bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods
Authors: Bengtsson Henrik , Ray Amrita , Spellman Paul , Speed Terence P. 
Published: February 2009

Abstract
Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more than one platform for the same set of samples, and it is natural to want to combine the different estimates in order to meet this demand. Estimates from different platforms show different degrees of attenuation of the true CN changes. Similar differences can be observed in CNs from the same platform run in different labs, or in the same lab, with different analytical methods. This is the reason why it is not straightforward to combine CN estimates from different sources (platforms, labs and analysis methods).
Results: We propose a single-sample multi source normalization that brings full-resolution CN estimates to the same scale across sources. The normalized CNs are such that for any underlying CN level, their mean level is the same regardless of the source, which make them better suited for being combined across sources, e.g. existing segmentation methods may be used to identify aberrant regions. We use microarray-based CN estimates from ‘The Cancer Genome Atlas’ (TCGA) project to illustrate and validate the method. We show that the normalized and combined data better separate two CN states at a given resolution. We conclude that it is possible to combine CNs from multiple sources such that the resolution becomes effectively larger, and when multiple platforms are combined, they also enhance the genome coverage by complementing each other in different regions.
Availability: A bounded-memory implementation is available in aroma.cn.
Contact: hb@stat.berkeley.edu
CoCAS: a ChIP-on-chip analysis suite
Authors: Benoukraf Touati , Cauchy Pierre , Fenouil Romain , Jeanniard Adrien , Koch Frederic , Jaeger Sébastien , Thieffry Denis , Imbert Jean , Andrau Jean-Christophe , Spicuglia Salvatore , Ferrier Pierre 
Published: February 2009

Abstract
Motivation: High-density tiling microarrays are increasingly used in combination with ChIP assays to study transcriptional regulation. To ease the analysis of the large amounts of data generated by this approach, we have developed ChIP-on-chip Analysis Suite (CoCAS), a standalone software suite which implements optimized ChIP-on-chip data normalization, improved peak detection, as well as quality control reports. Our software allows dye swap, replicate correlation and connects easily with genome browsers and other peak detection algorithms. CoCAS can readily be used on the latest generation of Agilent high-density arrays. Also, the implemented peak detection methods are suitable for other datasets, including ChIP-Seq output.
Availability: The software is available for download along with a sample dataset at http://www.ciml.univ-mrs.fr/software/ferrier.htm.
Contact: ferrier@ciml.univ-mrs.fr; andrau@ciml.univ-mrs.fr; spicuglia@ciml.univ-mrs.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Inhibition of platelet activation in rats with severe congestive heart failure by a novel endothelial nitric oxide synthase transcription enhancer
Authors: Schäfer Andreas , Fraccarollo Daniela , Widder Julian , Eigenthaler Martin , Ertl Georg , Bauersachs Johann 
Published: February 2009

AimsIncreased risk of thrombo‐embolic events in congestive heart failure (CHF) has been attributed to a hypercoagulable state including vascular endothelial dysfunction and reduced bioavailability of nitric oxide (NO) as well as platelet activation. We investigated whether treatment with a novel endothelial NO synthase (eNOS)‐transcription enhancer positively modulates systemic NO bioavailability and reduces platelet activation in rats with CHF.Methods and resultsAfter experimental myocardial infarction, male Wistar rats were treated with either placebo or the eNOS‐transcription enhancer, AVE9488 (25 ppm/day) for 10 weeks. In rats with severe CHF (left ventricular end‐diastolic pressure >15 mmHg), platelet vasodilator‐stimulated phosphoprotein (VASP)‐phosphorylation reflecting the integrity of the NO/cGMP pathway was significantly reduced (mean immunofluorescence at Ser157: Sham, 61.4 ± 9.1; CHF‐Placebo, 37.4 ± 4.9; P < 0.05; Ser239: Sham, 18.1 ± 2.5; CHF‐Placebo, 13.2 ± 0.6; P < 0.05). Platelet surface expression of P‐selectin and glycoprotein 53 were increased in CHF rats compared with sham‐operated animals. Chronic treatment with AVE9488 significantly enhanced platelet VASP‐phosphorylation in CHF rats (Ser157: 70.4 ± 16.2; Ser239: 19.3 ± 1.8). In parallel, platelet surface expression of P‐selectin and glycoprotein 53 was reduced in the treatment group.ConclusionPlatelet activation was evident in CHF rats. Therapy with the eNOS‐transcription enhancer, AVE9488, reduced platelet activation in parallel to normalization of platelet NO bioavailability.
Estimating tail-beat frequency using split-beam echosounders
Authors: Handegard Nils Olav , Pedersen Geir , Brix Ole 
Published: February 2009

AbstractHandegard, N. O., Pedersen, G., and Brix, O. 2009. Estimating tail-beat frequency using split-beam echosounders. – ICES Journal of Marine Science, 66: 1252–1258. Data from a standard split-beam echosounder are used to estimate tail-beat frequency within a dense herring (Clupea harengus L.) layer. The data were collected by lowering a horizontally projecting 38 kHz split-beam transducer into a herring layer at 245-m depth. Individual targets were concatenated into tracks, and a fast Fourier transform was used to estimate the periodogram of the backscattering strengths along each track. A simple model, assumed accurate under certain conditions, was used to relate the periodogram to tail-beat frequency. The requisite conditions are discussed. Examples of accurate tail-beat estimates from single high-quality tracks, which are consistent with statistics on all tracks in the test dataset, are presented. In addition, the cross periodogram between closely spaced individuals was calculated on selected tracks to estimate the relative phase between the adjacent tracks within the school. Finally, the potential use of this method to resolve schooling behaviour, improve target-strength estimates, and even estimate fish condition, is discussed.
Off-Pump Atrial Septal Defect Closure Using the Universal Cardiac Introducer®
Authors: Guiraudon Gerard M. , Jones Douglas L. , Bainbridge Daniel , Moore John T. , Wedlake Chris , Linte Cristian , Wiles Andrew , Peters Terry M. 
Published: February 2009

Objective Optimal atrial septal defect (ASD) closure should combine off-pump techniques with the effectiveness and versatility of open-heart techniques. We report our experience with off-pump ASD closure using the Universal Cardiac Introducer (UCI) in a porcine model. The goal was to create an ASD over the fossa ovale (FO) and position a patch over the ASD under ultrasound (US) imaging and augmented virtual reality guidance. Methods An US probe (tracked with a magnetic tracking system) was positioned into the esophagus (transesophageal echocardiographic probe) for real-time image-guidance. The right atrium (RA) of six pigs was exposed via a right lateral thoracotomy or medial sternotomy. The UCI was attached to the RA wall. A punching tool was introduced via the UCI, navigated and positioned, under US guidance, to create an ASD into the FO. A patch with its holder and a stapling device were introduced into the RA via the UCI. The patch was positioned on the ASD. Occlusion of the ASD was determined using US and Doppler imaging. Results The FO membrane was excised successfully in all animals. US image-guidance provided excellent visualization. The patch was positioned in all cases with complete occlusion of the ASD. The stapling device proved too bulky, impeding circumferential positioning. Conclusions Using the UCI, ASD closure was safe and feasible. US imaging, combined with virtual and augmented reality provided accurate navigating and positioning. This study also provided valuable information on the future design of anchoring devices for intracardiac procedures.
Endovascular Thoracic Aortic Aneurysm Repair without Angiography
Authors: Tozzi Piergiorgio , Marty Bettina , Ruchat Patrick , Ferrari Enrico , Siniscalchi Giuseppe , von Segesser Ludwig K. 
Published: February 2009

Objective Intravascular ultrasound (IVUS) generates high definition circumferential cross-sectional images and provides real-time readout of vascular dimensions, including visualization of vessel branches. We have used it as an alternative to angiography in the endovascular thoracic aneurysm repair work-up. Methods Out of consecutive 203 patients with descending thoracic aortic aneurysm, 89 (43.8%) received endovascular treatment [mean age, 68 ± 8 years; range, 29–82; male, 79 (88.7%); female, 10 (11.3%)] without using angiography during the endovascular procedure. IVUS (6 F, 12.5 MHz probe or 10 F 9 MHz) coupled with fluoroscopy for the placement of radiopaque markers was used for target site identification, landing zone measurement, device positioning, and assessment of endovascular repair. Results Hospital mortality was 4/89 (4.5%). Number of devices implanted in each patient was 1.2 (range, 1–3). X-ray exposure time was 12 ± 8 minutes. Median procedure time was 63 ± 20 minutes. Conversion to open surgery was necessary in one patient (1.1%) because of aortic dissection. In nine patients (10.1%) left subclavian artery was covered because of a short neck. Two patients (2.2%) had vascular access lesions and required surgical repair. One patient developed paraplegia (1.1%). Early endoleak was observed in eight patients (8.9%) and 4 (4.5%) required additional procedures (proximal or distal extensions). Late conversion was necessary in one patient (1.1%). Conclusions IVUS provides all information necessary for device selection, target site identification as well as safe and correct deployment of thoracic endoprostheses and makes periprocedural angiography unnecessary, thus avoiding the risk of renal failure because of contrast medium.
In Situ Investigation of Leaf Water Status by Portable Unilateral Nuclear Magnetic Resonance
Authors: Capitani Donatella , Brilli Federico , Mannina Luisa , Proietti Noemi , Loreto Francesco 
Published: February 2009

Abstract
A portable unilateral nuclear magnetic resonance (NMR) instrument was used to detect in field conditions the water status of leaves of herbaceous crops (Zea mays, Phaseolus vulgaris), mesophyllous trees (Populus nigra), and natural Mediterranean vegetation characterized by water-spending shrubs (Cistus incanus) and water-saving sclerophyllous trees (Quercus ilex). A good relationship was observed between NMR signal, leaf relative water content, and leaf transpiration in herbaceous leaves undergoing fast dehydration or slowly developing a drought stress. A relationship was also observed between NMR signal and water potential of Populus leaves during the development of a water stress and when leaves recovered from the stress. In the natural vegetation, the relationship between NMR signal and water status was found in Cistus, the species characterized by high transpiration rates, when measured during a drought stress period and after a rainfall. In the case of the sclerophyllous Quercus, the NMR signal, the relative water content, and the transpiration rate did not change at different leaf water status, possibly because a large amount of water is compartmentalized in cellular structures and macromolecules. The good association between NMR signal and relative water content was lost in leaves exposed for 24 h to dehydration or to an osmotic stress caused by polyethylene glycol feeding. At this time, the transverse relaxation time became longer than in leaves maintained under optimal water conditions, and two indicators of membrane damage, the ion leakage and the emission of products of membrane lipoxygenation [(Z)-3-hexenal, (Z)-3-hexenol, and (E)-2-hexenol], increased. These results taken all together give information on the physiological state of a leaf under a developing stress and show the usefulness of the NMR instrumentation for screening vegetation health and fitness in natural and cultivated conditions. It is concluded that the portable unilateral NMR instrument may be usefully employed in field conditions to monitor nondestructively the water status of plants and to assist agricultural practices, such as irrigation scheduling, to minimize stomatal closure and the consequent limitation to plant production.
Treatment with sirolimus results in complete responses in patients with autoimmune lymphoproliferative syndrome
Authors: Teachey David T. , Greiner Robert , Seif Alix , Attiyeh Edward , Bleesing Jack , Choi John , Manno Catherine , Rappaport Eric , Schwabe Dirk , Sheen Cecilia , Sullivan Kathleen E. , Zhuang Hongming , Wechsler Daniel S. , Grupp Stephan A. 
Published: February 2009

SummaryWe hypothesized that sirolimus, an mTOR inhibitor, may be effective in patients with autoimmune lymphoproliferative syndrome (ALPS) and treated patients who were intolerant to or failed other therapies. Four patients were treated for autoimmune cytopenias; all had a rapid complete or near complete response. Two patients were treated for autoimmune arthritis and colitis, demonstrating marked improvement. Three patients had complete resolution of lymphadenopathy and splenomegaly and all patients had a reduction in double negative T cells, a population hallmark of the disease. Based on these significant responses, we recommend that sirolimus be considered as second‐line therapy for patients with steroid‐refractory disease.
Hypertriglyceridaemia with bexarotene in cutaneous T cell lymphoma: the role of omega‐3 fatty acids
Authors: Musolino Antonino , Panebianco Michele , Zendri Enrico , Santini Marcello , Di Nuzzo Sergio , Ardizzoni Andrea 
Published: February 2009

SummaryBexarotene is approved for the treatment of cutaneous T cell lymphomas in patients refractory to at least one prior systemic therapy. Associated hypertriglyceridaemia requires monitoring, but can readily be managed with concomitant medication, such as fenofibrate. Here we report three cases of hypertriglyceridaemia secondary to bexarotene assumption, which was adequately managed with omega‐3 fatty acids. If fenofibate‐related side effects occur, or a statin is required to control low‐density lipoprotein‐cholesterol, omega‐3 fatty acids should be considered as a good alternative therapy to lower lipid levels during bexarotene treatment.
Pathogen trafficking pathways and host phosphoinositide metabolism
Authors: Weber Stefan S. , Ragaz Curdin , Hilbi Hubert 
Published: February 2009

SummaryPhosphoinositide (PI) glycerolipids are key regulators of eukaryotic signal transduction, cytoskeleton architecture and membrane dynamics. The host cell PI metabolism is targeted by intracellular bacterial pathogens, which evolved intricate strategies to modulate uptake processes and vesicle trafficking pathways. Upon entering eukaryotic host cells, pathogenic bacteria replicate in distinct vacuoles or in the host cytoplasm. Vacuolar pathogens manipulate PI levels to mimic or modify membranes of subcellular compartments and thereby establish their replicative niche. Legionella pneumophila, Brucella abortus, Mycobacterium tuberculosis and Salmonella enterica translocate effector proteins into the host cell, some of which anchor to the vacuolar membrane via PIs or enzymatically turnover PIs. Cytoplasmic pathogens target PI metabolism at the plasma membrane, thus modulating their uptake and antiapoptotic signalling pathways. Employing this strategy, Shigella flexneri directly injects a PI‐modifying effector protein, while Listeria monocytogenes exploits PI metabolism indirectly by binding to transmembrane receptors. Thus, regardless of the intracellular lifestyle of the pathogen, PI metabolism is critically involved in the interactions with host cells.
Educational level, coping, and psychological and physical aspects of quality of life in heart transplant candidates
Authors: Burker Eileen J. , Madan Alok , Evon Donna , Finkel Jerry B. , Mill Michael R. 
Published: February 2009

Abstract: Objective:  To determine whether demographic factors and coping strategies are related to quality of life in heart transplant candidates.Method:  Participants were 50 inpatients being evaluated for heart transplant. Coping was measured using the COPE Inventory (1) (J Pers Soc Psychol, 56, 1989, 267). Quality of life was assessed using the SF‐36 (2) (Health Survey: Manual and Interpretation Guide, Quality Metric Inc, Lincoln, RI, 2000).Results:  Higher education and less seeking of social support were independently associated with better physical functioning. Higher use of denial was associated with poorer mental health functioning.Conclusions:  In patients with significant physical limitations, years of education appears to be protective. Less seeking of social support was associated with better physical functioning perhaps because individuals who feel better physically do not feel the need to elicit support. Alternatively, the tendency to not seek assistance could stem from personality characteristics such as avoidance or optimism. Denial was associated with worse mental health functioning. Denying the existence of a stressor may be a high risk coping strategy for patients who are pre‐transplant and even more dangerous for those who are post‐transplant given the need to be alert to symptoms. Proactive identification of patients at risk for poorer quality of life will allow for more timely psychosocial interventions, which could impact post‐transplant outcomes.
Development of an activity of daily living scale for patients with COPD: The Activity of Daily Living Dyspnoea scale
Authors: YOZA Yoshiyasu , ARIYOSHI Koya , HONDA Sumihisa , TANIGUCHI Hiroyuki , SENJYU Hideaki 
Published: February 2009

ABSTRACTBackground and objective:  Patients with COPD often experience restriction in their activities of daily living (ADL) due to dyspnoea. This type of restriction is unique to patients with COPD and cannot be adequately evaluated by the generic ADL scales. This study developed an ADL scale (the Activity of Daily Living Dyspnoea scale (ADL‐D scale)) for patients with COPD and investigated its validity and internal consistency.Methods:  Patients with stable COPD were recruited and completed a pilot 26‐item questionnaire. Patients also performed the Incremental Shuttle Walk Test (ISWT), and completed the St. George's Respiratory Questionnaire (SGRQ) and Medical Research Council (MRC) dyspnoea grade.Results:  There were 83 male participants who completed the pilot questionnaire. Following the pilot, eight items that were not undertaken by the majority of subjects, and three items judged to be of low clinical importance by physical therapists were removed from the questionnaire. The final ADL‐D scale contained 15 items. Scores obtained with the ADL‐D scale were significantly correlated with the MRC dyspnoea grades, distance walked on the ISWT and SGRQ scores. The ADL‐D scores were significantly different across the five grades of the MRC dyspnoea grade. The ADL‐D scale showed high consistency (Chronbach's α coefficient of 0.96).Conclusions:  The ADL‐D scale is a useful scale for assessing impairments in ADL in Japanese male patients with COPD.
Small airways obstruction syndrome in clinical practice
Authors: CHEN Chiung‐Zuei , LIN Chien‐Chung , LEE Cheng‐Hung , CHANG Han‐Yu , HSIUE Tzuen‐Ren 
Published: February 2009

ABSTRACTBackground and objective:  Small airways obstruction syndrome (SAOS) is a particular pulmonary function test (PFT) pattern showing decreased VC and FEV1 but a normal FEV1/VC ratio and TLC. The significance of this syndrome in clinical practice has not been comprehensively investigated.Methods:  This study retrospectively identified all patients who had performed PFT that showed a SAOS pattern at a university teaching hospital over 1 year. A simple algorithm for differential diagnosis was developed and validated.Results:  Of the 3207 PFT performed, 153 (4.8%) showed a pattern indicating SAOS. Among these, a final diagnosis was confirmed for 85 (63.4%) of the patients. The causes of SAOS included both restrictive and obstructive lung diseases with the leading causes being early interstitial lung disease (n = 20; 23.3%), chest wall deformity (n = 12; 14.1%) and asthma (n = 10; 11.6%). Using a cut‐off point of TLC of <95% predicted value to identify restrictive ventilatory defects (P = 0.002) and of ≥95% predicted combined with RV/TLC ≥55% to identify obstructive ventilatory defects (P < 0.001), a simplified algorithm with good accuracy (86.6%) was identified. Validation in an independent group showed accuracy of 91%.Conclusions:  The PFT pattern called SAOS is not uncommon. The most common causes of SAOS were early interstitial lung disease, chest wall deformity and asthma. A diagnostic algorithm was proposed, which may help physicians' decision‐making in their daily practice.
Chronic intranasal administration of Aspergillus fumigatus spores leads to aggravation of airway inflammation and remodelling in asthmatic rats
Authors: GAO Fu‐Sheng , QIAO Jian‐Ou , ZHANG Yi , JIN Xian‐Qiao 
Published: February 2009

ABSTRACTBackground and objective:  Epidemiological evidence indicates a close link between exposure to fungi and deterioration of asthma. However, the role of fungi as an exogenous precipitant for initiation and progression of asthma has been incompletely explored. In this study, the effects of Aspergillus fumigatus exposure on airway inflammation and remodelling in a rat model of chronic asthma were investigated.Methods:  The rat model of chronic asthma was established by systemic sensitization and repeated challenge with ovalbumin (OVA). The asthmatic rats were exposed to chronic intranasal inhalation of A. fumigatus spores. Changes in airway inflammation, remodelling and BHR were measured after exposure to the fungus.Results:  Chronic inhalation of A. fumigatus spores elevated the production of T helper 2 (Th2) cytokines, increased the concentration of total serum IgE, and resulted in the recruitment of eosinophils and lymphocyte infiltration into the airways of asthmatic rats. Goblet cell hyperplasia, mucus hyperproduction and subepithelial collagen deposition were also induced by inhalation of the fungus. The remodelling changes induced by inhalation of the fungus paralleled the changes in BHR in this rat model of asthma.Conclusions:  Chronic exposure to A. fumigatus aggravated Th2 airway inflammation, promoted airway remodelling and increased BHR in OVA‐sensitized and ‐challenged rats.
Road ahead to respiratory health: Experts chart future research directions
Authors: HEFFNER John E. , HOLGATE Stephen T. , CHUNG Kian Fan , NIEDERMAN Michael S. , DALEY Charles L. , JETT James R. , STRADLING John R. , WELLS Athol U. , LIGHT Richard W. , TAPSON Victor F. , HANSELL David M. , PROVONOST Peter J. , LEE Y.C. Gary 
Published: February 2009

ABSTRACTRespiratory illnesses are a huge and rising burden to health‐care systems and societies worldwide. Research is crucial to tackle the enormous problem of chest diseases. However the vast number of research questions and available research approaches often creates confusion and risks dilution of resources by spreading them too diffusely. Clear research directions will help to use research funds efficiently to provide treatment advances that benefit patient care. This paper presents the visions of leading experts on future research directions, focusing on what should rather than what is going to be done. These opinions provide a guide for new investigators and a platform for intellectual debates through which coordinated research efforts can help progress towards respiratory health.