bluuebunny/crossref_metadata_2025 huggingface dataset:
The power of data mining in diagnosis of childhood pneumonia
Authors: Naydenova Elina , Tsanas Athanasios , Howie Stephen , Casals-Pascual Climent , De Vos Maarten
Published: July 2016

Childhood pneumonia is the leading cause of death of children under the age of 5 years globally. Diagnostic information on the presence of infection, severity and aetiology (bacterial versus viral) is crucial for appropriate treatment. However, the derivation of such information requires advanced equipment (such as X-rays) and clinical expertise to correctly assess observational clinical signs (such as chest indrawing); both of these are often unavailable in resource-constrained settings. In this study, these challenges were addressed through the development of a suite of data mining tools, facilitating automated diagnosis through quantifiable features. Findings were validated on a large dataset comprising 780 children diagnosed with pneumonia and 801 age-matched healthy controls. Pneumonia was identified via four quantifiable vital signs (98.2% sensitivity and 97.6% specificity). Moreover, it was shown that severity can be determined through a combination of three vital signs and two lung sounds (72.4% sensitivity and 82.2% specificity); addition of a conventional biomarker (C-reactive protein) further improved severity predictions (89.1% sensitivity and 81.3% specificity). Finally, we demonstrated that aetiology can be determined using three vital signs and a newly proposed biomarker (lipocalin-2) (81.8% sensitivity and 90.6% specificity). These results suggest that a suite of carefully designed machine learning tools can be used to support multi-faceted diagnosis of childhood pneumonia in resource-constrained settings, compensating for the shortage of expensive equipment and highly trained clinicians.
Evolving synergetic interactions
Authors: Wu Bin , Arranz Jordi , Du Jinming , Zhou Da , Traulsen Arne
Published: July 2016

Cooperators forgo their own interests to benefit others. This reduces their fitness and thus cooperators are not likely to spread based on natural selection. Nonetheless, cooperation is widespread on every level of biological organization ranging from bacterial communities to human society. Mathematical models can help to explain under which circumstances cooperation evolves. Evolutionary game theory is a powerful mathematical tool to depict the interactions between cooperators and defectors. Classical models typically involve either pairwise interactions between individuals or a linear superposition of these interactions. For interactions within groups, however, synergetic effects may arise: their outcome is not just the sum of its parts. This is because the payoffs via a single group interaction can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can such synergetic multiplayer games emerge from simpler pairwise interactions? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying such synergetic interactions.
Humanoid
infers Archimedes' principle: understanding physical relations and object affordances through cumulative learning experiences
Authors: Bhat Ajaz Ahmad , Mohan Vishwanathan , Sandini Giulio , Morasso Pietro
Published: July 2016

Emerging studies indicate that several species such as corvids, apes and children solve ‘The Crow and the Pitcher’ task (from Aesop's Fables) in diverse conditions. Hidden beneath this fascinating paradigm is a fundamental question: by cumulatively interacting with different objects, how can an agent abstract the underlying cause–effect relations to predict and creatively exploit potential affordances of novel objects in the context of sought goals? Re-enacting this Aesop's Fable task on a humanoid within an open-ended ‘learning–prediction–abstraction’ loop, we address this problem and (i) present a brain-guided neural framework that emulates rapid one-shot encoding of ongoing experiences into a long-term memory and (ii) propose four task-agnostic learning rules (elimination, growth, uncertainty and status quo) that correlate predictions from remembered past experiences with the unfolding present situation to gradually abstract the underlying causal relations. Driven by the proposed architecture, the ensuing robot behaviours illustrated causal learning and anticipation similar to natural agents. Results further demonstrate that by cumulatively interacting with few objects, the predictions of the robot in case of novel objects converge close to the physical law, i.e. the Archimedes principle: this being independent of both the objects explored during learning and the order of their cumulative exploration.
In vitroresponse of macrophages to ceramic scaffolds used for bone regeneration
Authors: Graney Pamela L. , Roohani-Esfahani Seyed-Iman , Zreiqat Hala , Spiller Kara L.
Published: July 2016

Macrophages, the primary cells of the inflammatory response, are major regulators of healing, and mediate both bone fracture healing and the inflammatory response to implanted biomaterials. However, their phenotypic contributions to biomaterial-mediated bone repair are incompletely understood. Therefore, we used gene expression and protein secretion analysis to investigate the interactionsin vitrobetween primary human monocyte-derived macrophages and ceramic scaffolds that have been shown to have varying degrees of success in promoting bone regenerationin vivo. Specifically, baghdadite (Ca3ZrSi2O9) and strontium–hardystonite–gahnite (Sr–Ca2ZnSi2O7–ZnAl2O4) scaffolds were chosen as two materials that enhanced bone regenerationin vivoin large defects under load compared with clinically used tricalcium phosphate–hydroxyapatite (TCP–HA). Principal component analysis revealed that the scaffolds differentially regulated macrophage phenotype. Temporal changes in gene expression included shifts in markers of pro-inflammatory M1, anti-inflammatory M2a and pro-remodelling M2c macrophage phenotypes. Of note, TCP–HA scaffolds promoted upregulation of many M1-related genes and downregulation of many M2a- and M2c-related genes. Effects of the scaffolds on macrophages were attributed primarily to direct cell–scaffold interactions because of only minor changes observed in transwell culture. Ultimately, elucidating macrophage–biomaterial interactions will facilitate the design of immunomodulatory biomaterials for bone repair.
Structural features of reconstituted wheat wax films
Authors: Pambou Elias , Li Zongyi , Campana Mario , Hughes Arwel , Clifton Luke , Gutfreund Philipp , Foundling Jill , Bell Gordon , Lu Jian R.
Published: July 2016

Cuticular waxes are essential for the well-being of all plants, from controlling the transport of water and nutrients across the plant surface to protecting them against external environmental attacks. Despite their significance, our current understanding regarding the structure and function of the wax film is limited. In this work, we have formed representative reconstituted wax film models of controlled thicknesses that facilitated an
ex vivo
study of plant cuticular wax film properties by neutron reflection (NR).
Triticum aestivum
L. (wheat) waxes were extracted from two different wheat straw samples, using two distinct extraction methods. Waxes extracted from harvested field-grown wheat straw using supercritical CO
2
are compared with waxes extracted from laboratory-grown wheat straw via wax dissolution by chloroform rinsing. Wax films were produced by spin-coating the two extracts onto silicon substrates. Atomic force microscopy and cryo-scanning electron microscopy imaging revealed that the two reconstituted wax film models are ultrathin and porous with characteristic nanoscale extrusions on the outer surface, mimicking the structure of epicuticular waxes found upon adaxial wheat leaf surfaces. On the basis of solid–liquid and solid–air NR and ellipsometric measurements, these wax films could be modelled into two representative layers, with the diffuse underlying layer fitted with thicknesses ranging from approximately 65 to 70 Å, whereas the surface extrusion region reached heights exceeding 200 Å. Moisture-controlled NR measurements indicated that water penetrated extensively into the wax films measured under saturated humidity and under water, causing them to hydrate and swell significantly. These studies have thus provided a useful structural basis that underlies the function of the epicuticular waxes in controlling the water transport of crops.
Odorant receptors can mediate axonal identity and gene choice via cAMP-independent mechanisms
Authors: Movahedi Kiavash , Grosmaitre Xavier , Feinstein Paul
Published: July 2016

Odorant receptors (ORs) control several aspects of cell fate in olfactory sensory neurons (OSNs), including singular gene choice and axonal identity. The mechanisms of OR-induced axon guidance have been suggested to principally rely on G-protein signalling. Here, we report that for a subset of OSNs, deleting G proteins or altering their levels of signalling does not affect axonal identity. Signalling-deficient ORs or surrogate receptors that are unable to couple to Gs/Golf still provide axons with distinct identities and the anterior–posterior targeting of axons does not correlate with the levels of cAMP produced by genetic modifications. In addition, we refine the models of negative feedback by showing that ectopic ORs can be robustly expressed without suppressing endogenous gene choice. In conclusion, our results uncover a new feature of ORs, showing that they can instruct axonal identity and regulate olfactory map formation independent of canonical G-protein signalling and cAMP production.
Dynamic phosphorylation of RelA on Ser42 and Ser45 in response to TNFα stimulation regulates DNA binding and transcription
Authors: Lanucara Francesco , Lam Connie , Mann Jelena , Monie Tom P. , Colombo Stefano A. P. , Holman Stephen W. , Boyd James , Dange Manohar C. , Mann Derek A. , White Michael R. H. , Eyers Claire E.
Published: July 2016

The NF-κB signalling module controls transcription through a network of protein kinases such as the IKKs, as well as inhibitory proteins (IκBs) and transcription factors including RelA/p65. Phosphorylation of the NF-κB subunits is critical for dictating system dynamics. Using both non-targeted discovery and quantitative selected reaction monitoring-targeted proteomics, we show that the cytokine TNFα induces dynamic multisite phosphorylation of RelA at a number of previously unidentified residues. Putative roles for many of these phosphorylation sites on RelA were predicted by modelling of various crystal structures. Stoichiometry of phosphorylation determination of Ser45 and Ser42 revealed preferential early phosphorylation of Ser45 in response to TNFα. Quantitative analyses subsequently confirmed differential roles for pSer42 and pSer45 in promoter-specific DNA binding and a role for both of these phosphosites in regulating transcription from the IL-6 promoter. These temporal dynamics suggest that RelA-mediated transcription is likely to be controlled by functionally distinct NF-κB proteoforms carrying different combinations of modifications, rather than a simple ‘one modification, one effect’ system.
Structural dissection of a complex
Bacteroides ovatus
gene locus conferring xyloglucan metabolism in the human gut
Authors: Hemsworth Glyn R. , Thompson Andrew J. , Stepper Judith , Sobala Łukasz F. , Coyle Travis , Larsbrink Johan , Spadiut Oliver , Goddard-Borger Ethan D. , Stubbs Keith A. , Brumer Harry , Davies Gideon J.
Published: July 2016

The human gastrointestinal tract harbours myriad bacterial species, collectively termed the microbiota, that strongly influence human health. Symbiotic members of our microbiota play a pivotal role in the digestion of complex carbohydrates that are otherwise recalcitrant to assimilation. Indeed, the intrinsic human polysaccharide-degrading enzyme repertoire is limited to various starch-based substrates; more complex polysaccharides demand microbial degradation. Select Bacteroidetes are responsible for the degradation of the ubiquitous vegetable xyloglucans (XyGs), through the concerted action of cohorts of enzymes and glycan-binding proteins encoded by specific xyloglucan utilization loci (XyGULs). Extending recent (meta)genomic, transcriptomic and biochemical analyses, significant questions remain regarding the structural biology of the molecular machinery required for XyG saccharification. Here, we reveal the three-dimensional structures of an α-xylosidase, a β-glucosidase, and two α-
l
-arabinofuranosidases from the
Bacteroides ovatus
XyGUL. Aided by bespoke ligand synthesis, our analyses highlight key adaptations in these enzymes that confer individual specificity for xyloglucan side chains and dictate concerted, stepwise disassembly of xyloglucan oligosaccharides. In harness with our recent structural characterization of the vanguard endo-xyloglucanse and cell-surface glycan-binding proteins, the present analysis provides a near-complete structural view of xyloglucan recognition and catalysis by XyGUL proteins.
Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population
Authors: Hoffman J. I. , Kowalski G. J. , Klimova A. , Eberhart-Phillips L. J. , Staniland I. J. , Baylis A. M. M.
Published: July 2016

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.
Johnson–Kendall–Roberts adhesive contact for a toroidal indenter
Authors: Argatov Ivan , Li Qiang , Pohrt Roman , Popov Valentin L.
Published: July 2016

The unilateral axisymmetric frictionless adhesive contact problem for a toroidal indenter and an elastic half-space is considered in the framework of the Johnson–Kendall–Roberts theory. In the case of a semi-fixed annular contact area, when one of the contact radii is fixed, while the other varies during indentation, we obtain the asymptotic solution of the adhesive contact problem based on the solution of the corresponding unilateral non-adhesive contact problem. In particular, the adhesive contact problem for Barber’s concave indenter is considered in detail. In the case when both contact radii are variable, we construct the leading-order asymptotic solution for a narrow annular contact area. It is found that for a v-shaped generalized toroidal indenter, the pull-off force is independent of the elastic properties of the indented solid.
Transient effects of drying creep in nanoporous solids: understanding the effects of nanoscale energy barriers
Authors: Sinko Robert , Vandamme Matthieu , Bažant Zdeněk P. , Keten Sinan
Published: July 2016

The Pickett effect is the phenomenon of creep enhancement during transient drying. It has been observed for many nanoporous solids, including concrete, wood and Kevlar. While the existing micromechanical models can partially explain this effect, they have yet to consider nanoscale dynamic effects of water in nanopores, which are believed to be of paramount importance. Here, we examine how creep deformations in a slit pore are accelerated by the motion of water due to drying forces using coarse-grained molecular dynamics simulations. We find that the drying that drives water flow in the nanopores lowers both the activation energy of pore walls sliding past one another and the apparent viscosity of confined water molecules. This lowering can be captured with an analytical Arrhenius relationship accounting for the role of water flow in overcoming the energy barriers. Notably, we use this model and simulation results to demonstrate that the drying creep strain is not linearly dependent on the applied creep stress at the nanopore level. Our findings establish the scaling relationships that explain how the creep driving force, drying force and fluid properties are related. Thus, we establish the nanoscale origins of the Pickett effect and provide strategies for minimizing the additional displacements arising from this effect.
Changes in physiological stress and behaviour in semi-free-ranging red-capped mangabeys (
Cercocebus torquatus
) following antiparasitic treatment
Authors: Friant Sagan , Ziegler Toni E. , Goldberg Tony L.
Published: July 2016

Parasites are ubiquitous in wildlife populations, but physiological and behavioural responses of hosts to infection are difficult to measure. We experimentally treated semi-free-ranging red-capped mangabeys (
Cercocebus torquatus
) in Nigeria with antiparasitic drugs and examined subsequent changes in glucocorticoid production and individual behaviour. Because both parasites and stress impact energy balance and health, we measured (i) behavioural time re-allocation via activity budgets, (ii) social relationships (e.g. social connectivity and dominance hierarchy stability) and (iii) body condition. We collected triplicate faecal samples (
n
= 441) from 49 individuals prior to and following treatment. Cortisol levels fluctuated in parallel with parasite abundance. Elevations in cortisol, but not parasitism, were related to reduced body condition. Behaviour also shifted according to infection status, with uninfected individuals spending more time foraging and less time resting and vigilant compared with when they were infected. Time spent feeding, travelling or socializing did not differ between pre- and post-treatment time periods. Group cohesion, but not dominance stability, changed following treatment, suggesting parasite-induced social avoidance. Together, these findings show a coordinated response to infection that promotes host tolerance through stress and energy conservation, reduces transmission risk and increases protection when infected hosts are vulnerable.
Fatal case of co-infection with dengue virus and Neisseria meningitidis during a dengue epidemic in the state of Rio de Janeiro, Brazil
Authors: de Filippis Ivano , Guerra Nunes Priscila Conrado , de Andrade Claudia Ferreira , Gonçalves Bianca de Santis , de Araújo Eliane Saraiva , Bezerra Itacirema de Oliveira , da Silva Ivan Rocha Ferreira , Nogueira Rita Maria , de Filippis Ana Maria Bispo
Published: July 2016

Introduction:

Dengue and meningococcal disease are caused by two different agents: a flavivirus and a Gram-negative bacterium, respectively. The first symptoms of both diseases can be indistinct and a rapid and accurate diagnosis is crucial, considering that both diseases are associated with high morbidity and mortality, representing a major public-health problem in Brazil.

Case presentation:

We report a fatal case of co-infection of dengue virus (DENV) and Neisseria meningitidis in a 54-year-old patient. The serum tested positive for DENV NS1 antigen, and N. meningitidis serogroup C was detected by nspA-PCR. Following the initial positive result for DENV infection, rRT-PCRwas performed and DENV-4 was confirmed.

Conclusion:

Our report highlights the importance of accurate differential diagnosis during periods of high circulation of DENV, in order to provide adequate management and an improved outcome.
The Influence of Lymphoid Reconstitution Kinetics on Clinical Outcomes in Allogeneic Stem Cell Transplantation
Authors: Kobulnicky David J , Sabo Roy T , Sharma Shashank , Shubar Ali Ali S , Kobulnicky Kristen , Roberts Catherine H , Clark William B , Chung Harold , McCarty John M , Toor Amir A
Published: July 2016

Lymphoid recovery following myeloablative stem cell transplantation (SCT) displays a logistic pattern of exponential growth followed by a plateau. Within this logistic framework, lymphoid recovery is characterized by the parametersR(slope of ascent),a(time of maximal rate of ascent) andK(plateau), the steady state lymphocyte count. A retrospective analysis of allogeneic SCT performed from 2008 to 2013 was undertaken to compare lymphoid recovery and clinical outcomes in 131 patients with acute myelogenous leukemia, acute lymphocytic leukemia and myelodysplastic syndromes. UsingPrismsoftware, a logistic curve was successfully fit to the absolute lymphocyte count recovery in all patients. Patients were classified according to the magnitude and rate of lymphoid recovery; pattern A achieved an ALC of > 1000/uL by day 45; pattern B an ALC 500 <x< 1000 /uL and pattern C, an ALC <500/uL. Pattern A was characterized by a higher mean K (p < 0.0001) compared with patterns B & C. Patients with patterns B and C were more likely to have mixed T cell chimerism at ninety days following SCT (p=0.01). There was a trend towards improved survival, (and relapse-free survival) in those with pattern A and B at one year compared to pattern C (p = 0.073). There was no difference in cGVHD (p=0.42) or relapse (p=0.45) between pattern types. CMV, aGVHD and relapse all were heralded by deviation from logistic behavior. Pattern C patients were more likely to require donor lymphocyte infusion (p=0.017). Weaning of Tacrolimus post-transplant was associated with a second, separate logistic expansion in some patients. This study demonstrated that lymphoid reconstitution follows a prototypical logistic recovery and that pattern observed correlates with T cell chimerism and need for DLI, and may influence survival.
A generalized quantitative antibody homeostasis model: regulation of B-cell development by BCR saturation and novel insights into bone marrow function
Authors: Prechl József
Published: July 2016

In a pair of articles we present a generalized quantitative model for the homeostatic function of clonal humoral immune system. In this first paper we describe the cycles of B-cell expansion and differentiation driven by B-cell receptor engagement.

The fate of a B cell is determined by the signals it receives via its antigen receptor at any point of its lifetime. We express BCR engagement as a function of apparent affinity and free antigen concentration, using the range of 10−14to 10−3M for both factors. We assume that for keeping their BCR responsive B cells must maintain partial BCR saturation, which is a narrow region defined by [Ag]≈KD. To remain in this region, B cells respond to changes in [Ag] by proliferation or apoptosis and modulate KDby changing BCR structure. We apply this framework to various niches of B-cell development, such as the bone marrow, blood, lymphoid follicles and germinal centers. We propose that clustered B cells in the bone marrow and in follicles present antigen to surrounding B cells by exposing antigen captured on complement and Fc receptors. The model suggests that antigen-dependent selection in the bone marrow results in 1) effector BI cells, which develop in blood as a consequence of the inexhaustible nature of soluble antigens, 2) memory cells that survive in antigen rich niches, identified as marginal zone B cells. Finally, the model implies that memory B cells could derive survival signals from abundant non-cognate antigens.
Genetic heterogeneity in depressive symptoms following the death of a spouse: Polygenic score analysis of the US Health and Retirement Study
Authors: Domingue Benjamin W. , Liu Hexuan , Okbay Aysu , Belsky Daniel W.
Published: July 2016

Experience of stressful life events is associated with risk of depression. Yet many exposed individuals do not become depressed. A controversial hypothesis is that genetic factors influence vulnerability to depression following stress. This hypothesis is most commonly tested with a “diathesis-stress” model, in which genes confer excess vulnerability. We tested an alternative model, in which genes may buffer against the depressogenic effects of life stress. We measured the hypothesized genetic buffer using a polygenic score derived from a published genome-wide association study (GWAS) of subjective wellbeing. We tested if married older adults who had higher polygenic scores were less vulnerable to depressive symptoms following the death of their spouse as compared to age-peers who had also lost their spouse and who had lower polygenic scores. We analyzed data from N=9,453 non-Hispanic white adults in the Health and Retirement Study (HRS), a population-representative longitudinal study of older adults in the United States. HRS adults with higher wellbeing polygenic scores experienced fewer depressive symptoms during follow-up. Those who survived death of their spouses during follow-up (n=1,829) experienced a sharp increase in depressive symptoms following the death and returned toward baseline over the following two years. Having a higher polygenic score buffered against increased depressive symptoms following a spouse's death. Effects were small and clinical relevance is uncertain, although polygenic score analyses may provide clues to behavioral pathways that can serve as therapeutic targets. Future studies of gene-environment interplay in depression may benefit from focus on genetics discovered for putative protective factors.
Robust ergodicity and tracking in antithetic integral control of stochastic biochemical reaction networks
Authors: Briat Corentin , Khammash Mustafa
Published: July 2016

Controlling stochastic reactions networks is a challenging problem with important implications in various fields such as systems and synthetic biology. Various regulation motifs have been discovered or posited over the recent years, the most recent one being the so-called Antithetic Integral Control (AIC) motif [1]. Several favorable properties for the AIC motif have been demonstrated for classes of reaction networks that satisfy certain irreducibility, ergodicity and output controllability conditions. Here we address the problem of verifying these conditions for large sets of reaction networks with fixed topology using two different approaches. The first one is quantitative and relies on the notion of interval matrices while the second one is qualitative and is based on sign properties of matrices. The obtained results lie in the same spirit as those obtained in [1] where properties of reaction networks are independently characterized in terms of control theoretic concepts, linear programming conditions and graph theoretic conditions.
Microbial Communities are Well Adapted to Disturbances in Energy Input
Authors: Fernandez-Gonzalez Nuria , Huber Julie A. , Vallino Joseph J.
Published: July 2016

Although microbial systems are well-suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20 day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function was used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appear inherently well-adapted to disturbances in energy input and that changes in community structure in both treatments are more dependent on internal dynamics than on external forcing. Results also show that the rare biosphere is critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, endogenous feedbacks were more important than exogenous drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics.

IMPORTANCE

Within the broader ecological context, biological communities are often viewed as stable and only experience succession or replacement when subject to external perturbations, such as changes in food availability or introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic ”unstable” communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating microbiomes in both host-associated and natural ecosystems.
Determination of the cationic distribution in oxidic thin films by resonant X-ray diffraction: the magnetoelectric compound Ga2−xFexO3
Authors: Lefevre Christophe , Thomasson Alexandre , Roulland Francois , Favre-Nicolin Vincent , Joly Yves , Wakabayashi Yusuke , Versini Gilles , Barre Sophie , Leuvrey Cedric , Demchenko Anna , Boudet Nathalie , Viart Nathalie
Published: July 2016

The cationic distribution is decisive for both the magnetic and electric properties of complex oxides. While it can be easily determined in bulk materials using classical methods such as X-ray or neutron diffraction, difficulties arise for thin films owing to the relatively small amount of material to probe. It is shown here that a full determination of the cationic site distribution in thin films is possible through an optimized processing of resonant elastic X-ray scattering experiments. The method is illustrated using gallium ferrite Ga2−xFexO3samples which have been the focus of an increasing number of studies this past decade. They indeed represent an alternative to the, to date, only room-temperature magnetoelectric compound BiFeO3. The methodology can be applied to determine the element distribution over the various crystallographic sites in any crystallized system.
Data systems for the Linac Coherent Light Source
Authors: Thayer J. , Damiani D. , Ford C. , Gaponenko I. , Kroeger W. , O'Grady C. , Pines J. , Tookey T. , Weaver M. , Perazzo A.
Published: July 2016

The data acquisition and data management systems for X-ray free-electron laser experiments at the Linac Coherent Light Source are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB s−1to the offline data storage, where experimental data and the relevant metadata are archived and made available for user analysis. A case study of a serial femtosecond crystallography pipeline is presented.
Collaboration in the consulting industry
Authors: Martensen Malte , Ryschka Stephanie , Blesik Till , Bick Markus
Published: July 2016

Purpose

– By studying the drivers of social collaboration the purpose of this paper is to describe how, and for what job-related purposes, social software is employed in the digital workplace. Focussing on consultants, who are considered to be part of a knowledge-intensive and innovative industry, factors that may influence the adoption of professional social software are explored. In addition, insights about socio-demographic differences as well as distinct consulting segments and use categories are provided.

Design/methodology/approach

– The Unified Theory of Acceptance and Use of Technologies (UTAUT) is the theoretical backbone of this research. The UTAUT model is expanded to fit the research goals, and the results from a quantitative study (n=341) are used to test the model.

Findings

– The results suggest that the adoption of social software is associated with the expectation that one’s work performance will improve. There are significant differences regarding age and gender in the use of social software for job-related purposes.

Practical implications

– Using the results of the study, social software suites can be tailored to users’ needs and preferences, which, in turn, may lead to higher levels of acceptance and intensity of use.

Originality/value

– Social software is already widely adopted for private purposes, and it is being used more and more within the digital workplace, too. However, little research has been conducted into how, and for what job-related purposes, social software is employed, or into the potential drivers for its adoption. The stakeholders in the research include scholars and practitioners alike.
Country of origin branding: an integrative perspective
Authors: Brodie Roderick J. , Benson-Rea Maureen
Published: July 2016

Purpose

A new conceptualization of the process of country of origin (COO) branding based on fresh theoretical foundations is developed. This paper aims to provide a strategic perspective that integrates extant views of COO branding, based on identity and image, with a relational perspective based on a process approach to developing collective brand meaning.

Design/methodology/approach

A systematic review of the literature on COO branding and geographical indicators is undertaken, together with a review of contemporary research on branding. Our framework conceptualizes COO branding as an integrating process that aligns a network of relationships to co-create collective meaning for the brand’s value propositions.

Findings

An illustrative case study provides empirical evidence to support the new theoretical framework.

Research limitations/implications

Issues for further research include exploring and refining the theoretical framework in other research contexts and investigating broader issues about how COO branding influences self and collective interests in business relationships and industry networks.

Practical implications

Adopting a broadened perspective of COO branding enables managers to understand how identity and image are integrated with their business relationships in the context of developing collective brand meaning. Providing a sustained strategic advantage for all network actors, an integrated COO branding process extends beyond developing a distinctive identity and image.

Originality/value

Accepted consumer, product, firm and place level perspectives of COO branding are challenged by developing and verifying a new integrated conceptualization of branding.
Turning inside out: perceived internal branding in customer-firm relationship building
Authors: Kang Doo Syen
Published: July 2016

Purpose

This paper aims to examine the strategic importance of perceived internal branding in building symbolic and behavioral relationships with a corporate in the service sector. Research on internal branding has been confined only to how internal staff understand brand values. Despite the importance of alignment between internal and external communication, little emphasis has been placed on consumers’ perception of how internal staff understand brand values. Even before experiencing service, consumers can shape their overall evaluation on service based on external communication about internal training and its congruence with brand values.

Design/methodology/approach

The theoretical model of cognitive, affective and behavioral responses is empirically tested using the structural equation modeling approach with a sample of 258 adults. Multiple group comparison is also conducted to identify the difference between user and non-user groups.

Findings

The findings indicate that perception of employees’ training and its congruence with external communication enables consumers to shape their cognitive and affective response toward a corporate, which is a source of future purchase intention. How consumers think about internal branding forms their attitudes and images of business and social conduct and enhances their behavioral intention.

Practical implications

The results imply that internal branding should not be limited to organizational communications but should be stretched into a critical topic for external communications. In particular, notable differences between user and non-user groups determined in the model provide further implications for corporate communication.

Originality/value

This paper stretches the concept of internal branding into the area of public interest. Theoretically, it tests a dual process model that suggests cognitive and affective antecedents in predicting consumer intention. Practically, it provides new ground for viewing internal affairs as part of a continuum of external communication and not a separate element of a corporation. The results are conducive to robust customer-firm relationship building in the service sector.
Stratified, precision or personalised medicine? Cancer services in the ‘real world’ of a London hospital
Authors: Day Sophie , Coombes R Charles , McGrath‐Lone Louise , Schoenborn Claudia , Ward Helen
Published: July 2016

We conducted ethnographic research in collaboration with a large, research‐intensive London breast cancer service in 2013–2014 so as to understand the practices and potential effects of stratified medicine. Stratified medicine is often seen as a synonym for both personalised and precision medicine but these three terms, we found, also related to distinct facets of treatment and care. Personalised medicine is the term adopted for the developing 2016 NHS England Strategy, in which breast cancer care is considered a prime example of improved biological precision and better patient outcomes. We asked how this biologically stratified medicine affected wider relations of care and treatment. We interviewed formally 33 patients and 23 of their carers, including healthcare workers; attended meetings associated with service improvements, medical decision‐making, public engagement, and scientific developments as well as following patients through waiting rooms, clinical consultations and other settings. We found that the translation of new protocols based on biological research introduced further complications into an already‐complex patient pathway. Combinations of new and historic forms of stratification had an impact on almost all patients, carers and staff, resulting in care that often felt less rather than more personal.
Optimal product variety in radio markets
Authors: Berry Steven , Eizenberg Alon , Waldfogel Joel
Published: July 2016

A vast theoretical literature explores inefficient market structures in free‐entry equilibria, and previous empirical work demonstrated that excessive entry may obtain in local radio markets. We extend that literature by relaxing the assumption that stations are symmetric, allowing for endogenous horizontal and (unobserved) vertical station differentiation. We find that, in most broadcasting formats, a social planner who takes into account the welfare of market participants eliminates 50%–60% of the observed stations. In 80%–94.9% of markets where high‐quality stations are observed, welfare could be unambiguously improved by converting one such station into low‐quality broadcasting, suggesting local overprovision of quality.
Optimal public funding for research: a theoretical analysis
Authors: De Fraja Gianni
Published: July 2016

This article studies how a government should distribute funds among research institutions and how it should allocate them to basic and applied research. Institutions differ in reputation and efficiency and have an information advantage. The government should award funding for basic research to induce the most productive institutions to carry out more applied research than they would like. Institutions with better reputation a do more research than otherwise identical ones, and applied research is inefficiently concentrated in the most efficient high‐reputation institutions. The article provides theoretical support for a dual‐channel funding mechanism but not for full economic costing.
Sporisorium scitamineum colonisation of sugarcane genotypes susceptible and resistant to smut revealed by GFP‐tagged strains
Authors: Carvalho G. , Quecine M.C. , Longatto D.P. , Peters L.P. , Almeida J.R. , Shyton T.G. , Silva M.M.L. , Crestana G.S. , Creste S. , Monteiro‐Vitorello C.B.
Published: July 2016

Sporisorium scitamineum is the causal agent of sugarcane smut disease. The fungus establishes a biotrophic interaction with sugarcane tissues, and unlike smut fungi of other monocot hosts, the primary meristem of sugarcane plants develops a whip‐like structure instead of a tumour‐like galls emerging from floral structures (tassels and ears). We examined (GFP)‐tagged S. scitamineum infecting tissues of three sugarcane genotypes with distinct responses to smut (susceptible, intermediate resistant and resistant). Mating compatible haploid cells gfp‐expressing were obtained by Agrobacterium tumefaciens‐mediated transformation (ATMT) using the integrative vector pFAT‐gfp. Regardless of the inoculation method (drop inoculation and hypodermal syringe inoculation), all genotypes were colonised by the fungus. GFP‐tagged strains of opposite mating reaction were able to: (a) grow in vitro as fluorescent yeast‐like cells; (b) generate infectious dikaryon; (c) penetrate sugarcane tissues; (d) colonise tissues by growing a filamentous network; and (e) form the characteristic highly branched hyphae within host cells. Fungal colonisation 160 DAI revealed an association of the fungus with vascular vessels disrupting their organisation in all three genotypes analysed. However, the resistant plants did not develop whips spanning the experiment time. The first whips emerged 76 DAI from plants of the susceptible genotype whereas for intermediate resistant plants whips were detected at 137 DAI. These whips were dissected and fluorescent sporogenesis and teliospore maturation were analysed. In vitro germination of recovered teliospores revealed after meiosis the formation of a three‐celled hyphal filament, where the fourth cell was likely maintained in the teliospore coat. These cells showed independent segregation of the gfp marker, as a result of gfp insertions in different chromosomes of each compatible haploid strain. This work presents the complete fungal life cycle of GFP‐marked S. scitamineum to study developmental stages in planta.
Seed treatment with salicylic acid invokes defence mechanism ofHelianthus annuusagainstOrobanche cumana
Authors: Yang C. , Hu L.Y. , Ali B. , Islam F. , Bai Q.J. , Yun X.P. , Yoneyama K. , Zhou W.J.
Published: July 2016

The root holoparasitic angiosperm sunflower broomrape (Orobanche cumana) specifically affects sunflower (Helianthus annuus) growth and causes severe damage all over the world. This investigation was designed to examine the protective effects of salicylic acid (SA) treatment to the seeds of anO. cumana‐susceptible cultivar of sunflower (TK0409). Sunflower seeds were pretreated with different concentrations (0, 0.5 and 1 mM) ofSAand inoculated withO. cumanafor 4 weeks.O. cumanainfection resulted in reduction in plant biomass, endogenousSAlevel, and the expression ofSA‐related genes includingpal,chsandNPR1. By contrast,O. cumanainfection enhanced the production of reactive oxygen species, activities of antioxidant enzymes as well as contents of phenolics and lignin. Seed treatment with 1 mMSAincreased sunflower biomass in terms of plant height, fresh weight and dry weight by 10%, 13% and 26%, respectively, via reducing the number and biomass of establishedO. cumana. The increase of hydrogen peroxide contents by 14% in the 1 mMSAtreated sunflower plants appeared to be because of the inhibition of ascorbate peroxidase and catalase by exogenousSA. The enhanced expression of pathogenesis‐related genes (PR3andPR12, encoding chitinase and defensin, respectively) after 4 weeks of inoculation indicated that systemic acquired resistance was induced in theSAtreated sunflower in which the level of endogenousSAwas also elevated in a dose‐dependent manner. The increased expression of a hypersensitive‐responsive (HR) genehsrindicated that the resistance of sunflowers might be associated with a hypersensitive reaction which was activated by exogenousSAtreatment.
Decreased Whole‐Body Fat Mass Produced by Chronic Alcohol Consumption is Associated with Activation of S6K1‐Mediated Protein Synthesis and Increased Autophagy in Epididymal White Adipose Tissue
Authors: Crowell Kristen T. , Steiner Jennifer L. , Coleman Catherine S. , Lang Charles H.
Published: July 2016

Background

Chronic alcohol consumption leads to a loss of white adipose tissue (WAT) but the underlying mechanisms for this lipodystrophy are not fully elucidated. This study tested the hypothesis that the reduction in WAT mass in chronic alcohol‐fed mice is associated with a decreased protein synthesis specifically related to impaired function of mammalian target of rapamycin (mTOR).

Methods

Adult male mice were provided an alcohol‐containing liquid diet for 24 weeks or an isonitrogenous isocaloric control diet. In vivo protein synthesis was determined at this time and thereafter epididymal WAT (eWAT) was excised for analysis of signal transduction pathways central to controling protein synthesis and degradation.

Results

While chronic alcohol feeding decreased whole‐body and eWAT mass, this was associated with a discordant increase in protein synthesis in eWAT. This increase was not associated with a change in mTOR, 4E‐BP1, Akt, or PRAS40 phosphorylation. Instead, a selective increase in phosphorylation of S6K1 and its downstream substrates, S6 and eIF4B was detected in alcohol‐fed mice. Alcohol also increased eEF2K phosphorylation and decreased eEF2 phosphorylation consistent with increased translation elongation. Alcohol increased Atg12‐5, LC3B‐I and ‐II, and ULK1 S555 phosphorylation, suggesting increased autophagy, while markers of apoptosis (cleaved caspase‐3 and ‐9, and PARP) were unchanged. Lipolytic enzymes (ATGL and HSL phosphorylation) were increased and lipogenic regulators (PPARγ and C/EBPα) were decreased in eWAT by alcohol. Although alcohol increased TNF‐α, IL‐6, and IL‐1β mRNA, no change in key components of the NLRP3 inflammasome (NLRP3, ACS, and cleaved caspase‐1) was detected suggesting alcohol did not increase pyroptosis. Plasma insulin did not differ between groups.

Conclusions

These results demonstrate that the alcohol‐induced decrease in whole‐body fat mass resulted in part from activation of autophagy in eWAT as protein synthesis was increased and mediated by the specific increase in the activity of S6K1.