bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating flight ranges to unravel migratory strategies: spring migration of continental Black-tailed Godwits Limosa limosa limosa
Authors: ALVES JOSé A. , LOURENçO PEDRO M. 
Published: September 2013

SummaryMapping migratory routes and the distribution of species during migration requires information collected over large scales (e.g. survey data), or the ability to follow specific movements (e.g. using tracking devices), which is often limited to a few individuals. For endangered species, such techniques may be impractical, but developments in flight range modelling allow inferences about migratory routes and potential site occupancy, given a few morphological parameters. We modelled flight range in a rapidly declining population of continental Black-tailed Godwits Limosa limosa limosa departing from a staging site in Iberia during spring migration and found that the vast majority of godwits are able to reach the breeding grounds in a single flight. Contrary to the traditional use of staging sites in France (and Morocco), godwits currently staging in Iberia are predicted to fly directly to The Netherlands and be present at breeding locations earlier than previously expected and observed. Despite harbouring approximately 75% of the total population during spring migration, Iberian staging sites currently lack any legal protection. Our example of the Black-tailed Godwit illustrates the potential of this approach to identify migration strategies and locate staging sites for species of conservation concern for which such information may be virtually absent.
Conservation of the Cinereous Vulture Aegypius monachus in Spain (1966–2011): a bibliometric review of threats, research and adaptive management
Authors: MORENO-OPO R. , MARGALIDA A. 
Published: September 2013

SummaryDetecting and quantifying threats and researching and implementing management actions are key to improving the conservation status of endangered species. Bibliometric analysis can constitute a useful tool for the evaluation of such questions from a long-term perspective. Taking as a case study the Cinereous Vulture Aegypius monachus in Spain, we tested relationships between population dynamics, research efforts, existing threats and conservation milestones. The population growth of the species (from 206 pairs in 1976 to 2,068 in 2011) was parallelled by the increase in the total number of publications, the number of articles in SCI journals and the number of published works dealing with aspects of conservation, threats and management. These results are discussed in terms of cause-effect relationships taking into account that the influence of other non-mutually exclusive factors could also probably explain such associations. Similarly, we analysed the trend of the Cinereous Vulture breeding population with respect to different threats and indices of food availability, obtaining a positive correlation with the increase in big-game hunting bags in Spain. With respect to conservation milestones, we concluded that the current situation is positive in terms of the protection of the species and its habitat, with the situation in relation to food availability being unclear. Finally, we reviewed the main conservation actions that have been taken for the species in Spain and how these have been progressively modified based on new scientific and technical evidence, as an example of adaptive management applied to conservation.
The value of stress perfusion cardiovascular magnetic resonance imaging for patients referred from the adult congenital heart disease clinic: 5-year experience at the Toronto General Hospital
Authors: Deva Djeven P. , Torres Felipe S. , Wald Rachel M. , Roche S. Lucy , Jimenez-Juan Laura , Oechslin Erwin N. , Crean Andrew M. 
Published: September 2013

AbstractBackground: Vasodilator stress perfusion cardiovascular magnetic resonance imaging is a clinically useful tool for detection of clinically significant myocardial ischaemia in adults. We report our 5-year retrospective experience with perfusion cardiovascular magnetic resonance in a large, quarternary adult congenital heart disease centre. Methods: We reviewed all cases of perfusion cardiovascular magnetic resonance in patients referred from the adult congenital heart disease service. Dipyridamole stress perfusion cardiovascular magnetic resonance was undertaken on commercially available 1.5 and 3 T cardiovascular magnetic resonance scanners. Late gadolinium enhancement imaging was performed 8–10 minutes after completion of the rest perfusion sequence. Navigator whole-heart coronary magnetic resonance angiography was also performed where feasible. Results of stress cardiovascular magnetic resonance were correlated with complementary imaging studies, surgery, and clinical outcomes. Results: Over 5 years, we performed 34 stress perfusion cardiovascular magnetic resonance examinations (11 positive). In all, 84% of patients had further investigations for ischaemia in addition to cardiovascular magnetic resonance. Within a subgroup of 19 patients who had definitive alternative assessment of their coronary arteries, stress perfusion cardiovascular magnetic resonance demonstrated a sensitivity of 82% and specificity of 100%. Of the 34 studies, two were false negatives, in which the aetiology of ischaemia was extrinsic arterial compression rather than intrinsic coronary luminal narrowing. Coronary abnormalities were identified in 71% of cases who had coronary magnetic resonance angiography. Conclusion: Stress perfusion cardiovascular magnetic resonance is a useful and accurate tool for investigation of myocardial ischaemia in an adult congenital heart disease population with suspected non-atherosclerotic coronary abnormalities.
Left ventricular strain and strain rates are decreased in children with normal fractional shortening after exposure to anthracycline chemotherapy
Authors: Moon Thomas J. , Miyamoto Shelley D. , Younoszai Adel K. , Landeck Bruce F. 
Published: September 2013

AbstractBackgroundAnthracycline chemotherapeutic agents carry the well-recognised risk of cardiotoxicity. Previous methods to evaluate cardiac function are useful, but have significant limitations. We sought to determine the left ventricular strain and strain rate of paediatric cancer patients with normal fractional shortening treated with anthracyclines using the latest ultrasound feature-tracking technology.Patients and methodsEchocardiograms on cancer patients before anthracycline exposure and following completion of treatment were retrospectively analysed using Velocity Vector Imaging software in the circumferential and longitudinal planes. The same analysis was performed on matched controls. Only patients with a fractional shortening ≥28% were included.ResultsIn all, 71 patients were identified with an age at diagnosis of 10.5 ± 4.7 years. The time from diagnosis to follow-up was 3.9 ± 4.0 years and the cumulative anthracycline dose was 356 ± 106 mg/m2. Following anthracycline exposure, paediatric cancer patients had a higher heart rate and a lower longitudinal strain, longitudinal diastolic strain rate, circumferential strain, and circumferential systolic and diastolic strain rate when compared with controls. Diastolic strain rate showed the greatest percent difference following anthracycline exposure versus controls.ConclusionDespite having a normal fractional shortening, children exposed to anthracyclines have subclinical derangement of their left ventricular deformation as measured by decreases in strain and strain rate in both the circumferential and longitudinal axis. In particular, there was a profound decrease in diastolic strain rate following anthracycline exposure compared with controls. Whether the decline of strain or strain rate can predict future risk of developing cardiomyopathy requires further investigation.
Chronic pain in children after cardiac surgery via sternotomy
Authors: Lauridsen Mette H. , Kristensen Anders D. , Hjortdal Vibeke E. , Jensen Troels S. , Nikolajsen Lone 
Published: September 2013

AbstractIntroductionChronic pain is common after sternotomy in adults with reported prevalence rates of 20–50%. So far, no studies have examined whether children develop chronic pain after sternotomy.Material and methodsPostal questionnaires were sent to 171 children 10–60 months after undergoing cardiac surgery via sternotomy at the age of 0–12 years. The children were asked to recall the intensity and duration of their post-operative pain, if necessary with the help from their parents, and to describe the intensity and character of any present pain. Another group of 13 children underwent quantitative sensory testing of the scar area 3 months after sternotomy.ResultsA total of 121 children, median (range) age 7.7 (4.2–16.9) years, answered the questionnaire. Their age at the time of surgery was median (range) 3.8 (0–12.9) years, and the follow-up period was median (range) 4 (0.8–5.1) years. In all, 26 children (21%) reported present pain and/or pain within the last week located in the scar area; in 12 (46%) out of the 26 children, the intensity was ≥4 on a numeric rating scale (0–10). Quantitative sensory testing of the scar area revealed sensory abnormalities – pinprick hyperalgesia and brush and cold allodynia – in 10 out of 13 children.ConclusionChronic pain after cardiac surgery via sternotomy in children is a problem that should not be neglected. The pain is likely to have a neuropathic component as suggested by the sensory abnormalities demonstrated by quantitative sensory testing.
Increasing functional modularity with residence time in the co-distribution of native and introduced vascular plants
Authors: Hui Cang , Richardson David M. , Pyšek Petr , Le Roux Johannes J. , Kučera Tomáš , Jarošík Vojtěch 
Published: September 2013

AbstractSpecies gain membership of regional assemblages by passing through multiple ecological and environmental filters. To capture the potential trajectory of structural changes in regional meta-communities driven by biological invasions, one can categorize species pools into assemblages of different residence times. Older assemblages, having passed through more environmental filters, should become more functionally ordered and structured. Here we calculate the level of compartmentalization (modularity) for three different-aged assemblages (neophytes, introduced after 1500 AD; archaeophytes, introduced before 1500 AD, and natives), including 2,054 species of vascular plants in 302 reserves in central Europe. Older assemblages are more compartmentalized than younger ones, with species composition, phylogenetic structure and habitat characteristics of the modules becoming increasingly distinctive. This sheds light on two mechanisms of how alien species are functionally incorporated into regional species pools: the settling-down hypothesis of diminishing stochasticity with residence time, and the niche-mosaic hypothesis of inlaid neutral modules in regional meta-communities.
MnO Nanoparticle@Mesoporous Carbon Composites Grown on Conducting Substrates Featuring High-performance Lithium-ion Battery, Supercapacitor and Sensor
Authors: Wang Tianyu , Peng Zheng , Wang Yuhang , Tang Jing , Zheng Gengfeng 
Published: September 2013

AbstractWe demonstrate a facile, two-step coating/calcination approach to grow a uniform MnO nanoparticle@mesoporous carbon (MnO@C) composite on conducting substrates, by direct coating of the Mn-oleate precursor solution without any conducting/binding reagents and subsequent thermal calcination. The monodispersed, sub-10 nm MnO nanoparticles offer high theoretical energy storage capacities and catalytic properties and the mesoporous carbon coating allows for enhanced electrolyte transport and charge transfer towards/from MnO surface. In addition, the direct growth and attachment of the MnO@C nanocomposite in the supporting conductive substrates provide much reduced contact resistances and efficient charge transfer. These excellent features allow the use of MnO@C nanocomposites as lithium-ion battery and supercapacitor electrodes for energy storage, with high reversible capacity at large current densities, as well as excellent cycling and mechanical stabilities. Moreover, this MnO@C nanocomposite has also demonstrated a high sensitivity for H2O2detection and also exhibited attractive potential for the tumor cell analysis.
Ionizing irradiation-induced radical stress stalls live meiotic chromosome movements by altering the actin cytoskeleton
Authors: Illner Doris , Scherthan Harry 
Published: September 2013

Significance
Sexual reproduction depends on breaking, pairing, and repairing the parental chromosomes by homologous recombination. Homologs are separated in the meiosis I division whose prophase sees extraordinary chromosome mobility in the presence of physiological dsDNA breaks (DSBs). Ionizing radiation (IR) induces unscheduled DSBs and radicals. The G2 and meiotic prophase of yeast is particularly resistant to IR with efficient cell killing requiring doses of up to 1,000 Gy. This investigation discloses that low-dose X irradiation stalls meiotic chromosome mobility via IR-induced oxidative damage to the actin cytoskeleton, while IR-induced DSBs persist in the presence of antioxidants. Altogether, the data disclose a unique low-dose radiation response in yeast that may protect IR-damaged meiotic chromosomes from unwanted interactions.
Public goods dilemma in asexual ant societies
Authors: Dobata Shigeto , Tsuji Kazuki 
Published: September 2013

SignificanceThis study reports experimental evidence for the “public goods dilemma” between cooperators and cheaters in an asexual ant society, in which cheating is always more rewarding for individuals but cooperation at the cost of individual fitness leads to better performance of groups. Although this dilemma provides the basic principle of social evolution, its experimental demonstration with underlying genetics and fitness evaluation for both cooperators and cheaters still lacks in societies other than microbial ones. By showing the striking evolutionary convergence between microbial societies and insect societies in fitness consequences and in phenotypic plasticity of cooperators against cheaters, our result suggests that a wide range of scales of cooperative systems could be understood in a unified manner.
Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules
Authors: Nonejuie Poochit , Burkart Michael , Pogliano Kit , Pogliano Joe 
Published: September 2013

Significance
Some bacteria have evolved resistance to nearly every known class of antibiotic, creating an urgent need for new ones that work by different mechanisms. However, there has been no simple way to determine how new antibiotics work. We have developed a unique method that provides a shortcut for understanding how antibiotics kill bacteria. This method can be used to sift through compounds to rapidly identify and characterize antibiotics that work against multidrug-resistant pathogens.
Entropic factors provide unusual reactivity and selectivity in epoxide-opening reactions promoted by water
Authors: Byers Jeffery A. , Jamison Timothy F. 
Published: September 2013

Significance
Mechanistic studies of a water-promoted cyclization reaction reveal that an unusual, multifaceted interaction between the organic substrate and water causes an otherwise disfavored chemical reaction. The combination of several factors leads to the unusual selectivity and highlights the beneficial features of water as a solvent in organic chemistry. Of particular importance is organization of the substrate, which is facilitated by synergistic interactions between the surprisingly simple organic substrate and water. In addition to providing insight into these important interactions, the results may be relevant to the biosynthetic origins of the ladder polyether natural products. These natural products are potent neurotoxins and are the active constituents of harmful algae blooms commonly referred to as “red tide.”
TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination
Authors: Berkseth Matt , Ikegami Kohta , Arur Swathi , Lieb Jason D. , Zarkower David 
Published: September 2013

Significance
Sex-determining genes have been identified in many animals, but how they impose sex specificity on development is poorly understood. We ask how the nematode sex-determining transcription factor Transformer 1 (TRA-1) regulates sex by identifying where in the genome TRA-1 binds and which nearby genes may be affected by this binding. We find that TRA-1 promotes female development primarily by preventing the expression of genes involved in male development. Among the genes repressed by TRA-1 are a number that control the timing of developmental events and also several that function upstream of TRA-1 in the global sex-determination pathway. The suite of TRA-1 targets presented here provides a resource to continue uncovering the basis of sex-specific development.
Use of autocorrelation scanning in DNA copy number analysis
Authors: Zhang Liangcai , Zhang Li 
Published: September 2013

AbstractMotivation: Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses.Method: We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes.Results: Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets.Contact: lzhangli@mdanderson.orgSupplementary information: Supplementary data are available at Bioinformatics online.
Integrated profiling of three dimensional cell culture models and 3D microscopy
Authors: Bilgin Cemal Cagatay , Kim Sun , Leung Elle , Chang Hang , Parvin Bahram 
Published: September 2013

Abstract
Motivation: Our goal is to develop a screening platform for quantitative profiling of colony organizations in 3D cell culture models. The 3D cell culture models, which are also imaged in 3D, are functional assays that mimic the in vivo characteristics of the tissue architecture more faithfully than the 2D cultures. However, they also introduce significant computational challenges, with the main barriers being the effects of growth conditions, fixations and inherent complexities in segmentation that need to be resolved in the 3D volume.
Results: A segmentation strategy has been developed to delineate each nucleus in a colony that overcomes (i) the effects of growth conditions, (ii) variations in chromatin distribution and (iii) ambiguities formed by perceptual boundaries from adjacent nuclei. The strategy uses a cascade of geometric filters that are insensitive to spatial non-uniformity and partitions a clump of nuclei based on the grouping of points of maximum curvature at the interface of two neighboring nuclei. These points of maximum curvature are clustered together based on their coplanarity and proximity to define dissecting planes that separate the touching nuclei. The proposed curvature-based partitioning method is validated with both synthetic and real data, and is shown to have a superior performance against previous techniques. Validation and sensitivity analysis are coupled with the experimental design that includes a non-transformed cell line and three tumorigenic cell lines, which covers a wide range of phenotypic diversity in breast cancer. Colony profiling, derived from nuclear segmentation, reveals distinct indices for the morphogenesis of each cell line.
Availability: All software are developed in ITK/VTK and are available at https://vision.lbl.gov/Software/3DMorphometry.
Contact: b_parvin@lbl.gov or hchang@lbl.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes
Authors: Gunawardana Yawwani , Niranjan Mahesan 
Published: September 2013

AbstractMotivation: Despite much dynamical cellular behaviour being achieved by accurate regulation of protein concentrations, messenger RNA abundances, measured by microarray technology, and more recently by deep sequencing techniques, are widely used as proxies for protein measurements. Although for some species and under some conditions, there is good correlation between transcriptome and proteome level measurements, such correlation is by no means universal due to post-transcriptional and post-translational regulation, both of which are highly prevalent in cells. Here, we seek to develop a data-driven machine learning approach to bridging the gap between these two levels of high-throughput omic measurements on Saccharomyces cerevisiae and deploy the model in a novel way to uncover mRNA-protein pairs that are candidates for post-translational regulation.Results: The application of feature selection by sparsity inducing regression (l1 norm regularization) leads to a stable set of features: i.e. mRNA, ribosomal occupancy, ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 to 5. A linear predictor used with these features is capable of predicting protein concentrations fairly accurately (). Proteins whose concentration cannot be predicted accurately, taken as outliers with respect to the predictor, are shown to have annotation evidence of post-translational modification, significantly more than random subsets of similar size . In a data mining sense, this work also shows a wider point that outliers with respect to a learning method can carry meaningful information about a problem domain.Contact: mn@ecs.soton.ac.uk
The puzzling radio source in the cool core cluster A2626
Authors: Gitti M. 
Published: September 2013

Abstract
We report on new Very Large Array (VLA) radio observations performed at 1.4 and 4.8 GHz with unprecedented sensitivity and angular resolution (∼1 arcsec) of the cool core cluster A2626, which is known to possess a radio mini-halo at its centre. The most unusual features of A2626 are two elongated radio features detected in previous observations to the north and south, having morphologies not common to the typical jet-lobe structures in cool cores. In our new sensitive images the two elongated features appears clearly as bright radio arcs, and we discover the presence of a new arc to the west. These radio arcs are not detected at 4.8 GHz, implying a steep (α &gt; 1) spectrum, and their origin is puzzling. After subtracting the flux density contributed by these discrete features from the total flux measured at low resolution, we estimate a residual 18.0 ± 1.8 mJy flux density of diffuse radio emission at 1.4 GHz. We therefore confirm the detection of diffuse radio emission, which appears distinct from the discrete radio arcs embedded in it. Although its radio power is lower (1.4 × 1023 W Hz−1) than previously known, the diffuse emission may still be classified as a radio mini-halo.