bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fano-like resonance emerging from magnetic and electric plasmon mode coupling in small arrays of gold particles
Authors: Bakhti Saïd , Tishchenko Alexandre V. , Zambrana-Puyalto Xavier , Bonod Nicolas , Dhuey Scott D. , Schuck P. James , Cabrini Stefano , Alayoglu Selim , Destouches Nathalie 
Published: September 2016

AbstractIn this work we theoretically and experimentally analyze the resonant behavior of individual 3 × 3 gold particle oligomers illuminated under normal and oblique incidence. While this structure hosts both dipolar and quadrupolar electric and magnetic delocalized modes, only dipolar electric and quadrupolar magnetic modes remain at normal incidence. These modes couple into a strongly asymmetric spectral response typical of a Fano-like resonance. In the basis of the coupled mode theory, an analytical representation of the optical extinction in terms of singular functions is used to identify the hybrid modes emerging from the electric and magnetic mode coupling and to interpret the asymmetric line profiles. Especially, we demonstrate that the characteristic Fano line shape results from the spectral interference of a broad hybrid mode with a sharp one. This structure presents a special feature in which the electric field intensity is confined on different lines of the oligomer depending on the illumination wavelength relative to the Fano dip. This Fano-type resonance is experimentally observed performing extinction cross section measurements on arrays of gold nano-disks. The vanishing of the Fano dip when increasing the incidence angle is also experimentally observed in accordance with numerical simulations.
Immunological efficacy of pneumococcal vaccine strategies in HIV-infected adults: a randomized clinical trial
Authors: Sadlier C. , O’Dea S. , Bennett K. , Dunne J. , Conlon N. , Bergin C. 
Published: September 2016

AbstractThe aim of this study was to compare the immunologic response to a prime-boost immunization strategy combining the 13-valent conjugate pneumococcal vaccine (PCV13) with the 23-valent polysaccharide pneumococcal vaccine (PPSV23) versus the PPSV23 alone in HIV-infected adults. HIV-infected adults were randomized to receive PCV13 at week 0 followed by PPSV23 at week 4 (n = 31, prime-boost group) or PPSV23 alone at week 4 (n = 33, PPSV23-alone group). Serotype specific IgG geometric mean concentration (GMC) and functional oposonophagocytic (OPA) geometric mean titer (GMT) were compared for 12 pneumococcal serotypes shared by both vaccines at week 8 and week 28. The prime-boost vaccine group were more likely to achieve a ≥2-fold increase in IgG GMC and a GMC >1 ug/ml at week 8 (odds ratio (OR) 2.00, 95% confidence interval (CI) 1.46–2.74, p < 0.01) and week 28 (OR 1.95, 95% CI 1.40–2.70, p < 0.01). Similarly, the prime-boost vaccine group were more likely to achieve a ≥4-fold increase in GMT at week 8 (OR 1.71, 95% CI 1.22–2.39, p < 0.01) and week 28 (OR 1.6, 95% CI 1.15–2.3, p < 0.01). This study adds to evidence supporting current pneumococcal vaccination recommendations combining the conjugate and polysaccharide pneumococcal vaccines in the United States and Europe for HIV-infected individuals.
Evanescent Wave-Assisted Symmetry Breaking of Gold Dipolar Nanoantennas
Authors: Yang Jhen-Hong , Chen Kuo-Ping 
Published: September 2016

AbstractSymmetry-breaking and scattering cancellation were observed in the dark-mode resonance of dipolar gold nanoantennas (NAs) on glass substrates coupled with oblique incidence and total internal reflection. With the assistance of evanescent waves, the coupling efficiency was twice as strong when the incidence angle was larger than the critical angle. The Hamiltonian equation and absorption spectra were used to analyze the hybridization model of symmetric dipolar gold NAs. The antibonding mode could be coupled successfully by both transverse-magnetic (TM) and transverse-electric (TE) polarizations to NAs when the dimers orientation is parallel to the propagation direction of evanescent waves.
A novel denitrifying methanotroph of the NC10 phylum and its microcolony
Authors: He Zhanfei , Cai Chaoyang , Wang Jiaqi , Xu Xinhua , Zheng Ping , Jetten Mike S. M. , Hu Baolan 
Published: September 2016

AbstractThe NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.
CRISPR-Cas9 enables conditional mutagenesis of challenging loci
Authors: Schick Joel A. , Seisenberger Claudia , Beig Joachim , Bürger Antje , Iyer Vivek , Maier Viola , Perera Sajith , Rosen Barry , Skarnes William C. , Wurst Wolfgang 
Published: September 2016

AbstractThe International Knockout Mouse Consortium (IKMC) has produced a genome-wide collection of 15,000 isogenic targeting vectors for conditional mutagenesis in C57BL/6N mice. Although most of the vectors have been used successfully in murine embryonic stem (ES) cells, there remain a set of nearly two thousand genes that have failed to target even after several attempts. Recent attention has turned to the use of new genome editing technology for the generation of mutant alleles in mice. Here, we demonstrate how Cas9-assisted targeting can be combined with the IKMC targeting vector resource to generate conditional alleles in genes that have previously eluded targeting using conventional methods.
Visualization of in vivo metabolic flows reveals accelerated utilization of glucose and lactate in penumbra of ischemic heart
Authors: Sugiura Yuki , Katsumata Yoshinori , Sano Motoaki , Honda Kurara , Kajimura Mayumi , Fukuda Keiichi , Suematsu Makoto 
Published: September 2016

AbstractAcute ischemia produces dynamic changes in labile metabolites. To capture snapshots of such acute metabolic changes, we utilized focused microwave treatment to fix metabolic flow in vivo in hearts of mice 10 min after ligation of the left anterior descending artery. The left ventricle was subdivided into short-axis serial slices and the metabolites were analyzed by capillary electrophoresis mass spectrometry and matrix-assisted laser desorption/ionization imaging mass spectrometry. These techniques allowed us to determine the fate of exogenously administered 13C6-glucose and 13C3-lactate. The penumbra regions, which are adjacent to the ischemic core, exhibited the greatest adenine nucleotide energy charge and an adenosine overflow extending from the ischemic core, which can cause ischemic hyperemia. Imaging analysis of metabolic pathway flows revealed that the penumbra executes accelerated glucose oxidation, with remaining lactate utilization for tricarboxylic acid cycle for energy compensation, suggesting unexpected metabolic interplays of the penumbra with the ischemic core and normoxic regions.
Using spatial uncertainty to manipulate the size of the attention focus
Authors: Huang Dan , Xue Linyan , Wang Xin , Chen Yao 
Published: September 2016

AbstractPreferentially processing behaviorally relevant information is vital for primate survival. In visuospatial attention studies, manipulating the spatial extent of attention focus is an important question. Although many studies have claimed to successfully adjust attention field size by either varying the uncertainty about the target location (spatial uncertainty) or adjusting the size of the cue orienting the attention focus, no systematic studies have assessed and compared the effectiveness of these methods. We used a multiple cue paradigm with 2.5° and 7.5° rings centered around a target position to measure the cue size effect, while the spatial uncertainty levels were manipulated by changing the number of cueing positions. We found that spatial uncertainty had a significant impact on reaction time during target detection, while the cue size effect was less robust. We also carefully varied the spatial scope of potential target locations within a small or large region and found that this amount of variation in spatial uncertainty can also significantly influence target detection speed. Our results indicate that adjusting spatial uncertainty is more effective than varying cue size when manipulating attention field size.
Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians
Authors: Wolfowicz Iliona , Baumgarten Sebastian , Voss Philipp A. , Hambleton Elizabeth A. , Voolstra Christian R. , Hatta Masayuki , Guse Annika 
Published: September 2016

AbstractSymbiosis, defined as the persistent association between two distinct species, is an evolutionary and ecologically critical phenomenon facilitating survival of both partners in diverse habitats. The biodiversity of coral reef ecosystems depends on a functional symbiosis with photosynthetic dinoflagellates of the highly diverse genus Symbiodinium, which reside in coral host cells and continuously support their nutrition. The mechanisms underlying symbiont selection to establish a stable endosymbiosis in non-symbiotic juvenile corals are unclear. Here we show for the first time that symbiont selection patterns for larvae of two Acropora coral species and the model anemone Aiptasia are similar under controlled conditions. We find that Aiptasia larvae distinguish between compatible and incompatible symbionts during uptake into the gastric cavity and phagocytosis. Using RNA-Seq, we identify a set of candidate genes potentially involved in symbiosis establishment. Together, our data complement existing molecular resources to mechanistically dissect symbiont phagocytosis in cnidarians under controlled conditions, thereby strengthening the role of Aiptasia larvae as a powerful model for cnidarian endosymbiosis establishment.
Anisotropic shrinkage of insect air sacs revealed in vivo by X-ray microtomography
Authors: Xu Liang , Chen Rongchang , Du Guohao , Yang Yiming , Wang Feixiang , Deng Biao , Xie Honglan , Xiao Tiqiao 
Published: September 2016

AbstractAir sacs are thought to be the bellows for insect respiration. However, their exact mechanism of action as a bellows remains unclear. A direct way to investigate this problem is in vivo observation of the changes in their three-dimensional structures. Therefore, four-dimensional X-ray phase contrast microtomography is employed to solve this puzzle. Quantitative analysis of three-dimensional image series reveals that the compression of the air sac during respiration in bell crickets exhibits obvious anisotropic characteristics both longitudinally and transversely. Volumetric changes of the tracheal trunks in the prothorax further strengthen the evidence of this finding. As a result, we conclude that the shrinkage and expansion of the insect air sac is anisotropic, contrary to the hypothesis of isotropy, thereby providing new knowledge for further research on the insect respiratory system.
Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study
Authors: Lu Liang-Xing , Wang Ying-Min , Srinivasan Bharathi Madurai , Asbahi Mohamed , Yang Joel K. W. , Zhang Yong-Wei 
Published: September 2016

AbstractWe perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures.
H-aggregate analysis of P3HT thin films-Capability and limitation of photoluminescence and UV/Vis spectroscopy
Authors: Ehrenreich Philipp , Birkhold Susanne T. , Zimmermann Eugen , Hu Hao , Kim Kwang-Dae , Weickert Jonas , Pfadler Thomas , Schmidt-Mende Lukas 
Published: September 2016

AbstractPolymer morphology and aggregation play an essential role for efficient charge carrier transport and charge separation in polymer-based electronic devices. It is a common method to apply the H-aggregate model to UV/Vis or photoluminescence spectra in order to analyze polymer aggregation. In this work we present strategies to obtain reliable and conclusive information on polymer aggregation and morphology based on the application of an H-aggregate analysis on UV/Vis and photoluminescence spectra. We demonstrate, with P3HT as model system, that thickness dependent reflection behavior can lead to misinterpretation of UV/Vis spectra within the H-aggregate model. Values for the exciton bandwidth can deviate by a factor of two for polymer thicknesses below 150 nm. In contrast, photoluminescence spectra are found to be a reliable basis for characterization of polymer aggregation due to their weaker dependence on the wavelength dependent refractive index of the polymer. We demonstrate this by studying the influence of surface characteristics on polymer aggregation for spin-coated thin-films that are commonly used in organic and hybrid solar cells.
A Multi-Serotype Approach Clarifies the Catabolite Control Protein A Regulon in the Major Human Pathogen Group A Streptococcus
Authors: DebRoy Sruti , Saldaña Miguel , Travisany Dante , Montano Andrew , Galloway-Peña Jessica , Horstmann Nicola , Yao Hui , González Mauricio , Maass Alejandro , Latorre Mauricio , Shelburne Samuel A. 
Published: September 2016

AbstractCatabolite control protein A (CcpA) is a highly conserved, master regulator of carbon source utilization in gram-positive bacteria, but the CcpA regulon remains ill-defined. In this study we aimed to clarify the CcpA regulon by determining the impact of CcpA-inactivation on the virulence and transcriptome of three distinct serotypes of the major human pathogen Group AStreptococcus(GAS). CcpA-inactivation significantly decreased GAS virulence in a broad array of animal challenge models consistent with the idea that CcpA is critical to gram-positive bacterial pathogenesis. Via comparative transcriptomics, we established that the GAS CcpA core regulon is enriched for highly conserved CcpA binding motifs (i.e.cresites). Conversely, strain-specific differences in the CcpA transcriptome seems to consist primarily of affected secondary networks. Refinement ofcresite composition via analysis of the core regulon facilitated development of a modifiedcreconsensus that shows promise for improved prediction of CcpA targets in other medically relevant gram-positive pathogens.
Conversion between two conformational states of KaiC is induced by ATP hydrolysis as a trigger for cyanobacterial circadian oscillation
Authors: Oyama Katsuaki , Azai Chihiro , Nakamura Kaori , Tanaka Syun , Terauchi Kazuki 
Published: September 2016

AbstractThe cyanobacterial circadian oscillator can be reconstituted in vitro by mixing three clock proteins, KaiA, KaiB and KaiC, with ATP. KaiC is the only protein with circadian rhythmic activities. In the present study, we tracked the complex formation of the three Kai proteins over time using blue native (BN) polyacrylamide gel electrophoresis (PAGE), in which proteins are charged with the anionic dye Coomassie brilliant blue (CBB). KaiC was separated as three bands: the KaiABC complex, KaiC hexamer and KaiC monomer. However, no KaiC monomer was observed using gel filtration chromatography and CBB-free native PAGE. These data indicate two conformational states of KaiC hexamer and show that the ground-state KaiC (gs-KaiC) is stable and competent-state KaiC (cs-KaiC) is labile and degraded into monomers by the binding of CBB. Repeated conversions from gs-KaiC to cs-KaiC were observed over 24 h using an in vitro reconstitution system. Phosphorylation of KaiC promoted the conversion from gs-KaiC to cs-KaiC. KaiA sustained the gs-KaiC state, and KaiB bound only cs-KaiC. An E77Q/E78Q-KaiC variant that lacked N-terminal ATPase activity remained in the gs-KaiC state. Taken together, ATP hydrolysis induces the formation of cs-KaiC and promotes the binding of KaiB, which is a trigger for circadian oscillations.
Regulation of CLC-1 chloride channel biosynthesis by FKBP8 and Hsp90β
Authors: Peng Yi-Jheng , Huang Jing-Jia , Wu Hao-Han , Hsieh Hsin-Ying , Wu Chia-Ying , Chen Shu-Ching , Chen Tsung-Yu , Tang Chih-Yung 
Published: September 2016

AbstractMutations in human CLC-1 chloride channel are associated with the skeletal muscle disorder myotonia congenita. The disease-causing mutant A531V manifests enhanced proteasomal degradation of CLC-1. We recently found that CLC-1 degradation is mediated by cullin 4 ubiquitin ligase complex. It is currently unclear how quality control and protein degradation systems coordinate with each other to process the biosynthesis of CLC-1. Herein we aim to ascertain the molecular nature of the protein quality control system for CLC-1. We identified three CLC-1-interacting proteins that are well-known heat shock protein 90 (Hsp90)-associated co-chaperones: FK506-binding protein 8 (FKBP8), activator of Hsp90 ATPase homolog 1 (Aha1), and Hsp70/Hsp90 organizing protein (HOP). These co-chaperones promote both the protein level and the functional expression of CLC-1 wild-type and A531V mutant. CLC-1 biosynthesis is also facilitated by the molecular chaperones Hsc70 and Hsp90β. The protein stability of CLC-1 is notably increased by FKBP8 and the Hsp90β inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG) that substantially suppresses cullin 4 expression. We further confirmed that cullin 4 may interact with Hsp90β and FKBP8. Our data are consistent with the idea that FKBP8 and Hsp90β play an essential role in the late phase of CLC-1 quality control by dynamically coordinating protein folding and degradation.
Hollow Gaussian beam generation through nonlinear interaction of photons with orbital angular momentum
Authors: Chaitanya N. Apurv , Jabir M. V. , Banerji J. , Samanta G. K. 
Published: September 2016

AbstractHollow Gaussian beams (HGB) are a special class of doughnut shaped beams that do not carry orbital angular momentum (OAM). Such beams have a wide range of applications in many fields including atomic optics, bio-photonics, atmospheric science and plasma physics. Till date, these beams have been generated using linear optical elements. Here, we show a new way of generating HGBs by three-wave mixing in a nonlinear crystal. Based on nonlinear interaction of photons having OAM and conservation of OAM in nonlinear processes, we experimentally generated ultrafast HGBs of order as high as 6 and power >180 mW at 355 nm. This generic concept can be extended to any wavelength, timescales (continuous-wave and ultrafast) and any orders. We show that the removal of azimuthal phase of vortices does not produce Gaussian beam. We also propose a new and only method to characterize the order of the HGBs.
Identification of p53-target genes in Danio rerio
Authors: Mandriani Barbara , Castellana Stefano , Rinaldi Carmela , Manzoni Marta , Venuto Santina , Rodriguez-Aznar Eva , Galceran Juan , Nieto M. Angela , Borsani Giuseppe , Monti Eugenio , Mazza Tommaso , Merla Giuseppe , Micale Lucia 
Published: September 2016

AbstractTo orchestrate the genomic response to cellular stress signals, p53 recognizes and binds to DNA containing specific and well-characterized p53-responsive elements (REs). Differences in RE sequences can strongly affect the p53 transactivation capacity and occur even between closely related species. Therefore, the identification and characterization of a species-specific p53 Binding sistes (BS) consensus sequence and of the associated target genes may help to provide new insights into the evolution of the p53 regulatory networks across different species. Although p53 functions were studied in a wide range of species, little is known about the p53-mediated transcriptional signature in Danio rerio. Here, we designed and biochemically validated a computational approach to identify novel p53 target genes in Danio rerio genome. Screening all the Danio rerio genome by pattern-matching-based analysis, we found p53 RE-like patterns proximal to 979 annotated Danio rerio genes. Prioritization analysis identified a subset of 134 candidate pattern-related genes, 31 of which have been investigated in further biochemical assays. Our study identified runx1, axin1, traf4a, hspa8, col4a5, necab2, and dnajc9 genes as novel direct p53 targets and 12 additional p53-controlled genes in Danio rerio genome. The proposed combinatorial approach resulted to be highly sensitive and robust for identifying new p53 target genes also in additional animal species.
Discovery of new diketopiperazines inhibiting Burkholderia cenocepacia quorum sensing in vitro and in vivo
Authors: Scoffone Viola C. , Chiarelli Laurent R. , Makarov Vadim , Brackman Gilles , Israyilova Aygun , Azzalin Alberto , Forneris Federico , Riabova Olga , Savina Svetlana , Coenye Tom , Riccardi Giovanna , Buroni Silvia 
Published: September 2016

AbstractBurkholderia cenocepacia, an opportunistic respiratory pathogen particularly relevant for cystic fibrosis patients, is difficult to eradicate due to its high level of resistance to most clinically relevant antimicrobials. Consequently, the discovery of new antimicrobials as well as molecules capable of inhibiting its virulence is mandatory. In this regard quorum sensing (QS) represents a good target for anti-virulence therapies, as it has been linked to biofilm formation and is important for the production of several virulence factors, including proteases and siderophores. Here, we report the discovery of new diketopiperazine inhibitors of theB. cenocepaciaacyl homoserine lactone synthase CepI, and report their anti-virulence properties. Out of ten different compounds assayed against recombinant CepI, four were effective inhibitors, with IC50values in the micromolar range. The best compounds interfered with protease and siderophore production, as well as with biofilm formation, and showed goodin vivoactivity in aCaenorhabditis elegansinfection model. These molecules were also tested in human cells and showed very low toxicity. Therefore, they could be considered forin vivocombined treatments with established or novel antimicrobials, to improve the current therapeutic strategies againstB.cenocepacia.