bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progress in understanding halo current at JET
Authors: Riccardo V. , Arnoux G. , Beaumont P. , Hacquin S. , Hobirk J. , Howell D. , Huber A. , Joffrin E. , Koslowski R. , Lam N. , Leggate H. , Rachlew E. , Sergienko G. , Stephen A. , Todd T. , Zerbini M. , Delogu R. , Grando L. , Marcuzzi D. , Peruzzo S. , Pomaro N. , Sonato P. 
Published: April 2009

The poloidal distribution of the halo current density on the top dump plate in JET can now be measured thanks to a new set of Rogowskii coils. These are the first measurements in JET able to offer an insight in the width of the halo current interaction with the wall. Therefore they offer both validation of the assumption made for JET disruption design criteria and one additional point in the extrapolation of the expected halo current width, and hence halo current density (and related local electro-mechanical loads on in-vessel components) for ITER. During upward events, the measured current density is consistent with the measured total poloidal halo current. The halo footprint extends over most of the upper dump plate, converting to a halo current flux tube width of ∼100 mm.
A set of four toridal field pick-up coils installed 90° apart now allows a more accurate measurement of the poloidal halo current, in particular its toroidal peaking factor, and direct comparison between halo and plasma asymmetries.
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures
Authors: Ryan Michael , Diekhans Mark , Lien Stephanie , Liu Yun , Karchin Rachel 
Published: April 2009

Abstract
Summary: LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features.
Availability: LS-SNP/PDB is available at http://ls-snp.icm.jhu.edu/ls-snp-pdb and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.
Contact: karchin@jhu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Many-core algorithms for statistical phylogenetics
Authors: Suchard Marc A. , Rambaut Andrew 
Published: April 2009

Abstract
Motivation: Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of synonymous and replacement substitutions and have the potential to more adequately model the process of protein-coding sequence evolution with a resulting increase in phylogenetic accuracy. Unfortunately, due to the high number of codon states, computational burden has largely thwarted phylogenetic reconstruction under codon models, particularly at the genomic-scale. Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units (GPUs), making use of the large number of processing cores to efficiently parallelize calculations even for large state-size models.
Results: We implement the approach in an existing Bayesian framework and apply the algorithms to estimating the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model. We see a near 90-fold speed increase over an optimized CPU-based computation and a &gt;140-fold increase over the currently available implementation, making this the first practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes.
Availability and implementation: Source code provided in BEAGLE: Broad-platform Evolutionary Analysis General Likelihood Evaluator, a cross-platform/processor library for phylogenetic likelihood computation (http://beagle-lib.googlecode.com/). We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (http://beast.bio.ed.ac.uk/).
Contact: msuchard@ucla.edu; a.rambaut@ed.ac.uk
ViaComplex: software for landscape analysis of gene expression networks in genomic context
Authors: Castro Mauro A. A. , Filho José L. Rybarczyk , Dalmolin Rodrigo J. S. , Sinigaglia Marialva , Moreira José C. F. , Mombach José C. M. , de Almeida Rita M. C. 
Published: April 2009

Abstract
ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res., 35, 1859–1867, 2007; Nucleic Acids Res., 36, 6269–6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these articles, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm.
Availability: http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: mauro@ufrgs.br or rita@if.ufrgs.br
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
Authors: Byun Yanga , Han Kyungsook 
Published: April 2009

Abstract
Motivation: Pseudoknots in RNA structures make visualization of RNA structures difficult. Even if a pseudoknot itself is represented without a crossing, visualization of the entire RNA structure with a pseudoknot often results in a drawing with crossings between the pseudoknot and other structural elements, and requires additional intervention by the user to ensure that the structure graph is overlap-free. Many programs such as web services prefer to obtain an overlap-free graph in one-shot rather than get a graph with overlaps to be edited. There are few programs for visualizing RNA pseudoknots, and PseudoViewer has been the almost only program that automatically draws RNA secondary structures with pseudoknots. The previous version of PseudoViewer visualizes all the known types of RNA pseudoknots as planar drawings, but visualizes some hypothetical pseudoknots as non-planar drawings.
Results: We developed a new version of PseudoViewer for efficiently visualizing large RNA structures with any types of pseudoknots, both known and hypothetical, as planar drawings in one-shot. It is about 10 times faster than the previous algorithm, and produces a more compact and aesthetic structure drawing. PseudoViewer3 supports both web services and web applications.
Availability: The new version of PseudoViewer, PseudoViewer3, is available at http://pseudoviewer.inha.ac.kr.
Contact: khan@inha.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria–Delbrück fluctuation analysis
Authors: Hall Brandon M. , Ma Chang-Xing , Liang Ping , Singh Keshav K. 
Published: April 2009

Abstract
Summary:The program Fluctuation AnaLysis CalculatOR (FALCOR) is a web tool designed for use with Luria–Delbrück fluctuation analysis to calculate the frequency and rate from various mutation assays in bacteria and yeast. Three calculation methods are available through this program: (i) Ma-Sandri-Sarkar Maximum Likelihood Estimator (MSS-MLE) method, (ii) Lea-Coulson method of the median (LC) and (iii) frequency.
Availability: The FALCOR rate calculator is currently accessible at http://www.mitochondria.org/protocols/FALCOR.html. This program is written as a Java™ Applet, requiring a web browser enabled with Sun MicroSystems' Java Virtual Machine.
Contact: brandon.hall@roswellpark.org
Metal-MACiE: a database of metals involved in biological catalysis
Authors: Andreini Claudia , Bertini Ivano , Cavallaro Gabriele , Holliday Gemma L. , Thornton Janet M. 
Published: April 2009

Abstract
Summary: Metal-MACiE is a new publicly available web-based database, held in MySQL, which aims to organize the available information on the properties and the roles of metals in the context of the catalytic mechanisms of metalloenzymes. Metal-MACiE, which currently covers 75% of metal-dependent enzyme commission (EC) sub-sub-classes and is continuously growing, exploits the existing MACiE database for the annotation of the reaction mechanisms. The two databases constitute complementary sources of information for enzymology, biochemistry and molecular pharmacology studies.
Availability: http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html
Contact: andreini@cerm.unifi.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Aquaporin-Mediated Reduction in Maize Root Hydraulic Conductivity Impacts Cell Turgor and Leaf Elongation Even without Changing Transpiration
Authors: Ehlert Christina , Maurel Christophe , Tardieu François , Simonneau Thierry 
Published: April 2009

Abstract
Root hydraulic conductivity in plants (Lpr) exhibits large variations in response to abiotic stimuli. In this study, we investigated the impact of dynamic, aquaporin-mediated changes of Lpr on leaf growth, water potential, and water flux throughout the plant. For this, we manipulated Lpr by subjecting roots to four independent treatments, with aquaporin inhibitors applied either to transpiring maize (Zea mays) plants grown in hydroponics or to detopped root systems for estimation of Lpr. The treatments were acid load at pH 6.0 and 5.0 and hydrogen peroxide and anoxia applied for 1 to 2 h and subsequently reversed. First, we established that acid load affected cell hydraulic conductivity in maize root cortex. Lpr was reduced by all treatments by 31% to 63%, with half-times of about 15 min, and partly recovered when treatments were reversed. Cell turgor measured in the elongating zone of leaves decreased synchronously with Lpr, and leaf elongation rate closely followed these changes across all treatments in a dose-dependent manner. Leaf and xylem water potentials also followed changes in Lpr. Stomatal conductance and rates of transpiration and water uptake were not affected by Lpr reduction under low evaporative demand. Increased evaporative demand, when combined with acid load at pH 6.0, induced stomatal closure and amplified all other responses without altering their synchrony. Root pressurization reversed the impact of acid load or anoxia on leaf elongation rate and water potential, further indicating that changes in turgor mediated the response of leaf growth to reductions in Lpr.
Comparison of risk factors and clinical responses to proton pump inhibitors in patients with erosive oesophagitis and non‐erosive reflux disease
Authors: LEE E. S. , KIM N. , LEE S. H. , PARK Y. S. , KIM J. W. , JEONG S. H. , LEE D. H. , JUNG H. C. , SONG I. S. 
Published: April 2009

SummaryBackground  There has been no report on the response to proton pump inhibitor (PPI) therapy and on‐demand or the relapse rate of non‐erosive reflux disease (NERD) and erosive oesophagitis in Korea.Aim  To compare the risk factors, clinical symptoms and PPI responses between patients with erosive oesophagitis and NERD patients.Methods  A survey was performed prospectively in the erosive oesophagitis (205 patients) and NERD group (200 patients). Clinical symptoms, risk factors and PPI responses were analysed. On‐demand therapy and the relapse rate of GERD symptoms were investigated during a one‐year follow‐up.Results  BMI ≥ 25 (OR 3.0, 95% CI 1.1–8.3), alcohol use (OR 2.9, 95% CI 1.0–8.3), hiatal hernia (OR 5.0, 95% CI 1.2–20) and triglyceride ≥150 mg/dL (OR 4.0, 95% CI 1.7–10) were more common in the erosive oesophagitis group than in the NERD group by multivariate analysis. The ratio of oesophageal to extra‐oesophageal symptoms was higher in the erosive oesophagitis group compared with the NERD group (P < 0.001). The PPI response rates at 8 weeks were different (P = 0.02); refractory rates were higher in the NERD group (16.7%) compared with the erosive oesophagitis group (6.0%). However, there was no significant difference between the two groups in on‐demand therapy or the relapse rate.Conclusion  These results suggest that the underlying pathogenic mechanisms of erosive oesophagitis and NERD are distinct.
Irradiated cultured apoptotic peripheral blood mononuclear cells regenerate infarcted myocardium
Authors: Ankersmit H. J. , Hoetzenecker K. , Dietl W. , Soleiman A. , Horvat R. , Wolfsberger M. , Gerner C. , Hacker S. , Mildner M. , Moser B. , Lichtenauer M. , Podesser B. K. 
Published: April 2009

AbstractBackground  Acute myocardial infarction (AMI) is followed by post AMI cardiac remodelling, often leading to congestive heart failure. Homing of c‐kit+ endothelial progenitor cells (EPC) has been thought to be the optimal source for regenerating infarcted myocardium.Methods  Immune function of viable peripheral blood mononuclear cells (PBMC) was evaluated after co‐culture with irradiated apoptotic PBMC (IA‐PBMC) in vitro. Viable PBMC, IA‐PBMC and culture supernatants (SN) thereof were obtained after 24 h. Reverse transcription polymerase chain reaction and enzyme‐linked immunosorbent assay were utilized to quantify interleukin‐8 (IL‐8), vascular endothelial growth factor, matrix metalloproteinase‐9 (MMP9) in PBMC, SN and SN exposed fibroblasts. Cell suspensions of viable‐ and IA‐PBMC were infused in an experimental rat AMI model. Immunohistological analysis was performed to detect inflammatory and pro‐angiogenic cells within 72 h post‐infarction. Functional data and determination of infarction size were quantified by echocardiography and Elastica van Gieson staining.Results  The IA‐PBMC attenuated immune reactivity and resulted in secretion of pro‐angiogenic IL‐8 and MMP9 in vitro. Fibroblasts exposed to viable and IA‐PBMC derived SN caused RNA increment of IL‐8 and MMP9. AMI rats that were infused with IA‐PBMC cell suspension evidenced enhanced homing of endothelial progenitor cells within 72 h as compared to control (medium alone, viable‐PBMC). Echocardiography showed a significant reduction in infarction size and improvement in post AMI remodelling as evidenced by an attenuated loss of ejection fraction.Conclusion  These data indicate that infusion of IA‐PBMC cell suspension in experimental AMI circumvented inflammation, caused preferential homing of regenerative EPC and replaced infarcted myocardium.
Repeatability and correlation of swimming performances and size over varying time‐scales in the guppy (Poecilia reticulata)
Authors: Oufiero Christopher E. , Garland Theodore 
Published: April 2009

Summary 1 Although the repeatability of a trait is of interest for several reasons, few studies have critically examined the repeatability or correlation of metrics of swimming performance. We quantified repeatability of three swimming performances (burst speed during a c‐start escape response, critical swimming speed [Ucrit], maximum speed [Umax]) and size/shape measures over short (within‐day), medium (days and weeks), and long (more than a year) time‐scales in a small poeciliid fish, the Trinidadian guppy (Poecilia reticulata). 2 We found that individual differences in most swimming performance metrics were repeatable on various time‐scales. Burst speed during c‐start was repeatable within a day, as well as over days and weeks, but it was not repeatable over the span of a year. However, the medium term repeatability was only statistically significant when accounting for the variation of individuals within a day and correcting for attenuation. Ucrit,Umax and size were repeatable on medium time‐scales, but only size and Umax were repeatable over the span of a year. Our index of shape was not statistically repeatable over any time‐scales. 3 When examining the correlations of performances and size, only a few traits were related to each other. Ucrit and Umax were significantly positively related to each other for trial 1 only, but not any of the others. Umax and the mean c‐start burst speed were correlated on trial 2 only. No other traits were significantly related to each other, and no performance traits were related to size or shape. Ucrit and Umax also did not differ in their overall mean values, suggesting that Umax, a more recently described assessment of fish swimming performance, may be a reliable alternative. 4 All traits, except our index of shape, shifted in their mean value over the span of a year. Ucrit and c‐start burst speed decreased significantly, consistent with previous findings on the effects of senescence on neuromuscular systems. However, Umax and size increased significantly over a year. 5 The measures of swimming performance used in this study are becoming widely used in ecological and evolutionary studies. Our results suggest that individual differences in these measures are relatively stable on various time‐scales. We found no significant relation of these performance metrics with body size or a simple index of shape, and few relations among the performance measures, suggesting that they measure different aspects of locomotor physiology and/or motivation under the test conditions used. Finally, while Ucrit and c‐start burst speed decreased over the span of the year, consistent with theories of senescence, Umax significantly increased over a year, suggesting that further studies of this recently described performance metric are needed.
Investigating biological control over soil carbon temperature sensitivity
Authors: BALSER TERI C. , WIXON DEVIN L. 
Published: April 2009

AbstractUnderstanding the temperature sensitivity of soil respiration is critical for predicting the response of ecosystems to climate change, yet the microbial communities responsible are rarely considered explicitly in studies or models. In this study, we assessed total microbial community composition, quantified bacterial respiration temperature response, and investigated the temperature dependence of bacterial carbon substrate utilization in tropical, temperate, and taiga soils (from Puerto Rico, California, and Alaska). Microbial community composition was characterized using phospholipid fatty acid analysis. Bacterial community respiration on a standardized set of substrates was ascertained using the BiOLOG™ substrate utilization assay incubated at four temperatures: 4, 12, 28, and 40 °C. First, we found that microbial communities from the three latitudes were compositionally distinct and that the bacterial component of the three communities had markedly different respiration temperature–response curves corresponding with their experienced temperature regimes. We use these data to highlight limitations of widely used temperature–response equations and investigate temperature‐dependent patterns of substrate utilization. We found that temperature response, in terms of both respiration rates and substrate use, varied for these bacterial communities independent of substrate quality or quantity interactions such as labile depletion. In contrast to the common assumption of heterotrophic microbial ubiquity, we found that bacterial community differences from these diverse systems appeared to determine both rates of respiration and patterns of carbon substrate usage. We suggest that microbial community composition‐specific responses to changing climate may be important in predicting the long‐term role of ecosystems in atmospheric CO2 dynamics.
Climate change induced hybridization in flying squirrels
Authors: GARROWAY COLIN J. , BOWMAN JEFF , CASCADEN TARA J. , HOLLOWAY GILLIAN L. , MAHAN CAROLYN G. , MALCOLM JAY R. , STEELE MICHAEL A. , TURNER GREGORY , WILSON PAUL J. 
Published: April 2009

AbstractThere is now unequivocal evidence for global climate change; however, its potential impacts on evolutionary processes remain unclear. Many species have responded to contemporary climate change through shifts in their geographic range. This could lead to increased sympatry between recently diverged species; likely increasing the potential for hybridization. Recently, following a series of warm winters, southern flying squirrels (Glaucomys volans) in Ontario, Canada rapidly expanded their northern range limit resulting in increased sympatry with the closely related northern flying squirrel (Glaucomys sabrinus). This provided the opportunity to test the prediction that contemporary climate change can act as a catalyst creating conditions for the formation of hybrid zones. Following extensive sampling and molecular analyses (nuclear and mitochondrial DNA), we identified the occurrence of hybridization between sympatricG. sabrinusandG. volans. There was evidence of backcrossing but not of extensive introgession, consistent with the hypothesis of recent rather than historic hybridization. To our knowledge, this is the first report of hybrid zone formation following a range expansion induced by contemporary climate change. This is also the first report of hybridization between North American flying squirrel species.
Dental Age Assessment: a comparison of 4‐ to 24‐year‐olds in the United Kingdom and an Australian population
Authors: PEIRIS TANYA SHYAMI , ROBERTS GRAHAM J. , PRABHU NEETA 
Published: April 2009

Background.  The physiological age of a person is determined by the degree of maturation of the different tissue systems. Children of the same chronological age (CA) can demonstrate different degrees of maturation. Dental age (DA) is based on the maturation of teeth. Tooth formation is a continuous process, where the developmental stages of the tooth can be sequenced and defined depending on the degree of mineralization. These stages can be visualized on a dental panoramic tomograph (DPT).Aim.  The aim of this study was to use a new method of Dental Age Assessment (DAA) to compare a United Kingdom (UK) and an Australian (AUS) population.Design.  The DPTs used are from the archives of the Westmead Centre for Oral Health (Westmead, Australia) and the King's College London Dental Institute. From the preliminary sample of 89 DPTs from each population, 77 were suitable for use as matched pairs. The radiographic technique used was developed by Demirjian and describes eight stages of tooth development. This was used in combination with numerical data derived from a meta‐analysis of a single UK subject.Results.  A significant difference was shown between the CA and DA of the AUS patients. The AUS patients were also shown to have a significant 0.82 years delay in their DA compared to the UK patients. The findings indicate a difference in AUS compared to UK patients. These results indicate the need to develop a reference data set for the AUS population for DAA.Conclusions.  This research is of significance in a number of clinical disciplines and can also be used to assist in age determination of subjects of unknown birth date to assist in forensic dentistry or social deliberations.