bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping the Tree of Life: Progress and Prospects
Authors: Pace Norman R. 
Published: November 2009

SUMMARY
The intent of this article is to provide a critical assessment of our current understanding of life's phylogenetic diversity. Phylogenetic comparison of gene sequences is a natural way to identify microorganisms and can also be used to infer the course of evolution. Three decades of molecular phylogenetic studies with various molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya. The sequence-based perspective on microbial identification additionally opened the way to the identification of environmental microbes without the requirement for culture, particularly through analysis of rRNA gene sequences. Environmental rRNA sequences, which now far outnumber those from cultivars, expand our knowledge of the extent of microbial diversity and contribute increasingly heavily to the emerging ToL. Although the three-domain structure of the ToL is established, the deep phylogenetic structure of each of the domains remains murky and sometimes controversial. Obstacles to accurate inference of deep phylogenetic relationships are both systematic, in molecular phylogenetic calculations, and practical, due to a paucity of sequence representation for many groups of organisms.
Jane Austen and Addison’s disease: an unconvincing diagnosis: Figure 1
Authors: White K G 
Published: November 2009

Jane Austen’s letters describe a two-year deterioration into bed-ridden exhaustion, with unusual colouring, bilious attacks and rheumatic pains.In 1964, Zachary Cope postulated tubercular Addison’s to explain her symptoms and her relatively pain-free illness. Literary scholars later countered this posthumous diagnosis on grounds that are not well substantiated, while medical authors supported his conclusion.Important symptoms reported by contemporary Addison’s patients—mental confusion, generalised pain and suffering, weight loss and anorexia—are absent from Jane Austen’s letters. Thus, by listening to the patient’s perspective, we can conclude it is unlikely that Addison’s disease caused Jane Austen’s demise.Disseminated bovine tuberculosis would offer a coherent explanation for her symptoms, so that Cope’s original suggestion of infective tuberculosis as the cause of her illness may have been correct.
DEVELOPING RADICAL SERVICE INNOVATIONS IN HEALTHCARE — THE ROLE OF DESIGN METHODS
Authors: BESSANT JOHN , MAHER LYNNE 
Published: November 2009

This paper looks at the management of service innovation. In particular, it explores the challenge of public services and argues that there is a need for new approaches to the ways which engage users as more active co-creators within the innovation process. It draws on wider research on radical innovation being carried out as part of a long-term international programme and reports on a series of case studies of experiments in the health sector in the UK using tools like ethnography and prototyping to enable innovation.The paper argues that a potentially valuable toolkit can be found in the field of design methods. By their nature, design tools are used to help articulate needs and give them shape and form; as such they are critical to the "front end" of any innovation process. Methods like ethnography allow for deep insights into user needs, including those not clearly articulated whilst prototyping provides the possibility of creating a set of "boundary objects" around which design discussions which include users and their perspectives can be carried out.
Algebrization
Authors: Aaronson Scott , Wigderson Avi 
Published: November 2009

Any proof of P ≠ NP will have to overcome two barriers:
relativization
and
natural proofs
. Yet over the last decade, we have seen circuit lower bounds (e.g., that PP does not have linear-size circuits) that overcome both barriers simultaneously. So the question arises of whether there is a third barrier to progress on the central questions in complexity theory.

In this article, we present such a barrier, which we call
algebraic relativization
or
algebrization
. The idea is that, when we relativize some complexity class inclusion, we should give the simulating machine access not only to an oracle
A
, but also to a low-degree extension of
A
over a finite field or ring.

We systematically go through basic results and open problems in complexity theory to delineate the power of the new algebrization barrier. First, we show that all known nonrelativizing results based on arithmetization---both inclusions such as IP = PSPACE and MIP = NEXP, and separations such as MA
EXP
⊄ P/poly---do indeed algebrize. Second, we show that almost all of the major open problems---including P versus NP, P versus RP, and NEXP versus P/poly---will require
non-algebrizing techniques
. In some cases, algebrization seems to explain exactly why progress stopped where it did: for example, why we have superlinear circuit lower bounds for PromiseMA but not for NP.

Our second set of results follows from lower bounds in a new model of
algebraic query complexity
, which we introduce in this article and which is interesting in its own right. Some of our lower bounds use direct combinatorial and algebraic arguments, while others stem from a surprising connection between our model and communication complexity. Using this connection, we are also able to give an MA-protocol for the Inner Product function with
O (√n
log
n
) communication (essentially matching a lower bound of Klauck), as well as a communication complexity conjecture whose truth would imply NL ≠ NP.
Privacy in location-aware systems
Authors: Freytag Johann-Christoph 
Published: November 2009

As our world becomes more and more proliferated by sensors and mobile devices - often connected by wireless networks - there is the urging need to develop appropriate abstractions for application development and deployment. Those abstractions should shield applications from the physical properties of the devices thereby allowing applications to focus on information processing based on global conceptual views (of the world) in form of context models.
This paper will briefly elaborate on the concern for privacy in location-aware systems by providing a few examples that should highlight the complexity of such concerns. We show that privacy needs well founded bases for handling user requirements appropriately. Additionally, we argue that privacy aspects in context model based systems should include and embed privacy protection and control mechanism as an integral part on all systems levels therefore increasing the usability of such systems from a user's point of view.
An autonomic framework for reliable multicast
Authors: Anastasopoulos Markos P. , Vasilakos Athanasios V. , Cottis Panayotis G. 
Published: November 2009

A major challenge in wireless terrestrial networks is to provide large-scale reliable multicast and broadcast services. The main problem limiting the scalability of such networks is feedback implosion, a problem arising when a large number of users transmit their feedback messages through the network, occupying a significant portion of system resources.
Inspired by social psychology, specifically from the bystander effect phenomenon, an autonomic framework for large-scale reliable multicast services is presented. The self-configuring and self-optimizing procedures of the proposed autonomic scheme are modeled using game theory. Through appropriate modeling and simulations of the proposed scheme carried out to evaluate its performance, it is found that the new approach suppresses feedback messages very effectively, while at the same time, it does not degrade the timely data transfer.
Probability Density Functions of Liquid Water Path and Cloud Amount of Marine Boundary Layer Clouds: Geographical and Seasonal Variations and Controlling Meteorological Factors
Authors: Kawai Hideaki , Teixeira João 
Published: November 2009

Abstract
The subgrid-scale variability of the liquid water path (LWP) of marine boundary layer clouds in areas that correspond to the typical grid size of large-scale (global climate and weather prediction) atmospheric models (200 km × 200 km) is investigated using geostationary satellite visible data. Geographical and seasonal variations of homogeneity, skewness, and kurtosis of probability density functions (PDFs) of LWP are discussed, in addition to cloud amount. It is clear that not only cloud amount but also these subgrid-scale statistics have well-defined geographical patterns and seasonal variations.
Furthermore, the meteorological factors that control subgrid-scale statistics of LWP that are related to boundary layer clouds are investigated using reanalysis data and PDFs of LWP data from satellites. Meteorological factors related to stability between 850 and 1000 hPa show high correlations with cloud amount and with the homogeneity, skewness, and kurtosis of PDFs of LWP of marine boundary layer clouds. The corrected gap of low-level moist static energy (CGLMSE) index, which is related to cloud-top entrainment instability, shows the highest correlation with the shape of LWP PDFs.
Assessing High-Latitude Winter Precipitation from Global Precipitation Analyses Using GRACE
Authors: Swenson Sean 
Published: November 2009

Abstract
This study compares cold-season, high-latitude precipitation estimates from two global, merged satellite–gauge precipitation analyses—Global Precipitation Climatology Project (GPCP) and Climate Prediction Center Merged Analysis of Precipitation (CMAP)—to total water storage anomalies produced from the Gravity Recovery and Climate Experiment (GRACE). In general, spatial patterns and interannual variability are highly correlated between the datasets, although significant differences are also observed. Differences vary by region but typically increase at higher latitudes. Furthermore, results indicate that the gauge undercatch correction used by GPCP may be overestimated. These comparisons may be useful for assessing precipitation estimates over large regions, where in situ gauge networks may be sparse.
Morning Precipitation Peak over the Strait of Malacca under a Calm Condition
Authors: Fujita Mikiko , Kimura Fujio , Yoshizaki Masanori 
Published: November 2009

Abstract
This paper describes the formation mechanism of morning maximum in the diurnal cycle of precipitation, at the Strait of Malacca under a calm condition, with a nonhydrostatic mesoscale numerical model and ship-based observational data. The morning precipitation peak at the strait is induced by the convergence of two cold outflows that have been produced by the precipitation systems in the previous evening over Sumatra and the Malay Peninsula. The outflows converge at the Strait of Malacca around midnight; a new precipitation system is thus generated and reaches its peak in the early morning. Sensitivity experiments using the numerical model suggest that the timing and position of the morning precipitation peak are affected by the width of the strait. In the case of the Strait of Malacca, its width favors the formation of the morning precipitation system around the center of the strait, which explains why its diurnal cycle of precipitation can be observed much clearer than those in other coastal areas over the Maritime Continent.
The sumoylation pathway is dysregulated in multiple myeloma and is associated with adverse patient outcome
Authors: Driscoll James J. , Pelluru Dheeraj , Lefkimmiatis Konstantinos , Fulciniti Mariateresa , Prabhala Rao H. , Greipp Philip R. , Barlogie Bart , Tai Yu-Tzu , Anderson Kenneth C. , Shaughnessy John D. , Annunziata Christina M. , Munshi Nikhil C. 
Published: November 2009

Abstract
Multiple myeloma (MM) is a plasma cell neoplasm that proceeds through a premalignant state of monoclonal gammopathy of unknown significance; however, the molecular events responsible for myelomagenesis remain uncharacterized. To identify cellular pathways deregulated in MM, we addressed that sumoylation is homologous to ubiquitination and results in the attachment of the ubiquitin-like protein Sumo onto target proteins. Sumoylation was markedly enhanced in MM patient lysates compared with normal plasma cells and expression profiling indicated a relative induction of sumoylation pathway genes. The Sumo-conjugating enzyme Ube2I, the Sumo-ligase PIAS1, and the Sumo-inducer ARF were elevated in MM patient samples and cell lines. Survival correlated with expression because 80% of patients with low UBE2I and PIAS1 were living 6 years after transplantation, whereas only 45% of patients with high expression survived 6 years. UBE2I encodes the sole Sumo-conjugating enzyme in mammalian cells and cells transfected with a dominant-negative sumoylation-deficient UBE2I mutant exhibited decreased survival after radiation exposure, impaired adhesion to bone marrow stroma cell and decreased bone marrow stroma cell–induced proliferation. UBE2I confers cells with multiple advantages to promote tumorigenesis and predicts decreased survival when combined with PIAS1. The sumoylation pathway is a novel therapeutic target with implications for existing proteasomal-based treatment strategies.
Liprin β1 is highly expressed in lymphatic vasculature and is important for lymphatic vessel integrity
Authors: Norrmén Camilla , Vandevelde Wouter , Ny Annelii , Saharinen Pipsa , Gentile Massimiliano , Haraldsen Guttorm , Puolakkainen Pauli , Lukanidin Eugene , Dewerchin Mieke , Alitalo Kari , Petrova Tatiana V. 
Published: November 2009

Abstract
The lymphatic vasculature is important for the regulation of tissue fluid homeostasis, immune response, and lipid absorption, and the development of in vitro models should allow for a better understanding of the mechanisms regulating lymphatic vascular growth, repair, and function. Here we report isolation and characterization of lymphatic endothelial cells from human intestine and show that intestinal lymphatic endothelial cells have a related but distinct gene expression profile from human dermal lymphatic endothelial cells. Furthermore, we identify liprin β1, a member of the family of LAR transmembrane tyrosine phosphatase-interacting proteins, as highly expressed in intestinal lymphatic endothelial cells in vitro and lymphatic vasculature in vivo, and show that it plays an important role in the maintenance of lymphatic vessel integrity in Xenopus tadpoles.
Frequent nocturnal awakening in early life is associated with nonatopic asthma in children
Authors: Kozyrskyj A. L. , Kendall G. E. , Zubrick S. R. , Newnham J. P. , Sly P. D. 
Published: November 2009

Sleep deprivation has become a common phenomenon of the Western world and is associated with a variety of medical problems in children. This retrospective longitudinal analysis of a community-based birth cohort was undertaken to determine whether frequent nocturnal awakening during early life was associated with the development of childhood asthma.2,398 children born to mothers recruited from the antenatal clinics of a single hospital in Perth, Australia during 1989–1991 were followed up at years 1, 2, 3, 6, 8, 10 and 14. Parent-completed questionnaires were analysed. The odds ratio for asthma at age 6 and 14 yrs in children with frequent nocturnal awakening during the first 3 yrs after birth was determined from multiple logistic regression.Following adjustment for asthma risk factors, co-sleeping and family stress, persistent nocturnal awakening was associated with nonatopic asthma at age 6 and 14 yrs (at age 14 yrs: OR 2.18, 95% CI 1.15–4.13) but not with atopic asthma.We found an increased risk of nonatopic asthma in children following frequent nocturnal awakening during the first 3 yrs of life. These hypothesis-generating data suggest the need for further systematic study of the effects of disordered sleep in early life on the development of asthma.
MRSA as a cause of lung infection including airway infection, community-acquired pneumonia and hospital-acquired pneumonia
Authors: Defres S. , Marwick C. , Nathwani D. 
Published: November 2009

Staphylococcus aureushas been recognised as a cause of community-acquired pneumonia, albeit uncommon, and an important cause of healthcare-associated (HA) pneumonia, including ventilator-associated pneumonia. Resistance ofS. aureusto methicillin developed shortly after its introduction into clinical practice. Since then, methicillin-resistantS. aureus(MRSA) has predominantly been a feature of hospital-acquired, or latterly HA, infections as the boundaries became more blurred between the community and hospital environments.However, more recently true community-acquired (CA)-MRSA infections have been detected and are becoming increasingly common, especially in the USA. Europe has not been immune to the development of MRSA in healthcare settings and although the prevalence of CA-MRSA is currently relatively low, there is the risk of wider spread. These new CA-MRSA strains appear to behave differently to HA-MRSA strains. Although predominantly causing skin and soft tissue infections, mainly as boils and abscesses requiring drainage, life threatening invasive infections including necrotising pneumonia can also occur. This article summarises the pathogenesis and clinical presentations of MRSA-related lung infections.
Ultrasound-guided transbronchial biopsy of solitary pulmonary nodules less than 20 mm
Authors: Eberhardt R. , Ernst A. , Herth F. J. F. 
Published: November 2009

Transbronchial biopsy of solitary pulmonary nodules (SPNs) is usually performed under fluoroscopic guidance, but success varies widely. Endobronchial ultrasonography (EBUS) may increase the likelihood of success. The ability of EBUS-guided transbronchial biopsy to sample SPNs of <20 mm in diameter was assessed.All patients seen between June 2004 and August 2007 in whom computed tomography identified a SPN of <20 mm underwent bronchoscopic general anaesthesia or moderate sedation for a radial EBUS-guided examination. If a typical ultrasonographic picture of solid tissue could be identified, specimens were taken through a catheter with forceps. If the node was not detected within 20 min, the procedure was terminated.Of 100 nodules detected in 100 consecutive patients, 67 (mean diameter 15 mm) were visualised using EBUS and biopsy specimens taken. A diagnosis was established for 46 (46%) patients. If the lesion was visualised by EBUS, the diagnostic success was 69% (46 out of 67). The 33 patients whose nodules could not be sampled underwent surgical biopsy. Pneumothorax occurred in three patients.For SPNs of <20 mm that can be detected using ultrasound, EBUS-guided transbronchial biopsy is safe and effective.
Primary ciliary dyskinesia: a consensus statement on diagnostic and treatment approaches in children
Authors: Barbato A. , Frischer T. , Kuehni C. E. , Snijders D. , Azevedo I. , Baktai G. , Bartoloni L. , Eber E. , Escribano A. , Haarman E. , Hesselmar B. , Hogg C. , Jorissen M. , Lucas J. , Nielsen K. G. , O'Callaghan C. , Omran H. , Pohunek P. , Strippoli M-P. F. , Bush A. 
Published: November 2009

Primary ciliary dyskinesia (PCD) is associated with abnormal ciliary structure and function, which results in retention of mucus and bacteria in the respiratory tract, leading to chronic oto-sino-pulmonary disease,situsabnormalities and abnormal sperm motility.The diagnosis of PCD requires the presence of the characteristic clinical phenotype and either specific ultrastructural ciliary defects identified by transmission electron microscopy or evidence of abnormal ciliary function.Although the management of children affected with PCD remains uncertain and evidence is limited, it remains important to follow-up these patients with an adequate and shared care system in order to prevent future lung damage.This European Respiratory Society consensus statement on the management of children with PCD formulates recommendations regarding diagnostic and therapeutic approaches in order to permit a more accurate approach in these patients. Large well-designed randomised controlled trials, with clear description of patients, are required in order to improve these recommendations on diagnostic and treatment approaches in this disease.
Pulmonary vascular dysfunction in end-stage cystic fibrosis: role of NF-κB and endothelin-1
Authors: Henno P. , Maurey C. , Danel C. , Bonnette P. , Souilamas R. , Stern M. , Delclaux C. , Lévy M. , Israël-Biet D. 
Published: November 2009

Pulmonary hypertension is rare in chronic respiratory diseases but has a strong impact on the prognosis and is partly underlined by factors other than hypoxaemia. The aim of the present study was to assess the potential role of endothelin-1 (ET-1) and nuclear factor (NF)-κB vasoconstrictive pathways in pulmonary hypertension.The effects of ET-1 receptors blockers (BQ 123 and 788) and of genistein were assessed on response to acetylcholine of pulmonary vascular rings from cystic fibrosis (CF) lung transplant recipients (n = 23). NF-κB and ET-1 receptor expression was immunodetected in pulmonary arteries and quantitated using Western blotting. ET-1 vascular content was quantitated using ELISA.In total, 14 out of 23 subjects exhibited strongly impaired pulmonary vasodilation (p<0.01versusnine out of 23 subjects with a normal response) associated with an activation of ET-1 receptors A and NF-κB pathways. Genistein restored vasodilation in subjects with an abnormal response.Pulmonary vascular dysfunction is frequent in end-stage CF, involving the NF-κB pathway and that of ET-1 through ET-1 receptor A (ETAR). These data leave a conceptual place for ETAR blockers and isoflavones in the management of the devastating vascular complication of chronic obstructive respiratory diseases such as CF.
Disseminated multiorgan MDR-TB resistant to virtually all first-line drugs
Authors: Sasse J. , Teichmann D. 
Published: November 2009

The emergence of multidrug-resistant tuberculosis (MDR-TB) is a major global concern since, despite a complex treatment regime, it still remains a lethal threat.A 21-yr-old male HIV-negative migrant from Burma presented with a disseminated tuberculosis affecting the lung, spleen, liver, mediastinal and abdominal lymph nodes. This particular strain ofMycobacterium tuberculosisproved to be resistant to all but one (pyrazinamide) of the first-line drugs,i.e.rifampicin, isoniazid and ethambutol, plus streptomycin, rifabutin and ofloxacin. On the mere account of its susceptibility concerning kanamycin it could not be labelled as extensively drug-resistant tuberculosis.After 1 month of a standard first-line four-drug regimen and a subsequent 4 months of second-line treatment with amikacin, moxifloxacin, terizidone, protionamide, linezolid and pyrazinamide, sputum cultures eventually yielded constantly negative results. Likewise, the organ manifestations decreased significantly, so as to be virtually undetectable in computed tomography scans after 1 yr of continuous treatment. A moderate pancytopenia reversed completely after dose adjustment of linezolid.Disseminated tuberculosis manifestations without typical pulmonary cavernous lesions are likely to represent primary infection rather than reactivation. Even a multiorgan disseminated MDR-TB with an extensive resistance pattern (including fluoroquinolones) can be successfully treated with an individual second-line treatment and result in considerably few adverse events.