bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ceiba: scalable visualization of phylogenies and 2D/3D image collections
Authors: Sanderson Michael J. 
Published: May 2014

Summary: Phylogenetic trees with hundreds of thousands of leaves are now being inferred from sequence data, posing significant challenges for visualization and exploratory analysis. Image data supplying valuable context for species in trees (and cues for exploring them) are becoming increasingly available in biodiversity databases and elsewhere but have rarely been built into tree visualization software in a scalable way. Ceiba lets the user explore large trees and inspect image collection arrays (sets of ‘homologous’ images) comprising mixtures of 2D and 3D image objects. Ceiba exploits recent improvements in graphics hardware, OpenGL toolkits and many standard high-performance computer graphics strategies, such as texture compression, level of detail control, culling, animations and image caching. Its tree layouts can be tuned by user-provided phylogenetic definitions of subtrees. The code has been extensively tested on phylogenies of up to 55 000 leaves and images.
Availability and implementation: A manual, datasets, source code (distributed under GPL) and binaries for OS X are available at http://sourceforge.net/projects/ceiba.
Contact: sanderm@email.arizona.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows
Authors: Bernard Elsa , Jacob Laurent , Mairal Julien , Vert Jean-Philippe 
Published: May 2014

Motivation: Several state-of-the-art methods for isoform identification and quantification are based on ℓ1-regularized regression, such as the Lasso. However, explicitly listing the—possibly exponentially—large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the ℓ1-penalty are either restricted to genes with few exons or only run the regression algorithm on a small set of preselected isoforms.Results: We introduce a new technique called FlipFlop, which can efficiently tackle the sparse estimation problem on the full set of candidate isoforms by using network flow optimization. Our technique removes the need of a preselection step, leading to better isoform identification while keeping a low computational cost. Experiments with synthetic and real RNA-Seq data confirm that our approach is more accurate than alternative methods and one of the fastest available.Availability and implementation: Source code is freely available as an R package from the Bioconductor Web site (http://www.bioconductor.org/), and more information is available at http://cbio.ensmp.fr/flipflop.Contact: Jean-Philippe.Vert@mines.orgSupplementary information: Supplementary Data are available at Bioinformatics online.
lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
Authors: Park Charny , Yu Namhee , Choi Ikjung , Kim Wankyu , Lee Sanghyuk 
Published: May 2014

Motivation: A number of long non-coding RNAs (lncRNAs) have been identified by deep sequencing methods, but their molecular and cellular functions are known only for a limited number of lncRNAs. Current databases on lncRNAs are mostly for cataloging purpose without providing in-depth information required to infer functions. A comprehensive resource on lncRNA function is an immediate need.
Results: We present a database for functional investigation of lncRNAs that encompasses annotation, sequence analysis, gene expression, protein binding and phylogenetic conservation. We have compiled lncRNAs for six species (human, mouse, zebrafish, fruit fly, worm and yeast) from ENSEMBL, HGNC, MGI and lncRNAdb. Each lncRNA was analyzed for coding potential and phylogenetic conservation in different lineages. Gene expression data of 208 RNA-Seq studies (4995 samples), collected from GEO, ENCODE, modENCODE and TCGA databases, were used to provide expression profiles in various tissues, diseases and developmental stages. Importantly, we analyzed RNA-Seq data to identify coexpressed mRNAs that would provide ample insights on lncRNA functions. The resulting gene list can be subject to enrichment analysis such as Gene Ontology or KEGG pathways. Furthermore, we compiled protein–lncRNA interactions by collecting and analyzing publicly available CLIP-seq or PAR-CLIP sequencing data. Finally, we explored evolutionarily conserved lncRNAs with correlated expression between human and six other organisms to identify functional lncRNAs. The whole contents are provided in a user-friendly web interface.
Availability and implementation: lncRNAtor is available at http://lncrnator.ewha.ac.kr/.
Contact: sanghyuk@ewha.ac.kr
Supplementary information: Supplementary Data are available at Bioinformatics online.
Successful Aging and Its Discontents: A Systematic Review of the Social Gerontology Literature
Authors: Martinson Marty , Berridge Clara 
Published: May 2014

Purpose of the Study:
The purpose of this study was to analyze the range of critiques of successful aging models and the suggestions for improvement as expressed in the social gerontology literature.

Design and Methods:
We conducted a systematic literature review using the following criteria: journal articles retrieved in the Abstracts in Social Gerontology, published 1987–2013, successful aging/ageing in the title or text (n = 453), a critique of successful aging models as a key component of the article. Sixty-seven articles met the criteria. Qualitative methods were used to identify key themes and inductively configure meanings across the range of critiques.

Results:
The critiques and remedies fell into 4 categories. The Add and Stir group suggested a multidimensional expansion of successful aging criteria and offered an array of additions. The Missing Voices group advocated for adding older adults’ subjective meanings of successful aging to established objective measures. The Hard Hitting Critiques group called for more just and inclusive frameworks that embrace diversity, avoid stigma and discrimination, and intervene at structural contexts of aging. The New Frames and Names group presented alternative ideal models often grounded in Eastern philosophies.

Implications:
The vast array of criteria that gerontologists collectively offered to expand Rowe and Kahn’s original successful model is symptomatic of the problem that a normative model is by definition exclusionary. Greater reflexivity about gerontology’s use of “successful aging” and other normative models is needed.
Does a strong particle accelerator arise very close to the light cylinder in a pulsar magnetosphere?
Authors: Hirotani K. 
Published: May 2014

Abstract
We examine if an efficient particle acceleration takes place by a magnetic-field-aligned electric field near the light cylinder in a rotating neutron star magnetosphere. Constructing the electric current density with the actual motion of collisionless plasmas, we express the rotationally induced Goldreich–Julian charge density as a function of position. It is demonstrated that the ‘light cylinder gap’, which emits very high energy photons via curvature process by virtue of a strong magnetic-field-aligned electric field very close to the light cylinder, will not arise in an actual pulsar magnetosphere.
Corticosteroid Effects on Sputum Culture in Pulmonary Tuberculosis: A Meta-Regression Analysis
Authors: Wallis Robert S. 
Published: May 2014

Abstract
Objectives.  There is increasing interest in the potential role of adjunctive anti-inflammatory therapy to accelerate tuberculosis (TB) treatment. Sputum culture conversion is an important biomarker predictor of durable TB cure.
Methods.  This study used meta-regression analysis to examine the relationship between corticosteroid dose and sputum culture conversion, using published data from controlled clinical trials including 1806 corticosteroid-treated TB patients.
Results.  Linear models with 2 or 3 variables, including corticosteroid dose and the proportion of culture positive control subjects, predicted therapeutic benefit of corticosteroids at 1 and 2 months. The 3-variable model predicted that 134 mg of prednisolone per day, given together with standard 4-drug TB chemotherapy, would reduce the proportion of positive culture at 2 months from 15% to 2%. The estimate accounts for a 50% reduction in steroid exposure due to rifampin. A proportion of 2% of subjects with positive cultures at 2 months has been proposed as a target for new 4-month TB regimens.
Conclusions.  These positive findings must be tempered by recognition that the metabolic and cardiovascular risks of corticosteroids administered at this dose for this duration are unlikely to be acceptable when examined from a patient-level benefit-risk perspective. In future research studies to shorten TB treatment, biologic anti-inflammatory therapies with similar therapeutic effects but superior safety profiles should be considered.
Higher Human T-Lymphotropic Virus Type 1 Subtype C Proviral Loads Are Associated With Bronchiectasis in Indigenous Australians: Results of a Case-Control Study
Authors: Einsiedel Lloyd , Cassar Olivier , Goeman Emma , Spelman Tim , Au Virginia , Hatami Saba , Joseph Sheela , Gessain Antoine 
Published: May 2014

AbstractBackground.  We previously suggested that infection with the human T-lymphotropic virus type 1 (HTLV-1) subtype C is associated with bronchiectasis among Indigenous Australians. Bronchiectasis might therefore result from an HTLV-1-mediated inflammatory process that is typically associated with a high HTLV-1 proviral load (PVL). Human T-lymphotropic virus type 1 PVL have not been reported for Indigenous Australians.Methods.  Thirty-six Indigenous adults admitted with bronchiectasis from June 1, 2008, to December 31, 2009 were prospectively recruited and matched by age, sex, and ethno-geographic origin to 36 controls. Case notes and chest high-resolution computed tomographs were reviewed, and pulmonary injury scores were calculated. A PVL assay for the HTLV-1c subtype that infects Indigenous Australians was developed and applied to this study. Clinical, radiological, and virological parameters were compared between groups and according to HTLV-1 serostatus.Results.  Human T-lymphotropic virus type 1 infection was the main predictor of bronchiectasis in a multivariable model (adjusted risk ratio [aRR], 1.84; 95% confidence interval [CI], 1.19–2.84; P = .006). Moreover, the median HTLV-1c PVL (interquartile range) for cases was &gt;100-fold that of controls (cases, 0.319 [0.007, 0.749]; controls, 0.003 [0.000, 0.051] per 100 peripheral blood lymphocytes; P = .007), and HTLV-1c PVL were closely correlated with radiologically determined pulmonary injury scores (Spearman's rho = 0.7457; P = .0000). Other predictors of bronchiectasis were positive Strongyloides serology (aRR, 1.69; 95% CI, 1.13–2.53) and childhood skin infections (aRR, 1.62; 95% CI, 1.07–2.44). Bronchiectasis was the major predictor of death (aRR, 2.71; 95% CI, 1.36–5.39; P = .004).Conclusions.  These data strongly support an etiological association between HTLV-1 infection and bronchiectasis in a socially disadvantaged population at risk of recurrent lower respiratory tract infections.
Bacteremia with Aerococcus sanguinicola: Case Series with Characterization of Virulence Properties
Authors: Senneby Erik , Eriksson Birger , Fagerholm Erik , Rasmussen Magnus 
Published: May 2014

Abstract
Background.  Since Aerococcus sanguinicola was designated as a species in 2001, only a few cases of bacteremia have been reported. The aim with this study was to describe the clinical presentation of A sanguinicola bacteremia and to determine the antibiotic susceptibility and the capacity of the bacteria to form biofilm and to induce platelet aggregation.
Methods.  Isolates of A sanguinicola from blood cultures were retrospectively identified from 2 clinical microbiology laboratories for 2006 to 2012. Species identity was confirmed through sequencing of the 16S rRNA gene. The medical charts of patients were reviewed. The minimum inhibitory concentration (MIC) for relevant antibiotics was determined. Biofilm formation was measured as the amount of crystal violet absorbed. Platelet aggregation was determined by aggregometry.
Results.  Eleven cases of A sanguinicola bacteremia were identified. All patients were male and the median age was 82 years (range 67–93). Nine patients fulfilled criteria for severe sepsis, and 2 patients died at hospital. Two patients were diagnosed with infective endocarditis. Most patients had underlying urinary tract diseases or an indwelling urinary tract catheter. Five patients suffered from dementia. None of the patients was treated with immunosuppressive medications. The MIC values of the isolates were in line with previous reports, with low MICs for penicillin, cefotaxime, and vancomycin. All 11 isolates produced biofilms but not all could induce platelet aggregation.
Conclusions.  A sanguinicola can cause severe infections in elderly men with urinary tract abnormalities and the bacteria possess potential virulence mechanisms.
Candida Pneumonia in Intensive Care Unit?
Authors: Schnabel Ronny M. , Linssen Catharina F. , Guion Nele , van Mook Walther N. , Bergmans Dennis C. 
Published: May 2014

AbstractIt has been questioned if Candida pneumonia exists as a clinical entity. Only histopathology can establish the definite diagnosis. Less invasive diagnostic strategies lack specificity and have been insufficiently validated. Scarcity of this pathomechanism and nonspecific clinical presentation make validation and the development of a clinical algorithm difficult. In the present study, we analyze whether Candida pneumonia exists in our critical care population. We used a bronchoalveolar lavage (BAL) specimen database that we have built in a structural diagnostic approach to ventilator-associated pneumonia for more than a decade consisting of 832 samples. Microbiological data were linked to clinical information and available autopsy data. We searched for critically ill patients with respiratory failure with no other microbiological or clinical explanation than exclusive presence of Candida species in BAL fluid. Five cases could be identified with Candida as the likely cause of pneumonia.
International Trade Puzzles: A Solution Linking Production and Preferences
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Authors: Caron Justin , Fally Thibault , Markusen James R. 
Published: May 2014

Abstract
International trade literature tends to focus heavily on the production side of general equilibrium, leaving us with a number of empirical puzzles. There is, for example, considerably less world trade than predicted by Heckscher-Ohlin-Vanek (HOV) models. Trade among rich countries is higher and trade between rich and poor countries lower than suggested by HOV and other supply-driven theories, and trade-to-GDP ratios are higher in rich countries. Our approach focuses on the relationship between characteristics of goods and services in production and characteristics of preferences. In particular, we find a strong and significant positive correlation of more than 45% between a good’s skilled-labor intensity and its income elasticity, even when accounting for trade costs and cross-country price differences. Exploring the implications of this correlation for empirical trade puzzles, we find that it can reduce HOV’s overprediction of the variance of the net factor content of trade relative to that in the data by about 60%. Since rich countries are relatively skilled-labor abundant, they are relatively specialized in consuming the same goods and services that they are specialized in producing, and so trade more with one another than with poor countries. We also find a positive sector-level correlation between income elasticity and a sector’s tradability, which helps explain the higher trade-to-GDP ratios in high-income relative to low-income countries.
First Report of Southern Blight of Swiss Chard (Beta vulgaris subsp. cicla) Caused by Sclerotium rolfsii in California
Authors: Koike S. T. 
Published: May 2014

In June 2013, a commercial organic planting of Swiss chard (Beta vulgaris subsp. cicla) in Monterey County, CA, showed symptoms of a soilborne disease. Early symptoms consisted of delayed and stunted growth, with wilting of foliage during the warmer times of the day. Initially, a light brown discoloration developed on stems at the soil line. As disease progressed, a dark brown necrosis extended up the main stem and down along the upper portion of the taproot. In advanced cases, the plants collapsed and died. Extensive white cottony mycelium and numerous brown, spherical sclerotia, approximately 1 mm in diameter, developed externally on the lower stem, crown, and adhering adjacent soil. For this particular planting, approximately 10% of the 0.4 ha was lost. Sequentially planted sets of chard placed in other parts of the farm were unaffected. Isolations from necrotic plant tissues, sclerotia, and white mycelium all resulted in recovery of the same white fungus that in culture produced identical sclerotia but no other reproductive structures. Based on white mycelium, sclerotia morphology, and the presence of clamp connections at hyphal septa, the fungus was identified as Sclerotium rolfsii (1). Pathogenicity was tested by growing isolates on potato dextrose agar, drying the resulting sclerotia for 48 h, then burying 5 to 8 sclerotia adjacent to the crowns of healthy Swiss chard plants grown in pots. Three isolates were tested using 24 plants per isolate. Six control plants were inoculated with sterilized sand. All plants were incubated in a greenhouse at 22 to 25°C. After 8 days, inoculated plants began to wilt. By 14 days after inoculation, 100% of the inoculated plants showed symptoms identical to those observed in the field. One half of the plants were used for re-isolations, from which S. rolfsii was recovered from all necrotic crown and stem tissues. The other half of the plants were maintained in the greenhouse; these plants later supported the development of sclerotia. Sand-inoculated control plants did not develop any disease symptoms. The experiment was repeated and the results were the same. To our knowledge, this is the first report of southern blight of Swiss chard in California. Southern blight has not previously been found in this cooler, western part of the county adjacent to the Pacific Ocean; southern blight has been documented on other crops such as pepper, tomato, and chives (3) in the warmer eastern and southern parts of Monterey County. S. rolfsii has been reported on Swiss chard in Louisiana, South Carolina, and Cuba (2). References: (1) K. H. Domsch et al. Compendium of Soil Fungi, 2nd edition. IHW-Verlag, Eching, Germany, 2007. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Syst. Mycol. Microbiol. Lab. Online publication, ARS, USDA. Retrieved July 26, 2013. (3) S. T. Koike et al. Plant Dis. 78:208, 1994.
Using Volume Index and Lateral Hepatic Angle to Differentiate Biliary Atresia From TPN‐Associated Cholestasis
Authors: Peng Steven Shinn‐Forng , Hsu Wen‐Ming , Chen Huey‐Ling , Mo Yuan‐Heng 
Published: May 2014

ABSTRACTObjectives:Differential diagnosis between biliary atresia (BA) and total parenteral nutrition–associated cholestasis (TPN‐AC) and early treatment for cholestatic infants are challenges for evaluating neonatal or infantile cholestasis. The aim of our retrospective study was to apply noninvasive indices of magnetic resonance images to differentiate BA from TPN‐AC.Methods:A total of 44 patients diagnosed as having BA (n = 30) or TPN‐AC (n = 14) were included in the present retrospective study and underwent abdominal magnetic resonance imaging to evaluate the possibility of BA. The left lateral hepatic angle was determined from the coronal image of the left portal vein and portal vein of segment II. Adjusted volume indices of the right hepatic lobe (AVIR) and left lateral segment (AVILL) were calculated as the product of 3 diameters (centimeters) divided by each patient's body weight.Results:The left lateral hepatic angles of patients with BA (74° ± 21°) were significantly larger than for patients with TPN‐AC (33° ± 9°) and controls (36° ± 5°, P < 0.05). AVILL of the BA (0.037 ± 0.012 cm3/g) and TPN‐AC groups (0.042 ± 0.030 cm3/g) were not significantly different (P = 0.61) but were significantly larger than for controls (0.020 ± 0.011 cm3/g) (P < 0.05). The right hepatic lobe to left lateral hepatic segment ratio (RLR) of patients with BA was significantly (P < 0.05) smaller (1.61 ± 0.58) than for patients with TPN‐AC (3.08 ± 2.43) and controls (2.98 ± 0.92). Patients with BA could have relative sparing and selective enlargement of the left lateral liver with a resultant lobar difference and blunt left lateral hepatic angle.Conclusions:Noninvasive indices of lobar difference and left lateral hepatic angle help differentiate patients with BA from those with TPN‐AC.
Background selection as baseline for nucleotide variation across theDrosophilagenome
Authors: Comeron Josep M 
Published: May 2014

ABSTRACTThe constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across theDrosophila melanogastergenome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps betweenDrosophilaspecies, suggest temporally variable recombination landscapes and thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages.