bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards understanding ELM mitigation: the effect of axisymmetric lobe structures near the X-point on ELM stability
Authors: Chapman I.T. , Kirk A. , Saarelma S. , Harrison J.R. , Scannell R. 
Published: November 2012

Abstract
The application of resonant magnetic perturbations (RMPs) with toroidal mode number n = 4 or n = 6 is observed to result in a significant increase in ELM frequency, despite a reduction in the edge pressure gradient. A picture for how type-I ELMs are mitigated, or destabilized, when magnetic perturbations are applied is proposed. Despite the magnetic perturbation incurring a drop in the pedestal pressure gradient, the critical pressure for an ELM to be triggered is dropped even further. Various mechanisms which could cause this degradation of the stability boundary are outlined. The stability of the edge of MAST H-mode plasmas has been tested when lobe structures are present in the separatrix after application of RMPs. The axisymmetric stability analysis presented here shows that when the plasma boundary is simulated with a model for the observed lobe structures included, the ballooning stability is degraded. This degradation in ballooning stability originates from the perturbed field lines dwelling in the region of unfavourable curvature due to the presence of lobe structures rather than the change in the plasma boundary shape.
FOLD-EM: automated fold recognition in medium- and low-resolution (4–15 Å) electron density maps
Authors: Saha Mitul , Morais Marc C. 
Published: November 2012

Abstract
Motivation: Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid approach to structure determination requires that an atomic resolution structure of each component, or a suitable homolog, is available. If neither is available, then the amount of structural information regarding that component is limited by the resolution of the cryo-EM map. However, even if a suitable homolog cannot be identified using sequence analysis, a search for structural homologs should still be performed because structural homology often persists throughout evolution even when sequence homology is undetectable, As macromolecules can often be described as a collection of independently folded domains, one way of searching for structural homologs would be to systematically fit representative domain structures from a protein domain database into the medium/low resolution cryo-EM map and return the best fits. Taken together, the best fitting non-overlapping structures would constitute a ‘mosaic’ backbone model of the assembly that could aid map interpretation and illuminate biological function.
Result: Using the computational principles of the Scale-Invariant Feature Transform (SIFT), we have developed FOLD-EM—a computational tool that can identify folded macromolecular domains in medium to low resolution (4–15 Å) electron density maps and return a model of the constituent polypeptides in a fully automated fashion. As a by-product, FOLD-EM can also do flexible multi-domain fitting that may provide insight into conformational changes that occur in macromolecular assemblies.
Availability and implementation: FOLD-EM is available at: http://cs.stanford.edu/~mitul/foldEM/, as a free open source software to the structural biology scientific community.
Contact: mitul@cs.stanford.edu or mcmorais@utmb.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
Authors: Pacini Clare , Iorio Francesco , Gonçalves Emanuel , Iskar Murat , Klabunde Thomas , Bork Peer , Saez-Rodriguez Julio 
Published: November 2012

Abstract
Summary: Drug versus Disease (DvD) provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories. Negatively correlated profiles can be used to generate hypotheses of drug-repurposing, whereas positively correlated profiles may be used to infer side effects of drugs. DvD allows users to compare drug and disease signatures with dynamic access to databases Array Express, Gene Expression Omnibus and data from the Connectivity Map.
Availability and implementation: R package (submitted to Bioconductor) under GPL 3 and Cytoscape plug-in freely available for download at www.ebi.ac.uk/saezrodriguez/DVD/.
Contact: saezrodriguez@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Systematic variation of the stellar initial mass function with velocity dispersion in early-type galaxies
Authors: Ferreras Ignacio , Barbera Francesco La , Rosa Ignacio G. de la , Vazdekis Alexandre , Carvalho Reinaldo R. de , Falcón-Barroso Jesús , Ricciardelli Elena 
Published: November 2012

Abstract
An essential component of galaxy formation theory is the stellar initial mass function (IMF) that describes the parent distribution of stellar mass in star-forming regions. We present observational evidence in a sample of early-type galaxies (ETGs) of a tight correlation between central velocity dispersion and the strength of several absorption features sensitive to the presence of low-mass stars. Our sample comprises ∼40 000 ETGs from the Spheroids Panchromatic Investigation in Different Environmental Regions survey (z ≲ 0.1). The data – extracted from the Sloan Digital Sky Survey – are combined, rejecting both noisy data, and spectra with contamination from telluric lines, resulting in a set of 18 stacked spectra at high signal-to-noise ratio (S/N ≳ 400 Å−1). A combined analysis of IMF-sensitive line strengths and spectral fitting is performed with the latest state-of-the-art population synthesis models (an extended version of the MILES models). A significant trend is found between IMF slope and velocity dispersion, towards an excess of low-mass stars in the most massive galaxies. Although we emphasize that accurate values of the IMF slope will require a detailed analysis of chemical composition (such as [α/Fe] or even individual element abundance ratios), the observed trends suggest that low-mass ETGs are better fitted by a Kroupa-like IMF, whereas massive galaxies require bottom-heavy IMFs, exceeding the Salpeter slope at σ ≳ 200 km s−1.
Internal shocks at the origin of the flat spectral energy distribution of compact jets
Authors: Malzac Julien 
Published: November 2012

Abstract
An internal shock model is proposed to interpret the radio to infrared (IR) emission of the compact jets observed in the hard spectral state of X-ray binaries. Assuming that the specific bulk Lorentz factor of the jet at its base varies with a flicker noise power spectrum [i.e. P(f) ∝ 1/f], we estimate the energy dissipation profile along the jet and the resulting partially self-absorbed synchrotron emission. For this type of velocity fluctuations, and a conical jet geometry, the shock dissipation at large distance from the black hole balances exactly the adiabatic losses. This leads to a flat radio to IR spectral energy distribution similar to that observed in compact jets.
First Report of Bacterial Leaf Spot of Rieger Begonia Caused by Xanthomonas campestris pv. begoniae in China
Authors: Zhou L. H. , Ji G. H. 
Published: November 2012

Rieger begonia are collectively referred to as a begonia hybrid group. Its global annual sales is 90,000,000 cutting seedlings. It is one of the top ten potted plants. In the summer of 2011, serious outbreaks of a suspected bacterial leaf spot disease were observed on five Rieger begonia cultivars (Dark Britt, Rebecca, Blitz, Barkos, and Borias). These plants were grown for potted cutting seedling production in commercial nurseries located in Shilin county of Yunnan Province, China. The initial symptoms of the disease were small circular or polygonal water-soaked needle spots on leaf margin that later these spots expanded and joined together, forming bigger inverted V-shaped necrotic specks (4). Yellow-pigmented bacterial colonies were consistently isolated from diseased leaves and stems on NA agar medium and incubated at 28°C. Twelve bacterial strains were isolated and used for further studies. All the isolates were Gram-negative, rod-shaped, motile, aerobic, and non-sporing. All of the bacterial strains isolated in the present study were identified as Xanthomonas campestris pv. begoniae (Xcb) based on biochemical and physiological identification (Biolog carbon source utilization analysis) and 16S rDNA sequences analysis and further pathogenicity determination (1). The results show that the sequence homology rate of HT1-1 (GenBank Accession No. JN648097) and X. euvesicatoria (syn. X. campestris pv vesicatoria) (GeneBank Accession No. AM039952) is 99%. This strongly suggests that the Rieger begonia isolates belong to X. campestris pv. begoniae (2). For Koch's postulates, 10 surface-disinfected young leaves from five susceptible Rieger begonia plants (cv. Dark Britt) were inoculated by spraying a phosphate-buffered saline suspension of each bacterial isolate (3.0 × 108 CFU/ml) onto the leaves (3). Controls were inoculated similarly with phosphate-buffered saline solution. All inoculated plants were covered with polyethylene bags for 24 h at 25°C and then put in the greenhouse. After inoculation, water-soaked and necrotic symptoms were observed on inoculated Rieger begonia leaves within 7 to 9 days. No symptoms were observed on controls. Bacteria were reisolated and confirmed to be identical to the original isolates by the methods described above. To our knowledge, this is the first report of Xcb causing leaf spot on Rieger begonia plants in China. The infection process of Xcb on Rieger begonia plants and rapid detection of this pathogen are underway. References: (1) M. R. Gillings et al. PNAS 12:102, 2005. (2) C. L. Oliver et al. Plant Dis. 4:96, 2012. (3) H. Ornek et al. New Dis. Rep. 13:40, 2006. (4) O. Pruvost et al. Plant Dis. 4:96, 2012.
The Mitochondrial Folylpolyglutamate Synthetase Gene Is Required for Nitrogen Utilization during Early Seedling Development in Arabidopsis
Authors: Jiang Ling , Liu Yanyan , Sun Hong , Han Yueting , Li Jinglai , Li Changkun , Guo Wenzhu , Meng Hongyan , Li Sha , Fan Yunliu , Zhang Chunyi 
Published: November 2012

Abstract
Investigations into the biochemical processes and regulatory mechanisms of nitrogen (N) utilization can aid in understanding how N is used efficiently in plants. This report describes a deficiency in N utilization in an Arabidopsis (Arabidopsis thaliana) transfer DNA insertion mutant of the mitochondrial folylpolyglutamate synthetase gene DFC, which catalyzes the conjugation of glutamate residues to the tetrahydrofolate during folate synthesis. The mutant seedlings displayed several metabolic changes that are typical of plant responses to low-N stress, including increased levels of starch and anthocyanin synthesis as well as decreased levels of soluble protein and free amino acid, as compared with those in wild-type seedlings when external N was sufficient. More striking changes were observed when dfc seedlings were grown under N-limited conditions, including shorter primary roots, fewer lateral roots, higher levels of glycine and carbon-N ratios, and lower N content than those in wild-type seedlings. Gene expression studies in mutant seedlings revealed altered transcript levels of several genes involved in folate biosynthesis and N metabolism. The biochemical and metabolic changes also suggested that N assimilation is drastically perturbed due to a loss of DFC function. The observation that elevated CO2 partly rescued the dfc phenotypes suggests that the alterations in N metabolism in dfc may be mainly due to a defect in photorespiration. These results indicate that DFC is required for N utilization in Arabidopsis and provide new insight into a potential interaction between folate and N metabolism.
Medical versus surgical termination of pregnancy in primigravid women—is the next delivery differently at risk? A population‐based register study
Authors: Männistö J , Mentula M , Bloigu A , Hemminki E , Gissler M , Heikinheimo O , Niinimäki M 
Published: November 2012

ObjectiveTo compare the effect of medical versus surgical termination of pregnancy (TOP), performed in primigravid women, on subsequent delivery.DesignPopulation‐based register study.SettingFinland 2000–2009.PopulationAll primigravid women (n = 8294) who underwent TOP during first trimester of pregnancy by medical (n = 3441) or surgical (n = 4853) method, and whose subsequent pregnancy resulted in singleton delivery.MethodsThe women were identified in the Finnish Register of Induced Abortions, and the data were linked to the Medical Birth and the Hospital Discharge Registries.Main outcome measuresRisk of preterm birth, low birthweight, small‐for‐gestational‐age (SGA) infant and placental complications (placenta praevia, placental abruption, retained placenta, placenta accreta).ResultsNo statistically significant differences in the incidences of preterm birth (4.0% in the medical group versus 4.9% in the surgical group), low birthweight (3.4% versus 4.0%), SGA infants (2.6% versus 2.9%) or placental complications (2.6% versus 2.8%) emerged between the two groups. After adjusting for various background factors, medical TOP was not associated with significantly altered risks of preterm birth (odds ratio [OR] 0.87, 95% confidence interval [95% CI] 0.68–1.13), low birthweight (OR 0.90, 95% CI 0.68–1.19), SGA infant (OR 0.87, 95% CI 0.64–1.20) or placental complications (OR 0.98, 95% CI 0.72–1.34) versus surgical TOP. In a sub‐analysis excluding women who underwent surgical evacuation following the index TOP, medical TOP was associated with a reduced risk of preterm birth (P < 0.01), but the difference became insignificant after adjusting for gestational age at the time of TOP, inter‐pregnancy interval, maternal age, cohabitation status, socio‐economic status, residence and smoking during pregnancy.ConclusionsA history of one medical versus surgical TOP, performed in primigravid women, is associated with similar obstetric risks in the subsequent delivery.
Analytical Thresholds and Sensitivity: Establishing RFU Thresholds for Forensic DNA Analysis,
Authors: Bregu Joli , Conklin Danielle , Coronado Elisse , Terrill Margaret , Cotton Robin W. , Grgicak Catherine M. 
Published: November 2012

AbstractDetermining appropriate analytical thresholds (ATs) for forensic DNA analysis is critical to maximize allele detection. In this study, six methods to determine ATs for forensic DNA purposes were examined and compared. Four of the methods rely on analysis of the baseline noise of a number of negatives, while two utilize the relationship between relative fluorescence unit signal and DNA input in the polymerase chain reaction (PCR) derived from a dilution series ranging from 1 to 0.06 ng. Results showed that when a substantial mass of DNA (i.e., >1 ng) was amplified, the baseline noise increased, suggesting the application of an AT derived from negatives should only be applied to samples with low levels of DNA. Further, the number and intensity of these noise peaks increased with increasing injection times, indicating that to maximize the ability to detect alleles, ATs should be validated for each post‐PCR procedure employed.
FDG PET/CT for the preoperative nodal staging of non‐small cell lung cancer in a tuberculosis‐endemic country: Are maximum standardized uptake values useful?
Authors: Lu Yu‐Yu , Wang Hsin‐Yi , Hsia Jiun‐Yi , Lin Wan‐Yu 
Published: November 2012

AbstractBackgroundThe aim of this study was to determine an optimum standardized uptake value threshold for identifying nodal metastasis in non‐small cell lung cancer (NSCLC) patients using Fluorine‐18 2‐fluoro‐2‐deoxy‐D‐glucose (FDG) positron emission tomography/computed tomography (PET/CT) in Taiwan, a tuberculosis‐endemic country. The variation in standardized uptake values of nodal metastasis among different NSCLC histological subtypes was also evaluated.MethodsWe retrospectively reviewed 75 NSCLC patients who had received FDG PET/CT before surgery. The diagnostic accuracy of FDG PET/CT for the preoperative nodal staging was evaluated by histopathologic findings.ResultsA total of 316 nodal stations were evaluated. The sensitivity and specificity of FDG PET/CT for nodal staging were 58.6% and 81.8%, respectively, using an SUV cut‐off of 2.6. With regard to the levels of mean SUVmax in true‐positive and false‐positive groups, there was no significant difference among different histological subtypes.ConclusionThe present study demonstrated that FDG PET/CT for pre‐operative nodal staging using SUVmax > 2.6 is a useful tool (with a higher specificity and a higher negative predictive value) to rule out the possibility of metastatic lymphadenopathy in operable patients with NSCLC.
Independent risk factors for infants who are small for gestational age by customised birthweight centiles in a multi‐ethnic New Zealand population
Authors: Anderson Ngaire H. , Sadler Lynn C. , Stewart Alistair W. , Fyfe Elaine M. , McCowan Lesley M.E. 
Published: November 2012

BackgroundInfants born small for gestational age (SGA) by customised birthweight centiles are at increased risk of adverse outcomes compared with those SGA by population centiles. Risk factors for customised SGA have not previously been described in a general obstetric population.AimTo determine independent risk factors for customised SGA in a multi‐ethnic New Zealand population.MethodsWe performed a retrospective cohort analysis of prospectively recorded maternity data from 2006 to 2009 at National Women's Health, Auckland, New Zealand. After exclusion of infants with congenital anomalies and missing data, our final study population was 26,254 singleton pregnancies. Multivariable logistic regression analysis adjusted for ethnicity, body mass index, maternal age, parity, smoking status, social deprivation, hypertensive disease, antepartum haemorrhage (APH), diabetes and relevant pre‐existing medical conditions.ResultsIndependent risk factors for SGA included obesity (adjusted odds ratio 1.24 [95% CI 1.11–1.39] relative to normal weight), maternal age ≥ 35 years (1.16 [1.05–1.30] relative to 20–29 years), nulliparity (1.13 [1.04–1.24] relative to parity 1), cigarette smoking (2.01 [1.79–2.27]), gestational hypertension (1.46 [1.21–1.75]), pre‐eclampsia (2.94 [2.49–3.48]), chronic hypertension (1.68 [1.34–2.09]), placental abruption (2.57 [1.74–3.78]) and APH of unknown origin (1.71 [1.45–2.00]). Gestational diabetes (0.80 [0.67–0.96]) and type 1 diabetes (0.26 [0.11–0.64]) were associated with reduced risk.ConclusionsWe report independent pregnancy risk factors for customised SGA in a general obstetric population. In contrast to population SGA, obesity is associated with increased risk. Our findings may help identify pregnancies that require increased fetal growth surveillance.
Grapefruit juice markedly increases the plasma concentrations and antiplatelet effects of ticagrelor in healthy subjects
Authors: Holmberg Mikko T. , Tornio Aleksi , Joutsi‐Korhonen Lotta , Neuvonen Mikko , Neuvonen Pertti J. , Lassila Riitta , Niemi Mikko , Backman Janne T. 
Published: November 2012

AimThis study examined the effects of grapefruit juice on the new P2Y12 inhibitor ticagrelor, which is a substrate of CYP3A4 and P‐glycoprotein.MethodsIn a randomized crossover study, 10 healthy volunteers ingested 200 ml of grapefruit juice or water thrice daily for 4 days. On day 3, they ingested a single 90 mg dose of ticagrelor.ResultsGrapefruit juice increased ticagrelor geometric mean peak plasma concentration (Cmax) to 165% (95% confidence interval 147, 184%) and area under the concentration–time curve (AUC(0,∞)) to 221% of control (95% confidence interval 200, 245%). The Cmax and AUC(0,34 h) (P < 0.05) but not the AUC(0,∞) of the active metabolite C12490XX were decreased significantly. Grapefruit juice had a minor effect on ticagrelor elimination half‐life prolonging it from 6.7 to 7.2 h (P = 0.036). In good correlation with the elevated plasma ticagrelor concentrations, grapefruit juice enhanced the antiplatelet effect of ticagrelor, assessed with VerifyNow® and Multiplate® methods, and postponed the recovery of platelet reactivity.ConclusionsGrapefruit juice increased ticagrelor exposure by more than two‐fold, leading to an enhanced and prolonged ticagrelor antiplatelet effect. The grapefruit juice–ticagrelor interaction seems clinically important and indicates the significance of intestinal metabolism to ticagrelor pharmacokinetics.
Shortening baroreflex delay in hypertrophic cardiomyopathy patients – an unknown effect of β‐blockers
Authors: Katarzynska‐Szymanska Agnieszka , Ochotny Romuald , Oko‐Sarnowska Zofia , Wachowiak‐Baszynska Hanna , Krauze Tomasz , Piskorski Jaroslaw , Gwizdala Adrian , Mitkowski Przemyslaw , Guzik Przemyslaw 
Published: November 2012

AimsHypertrophic cardiomyopathy (HCM) is characterized by left ventricular hypertrophy and impaired diastolic and systolic function. Abnormal sympathetic–parasympathetic balance is a potential stimulus for left ventricular hypertrophy in HCM patients. β‐Blockers are routinely used in HCM for their strong negative inotropic effect; however, these drugs also influence the sympathetic–parasympathetic balance. This study aimed to determine the autonomic control of the cardiovascular system and the autonomic effects of β‐blockers in HCM patients treated or untreated with β‐blockers.MethodsAmong 51 HCM outpatients (18–70 years old; 29 men) there were 19 individuals with no medication and 32 subjects treated with a β‐blocker. Fourteen age‐ and gender‐matched (23–70 years old; nine men) healthy volunteers were enrolled in the control group. Continuous, non‐invasive finger blood pressure was recorded during supine rest for 30 min. Autonomic regulation of the cardiovascular system was measured by heart rate variability and spontaneous baroreflex function (cross‐correlation sequence method).ResultsThe mean pulse interval, time domain and spectral measures of heart rate variability and baroreflex sensitivity were comparable between HCM patients, treated or not with β‐blockers, and the control group. However, the delay of the baroreflex was significantly longer in HCM patients who were not treated with β‐blockers [2.0 (1.6–2.3) s] in comparison with HCM patients receiving β‐blockers [1.4 (1.1–1.8) s; P = 0.0072] or control subjects [1.2 (0.8–1.8) s; P = 0.0025]. This delay did not differ between HCM patients treated with β‐blockers and the control group.ConclusionsHypertrophic cardiomyopathy not treated with β‐blockers is accompanied by prolonged baroreflex delay. The use of β‐blockers normalizes this delay.