bluuebunny/crossref_metadata_2025 huggingface dataset:
Graphene oxide hole transport layers for large area, high efficiency organic solar cells
Authors: Smith Chris T. G. , Rhodes Rhys W. , Beliatis Michail J. , Imalka Jayawardena K. D. G. , Rozanski Lynn J. , Mills Christopher A. , P. Silva S. Ravi
Published: August 2014

Graphene oxide (GO) is becoming increasingly popular for organic electronic applications. We present large active area (0.64 cm2), solution processable, poly[[9-(1-octylnonyl)-9H-carbazole-2,7-diyl]-2,5-thiophenediyl-2,1,3-benzothiadiazole-4,7-diyl-2,5-thiophenediyl]:[6,6]-Phenyl C71 butyric acid methyl ester (PCDTBT:PC70BM) organic photovoltaic (OPV) solar cells, incorporating GO hole transport layers (HTL). The power conversion efficiency (PCE) of ∼5% is the highest reported for OPV using this architecture. A comparative study of solution-processable devices has been undertaken to benchmark GO OPV performance with poly(3,4-ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS) HTL devices, confirming the viability of GO devices, with comparable PCEs, suitable as high chemical and thermal stability replacements for PEDOT:PSS in OPV.
Nucleation, transition, and maturing of the self-assembled Au droplets on various type-A GaAs substrates
Authors: Li Ming-Yu , Sui Mao , Kim Eun-Soo , Lee Jihoon
Published: August 2014

In this study, the fabrication of self-assembled Au droplets is successfully demonstrated on various type-A GaAs substrates: (711)A, (511)A, (411)A, and (311)A. The nucleation of the self-assembled tiny Au clusters is observed at 300 °C. As an intermediate stage, corrugated Au nanostructures are clearly observed at 350 °C on various type-A GaAs surfaces, rarely witnessed on other substrates. Based on the Volmer-Weber growth mode, the dome-shaped Au droplets with excellent uniformities are successfully fabricated between 500 and 550 °C. As a function of annealing temperature, the self-assembled Au droplets show the increased dimensions including average height and diameter, compensated by the decreased average density. Depending on the substrate indices utilized, the size and density of Au droplets show clear differences throughout the whole temperature range. The results are symmetrically analyzed by using atomic force microscope images, cross-sectional line-profiles, size and density plots, height distribution histograms, and Fourier filter transform power spectra.
Development of ferroelectric correlations in the quantum paraelectric and antiferrodistortive regimes in BaxSr1-xTiO3 (x ≤ 0.10)
Authors: Hassnain Jaffari G. , Mehmood Zahid , Iqbal Asad M. , Hasanain S. K. , Ismat Shah S.
Published: August 2014

The dielectric response ε(T)  of BaxSr1-xTiO3 (x ≤ 0.1) for compositions at and below the critical composition for the ferroelectric transition has been studied. With progressive Ba substitution, the growth of ferroelectric correlations and the weakening of the Antiferrodistortive (AFD) and the quantum paraelectric (QPE) effects have been studied by monitoring the changes in both the in and out of phase parts of the dielectric response. For the compositions close to pure SrTiO3 (x = 0 and x = 0.02), the temperature dependence exhibits a continuous rise in the in-phase part and no ferroelectric peak, consistent with the QPE behavior. With increasing Ba substitution, the low temperature behavior of the in phase part ε′ progressively changes from a continuous rise to exhibit a weak maximum and finally to a well developed cusp. For higher Ba concentrations, the low temperature peak (T ∼ 50K), which corresponds to ferroelectric correlations, becomes increasingly sharper until at the critical composition, x = 0.10, the system shows a single well defined ferroelectric peak. However, the out of phase response of the x = 0.1 composition exhibited a succession of three BaTiO3 type ferroelectric transitions. For x≤0.04, the out of phase part shows evidence of an ordering around T ∼ 100K, which is the expected AFD ordering temperature. The deviations of the ε′(T) data from the Curie-Weiss law have been analyzed within the frame work of two different theoretical models. It was determined that the dielectric behavior for lower concentrations of Ba (up to x ≤ 0.08) was explainable in terms of a model of non-interacting regions which are themselves homogeneously polarized and undergo a second order phase transition. For the phase boundary composition, i.e., x = 0.1, on the other hand, the data are explainable in terms of the Sherrington and Kirkpatrick model which includes the effects of weak correlations between the polar regions characterized by a glassy order parameter.
Novel magnetoelectric ceramic composites by control of the interface reactions in Fe2O3@BaTiO3 core-shell structures
Authors: Curecheriu Lavinia , Postolache Petronel , Buscaglia Maria Teresa , Buscaglia Vincenzo , Ianculescu Adelina , Mitoseriu Liliana
Published: August 2014

In the present work, composite ceramics of ferroelectric BaTiO3 (BT) with magnetic αFe2O3 were prepared from powders synthesized by two different methods: (a) core-shell powders of Fe2O3@BT and (b) Fe2O3-BT composites from mixed powders with the same composition. The M(H) loops at room temperature show a “wasp-waisted” character, with multiple components, determined as result of the formation of magnetic phases with contrasting coercivities (hard BaFe12O19 and soft Ba12Ti28Fe15O84 phases) in different ratios, as indicated by the magnetic first-order-reversal curves analysis. The core-shell composite ceramics generally showed slightly improved dielectric properties and smaller conductivity. The high field properties of composite ceramics show a strong nonlinearity in both cases, together with a reduction of zero field permittivity, making from these composites possible tunable materials interesting for applications. Their multifunctional character is enhanced by the presence of a complex magnetic character with soft/hard components.
Optimizing design and fabrication of microfluidic devices for cell cultures: An effective approach to control cell microenvironment in three dimensions
Authors: Pagano G. , Ventre M. , Iannone M. , Greco F. , Maffettone P. L. , Netti P. A.
Published: August 2014

The effects of gradients of bioactive molecules on the cell microenvironment are crucial in several biological processes, such as chemotaxis, angiogenesis, and tumor progression. The elucidation of the basic mechanisms regulating cell responses to gradients requires a tight control of the spatio-temporal features of such gradients. Microfluidics integrating 3D gels are useful tools to fulfill this requirement. However, even tiny flaws in the design or in the fabrication process may severely impair microenvironmental control, thus leading to inconsistent results. Here, we report a sequence of actions aimed at the design and fabrication of a reliable and robust microfluidic device integrated with collagen gel for cell culturing in 3D, subjected to a predetermined gradient of biomolecular signals. In particular, we developed a simple and effective solution to the frequently occurring technical problems of gas bubble formation and 3D matrix collapsing or detaching from the walls. The device here proposed, in Polydimethylsiloxane, was designed to improve the stability of the cell-laden hydrogel, where bubble deprived conditioning media flow laterally to the gel. We report the correct procedure to fill the device with the cell populated gel avoiding the entrapment of gas bubbles, yet maintaining cell viability. Numerical simulations and experiments with fluorescent probes demonstrated the establishment and stability of a concentration gradient across the gel. Finally, chemotaxis experiments of human Mesenchymal Stem Cells under the effects of Bone Morphogenetic Protein-2 gradients were performed in order to demonstrate the efficacy of the system in controlling cell microenvironment. The proposed procedure is sufficiently versatile and simple to be used also for different device geometries or experimental setups.
A sample-to-result system for blood coagulation tests on a microfluidic disk analyzer
Authors: Lin Chia-Hui , Liu Cheng-Yuan , Shih Chih-Hsin , Lu Chien-Hsing
Published: August 2014

In this report, we describe in detail a microfluidic analyzer, which is able to conduct blood coagulation tests using whole blood samples. Sample preparation steps, such as whole blood aliquoting and metering, plasma separation, decanting, and mixing with reagents were performed in sequence through microfluidic functions integrated on a disk. Both prothrombin time (PT) and activated partial thromboplastin time (aPTT) were carried out on the same platform and the test results can be reported in 5 min. Fifty clinical samples were tested for both PT and aPTT utilizing the microfluidic disk analyzer and the instrument used in hospitals. The test results showed good correlation and agreement between the two instruments.
Cell-cell proximity effects in multi-cell electroporation
Authors: Henslee Brian E. , Morss Andrew , Hu Xin , Lafyatis Gregory P. , James Lee L.
Published: August 2014

We report a fundamental study of how the electropermeabilization of a cell is affected by nearby cells. Previous researchers studying electroporation of dense suspensions of cells have observed, both theoretically and experimentally, that such samples cannot be treated simply as collections of independent cells. However, the complexity of those systems makes quantitative modeling difficult. We studied the change in the minimum applied electric field, the threshold field, required to affect electropermeabilization of a cell due to the presence of a second cell. Experimentally, we used optical tweezers to accurately position two cells in a custom fluidic electroporation device and measured the threshold field for electropermeabilization. We also captured video of the process. In parallel, finite element simulations of the electrostatic potential distributions in our systems were generated using the 3-layer model and the contact resistance methods. Reasonably good agreement with measurements was found assuming a model in which changes in a cell's threshold field were predicted from the calculated changes in the maximum voltage across the cell's membrane induced by the presence of a second cell. The threshold field required to electroporate a cell is changed ∼5%–10% by a nearby, nearly touching second cell. Cells aligned parallel to the porating field shield one another. Those oriented perpendicular to the field enhance the applied field's effect. In addition, we found that the dynamics of the electropermeabilization process are important in explaining observations for even our simple two-cell system.
Localized states in a semiconductor quantum ring with a tangent wire
Authors: Yang F. , Wu M. W.
Published: August 2014

We extend a special kind of localized state trapped at the intersection due to the geometric confinement, first proposed in a three-terminal-opening T-shaped structure [L. A. Openov, Europhys. Lett. 55, 539 (2001)], into a ring geometry with a tangent connection to the wire. In this ring geometry, there exists one localized state trapped at the intersection with energy lying inside the lowest subband. We systematically study this localized state and the resulting Fano-type interference due to the coupling between this localized state and the continuum ones. It is found that the increase of inner radius of the ring weakens the coupling to the continuum ones and the asymmetric Fano dip fades away. A wide energy gap in transmission appears due to the interplay of two types of antiresonances: the Fano-type antiresonance and the structure antiresonance. The size of this antiresonance gap can be modulated by adjusting the magnetic flux. Moreover, a large transmission amplitude can be obtained in the same gap area. The strong robustness of the antiresonance gap is demonstrated and shows the feasibility of the proposed geometry for a real application.
Unexpected magnetization enhancement in hydrogen plasma treated ferromagnetic (Zn,Cu)O film
Authors: Hu Liang , Zhu Liping , He Haiping , Ye Zhizhen
Published: August 2014

The effects of H+ incorporation on oxygen vacancies (HO+) on the giant ferromagnetic behavior (moment up to 3.26 μB/Cu) in ZnO:Cu polycrystalline films have been closely examined using different microstructural and magnetic characterization tools. Fine thermal stability (up to 450 °C) and low resistivity demonstrate a significant correlation between Cu 3d-states and HO+ donor defects in H plasma treated ZnO:Cu films, analogous to dual-donor (VO and Zni) defects mediated case. These HO+ donors can delocalize their electrons to the orbits of Cu atoms and contribute to a stronger spin-orbit coupling interaction. Suitable HO+ defect concentration and matched proportion between Cu2+ and Cu+ species ensure that orbital momentum shall not be quenched. Hence, unexpected moment enhancement, less than spin-orbit coupling upper limit (3.55 μB/Cu), can be also expected in this scenario. The manipulation from spin-only to spin-orbit coupling mode, using a facile thermally-mediated H plasma exposure way, will allow achieving spin transport based diluted magnetic semiconductor device.
Nonlinear switching dynamics in a photonic-crystal nanocavity
Authors: Yu Yi , Palushani Evarist , Heuck Mikkel , Vukovic Dragana , Peucheret Christophe , Yvind Kresten , Mork Jesper
Published: August 2014

We report the experimental observation of nonlinear switching dynamics in an InP photonic crystal nanocavity. Usually, the regime of relatively small cavity perturbations is explored, where the signal transmitted through the cavity follows the temporal variation of the cavity resonance. When the cavity is perturbed by strong pulses, we observe several nonlinear effects, i.e., saturation of the switching contrast, broadening of the switching window, and even initial reduction of the transmission. The effects are analyzed by comparison with nonlinear coupled mode theory and explained in terms of large dynamical variations of the cavity resonance in combination with nonlinear losses. The results provide insight into the nonlinear optical processes that govern the dynamics of nanocavities and are important for applications in optical signal processing, where one wants to optimize the switching contrast.
Improving charge transport property and energy transfer with carbon quantum dots in inverted polymer solar cells
Authors: Liu Chunyu , Chang Kaiwen , Guo Wenbin , Li Hao , Shen Liang , Chen Weiyou , Yan Dawei
Published: August 2014

Carbon quantum dots (Cdots) are synthesized by a simple method and introduced into active layer of polymer solar cells (PSCs). The performance of doped devices was apparently improved, and the highest power conversion efficiency of 7.05% was obtained, corresponding to a 28.2% enhancement compared with that of the contrast device. The charge transport properties, resistance, impedance, and transient absorption spectrum are systematically investigated to explore how the Cdots affect on PSCs performance. This study reveals the importance of Cdots in enhancing the efficiency of PSCs and gives insight into the mechanism of charge transport improvement.
Expansions of the solutions to the confluent Heun equation in terms of the Kummer confluent hypergeometric functions
Authors: Ishkhanyan T. A. , Ishkhanyan A. M.
Published: August 2014

We examine the series expansions of the solutions of the confluent Heun equation in terms of three different sets of the Kummer confluent hypergeometric functions. The coefficients of the expansions in general obey three-term recurrence relations defining double-sided infinite series; however, four-term and two-term relations are also possible in particular cases. The conditions for left- and/or right-side termination of the derived series are discussed.
Preparation of a heteroepitaxial LaxSryMnzO3/BiFeO3 bilayer by r.f. magnetron sputtering with various oxygen gas flow ratios
Authors: Naganuma H. , Ichinose T. , Begum H. A. , Sato S. , Han X. F. , Miyazaki T. , Bae In-T. , Oogane M. , Ando Y.
Published: August 2014

BiFeO3 (BFO) and LaxSryMnzO3 (LSMO) films were epitaxially grown on SrTiO3 (100) substrates by r.f. magnetron sputtering with various oxygen gas flow ratios (FO2). Compositional ratios of each atom in both of BFO and LSMO could be controlled kept to around 10 at.% by changing FO2. Adjusting the compositional ratio to La0.35Sr0.15Mn0.5O3 not only increase Tc of LSMO but also produces sufficient oxygen to form a perovskite lattice. For an LSMO/BFO heterostructure, detailed observation by cross sectional transmission electron microscopy (TEM) revealed that the lattice of rhombohedral (SG: R-3c) LSMO was shrank by a clamping effect from the SrTiO3 substrates, and then the BFO was grown in two layers: (i) an interfacial BFO layer (7 nm thick) with evenly shrunk a-axis and c-axis, and (ii) an upper BFO layer (25 nm thick) expanded along the c-axis. Neither misfit strain nor dislocations appeared at the interface between the shrunken BFO and LSMO layers, and these heterostructures did not show exchange bias. These results suggest that BFO is suitable for a tunneling barrier combine with LSMO electrode.
Thermal diffusivities of functionalized pentacene semiconductors
Authors: Zhang H. , Yao Y. , Payne Marcia M. , Anthony J. E. , Brill J. W.
Published: August 2014

We have measured the interlayer and in-plane (needle axis) thermal diffusivity of 6,13-bis(triisopropylsilylethynyl) pentacene. The needle axis value is comparable to the phonon thermal diffusivities of quasi-one dimensional organic metals with excellent π-orbital overlap, and its value suggests that a significant fraction of heat is carried by optical phonons. Furthermore, the interlayer (c-axis) thermal diffusivity is at least an order of magnitude larger, and this unusual anisotropy implies very strong dispersion of optical modes in the interlayer direction, presumably due to interactions between the silyl-containing side groups. Similar values for both in-plane and interlayer diffusivities have been observed for several other functionalized pentacene semiconductors with related structures.
Optimized two-color super resolution imaging of Drp1 during mitochondrial fission with a slow-switching Dronpa variant
Authors: Rosenbloom Alyssa B. , Lee Sang-Hyuk , To Milton , Lee Antony , Shin Jae Yen , Bustamante Carlos
Published: August 2014

Significance

Optimal performance of super resolution fluorescence localization microscopy relies on a clear understanding of the photo-physical properties of photoactivatable (photo-switchable) fluorescent proteins [PA(PS)-FPs] at the single-molecule level. Our comparative study of Dronpa and a novel variant, rsKame, demonstrates the crucial role of photo-switching kinetics in super resolution imaging. rsKame, with its superior properties, significantly broadens the green PA(PS)-FP palette. We demonstrate the efficacy of rsKame and our two-color super resolution imaging method (paired with PAmCherry1) by visualizing the inner and outer mitochondrial membranes and in situ structural parameters of dynamin related protein 1 helical rings during mitochondrial fission. Our two-color super resolution imaging method presented here is a reliable and user-friendly technique without complicated sample preparation.
Transmission of a signal that synchronizes cell movements in swarms of
Myxococcus xanthus
Authors: Kaiser Dale , Warrick Hans
Published: August 2014

Significance

Multicellular organisms, by necessity, form highly organized structures. The mechanisms required to construct these often dynamic structures are a challenge to understand.
Myxococcus xanthus
, a soil bacterium, builds two large structures: growing swarms and fruiting bodies. Because the cells are genetically identical, they rely on regulating protein activity and the levels of gene expression. Moreover, the long, flexible, rod-shaped cells modify each others’ behavior when they collide. By examining development of a
Myxococcus
swarm, testable rules can be proposed that rely only on cell behavior and cell–cell contact signaling. The mechanisms used by this prokaryote to form complex, dynamic multicellular structures might have been adapted for Hedgehog and Wnt morphogenetic signaling in animals.
ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments
Authors: Khan Imtiaz A. , Fraser Adam , Bray Mark-Anthony , Smith Paul J. , White Nick S. , Carpenter Anne E. , Errington Rachel J.
Published: August 2014

Motivation: Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments.

Availability and implementation: ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license.

Contact:  wpciak@cf.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cosi2: an efficient simulator of exact and approximate coalescent with selection
Authors: Shlyakhter Ilya , Sabeti Pardis C. , Schaffner Stephen F.
Published: August 2014

Motivation: Efficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection. Gene conversion is not supported by any published coalescent simulators that support selection.

Results: We describe cosi2, an efficient simulator that supports both exact and approximate coalescent simulation with positive selection. cosi2 improves on the speed of existing exact simulators, and permits further speedup in approximate mode while retaining support for selection. cosi2 supports a wide range of demographic scenarios, including recombination hot spots, gene conversion, population size changes, population structure and migration.

cosi2 implements coalescent machinery efficiently by tracking only a small subset of the Ancestral Recombination Graph, sampling only relevant recombination events, and using augmented skip lists to represent tracked genetic segments. To preserve support for selection in approximate mode, the Markov approximation is implemented not by moving along the chromosome but by performing a standard backwards-in-time coalescent simulation while restricting coalescence to node pairs with overlapping or near-overlapping genetic material. We describe the algorithms used by cosi2 and present comparisons with existing selection simulators.

Availability and implementation: A free C++ implementation of cosi2 is available at http://broadinstitute.org/mpg/cosi2.

Contact: ilya@broadinstitute.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inter-species pathway perturbation prediction via data-driven detection of functional homology
Authors: Hafemeister Christoph , Romero Roberto , Bilal Erhan , Meyer Pablo , Norel Raquel , Rhrissorrakrai Kahn , Bonneau Richard , Tarca Adi L.
Published: August 2014

Motivation: Experiments in animal models are often conducted to infer how humans will respond to stimuli by assuming that the same biological pathways will be affected in both organisms. The limitations of this assumption were tested in the IMPROVER Species Translation Challenge, where 52 stimuli were applied to both human and rat cells and perturbed pathways were identified. In the Inter-species Pathway Perturbation Prediction sub-challenge, multiple teams proposed methods to use rat transcription data from 26 stimuli to predict human gene set and pathway activity under the same perturbations. Submissions were evaluated using three performance metrics on data from the remaining 26 stimuli.

Results: We present two approaches, ranked second in this challenge, that do not rely on sequence-based orthology between rat and human genes to translate pathway perturbation state but instead identify transcriptional response orthologs across a set of training conditions. The translation from rat to human accomplished by these so-called direct methods is not dependent on the particular analysis method used to identify perturbed gene sets. In contrast, machine learning-based methods require performing a pathway analysis initially and then mapping the pathway activity between organisms. Unlike most machine learning approaches, direct methods can be used to predict the activation of a human pathway for a new (test) stimuli, even when that pathway was never activated by a training stimuli.

Availability: Gene expression data are available from ArrayExpress (accession E-MTAB-2091), while software implementations are available from http://bioinformaticsprb.med.wayne.edu?p=50 and http://goo.gl/hJny3h.

Contact:  christoph.hafemeister@nyu.edu or atarca@med.wayne.edu.

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Elevated Carbon Monoxide to Carbon Dioxide Ratio in the Exhaled Breath of Mice Treated With a Single Dose of Lipopolysaccharide
Authors: Langeroudi Arash Ghalyanchi , Hirsch Charlotte M. , Estabragh Azadeh Shojaee , Meinardi Simone , Blake Donald R. , Barbour Alan G.
Published: August 2014

Background.  Analysis of volatile organic chemicals in breath holds promise for noninvasive diagnosis and monitoring of patients, but investigation of this in experimental mouse models has been limited. Of particular interest is endogenous production of carbon monoxide as a biomarker of inflammation and, more particularly, during sepsis.

Methods.  Using a nose-only collection procedure for unanesthetized individual adult mice and sensitive gas chromatography of carbon monoxide (CO) and carbon dioxide (CO2) of sampled breath, we investigated the responses of mice to one-time injections with different doses of purified Escherichia coli lipopolysaccharide. Two strains of mice were examined: BALB/c and C3H, including an endotoxin-resistant mutant (HeJ) as well as the wild type (HOuJ).

Results.  The CO to CO2 ratio increased in a dose-responsive manner within hours in treated BALC/c mice but not control mice. The CO/CO2 values declined to the range of control mice within 48–72 h after the injection of lipopolysaccharide. Breath CO/CO2 values correlated with systemic inflammation biomarkers in serum and heme oxygenase-1 gene expression in blood. C3H/HOuJ mice, but not the HeJ mice, had similar increases of the CO/CO2 ratio in response to the endotoxin.

Conclusions.  Carbon monoxide concentrations in exhaled breath of at least 2 strains of mice increase in response to single injections of endotoxin. The magnitude of increase was similar to what was observed with a bacteremia model. These findings with an experimental model provide a rationale for further studies of normalized CO concentrations in human breath as an informative biomarker for staging and monitoring of sepsis.
Frontline Systemic Therapy With Pemetrexed–Platinum in Nonsquamous Non–Small-Cell Lung Cancer With Asymptomatic Brain Metastases
Authors: Alsidawi Samer , Chaudhary Rekha , Karim Nagla A.
Published: August 2014

The incidence of brain metastases from nonsquamous non–small-lung cancer is increasing as a result of superior imaging techniques for early detection of distant metastases. Although whole-brain radiation therapy and stereotactic radiosurgery along with systemic chemotherapy have shown to be effective in alleviating symptoms and improving outcomes, the approach to patients with asymptomatic brain metastases remains elusive. We explored the literature for a possible role of frontline systemic chemotherapy in asymptomatic brain metastases from nonsquamous non–small-lung cancer and found promising evidence that upfront systemic therapy with pemetrexed–platinum regimens might be a reasonable option for these patients and would forestall the need for upfront brain radiation therapy. More large-scale phase II and phase III clinical trials are needed to further investigate the frontline use of pemetrexed–platinum regimens in this setting.
Development of a genetic system for a model manganese-oxidizing proteobacterium, Leptothrix discophora SS1
Authors: Bocioaga Daniela , El Gheriany Iman A. , Lion Leonard W. , Ghiorse William C. , Shuler Michael L. , Hay Anthony G.
Published: August 2014

Understanding the molecular underpinnings of manganese oxidation in Leptothrix discophora SS1 has been hampered by the lack of a genetic system. In this report, we describe the development of a genetic system for L. discophora SS1. The antibiotic sensitivity was characterized, and a procedure for transformation with exogenous DNA via conjugation was developed and optimized, resulting in a maximum transfer frequency of 5.2×10−1 and a typical transfer frequency of the order of 1×10−3 transconjugants per donor. Genetic manipulation of L. discophora SS1 was demonstrated by disrupting pyrF via chromosomal integration with a plasmid containing a R6Kγ origin of replication through homologous recombination. This resulted in resistance to 5-fluoroorotidine, which was abolished by complementation with an ectopically expressed copy of pyrF cloned into pBBR1MCS. This system is expected to be amenable to a systematic genetic analysis of L. discophora SS1, including those genes responsible for manganese oxidation.
Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
Authors: Keane Orla M. , Toft Christina , Carretero-Paulet Lorenzo , Jones Gary W. , Fares Mario A.
Published: August 2014

Biological systems remain robust against certain genetic and environmental challenges. Robustness allows the exploration of ecological adaptations. It is unclear what factors contribute to increasing robustness. Gene duplication has been considered to increase genetic robustness through functional redundancy, accelerating the evolution of novel functions. However, recent findings have questioned the link between duplication and robustness. In particular, it remains elusive whether ancient duplicates still bear potential for innovation through preserved redundancy and robustness. Here we have investigated this question by evolving the yeast Saccharomyces cerevisiae for 2200 generations under conditions allowing the accumulation of deleterious mutations, and we put mechanisms of mutational robustness to a test. S. cerevisiae declined in fitness along the evolution experiment, but this decline decelerated in later passages, suggesting functional compensation of mutated genes. We resequenced 28 genomes from experimentally evolved S. cerevisiae lines and found more mutations in duplicates—mainly small-scale duplicates—than in singletons. Genetically interacting duplicates evolved similarly and fixed more amino acid–replacing mutations than expected. Regulatory robustness of the duplicates was supported by a larger enrichment for mutations at the promoters of duplicates than at those of singletons. Analyses of yeast gene expression conditions showed a larger variation in the duplicates’ expression than that of singletons under a range of stress conditions, sparking the idea that regulatory robustness allowed a wider range of phenotypic responses to environmental stresses, hence faster adaptations. Our data support the persistence of genetic and regulatory robustness in ancient duplicates and its role in adaptations to stresses.
Tree diversity and the role of non‐host neighbour tree species in reducing fungal pathogen infestation
Authors: Hantsch Lydia , Bien Steffen , Radatz Stine , Braun Uwe , Auge Harald , Bruelheide Helge
Published: August 2014

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non‐host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning.

We tested the effects of tree diversity and the proportion of neighbouring host and non‐host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non‐host neighbouring tree species.

Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro‐ and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species.

We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host‐specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non‐host neighbouring tree species on fungal species richness and infestation were, however, recorded.

Synthesis. For the first time, we experimentally demonstrated that for two common forestry tree species, foliar fungal pathogen richness and infestation depend on local biodiversity. Thus, local tree diversity can have positive impacts on ecosystem functioning in managed forests by decreasing the level of fungal pathogen infestation.
Occupation and its relationship with health and wellbeing: The threshold concept for occupational therapy
Authors: Fortune Tracy , Kennedy‐Jones Mary
Published: August 2014

Background/aim

We introduce the educational framework of ‘threshold concepts’ and discuss its utility in understanding the fundamental difficulties learners have in understanding ways of thinking and practising as occupational therapists. We propose that the relationship between occupation and health is a threshold concept for occupational therapy because of students' trouble in achieving lasting conceptual change in relation to their understanding of it.

Methods

The authors present and discuss key ideas drawn from educational writings on threshold concepts, review the emerging literature on threshold concepts in occupational therapy, and pose a series of questions in order to prompt consideration of the pedagogical issues requiring action by academic and fieldwork educators.

Results

Threshold concepts in occupational therapy have been considered in a primarily cross‐disciplinary sense, that is, the understandings that occupational therapy learners grapple with are relevant to learners in other disciplines. In contrast, we present a more narrowly defined conception that emphasises the ‘bounded‐ness’ of the concept to the discipline.

Conclusion

A threshold concept that captures the essential nature of occupational therapy is likely to be (highly) troublesome in terms of a learner's acquisition of it. Rather than simplifying these learning ‘jewels’ educators are encouraged to sit with the discomfort that they and the learner may experience as the learner struggles to grasp them. Moreover, they should reshape their curricula to provoke such struggles if transformative learning is to be the outcome.
Resveratrol Preserves Mitochondrial Function, Stimulates Mitochondrial Biogenesis, and Attenuates Oxidative Stress in Regulatory T Cells of Mice Fed a High‐Fat Diet
Authors: Wang Bin , Sun Jin , Ma Yuhua , Wu Guirong , Tian Yingjie , Shi Yonghui , Le Guowei
Published: August 2014

Consumption of high‐fat diet (HFD) is related with increased oxidative stress and dysfunctional mitochondria in many organs. The effects of resveratrol (trans‐3,5,4′‐trihydroxystilbene) that can protect T lymphocytes in various disease conditions on the HFD‐induced apoptosis of CD4+CD25+CD127low/− regulatory T cells (Tregs) were studied, and the possible mechanism was postulated. Resveratrol significantly decreased Tregs death induced by 20‐wk HFD, being associated with the reduction of reactive oxygen species production and the alleviation of HFD‐induced loss of mitochondrial membrane potential (Δψm) in Tregs. Furthermore, resveratrol increased the expression of factors that regulated mitochondrial biogenesis in Tregs. Finally, resveratrol recovered the HFD‐induced activation of apoptotic markers in Tregs. Resveratrol protected Tregs against HFD‐induced apoptosis by reducing oxidative stress, restoring mitochondrial functional activities, and stimulating mitochondrial biogenesis.
A Virtual Screening Method for Inhibitory Peptides of Angiotensin I–Converting Enzyme
Authors: Wu Hongxi , Liu Yalan , Guo Mingrong , Xie Jingli , Jiang XiaMin
Published: August 2014

Natural small peptides from foods have been proven to be efficient inhibitors of Angiotensin I–converting enzyme (ACE) for the regulation of blood pressure. The traditional ACE inhibitory peptides screening method is both time consuming and money costing, to the contrary, virtual screening method by computation can break these limitations. We establish a virtual screening method to obtain ACE inhibitory peptides with the help of Libdock module of Discovery Studio 3.5 software. A significant relationship between Libdock score and experimental IC50 was found, Libdock score = 10.063 log(1/IC50) + 68.08 (R2 = 0.62). The credibility of the relationship was confirmed by testing the coincidence of the estimated log(1/IC50) and measured log(1/IC50) (IC50 is 50% inhibitory concentration toward ACE, in μmol/L) of 5 synthetic ACE inhibitory peptides, which was virtual hydrolyzed and screened from a kind of seafood, Phascolosoma esculenta. Accordingly, Libdock method is a valid IC50 estimation tool and virtual screening method for small ACE inhibitory peptides.
Ultra‐Performance Liquid Chromatographic Determination of L‐Ergothioneine in Commercially Available Classes of Cow Milk
Authors: Sotgia Salvatore , Pisanu Elisabetta , Cambedda Debora , Pintus Gianfranco , Carru Ciriaco , Zinellu Angelo
Published: August 2014

A new efficient and sensitive precolumn hydrophilic interaction ultra‐performance liquid chromatography (HILIC‐UPLC) method was established for the quantitative determination of L‐ergothioneine (ERT) in milk. After derivatization of ERT with 7‐diethylamino‐3‐[4‐(iodoacetamido)phenyl]‐4‐methylcoumarin, chromatographic separation was achieved in a fairly short time, less than 5 min, on a 100 × 2.1 mm Waters Cortecs UPLC HILIC 1.6‐μm column, by using a mixture of 30 mmol/L ammonium acetate/acetonitrile (10:90, v/v) as a mobile phase flowing isocratically at 0.9 mL/min. Limit of detection and the limit of quantification were 0.03 and 0.10 μmol/L, respectively. The method exhibited linearity in a concentration range of 0.16 and 5.08 μmol/L. Mean recovery was 106.66%, whereas intra‐ and interassay precisions were determined to be within 6 RSD%. On average, ERT concentration in different commercially available classes of cow milk was found to be 0.442 ± 0.191 μmol/L, with the highest levels in the ultra‐high temperature milks and low values in the unprocessed and HTST whole milks. In this light, our experiments suggest that ERT could be used as a marker for the heat treatment of milk.
Analysis of the Subtropical Blackberry Cultivar Potential in Jelly Processing
Authors: Rios de Souza Vanessa , Aparecida Pimenta Pereira Patrícia , Carla Marques Pinheiro Ana , Carlos de Oliveira Lima Luiz , Pio Rafael , Queiroz Fabiana
Published: August 2014

In Brazil, there are numerous blackberry cultivars under cultivation, however, only a few cultivars, such as the Guarani, are displayed/used for processing. In this context the aim of this work was to study the effects of different Brazilian blackberry cultivars (Guarani, Brazos, Comanche, Tupy, Cherokee, Caingangue, and Choctaw) on the physicochemical characteristics, texture profiles and the consumer acceptance of the resulting jelly to identify the potential use of these cultivars in the jelly industry. It is feasible to produce blackberry jellies with the Tupy, Comanche, Brazos, Guarani, and Choctaw cultivars because these jellies demonstrated good acceptability combined with good productivity. Consumers were shown to have a preference for a less adhesive, more acidic jelly. This study provides a useful insight about the Brazilian blackberry cultivar potential in jelly processing.
Inhibitory Effects of Pomegranate Extracts on Recombinant Human Maltase–Glucoamylase
Authors: Kawakami Kayoko , Li Peng , Uraji Misugi , Hatanaka Tadashi , Ito Hideyuki
Published: August 2014

α‐Glucosidase inhibitors are currently used in the treatment of type 2 diabetes. In this study, we investigated the inhibitory activities of aril and pericarp extracts from pomegranates obtained various regions against recombinant human maltase–glucoamylase (MGAM). The inhibitory activities of the aril extracts tended to be stronger than those of the pericarp extracts. The Iranian aril extract was the most effective inhibitor. We investigated the polyphenol content of the pomegranate extracts using the Folin–Ciocalteu method. Among the aril extracts, the Iranian aril extract showed the highest polyphenol content. We further evaluated inhibitory activity against α‐glucosidase from the rat small intestine. Pomegranate extract used in this study showed slightly different inhibitory activities according to α‐glucosidase origin. Iranian aril extract was the most effective inhibitor of α‐glucosidases, especially recombinant human MGAM. Bioassay‐guided fractionation of the pomegranate arils led to identification of punicalagin and oenothein B as potent inhibitors of α‐glucosidase. Oenothein B showed inhibitory activity with a half‐maximal inhibitory concentration (IC50) value of 174 μM. Its potency was comparable to that of the α‐glucosidase inhibitor acarbose with an IC50 value of 170 μM. Dixon plot kinetic analysis of oenothein B showed a noncompetitive inhibition with a Ki value of 102 μM. These results suggest that pomegranate arils would be useful for suppressing postprandial hyperglycemia.
Extraction Efficiency of Hydrophilic and Lipophilic Antioxidants from Lyophilized Foods Using Pressurized Liquid Extraction and Manual Extraction
Authors: Watanabe Jun , Oki Tomoyuki , Takebayashi Jun , Takano‐Ishikawa Yuko
Published: August 2014

The efficient extraction of antioxidants from food samples is necessary in order to accurately measure their antioxidant capacities. α‐Tocopherol and gallic acid were spiked into samples of 5 lyophilized and pulverized vegetables and fruits (onion, cabbage, Satsuma mandarin orange, pumpkin, and spinach). The lipophilic and hydrophilic antioxidants in the samples were sequentially extracted with a mixed solvent of n‐hexane and dichloromethane, and then with acetic acid–acidified aqueous methanol. Duplicate samples were extracted: one set was extracted using an automated pressurized liquid extraction apparatus, and the other set was extracted manually. Spiked α‐tocopherol and gallic acid were recovered almost quantitatively in the extracted lipophilic and hydrophilic fractions, respectively, especially when pressurized liquid extraction was used. The expected increase in lipophilic oxygen radical absorbance capacity (L‐ORAC) due to spiking with α‐tocopherol, and the expected increase in 2,2‐diphenyl‐1‐picrylhydrazyl radical scavenging activities and total polyphenol content due to spiking with gallic acid, were all recovered in high yield. Relatively low recoveries, as reflected in the hydrophilic ORAC (H‐ORAC) value, were obtained following spiking with gallic acid, suggesting an interaction between gallic acid and endogenous antioxidants. The H‐ORAC values of gallic acid–spiked samples were almost the same as those of postadded (spiked) samples. These results clearly indicate that lipophilic and hydrophilic antioxidants are effectively extracted from lyophilized food, especially when pressurized liquid extraction is used.
An Improved Approach to Identify Irradiated Spices Using Electronic Nose, FTIR, and EPR Spectroscopy
Authors: Sanyal Bhaskar , Ahn Jae‐Jun , Maeng Jeong‐Hwan , Kyung Hyun‐Kyu , Lim Ha‐Kyeong , Sharma Arun , Kwon Joong‐Ho
Published: August 2014

Changes in cumin and chili powder from India resulting from electron‐beam irradiation were investigated using 3 analytical methods: electronic nose (E‐nose), Fourier transform infrared (FTIR) spectroscopy, and electron paramagnetic resonance (EPR) spectroscopy. The spices had been exposed to 6 to 14 kGy doses recommended for microbial decontamination. E‐nose measured a clear difference in flavor patterns of the irradiated spices in comparison with the nonirradiated samples. Principal component analysis further showed a dose‐dependent variation. FTIR spectra of the samples showed strong absorption bands at 3425, 3007 to 2854, and 1746 cm−1. However, both nonirradiated and irradiated spice samples had comparable patterns without any noteworthy changes in functional groups. EPR spectroscopy of the irradiated samples showed a radiation‐specific triplet signal at g = 2.006 with a hyper‐fine coupling constant of 3 mT confirming the results obtained with the E‐nose technique. Thus, E‐nose was found to be a potential tool to identify irradiated spices.
Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
Authors: Ho Simon Y. W. , Duchêne Sebastián , Duchêne David
Published: August 2014

Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed‐clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch‐specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed‐clock models are more appropriate for biological data. We present an R package, NELSI, that allows the evolution of DNA sequences to be simulated according to a range of clock models. Using data generated by this package, we assessed the ability of two Bayesian phylogenetic methods to distinguish among different relaxed‐clock models and to quantify rate variation among lineages. The results of our analyses show that rate autocorrelation is typically difficult to detect, even when there is complete taxon sampling. This provides a potential explanation for past failures to detect rate autocorrelation in a range of data sets.