed, yet few have been critically evaluated due to lack of labeled data (data with known identities and quantities). Although labeling techniques exist, they are limited in terms of confidence and accuracy. In silico simulators have recently been used to create complex data with known identities and quantities. We propose Java Mass Spectrometry Simulator (JAMSS): a fast, self-contained in silico simulator capable of generating simulated MS and LC-MS runs while providing meta information on the provenance of each generated signal. JAMSS improves upon previous in silico simulators in terms of its ease to install, minimal parameters, graphical user interface, multithreading capability, retention time shift model and reproducibility.
Availability and implementation: The simulator creates mzML 1.1.0. It is open source software licensed under the GPLv3. The software and source are available at https://github.com/optimusmoose/JAMSS.
Contact: 2robsmith@gmail.com
First Report of Phakopsora pachyrhizi Causing Rust on Soybean in Malawi
Authors: Murithi H. M. , Beed F. D. , Soko M. M. , Haudenshield J. S. , Hartman G. L. 
Published: November 2014

Soybean rust (SBR), caused by Phakopsora pachyrhizi, has become established in Africa since the first report in Uganda in 1996 (2). The urediniospores, as windborne propagules, have infested new regions of Africa, initiating SBR in many countries, including Ghana and Democratic Republic of the Congo in 2007 (4) and Tanzania in 2014 (3). No refereed reports have been published about rust in Malawi, but some people have indicated that soybean rust may have been observed as early as 2008. Typical symptoms and signs of SBR, including leaf yellowing and tan, sporulating uredinia, were observed on soybean in May 2014 during field surveys in the major soybean-growing areas of Malawi, including the central (Dowa, Mchinji, and Kasungu) and southern (Thyolo) regions in nine out of 12 sites surveyed. When microscopically examined, urediniospores were elliptical, echinulate, and hyaline to pale yellowish brown. Leaves exhibiting sporuliferous uredinia were sent by APHIS permit to the University of Illinois. To confirm the pathogen, symptomatic soybean leaf tissue of approximately 1 cm2 was excised from each of the samples, and DNA was extracted using the FastDNA Spin Kit (MP Biomedicals, Solon, OH), with further purification using the MicroElute DNA Clean-up Kit (Omega Bio-Tek, Norcross, GA). The resulting DNA was analyzed by quantitative PCR using published Taqman assays for P. pachyrhizi and P. meibomiae, with a multiplexed exogenous internal control reaction to validate negative results (1). P. pachyrhizi DNA was detected in excess of 180,000 genome equivalents/cm2 in all samples, indicating a substantial infection. P. meibomiae DNA was determined to be absent from all samples, within the limit of quantification of ~2 pg DNA/cm2. Urediniospores dislodged from three leaves and inoculated onto susceptible soybean cultivar Williams 82 produced tan lesions after 2 weeks of incubation in a detached-leaf assay. This is the first confirmed report of P. pachyrhizi causing rust on soybean in Malawi, putting at risk 14,000 ha currently under soybean production. The reports of soybean rust in Malawi and adjoining countries will alter soybean production practices and research interests. In some cases, foliar application of fungicides has increased and planting dates have been changed to avoid conditions that are most conducive for rust development. Efforts to understand the virulence and genetic diversity of the pathogen in the region are needed in order to develop and deploy resistant cultivars. References: (1) J. S. Haudenshield and G. L. Hartman. Plant Dis. 95:343, 2011. (2) R. Kawuki, et al. Afr. Crop Sci. J. 11:301, 2003. (3) H. M. Murithi et al. Plant Dis. 98:1586, 2014. (4) P. S. Ojiambo et al. Plant Dis. 91:1204, 2007.
Effectiveness of 14 Fungicides for Suppressing Lesions Caused by Phytophthora capsici on Inoculated Stems of Chile Pepper Seedlings
Authors: Matheron Michael E. , Porchas Martin 
Published: November 2014

Phytophthora blight, caused by the oomycete pathogen Phytophthora capsici, is an economically important disease in bell and chile pepper. Fourteen different fungicides were evaluated with respect to inhibition of stem lesion growth on chile pepper seedlings inoculated with mycelium or with zoospores of P. capsici 1 or 3 weeks after treatment of plant foliage and stems or roots. Fungicides containing ametoctradin + dimethomorph and fluopicolide were the most effective among tested products in both experiments across eight trial parameters (inoculum type, inoculation time after treatment, and fungicide application site). Other active ingredients, including acibenzolar-S-methyl, dimethomorph, fenamidone, ethaboxam, mandipropamid, mefenoxam, and oxathiapiprolin, were most effective in reducing stem lesion growth in three to seven of the eight trial parameters evaluated. Compared to nontreated plants, stem lesion inhibition ranged from 84.1 to 100%. Data from these trials demonstrate the comparative effectiveness of tested products under controlled environmental conditions favorable for disease development; however, confirmation of these findings is required in field trials, where plant and environmental conditions will be variable. Accepted for publication 18 September 2014. Published 1 November 2014.
Effects of Ultraprotective Ventilation, Extracorporeal Carbon Dioxide Removal, and Spontaneous Breathing on Lung Morphofunction and Inflammation in Experimental Severe Acute Respiratory Distress Syndrome
Authors: Güldner Andreas , Kiss Thomas , Bluth Thomas , Uhlig Christopher , Braune Anja , Carvalho Nadja , Quast Theresa , Rentzsch Ines , Huhle Robert , Spieth Peter , Richter Torsten , Saddy Felipe , Rocco Patricia R. M. , Kasper Michael , Koch Thea , Pelosi Paolo , de Abreu Marcelo Gama 
Published: November 2014

AbstractAbstract
In a model of severe acute respiratory distress syndrome in pigs, mechanical ventilation with 3 ml/kg tidal volume and extracorporeal carbon dioxide removal without spontaneous breathing slightly reduced lung histologic damage. Spontaneous breathing during ultraprotective ventilation improved gas exchange and distribution of ventilation, but pressure support increased lung inflammation.

Background:
To investigate the role of ultraprotective mechanical ventilation (UP-MV) and extracorporeal carbon dioxide removal with and without spontaneous breathing (SB) to improve respiratory function and lung protection in experimental severe acute respiratory distress syndrome.

Methods:
Severe acute respiratory distress syndrome was induced by saline lung lavage and mechanical ventilation (MV) with higher tidal volume (VT) in 28 anesthetized pigs (32.8 to 52.5 kg). Animals (n = 7 per group) were randomly assigned to 6 h of MV (airway pressure release ventilation) with: (1) conventional P-MV with VT ≈6 ml/kg (P-MVcontr); (2) UP-MV with VT ≈3 ml/kg (UP-MVcontr); (3) UP-MV with VT ≈3 ml/kg and SB (UP-MVspont); and (4) UP-MV with VT ≈3 ml/kg and pressure supported SB (UP-MVPS). In UP-MV groups, extracorporeal carbon dioxide removal was used.

Results:
The authors found that: (1) UP-MVcontr reduced diffuse alveolar damage score in dorsal lung zones (median[interquartile]) (12.0 [7.0 to 16.8] vs. 22.5 [13.8 to 40.8]), but worsened oxygenation and intrapulmonary shunt, compared to P-MVcontr; (2) UP-MVspont and UP-MVPS improved oxygenation and intrapulmonary shunt, and redistributed ventilation towards dorsal areas, as compared to UP-MVcontr; (3) compared to P-MVcontr, UP-MVcontr and UP-MVspont, UP-MVPS yielded higher levels of tumor necrosis factor-α (6.9 [6.5 to 10.1] vs. 2.8 [2.2 to 3.0], 3.6 [3.0 to 4.7] and 4.0 [2.8 to 4.4] pg/mg, respectively) and interleukin-8 (216.8 [113.5 to 343.5] vs. 59.8 [45.3 to 66.7], 37.6 [18.8 to 52.0], and 59.5 [36.1 to 79.7] pg/mg, respectively) in dorsal lung zones.

Conclusions:
In this model of severe acute respiratory distress syndrome, MV with VT ≈3 ml/kg and extracorporeal carbon dioxide removal without SB slightly reduced lung histologic damage, but not inflammation, as compared to MV with VT = 4 to 6 ml/kg. During UP-MV, pressure supported SB increased lung inflammation.
Faecal Calprotectin in Suspected Paediatric Inflammatory Bowel Disease
Authors: Degraeuwe Pieter L.J. , Beld Monique P.A. , Ashorn Merja , Canani Roberto Berni , Day Andrew S. , Diamanti Antonella , Fagerberg Ulrika L. , Henderson Paul , Kolho Kaija‐Leena , Van de Vijver Els , van Rheenen Patrick F. , Wilson David C. , Kessels Alfons G.H. 
Published: November 2014

ABSTRACTObjectives:The diagnostic accuracy of faecal calprotectin (FC) concentration for paediatric inflammatory bowel disease (IBD) is well described at the population level, but not at the individual level. We reassessed the diagnostic accuracy of FC in children with suspected IBD and developed an individual risk prediction rule using individual patient data.Methods:MEDLINE, EMBASE, DARE, and MEDION databases were searched to identify cohort studies evaluating the diagnostic performance of FC in paediatric patients suspected of having IBD. A standard study‐level meta‐analysis was performed. In an individual patient data meta‐analysis, we reanalysed the diagnostic accuracy on a merged patient dataset. Using logistic regression analysis we investigated whether and how the FC value and patient characteristics influence the diagnostic precision. A prediction rule was derived for use in clinical practice and implemented in a spreadsheet calculator.Results:According to the study‐level meta‐analysis (9 studies, describing 853 patients), FC has a high overall sensitivity of 0.97 (95% confidence interval [CI] 0.92–0.99) and a specificity of 0.70 (0.59–0.79) for diagnosing IBD. In the patient‐level pooled analysis of 742 patients from 8 diagnostic accuracy studies, we calculated that at an FC cutoff level of 50 μg/g there would be 17% (95% CI 15–20) false‐positive and 2% (1–3) false‐negative results. The final logistic regression model was based on individual data of 545 patients and included both FC level and age. The area under the receiver operating characteristic curve of this derived prediction model was 0.92 (95% CI 0.89–0.94).Conclusions:In high‐prevalence circumstances, FC can be used as a noninvasive biomarker of paediatric IBD with only a small risk of missing cases. To quantify the individual patients' risk, we developed a simple prediction model based on FC concentration and age. Although the derived prediction rule cannot substitute the clinical diagnostic process, it can help in selecting patients for endoscopic evaluation.
Gastrointestinal Manifestations in Diploid/Triploid Mixoploidy
Authors: Lalani Farida K. , Elsner Garrett L. , Lebel Robert Roger , Beg Mirza B. 
Published: November 2014

ABSTRACTA girl infant was delivered by cesarean section at 32 weeks of gestation because of growth arrest and poor movement patterns. The infant had feeding problems, which were based on gastroesophageal reflux, laryngomalacia, and decreased gut motility. Hypotonia was notable from the outset, and the patient eventually displayed significant delays in both motor and cognitive milestones. Meanwhile, lymphocytes had yielded a normal karyotype (46,XX), but at 2 years of age the patient underwent a skin biopsy and mosaicism because a 68,XX cell line was discovered in fibroblasts. At the age 6.4 years, the patient is short of stature below the 3rd percentile but has a weight at the 42nd percentile and head circumference above the 97th percentile. Other phenotypic features include low‐set ears, piebald irides and scalp hair, eyelid ptosis, strabismus, broad nasal bridge, anteverted nares, upswept eyebrows, hypoplastic teeth, pectus excavatum, hypoplastic labia, scoliosis, 3–4 finger syndactyly, and 2–3 toe syndactyly. We present this case with a review of the literature for mixoploidy (the rare event of mosaicism for diploid and triploid cell lines). We add to the existing data on the clinical features of diploid/triploid mixoploidy. The complexities of the gastrointestinal problems make this case unusual.
Inference of cell-cell interactions from population density characteristics and cell trajectories on static and growing domains
Authors: Ross Robert J.H. , Yates C.A. , Baker R.E. 
Published: November 2014

AbstractA key feature of cell migration is how cell movement is affected by cell-cell interactions. Furthermore, many cell migratory processes such as neural crest stem cell migration [1, 2] occur on growing domains or in the presence of a chemoattractant. Therefore, it is important to study interactions between migrating cells in the context of domain growth and directed motility. Here we compare discrete and continuum models describing the spatial and temporal evolution of a cell population for different types of cell-cell interactions on static and growing domains. We suggest that cell-cell interactions can be inferred from population density characteristics in the presence of motility bias, and these population density characteristics for different cell-cell interactions are conserved on both static and growing domains. We also study the expected displacement of a tagged cell, and show that different types of cell-cell interactions can give rise to cell trajectories with different characteristics. These characteristics are conserved in the presence of domain growth, however, they are diminished in the presence of motility bias. Our results are relevant for researchers who study the existence and role of cell-cell interactions in biological systems, so far as we suggest that different types of cell-cell interactions could be identified from cell density and trajectory data.