bluuebunny/crossref_metadata_2025_split huggingface dataset:
GOplot: an R package for visually combining expression data with functional analysis
Authors: Walter Wencke , Sánchez-Cabo Fátima , Ricote Mercedes 
Published: May 2015

Abstract
Summary: Despite the plethora of methods available for the functional analysis of omics data, obtaining comprehensive-yet detailed understanding of the results remains challenging. This is mainly due to the lack of publicly available tools for the visualization of this type of information. Here we present an R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings.
Availability and Implementation: The R package GOplot is available via CRAN-The Comprehensive R Archive Network: http://cran.r-project.org/web/packages/GOplot. The shiny web application of the Venn diagram can be found at: https://wwalter.shinyapps.io/Venn/. A detailed manual of the package with sample figures can be found at https://wencke.github.io/
Contact: fscabo@cnic.es or mricote@cnic.es
Quantifying 60 years of declining European eel (Anguilla anguilla L., 1758) fishery yields in Mediterranean coastal lagoons
Authors: Aalto Emilius , Capoccioni Fabrizio , Terradez Mas Juan , Schiavina Marcello , Leone Chiara , De Leo Giulio , Ciccotti Eleonora 
Published: May 2015

Abstract
The European eel Anguilla anguilla is thought to be in a multi-decadal decline across its range. Although its northern Atlantic sub-populations are well-studied, little is known about the historical trend and current status of eel stock in the Mediterranean Sea. To fill this gap, we gathered catch data for 86 lagoon fisheries in nine countries across the Mediterranean basin and analysed historical trends and geographical and environmental patterns. We found a region-wide decline in eel catch, beginning in the mid-1970s and exceeding the simultaneous decline in non-eel fisheries, as well as lower productivity in larger lagoons and those in the southern Mediterranean. Additionally, we developed a population dynamics model to provide a preliminary estimate of pristine, potential, and actual escapement of spawning adults (silver eels) across the Mediterranean basin under historical and current conditions. Model results suggest that current escapement is 35% of escapement at pristine biomass levels, &lt;40% target set by EC regulation 1100/2007. Furthermore, we estimate that a complete closure of lagoon fisheries would achieve 57% of pristine escapement under current recruitment levels. Though preliminary, this analysis represents a first step towards a full assessment of the role of the Mediterranean sub-population in overall eel stock recovery.
Regulatory B cells in human inflammatory and autoimmune diseases: from mouse models to clinical research
Authors: Miyagaki Tomomitsu , Fujimoto Manabu , Sato Shinichi 
Published: May 2015

AbstractB cells have been generally considered to be positive regulators of immune responses because of their ability to produce antigen-specific antibodies and to activate T cells through antigen presentation. Impairment of B cell development and function may cause inflammatory and autoimmune diseases. Recently, specific B cell subsets that can negatively regulate immune responses have been described in mouse models of a wide variety of inflammatory and autoimmune diseases. The concept of those B cells, termed regulatory B cells, is now recognized as important in the murine immune system. Among several regulatory B cell subsets, IL-10-producing regulatory B cells are the most widely investigated. On the basis of discoveries from studies of such mice, human regulatory B cells that produce IL-10 in most cases are becoming an active area of research. There have been emerging data suggesting the importance of human regulatory B cells in various diseases. Revealing the immune regulation mechanisms of human regulatory B cells in human inflammatory and autoimmune diseases could lead to the development of novel B cell targeted therapies. This review highlights the current knowledge on regulatory B cells, mainly IL-10-producing regulatory B cells, in animal models of inflammatory and autoimmune diseases and in clinical research using human samples.
Signals controlling the development and activity of regulatory B-lineage cells
Authors: Baba Yoshihiro , Matsumoto Masanori , Kurosaki Tomohiro 
Published: May 2015

Abstract
The fundamental concepts surrounding B cells with inhibitory function (regulatory B cells) are now being established. In the context of autoimmune and inflammatory animal models, B cells play an immunomodulatory role via IL-10 production and contribute to limitation of the pathogenesis. Recent studies have notably identified the human counterparts of these cells, which have been suggested to be relevant to the pathophysiology of disease. Clear criteria to identify these cell subsets and the key molecular mechanisms underlying their physiological features are required for understanding the big picture of regulatory B cells. Plasmablasts have recently been identified as a major IL-10-producing regulatory B-cell subset and Ca2+ signaling has furthermore been found to contribute to B-cell IL-10 expression. In this review, the signaling components controlling IL-10-dependent B-cell regulatory function and the development of IL-10-competent/-producing B cells and plasmablasts are discussed.
Innate response activator B cells: origins and functions
Authors: Chousterman Benjamin G. , Swirski Filip K. 
Published: May 2015

AbstractInnate response activator (IRA) B cells are a subset of B-1a derived B cells that produce the growth factors granulocyte macrophage colony stimulating factor and IL-3. In mouse models of sepsis and pneumonia, B-1a B cells residing in serosal sites recognize bacteria, migrate to the spleen or lung, and differentiate to IRA B cells that then contribute to the host response by amplifying inflammation and producing polyreactive IgM. In atherosclerosis, IRA B cells accumulate in the spleen, where they promote extramedullary hematopoiesis and activate classical dendritic cells. In this review, we focus on the ontogeny and function of IRA B cells in acute and chronic inflammation.
Witnessing the emergence of a carbon star
Authors: Guzman-Ramirez L. , Lagadec E. , Wesson R. , Zijlstra A. A. , Müller A. , Jones D. , Boffin H. M. J. , Sloan G. C. , Redman M. P. , Smette A. , Karakas A. I. , Nyman Lars-Åke 
Published: May 2015

Abstract
During the late stages of their evolution, Sun-like stars bring the products of nuclear burning to the surface. Most of the carbon in the Universe is believed to originate from stars with masses up to a few solar masses. Although there is a chemical dichotomy between oxygen-rich and carbon-rich evolved stars, the dredge-up itself has never been directly observed. In the last three decades, however, a few stars have been shown to display both carbon- and oxygen-rich material in their circumstellar envelopes. Two models have been proposed to explain this dual chemistry: one postulates that a recent dredge-up of carbon produced by nucleosynthesis inside the star during the Asymptotic Giant Branch changed the surface chemistry of the star. The other model postulates that oxygen-rich material exists in stable keplerian rotation around the central star. The two models make contradictory, testable, predictions on the location of the oxygen-rich material, either located further from the star than the carbon-rich gas, or very close to the star in a stable disc. Using the Faint Object InfraRed CAmera (FORCAST) instrument on board the Stratospheric Observatory for Infrared Astronomy (SOFIA) Telescope, we obtained images of the carbon-rich planetary nebula BD +30° 3639 which trace both carbon-rich polycyclic aromatic hydrocarbons and oxygen-rich silicate dust. With the superior spectral coverage of SOFIA, and using a 3D photoionization and dust radiative transfer model we prove that the O-rich material is distributed in a shell in the outer parts of the nebula, while the C-rich material is located in the inner parts of the nebula. These observations combined with the model, suggest a recent change in stellar surface composition for the double chemistry in this object. This is evidence for dredge-up occurring ∼103 yr ago.
Intermediate inclinations of type 2 Coronal-Line Forest AGN
Authors: Rose Marvin , Elvis Martin , Crenshaw Michael , Glidden Ana 
Published: May 2015

Abstract
Coronal-Line Forest Active Galactic Nuclei (CLiF AGN) are remarkable in the sense that they have a rich spectrum of dozens of coronal emission lines (e.g. [Fe vii], [Fe x] and [Ne v]) in their spectra. Rose, Elvis & Tadhunter suggest that the inner obscuring torus wall is the most likely location of the coronal line region in CLiF AGN, and the unusual strength of the forbidden high-ionization lines is due to a specific AGN-torus inclination angle. Here, we test this suggestion using mid-IR colours (4.6–22 μm) from the Wide-Field Infrared Survey Explorer for the CLiF AGN. We use the Fischer et al. result that showed that as the AGN-torus inclination becomes more face on, the Spitzer 5.5–30 μm colours become bluer. We show that the [W2−W4] colours for the CLiF AGN (〈[W2−W4]〉 = 5.92 ± 0.12) are intermediate between Sloan Digital Sky Survey (SDSS) type 1 (〈[W2−W4]〉 = 5.22 ± 0.01) and type 2 AGN (〈[W2−W4]〉 = 6.35 ± 0.03). This implies that the AGN-torus inclinations for the CLiF AGN are indeed intermediate, supporting the work of Rose, Elvis & Tadhunter. The confirmed relation between CLiF AGN and their viewing angle shows that CLiF AGN may be useful for our understanding of AGN unification.
Cognitive function, depression, fatigue and quality of life among
long-term survivors of head and neck cancer
Authors: Wilbers Joyce , Kappelle Arnoud C. , Versteeg Laura , Tuladhar Anil M. , Steens Stefan C.A. , Meijer Frederick J.A. , Boogerd Willem , Dorresteijn Lucille D. , Kaanders Johannes H. , Kessels Roy P.C. , van Dijk Ewoud J. 
Published: May 2015

Abstract

Background
Long-term cancer treatment complications become more prevalent as survival improves. Little is known about the psychological complications in long-term survivors of head and neck cancer (HNC). We investigated cognitive functioning and its relation with depression, fatigue, cognitive complaints, and brain lesions on MRI.

Methods
This study is part of a multicentre, prospective cohort study of 65 patients treated for HNC. A comprehensive neuropsychological assessment was combined with validated questionnaires on subjective memory complaints, depression, and fatigue after a median of 7 years follow-up. Results were compared with age- and education-adjusted normative data. Further, we evaluated cerebral white matter hyperintensities (WMH), brain volume, and infarctions on MRI.

Results
HNC patients had worse cognitive performance in two of the five assessed cognitive domains: episodic memory (z = −0.48, P = .003) and speed of information processing (z = −0.47, P < 0.001). Patients with fatigue performed worse than patients without fatigue on verbal fluency (mean difference in z-score 0.52, P = .02) and speed of information processing (0.49, P = .04). Patients with subjective memory complaints had a worse episodic memory performance (mean difference in z-score −0.96; P = .02). Patients with cerebral infarction(s) on MRI performed worse on fluency (mean difference in z-score 0.74, P = .005). A lower cognitive performance was not associated with depression, WMH or brain volume.

Conclusion
Long-term HNC survivors showed worse cognitive functioning 7 years after treatment. Cognitive function was associated with subjective complaints and fatigue, but not with depressive symptoms. Cerebral infarctions on MRI were correlated with cognitive function, whereas WMH, and brain volume were not.
Target observations for improving initialization of high-impact ocean-atmospheric environmental events forecasting
Authors: Mu Mu , Duan Wansuo , Chen Dake , Yu Weidong 
Published: May 2015

Abstract
In this paper, we emphasize the importance of accurate initial conditions in predicting high-impact ocean-atmospheric environmental events, such as El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), tropical cyclone (TC), and Kuroshio large meander (KLM), by reviewing recent progresses toward target observations for improving the initialization of these events forecasting. Since field observations are costly and will never be dense enough to fully cover the vast space of these events, it is necessary to develop methodologies that guide the design of efficient and effective observation strategy. Of particular interest is a method called conditional non-linear optimal perturbation (CNOP), which has been shown to be very useful in determining the sensitive areas for target observations applicable to the predictions of ENSO, IOD, TC, and KLM. Further studies are needed to understand the predictability of these events under the influence of climate change, and to explore the possibility of implementing field programs of target observations. These studies are challenging but are crucially important for improving our forecast skill of the high-impact ocean-atmospheric environmental events, and thus for disaster prevention, climate change mitigation, and sustainable socio-economic development.
Understanding nano effects in catalysis
Authors: Yang Fan , Deng Dehui , Pan Xiulian , Fu Qiang , Bao Xinhe 
Published: May 2015

AbstractCatalysis, as a key and enabling technology, plays an increasingly important role in fields ranging from energy, environment and agriculture to health care. Rational design and synthesis of highly efficient catalysts has become the ultimate goal of catalysis research. Thanks to the rapid development of nanoscience and nanotechnology, and in particular a theoretical understanding of the tuning of electronic structure in nanoscale systems, this element of design is becoming possible via precise control of nanoparticles’ composition, morphology, structure and electronic states. At the same time, it is important to develop tools for in situ characterization of nanocatalysts under realistic reaction conditions, and for monitoring the dynamics of catalysis with high spatial, temporal and energy resolution. In this review, we discuss confinement effects in nanocatalysis, a concept that our group has put forward and developed over several years. Taking the confined catalytic systems of carbon nanotubes, metal-confined nano-oxides and 2D layered nanocatalysts as examples, we summarize and analyze the fundamental concepts, the research methods and some of the key scientific issues involved in nanocatalysis. Moreover, we present a perspective on the challenges and opportunities in future research on nanocatalysis from the aspects of: (1) controlled synthesis of nanocatalysts and rational design of catalytically active centers; (2) in situ characterization of nanocatalysts and dynamics of catalytic processes; (3) computational chemistry with a complexity approximating that of experiments; and (4) scale-up and commercialization of nanocatalysts.
Behavioral Changes Associated with a Disruptive New Student in the Classroom
Authors: O'Brien Julie Stein , Taras Howard , Barton Scott , Sellick Pete , Stein Martin T. 
Published: May 2015

CASE: Marcus is a 10-year-old boy who was followed by his pediatrician for several years. She knows him as a socially engaged, active athlete, playing soccer and baseball, out-going, and a good student. He has been in good health without a significant medical history.
At the beginning of this academic year, a new student was placed in Marcus's fourth grade class. This student is disruptive, impulsive, and abusive. He has frequent violent outbursts, yelling, kicking, and throwing objects, including recently throwing a desk across the room. The school has made efforts to manage this student. The teacher sets up behavior contracts, and the school has temporarily suspended the child; however, the school is unable to remove the child from the classroom. Many students, including Marcus, have been significantly affected by this disruption.
Marcus describes the classroom environment as “tense.” He reports he is never sure what is going to make the student “so mad.” Over the last 3–4 months, Marcus developed nightmares, enuresis, and trichotillomania. The hair pulling is the most distressing feature for both Marcus and his parents. Marcus acknowledges that he is usually unaware of the behavior at first but then finds the sensation is relaxing. Afterward, he is typically embarrassed by the behavior. There is a family history of anxiety in both parents.
He has been seeing a psychologist with some mild improvement in his enuresis. However, the hair pulling has not improved and has worsened. They were seeking additional advice regarding the next steps.
Vaccines against enteric infections for the developing world
Authors: Czerkinsky Cecil , Holmgren Jan 
Published: May 2015

Since the first licensure of the Sabin oral polio vaccine more than 50 years ago, only eight enteric vaccines have been licensed for four disease indications, and all are given orally. While mucosal vaccines offer programmatically attractive tools for facilitating vaccine deployment, their development remains hampered by several factors:

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limited knowledge regarding the properties of the gut immune system during early life;

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lack of mucosal adjuvants, limiting mucosal vaccine development to live-attenuated or killed whole virus and bacterial vaccines;

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lack of correlates/surrogates of mucosal immune protection; and

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limited knowledge of the factors contributing to oral vaccine underperformance in children from developing countries.

There are now reasons to believe that the development of safe and effective mucosal adjuvants and of programmatically sound intervention strategies could enhance the efficacy of current and next-generation enteric vaccines, especially in lesser developed countries which are often co-endemic for enteric infections and malnutrition. These vaccines must be safe and affordable for the world's poorest, confer long-term protection and herd immunity, and must be able to contain epidemics.
ZIFA: Dimensionality reduction for zero-inflated single cell gene expression analysis
Authors: Pierson Emma , Yau Christopher 
Published: May 2015

AbstractSingle cell RNA-seq data allows insight into normal cellular function and diseases including cancer through the molecular characterisation of cellular state at the single-cell level. Dimensionality reduction of such high-dimensional datasets is essential for visualization and analysis, but single-cell RNA-seq data is challenging for classical dimensionality reduction methods because of the prevalence of dropout events leading to zero-inflated data. Here we develop a dimensionality reduction method, (Z)ero (I)nflated (F)actor (A)nalysis (ZIFA), which explicitly models the dropout characteristics, and show that it improves modelling accuracy on simulated and biological datasets.
The NADPH oxidase and microbial killing by neutrophils, with a particular emphasis on the proposed antimicrobial role of myeloperoxidase within the phagocytic vacuole
Authors: Levine Adam P. , Segal Anthony W. 
Published: May 2015

AbstractThis review is devoted to a consideration of the way in which the NADPH oxidase of neutrophils, NOX2, functions to enable the efficient killing of bacteria and fungi. It includes a critical examination of the current dogma that its primary purpose is the generation of hydrogen peroxide as substrate for myeloperoxide catalysed generation of hypochlorite. Instead it is demonstrated that NADPH oxidase functions to optimise the ionic and pH conditions within the vacuole for the solubilisation and optimal activity of the proteins released into this compartment from the cytoplasmic granules, which kill and digest the microbes. The general role of other NOX systems as electrochemical generators to alter the pH and ionic composition in compartments on either side of a membrane in plants and animals will also be examined.
Stretch Induced Hyperexcitability of Mice Callosal Pathway
Authors: Fan Anthony , Stebbings Kevin , Llano Daniel , Saif Taher 
Published: May 2015

AbstractMemory and learning are thought to result from changes in synaptic strength. Previous studies on synaptic physiology in brain slices have traditionally been focused on biochemical processes. Here, we demonstrate with experiments on mouse brain slices that central nervous system plasticity is also sensitive to mechanical stretch. This is important, given the host of clinical conditions involving changes in mechanical tension on the brain, and the normal role that mechanical tension plays in brain development. A novel platform is developed to investigate neural responses to mechanical stretching. Flavoprotein autofluoresence (FA) imaging was employed for measuring neural activity. We observed that synaptic excitability substantially increases after a small (2.5%) stretch was held for 10 minutes and released. The increase is accumulative, i.e. multiple stretch cycles further increase the excitability. We also developed analytical tools to quantify the spatial spread and response strength. Results show that the spatial spread is less stable in slices undergoing the stretch-unstretch cycle. FA amplitude and activation rate decrease as excitability increases in stretch cases but not in electrically enhanced cases. These results collectively demonstrate that a small stretch in physiological range can modulate neural activities significantly, suggesting that mechanical events can be employed as a novel tool for the modulation of neural plasticity.
Consumers’ willingness to pay for organic products in Thailand
Authors: Sriwaranun Yaowarat , Gan Christopher , Lee Minsoo , Cohen David A 
Published: May 2015

Purpose– The purpose of this paper is to investigate factors affecting consumers’ willingness to pay (WTP) a premium for organics.Design/methodology/approach– A self-administered questionnaire was used to collect data at five retail stores in metropolitan Bangkok. Exploratory factor analysis and the double-bound contingent valuation method were used for analysis.Findings– Results indicate WTP premiums of 88, 51 and 51 per cent for kale, jasmine rice and pork, respectively. Analysis indicates that respondents are willing to pay a premium if they have already purchased organic products, have good health, strong ethical and environmental concerns, think that organic products provide greater quality and health benefits, and reside in the city. Respondents with children, however, are less likely to pay a premium for organic products. Analysis also indicates that the price premium hinders purchase.Practical implications– Efforts should be made by policymakers, together with marketers and producers, to lower the price of organic products to attract more consumers.Originality/value– To enlarge the organic market, one must understand consumers’ preferences for organic products and the premium they will pay for them. This is not well-researched. Though several studies have investigated consumers’ behaviour towards environmentally friendly products in Thailand, there is little research on WTP. This lack is a major impediment to the growth of organic consumption and the development of organic product markets.