bluuebunny/crossref_metadata_2025 huggingface dataset:
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
Authors: Aßhauer Kathrin P. , Wemheuer Bernd , Daniel Rolf , Meinicke Peter
Published: May 2015

Motivation: The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data.

Results: Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches.

Availability and implementation: Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/.

Contact:  kasshau@gwdg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
MemGen: a general web server for the setup of lipid membrane simulation systems
Authors: Knight Christopher J. , Hub Jochen S.
Published: May 2015

Motivation: Molecular dynamics simulations provide atomic insight into the physicochemical characteristics of lipid membranes and hence, a wide range of force field families capable of modelling various lipid types have been developed in recent years. To model membranes in a biologically realistic lipid composition, simulation systems containing multiple different lipids must be assembled.

Results: We present a new web service called MemGen that is capable of setting up simulation systems of heterogenous lipid membranes. MemGen is not restricted to certain lipid force fields or lipid types, but instead builds membranes from uploaded structure files which may contain any kind of amphiphilic molecule. MemGen works with any all-atom or united-atom lipid representation.

Availability and implementation: MemGen is freely available without registration at http://memgen.uni-goettingen.de.

Contact:  jhub@gwdg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data
Authors: Kähärä Juhani , Lähdesmäki Harri
Published: May 2015

Motivation: Transcription factors (TFs) are a class of DNA-binding proteins that have a central role in regulating gene expression. To reveal mechanisms of transcriptional regulation, a number of computational tools have been proposed for predicting TF-DNA interaction sites. Recent studies have shown that genome-wide sequencing data on open chromatin sites from a DNase I hypersensitivity experiments (DNase-seq) has a great potential to map putative binding sites of all transcription factors in a single experiment. Thus, computational methods for analysing DNase-seq to accurately map TF-DNA interaction sites are highly needed.

Results: Here, we introduce a novel discriminative algorithm, BinDNase, for predicting TF-DNA interaction sites using DNase-seq data. BinDNase implements an efficient method for selecting and extracting informative features from DNase I signal for each TF, either at single nucleotide resolution or for larger regions. The method is applied to 57 transcription factors in cell line K562 and 31 transcription factors in cell line HepG2 using data from the ENCODE project. First, we show that BinDNase compares favourably to other supervised and unsupervised methods developed for TF-DNA interaction prediction using DNase-seq data. We demonstrate the importance to model each TF with a separate prediction model, reflecting TF-specific DNA accessibility around the TF-DNA interaction site. We also show that a highly standardised DNase-seq data (pre)processing is a requisite for accurate TF binding predictions and that sequencing depth has on average only a moderate effect on prediction accuracy. Finally, BinDNase’s binding predictions generalise to other cell types, thus making BinDNase a versatile tool for accurate TF binding prediction.

Availability and implementation: R implementation of the algorithm is available in: http://research.ics.aalto.fi/csb/software/bindnase/.

Contact:  juhani.kahara@aalto.fi

Supplementary information:  Supplemental data are available at Bioinformatics online.
Interactive analysis of large cancer copy number studies with Copy Number Explorer
Authors: Newman Scott
Published: May 2015

Summary: Copy number abnormalities (CNAs) such as somatically-acquired chromosomal deletions and duplications drive the development of cancer. As individual tumor genomes can contain tens or even hundreds of large and/or focal CNAs, a major difficulty is differentiating between important, recurrent pathogenic changes and benign changes unrelated to the subject’s phenotype. Here we present Copy Number Explorer, an interactive tool for mining large copy number datasets. Copy Number Explorer facilitates rapid visual and statistical identification of recurrent regions of gain or loss, identifies the genes most likely to drive CNA formation using the cghMCR method and identifies recurrently broken genes that may be disrupted or fused. The software also allows users to identify recurrent CNA regions that may be associated with differential survival.

Availability and Implementation: Copy Number Explorer is available under the GNU public license (GPL-3). Source code is available at: https://sourceforge.net/projects/copynumberexplorer/

Contact:  scott.newman@emory.edu
GOplot: an R package for visually combining expression data with functional analysis
Authors: Walter Wencke , Sánchez-Cabo Fátima , Ricote Mercedes
Published: May 2015

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

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, <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

B 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

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

Innate 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

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

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

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

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

Catalysis, 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.
Explaining Systematic Bias and Nontransparency in U.S. Social Security Administration Forecasts
Authors: Kashin Konstantin , King Gary , Soneji Samir
Published: May 2015

The accuracy of U.S. Social Security Administration (SSA) demographic and financial forecasts is crucial for the solvency of its Trust Funds, other government programs, industry decision-making, and the evidence base of many scholarly articles. Because SSA makes public insufficient replication information and uses antiquated statistical forecasting methods, no external group has ever been able to produce fully independent forecasts or evaluations of policy proposals to change the system. Yet, no systematic evaluation of SSA forecasts has ever been published by SSA or anyone else—until a companion paper to this one. We show that SSA's forecasting errors were approximately unbiased until about 2000, but then began to grow quickly, with increasingly overconfident uncertainty intervals. Moreover, the errors are largely in the same direction, making the Trust Funds look healthier than they are. We extend and then explain these findings with evidence from a large number of interviews with participants at every level of the forecasting and policy processes. We show that SSA's forecasting procedures meet all the conditions the modern social-psychology and statistical literatures demonstrate make bias likely. When those conditions mixed with potent new political forces trying to change Social Security, SSA's actuaries hunkered down, trying hard to insulate their forecasts from strong political pressures. Unfortunately, this led the actuaries into not incorporating the fact that retirees began living longer lives and drawing benefits longer than predicted. We show that fewer than 10% of their scorings of major policy proposals were statistically different from random noise as estimated from their policy forecasting error. We also show that the solution to this problem involves SSA or Congress implementing in government two of the central projects of political science over the last quarter century: (1) transparency in data and methods and (2) replacing with formal statistical models large numbers of ad hoc qualitative decisions too complex for unaided humans to make optimally.
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.
Is infant immunization by breastfeeding possible?
Authors: Verhasselt Valerie
Published: May 2015

Breastfeeding is known as the most efficient way to prevent infectious disease in early life. Maternal anti-microbial immunoglobulins transfer through milk confers passive immunity to the breastfed child while his immune system is maturing. Maternal milk also contains bioactive factors that will stimulate this maturation. From the literature on breastfeeding prevention of immune-mediated disease and more specifically from our experiments conducted in the field of allergic disease prevention, we propose that breastfeeding may also induce antigen-specific immune responses in the breastfed child. We found that early oral antigen exposure through breast milk leads to tolerance or immune priming depending on the nature of the antigen transferred and accompanying maternal milk cofactors. Here, we will discuss our data in the light of prevention of infectious disease and will propose that possible milk transfer of microbial antigen could affect actively the immune response in breastfed children and thereby their long-term susceptibility to infectious disease. Further research in this direction may lead to novel strategies of early life vaccination, taking advantage of the possibility to stimulate antigen-specific immune responses through breast milk.
Vaccinology in the era of high-throughput biology
Authors: Nakaya Helder I. , Pulendran Bali
Published: May 2015

Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced ‘experimental challenge models' in humans.
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.
Ferruginibacter paludis sp. nov., isolated from wetland freshwater, and emended descriptions of Ferruginibacter lapsinanis and Ferruginibacter alkalilentus
Authors: Kang Heeyoung , Kim Haneul , Joung Yochan , Jang Tae Yong , Joh Kiseong
Published: May 2015

A Gram-staining-negative, aerobic and rod-shaped bacterium, designated HME8881T, was isolated from a freshwater wetland located in the Republic of Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain HME8881T grouped with members of the genus Ferruginibacter. The most closely related species were Ferruginibacter lapsinanis HU1-HG42T (95.6  %), Ferruginibacter alkalilentus HU1-GD23T (95.1  %), ‘Ferruginibacter profundus’ DS48-5-3 (94.7  %) and Ferruginibacter yonginensis HME8442T (93.4  %). The major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 1G, C16 : 0 and iso-C17 : 0 3-OH. A polar lipid analysis revealed phosphatidylethanolamine, two unidentified aminolipids, three unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. DNA G+C content was 37.7 mol%. These results suggest that strain HME8881T represents a novel species of the genus Ferruginibacter, for which the name Ferruginibacter paludis sp. nov., is proposed with the type strain HME8881T ( = KCTC 42121T = CECT 8366T). In addition, emended descriptions of Ferruginibacter lapsinanis and Ferruginibacter alkalilentus are also proposed on the basis of new data obtained during this study.
ZIFA: Dimensionality reduction for zero-inflated single cell gene expression analysis
Authors: Pierson Emma , Yau Christopher
Published: May 2015

Single 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

This 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

Memory 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.
Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo
Authors: Lim Hee-Woong , Uhlenhaut N. Henriette , Rauch Alexander , Weiner Juliane , Hübner Sabine , Hübner Norbert , Won Kyoung-Jae , Lazar Mitchell A. , Tuckermann Jan , Steger David J.
Published: May 2015

Glucocorticoids (GCs) are commonly prescribed drugs, but their anti-inflammatory benefits are mitigated by metabolic side effects. Their transcriptional effects, including tissue-specific gene activation and repression, are mediated by the glucocorticoid receptor (GR), which is known to bind as a homodimer to a palindromic DNA sequence. Using ChIP-exo in mouse liver under endogenous corticosterone exposure, we report here that monomeric GR interaction with a half-site motif is more prevalent than homodimer binding. Monomers colocalize with lineage-determining transcription factors in both liver and primary macrophages, and the GR half-site motif drives transcription, suggesting that monomeric binding is fundamental to GR's tissue-specific functions. In response to exogenous GC in vivo, GR dimers assemble on chromatin near ligand-activated genes, concomitant with monomer evacuation of sites near repressed genes. Thus, pharmacological GCs mediate gene expression by favoring GR homodimer occupancy at classic palindromic sites at the expense of monomeric binding. The findings have important implications for improving therapies that target GR.
Crystal structure of dimethyl 2,5-bis[(diphenoxyphosphoryl)oxy]cyclohexa-1,4-diene-1,4-dicarboxylate
Authors: Gao Lei , Ma Zongshan , Yan Hong
Published: May 2015

In the title compound, C34H30O12P2, which was synthesizedviathe esterification of dimethyl 2,5-dioxo-1,4-cyclohexanedicarboxylate with diphenyl chlorophosphate, the molecule has crystallographic inversion symmetry. The dihedral angles between the plane of the cyclohexa-1,4-diene ring and those of the two benzene rings of the substituent phosphate groups are 41.0 (1) and 89.5 (1)°, while that with the ester group is 3.1 (3)°. In the crystal, only weak intermolecular C—H...O hydrogen bonds are present.
Crystal structure of poly[[μ-4-(hydroxymethyl)pyridine-κ2N:O][4-(hydroxymethyl)pyridine-κN](μ-thiocyanato-κ2N:S)(thiocyanato-κN)cadmium]
Authors: Werner Julia , Jess Inke , Näther Christian
Published: May 2015

The crystal structure of the title compound, [Cd(NCS)2(C6H7NO)2]nis made up of Cd2+cations that are coordinated by three thiocyanate ligands and three 4-(hydroxymethyl)pyridine ligands within distorted N4OS octahedra. The asymmetric unit consists of one Cd2+cation, two thiocyanate anions and two 4-(hydroxymethyl)pyridine ligands in general positions. Two Cd2+cations are linked by two μ-1,3N- andS-bonding thioycanate anions into dimers which are further linked into branched chains along [100] by two μ-1,6N- andO-bonding 4-(hydroxymethyl)pyridine ligands. One additionalN-bonded 4-(hydroxymethyl)pyridine ligand and one additionalN-bonded thiocyanate anion are only terminally bonded to the metal cation. Interchain O—H...S hydrogen bonds between the hydroxy H atoms and one of the thiocyanate S atoms connect the chains into a three-dimensional network.
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.
Going round in circles? Joint working between primary health and social care
Authors: Coleman Anna , Glendinning Caroline
Published: May 2015

Purpose

– The purpose of this paper is to examine research evidence on collaboration between primary and adult social care in strategic, rather than operational, activities at two different time points, following large-scale changes within the health and social care environments; and discuss the prospects for the future.

Design/methodology/approach

– This paper reports evidence from two substantial longitudinal studies (Dowling and Glendinning, 2003; Checkland et al., 2012) which followed the development of Primary Care Groups and Trusts (PCG/Ts) and Clinical Commissioning Groups (CCGs), respectively. Each used a combination of national surveys and local in-depth case studies to trace the early development of new structures and ways of working following major changes in the NHS and local government.

Findings

– PCG/Ts had limited success in collaborating with adult social care partners. Health and Well-being Boards offer a new overarching organisational framework for collaborative strategic working between GP-led CCGs and adult social care services. Mandated joint strategic needs assessments also provide a shared framework within which commissioning decisions by both CCGs and social services are made. However, there remains evidence of long-standing barriers, particularly differences in geographic boundaries and in organisational and professional cultures.

Research limitations/implications

– Evidence from both studies is based on the early years of the respective new organisations; later evidence may have yielded a different picture.

Originality/value

– This is the first paper reflecting on developments in strategic relations between primary and social care from researchers involved with two longitudinal investigations of the early development of PCG/Ts (1999-2002) and CCGs (2011-ongoing).
Social work: a “forgotten” piece of the integration jigsaw?
Authors: Hudson Annie
Published: May 2015

Purpose

– The article seeks to analyse the potential contribution of social work to integration debates. Social work has tended to be seen as marginal to these discussions despite the potential of social work expertise and leadership to help forge effective approaches to joined-up care. The purpose of this paper is to demonstrate how social work is well positioned to help lead and support practice focused change across social care and health. It also seeks to show how professional leadership can be a powerful vehicle for changing professional and organisational cultures.

Design/methodology/approach

– The paper draws on practice and research evidence to demonstrate the proposition that social work can make a powerful contribution to debates about integration.

Findings

– Three things could help build the cultural capital that is a pre-requisite to building integrated and joined-up approaches. First, the author needs to invest in developing the role of social workers and GPs working together as local professional and practice leaders. Second, there is a real risk that in any discussion about professional leadership and partnership, the author eclipses the singularly critical importance of engaging and involving users and carers in non tokenistic ways. Finally, the author needs to utilise better social work’s skills and knowledge in managing risk, building resilience and promoting social inclusion.

Research limitations/implications

– Further evaluation and research is needed about the potential for GPs and social workers to develop joined-up approaches to care for and support older and disabled people.

Practical implications

– Social workers need to be provided with the tools, support and space in which to develop their practice leadership role, including but not exclusively with GPs.

Originality/value

– This paper does not purport to offer any specifically originally research but rather some reflections on how social work expertise might better contribute to integration debates.
Australia's coal seam gas boom and the LNG entry result
Authors: Simshauser Paul , Nelson Tim
Published: May 2015

Queensland experienced extraordinary growth in booked 2P coal seam gas (CSG) reserves, rising from 3,400 PJ in 2005 to 41,200 PJ in 2013. Given annual domestic consumption of ca. 700 PJ/a, 2P reserves rapidly shifted from 14 to 72 years supply. Profit‐maximising firms sought to speed up commercialisation of reserves through the development of three liquefied natural gas (LNG) export plants at Gladstone. In this article, we present forecasts of Australia's east coast interconnected gas system with daily resolution using our dynamic partial equilibrium model. Modelling results show the rapid development of LNG plants combined with restrictive CSG development policies in NSW may result in unserved load from 2016. Relaxing development constraints or delaying construction of one LNG terminal by 1 year could have avoided the risk of Unserved Load events in the domestic gas market. Lessons can be learned from this CSG‐LNG boom scenario. Facilitating new gas supplies is the most efficient way of alleviating the impacts of the CSG‐LNG boom on domestic markets in the medium term. In the long‐term, Australian policymakers may consider the merits of a National Net Benefits Test to maximise welfare through appropriate coordination – as is done by policymakers in the USA – as opposed to protecting local industries through ‘domestic gas reservation policies’.
Use of Bacillus indicus HU36 as a probiotic culture in set‐type, recombined nonfat yoghurt production and its effects on quality
Authors: Erşan Sevcan , Gültekin‐Özgüven Mine , Berktaş İjlal , Erdem Özlem , Tuna Halide Ezgi , Gunes Gurbuz , Özçelik Beraat
Published: May 2015

Viability of a probiotic and carotenoid‐producing bacterium, Bacillus indicus HU36 in vegetative form, along with the yoghurt cultures in set‐type, recombined nonfat yoghurt and its effects on quality were determined during the storage at 4 °C. The number of B. indicus HU36 cells in yoghurt remained about 5 log cfu/mL after 14 days, but decreased to 3.5 log after 21 days. The bacterium resulted in increased yellowness, but did not affect the rheological properties of the yoghurt. Sensorial properties of the yoghurt were acceptable compared to a commercial probiotic yoghurt. B. indicus HU36 can thus be used as a probiotic culture in yoghurt production.
Cloning and structural characterization of juvenile hormone diol kinase in Spodoptera litura
Authors: Zeng Bao‐Juan , Lv Yuan , Zhang Li‐Li , Huang Li‐Hua , Feng Qi‐Li
Published: May 2015

Juvenile hormone (JH) is one of the key insect hormones that regulate metamorphosis. Juvenile hormone diol kinase (JHDK) is an enzyme involved in JH metabolism and catalyzes JH diol to form a polar end product, JH diol phosphate that has no JH activity. In this study, a JHDK complementary DNA (cDNA) was cloned from Spodoptera litura and the structure and expression of the gene was characterized. The cDNA was 714 base pairs in length and encoded a protein of 183 amino acids with a molecular mass of 21 kDa and an isoelectric point of 4.55. Based on the structure, three putative calcium binding motifs and guanosine triphosphate‐binding motifs were predicted in the protein. Modeling of the 3‐D structure showed that the protein consisted of eight α‐helixes linked with loops, with no β‐sheets. The gene was expressed in the epidermis, fat body and midgut of fifth and sixth instar larvae. The expression level in the epidermis was lower than in the fat body and midgut. The gene was expressed at higher levels at the early stages than in the later stages of fifth and sixth instar midgut and fat body. The results suggest that this gene may be involved in the regulation of the JH titer in larvae of S. litura.