bluuebunny/crossref_metadata_2025 huggingface dataset:
Antiquity's experience in adding an electronic element to a printed journal
Authors: Peachey Elizabeth , Chippindale Christopher
Published: November 2015

A conventional print publication, like ANTIQUITY has a choice in an electronic era: to remain print-only, to convert wholly to electronic format, or to find some hybrid or combination inbetween. ANTIQW has chosen to stay primarily in a print format (a conventional sewn paperback quarterly book) that is paid for by subscribers, and to develop alongside that a modest web presence that is free to anyone. Our circumstances are typical; so are both our uncertainty as to the future and the nature of our response so far. Very few publications – whether journals, magazines or newspapers – have left print to go fully electronic; many have a web presence, and those that have chosen to have none begin to appear as if they are thereby marginalizing themselves. This brief note reports why we tried, what we have done, how, and with what result.
Impact of methods used to express levels of circulating fatty acids on the degree and direction of associations with blood lipids in humans
Authors: Sergeant Susan , Ruczinski Ingo , Ivester Priscilla , Lee Tammy C. , Morgan Timothy M. , Nicklas Barbara J. , Mathias Rasika A. , Chilton Floyd H.
Published: November 2015

Numerous studies have examined relationships between disease biomarkers (such as blood lipids) and levels of circulating or cellular fatty acids. In such association studies, fatty acids have typically been expressed as the percentage of a particular fatty acid relative to the total fatty acids in a sample. Using two human cohorts, this study examined relationships between blood lipids (TAG, and LDL, HDL or total cholesterol) and circulating fatty acids expressed either as a percentage of total or as concentration in serum. The direction of the correlation between stearic acid, linoleic acid, dihomo-γ-linolenic acid, arachidonic acid and DHA and circulating TAG reversed when fatty acids were expressed as concentrationsv. a percentage of total. Similar reversals were observed for these fatty acids when examining their associations with the ratio of total cholesterol:HDL-cholesterol. This reversal pattern was replicated in serum samples from both human cohorts. The correlations between blood lipids and fatty acids expressed as a percentage of total could be mathematically modelled from the concentration data. These data reveal that the different methods of expressing fatty acids lead to dissimilar correlations between blood lipids and certain fatty acids. This study raises important questions about how such reversals in association patterns impact the interpretation of numerous association studies evaluating fatty acids and their relationships with disease biomarkers or risk.
Population genetic structure and migration patterns ofLiriomyza sativaein China: moderate subdivision and no Bridgehead effect revealed by microsatellites
Authors: Tang X.-T. , Ji Y. , Chang Y.-W. , Shen Y. , Tian Z.-H. , Gong W.-R. , Du Y.-Z.
Published: November 2015

WhileLiriomyza sativae(Diptera: Agromyzidae), an important invasive pest of ornamentals and vegetables has been found in China for the past two decades, few studies have focused on its genetics or route of invasive. In this study, we collected 288L. sativaeindividuals across 12 provinces to explore its population genetic structure and migration patterns in China using seven microsatellites. We found relatively low levels of genetic diversity but moderate population genetic structure (0.05 <FST< 0.15) inL. sativaefrom China. All populations deviated significantly from the Hardy–Weinberg equilibrium due to heterozygote deficiency. Molecular variance analysis revealed that more than 89% of variation was among samples within populations. A UPGMA dendrogram revealed that SH and GXNN populations formed one cluster separate from the other populations, which is in accordance with STRUCTURE and GENELAND analyses. A Mantel test indicated that genetic distance was not correlated to geographic distance (r= −0.0814,P= 0.7610), coupled with high levels of gene flow (M= 40.1–817.7), suggesting a possible anthropogenic influence on the spread ofL. sativaein China and on the effect of hosts. The trend of asymmetrical gene flow was from southern to northern populations in general and did not exhibit a Bridgehead effect during the course of invasion, as can be seen by the low genetic diversity of southern populations.
“Whatdunit?” Developmental changes in children's syntactically based sentence interpretation abilities and sensitivity to word order
Authors: MONTGOMERY JAMES W. , EVANS JULIA L. , GILLAM RONALD B. , SERGEEV ALEXANDER V. , FINNEY MIANISHA C.
Published: November 2015

Aim 1 of this study was to examine the developmental changes in typically developing English-speaking children's syntactically based sentence interpretation abilities and sensitivity to word order. Aim 2 was to determine the psychometric standing of the novel sentence interpretation task developed for this study, because we wish to use it later with children with specific language impairment. Children listened to semantically implausible sentences in which noun animacy and the natural affordance between the nouns were removed, thus controlling for event probability. Using this novel “whatdunit?” agent selection task, 256 children 7–11 years old listened to two structures with canonical word order and two with noncanonical word order. After each sentence, children selected as quickly as possible the picture of the noun they believed was “doing the action.” Children interpreted sentences with canonical word order with greater accuracy and speed than those with noncanonical word order. Older children (mean age = 10 years, 8 months) were more accurate and faster than younger children (mean age = 8 years, 1 month) across all sentence forms. Both older and younger children demonstrated similar error patterns across sentence type. The “whatdunit?” task also proved to have strong validity and reliability, making it suitable for studies with children with specific language impairment.
Perth punk and the construction of urbanity in a suburban city
Authors: Trainer Adam
Published: November 2015

As a musical form, punk is often associated with urbanity, as embodied in the scenes in both London and New York, and in an Australian national context by the scenes in Melbourne and Sydney. In Perth, Western Australia – a primarily middle-class suburban city without a distinct inner city – punk was expressed differently. While the music itself exemplified many of the stylistic traits associated with the genre, punk in Perth was articulated through the city's isolation, its affluence and its suburban nature. Utilising interviews with key players in the Perth punk scene of the late 1970s, this paper seeks to illustrate the ways in which urbanity was constructed and voiced through Perth punk, in a city that constructed itself in opposition to traditional notions of the inner city's urban lived environment.
Monitoring snow and ice surfaces on King George Island, Antarctic Peninsula, with high-resolution TerraSAR-X time series
Authors: Falk U. , Gieseke H. , Kotzur F. , Braun M.
Published: November 2015

Changes of glaciers and snow cover in polar regions affect a wide range of physical and ecosystem processes on land and in the adjacent marine environment. In this study, we investigated the potential of 11-day repeat high-resolution satellite image time series from the TerraSAR-X mission to derive glaciological and hydrological parameters on King George Island, Antarctica, between 25 October 2010 and 19 April 2011. The spatial pattern and temporal evolution of snow cover extent on ice-free areas can be monitored using multi-temporal coherence images. Synthetic aperture radar (SAR) coherence is used to map glacier extent of land-terminating glaciers with an average accuracy of 25 m. Multi-temporal SAR colour composites identify the position of the late summer snow line at ~220 m a.s.l. Glacier surface velocities are obtained from intensity feature-tracking. Surface velocities near the calving front of Fourcade Glacier were up to 1.8±0.01 m d-1. Using an intercept theorem based on fundamental geometric principles together with differential GPS field measurements, the ice discharge of Fourcade Glacier was estimated at 20 700±5500 m3d-1(corresponding to ~19±5 kt d-1). The rapidly changing surface conditions on King George Island and the lack of high-resolution digital elevation models for the region remain restrictions for the applicability of SAR data and the precision of derived products. Supplemental data are available athttp://dx.doi.org/10.1594/PANGAEA.853954.
On the Assessment of Paramedic Competence: A Narrative Review with Practice Implications
Authors: Tavares W. , Boet S.
Published: November 2015

Introduction

Paramedicine is experiencing significant growth in scope of practice, autonomy, and role in the health care system. Despite clinical governance models, the degree to which paramedicine ultimately can be safe and effective will be dependent on the individuals the profession deems suited to practice. This creates an imperative for those responsible for these decisions to ensure that assessments of paramedic competence are indeed accurate, trustworthy, and defensible.

Purpose

The purpose of this study was to explore and synthesize relevant theoretical foundations and literature informing best practices in performance-based assessment (PBA) of competence, as it might be applied to paramedicine, for design or evaluation of assessment programs.

Methods

A narrative review methodology was applied to focus intentionally, but broadly, on purpose relevant, theoretically derived research that could inform assessment protocols in paramedicine. Primary and secondary studies from a number of health professions that contributed to and informed best practices related to the assessment of paramedic clinical competence were included and synthesized.

Results

Multiple conceptual frameworks, psychometric requirements, and emerging lines of research are forwarded. Seventeen practice implications are derived to promote understanding as well as best practices and evaluation criteria for educators, employers, and/or licensing/certifying bodies when considering the assessment of paramedic competence.

Conclusions

The assessment of paramedic competence is a complex process requiring an understanding, appreciation for, and integration of conceptual and psychometric principles. The field of PBA is advancing rapidly with numerous opportunities for research.

TavaresW,BoetS.On the assessment of paramedic competence: a narrative review with practice implications.Prehosp Disaster Med.2016;31(1):64–73.
Quantum-enabled temporal and spectral mode conversion of microwave signals
Authors: Andrews R. W. , Reed A. P. , Cicak K. , Teufel J. D. , Lehnert K. W.
Published: November 2015

Electromagnetic waves are ideal candidates for transmitting information in a quantum network as they can be routed rapidly and efficiently between locations using optical fibres or microwave cables. Yet linking quantum-enabled devices with cables has proved difficult because most cavity or circuit quantum electrodynamics systems used in quantum information processing can only absorb and emit signals with a specific frequency and temporal envelope. Here we show that the temporal and spectral content of microwave-frequency electromagnetic signals can be arbitrarily manipulated with a flexible aluminium drumhead embedded in a microwave circuit. The aluminium drumhead simultaneously forms a mechanical oscillator and a tunable capacitor. This device offers a way to build quantum microwave networks using separate and otherwise mismatched components. Furthermore, it will enable the preparation of non-classical states of motion by capturing non-classical microwave signals prepared by the most coherent circuit quantum electrodynamics systems.
Exploring the phase diagram of the two-impurity Kondo problem
Authors: Spinelli A. , Gerrits M. , Toskovic R. , Bryant B. , Ternes M. , Otte A. F.
Published: November 2015

A system of two exchange-coupled Kondo impurities in a magnetic field gives rise to a rich phase space hosting a multitude of correlated phenomena. Magnetic atoms on surfaces probed through scanning tunnelling microscopy provide an excellent platform to investigate coupled impurities, but typical high Kondo temperatures prevent field-dependent studies from being performed, rendering large parts of the phase space inaccessible. We present a study of pairs of Co atoms on insulating Cu2N/Cu(100), which each have a Kondo temperature of only 2.6 K. The pairs are designed to have interaction strengths similar to the Kondo temperature. By applying a sufficiently strong magnetic field, we are able to access a new phase in which the two coupled impurities are simultaneously screened. Comparison of differential conductance spectra taken on the atoms to simulated curves, calculated using a third-order transport model, allows us to independently determine the degree of Kondo screening in each phase.
Multiple region whole-exome sequencing reveals dramatically evolving intratumor genomic heterogeneity in esophageal squamous cell carcinoma
Authors: Cao W , Wu W , Yan M , Tian F , Ma C , Zhang Q , Li X , Han P , Liu Z , Gu J , Biddle F G
Published: November 2015

Cancer is a disease of genome instability and genomic alterations; now, genomic heterogeneity is rapidly emerging as a defining feature of cancer, both within and between tumors. Motivation for our pilot study of tumor heterogeneity in esophageal squamous cell carcinoma (ESCC) is that it is not well studied, but the highest incidences of esophageal cancers are found in China and ESCC is the most common type. We profiled the mutations and changes in copy number that were identified by whole-exome sequencing and array-based comparative genomic hybridization in multiple regions within an ESCC from two patients. The average mutational heterogeneity rate was 90% in all regions of the individual tumors in each patient; most somatic point mutations were nonsynonymous substitutions, small Indels occurred in untranslated regions of genes, and copy number alterations varied among multiple regions of a tumor. Independent Sanger sequencing technology confirmed selected gene mutations with more than 88% concordance. Phylogenetic analysis of the somatic mutation frequency demonstrated that multiple, genomically heterogeneous divergent clones evolve and co-exist within a primary ESCC and metastatic subclones result from the dispersal and adaptation of an initially non-metastatic parental clone. Therefore, a single-region sampling will not reflect the evolving architecture of a genomically heterogeneous landscape of mutations in ESCC tumors and the divergent complexity of this genomic heterogeneity among patients will complicate any promise of a simple genetic or epigenetic diagnostic signature in ESCC. We conclude that any potential for informative biomarker discovery in ESCC and targeted personalized therapies will require a deeper understanding of the functional biology of the ontogeny and phylogeny of the tumor heterogeneity.
Long-period ocean-bottom motions in the source areas of large subduction earthquakes
Authors: Nakamura Takeshi , Takenaka Hiroshi , Okamoto Taro , Ohori Michihiro , Tsuboi Seiji
Published: November 2015

Long-period ground motions in plain and basin areas on land can cause large-scale, severe damage to structures and buildings and have been widely investigated for disaster prevention and mitigation. However, such motions in ocean-bottom areas are poorly studied because of their relative insignificance in uninhabited areas and the lack of ocean-bottom strong-motion data. Here, we report on evidence for the development of long-period (10–20 s) motions using deep ocean-bottom data. The waveforms and spectrograms demonstrate prolonged and amplified motions that are inconsistent with attenuation patterns of ground motions on land. Simulated waveforms reproducing observed ocean-bottom data demonstrate substantial contributions of thick low-velocity sediment layers to development of these motions. This development, which could affect magnitude estimates and finite fault slip modelling because of its critical period ranges on their estimations, may be common in the source areas of subduction earthquakes where thick, low-velocity sediment layers are present.
Lowering N2O emissions from soils using eucalypt biochar: the importance of redox reactions
Authors: Quin P , Joseph S , Husson O , Donne S , Mitchell D , Munroe P , Phelan D , Cowie A , Van Zwieten L
Published: November 2015

Agricultural soils are the primary anthropogenic source of atmospheric nitrous oxide (N2O), contributing to global warming and depletion of stratospheric ozone. Biochar addition has shown potential to lower soil N2O emission, with the mechanisms remaining unclear. We incubated eucalypt biochar (550 °C) – 0, 1 and 5% (w/w) in Ferralsol at 3 water regimes (12, 39 and 54% WFPS) – in a soil column, following gamma irradiation. After N2O was injected at the base of the soil column, in the 0% biochar control 100% of expected injected N2O was released into headspace, declining to 67% in the 5% amendment. In a 100% biochar column at 6% WFPS, only 16% of the expected N2O was observed. X-ray photoelectron spectroscopy identified changes in surface functional groups suggesting interactions between N2O and the biochar surfaces. We have shown increases in -O-C = N /pyridine pyrrole/NH3, suggesting reactions between N2O and the carbon (C) matrix upon exposure to N2O. With increasing rates of biochar application, higher pH adjusted redox potentials were observed at the lower water contents. Evidence suggests that biochar has taken part in redox reactions reducing N2O to dinitrogen (N2), in addition to adsorption of N2O.
The glassy random laser: replica symmetry breaking in the intensity fluctuations of emission spectra
Authors: Antenucci Fabrizio , Crisanti Andrea , Leuzzi Luca
Published: November 2015

The behavior of a newly introduced overlap parameter, measuring the correlation between intensity fluctuations of waves in random media, is analyzed in different physical regimes, with varying amount of disorder and non-linearity. This order parameter allows to identify the laser transition in random media and describes its possible glassy nature in terms of emission spectra data, the only data so far accessible in random laser measurements. The theoretical analysis is performed in terms of the complex spherical spin-glass model, a statistical mechanical model describing the onset and the behavior of random lasers in open cavities. Replica Symmetry Breaking theory allows to discern different kinds of randomness in the high pumping regime, including the most complex and intriguing glassy randomness. The outcome of the theoretical study is, eventually, compared to recent intensity fluctuation overlap measurements demonstrating the validity of the theory and providing a straightforward interpretation of qualitatively different spectral behaviors in different random lasers.
P311 promotes renal fibrosis via TGFβ1/Smad signaling
Authors: Yao Zhihui , Yang Sisi , He Weifeng , Li Lian , Xu Rui , Zhang Xiaorong , Li Haisheng , Zhan Rixing , Sun Wei , Tan Jianglin , Zhou Junyi , Luo Gaoxing , Wu Jun
Published: November 2015

P311, a gene that was identified in 1993, has been found to have diverse biological functions in processes such as cell proliferation, migration and differentiation. However, its role in fibrosis is unknown. We previously observed that P311 is highly expressed in skin hypertrophic scars. In this study, P311 over-expression was detected in a subset of tubular epithelial cells in clinical biopsy specimens of renal fibrosis; this over-expression, was found concurrent with α-smooth muscle actin (α-SMA) and transforming growth factor beta1 (TGFβ1) expression. Subsequently, these results were verified in a mouse experimental renal fibrosis model induced by unilateral ureteral obstruction. The interstitial deposition of collagen, α-SMA and TGF-β1 expression and macrophage infiltration were dramatically decreased when P311 was knocked out. Moreover, TGFβ/Smad signaling had a critical effect on the promotion of renal fibrosis by P311. In conclusion, this study demonstrate that P311 plays a key role in renal fibrosis via TGFβ1/Smad signaling, which could be a novel target for the management of renal fibrosis.
Compact Shielding of Graphene Monolayer Leads to Extraordinary SERS-Active Substrate with Large-Area Uniformity and Long-Term Stability
Authors: Liu Xiangjiang , Wang Jiajun , Wu Yichen , Fan Tianren , Xu Yang , Tang Longhua , Ying Yibin
Published: November 2015

Surface-enhanced Raman scattering (SERS) can significantly boost the inherently weak Raman scattering signal and provide detailed structural information and binding nature of the molecules on the surface. Despite the long history of this technology, SERS has yet to become a sophisticated analytical tool in practical applications. A major obstacle is the absence of high-quality and stable SERS-active substrate. In this work, we report a monolayer graphene-shielded periodic metallic nanostructure as large-area uniform and long-term stable SERS substrate. The monolayer graphene acting as a corrosion barrier, not only greatly enhanced stability, but also endowed many new features to the substrate, such as alleviating the photo-induced damages and improving the detection sensitivity for certain analytes that are weakly adsorbed on the conventional metallic substrates. Besides, our fabrication strategy were also capable of fabricating the reproducible SERS sensing spots array, which may serve as a promising high-throughput or multi-analyte sensing platform. Taken together, the graphene-shielded SERS substrate holds great promise both in fundamental studies of the SERS effect and many practical fields.
Impacts of IOD, ENSO and ENSO Modoki on the Australian Winter Wheat Yields in Recent Decades
Authors: Yuan Chaoxia , Yamagata Toshio
Published: November 2015

Impacts of the Indian Ocean Dipole (IOD), two different types of El Niño/Southern Oscillation (ENSO): canonical ENSO and ENSO Modoki, on the year-to-year winter wheat yield variations in Australia have been investigated. It is found that IOD plays a dominant role in the recent three decades; the wheat yield is reduced (increased) by −28.4% (12.8%) in the positive (negative) IOD years. Although the canonical ENSO appears to be responsible for the wheat yield variations, its influences are largely counted by IOD owing to their frequent co-occurrence. In contrast, the ENSO Modoki may have its distinct impacts on the wheat yield variations, but they are much smaller compared to those of IOD. Both the observed April-May and the predicted September-November IOD indices by the SINTEX-F ocean-atmosphere coupled model initialized on April 1st just before the sowing season explain ~15% of the observed year-to-year wheat yield variances. The present study may lead to a possible scheme for predicting wheat yield variations in Australia in advance by use of simple climate mode indices.
Human Granulocyte Macrophage Colony-Stimulating Factor Enhances Antibiotic Susceptibility of Pseudomonas aeruginosa Persister Cells
Authors: Choudhary Geetika S. , Yao Xiangyu , Wang Jing , Peng Bo , Bader Rebecca A. , Ren Dacheng
Published: November 2015

Bacterial persister cells are highly tolerant to antibiotics and cause chronic infections. However, little is known about the interaction between host immune systems with this subpopulation of metabolically inactive cells and direct effects of host immune factors (in the absence of immune cells) on persister cells have not been studied. Here we report that human granulocyte macrophage-colony stimulating factor (GM-CSF) can sensitize the persister cells of Pseudomonas aeruginosa PAO1 and PDO300 to multiple antibiotics including ciprofloxacin, tobramycin, tetracycline and gentamicin. GM-CSF also sensitized the biofilm cells of P. aeruginosa PAO1 and PDO300 to tobramycin in the presence of biofilm matrix degrading enzymes. The DNA microarray and qPCR results indicated that GM-CSF induced the genes for flagellar motility and pyocin production in the persister cells, but not the normal cells of P. aeruginosa PAO1. Consistently, the supernatants from GM-CSF treated P. aeruginosa PAO1 persister cell suspensions were found cidal to the pyocin sensitive strain P. aeruginosa PAK. Collectively, these findings suggest that host immune factors and bacterial persisters may directly interact, leading to enhanced susceptibility of persister cells to antibiotics.
Isolation of exosomes by differential centrifugation: Theoretical analysis of a commonly used protocol
Authors: Livshits Mikhail A. , Khomyakova Elena , Evtushenko Evgeniy G. , Lazarev Vassili N. , Kulemin Nikolay A. , Semina Svetlana E. , Generozov Edward V. , Govorun Vadim M.
Published: November 2015

Exosomes, small (40–100 nm) extracellular membranous vesicles, attract enormous research interest because they are carriers of disease markers and a prospective delivery system for therapeutic agents. Differential centrifugation, the prevalent method of exosome isolation, frequently produces dissimilar and improper results because of the faulty practice of using a common centrifugation protocol with different rotors. Moreover, as recommended by suppliers, adjusting the centrifugation duration according to rotor K-factors does not work for “fixed-angle” rotors. For both types of rotors – “swinging bucket” and “fixed-angle” – we express the theoretically expected proportion of pelleted vesicles of a given size and the “cut-off” size of completely sedimented vesicles as dependent on the centrifugation force and duration and the sedimentation path-lengths. The proper centrifugation conditions can be selected using relatively simple theoretical estimates of the “cut-off” sizes of vesicles. Experimental verification on exosomes isolated from HT29 cell culture supernatant confirmed the main theoretical statements. Measured by the nanoparticle tracking analysis (NTA) technique, the concentration and size distribution of the vesicles after centrifugation agree with those theoretically expected. To simplify this “cut-off”-size-based adjustment of centrifugation protocol for any rotor, we developed a web-calculator.
Local structure of human hair spatially resolved by sub-micron X-ray beam
Authors: Stanić Vesna , Bettini Jefferson , Montoro Fabiano Emmanuel , Stein Aaron , Evans-Lutterodt Kenneth
Published: November 2015

Human hair has three main regions, the medulla, the cortex and the cuticle. An existing model for the cortex suggests that the α-keratin- based intermediate filaments (IFs) align with the hair’s axis, but are orientationally disordered in-plane. We found that there is a new region in the cortex near the cuticle’s boundary in which the IFs are aligned with the hair’s axis, but additionally, they are orientationally ordered in-plane due to the presence of the cuticle/hair boundary. Further into the cortex, the IF arrangement becomes disordered, eventually losing all in-plane orientation. We also find that in the cuticle, a key diffraction feature is absent, indicating the presence of the β-keratin rather than that of the α-keratin phase. This is direct structural evidence that the cuticle contains β-keratin sheets. This work highlights the importance of using a sub-micron x-ray beam to unravel the structures of poorly ordered, multi-phase systems.
Confirmation of co-denitrification in grazed grassland
Authors: Selbie Diana R. , Lanigan Gary J. , Laughlin Ronald J. , Di Hong J. , Moir James L. , Cameron Keith C. , Clough Tim J. , Watson Catherine J. , Grant James , Somers Cathal , Richards Karl G.
Published: November 2015

Pasture-based livestock systems are often associated with losses of reactive forms of nitrogen (N) to the environment. Research has focused on losses to air and water due to the health, economic and environmental impacts of reactive N. Di-nitrogen (N2) emissions are still poorly characterized, both in terms of the processes involved and their magnitude, due to financial and methodological constraints. Relatively few studies have focused on quantifying N2 losses in vivo and fewer still have examined the relative contribution of the different N2 emission processes, particularly in grazed pastures. We used a combination of a high 15N isotopic enrichment of applied N with a high precision of determination of 15N isotopic enrichment by isotope-ratio mass spectrometry to measure N2 emissions in the field. We report that 55.8 g N m−2 (95%, CI 38 to 77 g m−2) was emitted as N2 by the process of co-denitrification in pastoral soils over 123 days following urine deposition (100 g N m−2), compared to only 1.1 g N m−2 (0.4 to 2.8 g m−2) from denitrification. This study provides strong evidence for co-denitrification as a major N2 production pathway, which has significant implications for understanding the N budgets of pastoral ecosystems.
Electric-field-assisted formation of an interfacial double-donor molecule in silicon nano-transistors
Authors: Samanta Arup , Moraru Daniel , Mizuno Takeshi , Tabe Michiharu
Published: November 2015

Control of coupling of dopant atoms in silicon nanostructures is a fundamental challenge for dopant-based applications. However, it is difficult to find systems of only a few dopants that can be directly addressed and, therefore, experimental demonstration has not yet been obtained. In this work, we identify pairs of donor atoms in the nano-channel of a silicon field-effect transistor and demonstrate merging of the donor-induced potential wells at the interface by applying vertical electric field. This system can be described as an interfacial double-donor molecule. Single-electron tunneling current is used to probe the modification of the potential well. When merging occurs at the interface, the gate capacitance of the potential well suddenly increases, leading to an abrupt shift of the tunneling current peak to lower gate voltages. This is due to the decrease of the system’s charging energy, as confirmed by Coulomb blockade simulations. These results represent the first experimental observation of electric-field-assisted formation of an interfacial double-donor molecule, opening a pathway for designing functional devices using multiple coupled dopant atoms.
Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta)
Authors: Shao Renfu , Barker Stephen C , Li Hu , Song Simon , Poudel Shreekanta , Su Yuan
Published: November 2015

Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9–20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis – the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5–4.2 kb in size and has 2–6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago.
Dopant morphology as the factor limiting graphene conductivity
Authors: Hofmann Mario , Hsieh Ya-Ping , Chang Kai-Wen , Tsai He-Guang , Chen Tzung-Te
Published: November 2015

Graphene’s low intrinsic carrier concentration necessitates extrinsic doping to enhance its conductivity and improve its performance for application as electrodes or transparent conductors. Despite this importance limited knowledge of the doping process at application-relevant conditions exists. Employing in-situ carrier transport and Raman characterization of different dopants, we here explore the fundamental mechanisms limiting the effectiveness of doping at different doping levels. Three distinct transport regimes for increasing dopant concentration could be identified. First the agglomeration of dopants into clusters provides a route to increase the graphene conductivity through formation of ordered scatterers. As the cluster grows, the charge transfer efficiency between graphene and additional dopants decreases due to emerging polarization effects. Finally, large dopant clusters hinder the carrier motion and cause percolative transport that leads to an unexpected change of the Hall effect. The presented results help identifying the range of beneficial doping density and guide the choice of suitable dopants for graphene’s future applications.
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement
Authors: De Vega Jose J. , Ayling Sarah , Hegarty Matthew , Kudrna Dave , Goicoechea Jose L. , Ergon Åshild , Rognli Odd A. , Jones Charlotte , Swain Martin , Geurts Rene , Lang Chunting , Mayer Klaus F. X. , Rössner Stephan , Yates Steven , Webb Kathleen J. , Donnison Iain S. , Oldroyd Giles E. D. , Wing Rod A. , Caccamo Mario , Powell Wayne , Abberton Michael T. , Skøt Leif
Published: November 2015

Red clover (Trifolium pratense L.) is a globally significant forage legume in pastoral livestock farming systems. It is an attractive component of grassland farming, because of its high yield and protein content, nutritional value and ability to fix atmospheric nitrogen. Enhancing its role further in sustainable agriculture requires genetic improvement of persistency, disease resistance and tolerance to grazing. To help address these challenges, we have assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. Genotyping by sequencing of a synthetic population of 86 genotypes show that the number of markers required for genomics-based breeding approaches is tractable, making red clover a suitable candidate for association studies and genomic selection.
Electrospun interconnected Fe-N/C nanofiber networks as efficient electrocatalysts for oxygen reduction reaction in acidic media
Authors: Wu Nan , Wang Yingde , Lei Yongpeng , Wang Bing , Han Cheng , Gou Yanzi , Shi Qi , Fang Dong
Published: November 2015

One-dimensional electrospun nanofibers have emerged as a potential candidate for high-performance oxygen reduction reaction (ORR) catalysts. However, contact resistance among the neighbouring nanofibers hinders the electron transport. Here, we report the preparation of interconnected Fe-N/C nanofiber networks (Fe-N/C NNs) with low electrical resistanceviaelectrospinning followed by maturing and pyrolysis. The Fe-N/C NNs show excellent ORR activity with onset and half-wave potential of 55 and 108 mV less than those of Pt/C catalyst in 0.5 M H2SO4. Intriguingly, the resulting Fe-N/C NNs exhibit 34% higher peak current density and superior durability than generic Fe-N/C ones with similar microstructure and chemical compositions. Additionally, it also displays much better durability and methanol tolerance than Pt/C catalyst. The higher electroactivity is mainly due to the more effective electron transport between the interconnected nanofibers. Thus, our findings provide a novel insight into the design of functional electrospun nanofibers for the application in energy storage and conversion fields.
Environmentally friendly method to grow wide-bandgap semiconductor aluminum nitride crystals: Elementary source vapor phase epitaxy
Authors: Wu PeiTsen , Funato Mitsuru , Kawakami Yoichi
Published: November 2015

Aluminum nitride (AlN) has attracted increasing interest as an optoelectronic material in the deep ultraviolet spectral range due to its wide bandgap of 6.0 eV (207 nm wavelength) at room temperature. Because AlN bulk single crystals are ideal device substrates for such applications, the crystal growth of bulky AlN has been extensively studied. Two growth methods seem especially promising: hydride vapor phase epitaxy (HVPE) and sublimation. However, the former requires hazardous gases such as hydrochloric acid and ammonia, while the latter needs extremely high growth temperatures around 2000 °C. Herein we propose a novel vapor-phase-epitaxy-based growth method for AlN that does not use toxic materials; the source precursors are elementary aluminum and nitrogen gas. To prepare our AlN, we constructed a new growth apparatus, which realizes growth of AlN single crystals at a rate of ~18 μm/h at 1550 °C using argon as the source transfer via the simple reaction Al + 1/2N2 → AlN. This growth rate is comparable to that by HVPE and the growth temperature is much lower than that in sublimation. Thus, this study opens up a novel route to achieve environmentally friendly growth of AlN.
Therapeutic effect of baicalin on experimental autoimmune encephalomyelitis is mediated by SOCS3 regulatory pathway
Authors: Zhang Yuan , Li Xing , Ciric Bogoljub , Ma Cun-Gen , Gran Bruno , Rostami Abdolmohamad , Zhang Guang-Xian
Published: November 2015

Natural compounds derived from medicinal plants have long been considered a rich source of novel therapeutic agents. Baicalin (Ba) is a bioactive flavonoid compound derived from the root of Scutellaria baicalensis, an herb widely used in traditional medicine for the treatment of various inflammatory diseases. In this study, we investigate the effects and mechanism of action of Ba in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). Ba treatment effectively ameliorated clinical disease severity in myelin oligodendrocyte glycoprotein (MOG)35–55 peptide-induced EAE and reduced inflammation and demyelination of the central nervous system (CNS). Ba reduced infiltration of immune cells into the CNS, inhibited expression of proinflammatory molecules and chemokines and prevented Th1 and Th17 cell differentiation via STAT/NFκB signaling pathways. Further, we showed that SOCS3 induction is essential to the effects of Ba, given that the inhibitory effect of Ba on pathogenic Th17 responses was largely abolished when SOCS3 signaling was knocked down. Taken together, our findings demonstrate that Ba has significant potential as a novel anti-inflammatory agent for therapy of autoimmune diseases such as MS.
Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway
Authors: Yang Mingyi , Lin Xiaolin , Rowe Alexander , Rognes Torbjørn , Eide Lars , Bjørås Magnar
Published: November 2015

The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3), antioxidant genes (PRDX4, PTGS1 and CYGB) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and RPRM) and apoptosis (i.e. CytC and CASP9). We demonstrated that OXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress and increase protein expression of the apoptosis initiator protease CASP9. In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.
Compact Optical Fiber 3D Shape Sensor Based on a Pair of Orthogonal Tilted Fiber Bragg Gratings
Authors: Feng Dingyi , Zhou Wenjun , Qiao Xueguang , Albert Jacques
Published: November 2015

In this work, a compact fiber-optic 3D shape sensor consisting of two serially connected 2° tilted fiber Bragg gratings (TFBGs) is proposed, where the orientations of the grating planes of the two TFBGs are orthogonal. The measurement of the reflective transmission spectrum from the pair of TFBGs was implemented by Fresnel reflection of the cleaved fiber end. The two groups of cladding mode resonances in the reflection spectrum respond differentially to bending, which allows for the unique determination of the magnitude and orientation of the bend plane (i.e. with a ± 180 degree uncertainty). Bending responses ranging from −0.33 to + 0.21 dB/m−1 (depending on orientation) are experimentally demonstrated with bending from 0 to 3.03 m−1. In the third (axial) direction, the strain is obtained directly by the shift of the TFBG Bragg wavelengths with a sensitivity of 1.06 pm/με.
Observed deep energetic eddies by seamount wake
Authors: Chen Gengxin , Wang Dongxiao , Dong Changming , Zu Tingting , Xue Huijie , Shu Yeqiang , Chu Xiaoqing , Qi Yiquan , Chen Hui
Published: November 2015

Despite numerous surface eddies are observed in the ocean, deep eddies (a type of eddies which have no footprints at the sea surface) are much less reported in the literature due to the scarcity of their observation. In this letter, from recently collected current and temperature data by mooring arrays, a deep energetic and baroclinic eddy is detected in the northwestern South China Sea (SCS) with its intensity, size, polarity and structure being characterized. It remarkably deepens isotherm at deep layers by the amplitude of ~120 m and induces a maximal velocity amplitude about 0.18 m/s, which is far larger than the median velocity (0.02 m/s). The deep eddy is generated in a wake when a steering flow in the upper layer passes a seamount, induced by a surface cyclonic eddy. More observations suggest that the deep eddy should not be an episode in the area. Deep eddies significantly increase the velocity intensity and enhance the mixing in the deep ocean, also have potential implication for deep-sea sediments transport.
Drug target prioritization by perturbed gene expression and network information
Authors: Isik Zerrin , Baldow Christoph , Cannistraci Carlo Vittorio , Schroeder Michael
Published: November 2015

Drugs bind to their target proteins, which interact with downstream effectors and ultimately perturb the transcriptome of a cancer cell. These perturbations reveal information about their source, i.e., drugs’ targets. Here, we investigate whether these perturbations and protein interaction networks can uncover drug targets and key pathways. We performed the first systematic analysis of over 500 drugs from the Connectivity Map. First, we show that the gene expression of drug targets is usually not significantly affected by the drug perturbation. Hence, expression changes after drug treatment on their own are not sufficient to identify drug targets. However, ranking of candidate drug targets by network topological measures prioritizes the targets. We introduce a novel measure, local radiality, which combines perturbed genes and functional interaction network information. The new measure outperforms other methods in target prioritization and proposes cancer-specific pathways from drugs to affected genes for the first time. Local radiality identifies more diverse targets with fewer neighbors and possibly less side effects.
Migratory Restlessness and the Role of Androgen for Increasing Behavioral Drive in the Spawning Migration of the Japanese eel
Authors: Sudo Ryusuke , Tsukamoto Katsumi
Published: November 2015

Migratory restlessness refers to a type of locomotor activity observed just before the onset of a migration. This behavior is primarily known in birds, where it is considered to be an indicator of the urge for migration. In contrast, little is known about migratory restlessness in fishes. To confirm migratory restlessness in a fish, we measured the locomotor activity of the Japanese eel, Anguilla japonica during its migration season. Migratory-phase silver eels showed higher locomotor activity in aquaria than yellow eels at the non-migratiory growth-phase. Silver eels stayed outside of their shelters for longer durations in dark periods than yellow eels and were active even in light periods when yellow eels were inactive in the shelters. Silver eels had higher levels of the androgen hormone 11-ketotestosterone at the end of experiment than yellow eels. Administration of 11-ketotesosterone to yellow eels induced higher levels of locomotor activity than that observed in non-treated controls. These findings suggest that anguillid eels exhibit migratory restlessness just before their spawning migration and that 11-ketotestosterone may be involved in the onset of this behavior.
In situ fabrication of high-performance Ni-GDC-nanocube core-shell anode for low-temperature solid-oxide fuel cells
Authors: Yamamoto Kazuhiro , Qiu Nan , Ohara Satoshi
Published: November 2015

A core–shell anode consisting of nickel–gadolinium-doped-ceria (Ni–GDC) nanocubes was directly fabricated by a chemical process in a solution containing a nickel source and GDC nanocubes covered with highly reactive {001} facets. The cermet anode effectively generated a Ni metal framework even at 500 °C with the growth of the Ni spheres. Anode fabrication at such a low temperature without any sintering could insert a finely nanostructured layer close to the interface between the electrolyte and the anode. The maximum power density of the attractive anode was 97 mW cm–2, which is higher than that of a conventional NiO–GDC anode prepared by an aerosol process at 55 mW cm–2 and 600 °C, followed by sintering at 1300 °C. Furthermore, the macro- and microstructure of the Ni–GDC-nanocube anode were preserved before and after the power-generation test at 700 °C. Especially, the reactive {001} facets were stabled even after generation test, which served to reduce the activation energy for fuel oxidation successfully.
Genome-wide expression analysis offers new insights into the origin and evolution of Physcomitrella patens stress response
Authors: Khraiwesh Basel , Qudeimat Enas , Thimma Manjula , Chaiboonchoe Amphun , Jijakli Kenan , Alzahmi Amnah , Arnoux Marc , Salehi-Ashtiani Kourosh
Published: November 2015

Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a key evolutionary position bridging the gap between green algae and higher plants and because it exhibits a well-developed stress tolerance, it is an excellent model for such exploration. Here, we have used Physcomitrella patens to study genome-wide responses to abiotic stress through transcriptomic analysis by a high-throughput sequencing platform. We report a comprehensive analysis of transcriptome dynamics, defining profiles of elicited gene regulation responses to abiotic stress-associated hormone Abscisic Acid (ABA), cold, drought and salt treatments. We identified more than 20,000 genes expressed under each aforementioned stress treatments, of which 9,668 display differential expression in response to stress. The comparison of Physcomitrella patens stress regulated genes with unicellular algae, vascular and flowering plants revealed genomic delineation concomitant with the evolutionary movement to land, including a general gene family complexity and loss of genes associated with different functional groups.